Download structure of proteins

Biomolecules
PROTEINS
Introduction
Proteins are the most abundant organic molecules present in cells(table1).They constitute
about 50% or more of dry weight. Proteins are intimately connected with all phases of physical
and chemical activities in the life of a cell. They are ,therefore, essential to cell structure and
function.
COMPONENT PERCENTAGE OF TOTAL CELLULAR MAS
COMPOSITION OF PROTEINS:
A large number of proteins have been isolated in pure crystalline forms. All contain carbon,
hydrogen, nitrogen and oxygen. Some proteins may contain additional elements particularly,
sulphur, phosphorous, iron, zinc, copper and magnesium.
All proteins are macromolecules because of their very high molecular weights .They are
polymers of amino acids i.e. chain like molecules produced by joining a number of small units
of amino acids called MONOMERS. These amino acids are therefore appropriately called as
“Building blocks of proteins”. The amino acids are linked by covalent peptide bonds. Each
amino acid is a nitrogenous compound consisting of an acidic carboxyl (-COOH) group, basic
amino (-NH2) group, a hydrogen atom and a distinct R group bonded to the carbon atom. An R
group is also referred to as SIDE CHAIN.
In aqueous solution, the carboxyl group of the amino acid gets dissociated and becomes
negatively charged while the amino group becomes positively charged. Thus ,amino acids
exist as dipolar molecules or ZWITTER IONS which are electrically neutral with no net
charge. When a zwitter ion i:e amino acid is dissolved in water, it can either act as an acid
(proton donor) or as a base (proton acceptor) and therefore are amphoteric (Greek, amphi,
means “both”). They are also called ampholytes (abbreviated from “amphoteric–electrolytes”)
because of their acid-base behaviour.
R group can be as simple as a H atom (e.g. in Glycine), a methyl group or more complex
structure. On the basis of R group, there are 20 types of amino acids out of which some are
essential amino acids which we obtain from the diet /food, while the non essential amino acids
can be made by our body from essential ones.
Individual amino acids can be linked by forming covalent bond called PEPTIDE BOND.The
bond is formed between alpha carboxyl group of one amino acid and alpha amino group of
the next one.Water is eliminated in this process
STRUCTURE OF PROTEINS
Biologists describe the protein structure at four different levels of structural organisation:
1. Primary Structure 2. Secondary Structure 3. Tertiary Structure and 4. Quaternary Structure
1. Primary structure of a protein is relatively simple and refers to the amino acid sequence
of the peptide chain with amino groups at the left and carboxy group at the right end,
for example tripeptide, Glutathione. The sequence of amino acid is always read from the
N-terminus to the C-terminus i.e. from left to right.
2. Secondary structure refers to the foldings and bendings of the linear peptide chain. Two
types of seconday structures are known
(a) Alpha helix structure where the peptide chain is coiled e.g. proteins of wool,hair and other
fibrous structures.
(b) Beta pleated sheets – in which the peptide chain forms a zigzag pattern as observed in silk.
3. Tertiary Structure: The secondary structure, in turn, may fold in certain specific patterns
to produce the twisted three dimensional or tertiary structure of protein. The tertiary
structure of protein specifies its shape and thereby its biological activity. This shape is
known as the native conformation of protein. The tertiary structure is stabilized by
hydrogen bond and other bonds.has b
esince then.
4. Quaternary structure is the assembly of two or more poly peptides which are individually
folded and arranged in relation to each other.
GENERAL REACTIONS OF PROTEINS:
Small
amounts of concentrated mineral acids cause heavy precipitation of proteins but
further addition of acid re-dissolves the protein and hydrolysis may occur later.
Alkalis do not precipitate proteins but hydrolysis and oxidative decomposition occurs.
Heavy metals act as protein precipitants, depending upon the hydrogen ion concentration,
temperature and the presence of other electrolytes.
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Heat
will coagulate many proteins although the effective temperature may range from
38 – 750C. Various factors influence coagulation but the protein is most easily coagulated
at its iso-electric point.
Denaturation of protein results in an unfolding of the molecule destroying hydrogen and
non polar bonds as well.
QUALITATIVE TEST FOR AMINO ACIDS AND PROTEINS:
There are various qualitative test for detection of amino acid in a sample. Some of these tests
are general and are given by all the amino acids while others are specific for a particular
amino acid. Ninhydrin test result is positive for alpha amino acids, proteins and also peptides.
