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Tutorial 2

1. You must remember all 20 amino acids found naturally in proteins by heart and be able to write an equation leading to the formation of peptide bond. In addition, you must be able to identify this bond from a given structure of peptide or polypeptide.

Figures below illustrate the structures of the 20 amino acids found naturally in proteins. The structures are drawn in the ionized form in which they would be found in cells.

Reference: Schumm DE. 1995. Essentials of biochemistry, 2nd edn. Little, Brown and Company, New York, pp. 108-109.

* Typo for lysine in the figure, it should not be "lycine"

2. D (Dextrorotatory, +) and L (Levorotatory, -) sugars, the configuration of the asymmetric carbon atom farthest from the aldehyde or ketone group determines whether a monosaccharide belongs to the D or L series. In the D form, the hydroxyl group is on the right; in the L form, it is on the left.

Note that asymmetric carbon atom (or achiral) has four different chemical groups attached to it.

Sugars of the D series are the most common in nature.
All of the 20 amino acids except glycine (Why glycine ? what is so special about it ?) are of L-configuration.

Note : Use L-, D- system only for sugars and amino acids, for other chiral compounds use R (rectus = right) & S (sinister = left) system instead because this is a standard method (also called "absolute" convention) of describing stereochemical configuration nowadays (but D-L terminology is still commonly used by biochemists & chemical manufacturers as you may observe from the chemical shelves in laboratory), (You should find & read about Cahn-Ingold-Prelog priority system, also read more about the unreliability of L-, D- system in some cases & find out why L-, D- system is sometimes called "reference" method)

Reference :

There is no direct conversion of L-, D- system to R-, S- system, for example, L-phenylacetylcarbinol may be the same as R-phenylacetylcarbinol but L-glyceraldehyde is actually S-glyceraldehyde. So, we can not say L- is equivalent to R- or D- is equivalent to S- and vice versa.

(Are you convinced that L-glyceraldehyde is S-glyceraldehyde and D-glyceraldehyde is R-glyceraldehyde ? (see picture below), if not you have to read R-, S- system rule again, priorities for groups common in carbohydrate chemistry are -OR > -OH > -NH2 > CO2H > CHO > CH2OH > CH3 > H).

Interesting learning weblinks
Introduction to L, D and R, S configuration system
Introduction to chirality and enantiomers
Structure of various sugars

Stereoisomers : have the same chemical formula but differ in the position of the functional groups on one or more of their asymmetric carbons.

Enantiomers : are stereoisomers that are mirror images of each other.

Epimers : are stereoisomers that differ in the position of the hydroxyl group at only one asymmetric carbon, for example, D-glucose and D-galactose (search for their structures to see the difference clearly) are epimers that differ at carbon 4.

Diastereoisomers : see definition below

(What is the difference between Fischer & Haworth projection ?)

Exercise 1:
Use the skills you have just developed, confirm the following optical stereoisomers of various monosaccharides

Reference: ISISTM Draw 2.3 (2000), MDL Information system.

3. For those who like to practice more on "net charge" and "pI" of a peptide. Try this question; What is the net charge of an oligopeptide in pH range of 1 - 14, also calculate it's pI; (this oligopeptide is in order from the C-terminus to the N-terminus; serine, glutamic acid, methionine, histidine, lysine and alanine).


4. Dipeptide results from the linkage of two amino acids. An amide bond (a type of covalent bond) between alpha-amino and alpha-carboxyl groups is formed when two amino acids are linked together. A water molecule is also eliminated from this reaction as shown below.

(To gain more experiences, you should practice writing "peptide bond formation reactions" between any two of twenty naturally occurring amino acids given above, 20C2 = 190 reactions are possible for any set of two distinct amino acids)

Tetrapeptide shown below results from further peptide bond formation on the free N-terminus and C-terminus of dipeptide glycylalanine with glutamic acid and lysine respectively.

Reference: Mathews CK, van Holde KE. 1990. Biochemistry. Benjamin/Cummings Publishing, New York, pp. 142-143.

5. All proteins are polypeptides. (Find out about variety of proteins and their roles in living organisms, how many different kinds of proteins are there in each type of cell ?)

The picture below illustrates the three-dimensional structure of myoglobin, a type of protein. This paintings emphasizes both the complexity and specificity of protein structure. From Kendrew JC (1961), "The three-dimensional structure of a protein molecule", Scientific American.

Proteins can be classified into four type of structures, namely; primary, secondary, tertiary and quaternary, respectively. The primary structure is the sequence of amino acids along the polypeptide chain, by convention, the sequence is written from left to right starting with the N-terminal amino acid. Secondary structure involves a-helices, b-sheets, and other types of folding patterns (also called supersecondary structures) such as helix-turn-helix, leucine zipper, zinc finger, random coils. (Search for the pictures of various secondary structure of proteins). Three-dimensional conformation of a protein can be refered to the tertiary structure, this involves electrostatic and hydrophobic interactions and hydrogen and disulfide bonds. Special arrangement of protein subunits (What is protein subunits ?) with more than one polypeptide chain results in quaternary structure, the subunits are joined together by noncovalent interactions similar to those found in tertiary structure. (What are the meanings of denaturation and renaturation ? How do they affect protein structures ?).

We will concentrate more on the various types of polypeptide chains (secondary structure) of proteins. A peptide chain backbone can be visualized as a series of playing cards, each card representing a planar peptide group. The arrangement of these cards is described by rotation angles, frequently called Ramachandran angles (after their creater GN Ramachandran). The rotation around the Ca-N bond is called f (phi) and the angle of rotation around the Ca-C bond is designated y (psi), as shown in the picture below.

Reference : Campbell MK. 1995. Biochemistry, 2nd edition. Saunders College, Philadelphia, p. 90

We can use Ramachandran plot (see below) to determine various secondary structures based on coordinate of rotation angles. The white areas correspond to those allowed when side chains are alanines. Circles with symbols correspond to important secondary structures. The dark contour lines running across the graph correspond to various values of n. Where values of n are positive, the helix is right handed; where negative, it is left handed. Areas for right helices are in red; those for left helices in blue.

Reference: Mathews CK, van Holde KE. 1990. Biochemistry. Benjamin/Cummings Publishing, New York, p. 178.

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