biochem semifinal 1

Immunoglobulins.

. Proteins are involved in defence function. They act against bacterial or viral infection.

Enterotoxin of cholera microorganism

. Some toxins are proteins

Ceruloplasmin:

: A copper binding plasma protein and function as ferrooxidase and converts

α-Lipoprotein:

: Functions in the transport of lipids (HDL). It transports cholesterol from extra hepatic tissue to liver

Fibrinogen

: It is similar to globulins because it is precipitated by half saturation with ammonium sulfate. It is a fibrous or filamentous protein. It is the precursor of fibrin, the blood clotting substances

α1-Globulin:

: Mainly α1-antitrypsin. It is a protease inhibitor. It is the major component of α1-fraction and accounts more than 90%. It inhibits trypsin, chymotrypsin, elastase and neutral protease. The major function of α1-antitrypsin is the protection of pulmonary tissue and other tissues from the destructive action of proteases.

Isoelectric point:

: Proteins have characteristic isoelectric points. At the isoelectric point its net charge is zero because the number of positive charges are equal to number of negative charges. So proteins are insoluble or have minimum solubility at isoelectric point. This property is used for the isolation of casein from milk. The isoelectric point for casein is 4.6. If the pH of the surrounding is raised above the isoelectric point, the protein is negatively charged i.e., it exists as anion. Likewise, if the pH of the surrounding is lowered, the protein is positively charged i.e., it exist as cation. Further, proteins do not move in an electrical field at isoelectric point like amino acids. However, if the pH of the medium is raised or lowered protein moves towards anode or cathode respectively. This property is exploited for the separation of proteins.

. Histones

: Soluble in water and dilute acids

Primary derived proteins

: They are formed from natural proteins by the action of heat or alcohol etc. The peptide bonds are not hydrolysed. They are synonymous with denatured proteins.

) Secondary derived proteins

: They are formed from partial hydrolysis of proteins. Examples: Proteoses, peptone, gelatin, and peptides

Internal hydrogen bonds

Amino acid side chains are involved in the hydrogen bond formation. Hydroxyl group of serine, threonine, the amino groups and carbonyl oxygen of glutamine and aspargine, the ring nitrogen of histidine participates in internal hydrogen bond formation

Derived proteins

As the name implies this class of proteins are formed from simple and conjugated proteins

Prothrombin:

Blood clotting factor

Charge properties:

Charge of a protein depends on the surroundings like amino acids. So, by changing the pH of surroundings the charge of protein can be altered. This property is used for separation of proteins

triple Helix

Collagen present in skin, cartilage, bone and tendons consists of left handed helix as basic unit. Three left handed helices are wrapped around each other to right handed super secondary structure triple helix

proteins.

Enzymes which catalyze chemical reactions in the body are

Native conformation

Finally native conformation develops from molten globule state after several minor conformational changes and rearrangements

Secondary Structure

Folding of polypeptide chain along its long axis is called as secondary structure of protein. Folding of polypeptide chain can be ordered, disordered or random. Secondary structure is often referred as conformation. So, proteins has ordered secondary structure or conformation and random or disordered secondary structure or conformation.

β-turn or β-bends (Reverse Turn)

Hair pin turn of a polypeptide chain is called as β-turn. The change in the direction of a polypeptide chain is achieved by β-turn. β-turn connects anti parallel β-sheets. Usually four aminoacids make up β-turn. Gly, Ser, Asp, proline are involved in β-turns. (Fig. 3.5a)

Insulin

Hormones are proteins. They control many biochemical events

Random Coil (Disordered) Conformation

Regions of proteins that are not organized as helices and pleated sheet are said to be present in random coil conformation. These are also equally important for biological function of proteins as those of helices and β-pleated sheet

Super Secondary Structure

In some globular proteins regions of α-helix and β-pleated sheet join to form super secondary structure or motifs. They are very important for biological function. (Fig. 3.5b

Oligomer formation

In the case of multimeric or oligomeric proteins after attaining specific conformation protomers or sub-units may assemble into native like structure initially. After some realignments it ultimately gives rise to final conformation of oligomer

) Disulfide isomerase

In the newly formed protein molecules -SH groups of cysteine residues may form several intra or inter disulfide linkages. However, only few disulfide linkages may be essential for proper protein folding. The disulfide isomerase favours formation of such disulfide linkages by breaking unwanted linkages formed.

) Molten globule

In the next step domains from molten globule state in which secondary structure predominates and tertiary structure is highly diso

Sclero proteins:

Insoluble in water and dilute acids and alkalies.

β-Lipoproteins:

Involved in the transport of cholesterol from liver to extrahepatic tissue

Ig A class

It accounts for 10-20% of immunoglobulins. Its basic composition is (α2L2), SCJ and it also exists as multimer of the basic unit (α2L2)n where n = 1, 2, 3 etc. It is the chief antibody present in mucous secretions of lungs and gastrointestinal tract.

