Nucleic Acids

Nucleic acids are found in all living cells and form the genetic material, thus being responsible for storage and replication of genetic information.

Nucleic acids are also closely associated with protein synthesis and enhance the expression of genetic information .

Nucleic acids are high molecular weight polymers composed of structures called nucleotides as repeating units.

Nucleotides are joined by covalent bond to form a long molecule (polynucleotide). This joined nucleotide make a nucleic acids.

Both DNA and RNA are nucleic acid or polynucleotide.

A nucleotide is made up of three small molecules:a)A phosphate group or phosphoric acid b)A pentose sugar either deoxyribose or ribose c)A nitrogenous base, either thymine, adenine, guanine, cytosine or uracil.

If the nucleotides contain ribose, the resulting polynucleotide is ribonucleic acid (RNA)

If the nucleotides contain deoxyribose, the resulting polynucleotide is deoxyribonucleic acid (DNA)

DNA molecules are much longer than RNA molecules and quite enormous.

RNA (Ribonucleic acid)

• Found in nucleus, mitochondria, chloroplast, cell wall•RNA nucleotide may contain several thousand nucleotides.•The four possible bases of RNA are adenine, guanine, cytosine, uracil and they never contain thymine.

Types of RNAsBroadly classified as genetic RNA and non-genetic RNA.Genetic RNA: In most of the plant viruses, the genetic material is RNA as DNA is absent. Genetic RNA contain information which is normally found in DNA in higher organism( RNA replaced DNA)Categories of genetic RNA:a)Double stranded RNA- generally follow rule of base paring as in case of DNAb)Single stranded RNA in covalently closed circlec)Single stranded RNA in a linear form

Non-genetic RNA: in organism where DNA is present, RNA does not serve as genetic material. The non-genetic RNA is synthesized on DNA.

Types of non-genetic RNA:

1) Ribosomal RNA (rRNA) Found in ribosomes of the cell, Most stable type Up to 80% of the total cellular RNA In 70s type of ribosome, there are three molecules of RNA In 80s type of ribosome, four molecules of RNA are found rRNA exposed at the surface of the ribosome is double stranded & the

portion associated with internal proteins remains single stranded Participate in translation & translocation process of protein synthesis

2) Messenger RNA (mRNA)•Consist of less than 5% of total cellular RNA• RNA has been isolated from many plants• Variable stability•Single stranded & has no definite organisation• Carries the information needed for synthesis of protein from the nucleus to the sites of protein synthesis, hence called mRNA•Synthesized in the nucleus during transcription from one strand of DNA in the presence of enzyme RNA- polymerase.•Then transported through nuclear pore to the cytoplasm which spread on the surface of ribosomes & participate in protein synthesis.• in eukaryotic cell, mRNA is not formed directly from DNA, rether it is processed through hnRNA

3) Transfer RNA (tRNA) • consist of 15% of total cellular RNA•Is the smallest of RNA molecules being composed of 75-80 nucleotides.•Transfer RNA function as amino-acid carrying molecules during protein synthesis.•There is at least one specific tRNA for each of the twenty amino acids.•Freely present in cytoplasm•All tRNA contain several unusual bases due to methylation of normal bases.•tRNA looks like an L-shaped molecule in three dimensional view.•tRNA has two ends, one end to link with amino acid (acceptor end) & the other anticodon end to link with mRNA.

DNA (Deoxyribonucleic acid)

• DNA molecules contain two poly nucleotide strands. The strands are held together by hydrogen bonds between the bases.

•Watson & Crick in 1953 proposed that DNA molecule was double helix with two right handed polynucleotide chains coiled around a common axis.

•The four possible bases of DNA are adenine, guanine, cytosine and thymine and DNA molecules never contain uracil.

•Hydrogen bond can be formed only between complementary pairs: cytosine with guanine and adenine with thymine.

•This complementary base paring is the basis of the way in which information on DNA can be copied, either to be passed on to a new generation or to be used for building proteins.

DNA NucleotideDNA Nucleotide

OO=P-O O

PhosphatePhosphate GroupGroup

NNitrogenous baseNitrogenous base (A, G, C, or T)(A, G, C, or T)

CH2

O

C1C4

C3 C2

5

SugarSugar(deoxyribose)(deoxyribose)

• Because of highly polar phosphate located on the outside of double helix,DNA is a polyanion and readily binds various cations to maintain charge neutrality.•Phosphate group bind monovalent and divalent cations, various organic molecules such as amines and histones in higher cell chromosomes.

Different types of DNA:B-DNA & Z-DNA. The alternative form differs in bases per turn & spacing between base pairs along the helical axis.

