. Proteins3. Protein structure Page 11Figure 8The a -helix.3.2 Secondary structure (continued)We can describe the arrangement of atoms around the peptide link (the conformation ) by giving the degree and direction in which the C a- CO and N-Ca bonds are rotated. When a number of successive peptide links have identical rotations the polypeptide chain takes up a particular secondary structure. There are several types of secondary structure, but we will concentrate on just two: the a -helix and the b -pleated sheet. In both cases you will see how the regular conformation allows the structure to be stabilised by forming many relatively strong hydrogen bonds. 
Amino Acids: Protein Building Blocks Science, Tech, Math ›Science Amino Acids: Protein Building Blocks Share Flipboard Email Printby Regina Bailey Updated October 23, 2017An amino acid is an organic molecule that, when linked together with other amino acids, forms a protein. Amino acids are essential to life because the proteins they form are involved in virtually all cell functions. Some proteins function as enzymes, some as antibodies, while others provide structural support. Although there are hundreds of amino acids found in nature, proteins are constructed from a set of 20 amino acids. Structure Basic Amino Acid Structure: alpha carbon, hydrogen atom, carboxyl group, amino group, "R" group (side chain). Yassine Mrabet/Wikimedia Commons Generally, amino acids have the following structural properties: A carbon (the alpha carbon)A hydrogen atom (H)A Carboxyl group (-COOH)An Amino group (-NH 2)A "variable" group or "R" group All amino acids have the alpha carbon bonded to a hydrogen atom, carboxyl group, and amino group. The "R" group varies among amino acids and determines the differences between these protein monomers. The amino acid sequence of a protein is determined by the information found in the cellular genetic code. The genetic code is the sequence of nucleotide bases in nucleic acids ( DNA and RNA) that code for amino acids. These gene codes not only determine the order of amino acids in a protein, but they also determine a protein's structure and function. Amino Acid Groups Amino acids can be classified into four general groups based on the properties of the "R" group in each amino acid. Amino acids can be polar, nonpolar, positively charged, or negatively charged. Polar amino acids have "R" groups that are hydrophilic, meaning that they seek contact with aqueous solutions. Nonpolar amino acids are the opposite (hydrophobic) in that they avoid contact with liquid. These interactions play a major role in protein folding and give proteins their 3-D structure. Below is a listing of the 20 amino acids grouped by their "R" group properties. The nonpolar amino acids are hydrophobic, while the remaining groups are hydrophilic. Nonpolar Amino Acids Ala: Alanine Gly: Glycine Ile: Isoleucine Leu: Leucine Met: Methionine Trp: Tryptophan Phe: Phenylalanine Pro: Proline Val: Valine Polar Amino Acids Cys: Cysteine Ser: Serine Thr: Threonine Tyr: Tyrosine Asn: Asparagine Gln: Glutamine Polar Basic Amino Acids (Positively Charged)His: Histidine Lys: Lysine Arg: Arginine Polar Acidic Amino Acids (Negatively Charged)Asp: Aspartate Glu: Glutamate While amino acids are necessary for life, not all of them can be produced naturally in the body. Of the 20 amino acids, 11 can be produced naturally. These nonessential amino acids are alanine, arginine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, and tyrosine. With the exception of tyrosine, nonessential amino acids are synthesized from products or intermediates of crucial metabolic pathways. For example, alanine and aspartate are derived from substances produced during cellular respiration. Alanine is synthesized from pyruvate, a product of glycolysis. Aspartate is synthesized from oxaloacetate, an intermediate of the citric acid cycle. Six of the nonessential amino acids (arginine, cysteine, glutamine, glycine, proline, and tyrosine) are considered conditionally essential as dietary supplementation may be required during the course of an illness or in children. Amino acids that can not be produced naturally are called essential amino acids. They are histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. Essential amino acids must be acquired through diet. Common food sources for these amino acids include eggs, soy protein, and whitefish. Unlike humans, plants are capable of synthesizing all 20 amino acids. Amino Acids and Protein Synthesis Colored transmission electron micrograph of deoxyribonucleic acid, (DNA pink), transcription coupled with translation in the bacterium Escherichia coli. During transcription, complementary messenger ribonucleic acid (m RNA) strands (green) are synthesized and immediately translated by ribosomes (blue). The enzyme RNA polymerase recognizes a start sign on the DNA strand and moves along the strand building the m RNA. m RNA is the intermediary between DNA and its protein product. DR ELENA KISELEVA/SCIENCE PHOTO LIBRARY/Getty Images Proteins are produced through the processes of DNA transcription and translation. In protein synthesis, DNA is first transcribed or copied into RNA. The resulting RNA transcript or messenger RNA (m RNA) is then translated to produce amino acids from the transcribed genetic code. Organelles called ribosomes and another RNA molecule called transfer RNA help to translate m RNA. The resulting amino acids are joined together through dehydration synthesis, a process in which a peptide bond is formed between the amino acids. A polypeptide chain is formed when a number of amino acids are linked together by peptide bonds. After several modifications, the polypeptide chain becomes a fully functioning protein. One or more polypeptide chains twisted into a 3-D structure form a protein. Biological Polymers While amino acids and proteins play an essential role in the survival of living organisms, there are other biological polymers that are also necessary for normal biological functioning. Along with proteins, carbohydrates, lipids, and nucleic acids constitute the four major classes of organic compounds in living cells .cite  Proteins Proteins Amino Acids Proteins are the most diverse biomolecules on Earth, performing many functions required for life. Protein enzymes are biological catalysts, maintaining life by regulating where and when cellular reactions occur. Structural proteins provide internal and external support to protect and maintain cell shape. For example, keratins are an important class of structural proteins found in the hair, skin, nails, and feathers of animals. Motility proteins provide the basis for cellular and whole organism movement, including muscle motor proteins that can move entire animals! Membrane proteins transmit signals during cell-to-cell communication, transport molecules into and out of cells, and protect living organisms by identifying and flagging invaders. Protein functions are so diverse because of the many unique three-dimensional structures protein polymers form. Despite such variety, proteins also share several specific structural characteristics in their monomers, the amino acids. Structural similarities among amino acids make protein synthesis a uniform and regulated process; however, each amino acid contains a unique structural component as well. Specific differences between each amino acid interact to create unique three-dimensional protein structures. Combined, the similarities and differences between amino acids explain how cells can build a diverse pool of proteins from the same set of building blocks. In every amino acid, one central carbon atom exists - the alpha-carbon (α-carbon). Of the four atom groups covalently bonded to the α-carbon, three are the same in all amino acids. The α-carbon is always directly bonded to one amino group and to one carboxyl group (carboxylic acid). The name amino acid derives from the presence of these two functional groups (amino + acid). All amino acids share a third common covalent bond to a hydrogen atom, but the fourth atom (or atomic group) bonded to the α-carbon is unique in each amino acid. The fourth α-carbon bond may link to another single hydrogen atom, as in glycine, or to a group of atoms. Atom groups range in both size and polarity or charge. For example, lysine contains a large and ionic atom group. For simplicity, when a specific amino acid is not identified, biologists use the term “R-group” to refer to the fourth atom or group bonded to the α-carbon. The term “R” signifies the rest of the molecule and is used when discussing general structure and reactivity of amino acids without complicating a structure by inclusion of R-group details. Protein synthesis involves building a polymer of amino acids with complex three-dimensional structure. Dehydration synthesis forms a peptide bond between amino acids and releases a water molecule. A dipeptide forms when a peptide bond is created between two individual amino acids, connecting the carboxyl-group carbon of one amino acid and the amino-group nitrogen of another amino acid. As additional amino acids are bonded through dehydration synthesis, a short chain ( peptide) grows. Polypeptides are formed as peptide chain lengths reach one hundred or more amino acids. Proteins form as amino acids in one or more polypeptides chemically interact to create a complex three-dimensional structure. Living organisms synthesize almost all proteins using only twenty different amino acids. Polypeptides form a unique three-dimensional structure based on the type and position (sequence) of these amino acids. Within the sequence, amino acid R-groups form chemical interactions that create a specific three-dimensional structure. These R-groups are commonly called “side chains” because they are not involved in the peptide bonds. The R-groups stick out on the side of a polypeptide, freeing them to chemically interact with one another. Side chain interactions form each protein’s specific structure, a structure uniquely capable of performing that protein’s cellular function. Functional Groups of Proteins This activity tests your ability to identify functional groups of amino acids in proteins. Launch Activity Building and Breaking Proteins This activity tests your ability to identify the reactants and products in protein synthesis and hydrolysis. Launch Activity Protein Structure and Function Unlike polysaccharides, polypeptide chains are assembled with a wide variety of amino acids in each polymer. The set of twenty amino acids commonly found in biological proteins is directly responsible for the diversity of protein structures in living cells. Each protein differs in several aspects that determine structure and, therefore, function. A protein may be composed of one or more polypeptide strands. A cell’s genes determine the length of each polypeptide strand, as well as the type and position of each amino acid in the sequence. Together, these factors determine protein structure, which determines the function a protein can perform. How does protein structure determine function? The three-dimensional shape of each protein is perfectly suited to perform one specific function. For example, aquaporins are channel proteins that form small tunnels through a cell membrane. The internal surface of aquaporin tunnels possesses a specific diameter and polarity. This structure is perfectly designed to transport water molecules but very little else, providing specificity and function. If protein structure changes, so does a protein’s ability to function. Knowing the importance of protein structure in determining function, how then is protein structure determined? To answer this, we must first ask how only twenty amino acids can create the diversity of proteins we see in living organisms. This diversity is easily explained by the way polypeptides form a sequence. Imagine creating a dipeptide using the twenty common amino acids. Twenty options exist for the first position, and twenty options exist for the second position of this two amino acid peptide. Math calculations tell us that we could synthesize four hundred different dipeptides! For every additional amino acid in a peptide, we multiply this number of options by twenty again. With more than one hundred amino acids in the average sequence, imagine how many different polypeptides may exist in nature!In addition to increasing variation, each of the twenty common amino acids plays a vital role in the structure and function of proteins in all living organisms. While producers like plants synthesize all twenty common amino acids, consumers, who obtain energy by eating biomolecules, rely on dietary intake to obtain one or more amino acids. Humans synthesize ten of the twenty common amino acids, but the remaining ten must be obtained through diet. Although all amino acids are necessary for human life, the “ essential amino acids ” are the ones humans cannot synthesize on their own. Eating protein-rich foods provides these essential amino acids to the cells. Directed by genes, living organisms synthesize polypeptides using amino acids. The unique order of amino acids in a polypeptide is called the primary structure and represents the first level of a protein’s three-dimensional structure (conformation). The primary structure determines every additional level of chemical interactions, directing the formation of a protein’s final conformation. If structure determines function, how does the primary sequence of amino acids determine a three-dimensional structure? In a process called protein folding, stable chemical interactions form between amino acids in a protein, bending and twisting the polymer into a three-dimensional shape. Protein folding sometimes requires help by molecular chaperone proteins that bind newly forming polypeptides and assist with structure formation. Protein folding involves three layers of chemical interactions, termed secondary, tertiary, and quaternary structure. Secondary structure is created as hydrogen bonds form between nearby amino acids during protein synthesis. Hydrogen bonds in secondary structure involve the polar amino and carboxyl groups of amino acids, but do not involve R-groups. As the peptide chain continues to grow, interactions between amino acid side chains (R-groups) form the tertiary structure of a polypeptide. Side chains interact with one another by:formation of side-chain hydrogen bonds.aggregation of hydrophobic side-chains.formation of ionic (salt bridge) bonds and covalent (disulfide bridge) bonds. Although all chemical interactions are important to tertiary structure, proteins fold mainly in response to which side chains are able to form hydrogen bonds with water. Because water molecules are most of a cell’s interior solution, nonpolar side chains are excluded from solution and aggregate as hydrogen bonds form with polar and ionic side chains. These hydrophobic interactions are the strongest determinant of tertiary structure. In some proteins, folding is complete after formation of tertiary structure. In others, multiple polypeptide chains combine to form a fourth level of structure, quaternary structure. Quaternary structure involves two or more polypeptides folding together through the same types of chemical interactions that formed the tertiary structure. In quaternary structure, the side-chains of different polypeptides form hydrogen bonds, hydrophobic interactions, and chemical bonds with one another. Hemoglobin, the protein that carries oxygen through the bloodstream, consists of four polypeptides. What if something disrupts protein structure? Extreme heat, changes in p H, and chemical toxins are only a few causes of protein denaturation, the loss of natural protein structure. Some proteins are capable of refolding, but most proteins are unable to recover from significant loss of protein structure. For example, cooking an egg permanently denatures its proteins, changing the appearance and texture of the egg. Living cells expend considerable effort to maintain homeostasis by controlling their internal environment because unexpected changes can destroy a cell’s proteins, killing the cell. Because protein function relies on precise structure formation, protein folding is a key topic of scientific study. Many biochemists devote their entire careers to finding ways to predict how proteins will fold and how mutations will affect protein structure and function. Mutations that change a protein’s primary sequence can lead to massive changes in protein structure and eliminate or change function, resulting in disease or death. Occasionally, mutations lead to improved or new functions benefittting the organism. Rare beneficial mutations spread through populations through natural selection, leading to evolutionary change. Protein Denaturation This animation illustrates the process of denaturation. Protein Terms This activity tests your ability to match terms related to proteins with their definitions. Launch Activityprotein foldingx Match the terms to the definitions. Select the correct term for each definition when it's highlighted by the red arrow.secondary structuretertiary structuredenaturationprimary structure Nextmolecular chaperonequaternary structurechemical and hydrophobic interactions in side chains of multiple polypeptidesprocess of losing protein structurechemical and hydrophobic interactions between side chains in a polypeptidehydrogen bonding between amino acid and carboxyl groups in a popypeptideprotein that binds to polypeptides and assists with the protein folding processsequence of amino acids in a polypeptideprocess of forming protein structure Great work! You have correctly identified some of the many pathways through the endomembrane system. Definitions Termsi  What Are Examples of Fibrous Proteins? Full Answer Collagen is the most abundant fibrous protein in the human body. A typical collagen molecule contains three polypeptide chains joined together by hydrogen bonds in the chain. Collagen is mostly found in the bones, skin and connective tissues within the body. It provides structural strength, support and a degree of elasticity to the body tissues. Keratin has a seven amino acid repeating structure. There are more than twenty-five variations of keratin in the cells of mammals. In humans, keratin is mostly found in hair and nails while in animals it is found in feathers, wool and horns. Keratin provides strength to the body tissues. Elastin gives connective tissues and organs rigidity, so that they can stretch, recoil and return to their original state. It also plays a vital role in maintaining and supporting healthy cells. Fibronectin molecule has a rod like structure in which three polypeptides are wound around each other. Fibronectin is involved in many cellular processes, including cell migration/adhesion, blood clotting, embryogenesis and tissue repair. Learn more about Muscles Sources:examples.yourdictionary.com chemistryexplained.com medicalnewstoday.com callutheran.edubiog1445.org  Chapter 3 Protein Structure and Function 58 terms kdunphy Chapter 3 Protein Structure and Function Learn Flashcards Write Spell Test Match Gravity Advertisement Upgrade to remove ads Sortamino acids most of these molecules are composed of just 20 different building blockscell theory step 1 chemical evolution began with the production of small organic compounds from reactancts such as H2, N2, NH3, and CO2.cell theory step 2 these small, simple organic compounds reacted to form mid-sized molecules, such as amino acids, nucleotides, and sugars.cell theory step 3 mid-sized, building block molecules linked to form the types of large molecules found in cells today, including proteins, nucleic acids, and complex carbs. Each of these large molecules is composed of distinctive chemical sub-units that join together: proteins are composed of amino acids, nucleic acids are composed of nucleotides, and complex carbs are composed of sugars.cell theory step 4 life became possible when one of these large, complex molecules acquired the ability to replicate itself. By increasing in copy number, this molecule would then emerge from the pool of chemicals. At that point, life had begun-- chemical evolution gave way to biological evolutionhydrophobic do not interact with waterhydrophilic interact readily with watermonomer "one-part" a molecular sub-unit such as an amino acid, a nucleotide, or a sugarpolymer "many parts" when