Ninhydrin reagent is a strong oxidizing agent which reacts with amino acid to give purple
colour due to the formation of a complex called Ruhemann’s purple.
FUNCTIONS OF PROTEINS:
Proteins play very important roles in almost all biological processes:
1) Enzyme catalysis: Nearly all chemical reactions in biological systems are catalyzed by
specific macromolecules called ENZYMES. Almost all enzymes are proteins but there
are some nucleic acids that exhibit catalytic properties and are called RIBOZYME.
2) Transport and storage: Many small molecules and ions are transported by specific
proteins, for example, Hemoglobin transports oxygen in RBCs while Mb, a related
protein stores oxygen. Iron is carried in the plasma of blood by transferring and is stored
in liver as a complex with ferritin.
3) Coordinated motion: Muscle contraction is accomplished by the sliding motion of two
kinds of protein filaments viz. actin and myosin.
4) Mechanical support: Collagen a fibrous protein provides high tensile strength to skin
and tendon.
5) Immune protection: Antibodies are highly specific proteins that play a vital role in
providing protection against foreign antigens and pathogens such as viruses and
bacteria.
6) Generation and transmission of nerve impulses: A large number of receptor proteins
are involved in responding to specific stimuli, for example, rhodopsin.
7) Control of growth and differentiation: Controlled sequential expression of genetic
information is a must for the coordination of growth and differentiation of cells. Proteins
play a vital role in the expression of genome.
ENZYMES
Enzymes are catalytic proteins. Although the catalytic activity of enzymes was formerly thought
to be expressed only in intact cells hence the term enzyme, that is, “in yeast”, most enzymes may
be extracted from cells without loss of their biological activity. They can, therefore be studied
outside the living cells. They are colloidal, high molecular weight, non dialysable, denaturable,
structurally diverse group of proteins. Biochemical reactions taking place within the living cells
are catalysed by enzymes (hence the name biocatalyst). Enzyme containing extracts are used in
studies of metabolic reactions and even as catalysts in the industrial synthesis of biologically
active compounds such as hormones and drugs.
Enzymes increase the rate of reaction without themselves undergoing any change and without
altering the equilibrium of the reaction. The speed with which the enzyme catalyses a reaction is
called velocity or the rate of reaction. It is denoted as ‘V’. The substance on which the enzyme
acts is called substrate (S) and the new substance generated after the reaction is called product
(P). Most enzymes get denatured at high temperature except that of thermophillic organisms.
Naming and Classification of Enzymes
A large number of enzymes have been isolated and studied. These enzymes have been named
and classified by International Union of Bio-Chemist (IUB) in 1961 on the type of reaction
they catalyze.
The six major classes are:1. OXIDOREDUCTASES: This class comprises the enzymes which were earlier called
dehydrogenases, oxidases, hydroxylases etc. The group, includes those enzymes which
bring about oxidation reduction reaction between two substrates
2. TRANSFERASES: Enzymes which catalyze the transfer of a group G (other than
hydrogen) between a pair of substrates S and S’ are called transferases.
3. HYDROLASES: These catalyse the hydrolysis of glycosidic, ester, ether, peptide, C-C,
C-halide, P-N bonds.
4. LYASES (DESMOLASES) : These are those enzymes that catalyze the removal of
groups from substrate by mechanism other than hydrolysis leaving double bonds.
5. ISOMERASES: - Enzymes that catalyse interconversion of optical, geometric or
positional isomers by intramolecular rearrangement of atoms.
6. LIGASES :- (Ligase = to bind) or Synthetase. These are the enzymes catalysing the
linking together of two compounds, for example, joining of C-O, C-S, C-N, P-O.
bonds.
Isoenzymes/Isozymes : Many enzymes occur in more than one molecular form in the same
cell/ tissue/species. Since they possess different kinetic properties and different amino acid
composition, these multiple forms of enzymes are called Isoenzymes or Isozymes for example
LDH exist in 5 possible forms in various organs of most vertebrates.ty
Factors affecting enzyme activity
Various factors affect the activity of enzymes. These are substrate concentration, reaction
temperature and pH of the reaction medium.
Mechanism of Enzyme Action :Activation Energy (delta G) is the energy required for
the formation of transition state. When an enzyme-substrate complex is formed an enzyme
increases the rate of reaction by lowering the activation energy. After the substrate fits into the
active site of the enzyme, free energy is released and it is called intrinsic binding energy.
