- The ORDER of the building blocks in the chain determines the character and function.
-
The Amino Acid is a very simple small molecule built from an acidic (carboxyl) group and a basic (amino) group linked by a carbon (called Cα) atom.
-
The carboxyl group is a weak acid and the amino group is a weak base. In the pH range 4-9 both the basic and acidic groups are ionised and the amino acid is a zwitterion (provided there is no charge on the side chain R!). A zwitterion is an ionic molecule with no net charge.
EXERCISE 1: Each member of the team should first construct a model of glycine as it exists in its zwitterionic form at pH7. To make things easier later the carboxyl group is represented with a single and a double bond rather than delocalised, and the two hole linear H and O are used as shown. Use the medium grey links for all single covalent bonds and the long flexible links for the double bond.
SIDE CHAINS
-
The single amino acid building block has twenty variations. The variation is in the part labelled R - twenty different small groups of atoms (known as SIDE CHAINS) can be attached to the central carbon atom (Cα) at this position.
-
R might simply be a hydrogen (the amino acid glycine), or it might be another carbon with hydrogens or small chains of other atoms attached. Generally the atoms in the SIDE CHAINS are Carbon, Hydrogen, Nitrogen, Oxygen. Two of the 20 variations contain Sulphur.
- The atoms in the side chain determine the character of each of the twenty amino acids. Some side chains are acidic (carboxyl groups), some are basic (amino groups), some are neutral. Some contain only C and H while others also contain O or N or both.
The twenty amino acids
- Each of the twenty amino acids has a three letter and single letter code:
eg Valine, Val or V Phenylalanine, Phe or F Tyrosine, Tyr or Y
AMINO ACID SIDE CHAINS
Some examples of amino acid side chains (R) which are attached to Cα. There are 20 different side chains. Atoms in the amino acid side chains generally determine its nature and properties.
Asymmetry around the alpha carbon.
The alpha carbon Cα is tetrahedral and connected by single bonds to 4 different groups
Cα is therefore chiral, and the amino acid can exists as 2 enantiomers
Enantiomers.
-
also known as optical isomers
- can only be interconverted by breaking a chemical bond (like all isomers)
- exist as 2 mirror images, D and L forms
-
only L-amino acids are found in proteins (why?)
EXERCISE 2. Starting with one of your teams glycines, remove one of the hydrogens attached to the α-carbon and add a methyl group to form alanine. The α-carbon of alanine is asymmetric; namely all four substituents are different. There are two ways of arranging the substituents around the α-carbon atom. Viewing the α-carbon down the H → C bond, note the positions of the other substituents. In the L- form the other three substituents in clockwise order are CarbOxylate - R - amiNo (CO-R-N rule) while in the D form the sequence is amino - R - carboxylate. Which form of alanine have you made?
EXERCISE 3. Convert the other of your team's glycines to the enantiomeric (optical isomer) form of alanine to the one you have already made. Compare the two structures and verify to your own satisfaction that they are non-superimposable and mirror images of each other.
EXERCISE 4. Convert the D-amino acid of your pair of alanines to glycine.
EXERCISE 5. One member of your team should then, similarly, make up a molecular model of L- glutamate and the other member L-cysteine: Use single bonds for the delocalised acidic side chain group. Check your models with a demonstrator (see next page).
FROM AMINO ACIDS TO PROTEINS
- Proteins are built from amino acid building blocks joined together in long chains
-
The amino acid sequence of the protein is called the PRIMARY STRUCTURE.
- Protein sequences vary enormously in length, some protein sequences being up to 2,500 amino acids long. Most are 200-500.
-
The amino acids are linked together by the PEPTIDE BOND formed between the N of one amino acid and the C of the next, with the elimination of water.
THE PEPTIDE PLANE
The peptide bond CN has double bond character and no rotation about this bond is allowed. The N and C are both trigonal planar and therefore the whole unit is planar: We may describe the protein as consisting of a long chain of linked peptide planes
EXERCISE 6. Construct two dipeptides by linking together the four amino acids you have already made in two pairs:
e.g.