a large number of monomers are bonded togetherpolymerization the process of linking monomers togethermacromolecule a very large molecule that is made up of smaller molecules joined togethercondensation reactions or dehydration reactions when monomers polymerize, the newly formed bond results in a loss of a water moleculepeptide bond the C-N covalent bond that results from this condensation reaction R-group orientation the side chains present in each residue extend out from the backbone, making it possible for them to interact with each other and with waterdirectionality there is an amino group on one end of the backbone and a carboxyl group on the other. The end sequence that has the free amino group is called the N-terminus, or amino-terminus, and the end with the free carboxyl group is called the C-terminus, or carboxy-terminus. By convention, biologists always write amino acid sequences from the N-terminus to the C-terminus, because the N-terminus is the start of the chain when proteins are synthesized in cells.flexibility although the peptide bond itself canot rotate because of its double-bond nature, the single bonds on either side of the peptide bond can rotate.oligopeptide when feweer than 50 amino acids are linked together in this waypolypeptides when more than 50 amino acids are linked together in this wayprotein used to describe any chain of amino acid residues, but formally protein refers to the complete, functional form of the moleculeprimary struture the unique sequence of amino acids in a proteinsecondary structure is created in part by hydrogen bonding between components of the peptide-bonded backbonealpha helix the polypeptide's backbone is coiledbeta-pleated sheet segments of a peptide chain bend 180 degrees and then fold in the same pleanetertiary structure a polypeptide results from interactions between R-groups or between R-groups and the backbone.hydrogen bonding hydrogen bonds form between polar R-groups and opposite partial charges either in the peptide backbone or other R-groupsvan der Waals interactions once hydrophobic side chains are close to one another, their association is further stabilized by electrical attractionsdisulfide "two sulfurs" bonds are frequently referred to as bridges, because they create strong links between distinct regions of the same polypeptide or two separate polypeptidesquaternary structure the combination of polypeptides, referred to as subunitsmacromolecular machines groups of multiple proteins that assemble to carry out a particular function Quarternary structure is based on tertiary structure which is based in part on secondary structure which is based on primary structure ...denatured unfoldedmolecular chaperones folding is often facilitated by specific proteinsprions proteinaceous infectious particlesenzyme a protein that functions as a catalystcatalyze speed updefense proteins called antibodies and complement proteins attack and destroy viruses and bacteria that cause diseasemovement motor proteins and contractile proteins are responsible for moving the cell itself, or moving large molecules and other types of cargo inside the cell.signaling proteins are involved in carrying and receiving signals from cell to cell inside the body. If sugar levels in your blood are low, a small protein called glucagon will bind to receptor proteins on your liver cells, triggering enzymes inside to release sugar into your bloodstream.structure structural proteins make up body components such as fingernails and hair, and define the shape of individual cells. Structural proteins keep red blood cells flexible and in their normal disc-like shape.transport proteins allow particular molecules to enter and exit cells or carry them throughout the body. Hemoglobin is a particularly well studied transport protein, but virtually every cell is studded with membrane proteins that control the passage of specific molecules and ions.substrates reactant moleculesactive site catalysis usually occurs IFU- you should be able to explain how you could use the structural formula of an amino acid to determine if it is acidic, basic, uncharged polar, or nonpolar Look at the R-group of the amino acid. If there is a positive charge, then it is basic. If there is a negative charge, then its an acid. If it has no charge, but there is an oxygen atom, then it is polar uncharged. If there is no charge or oxygen, then it is nonpolaryou should be able to predict where nonpolar amino acid residues would be found in a globular protein, such as trypsin molecule. nonpolar amino acid residues would be found in the interior of a globular protein, grouped with other nonpolar residues due to hydrophobic interactionsyou should be able to identify one way the process of folding in calmodulin and infectious prions is similar Both calmodulin and infectious prions require some form of induction to achieve their active conformations. Calcium ions are required for calmodulin to fold into its functional structure while prions are induced to change their shape by other, improperly folded prion proteinsyou should be able to provide the characteristics of proteins that make them especially useful for the following cellular activities: catalysis, defense, and signaling. Catalysis- proteins are made of amino acids, which have many reactive functional groups, and can fold into different shapes that allow the formation of active sites. Defense- similar to catalysis, the chemical properties and capacity for different shapes allows proteins to be made that can attach to virtually any type of invading virus or cell. Signaling- the flexibility in protein structure allows protein activities to be quickly turned on or off based on binding to signal molecules or ions.what 2 functional groups are present on every amino acid? dtwenty different amino acids are found in the proteins of cells. what distinguishes these molecules? the atoms and functional groups found in the side chains By convention, biologists write the sequence of amino acids in a polypeptide in which direction? bin a polypeptide, what bonds are responsible for the secondary structure called an alpha helix? b Where is the information stored that directs different polypeptides to fold into different shapes? the order and type of amino acids contains the information that directs folding What is an active site? the position in an enzyme where substrates bindexplain how water participates in the development of of the interactions that glue non-polar amino acids together in the interior of globular proteins. because the non polar amino avid residues are not able to interact with water solvent, they are crowded together in the interior of a protein and surrounded by a network of hydrogen-bonded water molecules. This crowding leads to the development of van der Waals interactions that help glue the non polar side chains together If amino acids were mixed together in a solution, resembling the prebiotic soup, would they spontaneously polymerize into polypeptides? why or why not? No, polymerization is a non-spontaneous reaction because the product molecules have lower entropy than the free form of the reactants and there would be nothing to prevent hydrolysis from reversing the reactionprovide an example of how a specific shape of a protein is correlated with its function Many possible correct answers, including 1) the prescence of an active site in an enzyme that is precisely shaped to fit a substrate or substrates in the correct orientation for a reaction to occur 2) the doughnut shape of porin that allows certain substances to pass through it 3) the cable shape of collagen to provide structural support for cells and tissues.a major theme in this chapter is that the structure of molecules correlates with their function. Use this theme to explain why proteins can perform so many different functions in organisms and why enzymes are such effective catalysts proteins are highly variable in overall shape and chemical properties due to variation in the composition of R-groups and the array of secondary through quaternary structures that are possible. This variation allows them to fulfill many different roles in the cell. Diversity in the shape and reactivity of active sites also makes them effective catalysts.why are proteins not considered to be good candidate for the first living molecule? The cannot serve as a template for replicationif proteins folded only into rigid, inflexible structures, how might this affect the cell's ability to regulate protein function In many proteins, especially those involved in cell signaling, their structure is affected by binding to other molecules or ions. Since the Shape of the protein is directly involved in its function, the protein's activity is regulated by controlling how it is folded. If proteins were inflexible, this type of control could not occur.  What is the difference between the secondary, tertiary, and quaternary structures of protein? Science & Mathematics Biology What is the difference between the secondary, tertiary, and quaternary structures of protein? Follow 3 answers Answers Relevance Rating Newest Oldest Best Answer: Levels of Protein Structure Structural features of proteins are usually described at four levels of complexity: Primary structure: the linear arrangment of amino acids in a protein and the location of covalent linkages such as disulfide bonds between amino acids. Secondary structure: areas of folding or coiling within a protein; examples include alpha helices and pleated sheets, which are stabilized by hydrogen bonding. Tertiary structure: the final three-dimensional structure of a protein, which results from a large number of non-covalent interactions between amino acids. Quaternary structure: non-covalent interactions that bind multiple polypeptides into a single, larger protein. Hemoglobin has quaternary structure due to association of two alpha globin and two beta globin polyproteins. Source (s):http://www.vivo.colostate.edu/hbooks/gen...http://www.chemguide.co.uk/organicprops/... Peter S · 8 years ago5 0 Comment In addition to that, The tertiary and the quaternary ones are complete.ariane · 2 years ago0 1 Commentwhat is the similarity of tertary and quaternary protiensmahani2002 · 5 years ago0 2 Comment Maybe you would like to learn more about one of these? Find Email Marketing Software Consolidate Your Student Loans Best Home Security System? Portfolio Management Options  Protein structure? Science & Mathematics Biology Protein structure?1 what is meant by the term 'secondary structure' when appiled to protein structure? 2 how the structure of the peptide group leads to the formation of secondary structure? 3 what is the main driving force that leads a polypeptide with regions of secondary structure to fold in an aqueous environment to... show more Follow 5 answers Answers Relevance Rating Newest Oldest Best Answer: 1 and 2) Proteins fold in three dimensions. Protein structure is organized hierarchically from so-called primary structure to quaternary structure. Higher-level structures are motifs and domains. The primary structure is the sequence of residues in the polypedptide chain. Secondary structure is a local regulary occuring structure in proteins and is mainly formed through hydrogen bonds between backbone atoms, mainly of the R-portion of aminoacids. So-called random coils, loops or turns don't have a stable secondary structure. There are two types of stable secondary structures: Alpha helices and beta-sheets. Alpha-helices and beta-sheets are preferably located at the core of the protein, whereat loops prefer to reside in outer regions. 3) Tertiary structure describes the packing of alpha-helices, beta-sheets and random coils with respect to each other on the level of one whole polypeptide chain. Included in this description is the spatial relationship of different secondary structures to one another within a polypeptide chain and how these secondary structures themselves fold into the three-dimensional form of the protein. The interactions of different domains is governed by several forces: These include hydrogen bonding, hydrophobic interactions, electrostatic interactions and van der Waals forces. The reason why secondary structures organize themselves in tertiary structures in an aqueous environment is because this is the "lowest" energy solution for the environment. Jesus is my Savior · 1 decade ago2 0 Comment1. secondary structure is the common repeating three dimensional units in the protein (as opposed to primary structure which is just the sequence of the amino acids), most commonly alpha helix or beta pleated sheet. 2. peptide groups (peptide bonds) hold the amino acids together in the chain or backbone of the protein, but they are also involved in hydrogen bonding between amino acids at a distance from each other, which leads to the contorsion of the chain which results in e.g. and alpha helix 3. again, a combination of hydrogen bonding within the secondary structure and the hydrophobicity of the side chains on the outside causes the secondary structure to folddrjaycat · 1 decade ago0 0 Comment1-the secondary structure of the protein is when the single chain (primary structure) of polypeptides for hydrogen bonds with itself to form a helix known as the alpha helix (single helix shape) or it forms hyrogen bonds when it fols on itslef to form beta pleted sheets (zigzag shape). 2- the structure is a chain of amino acids, some of the amino acids for hydrogen bonds with other amino acids furthur away from them to form the secondary structure. the tertiary structure is made between the cystine amino acids which form disulphide bonds with each other (cystine amino acids only), this turns is into a tertiary structure. there is also the quaternary structure which is made os the whole tertiary structure sitting on itself, forming ionic and hydrophibic bonds. there are different types of chaines of amino acids involved, (primary, secondary and tertiary) joined together. Anonymous · 1 decade ago0 0 Comment Proteins are an important class of biological macromolecules present in all biological organisms, made up of such elements as carbon, hydrogen, nitrogen, oxygen, and sulfur. All proteins are polymers of amino acids. The polymers, also known as peptides consist of a sequence of 20 different L-α-amino acids, also referred to as residues. For chains under 40 residues the term peptide is frequently used instead of protein. To be able to perform their biological function, proteins fold into one, or more, specific spatial conformations, driven by a number of noncovalent interactions such as hydrogen bonding, ionic interactions, Van der Waals' forces and hydrophobic packing. In order to understand the functions of proteins at a molecular level, it is often necessary to determine the three dimensional structure of proteins. This is the topic of the scientific field of structural biology, that employs techniques such as X-ray crystallography or NMR spectroscopy, to determine the structure of proteins. A certain number of residues is necessary to perform a particular biochemical function, and around 40-50 residues appears to be the lower limit for a functional domain size. Protein sizes range from this lower limit to several thousand residues in multi-functional or structural proteins. However, the current estimate for the average protein length is around 300 residues. Very large aggregates can be formed from protein subunits, for example many thousand actin molecules assemble into an actin filament Biochemists refer to four distinct aspects of a protein's structure: Primary structure: the amino acid sequence of the peptide chains Secondary structure: highly regular sub-structures--alpha helix and strands of beta sheet. Secondary structures are locally defined, meaning that there can be many different secondary motifs present in one single protein molecule Tertiary structure: Three-dimensional structure of a single protein molecule; a spatial arrangement of the secondary structures Quaternary structure: complex of several protein molecules or polypeptide chains, usually called protein subunits in this context, which function as part of the larger assembly or protein complex. In addition to these levels of structure, a protein may shift between several similar structures in performing its biological function. In the context of these functional rearrangements, these tertiary or quaternary structures are usually referred to as "conformations," and transitions between them are called conformational changes. The primary structure is held together by covalent peptide bonds, which are made during the process of translation. The two ends of the amino acid chain are referred to as the carboxy terminus (C-terminus) and the amino terminus (N-terminus) based on the nature of the free group on each extremity. The various types of secondary structure are defined by their patterns of hydrogen bonds between the main-chain peptide groups. However, these hydrogen bonds are generally not stable in themselves, since the water-amide hydrogen bond is generally more favorable than the amide-amide hydrogen bond. Thus, secondary structure is stable only when the local concentration of water is sufficiently low, e.g., in the molten globule or fully folded states. Similarly, the formation of molten globules and tertiary structure is driven mainly by structurally non-specific interactions, such as the rough propensities of the amino acids and hydrophobic interactions. However, the tertiary structure is fixed only when the parts of a protein domain are locked into place by structurally specific interactions, such as ionic interactions (salt bridges), hydrogen bonds and the tight packing of side chains. The tertiary structure of extracellular proteins can also be stabilized by disulfide bonds, which reduce the entropy of the unfolded state; disulfide bonds are extremely rare in cytosolic proteins, since the cytosol is generally a reducing environment The sequence of the different amino acids is called the primary structure of the peptide or protein. Counting of residues always starts at the N-terminal end (NH2-group), which is the end, where the amino group is not involved in a peptide bond. The primary structure of a protein is determined by the gene corresponding to the protein. A specific sequence of nucleotides in DNA is transcribed into m RNA, which is read by the ribosome in a process called translation. The sequence of a protein is unique to that protein, and defines the structure and function of the protein. The sequence of a protein can be determined by methods such as Edman degradation or tandem mass spectrometry. Often however, it is read directly from the sequence of the gene using the genetic code. Post-transcriptional modifications such as disulfide formation, phosphorylations and glycosylations are usually also considered a part of the primary structure, and cannot be read from the gene. By building models of peptides using known information about bond lengths and angles, the first elements of secondary structure, the alpha helix and the beta sheet, were suggested in 1951 by Linus Pauling and coworkers. [1] Both the alpha helix and the beta-sheet represent a way of saturating all the hydrogen bond donors and acceptors in the peptide backbone. These secondary structure elements only depend on properties that all the residues have in common, explaining why they occur frequently in most proteins. Since then other elements of secondary structure have been discovered such as various loops and other forms of helices. The part of the backbone that is not in a regular secondary structure is said to be random coil. Each of these two secondary structure elements have a regular geometry, meaning they are constrained to specific values of the dihedral angles ψ and φ. Thus the can be found in a specific region of the Ramachandran plot. The elements of secondary structure are usually folded into a compact shape using a variety of loops and turns. The formation of tertiary structure is usually driven by the burial of hydrophobic residues, but other interactions such as hydrogen bonding, ionic interactions and disulfide bonds can also stabilize a the tertiary structure. The tertiary structure encompasses all the noncovalent interactions that are not considered secondary structure, and is what defines the overall fold of the protein, and is usually indispensable for the function of the protein. The quarternary structure is the interaction between several chains of peptide bonds. The individual chains are called subunits. The individual subunits are not necessarily covalently connected, but might be connected by a disulfide bond. Not all proteins have quarternary structure, since they might be functional as monomers. The quarternary structure is stabilized by the same range of interactions as the tertiary structure. Complexes of two or more polypeptides (i.e. multiple subunits) are called multimers. Specifically it would be called a dimer if it contains two subunits, a trimer if it contains three subunits, and a tetramer if it contains four subunits. Multimers made up of identical subunits may be referred to with a prefix of "homo-" (e.g. a homotetramer) and those made up of different subunits may be referred to with a prefix of "hetero-" (e.g. a heterodimer). Source (s):bookswatsup · 1 decade ago0 1 Comment THANKS? · 2 years ago0 0 Comment Perhaps you would like to learn more about one of these? Time for a Caribbean cruise? How Does Cloud Computing Work? Want to build your own website? Need Home Equity Loan Options?  . The Giant Molecules of Life Proteins Amino Acids The building blocks of all proteins are the amino acids. There are about 20 common amino acids, all but one of them have a structure based on a single atom of carbon, to which is attached four different atoms or groups of atoms; a hydrogen atom, an amine group, a carboxylic acid group and a variable group (called here an R-group ). It is the varying chemical structure and properties of the R-group that make the amino acids different from one another. About 9 amino acids have non-polar R-groups and are relatively hydrophobic. Another 6 amino acids have strongly polar R-groups which readily attract water molecules. These are hydrophilic amino acids. The remainder, about 5 amino acids, have R-groups which can ionize. At normal cellular p H's these R-groups become electrically charged, making them even more hydrophilic than the polar amino acids. Some of the Amino Acids Amino Acid Abreviation% in hemoglobin # molecules in insulin Year discovered Alanine Ala 9.0 3 1875Aspartic Acid Asp 9.6 0 1868Glutamic Acid Glu 6.6 4 1866Histidine His 8.8 2 1896Leucine Leu 14.0 6 1819Proline Pro 4.8 1 1901Serine Ser 4.4 3 1865Tyrosine Tyr 2.9 4 1846Polypeptides I: Primary Structure Polymers of amino acids are called "polypeptides", a name which comes from the type of bond holding the chains of amino acids together. In a joining reaction called a "condensation" or "dehydration synthesis" the nitrogen atom of one amino acid is directly linked to the carbon atom in the acid group of the second amino acid. During this molecular rearrangement, a molecule of water is produced. The resulting group of atoms, which hold the amino acids together, is called a peptide bond. Any of the 20 different amino acids can occur in any position along a polypeptide chain. This means that there is a very large number of possible chains, even at lengths of only a few amino acids. The number, and sequence, of amino acids in a polypeptide chain is called the primary structure. Every type of polypeptide produced by a cell has a different primary structure. This is a carefully controlled property of the chain and is regulated by the genetic code found in the genes and DNA molecules. All the other properties of polypeptides and proteins stem from the primary structure. Polypeptides II: Secondary Structure In water, polypeptides act and react with themselves and with their environment. The sum of all the forces acting on the complex chains, and their chemical R-groups, bends, twists and forces the polypeptide into fantastic shapes. They coil and fold into complicated three dimensional conformations which are critical to their roles and properties inside cells. The lowest level of three dimensional shape is called the secondary structure. Three types of common secondary structure can be recognized. Random Walk is seen in regions of polypeptide where the constituent R-groups act and react to one another. A positively charged R-group could be attracted to a negatively charged R-group forcing the chain to bend until the two R-groups come close together. Alternatively, a second positively charged R-group further down the chain would be repelled by the first positive charge. The chain would stretch out so as to put the largest possible distance between these charges. Beta Pleated Sheet is a flexible, strong configuration in which alternate R-groups extend away from the backbone of the chain in opposite directions. This produces a zig-zag effect which is held in place by cross linking hydrogen bonds between adjacent chains. Silk protein, beta-keratin, spider webs, your nails, all contain proteins with high proportions of beta pleated sheet. These proteins resist stretching since their chains are almost fully extended as it is. Alpha Helix is a common form of secondary structure seen in many proteins. A series of weak hydrogen bonds form between the atoms of one peptide bond and the atoms of another peptide bond about 3 amino acids further down the chain. These tiny interactions, are, never the less, strong enough to coil the polypeptide into an alpha helix; a structure that looks some what as if the chain of amino acids had been wrapped around a cylinder. These spiral, helical molecules can be stretched. Some proteins, with high helical content, extend easily. Hair and wool readily stretch, but, when the force is released, the helix snaps back into its original conformation, and the protein returns to its original shape. Tertiary Structure; becoming a protein Most proteins fold into complex, three dimensional, globular shapes. Hydrophilic R-groups interact positively with the surrounding water. The entire chain twists until the maximum number of these groups are in full contact with the surrounding water. The interplay between water and the hydrophilic R-groups support the huge protein molecule and help keep it in solution. Conversely, the hydrophobic R-groups become buried deep within the folding macromolecule, far away from the water molecules. These forces, together with other cross-linking effects, hold the giant structure in a three dimensional shape which is distinctive and unique to that protein. It is at this level of structure that many proteins take on their cellular role or function. As a polypeptide chain, the molecule had no special properties, but as a three dimensional protein, the molecule is capable of performing an astonishing variety of feats. Globular proteins catalyze chemical reactions, others act as defending antibodies within the immune system, and yet others trigger violent bodily reactions as they travel through the blood. Quaternary Structure Some globular proteins come together in complexes consisting of two or more subunits. Attached to these subunits can be other, non protein, molecules such as polysaccharides. These higher levels of structure can be seen in a protein molecule such as hemoglobin, a large, four subunit globular protein with four additional non protein additions. This protein carries oxygen around in the blood. Denaturation. Most of the special properties of proteins stem from their unique three dimensional shapes. When this shape is lost, the protein ceases to function. The process of changing the shape of a protein so that the function is lost is called denaturation. Proteins are easily denatured by heat. When protein molecules are boiled their properties change. For example, they frequently become insoluble and remain so even when the solution is cooled. Boiling an egg causes the irreversible denaturation of all the proteins it contains, the "white" of the egg, a globular protein, changes shape and hardens into a solid. This denatured protein has the same primary structure as the original protein, but the tertiary structure has been lost; so have all the critical properties of the original or native protein. Denaturation can be brought about in other ways as well as heat. All proteins can be denatured by extremes of p H; alkaline or acid. They are sensitive to organic solvents and soaps. Beating an egg white will cause mechanical denaturation by increasing the surface area of the liquid. Surface tension then pulls the protein out of shape. *** Make a Dipeptide ***  The Function and Structure of Proteins Science, Tech, Math ›Science The Function and Structure of Proteins Share Flipboard Email Print Laguna Design / Science Photo Library / Getty Imagesby Regina Bailey Updated October 16, 2017Proteins are very important molecules in our cells and are essential for all living organisms. By weight, proteins are collectively the major component of the dry weight of cells and are involved in virtually all cell functions. Each protein within the body has a specific function, from cellular support to cell signaling and cellular locomotion. In total, there are seven types of proteins, including antibodies, enzymes, and some types of hormones, such as insulin. While proteins have many diverse functions, all are typically constructed from one set of 20 amino acids. The structure of a protein may be globular or fibrous, and the design helps each protein with their particular function. In all, proteins are absolutely fascinating and a complex subject. Let's explore the basics of these essential molecules and discover what they do for us. Antibodies Antibodies are specialized proteins involved in defending the body from antigens (foreign invaders). They can travel through the bloodstream and are utilized by the immune system to identify and defend against bacteria, viruses, and other foreign intruders. One way antibodies counteract antigens is by immobilizing them so they can be destroyed by white blood cells. Contractile Proteins Contractile proteins are responsible for muscle contraction and movement. Examples of these proteins include actin and myosin. Enzymes Enzymes are proteins that facilitate biochemical reactions. They are often referred to as catalysts because they speed up chemical reactions. Enzymes include lactase and pepsin, which you might hear of often when learning about specialty diets or digestive medical conditions. Lactase breaks down the sugar lactose found in milk. Pepsin is a digestive enzyme that works in the stomach to break down proteins in food. Hormonal Proteins Hormonal proteins are messenger proteins which help to coordinate certain bodily activities. Examples include insulin, oxytocin, and somatotropin. Insulin regulates glucose metabolism by controlling the blood-sugar concentration. Oxytocin stimulates contractions during childbirth. Somatotropin is a growth hormone that stimulates protein production in muscle cells. Structural Proteins Structural proteins are fibrous and stringy and because of this formation, they provide support for various body parts. Examples include keratin, collagen, and elastin. Keratins strengthen protective coverings such as skin, hair, quills, feathers, horns, and beaks. Collagens and elastin provide support for connective tissues such as tendons and ligaments. Storage Proteins Storage proteins store amino acids for the body to use later. Examples include ovalbumin, which is found in egg whites, and casein, a milk-based protein. Ferritin is another protein that stores iron in the transport protein, hemoglobin. Transport Proteins Transport proteins are carrier proteins which move molecules from one place to another around the body. Hemoglobin is one of these and is responsible for transporting oxygen through the blood via red blood cells. Cytochromes are another that operate in the electron transport chain as electron carrier proteins. Amino Acids and Polypeptide Chains Amino acids are the building blocks of all proteins, no matter their function. Most amino acids follow a particular structural property in which a carbon (the alpha carbon) is bonded to four different groups: A hydrogen atom (H)A Carboxyl group (-COOH)An Amino group (-NH2)A "variable" group Of the 20 amino acids that typically make up proteins, the "variable" group determines the differences among the amino acids. All amino acids have the hydrogen atom, carboxyl group, and amino group bonds. Amino acids are joined together through dehydration synthesis to form a peptide bond. When a number of amino acids are linked together by peptide bonds, a polypeptide chain is formed. One or more polypeptide chains twisted into a 3-D shape forms a protein. Protein Structure We can divide the structure of protein molecules into two general classes: globular proteins and fibrous proteins. Globular proteins are generally compact, soluble, and spherical in shape. Fibrous proteins are typically elongated and insoluble. Globular and fibrous proteins may exhibit one or more types of protein structure. There are four levels of protein structure: primary, secondary, tertiary, and quaternary. These levels are distinguished from one another by the degree of complexity in the polypeptide chain. A single protein molecule may contain one or more of these protein structure types. The structure of a protein determines its function. For example, collagen has a super-coiled helical shape. It is long, stringy, strong, and resembles a rope, which is great for providing support. Hemoglobin, on the other hand, is a globular protein that is folded and compact. Its spherical shape is useful for maneuvering through blood vessels. In some cases, a protein may contain a non-peptide group. These are called cofactors and some, such as coenzymes, are organic. Others are an inorganic group, such as a metal ion or iron-sulfur cluster. Protein Synthesis Proteins are synthesized in the body through a process called translation. Translation occurs in the cytoplasm and involves the translation of genetic codes into proteins. The gene codes are assembled during DNA transcription, where DNA is transcribed into an RNA transcript. Cell structures called ribosomes help translate the gene codes in RNA into polypeptide chains that undergo several modifications before becoming fully functioning proteins.cite  . Exploring the Molecules of Life: Proteins What is the major function of proteins in the human body? Why does having a perm (or permanent) make your hair curly? Proteins are the most important biological compounds needed for life and are used for many purposes in the human body. They act as the structural materials in humans and animals as cellulose does in plants. Enzymes are proteins that catalyze the body's chemical reactions. Proteins make up muscles that aid in movement. The curl from a perm involves the resetting of attractive forces in the protein of hair. Proteins are made up of chains of amino acids. For example, here is the simplest amino acid glycine. Can you find what element is present in proteins that is not present in carbohydrates? What is the oxygen-containing functional group? Amino acids are organic compounds that contain an amine group (- N H 2) bonded to a carbon atom that is bonded to a carboxylic acid group (- C OO H) as seen below. Remember you saw the carboxylic acid group in fatty acids. C an you find the two functional groups above? For glycine the R group is a hydrogen, H. Other side chains or R groups make up other amino acids. There are about 20 amino acids that naturally form in nature. We can classify amino acids into four major groups, each characterized by its type of side chain: non-polar, polar but neutral, acidic, and basic. Click here to go to a good site displaying the amino acids. Amino acids can bond together forming what is called a peptide bond (which is also called a amide linkage) . The amine group (- N H 2 ) of one amino acid bonds to the carboxylic acid group (- C OO H ) of another amino acid as seen below for the general case, where the R groups are different. Here is an example of phenylalanine and lysine combining together. The product, phe-lys, does not have any hydrogen showing to make viewing easier. Orient the individual amino acids to help see how they combine. For the two linked amino acids or phe-lys, you may want to right click and select 2D structure to compare to the reaction above.phenylalanine lysine the two linked Can you see where these two amino acids will come together to form a bond? Describe it. Looking at the structure of combination of the two, what is lost when the two amino acids bond together? Peptide bonds are formed by loosing an (- O H ) and a (- H ). What do you call two amino acids bonded together? Could you bond a third amino acid to the two-bonded amino acids above? Why or why not? Two amino acids bonded together produce a dipeptide. Di means two, therefore if three are bonded together the product is a tripeptide. If many amino acids are bonded together the product would be a polypeptide. Notice that there is still an amine group and a carboxylic acid group in the final product. What do long chains of amino acids produce? When many amino acids bond together they form a protein, which is used in many functions in living organism. Can phenylalanine and lysine be bonded a different way to get the same product? As you can see (phe-lys) and (lys-phe) are not the same products. These are two different dipeptides. They have the same formula but they both have different properties. They are known as isomers. Isomers are compounds that are different in properties but they have the same molecular formula. To link a pair of amino acids together requires one peptide linkage. How many peptide linkages occur in a tripeptide? How many in a tetrapeptide? Click here to go to a website that will allow you to build a polypeptide. Here is a longer chain of amino acids. Does the main part of the amino acid chain look like a hydrocarbon chain? Can you count how many amino acid linkages make up this chain? How many amino acids actually make up this chain? There are six amino acids present in this chain. Can you see them? Can you also name each individual amino acid in this chain? Click here to go to the site to see the individual structures, names and official abbreviations of the 20 amino acids found in nature. Here is the sequence of amino acids that make up hexapeptide above:val-cys-lys-asp-phe-cys The order of the linkage of amino acids or the sequence is the basis of the primary structure of proteins. Here is a brief table of proteins with their function, number of amino acids, and the resultant molar mass. Protein Function Number of amino acids Molar Mass (g/mole)Insulin enzyme for sugar metabolism 51 6000Cytochrome c enzyme for cell respiration 104 16000Growth Hormone used in anti-aging treatment 191 49000Hemoglobin oxygen transport in blood 574 65000Hexokinase enzyme for glycolysis 730 96000Gamma Globulin part of immune system in blood 1320 176000Myosin muscle action 6100 800000Modified from: Seager & Slabaugh , Organic and Biochemistry for Today, 4th ed, Brooks/Cole (2000)Here is a simplified protein structure that is made up of nine amino acids. How does this structure in terms of the backbone (not the number of amino acids) differ from the hexapeptide above? How would you describe the shape of each structure? Be sure to click on the molecule to move it around so you can see this. Selected hydrogen atoms have been removed to make viewing of the structure easier. The structure above is an alpha helix that has been simplified by removing the side chains, or R groups. What attractive force holds the helix in its shape? ( Right click on the image, go to options, then select display hydrogen bonds. )The structure below is more realistic as it displays different amino acids in the helix. Be sure to click on the molecule to move it around so you can see the nature of the helix. Now look at the simplified structure composed of only glycine below. What is the structural difference between this one and the two helix proteins above? Do you think that you can find where hydrogen bonding will take place? The three chains in this structure above are aligned parallel to each other and they are held together by hydrogen bonding. Here is a real sheet protein, composed of many amino acid. See if you can see the sheet structure. If you right click, go to display and then select cartoon, you may be able to visualize the structure easier. These proteins are known as sheet proteins. The helix and sheet structures are the two most common secondary