Enzyme substrate binding can be explained by two models namely
(1) Fischer’s Lock & Key Model (2) Koshland’s Induced Fit Model.
According to first model, the active site of the enzyme is rigid and predetermined to be
complementary to the substrate. Thus the substrate fits into the active site like lock and key.
In second model, the active site of enzyme is flexible and changes shape on binding with the
substrate i.e. the complementarity is induced after the binding of substrate to the enzyme.
ENZYME INHIBITION
1) Competitive Inhibition (reversible)
The inhibition in which substrate analogs bind to active sites of enzymes and inhibit
their activity is called competitive inhibition.
Example- i) Succinate dehydrogenase is inhibited by its competitor Malonate.
ii) Sulpha drugs are substrate analogs of p-amino benzoic acid used in folic acid
synthesis in bacterial cells,hence these drugs are used to kill bacteria.
2) Non-competitive Inhibition (irreversible)
The inhibition in which the inhibitor substance can bind to an enzyme,other than
active site and destroy sulphahydryl group of enzyme.
Example- Toxic metals,CO,CN poisoning of cytochrome oxidase
NUCLEIC ACIDS (Polynucleotides)
Nucleic acid, like proteins occur in all living cells. They derive their name because of their
primary occurrence in the nucleus and acidic nature.
There are 2 types of nucleic acids : DNA- deoxyribonucleic acid and RNA - ribonucleic acid
depending upon the presence of deoxyribose and ribose pentose sugar respectively. The
monomeric unit of DNA are called deoxyribonucleiotides and those of RNA are called
ribonucleotides.
Each nucleotide contains 3 structural units- A nitrogenous heterocyclic base which is a
derivative of either pyrimidine or purine base, a pentose sugar and a molecule of phosphoric
acid.
When the phosphate group of a nucleotide is removed by hydrolysis, the structure remaining is
called a nucleoside. Therefore, Nucleotides are the 5’ phosphates of the corresponding
nucleoside.
DNA is the major component of chromosome. DNA is also found in chloroplast and
mitochondria.DNA is genetic material of all prokaryotes and of many viral particles. RNA is
found mostly in the cytoplasm and in plant virus
Two types of nitrogenous bases are found in nucleic acid viz. purine and pyrimidine .Adenine
(A) and guanine(G) are purine bases while cytosine(C), thymine(T) and uracil(U) are pyrimidine
bases.
DNA (Deoxyribonucleic acid)
DNA is composed of A,G,C and T ; RNA is composed of A,G,C and U.
In nucleic acid strands, successive nucleotides are linked by phosphodiester bond.This is a
bond formed between the 5’ phosphate group of one nucleotide and 3’ hydroxyl group of
the adjacent nucleotides.
In 1953, James Watson and Francis Crick deduced the three dimensional structure of DNA and
got nobel prize in 1962 along with Maurice Wilkins. This brilliant accomplishment is ranked as
one of the most significant in the history of biology because it paved the way to understanding
of genetics.
The salient features of their model are:
1. Two helical polynucleotide chains are coiled around a common axis. The chains run in
opposite directions.
2. The purine and pyrimidine bases are on the inside of the helix, whereas the phosphate
and deoxyribose units are on the outside. The planes of the bases are perpendicular to the
helix axis. The planes of the sugars are nearly at right angles to those of the bases.
3. The two chains are held together by hydrogen bonds between pairs of bases. Adenine is
always paired with thymine. Guanine is always paired with cytosine
4. The sequence of bases along a polynucleotide chain is not restricted in any way. The precise
sequence of bases carries the genetic information.
5. Within the structure of the nucleic acids,a pyrimidine or purine is linked to the sugar to
give a Nucleoside.
Biochemical Test to check the presence of DNA:
DNA can be studied by a specific cytochemical staining method which involves mild acid
hydrolysis of the fixed tissue to remove purines thus unmasking the aldehyde groups of DNA
which are treated with Leucofuchsin (Schiff’s reagent) resulting in a purple colour. This
reaction is positive in the nucleus and negative in the cytoplasm.
TYPES OF DNA
1) Right handed DNA-Twisting of the helix is in clockwise manner, for example, Watson
and Crick proposed B-DNA
2. Left handed DNA-Twisting of the helix is in anticlockwise manner. Example-Z-DNA
discovered by Rich
TYPES OF RNA:
1) Messenger RNA (mRNA) 2) Transfer RNA (t-RNA) and 3) Ribosomal RNA (r-RNA)