Similarities: • both have double helical organisation•Two strands in both run antiparallel•In both G ≡ C parings are found

Z- DNA B-DNA

It shows left handed helical sense It shows right handed helical sense

Phosphate backbone follows a zig- zag course

Phosphate backbone is regular

The sugar molecules show alternating orientation so that repeating unit is dinucleotide

Orientation of sugar molecules is not alternating & the repeating unit is mononucleotide

One complete turn of DNA has 12 base pairs or 6 repeating dinucleotide

One complete turn has only 10 base pair or 10 repeat units

The angle of twist per repeat unit is 60° The angle of twist per repeat unit is 34°

The length of one complete turn is 45Å The length of one complete turn is 34Å

The diameter of DNA molecule is 18 Å The diameter of DNA molecule is 20 Å

ZZBB

Enzymes and Co-enzymes

Mayrback (1952)- enzymes are simple or compound proteins acting as specific catalysts. organic substances capable of catalysing chemical reactions in the living systems

Dixon and Webb (1964)- ENZYME is a protein with catalytic properties due to its power of specific activation.

enzymes are catalyst. catalyst are able to increase the rate of a chemical reaction without a increase in temperature. Catalyst must function by lowering the level of activation energy. When the product is formed, the catalyst is regenerated unchanged and can be used again.

very small amount of enzyme catalyze the conversion of large molecules of substrate (the substance in which the enzyme acts and which is thereby activated.

Nature of Enzymes

• Enzymes are biocatalysts produced in the protoplasm. • Intra-cellular enzymes/endoenzymes : which acts within the cell•Extra-cellular enzymes/ exoenzymes : diffuse out of the cell to act upon some outside substrates

Properties of Enzyme:a.Enzymes are colloidal in nature- being colloidal in nature provides large surface area for a reaction to take place. Being colloidal in nature, enzymes are hydrophillic in nature anf form hydrosol in free state.b.Enzymes can reacts with both acidic and alkaline substances (amphoteric in nature)c.Enzyme show sensitivity d.Enzyme molecules are larger than substrate molecules.

e. Enzyme are thermolabile (heat sensitive)

• rise in temperature results in an increase in the rate of enzymic reactions until a temperature is reached when the rate falls sharply.

• when the temperature increases, the rate at which enzyme-substrate collisions increases. Hence, the rate of reaction will also increases.

• But, high temperature denatured the enzyme. High temperature cause hydrogen bonds and hydrophillic interactions to break in the enzyme molecules so that it begins to lose its shape.• optimum temperature: the temperature at which the rate of reaction can take place fastest. Optimum temperature for plants= 25°C

f. enzymes are specific : enzymes are specific in their actions, that is they react with only particular substrate. This type of nature of enzyme is called the specificity of enzyme.

g. Enzyme activity is controlled by pH:-pH changes can affect the structure of an enzyme molecule and so it affects its ability to bind and act on its substrate.-- changes in pH affects ionic bonds that are holding the enzyme in shape, and may also affect the R- groups in the active site which form temporary bonds with the substrate.-Most enzymes act over only a very narrow range of pH. The optimum pH is normally around 7.

h. Enzyme lowers down the activation energy of reactions.

Structure and compositions of enzyme

enzyme are proteinaceous in natureEnzyme may entirely consist of protein or may contain a non-protein part. if an enzyme consists only of protein, it is called simple protein enzyme. if it contains another group it is called conjugated protein enzyme.•many enzymes require the presence of another non-protein, non-catalyst substance in order to function. These substances are called coenzyme or cofactors.

• biologist use cofactors for simple molecules and coenzyme for complex organic molecules.

•Both coenzyme and cofactors works by binding with enzyme.

•Coenzymes, which are tightly bound to the enzyme molecule is called prosthetic groups.

• a true prosthetic group is one which remains attached to one enzyme throughout its whole catalytic activity.•AMP, ADP, ATP, NAD, NADP, FAD

Classification of enzymesClassified into six major groups based on chemical reaction that they catalyze:

1. Oxidoreductases: Enzyme that catalyze oxidation-reduction reactions and so are closely

related to respiratory processes in the cell. eg: dehydrogenases, oxidases, reductases2. Transferases: Catalyse the transfer of variouss groups such as one-carbon groups, glycosyl groups, or the phosphate groups from substrate to acceptor molecule. eg: transaminases, kinases3. Hydrolases: These enzymes catalyse a wide range of hydrolytic reaction. They cause addition of water to a variety of bonds and results in cleavage of the substrate.

4. Lyases: results in direct removal of groups from substrate nonhydrolytically. eg: fumarase, carboxylase, aldolase

5. Isomerases: enzyme that bring about isomerizations. It includes the racemerases and

epimeraces which catalyse the interconversion of sterioisomers of amino acids and sugars respectively.

6. Ligases/ synthetases: these enzyme catalyse the synthesis of different types of bonds such as C-C, C-N, C-S, C-O

eg: pyruvate carboxylase

Mode of Enzyme actionKey-Lock theory:•Proposed by Fischer but later advanced by Paul Fildes & D.D. Woods.•As a particular lock can be opened by a particular key, in the same way a particular enzyme acts on a particular substrate. The substrate molecule gets fitted upon an enzyme and decomposes into products.•The shape of the active site (binding site) of the enzyme, matches the shape of the substrate. Allowing the two molecules to bind during the chemical reaction.

Induced fit-theory:

• By Michaelis-Menton• active site of the substrate and enzyme fit into each other and they may combine to form an active complex.

• all enzyme has active sites. In most of the enzymes, when substrate slots into active site, the shape of the whole enzyme changes slightly so that it can accommodate the substrate better. This is called induced fit.

• The arrival of the substrate molecules causes or induces, a change in the shape of enzyme which makes the substrate fit perfectly into the active site.