Proteins and Enzymes-Structure and Function, Biology tutorial

Structure of Proteins:

i) Primary Structure: Primary structure of protein is linear sequential order of amino acid residues making up its polypeptide chain. Focal point is peptide linkage between each of amino acids; no other forces or bonds are involved in term.

aa1-aa2-aa3-aa4-aa5-aa6-aa7.............aan

ii) Secondary Structure: After amino acids have been joined sequentially by peptide bonds, protein chain suffers coiling into helix (spiral of fixed diameter; i.e. cock-screw shape. This secondary feature are enabled by hydrogen bonding, between O2 and H2 atoms near peptide linkage

iii) Tertiary Structure: This is folding of helix or sheet at characteristic places to generate complex, fairly rigid interaction. Folding usually occurs from interactions between amino acid residues comparatively far apart in sequence. Term conformation refers to participation of secondary and tertiary structures of polypeptide chains in molding structure of protein and is of great significance in finding fine structure and unique catalytic properties of biologically active proteins (i.e. enzymes and carriers); change from accurate conformation may lead to loss of activity.

iv) Quaternary Structure: This is formed when two or more polypeptide chains come together to create one complex active protein molecule. Each subunit has its own independent three-dimensional conformation quaternary structure is stabilized by weak interactions rather than by covalent bonds. Example of protein with quaternary structure is haeme of haemoglobin that has paired each of α and a β chain.

Classification of Proteins:

Within these measures there are two categories of proteins that is Fibrous and Globular proteins.

a) Fibrous Proteins: are made up of individual elongated filamentous polypeptide chains arranged in parallel rows, and attached laterally by numerous kinds of cross-linkages to create sheets of fibres that are quite stable, tough and insoluble in water and dilute salt solutions. Examples of fibrous proteins comprise structural proteins like keratin (found in skin and feathers) collagen (found in skin, cartilage and bone) and silk.

b) Globular Proteins: Contrary to fibrous proteins, has a polypeptide chain that are widely folded and compact, with little, if any room for molecules of water in interior. They are folded to generate roughly spherical shapes, with all polar R groups of amino acids on outside and are hydrated; on inside are hydrophobic R groups which therefore repel water from interior. These include enzymes, few animal hormones (e.g. vasopresin, oxytocin, adrenocorticotrophic hormone (ACTH), and insulin), transport proteins (e.g. haemoglobin) cytochrome C (involved in aerobic respiration).

Enzymes:

An enzyme is protein which is synthesized in living cell and catalyses or speeds up thermodynamically possible reaction so that rate of reaction is compatible with biochemical process necessary for maintenance of cell. Enzyme in no way alters equilibrium constant (km) or ΔG (free energy change) of a reaction. Enzymes, being proteins can be denatured by (a) heat (b) strong acids and bases (c) organic solvents (d) temperatures or other materials that denature proteins.

Mechanism of enzyme Action:

Molecules of any compound are always in constant motion, speed depending on nature of compound i.e. gas, liquid or solids (gas molecules are much freer than liquid molecules and far much freer than solid molecules). Enzymes function by increasing proportion of molecules having enough energy to react, therefore speeding rate of reaction.

For substrate to be converted to product energy barrier, ΔG, should be

S+E ↔ P+E    (Where S = Substrate, E = enzyme P = product)

Overcome. This barrier is known as energy of activation (ΔG). Enzyme really reduces this hill, barrier, or energy of activation for hydrolysis of sucrose to glucose and fructose subunits is about 32,000 calories per mole, but the presence of the enzyme invertase lowers it to about 9.400 calories thus an enzyme catalyzed reaction proceeds at a tremendously faster rate than would the same non-catalyzed reaction.

Effect of Enzyme Concentration and Substrate Concentration:

Enzyme-catalyzed reaction at varying substrate concentration is diphasic. With fixed enzyme concentration, increase of substrate will result at first in very rapid rise in velocity or reaction rate. As substrate concentration continues to increase, though, rate of reaction starts to slow down until, with large substrate concentration, no further change in velocity is seen.

Factors which affect Enzyme Activity:

Enzymes, being proteins, are affected by same factor which affect proteins. Enzymes are affected by such factors as temperature, pH, salt concentration etc.

Effect of Temperature:

Non-catalyzed reaction can be greatly increased by raising temperature of environment. Though, such a condition can be extremely unfavorable in living cell. In fact, enzymes being proteins are sensitive to elevated temperatures that results in denaturation of enzyme protein, by decreasing effective concentration of enzyme and therefore decreasing reaction rate. Enzyme activity is strongly influenced by temperature. As the temperature increase so does the reaction.

Effect of pH:

As enzymes are proteins, changes in hydrogen ion concentrations or pH, deeply affect ionic character of amino (NH2) and carboxylic (COOH) groups of protein; so also will it affect changes on exposed "R" groups; it will therefore affect whole charges carried on protein. Low or high pH values can cause substantial denaturation and therefore inactivation of enzyme protein

Specificity:

One significant feature of enzyme is its substrate specificity. This is due to conformation of complex protein molecule, uniqueness of its active site and structural configuration of substrate molecule that make enzyme and its substrate fit in like lock and key. Hence and enzyme will select only specific compounds for attack.

