Answers are supposed to be in essay-form, should have supportive evidence, examp

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Answers are supposed to be in essay-form, should have supportive evidence, examples and diagram.



1. Describe protein structure and its interaction, explain protein activation, inhibition, co-factors and ligands Answers are supposed to be in essay-form, should have supportive evidence, examples and diagram.



1. Describe protein structure and its interaction, explain protein activation, inhibition, co-factors and ligands Answers are supposed to be in essay-form, should have supportive evidence, examples and diagram.

Explanation / Answer

STRUCTURE OF PROTEIN

Primary Structure in Proteins

The primary structure of peptides and proteins refers to the linear number and order of the amino acids present. The convention for the designation of the order of aminoacids is that the N-terminal end (ie, the end bearing the residue with the free -amino group) is to the left and the C-terminal end (ie, the end with the residue containing a free -carboxyl group) is to the right.

Secondary Structure in Proteins

The ordered array of amino acids in a protein confers regular conforma ional forms upon that protein . These conform ations constitute the secondary structures of a protein . In general , proteins fold into 2 broad classes of structure termed globular proteins or fibrous proteins. Globular proteins are com pactly folded and coiled, whereas, fibrous proteins are more filamentous or elongated. It is the partial double bond character of the peptide bond that defines the conformations a polypeptide chain may assume. Within a single protein , different regions of the polypeptide chain may assume different conformations determined by the primary sequence of the amino acids.

Tertiary Structure of Proteins

Tertiary structure refers to the complete 3-dimensional structure of the polypeptide units of a given protein . Included in this description is the spatial relationship of different secondary structures to on e another within a polypeptide chain and how these secondary structures themselves fold into the 3-dimensional form of the protein . Secondary structures of proteins often constitute distinct domains. Therefore, tertiary structure also describes the relationship of different domains to one an other within a protein

FORCES CONTROLLING PROTEIN STRUCTURE

The interaction of different domains is governed by several forces: These include hydrogen bonding , hydrophobic interactions, electrostatic interactions, and vander Waals forces.

Hydrogen Bonding

Poly peptides contain numerous proton donors and acceptors both in their back bone and in the R-groups of the amino acids. The environment in which proteins are found also contains the ample H-bond donors and acceptors of the water molecule. Hbonding , therefore, occurs not only within and between polypeptide chains but with the surrounding aqueous medium .

Hydrophobic Forces

Proteins are composed of amino acids that contain either hydrophilic or hydrophobic R-groups. It is the nature of interaction of different R-groups with the aqueous environment that plays a major role in shaping protein structure. The spontaneous folded state of globular proteins is a reflection of a balance between the opposing energetics of H-bondin g between hydrophilic R-groups and the aqueous environment and the repulsion from the aqueous environment by the hydrophobic R-groups. The hydrophobicity of certain amino acid R-groups tends to drive them away from the exterior of proteins and into the interior. This driving force restricts the available conformations into which a protein may fold.

Electrostatic Forces

Elecrostatic forces are mainly of 3 types: charge-charge, charge-dipole, and dipoledipole. Typical ch arge-charge interactions that favor protein foldin g are those between oppositely charged R-groups such as K or R an d D or E. A substantial 100 component of the energy involved in protein folding is charge-dipole interactions. This refers to the interaction of ionized R-groups of amino acids with the dipole of the water molecule.

van der Waals Forces

There are both attractive and repulsive van der Waals forces that control protein foldin g . Attractive van der Waals forces involve the interactions among induced dipoles that arise from fluctuations in the charge densities that occur between adjacent uncharged non bonded atoms. Repulsive vander Waals forces involve the interactions that occur when uncharged non bonded atoms come very close together but donot induce dipoles. The repulsion is the result of the electron –electron repulsion that occurs as 2 clouds of electrons beg into overlap.

Cofactors

The first type of enzyme partner is a group called cofactors, or molecules that increase the rate of reaction or are required for enzyme function. Cofactors are not proteins but rather help proteins, such as enzymes, although they can also help non-enzyme proteins as well. Examples of cofactors include metal ions like iron and zinc.

A specific type of cofactor, coenzymes, are organic molecules that bind to enzymes and help them function. coenzymes are not really enzymes. As the prefix 'co-' suggests, they work with enzymes. Many coenzymes are derived from vitamins.

These molecules often sit at the active site of an enzyme and aid in recognizing, attracting, or repulsing a substrate or product. A substrate is the molecule upon which an enzyme catalyzes a reaction. Coenzymes can also shuttle chemical groups from one enzyme to another enzyme. Coenzymes bind loosely to enzymes, while another group of cofactors do not

An enzyme activator is a molecule that positively regulates an enzyme's activity. Many enzymes require activators to begin or continue a process, recognize a substrate, or reach their maximum reaction rate. On the flip-side of enzyme activation is inactivation. This is achieved by an inhibitor, or a molecule that binds to an enzyme and disrupts its activity. Activators are the green light of enzyme regulation, while inhibitors are the red light of enzyme regulation. Neither activators nor inhibitors are substrates. These regulators can be proteins or other molecules.

Competitive INHIBITION

Inhibition can be either competitive or noncompetitive and is often reversible. a normal enzymatic interaction, an enzyme will recognize and bind to a substrate in order to catalyze a reaction. It will then release the products.

LIGANDS

Ligands are small molecules that transmit signals in between or within cells. Ligands exert their effects by binding to cellular proteins called receptors. The ligand is like the baton and the receptor is like the next runner in line. After binding to the ligand, the receptor can then send additional signals to other parts of the cell.

Ligands such as hormones that bind to and activate receptor proteins are termed cofactors or coactivators, whereas molecules that inhibit receptor proteins are termed corepressors. Ligand binding to the receptors activates the G protein, which then activates an enzyme to activate the effector.

There are two main types of ligands, ligands that bind to receptors inside the cell, called intracellular ligands, and ligands that bind to receptors outside the cell, called extracellular ligands.

COENZYMES

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