NAME:KIMELI RICHARD

REG NO: MIC/513/011

COURSE: MOLECULAR GENETICS

COURSE CODE MIC 414

TASK :ASSIGNMENT
 .

Definition of an enzyme
.

Enzymes are protein macromolecules.

o They have a defined amino acid sequence, and are typically 100-500 amino acids
long.

o They have a defined three-dimensional structure.

Enzymes are catalysts.

o They act as a catalyst to a chemical or biochemical reaction, with a defined

mechanism.

o They increase the speed of that reaction, typically by 106-1014 times faster than the
rate of the uncatalysed reaction.

o They are selective for a single substrate.

o They are stereospecific, meaning the reaction produces a single product.

o
Enzyme structure
Primary structure

Enzymes are made up of amino acids which are linked together via amide (peptide) bonds in a
linear chain. This is the primary structure. The resulting amino acid chain is called a
polypeptide or protein. The specific order of amino acids in the protein is encoded by the DNA
sequence of the corresponding gene. There are 20 different standard L--amino acids used by
cells for protein construction. Amino acids, as their name indicates, contain both a basic amino
group and an acidic carboxyl group. This difunctionality allows the individual amino acids to
join together in long chains by forming peptide bonds: amide bonds between the -NH2 of one
amino acid and the -COOH of another. Sequences with fewer than 50 amino acids are generally
referred to as peptides, while the terms protein or polypeptide are used for longer sequences. A
protein can be made up of one or more polypeptide molecules. The end of the peptide or protein
sequence with a free carboxyl group is called the carboxy-terminus or C-terminus. The terms
amino-terminus or N-terminus describe the end of the sequence with a free -amino group.

The amino acids differ in structure by the substituent on their side chains. These side chains
confer different chemical, physical and structural properties to the final peptide or protein. The
structures of the 20 amino acids commonly found in proteins are shown in Figure 1. Each amino
acid has both a one-letter and three-letter abbreviation. These abbreviations are commonly used
to simplify the written sequence of a peptide or protein.

Depending on the side-chain substituent, an amino acid can be classified as being acidic, basic or
neutral. Although 20 amino acids are required for synthesis of various proteins found in humans,
we can synthesize only 10. The remaining 10 are called essential amino acids and must be
obtained in the diet.

The amino acid sequence of a protein is encoded in DNA. Proteins are synthesized by a series of
steps called transcription (the use of a DNA strand to make a complimentary messenger RNA
strand - mRNA) and translation (the mRNA sequence is used as a template to guide the synthesis
of the chain of amino acids which make up the protein). Often, post-translational modifications,
such as glycosylation or phosphorylation, occur which are necessary for the biological function
of the protein. While the amino acid sequence makes up the primary structure of the protein, the
chemical/biological properties of the protein are very much dependent on the three-dimensional
or tertiary structure.
Secondary structure

Because the hydrogen in the amide group (NH2) and the oxygen in the carboxyl group (COOH)
of each amino acid can hydrogen bond with each other, this means that the amino acids in the
same chain can interact with each other. As a result, the protein chain can fold up on itself, and it
can fold up in two ways, resulting in two secondary structures: it can either wrap round
forming the -helix, or it can fold on top of itself forming the -sheet.

The -helix is a right-handed coiled strand. The side-chain substituents of the amino acid groups
in an -helix extend to the outside. Hydrogen bonds form between the oxygen of the C=O of
each peptide bond in the strand and the hydrogen of the N-H group of the peptide bond four
amino acids below it in the helix. The hydrogen bonds make this structure especially stable. The
side-chain substituents of the amino acids fit in beside the N-H groups.

The hydrogen bonding in a -sheet is between strands (inter-strand) rather than within strands
(intra-strand). The sheet conformation consists of pairs of strands lying side-by-side. The
carbonyl oxygens in one strand hydrogen bond with the amino hydrogens of the adjacent strand.
The two strands can be either parallel or anti-parallel depending on whether the strand directions
(N-terminus to C-terminus) are the same or opposite. The anti-parallel -sheet is more stable due
to the more well-aligned hydrogen bonds If the direction alternates between every fold, it forms
an anti-parallel sheet; if it remains the same direction, it forms a parallel sheet.