structures in proteins. The structure of myoglobin, which aids in oxygen transport to muscles, is given below. How does myoglobin compare to the other proteins shown above? Let's change the display of the protein- Right click on the image, go to display, then select cartoons. Is the chain of amino acids one continuous chain? Myoglobin is one continuous chain of amino acids that is folded and twisted. This folding and twisting forms the basis of the tertiary structure of a protein. What attractive forces do you think keeps the folds in place? The structure of insulin is given below. Do you see any similarities in the structure with those of the helix and sheet structures you have seen already? Let's change the display of the protein- Right click on the image, go to display, then select cartoons. Now what do you notice about the structure of insulin? Is the chain of amino acids one continuous chain? Is there any sulfur in the protein? Insulin is the hormone in the body that regulates the blood's glucose level. It is a small protein that only consists of 51 amino acids and contains two polypetide chains linked together. The structure of insulin is an example of a protein with a quaternary structure. The adjacent sulfurs in the cysteine forms disulfide linkages to help hold the structure along with hydrogen bonding. Here is an excellent tutorial on insulin- click here . (must use Netscape to view)Compare the structure of hemoglobin, which transports oxygen in blood, given below with that of insulin. Be sure to right click on the image, go to display, then select cartoons. What do you notice about the difference in structure? Now right click again on the image of hemoglobin, go to color, then select chain. How many subunits in hemoglobin? Insulin and hemoglobin are examples of proteins with quaternary structure. Quaternary structure is the highest level of protein organization and it only applies to proteins with more than one polypeptide chain. The four subunits of amino acids are held tightly together in a compact shape as you can see with hemoglobin. However not all proteins have a quaternary structure. The tertiary and quaternary structures of proteins are aided by a number of attractive forces which include hydrogen bonding and the three below:1. d isulfide linkages between -SH groups to form -S-S- from the occurrence of cysteine2. salt bridges between ionized -COO - and -NH 3+3. hydrophobic interactions between non-polar groups such as phenyl groups from phenylalanine The molar mass of a protein can be experimentally determined by osmotic pressure measurements. How might you estimate the number of amino acids in a protein from its molar mass? In a protein with a very specific biological function, does changing one of the amino acids in the sequence make any different how the protein functions? Do a web search on sickle cell anemia to find out. Here is the structure of concanavalin A monomer. How would you describe this protein in terms of its primary, secondary, tertiary, and quaternary structure? This monomer has a molar mass of 18,000 g/mole. How many amino acids in the monomer? Is this a continuous chain of amino acids? For more information on the concanavalin A monomer- click here. An excellent website on proteins and amino acids can be found at UCSB by Duane Sears - click here . Then click on the TABS near the top of the page. Many of the structures on this page are from the molecules collection available at the NSF-funded C4 Project at Cabrillo Community College. Return to Exploring the Molecules of Life homepage.  Biomolecular structure From Wikipedia, the free encyclopedianavigation search It has been suggested that this article be merged with Structural biology. ( Discuss) Proposed since February 2018. This article may be confusing or unclear to readers. Please help us clarify the article. There might be a discussion about this on the talk page. (February 2016) ( Learn how and when to remove this template message)Interactive diagram of protein structure, using PCNA as an example. ( PDB: 1AXC ) Interactive image of nucleic acid structure (primary, secondary, tertiary, and quaternary) using DNA helices and examples from the VS ribozyme and telomerase and nucleosome. ( PDB: ADNA, 1BNA, 4OCB, 4R4V, 1YMO, 1EQZ )Biomolecular structure is the intricate folded, three-dimensional shape that is formed by a molecule of protein, DNA, or RNA, and that is important to its function. The structure of these molecules may be considered at any of several length scales ranging from the level of individual atoms to the relationships among entire protein subunits. This useful distinction among scales is often expressed as a decomposition of molecular structure into four levels: primary, secondary, tertiary, and quaternary. The scaffold for this multiscale organization of the molecule arises at the secondary level, where the fundamental structural elements are the molecule's various hydrogen bonds. This leads to several recognizable domains of protein structure and nucleic acid structure, including such secondary-structure features as alpha helixes and beta sheets for proteins, and hairpin loops, bulges, and internal loops for nucleic acids. The terms primary, secondary, tertiary, and quaternary structure were introduced by Kaj Ulrik Linderstrøm-Lang in his 1951 Lane Medical Lectures at Stanford University. Contents [ hide ]1 Primary structure2 Secondary structure3 Tertiary structure4 Quaternary structure5 Structure determination6 Structure prediction7 Design8 Other biomolecules9 See also10 References Primary structure [ edit]Further information: Protein primary structure and Nucleic acid primary structure The primary structure of a biopolymer is the exact specification of its atomic composition and the chemical bonds connecting those atoms (including stereochemistry ). For a typical unbranched, un-crosslinked biopolymer (such as a molecule of a typical intracellular protein, or of DNA or RNA ), the primary structure is equivalent to specifying the sequence of its monomeric subunits, such as peptides or nucleotides. Primary structure is sometimes mistakenly termed primary sequence, but there is no such term, as well as no parallel concept of secondary or tertiary sequence. By convention, the primary structure of a protein is reported starting from the amino terminal (N) to the carboxyl terminal (C), while the primary structure of DNA or RNA molecule is reported from the 5′ end to the 3′ end. The primary structure of a nucleic acid molecule refers to the exact sequence of nucleotides that comprise the whole molecule. Often, the primary structure encodes sequence motifs that are of functional importance. Some examples of such motifs are: the C/D [1] and H/ACA boxes [2] of sno RNAs, LSm binding site found in spliceosomal RNAs such as U1, U2, U4, U5, U6, U12 and U3, the Shine-Dalgarno sequence, [3] the Kozak consensus sequence [4] and the RNA polymerase III terminator. [5]Secondary structure [ edit]Further information: Protein secondary structure and Nucleic acid secondary structure Secondary (inset) and tertiary structure of t RNA demonstrating coaxial stacking PDB: 6TNA 6TNA )The secondary structure is the pattern of hydrogen bonds in a biopolymer. These determine the general three-dimensional form of local segments of the biopolymers, but does not describe the global structure of specific atomic positions in three-dimensional space, which are considered to be tertiary structure. Secondary structure is formally defined by the hydrogen bonds of the biopolymer, as observed in an atomic-resolution structure. In proteins, the secondary structure is defined by patterns of hydrogen bonds between backbone amine and carboxyl groups (sidechain–mainchain and sidechain–sidechain hydrogen bonds are irrelevant), where the DSSP definition of a hydrogen bond is used. In nucleic acids, the secondary structure is defined by the hydrogen bonding between the nitrogenous bases. For proteins, however, the hydrogen bonding is correlated with other structural features, which has given rise to less formal definitions of secondary structure. For example, in general residues in protein, helices adopt backbone dihedral angles in some region of the Ramachandran plot; thus, a segment of residues with such dihedral angles is often called a helix, regardless of whether it has the correct hydrogen bonds. Many other less formal definitions have been proposed, often applying concepts from the differential geometry of curves, such as curvature and torsion. Structural biologists solving a new atomic-resolution structure will sometimes assign its secondary structure by eye and record their assignments in the corresponding Protein Data Bank (PDB) file. The secondary structure of a nucleic acid molecule refers to the base pairing interactions within one molecule or set of interacting molecules. The secondary structure of biological RNA's can often be uniquely decomposed into stems and loops. Often, these elements or combinations of them can be further classified, e.g. tetraloops, pseudoknots and stem loops. There are many secondary structure elements of functional importance to biological RNA. Famous examples include the Rho-independent terminator stem loops and the transfer RNA (t RNA) cloverleaf. There is a minor industry of researchers attempting to determine the secondary structure of RNA molecules. Approaches include both experimental and computational methods (see also the List of RNA structure prediction software ). Tertiary structure [ edit]Further information: Protein tertiary structure and Nucleic acid tertiary structure The tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates. [6] Proteins and nucleic acids fold into complex three-dimensional structures which result in the molecules' functions. While such structures are diverse and complex, they are often composed of recurring, recognizable tertiary structure motifs and domains that serve as molecular building blocks. Tertiary structure is considered to be largely determined by the biomolecule's primary structure (its sequence of amino acids or nucleotides ). Quaternary structure [ edit]Further information: Protein quaternary structure and Nucleic acid quaternary structure The quaternary structure refers to the number and arrangement of multiple protein molecules in a multi-subunit complex. For nucleic acids, the term is less common, but can refer to the higher-level organization of DNA in chromatin, [7] including its interactions with histones, or to the interactions between separate RNA units in the ribosome [8] [9] or spliceosome. Structure determination [ edit]Further information: Protein structure and Nucleic acid structure determination Structure probing is the process by which biochemical techniques are used to determine biomolecular structure. [10] This analysis can be used to define the patterns that can be used to infer the molecular structure, experimental analysis of molecular structure and function, and further understanding on development of smaller molecules for further biological research. [11] Structure probing analysis can be done through many different methods, which include chemical probing, hydroxyl radical probing, nucleotide analog interference mapping (NAIM), and in-line probing. [10]Protein and nucleic acid structures can be determined using either nuclear magnetic resonance spectroscopy ( NMR) or X-ray crystallography or single-particle cryo electron microscopy ( cryo EM ). The first published reports for DNA (by Rosalind Franklin and Raymond Gosling in 1953) of A-DNA X-ray diffraction patterns —and also B-DNA—used analyses based on Patterson function transforms that provided only a limited amount of structural information for oriented fibers of DNA isolated from calf thymus. [12] [13] An alternate analysis was then proposed by Wilkins et al. in 1953 for B-DNA X-ray diffraction and scattering patterns of hydrated, bacterial-oriented DNA fibers and trout sperm heads in terms of squares of Bessel functions. [14] Although the '`B-DNA form' is most common under the conditions found in cells, [15] it is not a well-defined conformation but a family or fuzzy set of DNA conformations that occur at the high hydration levels present in a wide variety of living cells. [16] Their corresponding X-ray diffraction & scattering patterns are characteristic of molecular paracrystals with a significant degree of disorder (over 20%), [17] [18] and the structure is not tractable using only the standard analysis. In contrast, the standard analysis, involving only Fourier transforms of Bessel functions [19] and DNA molecular models, is still routinely used to analyze A-DNA and Z-DNA X-ray diffraction patterns. [20]Structure prediction [ edit]Saccharomyces cerevisiae t RNA-Phe structure space: the energies and structures were calculated using RNAsubopt and the structure distances computed using RNAdistance. Further information: Protein structure prediction and Nucleic acid structure prediction Biomolecular structure prediction is the prediction of the three-dimensional structure of a protein from its amino acid sequence, or of a nucleic acid from its nucleobase (base) sequence. In other words, it is the prediction of secondary and tertiary structure from its primary structure. Structure prediction is the inverse of biomolecular design, as in rational design, protein design, nucleic acid design, and biomolecular engineering. Protein structure prediction is one of the most important goals pursued by bioinformatics and theoretical chemistry. Protein structure prediction is of high importance in medicine (for example, in drug design) and biotechnology (for example, in the design of novel enzymes ). Every two years, the performance of current methods is assessed in the Critical Assessment of protein Structure Prediction ( CASP) experiment. There has also been a significant amount of bioinformatics research directed at the RNA structure prediction problem. A common problem for researchers working with RNA is to determine the three-dimensional structure of the molecule given only the nucleic acid sequence. However, in the case of RNA, much of the final structure is determined by the secondary structure or intra-molecular base-pairing interactions of the molecule. This is shown by the high conservation of base pairings across diverse species. Secondary structure of small nucleic acid molecules is determined largely by strong, local interactions such as hydrogen bonds and base stacking. Summing the free energy for such interactions, usually using a nearest-neighbor method, provides an approximation for the stability of given structure. [21] The most straightforward way to find the lowest free energy structure would be to generate all possible structures and calculate the free energy for them, but the number of possible structures for a sequence increases exponentially with the length of the molecule. [22] For longer molecules, the number of possible secondary structures is vast. [21]Sequence covariation methods rely on the existence of a data set composed of multiple homologous RNA sequences with related but dissimilar sequences. These methods analyze the covariation of individual base sites in evolution; maintenance at two widely separated sites of a pair of base-pairing nucleotides indicates the presence of a structurally required hydrogen bond between those positions. The general problem of pseudoknot prediction has been shown to be NP-complete. [23]Design [ edit]Further information: Protein design and Nucleic acid design Biomolecular design can be considered the inverse of structure prediction. In structure prediction, the structure is determined from a known sequence, whereas, in protein or nucleic acid design, a sequence that will form a desired structure is generated. Other biomolecules [ edit]This section needs expansion. You can help by adding to it. (April 2010)Other biomolecules, such as polysaccharides, polyphenols and lipids, can also have higher-order structure of biological consequence. See also [ edit]Molecular and cellular biology portal Comparison of nucleic acid simulation software Gene structure List of RNA structure prediction software Non-coding RNAReferences [ edit]^ Samarsky, D. A.; Fournier, M. J.; Singer, R. H.; Bertrand, E. (1998). "The sno RNA box C/D motif directs nucleolar targeting and also couples sno RNA synthesis and localization". EMBO J. 17 (13): 3747–3757. doi: 10.1093/emboj/17.13.3747. PMC 1170710. PMID 9649444.^ Ganot, Philippe; Caizergues-Ferrer, Michèle; Kiss, Tamás (1 April 1997). "The family of box ACA small nucleolar RNAs is defined by an evolutionarily conserved secondary structure and ubiquitous sequence elements essential for RNA accumulation". Genes Dev. 11 (7): 941–956. doi: 10.1101/gad.11.7.941. PMID 9106664.^ Shine, J.; Dalgarno, L. (1975). "Determinant of cistron specificity in bacterial ribosomes". Nature. 254 (5495): 34–38. Bibcode: 1975Natur.254...34S. doi: 10.1038/254034a0. PMID 803646.^ Kozak, M. (October 1987). "An analysis of 5′-noncoding sequences from 699 vertebrate messenger RNAs". Nucleic Acids Res. 15 (20): 8125–8148. doi: 10.1093/nar/15.20.8125. PMC 306349. PMID 3313277.^ Bogenhagen, D. F.; Brown, D. D. (1981). "Nucleotide sequences in Xenopus 5S DNA required for transcription termination". Cell. 24 (1): 261–270. doi: 10.1016/0092-8674 (81)90522-5. PMID 6263489.^ IUPAC, Compendium of Chemical Terminology, 2nd ed. (the "Gold Book") (1997). Online corrected version: (2006–) " tertiary structure ".^ Sipski, M. Leonide; Wagner, Thomas E. (1977). "Probing DNA quaternary ordering with circular dichroism spectroscopy: Studies of equine sperm chromosomal fibers". Biopolymers. 16 (3): 573–582. doi: 10.1002/bip.1977.360160308. PMID 843604.^ Noller, H. F. (1984). "Structure of Ribosomal RNA". Annual Review of Biochemistry. 53: 119–162. doi: 10.1146/annurev.bi.53.070184.001003. PMID 6206780.^ Nissen, P.; Ippolito, J. A.; Ban, N.; Moore, P. B.; Steitz, T. A. (2001). "RNA tertiary interactions in the large ribosomal subunit: The A-minor motif". Proceedings of the National Academy of Sciences of the United States of America. 98 (9): 4899–4903. Bibcode: 2001PNAS...98.4899N. doi: 10.1073/pnas.081082398. PMC 33135. PMID 11296253.^ a b Teunissen, A. W. M. (1979). RNA Structure Probing: Biochemical structure analysis of autoimmune-related RNA molecules. pp. 1–27. ISBN 90-901323-4-1.^ Pace, N. R.; Thomas, B. C.; Woese, C. R. (1999). Probing RNA Structure, Function, and History by Comparative Analysis. Cold Spring Harbor Laboratory Press. pp. 113–117. ISBN 0-87969-589-7.^ Franklin, R. E.; Gosling, R. G. (6 March 1953). "The Structure of Sodium Thymonucleate Fibres (I. The Influence of Water Content, and II. The Cylindrically Symmetrical Patterson Function)". Acta Crystallogr. 6: 673–678. doi: 10.1107/s0365110x53001939.^ Franklin, R. E.; Gosling, R. G. (1953). "Molecular Configuration in Sodium Thymonucleate" (PDF). Nature. 171 (4356): 740–741. Bibcode: 1953Natur.171..740F. doi: 10.1038/171740a0. PMID 13054694.^ Wilkins, M. H. F.; Stokes, A. R.; Wilson, H. R. (1953). "Molecular Structure of Deoxypentose Nucleic Acids" (PDF). Nature. 171 (4356): 738–740. Bibcode: 1953Natur.171..738W. doi: 10.1038/171738a0. PMID 13054693.^ Leslie, A. G.; Arnott, S.; Chandrasekaran, R.; Ratliff, R. L. (1980). "Polymorphism of DNA double helices". J. Mol. Biol. 143 (1): 49–72. doi: 10.1016/0022-2836 (80)90124-2. PMID 7441761.^ Baianu, I. C. (1980). "Structural Order and Partial Disorder in Biological systems". Bull. Math. Biol. 42 (1): 137–41. doi: 10.1007/BF02462372.^ Hosemann, R.; Bagchi, R. N. (1962). Direct analysis of diffraction by matter. Amsterdam/New York: North-Holland.^ Baianu, I. C. (1978). "X-ray scattering by partially disordered membrane systems". Acta Crystallogr. A. 34: 751–753. Bibcode: 1978Ac Cr A..34..751B. doi: 10.1107/s0567739478001540.^ "Bessel functions and diffraction by helical structures". planetphysics.org. [ permanent dead link]^ "X-Ray Diffraction Patterns of Double-Helical Deoxyribonucleic Acid (DNA) Crystals". planetphysics.org. Archived from the original on 24 July 2009.^ a b Mathews, D. H. (2006). "Revolutions in RNA secondary structure prediction". J. Mol. Biol. 359: 526–532. doi: 10.1016/j.jmb.2006.01.067. PMID 16500677.^ Zuker, M.; Sankoff, D. (1984). "RNA secondary structures and their prediction". Bull. Math. Biol. 46: 591–621. doi: 10.1016/s0092-8240 (84)80062-2.