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Proteins

Medical Review: No
Date: 2017-11-01

 

Section 01: Structure, Functions and Properties of Amino Acids

Enzymes are proteins proteinase facilitate biochemical reactions, for example, pepsin. Antibodies are produced by the immune system to help remove foreign substances and fight infections. DNA-associated proteins regulate chromosome structure during cell division and/or play a role in regulating gene expression, for example, histones and cohesion proteins. Contractile proteins for example, actin and myosin. Structural proteins such as collagen and elastin. Hormone proteins co-ordinate bodily functions, for example, insulin and Transport proteins for example, haemoglobin. 

Proteins are very large molecules composed of combinations of 20 different amino acids. All proteins (peptides and polypeptides) are polymers of alpha amino acids. There are 20 α-amino acids that are relevant to the make-up of all proteins. e.g., tyrosine in the formation of thyroid hormones or glutamate acting as a neurotransmitter.

Structure of Amino Acids; The α-amino acids in peptides and proteins consist of a carboxylic acid(–COOH) and an amino (–NH2) functional group attached to the same tetrahedral carbon atom. This carbon is the α-carbon. Distinct R-groups, which distinguish one amino acid from another, are also attached to the alpha-carbon. The fourth substitution on the tetrahedral α-carbon of amino acids is hydrogen

Properties of Amino Acids are:

1. Hydrophobicity and Hydrophilicity of Amino Acids: Each of the 20 α-amino acids found in proteins can be distinguished by the R group substitution on the α-carbon atom. There are two broad classes of amino acids based upon whether the R-group is Hydrophobic and Hydrophilic

2. Acid-Base Properties of the Amino Acids: The α–COOH and α–NH2 groups in amino acids are capable of ionizing (as are the acidic and basic R-groups of the amino acids). As a result of their ionizability, the following ionic equilibrium reactions may be written: The equilibrium reactions, as written, demonstrate that amino acids contain at least two weak acidic groups. An amino acid with no ionizable R-group would be electrically neutral at this pH. This species is called a zwitterion.

3. Optical Properties of the Amino Acids: Chirality describes the handedness of a molecule that is observable by the ability of a molecule to rotate the plane of polarized light either to the right (dextrorotatory) or to the left (levorotatory).  All of the amino acids in proteins exhibit the same absolute steric configuration as L-glyceraldehyde. Therefore, they are all L-α-amino acids. D-amino acids are often found in polypeptide antibiotics.

 

Section 02: Different Structures of Protein

The Peptide-bond formation is a condensation reaction leading to the polymerization of amino acids into peptides and proteins. The simplest peptide, a dipeptide, contains a single peptide bond formed by the condensation of the carboxyl group of one amino acid with the amino group of the second with the concomitant elimination of water. Functional Significance of Amino Acid R-Groups involves the imidazole ring of histidine allows it to act as either a proton donor or acceptor at physiological pH

Structure of proteins are: Primary Structure of Proteins: The primary structure is held together by peptide bonds that are made during the process of protein biosynthesis. Size of the protein molecule can be determined by SDS-PAGE (sodium dodecyl sulphate polyacrylamide gel electrophoresis) or electrospray-mass spectrometry (ES-MS).

Secondary Structure of Proteins. There are mainly four patterns of secondary structures observed in various protein molecules: alpha helix, beta pleated sheet, random coil, and beta turn. The intra-strand hydrogen bonding makes the protein more strong, rigid, and inflexible.

Tertiary Structure of Proteins: The regular polypeptide structures with the complete, compact folding into tertiary structure that the proteins attain their “native conformation” and become active proteins (as a result of the creation of active sites).

Quaternary Structure of Protein: Some proteins are made of more than one polypeptide chain. These proteins are referred to as multimeric proteins. Examples include haemoglobin (blood protein involved in oxygen transport), which has four subunits. Pyruvate dehydrogenase (mitochondrial protein involved in energy metabolism) has 72 subunits. The main molecular interactions involved in the assembly of subunits and formation of quaternary structures include hydrophobic and electrostatic attractions in addition to the weak Van der Waal’s attractions.

 

Section 03: Structure of Immunoglobulins

Immunoglobulin Family is A family of proteins that can be created to bind to almost any molecule. Antibodies (immunoglobulins) are made in response to a foreign molecule like bacteria, virus, pollen called the antigen, Bind together tightly and therefore inactivates the antigen or marks it for destruction. Y-shaped molecules with 2 binding sites at the upper ends of the Y. The loops of polypeptides on the end of the binding site are what imparts the recognition of the antigen. Changes in the sequence of the loops make the antibody recognize different antigens - specificity

Immunoglobulins and their Biochemical Function: IgG is found in the surface of the B-cells that have not been exposed to antigens. Ig E plays an important role in allergic reactions and increase in worm infestations. IgA is found mainly in mucosal secretions, tears, colostrum and milk. These are the initial defense in mucosa against pathogen agents. IgM antibodies are expressed in the surface of B-cells and are found primarily in plasma. They promote phagocytosis and activate the complement system. Immunoglobulins containing alpha chains are called IgA.

 IgA is found mainly in mucosal secretions, tears, colostrum and milk. These are the initial defense in mucosas against pathogen agents. They appear usually as dimmers of (LH)2 units. IgM contain mu heavy chains. IgM antibodies are expressed in the surface of B-cells and are found primarily in plasma. They are the first antibodies produced in significant quantities against an antigen. They promote phagocytosis and activate the complement system.

 

Section 04: Techniques of Proteins Separation

In this section of lecture Separation of Proteins by Salting Out, and Electrophoresis and Centrifugation are explained in detail. There are three basic Protein Separation Techniques that are discussed in this section of lecture. First technique is Electrophoresis, Electrophoresis is the one of the most common method that is used to separate the protein. In this procedure electric field is applied and protein is denatured. In this technique current is provided from cathode to anode, and direction of protein will be downward.

Second technique for protein separation is Salting out procedure. In this procedure at higher ionic strength, the solubility of proteins decreases. Ammonium Sulphate is the most preferred salt used in biochemistry for salting out proteins. This is because it has very high solubility (close to 4 M at zero degree Celsius). Centrifugation is the third technique used for protein separation. This is the most common technique to be used in the laboratories. In this technique Tissue Homogenization is used. Proteins are separated according to their density gradient and tissues are homogenised. 

 

Section 04: Important Proteins

In the last section of this lecture, educator describes some more important proteins and their functions. Collagen are present is Connective tissues and they give tensile strength. Thrombin is present in blood and their function is to provide blood coating. Trypsin are present in Pancreatic juice and they cleaves the polypeptide during protein digestion.

Amylase are also important protein and their site of location is salivary secretion and their function if to starch hydrolysis. Insulin is secreted by islet cells of pancreas into blood stream and they control the blood sugar level. Immunoglobulins are present is blood and they provide Immunity. Endorphins are present in brain and their function is to regulate the brain activities.

Tanveer, Hafsa
  • Academics:  MS
  • Specialization: Biochemistry
  • Current: Research Associate
  • University: NUST
  • Location: Islamabad, Pakistan
  •      
  • Course: Biochemistry
  • Clinical Years:  -
  • Teaching Years: 1

Hafsa Tanveer is an MLS Educator.

2 lectures