1(a) Write short note on the structural features of amino acids.
Solution
Amino acids are the monomers that make up proteins. Each amino acid has the same
fundamental 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
to a hydrogen atom.
(10 mks)
(b) Classify the twenty amino acids commonly found in proteins according to their charge
and polarity and draw the structures of at least two examples in each categories.
Solution
Nonpolar Side Chains
There are eight amino acids with nonpolar side chains. Glycine, alanine, and proline
have small, nonpolar side chains and are all weakly hydrophobic. Phenylalanine,
valine, leucine, isoleucine, and methionine have larger side chains and are more
strongly hydrophobic.
(10 mks)
Polar, Uncharged Side Chains - There are also eight amino acids with polar, uncharged side
chains.
(a) Polar Amino Acids with no Charge
These amino acids do not have any charge on the 'R' group. These amino acids participate in
hydrogen bonding of protein structure. The amino acids in this group are serine,
threonine, tyrosine, cysteine, glutamine and aspargine.
(10 mks)
(b) Polar Amino Acids with Negative Charge
Polar amino acids with negative charge have more carboxyl groups than amino groups
making them acidic. The amino acids, which have negative charge on the 'R' group
are placed in this category. They are called as dicarboxylic mono-amino acids. They
are aspartic acid and glutamic acid.
(10 mks)
(c) Polar Amino Acids with Positive Charge
Polar amino acids with positive charge have more amino groups as compared to carboxyl
groups making it basic. The amino acids, which have positive charge on the 'R' group
are placed in this category. They are lysine, arginine and histidine.
(10 mks)
2(a) Briefly describe the primary and secondary protein structure and illustrate with
diagram when necessary.
Solution
Primary structure
The primary structure of a protein refers to the linear sequence of amino acids in the
polypeptide chain. The primary structure is held together by covalent bonds such as peptide
bonds, which are made during the process of protein biosynthesis. The two ends of
the polypeptide chain are referred to as the carboxyl terminus (C-terminus) and the amino
terminus (N-terminus) based on the nature of the free group on each extremity. 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 mRNA, which is read by
the ribosome in a process called translation.
(15 mks)
Secondary structure
Secondary structure refers to highly regular local sub-structures on the actual polypeptide
backbone chain. Two main types of secondary structure are the α-helix and the β-strand or βsheets. These secondary structures are defined by patterns of hydrogen bonds between the
main-chain peptide groups. They have a regular geometry, being constrained to specific
values of the dihedral angles ψ and φ on the Ramachandran plot. Both the α-helix and the βsheet represent a way of saturating all the hydrogen bond donors and acceptors in the peptide
backbone. Some parts of the protein are ordered but do not form any regular structures. They
should not be confused with random coil, an unfolded polypeptide chain lacking any fixed
three-dimensional structure. Several sequential secondary structures may form a
"supersecondary unit".
(15 mks)
(b) Define the following;
(i) Biomolecules
(ii) Peptide bond
(iii) Disulfide bond
(iv) Hydrogen bond
Solution
(i) BIOLMOLECULES
These are the substances which are present exclusively in the living organisms. They are
formed in the body by biological means and manage the physiology and growth. There are
many biomolecules in nature and one can read them in detail in biochemistry.
Biochemistry describes their formation, physiological role and any deficiency diseases. The
biomolecules are present in the body of humans, animals and plants. Their primary formation
from the basic elements seems to occur in plants. Once formed, these molecules then pass on
to animals through the food chain. They are large macromolecules such
as proteins, carbohydrates, lipids, and nucleic acids, as well as small molecules such as
primary metabolites, secondary metabolites, and natural products. (5 mks)
(ii) PEPTIDE BOND
A peptide bond is a chemical bond formed between two molecules when the carboxyl group
of one molecule reacts with the amino group of the other molecule, releasing a molecule of
water (H2O). This is a dehydration synthesis reaction (also known as a condensation
reaction), and usually occurs between amino acids.
(5 mks)
(iii) DISULFIDE BOND
A disulfide bond, also called an S-S bond, ordisulfide bridge, is a covalent bond derived from
two thiol groups. In biochemistry, the terminology R-S-S-R connectivity is commonly used
to describe the overall linkages. The most common way of creating this bondis by the
oxidation of sulfhydryl groups.
(5 mks)
(iv) HYDROGEN BOND
A hydrogen bond is the electrostatic attraction between two polar groups that occurs when
a hydrogen (H) atom covalently bound to a highly electronegative atom such
as nitrogen (N), oxygen (O), or fluorine (F) experiences the electrostatic field of another
highly electronegative atom nearby. Hydrogen bonds can occur between molecules
(intermolecular) or within different parts of a single molecule (intramolecular). This type of
bond can occur in inorganic molecules such as water and in organic molecules like proteins.
In the secondary structure of proteins, hydrogen bonds are formed between the backbone
oxygens and amide hydrogens.
(5 mks)