Evolutionary Trends in Enzymes:

Through several different proteins could be created from random arrangements of amino acids, enzyme proteins in different organisms are amazingly similar. This resemblance results partially from evolutionary relationships. Protein should have specific shape to catalyze specific reaction. Several reactions in diverse organisms are the same. Thus enzymes which perform same function in different plants and animals should have analogous structures.

Action of Enzyme:

Several enzymes have their catalytic activity stimulated by nonsubstrate molecules that are known jointly as activators. Examples of activators are cofactors and coenzymes. Other substances retard or inhibit enzyme activity. These are called as inhibitors; of these there are those which compete with substrates for enzyme and those that don't compete i.e. competitive and non-competitive inhibitors respectively.

Activators:

(a) Cofactors:

Several enzymes need small heat-stable molecules, called as cofactors, for their activity. Frequently such cofactors are metal ions like magnesium and sodium ions. Cofactor may from weak association with enzyme such that they can be removed by dialysis - (if enzyme - cofactor complex is put in the dialysis bag (e.g. cellophane sac)).

(b) Coenzymes:

The group of relatively small non-protein organic molecules those are necessary for activities of some enzymes. Coenzymes vary from simpler (metal ions) cofactors in that they are quite complex molecules. Few coenzymes (e.g. NAD+ or NADPT, FAD+) are involved in transferring electrons, protons or groups of atoms form one reaction to another and these really participate in reaction of one of the substrates.

Inhibitors:

These are substances which hinder performance of enzyme. Their action can be reversible or irreversible, competitive or noncompetitive.

(a) Irreversible Inhibitors: The irreversible inhibitor forms the covalent bond with the specific function, typically amino acid residue that may, in some manner, be related with catalytic activity of enzyme. Inhibitor can't be released by dilution or dialysis. Concentration, and therefore velocity of active enzyme is lowered in proportion to concentration of inhibitor and therefore effect is that of a non-competitive inhibition.

(b) Reversible Inhibition: This involves equilibrium between enzyme and inhibitor. There are three different kinds of reversible inhibition.

(c) Competitive Inhibition: As an enzyme should physically combine with substance to form enzyme - substrate complex a molecule other than substrate will inhibit action of enzyme competitively if it combines reversibly with same site on enzyme as substrate. Therefore, in presence of both substrate and inhibitor, enzyme can take part in two distinct reactions either inhibitor may not be structurally related to natural substrate, but combines with enzyme at or near active site.

Non-Competitive Inhibition:

The non-competitive inhibitor is usually thought to combine with enzyme in some way that may not prevent extra binding of substrate. Several non-competitive inhibitors act by causing conformational changes in enzymes they inhibit in such a way that catalytic site is disrupted; though substrate binds, catalytic activity of enzyme is greatly reduced.

Relationship between Enzyme Structure and Activity:

1. At level of primary structure, a alteration of amino acid sequence in region of active center will deform active site and may prevent enzyme from combining with substrate or from performing reaction.

2. Also, any amino acid substitution that causes charge in reactive amino acid side chains (serine, histidine, glutamic, acid etc) at active center will interfere with catalytic activity.

3. If secondary (2o) or tertiary (3o) structure of enzyme is modified by inhibitor or activator, or by some changes in conditions, this can influence activity of enzyme by modifying accessibility of substrate to active center or by altering the orientation of catalytic groups.

Isoenzymes:

Even within single cell, some enzymes exist in more than one molecular form. These numerous forms of same enzyme are known as isoenzymes. These comprise of different polypeptide chains. For instance, lactic dehydrogenase contains four subunits, each of which may be either of 2 polypeptide chains with different amino acid sequences. All the isoenzymes have same molecular weights and catalyze same reaction, though they have different Km values for lactic acid.

Classification of Enzymes:

Enzymes are usually classified in six major groups depending on type of reactions they are involved in.

1. Oxidoreductases: are involved in biological oxidation and reduction reactions - and so are directly related to respiratory processes in cell i.e. respiration and fermentation. This class includes (i) dehydrogenases that bring about oxidation in conjunction with coenzymes like NAD+ and NADP+ that act as hydrogen acceptors. (ii) peroxidases that are hydrogen peroxide (H2O2) as oxidant (iii) hydroxylases that introduce hydroxyl groups (iv) oxygenases that introduce molecular oxygen in place of double bonds in substrate.

2. Transferases: catalyze transfer of one carbon group (methyl, formyl, carboxyl, aldehydyl or ketonic groups, alkyl groups, and sulfide containing groups from substrate to acceptor molecules.

3. Hydrolases: Comprise esterases, phosphatases, glycosidases, peptidases etc that hydrolyze esters, phosphatase, glycosidic and peptide bonds by introduction of water.

4. Lyases: remove groups from substrates (not by hydrolysis) leaving double bonds. This class also comprises decarboxylases (which release CO2 from different substrates).

5. Isomerases: Comprise epimerases, racemoces, cis-trans isomerases, intramolecular oxidoredectases and intra molecular transferaces that catalyze interconversion of stereoisoers of amino acids and sugars respectively.

6 Ligases: catalyze joining together of two molecules couples with breakdown of pyrophosphate bond in ATP or similar triphosphate also called as synthetases, these enzymes are involved in such significant reactions as linkage of amino acids to transfer RNA (tRNA) in first state of protein synthesis.

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