Tertiary structure

As a consequence of the folding-up of the 2D linear chain in the secondary structure, the protein
can fold up further and in doing so gains a three-dimensional structure. This is its tertiary
structure. Although the three-dimensional shape of a protein may seem irregular and random, it
is fashioned by many stabilizing forces due to bonding interactions between the side-chain
groups of the amino acids.

Under physiologic conditions, the hydrophobic side-chains of neutral, non-polar amino acids
such as phenylalanine or isoleucine tend to be buried on the interior of the protein molecule
thereby shielding them from the aqueous medium. The alkyl groups of alanine, valine, leucine
and isoleucine often form hydrophobic interactions between one-another, while aromatic groups
such as those of phenylalanine and tryosine often stack together. Acidic or basic amino acid side-
chains will generally be exposed on the surface of the protein as they are hydrophilic.

The formation of disulfide bridges by oxidation of the sulfhydryl groups on cysteine is an

important aspect of the stabilization of protein tertiary structure, allowing different parts of the
protein chain to be held together covalently. Additionally, hydrogen bonds may form between
different side-chain groups. As with disulfide bridges, these hydrogen bonds can bring together
two parts of a chain that are some distance away in terms of sequence. Salt bridges, ionic
interactions between positively and negatively charged sites on amino acid side chains, also help
to stabilize the tertiary structure of a protein.

quaternary structure

Many enzymes are actually assemblies of more than one polypeptide chain, which in the context
of the larger assemblage are known as protein subunits. In addition to the tertiary structure of the
subunits, multiple-subunit proteins possess a quaternary structure, which is the arrangement
into which the subunits assemble. Enzymes composed of subunits with diverse functions are
sometimes called holoenzymes, in which some parts may be known as regulatory subunits and
the functional core is known as the catalytic subunit. Examples of proteins with quaternary
structure include hemoglobin, DNA polymerase, and ion channels. Other assemblies referred to
instead as multiprotein complexes also possess quaternary structure. Examples include
nucleosomes and microtubules. Changes in quaternary structure can occur through
conformational changes within individual subunits or through reorientation of the subunits
relative to each other. It is through such changes, which underlie cooperativity and allostery in
"multimeric" enzymes, that many proteins undergo regulation and perform their physiological
function.

The above definition follows a classical approach to biochemistry, established at times when the
distinction between a protein and a functional, proteinaceous unit was difficult to elucidate. More
recently, people refer to protein-protein interaction when discussing quaternary structure of
proteins and consider all assemblies of proteins as protein complexes
Substrate binding
All enzymes have an active site, where the reaction is catalysed. This part of the enzyme has the
right shape and functional groups to bind to the reacting molecules (called the substrate). Hence
the active site contains a small number of catalytic amino acids, which are essential in catalysing
the reaction. The substrate molecule can bind to the active site via non-covalent interactions:

1. electrostatic interactions

for example, those amino acids in section A of this list will attract an oppositely charged
substrate.

2. hydrogen bonding

typically between the amide and carboxyl groups of the amino acid can hydrogen bonds
form with the substrate.

3. Van der Waals interactions

.
REFERENCES
Jurgensen SR, Wood DC, Mahler JC, Harrison JH. The immobilization of
mitochondrial malate dehydrogenase on Sepharose beads and the
demonstration of catalytically active subunits. J Biol Chem. 1981 Mar
10;256(5):23832388. [PubMed]
Kelly CA, Nishiyama M, Ohnishi Y, Beppu T, Birktoft JJ. Determinants of
protein thermostability observed in the 1.9-A crystal structure of malate
dehydrogenase from the thermophilic bacterium Thermus flavus.
Biochemistry. 1993 Apr 20;32(15):39133922. [PubMed]
McEvily AJ, Mullinax TR, Dulin DR, Harrison JH. Regulation of mitochondrial
malate dehydrogenase: kinetic modulation independent of subunit
interaction. Arch Biochem Biophys. 1985 Apr;238(1):229236. [PubMed]

Mullinax TR, Mock JN, McEvily AJ, Harrison JH. Regulation of mitochondrial
malate dehydrogenase. Evidence for an allosteric citrate-binding site. J Biol
Chem. 1982 Nov 25;257(22):1323313239. [PubMedhydrophobic interactions