^ Lyngsø, R. B.; Pedersen, C. N. (2000). "RNA pseudoknot prediction in energy-based models". J. Comput. Biol. 7 (3–4): 409–427. doi: 10.1089/106652700750050862. PMID 11108471. [ hide]v t e Biomolecular structure Protein structure Primary Secondary Tertiary Quaternary Determination Prediction Design Thermodynamics Nucleic acid structure Primary Secondary Tertiary Quaternary Determination Prediction Design Thermodynamics See also Protein Protein domain Protein engineering Nucleic acid DNA RNA Nucleic acid double helix Categories: Biomolecules  Amino Acids Amino Acids The naturally occurring amino acids have a common structure. Amino acids, as the name implies, have two functional groups, an amino group (–NH 2) and a carboxyl group (–COOH). These groups are joined to a single (aliphatic) carbon. In organic chemistry, the carbon directly attached to a carboxyl group is the alpha (α) position, so the amino acids in proteins are all alpha‐amino acids. The side chains that distinguish one amino acid from another are attached to the alpha carbon, so the structures are often written as shown in Figure, where R stands for one of the 20 side chains: Figure 1The amino acids found in proteins have a common stereochemistry. In the structure illustrated in Figure, the amino group is always to the left side of the alpha carbon. In organic chemistry, this stereochemistry is referred to as L (for levo, meaning left). Thus, the amino acids found in proteins are L‐alpha amino acids. (Biochemists, being creatures of habit, usually do not refer to amino acid stereochemistry in the R and S nomenclature.) A few D‐amino acids are found in nature, although not in cellular proteins. (The D comes from dextro, meaning right.) For example, some peptide antibiotics, such as bacitracin, contain D‐amino acids. The carboxyll and amino groups of the amino acids can respectively donate a proton to and accept a proton from water. This exchange happens simultaneously in solution so that the amino acids form doubly ionized species, termed zwitterions (from German zwei, meaning two) in solution. The formation of zwitterions can be rationalized from the principles of acid‐base chemistry. The strongest acid that can exist in water is the conjugate acid of water, the hydronium ion, H 3 O +. Carboxyllic acids are stronger acids than water, so the carboxyl group of an amino acid (p K a near 2) will donate a proton to water. Similarly, α‐amino groups (p K a greater than 9) are stronger bases than water and will accept a proton from water. Amino acids in water, therefore, have the general structure: Amino acid side chains The side chains of amino acids give them their different chemical properties and allow proteins to have so many different structures. How many proteins are possible? Protein chains generally vary in size from 100 to 1,000 amino acids in length. Even if limited to the smallest chain length, there would be 20 100, over 10 130 —that is, 1 with 130 zeroes after it—possible primary structures. (Again, remember that the number of elementary particles in the universe is estimated to be 10 80 .) Obviously, not all these potential proteins exist in nature. Instead, the primary structures of proteins are related to each other, and almost all proteins have homologues, that is, other proteins sharing a common ancestor. What homologues are possible? In general, homologous proteins share some short amino acid sequences exactly. In other cases, the differences result in the substitution of one amino acid side chain by another chemically similar one. Six classes of amino acid side chains exist; within a group, the amino acid side chains are chemically similar. Substitution of one amino acid side chain for another one within the same group is known as conservative substitution. Homologous proteins are related by conservative amino acid substitutions, as in Figure. Although nonconservative substitutions are tolerated at some positions in the primary sequence of a protein, the general rule illustrated in Figure is followed when evaluating the relationship of two protein primary sequences. (The dashes indicate that all three proteins have the same amino acid at that position—these are highly homologous proteins, indeed! )Figure 2Aliphatic amino acids. The side chains of glycine, alanine, valine, leucine, and isoleucine, shown in Figure, contain saturated carbon‐carbon and carbon‐hydrogen bonds only. Thinking of glycine as containing a side chain can be somewhat confusing because the fourth substituent on the α‐carbon is only a single hydrogen atom. Alone among the 20 amino acids, glycine is not optically active; the D‐ and L‐ nomenclature is irrelevant. Alanine has a methyl group for its side chain, valine a 3‐carbon side chain, while leucine and isoleucine have 4‐carbon side chains. Figure 3Aromatic amino acids. Phenylalanine, tyrosine, and tryptophan contain ring systems. In order of increasing complexity, phenylalanine has a benzyl group, while tyrosine is phenylalanine with an added hydroxyl group in the trans position relative to the methyl group. Tryptophan has two rings, one of which contains a nitrogen atom. The nitrogen is not ionizable at biologically relevant p H values. Ionizable basic amino acids. Histidine, lysine, and arginine each have a nitrogen atom which, unlike the nitrogen of tryptophan, is ionized at the p H ranges found in the cell. Histidine has a 5‐member imidazole ring. One of the two nitrogen ions has a p K a near 7.0. This means that, at the neutral p H values found in cells, about half of the histidine molecules will have their side chains protonated (that is, with a positive charge) and about half will have their side chains unprotonated and uncharged. Histidine is often used in enzymes to bind and release protons during the enzymatic reaction. Lysine and arginine are almost fully ionized at the p H values found in the cell. Lysine's p K a is greater than 9; therefore, it will be > 99% protonated in the cell. Arginine's side chain is even more basic; its p K a is > 12. Therefore, these amino acids have a net positive charge in the cell. Carboxyllate‐containing amino acids. Aspartic acid and asparagine have four carbons; glutamic acid and glutamine have five carbons in all. Aspartic acid has a carboxyllic acid, and aspargine has an amide side chain. Similarly, glutamic acid has a carboxyllic acid side group, and glutamine has an amide group. The p K a ’s of the side chain carboxyll groups in aspartate and glutamate are near 4.0. Therefore, these side chain groups are almost fully ionized in the neutral conditions found in cells and are negatively charged. Hydroxyl and sulfur-containing side chains Serine and cysteinecan be thought of as being related to alanine. Serine is alanine with a hydroxyl (–OH) group and cysteine is alanine with a sulfhydryl (–SH) group. Threonine has four carbons, with a hydroxyl group on the beta carbon. The beta carbon is next to the one containing the alpha carbon (the alpha carbon has the amino group on it). The presence of the hydroxyl group on threonine means that the beta carbon of threonine is optically active, in addition to the alpha carbon. As the name suggests, the –OH group has the D configuration, or threo to the alpha carbon. (The other possible stereochemistry is erythro—think of the letter E to remember this term. The arms of the E point in the same direction. )Methionine has a methyl group on its sulfur. The backbone of methionine has one more carbon than does cysteine. (Cysteine with an extra carbon is termed homocysteine; homocysteine is an intermediate in the biosynthesis of methionine. )The cyclic amino acid Prolineis the odd one out among the amino acids. It has four carbons, with the alpha amino group bonded not only to the alpha carbon but also to the last side chain carbon. The cyclic side chain means that proline is conformationally rigid. That is, the carbon‐carbon bonds of proline do not rotate in solution. Other amino acids are more flexible in solution. Peptide bond. The peptide bond joins the carboxyl and amino groups of amino acids. When activated, carboxyllic acids and amines form amides. Amino acids are bifunctional, with each amino acid having both amino and carboxyl groups. Peptides are composed of amino acids joined head to tail with amide bonds. Peptides are classified according to their chain length. Oligopeptides are shorter than polypeptides, although no defined transition exists between the two forms. The joining of amino acids to form a peptide bond occurs formally (although the mechanism of its formation is more complicated) in the following way: Note that two amino acids can form a dipeptide (a peptide composed of two units) in either of two ways. For example, glycine and alanine can form glycylalanine (gly‐ala) or alanylglycine (ala ‐ gly): No matter which arrangement occurs, each dipeptide will have one free amino group and one free carboxyl group. Peptide sequences are written in the direction from the amino to the carboxyl end. Peptide bond structure. The peptide bond structure favors coplanar N, C, and O atoms. Although a peptide bond is formally a carbon‐nitrogen single bond, the unpaired electrons on the carboxyl oxygen and on the nitrogen can overlap through their pi orbitals to make the three‐atom system partially double‐bonded in character. The partially double‐bonded system makes it harder to rotate the peptide bond in solution. As a result, peptide bonds can exist in one of two conformational isomers, with the two carbons either cis or trans to each other. Usually, the trans conformation is favored. Proline is an exceptional case because its peptide bond does not have a hydrogen, making the cis and trans isomers harder to change one for the other: Proline usually is found in the trans isomer, although conversion (isomerization) between the cis and trans forms can be catalyzed by specific enzymes.  . Chapter 27: Amino Acids, Peptides and Proteinsa -Amino Acids The generic structure of an a -amino acid The 20 naturally occurring a -amino acids used by cells to synthesise proteins can be generally represented by the generic formula shown above. The means the main difference between the various amino acids lies in the structure of the " R " group. These 20 a -amino acids can be sub-classified according to how the properties of other functional groups in the " R " group influence the system.non-polar side chains ( e.g. alkyl groups)polar ( e.g. amides, alcohols)acidic ( e.g. carboxylic acids, phenols)basic ( e.g. amines)Question : Which common amino acid doesn't quite fit the generic formula ? Amino acids with non-polar side chains. The hydrophobic side chains are chemically unreactive and tend to aggregate rather than be exposed to the aqueous environment, so they tend to found on the interior of proteins. Hydrophobic means "water hating" - remember "oil and water don't mix" and "like dissolves like" - this is because non-polar hydrocarbons do not interact with polar water molecules in an energetically favourable way - they would rather interact with another non-polar hydrocarbon molecule : this it the hydrophobic effect - the aggregation of non-polar systems in an aqueous environment. (see also " micelles ")Amino acid Abbreviations Structural Formula 3D-representation Glycine Gly (G)Alanine Ala (A)Valine Val (V)Leucine Leu (L)Isoleucine Ile (I)Methionine Met (M)Proline Pro (P)Phenylalanine Phe (F)Tryptophan Trp (W)Amino acids with polar side chains. These are side chains can be involved in hydrogen bonding interactions. Cysteine is important because of its ability to form disulfide bonds. Amino acid Abbreviations Structural Formula 3D-representation Asparagine Asn (N)Glutamine Gln (Q)Serine Ser (S)Threonine Thr (T)Tyrosine Tyr (Y)Cysteine Cys (C)Amino acids with acidic side chains. These carboxylate group will be -ve at physiological p H. Often involved at the active sites of enzymes, in hydrogen bonding interactions and in acid/base type reactivity. Amino acid Abbreviations Structural Formula 3D-representation Aspartic acid Asp (D)Glutamic acid Glu (E)Amino acids with basic side chains. Often involved at the active sites of enzymes, in hydrogen bonding interactions and in acid/base type reactivity ( e.g. histidine)Amino acid Abbreviations Structural Formula 3D-representation Lysine Lys (K)Arginine Arg (R)Histidine His (H)  structural differences between fibrous and globular proteins. structural differences between fibrous and globular proteins. Extracts from this document... Introduction Question: Explain with examples, the structural differences between fibrous and globular proteins. A globular protein has a fixed specific sequence of amino acids that are non-repetitive while a fibrous protein has a repetitive regular sequence of amino acid. For example, haemoglobin, a globular protein is made up of 4 polypeptide chains to form a tetramer (?2?2), composed of two identical alpha-beta (??) dimers. Collagen, a fibrous protein, has a primary structure characterized by a repeating tripeptide sequence of Glycine - X - Y. ...read more. Middlechains and 2? chains. These four subunits are packed to form an overall spherically shaped molecule. However, collagen, a fibrous protein, is formed with three polypeptide chains lie parallel and wind round one another, forming a tropocollagen. The tropocollagen molecules lie side by side and are linked to each other giving a collagen fibril. A globular protein has its length of polypeptide always identical in two examples of the same globular protein where else a fibrous protein has its length of polypeptide chain varying in two examples of the same fibrous protein. ...read more. Conclusion Y rotates around hydroxyproline and hydroxylysine so the length of polypeptide chains differ. A globular protein is held primarily by numerous intra- and inter-molecular non-convalent bonds, such as hydrogen, ionic bonds while a fibrous proteins are held due to numerous intra- and inter- molecular hydrogen and disulphide bonds. For example, haemoglobin, a globular protein, is basically held together by interchain hydrophobic interatctions, with hydrogen and ionic bonds occurring. On the other hand, collagen, a fibrous protein, has its triple helix held together by extensive network of hydrogen bonds. Tropocollagen of collagen is also held by covalent cross-links to give the collagen fibre strength and rigidity. ?? ?? ?? ?? ...read more. The above preview is unformatted text This student written piece of work is one of many that can be found in our AS and A Level Molecules & Cells section. Found what you're looking for? Start learning 29% faster today150,000+ documents available Just £6.99 a month Get Full Access Nowor Learn more  . Example of Homologous Structure A homologous structure is a structure which is shared or similar between organisms through shared ancestry. The importance of homologous structures is that they provide a track of the evolutionary paths and divergences between species and sub species. In some cases homologous structures are also related to instantly recognizable behavioral characteristics like bird's beaks, which are modified in different subspecies by their varying environments. The homologous structures define the behavior pattern and help define the various structural modifications created by different behaviors. Examples of Homologous Structure: Rodent teeth Hooves in species of camels, goats, sheep and cattle Hands and feet in primates Bird feathers Shark morphology http://en.wikipedia.org/wiki/Homology_%28biology%29#Homology_of_structures_in_evolution Image Example of Homologous Structure: The wings of pterosaurs (1), bats (2) and birds (3) are analogous: they serve the same function and are similar in structure, but each evolved independently. Diagram of the skulls of a monitor lizard and a crocodile with homologous bones coloured the same colours.  . Aliphatic Amino Acids Aliphatic R groups are nonpolar and hydrophobic. Hydrophobicity increases with increasing number of C atoms in the hydrocarbon chain. Although these amino acids prefer to remain inside protein molecules, alanine and glycine are ambivalent, meaning that they can be inside or outside the protein molecule. Glycine has such a small side chain that it does not have much effect on the hydrophobic interactions. The structures below are shown in the ionization state that predominates at p H 7. Less hydrophobic More hydrophobic  Four Levels of Protein Structure 4 terms sofiamuscatello Four Levels of Protein Structure Learn Flashcards Write Spell Test Match Gravity Advertisement Upgrade to remove ads Like this study set? Create a free account to save it. Create a free account Maybe later Sort Primary Structure Amino Acid is ordered by DNA and held by a peptide bond between C of Acid group, and N of adjacent amino group. A dehydration synthesis removes H2O. Draw (N-C-C-N-C-C)<- peptide bond... dipeptide Secondary Structure There are two geometric shapes to the Polypeptide, alpha and beta, which both have hydrogen bonds holding them together. Hydrogen bonds are the weak interactions between Oxygen, which carries a negative charge, and Hydrogen which carries a positive charge. The interaction is due to charge attractions (polar). Draw alpha: springy Beta: zigzag line Tertiary Structure When R groups come in contact with each other they will bond in 4 different ways. The first way, is an ionic bond. The charged R groups come together and give away and accept electrons. The second bond, is a hydrogen bond, which was explained about in the secondary structure. The third bond is Vander Waals. Nonpolar groups in close proximity bond due to similar atomic properties. And the last bond is the sulfur bond, or Disulfide Bridge. Two amino acids with sulfur R groups in close proximity lock the area tightly. This is a permanent arrangement and creates a denser configuration. Quaternary Structure Many proteins are finished after tertiary, but in quaternary structure the bonds are the same as in tertiary  Biology, Eighth Edition (Raven) Biology, Eighth Edition (Raven)Chapter 3: The Chemical Building Blocks of Life Protein Denaturation Why do we cook many kinds of food before we eat them? Most foods that have a significant amount of protein are cooked before consumption. Proteins are chains of amino acids. The sequence of amino acids in a chain is known as the primary structure of a protein. The chains fold up to form complex three dimensional shapes. The chains can fold on themselves locally (secondary structure) and wrap around themselves to form a specific three dimensional shape (tertiary structure). The secondary/tertiary structure of a folded protein is directly related to the function of that protein. For example, enzymes are proteins that catalyze reactions. They have binding sites that interact with other molecules. These binding sites are created through the folding of the amino acid chains that gives rise to the three dimensional shape of the enzyme. Proteins can be denatured through exposure to heat or chemicals. Denatured proteins lose their three dimensional structure and thus their function. Cooking food denatures the proteins found in the food and makes digestion more efficient. View the animation below, then complete the quiz to test your knowledge of the concept.1. What type of bonds link individual amino acids together? A) peptide bonds B) polymerizing bonds C) hydrogen bonds D) organic bonds2. The helix that forms in a protein chain as a result of hydrogen bonds and other weak forces is an example of A) primary structure of protein. B) secondary structure of protein. C) tertiary structure of protein. D) non-linear structure of protein.3. In the stable form of protein, what is generally oriented to the interior of the protein molecule? A) large portions B) random portions C) hydrophobic portions D) hydrophilic portions4. When an egg is fried, what happens to the protein in the egg? A) amino acids form new proteins B) the heat converts the protein into water C) because the heat removes water, the hydrophilic amino acids leave the pan D) the protein is denatured5. When forming a semi-solid gel such as gelatin, what type of molecule does the process of protein coagulation entrap? A) protein B) water C) carbohydrate D) lipid  Ch.19 Amino Acids and Proteins 43 terms thirdeb7Ch.19 Amino Acids and Proteins Learn Flashcards Write Spell Test Match Gravity Advertisement Upgrade to remove ads