3. Ig M class

It accounts for about 5-10% of total immunoglobulins. Like Ig A class, it is also a multimer of basic tetramer. Its composition is (µ2L2)5 J i.e., it is a pentamer of basic unit. The H chains are joined by JC chain. When these are present in secretions of mucous membranes they may contain SC component also. It is the largest of all the immunoglobulins (Fig. 3.15b) Ig M act as antigen receptor on B-lymphocytes. It is also involved in complement fixation. Ig M molecules are first to appear in infancy

4. Ig D class

It accounts less than 0.5% of total immunoglobulins. Its composition is δ2L2. The biological activity of Ig D appears to be limited. It is not a secretory antibody. It is involved in the initiation of alternate pathway of complement fixation.

Cis-trans prolyl isomerase

It aids folding process by catalyzing inter conversion of cis-trans peptide bonds of proline residues of folding protein

Haptoglobulin

It combines with haemoglobin in order to remove it from the circulation. Kidney can not filter haemoglobin-haptoglobin complex because of it

. Ig G class

It constitutes 70 to 80% serum immunoglobulins. Its composition is γ2L2 (γ2k2 or γ2λ2). It is the only class of antibody that is capable of crossing the placental barrier from the maternal to fetal circulation.

α2-Macroglobulin:

It functions as protease inhibitor. It combines with proteases and facilitates their removal from circulation. It also binds with cytokines and involved in zinc transport

Prealbumin:

It is a component of globulin fraction. Though it is a globulin by nature it is named as prealbumin because it migrates ahead of a albumin in electrophoresis. It is a carrier of thyroxine, Vitamin A and binds calcium.

. Multiplemyeloma

It is a malignant disease of single clone (cell type) of plasma cells of the bone marrow. These plasma cells proliferate throughout bone marrow. Other bone marrow cells are reduced. Tumours of the plasma cells produce myeloma proteins.

β-Globulins:

It is an iron transport protein

Erythropoietin:

It is involved in erythropoiesis

. Ig E class

It is least concentrated and has shortest life span of all the immunoglobulins. Its composition is ε2L2. Ig E concentration increases in allergic reactions. It is a surface antibody of cells involved in anaphylactic response. The constant region of the antibody is bound to membrane receptor of leukocytes or mast cells and variable region is exposed to the outer surface. When the specific antigen reacts with antibody, it triggers the cells to release histamine and other vasoactive amines. The Ig E class also found in secretions of lungs and gut but the Ig Es lack the J chain and SC part found in Ig As and Ig Ms.

Complement-3

It is one of the member of complement system present in plasma. It is involved in phagocytosis

Pseudocholinesterase:

It is only functional enzyme present in plasma. It hydrolyzes acetylcholine.

α1-Fetoprotein:

It is present only in fetal serum. Its presence in non-foetal serum indicates primary carcinoma of liver. It is referred as tumour marker.

Agammaglobulinemia

It is x-chromosome linked and affects only males. γ-globulins are absent in plasma of these patients. So they are prone to infections.

Albumin:

Not precipitated by half-saturated ammonium sulfate

Fibrous proteins:

Poly peptide chains are extended along one axis.

Globular proteins:

Polypeptide chain(s) of these proteins are folded into compact globular (Spherical) shape

Globulin:

Precipitated by half-saturated ammonium sulfate.

. Hypogammaglobulinemia

Production of γ-globulins is decreased in these cases.

Plasma proteins

Proteins act as buffers.

Prions which cause mad cow disease are proteins.

Proteins are infective agents

Histones.

Proteins are involved in the gene expression. They control gene expression and translation

Haemoglobin transports oxygen.

Proteins are involved in the transport of substances in the body

Quaternary Structure

Proteins containing two or more polypeptide chains possess quaternary structure. These proteins are called as oligomers. The individual polypeptide chains are called as protomer, monomers or subunits. The protomers are united by forces other than covalent bonds. Occasionally, they may be joined by disulfide bonds. (Fig. 3.8

Avidin of egg.

Proteins function as anti-vitamins

Casein of milk, Ferritin that stores iron

Proteins serve as nutrients. Proteins are also involved in storage function

. Proteins act as buffers:

Since proteins are amphoteric substances, they act as buffers. Hemoglobin (Hb) of erythrocytes and plasma proteins are important buffers. Hb accounts for 60% of buffering action with in erythrocytes and plasma proteins contributes to 20% of buffering action of blood.