- glycine- glutamate 2. alanine-serine
The peptide bonds are planar and will be shown in your model by double bonds, thus preventing free rotation around the C - N bond. Remember that the bond has only partial double bond character. The Cα carbons in your dipeptide should be trans.
Rotational flexibility of linked peptide planes
Rotation about the Cα-N single bond is allowed.
EXERCISE 7. Investigate possible conformations of your dipeptides by rotation about the Cα-N and Cα-C bonds. Try and find conformations that maximise the distance between the atoms which are bonded to the main chain C, N and Cα. Discuss your findings with a demonstrator.
FROM PEPTIDE PLANES TO PROTEINS
Peptide planes are
linked by common Cα
and can rotate with
respect to each other
Side view
Two-dimensional representation
PROTEIN FOLDS UP IN THREE DIMENSIONS
EXERCISE 8. Join your two dipeptides together to make an oligopeptide of four amino acids. Investigate the possible conformations by rotations about the Cα-C and Cα-N single bonds. You should discover that there are many possible conformations but only a few that maximise distances between atoms as before.
EXERCISE 9. Now your team should make a valine or a histidine (use C3 and N3 in the ring). Add your valine or histidine to one end of your peptide.
SECONDARY STRUCTURE
The protein folds up with short segments of the polypeptide chain (perhaps 6-20 amino acids) in regular arrangements - these arrangements are known as SECONDARY STRUCTURE. These regular arrangements tend to maximise distances between atoms in adjacent amino acids. There are only a few ways that this can be achieved.
The first of the secondary structure folding patterns is known as the β-strand. In the β-strand the chain is extended in a 'straight' line and the peptide planes form a 'crinkled' plane.
In the β-strand side chains stick out alternately above and below the 'plane' of the strand.
EXERCISE 10. Form your oligopeptide into a β strand. Check your result with a demonstrator.
In most cases several of these beta strands join together to form a β-sheet where adjacent strands are hydrogen bonded together via main chain C=O to main chain N-H hydrogen bonds (C=O∙∙∙∙∙H-N).
EXERCISE 11. Line up your β strand with that of another group or groups so that all the C=O and N-H groups are positioned to make hydrogen bonds. The hydrogen bonds may be formed by linking the oxygens (2-hole linear) with the 2-hole nitrogen hydrogens using the purple links. Now remove the H-bonds, turn one of the strands round and verify that there are two ways of forming a beta sheet (parallel and antiparallel strands).
The second of these arrangements is the α-helix where the chain winds around to form a helix.
The side chains stick out away from the body of the helix. Except for some FRAMEWORK proteins, α-helices are always right handed. There are 3.6 amino acids (or peptide planes) (0.54nm) per turn.
EXERCISE 12. Retreive the individual oligopetides from the β-sheet and try to form them into an α helix. You should discover that the main chain C=O and N=H groups all point approximately along the helix, and that hydrogen bonds can be made between the C=O of one peptide plane and the N-H of another 4 planes further along the helix.
The final three-dimensional structure of the folded protein sequence is known as the TERTIARY STRUCTURE.
GLOBULAR proteins (eg. enzymes, carriers such as haemoglobin, antibodies) are folded up into a compact "blob". Almost all globular proteins, however big or small, have some parts of their chain of amino acids arranged as α-helices, β-strands, or both. Many globular proteins are formed from collections of α-helices and/or β-strands which are arranged in a similar way. However, although the overall shape and appearance (the tertiary structure) of many such proteins is similar, the differences in amino acid sequence, along with the structural changes they produce, give rise to distinctly different properties.
In FRAMEWORK or FIBROUS proteins (eg, keratin, collagen), the entire amino acid chain is folded into a single secondary structure conformation such as a helix (α-keratin, collagen) or strand (silk). Hair and fingernails are formed from α keratin, while skin, bones tendons are formed from collagen.