Sort Which of the following is NOT a function of proteins? stores the genetic information of a living organism. The peptide bonds that combine amino acids in a protein are amide bonds. The bonds that are important in the secondary structure of a protein are hydrogen bonds. Which of the following is a secondary protein structure? α helix. What type of interaction would you expect between the following two R groups in the tertiary structure of a protein? salt bridges. What kinds of interactions are NOT part of tertiary protein structure? peptide bonds. Acids and bases denature a protein by disrupting ionic bonds and hydrogen bonds. Heat denatures a protein by disrupting hydrophobic bonds and hydrogen bonds. The secondary structure of collagen is distinguished by a braided triple helix. Collagen, a protein found in tendons and cartilage, would be classified as a __________ protein. structural. The fibrous protein responsible for the structure of hair and wool is keratin. In the peptide Ala-Try-Gly-Phe, the N-terminal amino acid is alanine. In the peptide Ser-Cys-Ala-Gly, the C-terminal end is glycine. Which of the following shows all of the tripeptides that can be formed from one molecule each of glycine (Gly), valine (Val), and leucine (Leu)? Gly Val Leu, Gly Leu Val, Val Leu Gly, Val Gly Leu, Leu Gly Val, Leu Val Gly. Which of the following shows all of the tripeptides that can be formed from one molecule each of lysine (Lys), threonine (Thr), and histidine (His)? Lys Thr His, Lys His Thr, His Thr Lys, His Lys Thr, Thr Lys His, Thr His Lys. A peptide bond contains which kind of functional group? amide. A chain made of more than 50 amino acids is usually referred to as a/an protein. Which of the following is an example of a secondary protein structure? a helix. The α helix of the secondary structure of a protein is held together by __________ between two widely separated parts of a protein chain. hydrogen bonds. In the β-pleated sheet secondary structure of a protein, two or more amino acid sequences in separate parts of the protein are held together in a zig-zag conformation, by hydrogen bonding. Sucrase, the protein that facilitates the hydrolysis of sucrose, would be classified as a __________ protein. catalytic. A completely vegetarian diet will contain all the essential amino acids if it includes rice and beans. In insulin, two peptide chains are held together in a single unit by disulfide bridges. Hemoglobin is an example of a protein with a globular structure. Within hemoglobin, the heme functions as an oxygen carrier. Hemoglobin has a total of __________ protein chains in its quaternary structure four. Wool is primarily made up of protein. In sickle-cell anemia, the hemoglobin molecules clump together into insoluble fibers. The structural formulas of amino acids are the same EXCEPT for the side (R) group. Denaturation of a protein disrupts the secondary, tertiary, or quaternary structure of a protein. One heavy metal that can cause denaturation of a protein is silver. Heavy metals denature proteins by disrupting disulfide bonds. An acid can denature a protein by disrupting hydrogen bonds between R groups chains. Glycine is the only naturally occurring amino acid that is achiral. In a typical amino acid zwitterion, the carboxylate end is negatively charged. Methionine is an amino acid that contains a sulfur atom. Disulfide bonds in a protein chain connect two cysteine residues. At a p H > 9, the zwitterion of glycine will have a net negative charge. The following amino acid R group chain is hydrophobic. At a p H < 5, the zwitterion for alanine (p I = 6) will have a net positive charge. Consider a mixture of the amino acids lysine (p I = 9.7), tyrosine (p I = 5.7), and glutamic acid (p I = 3.2). At a p H 5.7, if it is subjected to an electric current, __________ will migrate towards the positive electrode (+). Glutamic acid. Consider a mixture of the amino acids lysine (p I = 9.7), tyrosine (p I = 5.7), and glutamic acid (p I = 3.2) at a p H 5.7 that is subjected to an electric current. __________ will remain stationary. Tyrosine. A basic amino acid has an R group that contains an amine group.  Learn About the 4 Types of Protein Structure Science, Tech, Math ›Science Learn About the 4 Types of Protein Structure Share Flipboard Email Print Protein structure types: primary, secondary, tertiary, and quaternary. Holger87/Creative Commons Attribution- Share Alike 3.0 Unported licenseby Regina Bailey Updated October 17, 2017Proteins are biological polymers composed of amino acids. Amino acids, linked together by peptide bonds, form a polypeptide chain. One or more polypeptide chains twisted into a 3-D shape form a protein. Proteins have complex shapes that include various folds, loops, and curves. Folding in proteins happens spontaneously. Chemical bonding between portions of the polypeptide chain aid in holding the protein together and giving it its shape. There are two general classes of protein molecules: globular proteins and fibrous proteins. Globular proteins are generally compact, soluble, and spherical in shape. Fibrous proteins are typically elongated and insoluble. Globular and fibrous proteins may exhibit one or more of four types of protein structure. These structure types are called primary, secondary, tertiary, and quaternary structure. Protein Structure Types The four levels of protein structure are distinguished from one another by the degree of complexity in the polypeptide chain. A single protein molecule may contain one or more of the protein structure types. Primary Structure - describes the unique order in which amino acids are linked together to form a protein. Proteins are constructed from a set of 20 amino acids. Generally, amino acids have the following structural properties: A carbon (the alpha carbon) bonded to the four groups below: A hydrogen atom (H)A Carboxyl group (-COOH)An Amino group (-NH2)A "variable" group or "R" group All amino acids have the alpha carbon bonded to a hydrogen atom, carboxyl group, and amino group. The "R" group varies among amino acids and determines the differences between these protein monomers. The amino acid sequence of a protein is determined by the information found in the cellular genetic code. The order of amino acids in a polypeptide chain is unique and specific to a particular protein. Altering a single amino acid causes a gene mutation, which most often results in a non-functioning protein. Secondary Structure - refers to the coiling or folding of a polypeptide chain that gives the protein its 3-D shape. There are two types of secondary structures observed in proteins. One type is the alpha (α) helix structure. This structure resembles a coiled spring and is secured by hydrogen bonding in the polypeptide chain. The second type of secondary structure in proteins is the beta (β) pleated sheet. This structure appears to be folded or pleated and is held together by hydrogen bonding between polypeptide units of the folded chain that lie adjacent to one another. Tertiary Structure - refers to the comprehensive 3-D structure of the polypeptide chain of a protein. There are several types of bonds and forces that hold a protein in its tertiary structure. Hydrophobic interactions greatly contribute to the folding and shaping of a protein. The "R" group of the amino acid is either hydrophobic or hydrophilic. The amino acids with hydrophilic "R" groups will seek contact with their aqueous environment, while amino acids with hydrophobic "R" groups will seek to avoid water and position themselves towards the center of the protein. Hydrogen bonding in the polypeptide chain and between amino acid "R" groups helps to stabilize protein structure by holding the protein in the shape established by the hydrophobic interactions. Due to protein folding, ionic bonding can occur between the positively and negatively charged "R" groups that come in close contact with one another. Folding can also result in covalent bonding between the "R" groups of cysteine amino acids. This type of bonding forms what is called a disulfide bridge. Interactions called van der Waals forces also assist in the stabilization of protein structure. These interactions pertain to the attractive and repulsive forces that occur between molecules that become polarized. These forces contribute to the bonding that occurs between molecules. Quaternary Structure - refers to the structure of a protein macromolecule formed by interactions between multiple polypeptide chains. Each polypeptide chain is referred to as a subunit. Proteins with quaternary structure may consist of more than one of the same type of protein subunit. They may also be composed of different subunits. Hemoglobin is an example of a protein with quaternary structure. Hemoglobin, found in the blood, is an iron-containing protein that binds oxygen molecules. It contains four subunits: two alpha subunits and two beta subunits. How to Determine Protein Structure Type The three-dimensional shape of a protein is determined by its primary structure. The order of amino acids establishes a protein's structure and specific function. The distinct instructions for the order of amino acids are designated by the genes in a cell. When a cell perceives a need for protein synthesis, the DNA unravels and is transcribed into an RNA copy of the genetic code. This process is called DNA transcription. The RNA copy is then translated to produce a protein. The genetic information in the DNA determines the specific sequence of amino acids and the specific protein that is produced. Proteins are examples of one type of biological polymer. Along with proteins, carbohydrates , lipids, and nucleic acids constitute the four major classes of organic compounds in living cells .cite  Introduction Introduction Have you ever wondered why egg whites go from clear to opaque when you fry an egg? If so, this section is for you!Egg whites contain large amounts of proteins called albumins, and the albumins normally have a specific 3D shape, thanks to bonds formed between different amino acids in the protein. Heating causes these bonds to break and exposes hydrophobic (water-hating) amino acids usually kept on the inside of the protein 1, 2. The hydrophobic amino acids, trying to get away from the water surrounding them in the egg white, will stick to one another, forming a protein network that gives the egg white structure while turning it white and opaque. Ta-da! Thank you, protein denaturation, for another delicious breakfast. As we mentioned in the last article on proteins and amino acids, the shape of a protein is very important to its function. To understand how a protein gets its final shape or conformation, we need to understand the four levels of protein structure: primary, secondary, tertiary, and quaternary. Primary structure The simplest level of protein structure, primary structure, is simply the sequence of amino acids in a polypeptide chain. For example, the hormone insulin has two polypeptide chains, A and B, shown in diagram below. (The insulin molecule shown here is cow insulin, although its structure is similar to that of human insulin.) Each chain has its own set of amino acids, assembled in a particular order. For instance, the sequence of the A chain starts with glycine at the N-terminus and ends with asparagine at the C-terminus, and is different from the sequence of the B chain. [What's up with those S-S bonds? ]You may notice that the insulin chains are linked together by sulfur-containing bonds between cysteines. Don’t let yourself get confused: although these bonds are an important part of insulin’s overall structure, they are not part of its primary structure! We’ll talk more about these bonds, called disulfide bonds, in later sections.image credit: Open Stax Biology. The sequence of a protein is determined by the DNA of the gene that encodes the protein (or that encodes a portion of the protein, for multi-subunit proteins). A change in the gene's DNA sequence may lead to a change in the amino acid sequence of the protein. Even changing just one amino acid in a protein’s sequence can affect the protein’s overall structure and function. For instance, a single amino acid change is associated with sickle cell anemia, an inherited disease that affects red blood cells. In sickle cell anemia, one of the polypeptide chains that make up hemoglobin, the protein that carries oxygen in the blood, has a slight sequence change. The glutamate that is normally the seventh amino acid of the hemoglobin β chain (one of two types of protein chains that make up hemoglobin) is replaced by a valine. This substitution is shown for a fragment of the β chain in the diagram below. Image modified from Open Stax Biology. What is most remarkable to consider is that a hemoglobin molecule is made up of two α chains and two β chains, each consisting of about 150 amino acids, for a total of about 600 amino acids in the whole protein. The difference between a normal hemoglobin molecule and a sickle cell molecule is just 2 amino acids out of the approximately 600. A person whose body makes only sickle cell hemoglobin will suffer symptoms of sickle cell anemia. These occur because the glutamate-to-valine amino acid change makes the hemoglobin molecules assemble into long fibers. The fibers distort disc-shaped red blood cells into crescent shapes. Examples of “sickled” cells can be seen mixed with normal, disc-like cells in the blood sample below. Image credit: Open Stax Biology modification of work by Ed Uthman; scale-bar data from Matt Russell. The sickled cells get stuck as they try to pass through blood vessels. The stuck cells impair blood flow and can cause serious health problems for people with sickle cell anemia, including breathlessness, dizziness, headaches, and abdominal pain. Secondary structure The next level of protein structure, secondary structure, refers to local folded structures that form within a polypeptide due to interactions between atoms of the backbone. (The backbone just refers to the polypeptide chain apart from the R groups – so all we mean here is that secondary structure does not involve R group atoms.) The most common types of secondary structures are the α helix and the β pleated sheet. Both structures are held in shape by hydrogen bonds, which form between the carbonyl O of one amino acid and the amino H of another. Image credit: Open Stax Biology. In an α helix, the carbonyl (C=O) of one amino acid is hydrogen bonded to the amino H (N-H) of an amino acid that is four down the chain. (E.g., the carbonyl of amino acid 1 would form a hydrogen bond to the N-H of amino acid 5.) This pattern of bonding pulls the polypeptide chain into a helical structure that resembles a curled ribbon, with each turn of the helix containing 3.6 amino acids. The R groups of the amino acids stick outward from the α helix, where they are free to interact 3. In a β pleated sheet, two or more segments of a polypeptide chain line up next to each other, forming a sheet-like structure held together by hydrogen bonds. The hydrogen bonds form between carbonyl and amino groups of backbone, while the R groups extend above and below the plane of the sheet 3. The strands of a β pleated sheet may be parallel, pointing in the same direction (meaning that their N- and C-termini match up), or antiparallel, pointing in opposite directions (meaning that the N-terminus of one strand is positioned next to the C-terminus of the other). Certain amino acids are more or less likely to be found in α-helices or β pleated sheets. For instance, the amino acid proline is sometimes called a “helix breaker” because its unusual R group (which bonds to the amino group to form a ring) creates a bend in the chain and is not compatible with helix formation 4. Proline is typically found in bends, unstructured regions between secondary structures. Similarly, amino acids such as tryptophan, tyrosine, and phenylalanine, which have large ring structures in their R groups, are often found in β pleated sheets, perhaps because the β pleated sheet structure provides plenty of space for the side chains 4. Many proteins contain both α helices and β pleated sheets, though some contain just one type of secondary structure (or do not form either type). Tertiary structure The overall three-dimensional structure of a polypeptide is called its tertiary structure. The tertiary structure is primarily due to interactions between the R groups of the amino acids that make up the protein. R group interactions that contribute to tertiary structure include hydrogen bonding, ionic bonding, dipole-dipole interactions, and London dispersion forces – basically, the whole gamut of non-covalent bonds. For example, R groups with like charges repel one another, while those with opposite charges can form an ionic bond. Similarly, polar R groups can form hydrogen bonds and other dipole-dipole interactions. Also important to tertiary structure are hydrophobic interactions, in which amino acids with nonpolar, hydrophobic R groups cluster together on the inside of the protein, leaving hydrophilic amino acids on the outside to interact with surrounding water molecules. Finally, there’s one special type of covalent bond that can contribute to tertiary structure: the disulfide bond. Disulfide bonds, covalent linkages between the sulfur-containing side chains of cysteines, are much stronger than the other types of bonds that contribute to tertiary structure. They act like molecular "safety pins," keeping parts of the polypeptide firmly attached to one another. Image modified from Open Stax Biology. Quaternary structure Many proteins are made up of a single polypeptide chain and have only three levels of structure (the ones we’ve just discussed). However, some proteins are made up of multiple polypeptide chains, also known as subunits. When these subunits come together, they give the protein its quaternary structure. We’ve already encountered one example of a protein with quaternary structure: hemoglobin. As mentioned earlier, hemoglobin carries oxygen in the blood and is made up of four subunits, two each of the α and β types. Another example is DNA polymerase, an enzyme that synthesizes new strands of DNA and is composed of ten subunits 5. In general, the same types of interactions that contribute to tertiary structure (mostly weak interactions, such as hydrogen bonding and London dispersion forces) also hold the subunits together to give quaternary structure. Image modified from Open Stax Biology's modification of work by the National Human Genome Research Institute. Denaturation and protein folding Each protein has its own unique shape. If the temperature or p H of a protein's environment is changed, or if it is exposed to chemicals, these interactions may be disrupted, causing the protein to lose its three-dimensional structure and turn back into an unstructured string of amino acids. When a protein loses its higher-order structure, but not its primary sequence, it is said to be denatured. Denatured proteins are usually non-functional. For some proteins, denaturation can be reversed. Since the primary structure of the polypeptide is still intact (the amino acids haven’t split up), it may be able to re-fold into its functional form if it's returned to its normal environment. Other times, however, denaturation is permanent. One example of irreversible protein denaturation is when an egg is fried. The albumin protein in the liquid egg white becomes opaque and solid as it is denatured by the heat of the stove, and will not return to its original, raw-egg state even when cooled down. Researchers have found that some proteins can re-fold after denaturation even when they are alone in a test tube. Since these proteins can go from unstructured to folded all by themselves, their amino acid sequences must contain all the information needed for folding. However, not all proteins are able to pull off this trick, and how proteins normally fold in a cell appears to be more complicated. Many proteins don’t fold by themselves, but instead get assistance from chaperone proteins (chaperonins). [Attribution and references]Attribution: This article is a modified derivative of “ Proteins ,” by Open Stax College, Biology ( CC BY 3.0 ). Download the original article for free at http://cnx.org/contents/185cbf87-c72e-48f5-b51e-f14f21b5eabd@9.85:13/Biology. The modified article is licensed under a CC BY-NC-SA 4.0 license. Works cited: Watt, Jeremy. (2010, February 1). The denatured egg white. In Moment of science. Retrieved from http://indianapublicmedia.org/amomentofscience/denatured_egg_white/. Egg white. (2015, July 20). Retrieved July 25, 2015 from Wikipedia: https://en.wikipedia.org/wiki/Egg_white. Berg, J. M., Tymoczko, J. L., and Stryer, L. (2002). Secondary structure: Polypeptide chains can fold into regular structures such as the alpha helix, the beta sheet, and turns and loops. In Biochemistry (5th ed., section 3.3). New York, NY: W. H. Freeman. Retrieved from http://www.ncbi.nlm.nih.gov/books/NBK22580/. Protein secondary structure. (2015, June 16). Retrieved July 25, 2015 from Wikipedia: https://en.wikipedia.org/wiki/Protein_secondary_structure. Marians, K. J., Hiasa, H., Kim, D. R., and Mc Henry, C. S. (1998). Role of the Core DNA Polymerase III Subunits at the Replication Fork. J. Biol. Chem., 273, 2452-2457. http://doi.org/10.1074/jbc.273.4.2452. Additional references: Berg, J. M., Tymoczko, J. L., and Stryer, L. (2002). Secondary structure: Polypeptide chains can fold into regular structures such as the alpha helix, the beta sheet, and turns and loops. In Biochemistry (5th ed., section 3.3). New York, NY: W. H. Freeman. Retrieved from http://www.ncbi.nlm.nih.gov/books/NBK22580/. Berg, J. M., Tymoczko, J. L., and Stryer, L. (2002). Tertiary structure: Water-soluble proteins fold Into compact structures with nonpolar cores. In Biochemistry (5th ed., section 3.4). New York, NY: W. H. Freeman. Retrieved from http://www.ncbi.nlm.nih.gov/books/NBK22375/. Egg white. (2015, July 20). Retrieved July 25, 2015 from Wikipedia: https://en.wikipedia.org/wiki/Egg_white. Keratin. (2015, 24 July). Retrieved July 25, 2015 from Wikipedia: https://en.wikipedia.org/wiki/Keratin. Protein secondary structure. (2015, June 16). Retrieved July 25, 2015 from Wikipedia: https://en.wikipedia.org/wiki/Protein_secondary_structure. Protein quaternary structure. (2015, July 21). Retrieved July 25, 2015 from Wikipedia: https://en.wikipedia.org/wiki/Protein_quaternary_structure. Raven, P. H., Johnson, G. B., Mason, K. A., Losos, J. B., and Singer, S. R. (2014). Proteins: Molecules with diverse structures and functions. In Biology (10th ed., AP ed., pp. 44-53). New York, NY: Mc Graw-Hill. Reece, J. B., Urry, L. A., Cain, M. L., Wasserman, S. A., Minorsky, P. V., and Jackson, R. B. (2011). Proteins include a diversity of structures, resulting in a wide range of functions. In Campbell biology (10th ed., pp. 75-84). San Francisco, CA: Pearson. Watt, Jeremy. (2010, February 1). The denatured egg white. In Moment of science. Retrieved from http://indianapublicmedia.org/amomentofscience/denatured_egg_white/.  . PROTEINS AS ENZYMESThis page is an introduction to how proteins can work as enzymes - biological catalysts. You should realise that this is written to cover the needs of a number of UK-based chemistry syllabuses for 16 - 18 year olds. If you want detailed knowledge about enzymes for a biology or biochemistry course, you are probably in the wrong place! This is just an introduction. Note: This page follows on from a page about protein structure. If you don't have a reasonable knowledge of the structure of proteins and the sorts of attractions that can be found in them, you may not understand bits of the present page. Read the protein structure page first and come back here later. Important: The specific examples of the enzymes that you will find on this page are only intended to give you a feel for the way that enzymes work. Unless your syllabus specifically asks for a particular enzyme, there is no need for you to remember the details. Enzymes as catalysts Enzymes are mainly globular proteins - protein molecules where the tertiary structure has given the molecule a generally rounded, ball shape (although perhaps a very squashed ball in some cases). The other type of proteins (fibrous proteins) have long thin structures and are found in tissues like muscle and hair. We aren't interested in those in this topic. These globular proteins can be amazingly active catalysts. You are probably familiar with the use of catalysts like manganese (IV) oxide in decomposing hydrogen peroxide to give oxygen and water. The enzyme catalase will also do this - but at a spectacular rate compared with inorganic catalysts. One molecule of catalase can decompose almost a hundred thousand molecules of hydrogen peroxide every second. That's very impressive!This is a model of catalase, showing the globular structure - a bit like a tangled mass of string: Note: This diagram was obtained from the RCSB Protein Data Bank. You should be able to identify the alpha-helices and beta-pleated sheets. If you can't, you obviously didn't read the page about protein structure mentioned above!If you look very carefully, you might also spot two pink, non-protein structures hidden in the main structure. More about these in a while . . . An important point about enzymes is that they are very specific about what they can catalyse. Even small changes in the reactant molecule can stop the enzyme from catalysing its reaction. The reason for this lies in the active site present in the enzyme . . . Active sites Active sites are cracks or hollows on the surface of the enzyme caused by the way the protein folds itself up into its tertiary structure. Molecules of just the right shape, and with just the right arrangement of attractive groups (see later) can fit into these active sites. Other molecules won't fit or won't have the right groups to bind to the surface of the active site. The usual analogy for this is a key fitting into a lock. For the key to work properly it has to fit exactly into the lock. In chemistry, we would describe the molecule which is actually going to react (the purple one in the diagram) as the reactant. In biology and biochemistry, the reactant in an enzyme reaction is known instead as the substrate . You mustn't take this picture of the way a substrate fits into its enzyme too literally. What is just as important as the physical shape of the substrate are the bonds which it can form with the enzyme. Enzymes are protein molecules - long chains of amino acid residues. Remember that sticking out all along those chains are the side groups of the amino acids - the "R" groups that we talked about on the page about protein structure. Active sites, of course, have these "R" groups lining them as well - typically from about 3 to 12 in an active site. The next diagram shows an imaginary active site: Remember that these "R" groups contain the sort of features which are responsible for the tertiary structure in proteins. For example, they may contain ionic groups like -NH 3+ or -COO -, or -OH groups which can hydrogen bond, or hydrocarbon chains or rings which can contribute to van der Waals forces. Groups like these help a substrate to attach to the active site - but only if the substrate molecule has an arrangement of groups in the right places to interact with those on the enzyme. The diagram shows a possible set of interactions involving two ionic bonds and a hydrogen bond. The groups shown with + or - signs are obvious. The ones with the "H"s in them are groups capable of hydrogen bonding. It is possible that one or more of the unused "R" groups in the active site could also be helping with van der Waals attractions between them and the substrate. If the arrangement of the groups on the active site or the substrate was even slightly different, the bonding almost certainly wouldn't be as good - and in that sense, a different substrate wouldn't fit the active site on the enzyme. This process of the catalyst reacting with the substrate and eventually forming products is often summarised as:. . . where E is the enzyme, S the substrate and P the products. The formation of the complex is reversible - the substrate could obviously just break away again before it converted into products. The second stage is shown as one-way, but might be reversible in some cases. It would depend on the energetics of the reaction. So why does attaching itself to an enzyme increase the rate at which the substrate converts into products? It isn't at all obvious why that should be - and most sources providing information at this introductory level just gloss over it or talk about it in vague general terms (which is what I am going to be forced to do, because I can't find a simple example to talk about!). Catalysts in general (and enzymes are no exception) work by providing the reaction with a route with a lower activation energy. Attaching the substrate to the active site must allow electron movements which end up in bonds breaking much more easily than if the enzyme wasn't there. Strangely, it is much easier to see what might be happening in other cases where the situation is a bit more complicated . . . Enzyme cofactors What we have said so far is a major over-simplification for most enzymes. Most enzymes aren't in fact just pure protein molecules. Other non-protein bits and pieces are needed to make them work. These are known as cofactors. In the absence of the right cofactor, the enzyme doesn't work. For those of you who like collecting obscure words, the inactive protein molecule is known as an apoenzyme. When the cofactor is in place so that it becomes an active enzyme, it is called a holoenzyme. Note: If you don't collect obscure words, don't worry about these! Neither of them occurs in the syllabuses I am trying to cover with this material. I have spent a lifetime in chemistry education without having come across either of them until researching this!There are two basically different sorts of cofactors. Some are bound tightly to the protein molecule so that they become a part of the enzyme - these are called prosthetic groups. Some are entirely free of the enzyme and attach themselves to the active site alongside the substrate - these are called coenzymes. Prosthetic groups Prosthetic groups can be as simple as a single metal ion bound into the enzyme's structure, or may be a more complicated organic molecule (which might also contain a metal ion). The enzymes carbonic anhydrase and catalase are simple examples of the two types. Zinc ions in carbonic anhydrase Carbonic anhydrase is an enzyme which catalyses the conversion of carbon dioxide into hydrogencarbonate ions (or the reverse) in the cell. (If you look this up elsewhere, you will find that biochemists tend to persist in calling hydrogencarbonate by its old name, bicarbonate! )In fact, there are a whole family of carbonic anhydrases all based around different proteins, but all of them have a zinc ion bound up in the active site. In this case, the mechanism is well understood and simple. We'll look at this in some detail, because it is a good illustration of how enzymes work. Important: This is just an example! If you are doing a UK-based chemistry syllabus for 16 - 18 year olds, there is almost certainly no need to learn this. If in doubt, check your syllabus. If it doesn't explicitly ask for this reaction in detail, you don't need to learn it. To repeat - I'm just using it to illustrate how enzymes carry out a simple reaction. The zinc ion is bound to the protein chain via three links to separate histidine residues in the chain - shown in pink in the picture of one version of carbonic anhydrase. The zinc is also attached to an -OH group - shown in the picture using red for the oxygen and white for the hydrogen. Note: This diagram comes from Wikipedia. I have no reason to doubt its accuracy, but I can't guarantee it. As far as I have been able to find out, all the various forms of carbonic anhydrase have the zinc ion bound to three histidine residues in this way - irrespective of what is happening in the rest of the protein molecule. If I am wrong about this generalisation, could you please let me know via the address on the about this site page. The structure of the amino acid histidine is . . .. . . and when it is a part of a protein chain, it is joined up like this: If you look at the model of the arrangement around the zinc ion in the picture above, you should at least be able to pick out the ring part of the three molecules. The zinc ion is bound to these histidine rings via dative covalent (co-ordinate covalent) bonds from lone pairs on the nitrogen atoms. Simplifying the structure around the zinc . . . The arrangement of the four groups around the zinc is approximately tetrahedral. Notice that I have distorted the usual roughly tetrahedral arrangement of electron pairs around the oxygen - that's just to keep the diagram as clear as possible. So that's the structure around the zinc. How does this catalyse the reaction between carbon dioxide and water? A carbon dioxide molecule is held by a nearby part of the active site so that one of the lone pairs on the oxygen is pointing straight at the carbon atom in the middle of the carbon dioxide molecule. Attaching it to the enzyme also increases the existing polarity of the carbon-oxygen bonds. If you have done any work on organic reaction mechanisms at all, then it is pretty obvious what is going to happen. The lone pair forms a bond with the carbon atom and part of one of the carbon-oxygen bonds breaks and leaves the oxygen atom with a negative charge on it. What you now have is a hydrogencarbonate ion attached to the zinc. The next diagram shows this broken away and replaced with a water molecule from the cell solution. All that now needs to happen to get the catalyst back to where it started is for the water to lose a hydrogen ion. This is transferred by another water molecule to a nearby amino acid residue with a nitrogen in the "R" group - and eventually, by a series of similar transfers, out of the active site completely.. . . and the carbonic anhydrase enzyme can do this sequence of reactions about a million times a second. This is a wonderful piece of molecular machinery!Let me repeat yet again: If you are doing a UK-based chemistry exam for 16 - 18 year olds, you are unlikely to need details of this reaction. I've talked it through in some detail to show that although enzymes are complicated molecules, all they do is some basic chemistry. It is just that this particular example is a lot easier to understand than most!The haem (US: heme) group in catalase Remember the model of catalase from further up the page . . . At the time, I mentioned the non-protein groups which this contains, shown in pink in the picture. These are haem (US: heme) groups bound to the protein molecule, and an essential part of the working of the catalase. The haem group is a good example of a prosthetic group. If it wasn't there, the protein molecule wouldn't work as a catalyst. The haem groups contain an iron (III) ion bound into a ring molecule - one of a number of related molecules called porphyrins. The iron is locked into the centre of the porphyrin molecule via dative covalent bonds from four nitrogen atoms in the ring structure. There are various types of porphyrin, so there are various different haem groups. The one we are interested in is called haem B, and a model of the haem B group (with the iron (III) ion in grey at the centre) looks like this: Note: This diagram comes from Wikipedia, and you will also find a proper structure for the group on the page you will get to by following this link if you are interested (and a lot more information that you probably won't want to know about!). You may have come across haemoglobin in the transport of oxygen around the blood. This is the same haem group that is at the heart of that - with one small difference. In haemoglobin, the iron is present as iron (II) rather than iron (III). The reaction that catalase carries out is the decomposition of hydrogen peroxide into water and oxygen. A lot of work has been done on the mechanism for this reaction, but I am only going to give you a simplified version rather than describe it in full. Although it looks fairly simple on the surface, there are a lot of hidden things going on to complicate it. Essentially the reaction happens in two stages and involves the iron changing its oxidation state. An easy change of oxidation state is one of the main characteristics of transition metals. In the lab, iron commonly has two oxidation states (as well as zero in the metal itself), +2 and +3, and changes readily from one to the other. In catalase, the change is from +3 to the far less common +4 and back again. In the first stage there is a reaction between a hydrogen peroxide molecule and the active site to give: The "Enzyme" in the equation refers to everything (haem group and protein) apart from the iron ion. The " (III)" and " (IV)" are the oxidation states of the iron in both cases. This equation (and the next one) are NOT proper chemical equations. They are just summaries of the most obvious things which have happened. The new arrangement around the iron then reacts with a second hydrogen peroxide to regenerate the original structure and produce oxygen and a second molecule of water. What is hidden away in this simplification are the other things that are happening at the same time - for example, the rest of the haem group and some of the amino acid residues around the active site are also changed during each stage of the reaction. And if you think about what has to happen to the hydrogen peroxide molecule in both reactions, it has to be more complicated than this suggests. Hydrogen peroxide is joined up as H-O-O-H, and yet both hydrogens end up attached to the same oxygen. That is quite a complicated thing to arrange in small steps in a mechanism, and involves hydrogen ions being transferred via amino acids residues in the active site. So do you need to remember all this for chemistry purposes at this level? No - not unless your syllabus specifically asks you for it. It is basically just an illustration of the term "prosthetic group". It also shows that even in a biochemical situation, transition metals behave in the same sort of way as they do in inorganic chemistry - they form complexes, and they change their oxidation state. And if you want to follow this up to look in detail at what is happening, you will find the same sort of interactions around the active site that we looked at in the simpler case of carbonic anydrase. (But please don't waste time on this unless you have to - it is seriously complicated! )Coenzymes Coenzymes are another form of cofactor. They are different from prosthetic groups in that they aren't permanently attached to the protein molecule. Instead, coenzymes attach themselves to the active site alongside the substrate, and the reaction involves both of them. Once they have reacted, they both leave the active site - both changed in some way. A simple diagram showing a substrate and coenzyme together in the active site might look like this: It is much easier to understand this with a (relatively) simple example. NAD+ as coenzyme with alcohol dehydrogenase Alcohol dehydrogenase is an enzyme which starts the process by which alcohol (ethanol) in the blood is oxidised to harmless products. The name "dehydrogenase" suggests that it is oxidising the ethanol by removing hydrogens from it. The reaction is actually between ethanol and the coenzyme NAD+ attached side-by-side to the active site of the protein molecule. NAD+ is a commonly used coenzyme in all sorts of redox reactions in the cell. NAD+ stands for nicotinamide adenine dinucleotide. The plus sign which is a part of its name is because it carries a positive charge on a nitrogen atom in the structure. The "nicotinamide" part of the structure comes from the vitamin variously called vitamin B3, niacin or nicotinic acid. Several important coenzymes are derived from vitamins. Note: I'm not going to confuse you with the structures of NAD+ or even nicotinic acid - this page is already long enough! If you are interested, they are easy to find via a Google search. In common with what I have done on the rest of this page, this is just an example to illustrate how a coenzyme works which is reasonably easy to understand. You are unlikely to need details for any chemistry exam at this level. Ethanol is oxidised by a reaction with NAD+ helped by the active site of the enzyme. At the end of the reaction, ethanal (acetaldehyde) is formed, and the NAD+ has been converted into another compound known as NADH. As far as the NAD+ is concerned, it has picked up a hydrogen atom together with an extra electron which has neutralised the charge. Both major products - ethanal and NADH - leave the active site and are processed further in other cell reactions. The very poisonous ethanal is oxidised at once to ethanoic acid using a different enzyme, but again using NAD+ as the coenzyme. And the ethanoic acid from that reacts on through a whole set of further enzyme-controlled reactions to eventually end up as carbon dioxide and water. What about the NADH? This is a coenzyme in its own right, and takes part in reactions where something needs reducing. The hydrogen atom and the extra electron that it picked up from the ethanol are given to something else. In the process, of course, the NADH gets oxidised back to NAD+ again. In general terms, for a substrate S which needs reducing: And one final time - do you need to remember any of this? No, unless this particular example is on your syllabus. Note: Because this page is getting so long, and because there is still quite a bit of enzyme chemistry to talk about, it continues on another two pages. You will find the link to the first of these below. What follows is a page about the effect of substrate concentration, temperature and p H on enzymes, and then a further page about enzyme inhibitors. Questions to test your understanding If this is the first set of questions you have done, please read the introductory page before you start. You will need to use the BACK BUTTON on your browser to come back here afterwards.questions on proteins as enzymesanswers Where would you like to go now? To continue to the next page about enzymes . . . To the amino acid and proteins menu . . . To the menu of other organic compounds . . . To Main Menu . . .