Protamins:

Soluble in ammonia and water

Glutelins:

Soluble in dilute acids and alkalies

Prolamines:

Soluble in dilute alcohol and insoluble in water and alcohol

Albumins:

Soluble in water and salt solutions

α-keratin is present in hair and epidermis.

Some proteins are components of structures of tissues.

Muscle proteins

Some proteins have role in contraction of muscles

Collagen and elastin of bone matrix and ligaments.

Some proteins provide structural strength and elasticity to the organs and vascular system

. Autoimmune disorders

Sometimes body rejects its own proteins which becomes antigenic. This results in auto immune disorders due to production of antibodies against its own proteins. Rheumatoid arthritis is known auto immune disorder.

Globulins:

Sparingly soluble in water but soluble in salt solutions.

Primary Structure

The linear sequence of amino acid residues in a polypeptide chain is called

Hydrophobic interactions

The non-polar side chains of neutral amino acids tend to associate in proteins. These are called as hydrophobic interactions. They play significant role in maintaining tertiary structure

α2-Globulins:

The α2-fraction of globulins includes.

Vander waals interactions

These are the weak interactions between uncharged groups of protein molecule. They also contribute to the stability of proteins.

B. Electrostatic bonds

These bonds are formed between oppositely charged groups of amino acid side chains. The ε-amino groups of lysine is positively charged and second (non-α-) carboxyl group of aspartic acid is negatively charged at physiological or body pH. These interact electrostatically to stabilize tertiary structure of protein. They are also called as salt bridges

Chaperons (Chaperonins

These proteins aid protein folding process by preventing formation of aggregates. Usually aggregate formation slows down protein folding process.

Conjugated proteins:

They are proteins containing non-protein part attached to the protein part. The non-protein part is linked to protein through covalent bond, non-covalent bond and hydrophobic interaction. The non-protein part is loosely called as prosthetic group. On hydrolysis, these proteins yield non-protein compounds and amino acids

Primary Structure of Insulin

This protein consist of two polypeptide chains A and B. The two chains are covalently linked by disulfide bonds. The A chain has N-terminal glycine and C-terminal aspargine. The B chain has phenylalanine and alanine as N-and C-terminal residues, respectively. Insulin is a hormone and its molecular weight is 5,700 (Fig. 3.1b)

Simple proteins:

are made up of amino acids only. On hydrolysis, they yield only amino acids.

Tertiary Structure

Three-dimensional folding of polypeptide chain is called as tertiary structure. It consists of regions of α-helices, β-pleated sheet, β-turns, motifs and random coil conformations. Interrelationships between these structures are also a part of tertiary structure (Fig. 3.6).

Retinolbinding protein

Transport of Vit A

Thyroxine binding globulin

Transport of thyroxine

Albumin

accounts for 75% of the osmotic pressure (25 mm Hg) in blood and responsible for maintenance of blood volume

α1-Acid glycoprotein (AAG)

another major component of α1-globulins. It increases in plasma in inflammatory conditions.

proteins

are also called as polypeptides because they contain many peptide bonds.

Edman's reagent

for the determination of amino acid sequence of a protein from the N-terminus. Edmans reagent not only identifies N-terminus but also when used repeatedly provides complete sequence of the polypeptide chain. In Edman's reaction, the polypeptide chain is shortened by only one residue and rest of the polypeptide remains intact. The reaction is repeated and second residue is determined. By continued repetition, complete sequence of protein is determined starting from N-terminus

Hydrogen bond

is a weak ionic interaction between positively charged hydrogen atom and negatively charged atoms like oxygen, nitrogen, sulfur etc. It is indicated with broken lines (---).

Liver

is the sole source of albumin, prothrombin and fibrinogen. Most of the α and β globulins are also of hepatic origin. γ-globulins are derived from lymphocytes.

Denaturation of Proteins

s loss of native conformation

Sanger's reagent

to determine the amino acid sequence of a polypeptide chain from N-terminus. Sanger's reagent can be used to determine only one amino acid at a time because FDNB reacts with other amino acids. FDNB arylates free amino acid group and produces intense yellow 2, 4-dinitrophenyl residues of amino acids. These derivatives are separated by chromatography and identified (

The polypeptide chain of α-keratin,

which is present in hair, nails, epidermis of the skin is arranged. given to this type of structure because it was first ordered structure noticed in proteins

Polypeptide chain of β-keratin,

which is present in silk fibroin and spider web is arranged.

Domains formation

α-helical, β-pleated sheet, β-bend containing domains are formed in the initial step of folding of polypeptide chain. This self assembling process mostly depends on primary structure. It involves extensive interaction among amino acids residues side chains of polypeptide chain. It is governed by thermodynamic principles like free energy etc

Super Helix

α-keratin consist of right handed α-helix as basic unit. Three such α-helices get cross linked by disulfide bonds and form super secondary structure.