© Jim Clark 2007 (modified May 2016)  . Hydrophobic Interactions: Soluble globular proteins fold so that hydrophobic side chains are mostly sequestered in the core of the protein. The removal of the non-polar groups from water (i.e. the hydrophobic effect) is the primary force stabilizing tertiary structure. Most polar amino acid side chains are on the outside surface so they can hydrogen bond to water to solubilize the protein. Salt Bridges: Protein fold so that positively charged side chains are often located adjacent to negatively charged side chains. The salt bridge or ionic bond between the charged functional groups helps stabilize the tertiary structure. Hydrogen Bonds: Folding is also stabilized by hydrogen bonds that form between the polar hydrogen of one amino acid and a lone pair of electrons on another (note: hydrogen atoms do not usually display in pdb files). Covalent Bonds: Some proteins are cross-linked with covalent bonds. The most common is a disulfide bond between the sulfur atoms of two cysteines. These are most common in extracellular proteins.  PROTEINS Proteins in the human body have a wide range of functions which include: Hormones (insulin, testosterone), Muscle Fibers (actin, muasin), Carrier Protein (Oxygen carrying hemoglobin), Structure/ Support (nails/ hair), Enzymes (biological catalyst), Membrane Transport (Na/ K pump), Cell-to-Cell Recognition, Antibodies. Structure Proteins are polymers made up of amino acid subunits bonded together by peptide bonds. This occurs by a condensation reaction. Primary Structure Given by the sequence of amino acids in the polypeptide. Controls all levels of further folding. All proteins have an amino terminal end and a carboxyl terminal end. These ends are significant to the sequencing of a polypeptide. Insulin was the first protein to be sequenced. Our DNA codes for the sequence of every protein our cells make. A change in one amino acid residue can alter the final shape of the protein making it dysfunctional. This is the root cause of genetic disorders (e.g. sickle cell anemia hemoglobin defect). Secondary Structure Second level of folding due to hydrogen bonding between main chain amino and carbonyl groupsα-helix:springy/ flexibleβ-sheet: Hydrogen bonding (e.g silk)High tensile strength due to hydrogen bonding Tertiary Structurefurther folding and super coiling of the polypeptidecontrolled by interactions (covalent, ionic, van der Waals) between the R-groups or side chains of the amino acids Interacts with watery environment of the cytoplasm to drive folding process. Gives protein a specific 3-dimensional shape and a specific function. What would happen to the protein if these bonds were broken? Denaturation Quaternary Structure Two or more polypeptides interacting to form a functional protein Metal ions may be part of the protein structure as in Hemoglobin with Fe 2+Allows for very specific activity of the protein due to detailed globular shape andcollagen triple helix Indivisible, tensile (strong), flexible Responsible for skin elasticity4 heme groups allows it to bind 4 oxygen molecules Successive oxygen binding is accelerated1 st oxygen is hardest to bind Allosteric Co-operativity Property of quaternary structure Activates activity of a protein through its initial bonding Related posts: CELL-MEDIATED IMMUNE RESPONSEBIOLOGICAL MOLECULESDiagnosing Blood Diseases Analysis Questions ORGANIC REACTIONSBreathing Lab: Discussion Questions/ Answers Tags: Allosteric Co-operativity amino terminal antibodies carboxyl terminal Carrier Protein (Oxygen carrying hemoglobin) Cell-to-Cell Recognitioncondensation reaction Denaturation Enzymes (biological catalyst) Hemoglobin Membrane Transport (Na/ K pump) muasin) Muscle Fibers (actin Primary Structure Proteins in the human body have a wide range of functions which include: Hormones (insulin Quaternary Structure Secondary Structure Structure/ Support (nails/ hair) Tertiary Structure testosterone) α-helix β-sheet Share this post Author: Schoolworkhelper Editorial Teamhttps://schoolworkhelper.net/Article last reviewed: 2017 | St. Rosemary Institution © 2010-2018 | Creative Commons 4.0  How Does Hemoglobin Show the Four Levels of Protein Structure? Written by Jillian O'Keeffe Related Articles1What Is the Chemical Makeup of Sebum?2How Does Chemiosmosis Work in Mitochondria?3Chemical Structure of Testosterone4Enzyme Activity in Photosynthesis The structure of the hemoglobin molecule is essential to its function, which is carrying oxygen around the body. Fitting together like a jigsaw that opens up to accept new oxygen, hemoglobin is made up of different proteins with specific amino acid sequences. The overall structure can be interpreted in four different ways. Primary Structure At its simplest level, hemoglobin is made up of amino acids stuck together in chains. These chains are polypeptides that are also stuck to a heme molecule, which is where the oxygen will eventually stick. Hemoglobin is different than other proteins because its individual polypeptides, of which there are four, are called globins instead of simply protein subunits. Secondary Structure The most common secondary protein structures are the alpha helix and the beta-pleated sheet, and each globin contains eight alpha helices. The alpha helices are a result of each globin interacting with itself to form stable structures. Tertiary Structure Tertiary structure describes how each globin bends in space. The heme molecule is important for the tertiary bending structure of hemoglobin, as it helps twist the globins into shape by connecting to histidine residues on them. Quaternary Structure Of the four globins that make up hemoglobin, two are identical and called alpha chains, and the other two are called beta chains and are also identical. They can also be called alpha-globins and beta-globins. The quaternary structure of hemoglobin is these units fitting together. References Springfield Technical Community College: Hemoglobin BRS Biochemistry, Molecular Biology and Genetics; Todd A. Swanson, Sandra I. Kim and Marc J. Glucksman California State University San Marcos: Biomolecular Tutorials Resources Mc Graw-Hill Higher Education: The Four Levels of Protein Structure About the Author Jillian O'Keeffe has been a freelance writer since 2009. Her work appears in regional Irish newspapers including "The Connacht Tribune" and the "Sentinel." O'Keeffe has a Master of Arts in journalism from the National University of Ireland, Galway and a Bachelor of Science in microbiology from University College Cork. Photo Credits Liquidlibrary/liquidlibrary/Getty Images  Introduction Introduction We tend to think of protein as a mass noun: a homogeneous substance, something that your diet should contain in a certain proportion. But if you ever work in a molecular biology lab (say, for a summer internship), protein may start to look very different to you. How so? Well, you may see firsthand that protein isn’t just a single substance. Instead, there are lots and lots of different proteins in an organism, or even in a single cell. They come in every size, shape, and type you can imagine, and each one has a unique and specific job. Some are structural parts, giving cells shape or helping them move. Others act as signals, drifting between cells like messages in a bottle. Still others are metabolic enzymes, putting together or snapping apart biomolecules needed by the cell. And, odds are, one of these unique molecular players will become yours for the duration of your research!Proteins are among the most abundant organic molecules in living systems and are way more diverse in structure and function than other classes of macromolecules. A single cell can contain thousands of proteins, each with a unique function. Although their structures, like their functions, vary greatly, all proteins are made up of one or more chains of amino acids. In this article, we will look in more detail at the building blocks, structures, and roles of proteins. Types and functions of proteins Proteins can play a wide array of roles in a cell or organism. Here, we’ll touch on a few examples of common protein types that may be familiar to you, and that are important in the biology of many organisms (including us). Enzymes Enzymes act as catalysts in biochemical reactions, meaning that they speed the reactions up. Each enzyme recognizes one or more substrates, the molecules that serve as starting material for the reaction it catalyzes. Different enzymes participate in different types of reactions and may break down, link up, or rearrange their substrates. One example of an enzyme found in your body is salivary amylase, which breaks amylose (a kind of starch) down into smaller sugars. The amylose doesn’t taste very sweet, but the smaller sugars do. This is why starchy foods often taste sweeter if you chew them for longer: you’re giving salivary amylase time to get to work. Hormones Hormones are long-distance chemical signals released by endocrine cells (like the cells of your pituitary gland). They control specific physiological processes, such as growth, development, metabolism, and reproduction. While some hormones are steroid-based (see the article on lipids ), others are proteins. These protein-based hormones are commonly called peptide hormones. For example, insulin is an important peptide hormone that helps regulate blood glucose levels. When blood glucose rises (for instance, after you eat a meal), specialized cells in the pancreas release insulin. The insulin binds to cells in the liver and other parts of the body, causing them to take up the glucose. This process helps return blood sugar to its normal, resting level. Some additional types of proteins and their functions are listed in the table below: Protein types and functions Role Examples Functions Digestive enzyme Amylase, lipase, pepsin Break down nutrients in food into small pieces that can be readily absorbed Transport Hemoglobin Carry substances throughout the body in blood or lymph Structure Actin, tubulin, keratin Build different structures, like the cytoskeleton Hormone signaling Insulin, glucagon Coordinate the activity of different body systems Defense Antibodies Protect the body from foreign pathogens Contraction Myosin Carry out muscle contraction Storage Legume storage proteins, egg white (albumin) Provide food for the early development of the embryo or the seedling Table modified from Open Stax College, Biology. Proteins come in many different shapes and sizes. Some are globular (roughly spherical) in shape, whereas others form long, thin fibers. For example, the hemoglobin protein that carries oxygen in the blood is a globular protein, while collagen, found in our skin, is a fibrous protein. A protein’s shape is critical to its function, and, as we’ll see in the next article, many different types of chemical bonds may be important in maintaining this shape. Changes in temperature and p H, as well as the presence of certain chemicals, may disrupt a protein’s shape and cause it to lose functionality, a process known as denaturation. Amino acids Amino acids are the monomers that make up proteins. Specifically, a protein is made up of one or more linear chains of amino acids, each of which is called a polypeptide. (We'll see where this name comes from a little further down the page.) There are 2 0 types of amino acids commonly found in proteins. Image credit: Open Stax Biology. Amino acids share a basic structure, which consists of a central carbon atom, also known as the alpha (α) carbon, bonded to an amino group ( NH 2 ), a carboxyl group ( COOH ), and a hydrogen atom. Although the generalized amino acid shown above is shown with its amino and carboxyl groups neutral for simplicity, this is not actually the state in which an amino acid would typically be found. At physiological p H ( 7. 2 - 7. 4 ), the amino group is typically protonated and bears a positive charge, while the carboxyl group is typically deprotonated and bears a negative charge. Every amino acid also has another atom or group of atoms bonded to the central atom, known as the R group, which determines the identity of the amino acid. For instance, if the R group is a hydrogen atom, then the amino acid is glycine, while if it’s a methyl ( CH 3) group, the amino acid is alanine. The twenty common amino acids are shown in the chart below, with their R groups highlighted in blue. Image modified from Open Stax Biology. The properties of the side chain determine an amino acid’s chemical behavior (that is, whether it is considered acidic, basic, polar, or nonpolar). For example, amino acids such as valine and leucine are nonpolar and hydrophobic, while amino acids like serine and glutamine have hydrophilic side chains and are polar. Some amino acids, such as lysine and arginine, have side chains that are positively charged at physiological p H and are considered basic amino acids. (Histidine is sometimes put in this group too, although it is mostly deprotonated at physiological p H.) Aspartate and glutamate, on the other hand, are negatively charged at physiological p H and are considered acidic. A few other amino acids have R groups with special properties, and these will prove to be important when we look at protein structure: Proline has an R group that’s linked back to its own amino group, forming a ring structure. This makes it an exception to the typical structure of an amino acid, since it no longer has the standard NH 3+ amino group. If you think that ring structure looks a little awkward, you’re right: proline often causes bends or kinks in amino acid chains. Cysteine contains a thiol (-SH) group and can form covalent bonds with other cysteines. We'll see why this is important to protein structure and function in the article on orders of protein structure Finally, there are a few other “non-canonical” amino acids that are found in proteins only under certain conditions. [Click here for cool details! ]You may not need to know about these for your biology class, but they’re pretty darn interesting!One is N -formylmethionine (abbreviated f Met), which is often the first amino acid of protein chains produced by bacteria. It’s similar in structure to methionine, but with an oxygen-containing group added to the amino group 1. Another is pyrrolysine, which looks similar to lysine but has an extra ring-containing group attached to the end of the R group. Pyrrolysine is found mostly in the proteins of microorganisms called methanogenic (methane-producing) archaea 2. Finally, selenocysteine is found in many different types of organisms, including humans, and is used to build selenium-containing proteins. Selenium is highly reactive, so this amino acid must be handled with care: it is specified in the genetic code, and added to protein chains, in a different way than a normal amino acid. Structurally, selenocysteine looks just like cysteine, but with a –Se H group in place of the –SH group 4. Peptide bonds Each protein in your cells consists of one or more polypeptide chains. Each of these polypeptide chains is made up of amino acids, linked together in a specific order. A polypeptide is kind of like a long word that is "spelled out" in amino acid letters 4. The chemical properties and order of the amino acids are key in determining the structure and function of the polypeptide, and the protein it's part of. But how are amino acids actually linked together in chains? The amino acids of a polypeptide are attached to their neighbors by covalent bonds known as a peptide bonds. Each bond forms in a dehydration synthesis (condensation) reaction. During protein synthesis, the carboxyl group of the amino acid at the end of the growing polypeptide chain chain reacts with the amino group of an incoming amino acid, releasing a molecule of water. The resulting bond between amino acids is a peptide bond Image modified from Open Stax Biology. Because of the structure of the amino acids, a polypeptide chain has directionality, meaning that it has two ends that are chemically distinct from one another. At one end, the polypeptide has a free amino group, and this end is called the amino terminus (or N-terminus). The other end, which has a free carboxyl group, is known as the carboxyl terminus (or C-terminus). The N-terminus is on the left and the C-terminus is on the right for the very short polypeptide shown above. How do we go from the amino acid sequence of a polypeptide to the three-dimensional structure of a mature, functional protein? To learn how interactions between amino acids cause a protein to fold into its mature shape, I highly recommend the video on orders of protein structure. [Attribution and references]Attribution: This article is a modified derivative of “ Proteins ,” by Open Stax College, Biology ( CC BY 3.0 ). Download the original article for free at http://cnx.org/contents/185cbf87-c72e-48f5-b51e-f14f21b5eabd@9.85:13/Biology. The modified article is licensed under a CC BY-NC-SA 4.0 license. Works cited: N-formylmethionine. (2014, July 7). Retrieved July 25, 2015 from Wikipedia: https://en.wikipedia.org/wiki/N-Formylmethionine. Pyrrolysine. (2015, May 5). Retrieved July 25, 2015 from Wikipedia: https://en.wikipedia.org/wiki/Pyrrolysine. Selenocysteine. (2015, July 7). Retrieved July 25, 2015 from Wikipedia: https://en.wikipedia.org/wiki/Selenocysteine. Reece, J. B., Urry, L. A., Cain, M. L., Wasserman, S. A., Minorsky, P. V., and Jackson, R. B. (2011). Figure 5.18. Levels of protein structure. In Campbell Biology (10th ed., p. 80). San Francisco, CA: Pearson. Additional references: Amino acid. (2015, July 19). Retrieved July 25, 2015 from Wikipedia: https://en.wikipedia.org/wiki/Amino_acid. Amino acids. (2015, September 9). In Med Line Plus. Retrieved from https://www.nlm.nih.gov/medlineplus/ency/article/002222.htm. Maltose. (2015, July 20). Retrieved July 25, 2015 from Wikipedia: https://en.wikipedia.org/wiki/Maltose. N-formylmethionine. (2014, July 7). Retrieved July 25, 2015 from Wikipedia: https://en.wikipedia.org/wiki/N-Formylmethionine. Pyrrolysine. (2015, May 5). Retrieved July 25, 2015 from Wikipedia: https://en.wikipedia.org/wiki/Pyrrolysine. Raven, P. H., Johnson, G. B., Mason, K. A., Losos, J. B., and Singer, S. R. (2014). Proteins: Molecules with diverse structures and functions. In Biology (10th ed., AP ed., pp. 44-53. New York, NY: Mc Graw-Hill. Reece, J. B., Urry, L. A., Cain, M. L., Wasserman, S. A., Minorsky, P. V., and Jackson, R. B. (2011). Proteins include a diversity of structures, resulting in a wide range of functions. In Campbell biology (10th ed., pp. 75-84). San Francisco, CA: Pearson. Selenocysteine. (2015, July 7). Retrieved July 25, 2015 from Wikipedia: https://en.wikipedia.org/wiki/Selenocysteine. 