Lecture 4

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ءايبولأا فزشأ ىلع ملاسلاو ةلاصلاو

Lecture 4

NUCLEIC ACIDS

1- They are the most important macromolecules in the cells of all microorganisms

2- They are carriers of genetic information 3-There have Two forms (RNA and DNA)

Composition and structure of nucleic acids

Nucleic acid molecule is a polymers of monomeric unit called

nucleotides. These nucleotide monomer unit are joined by the formation of phosphodiester bond

NUCLEIC ACIDS

Phosphodiester Bond

- Phosphate linkage that connects two sugars by ester linkage

- Diester bond is one which involves two ester bond

- Phosphodiester bond will be formed between any two adjacent nucleotides (bet.

The 5’ phosphate of one nucleotide and the 3’ hydroxyl of another)

Nucleotide

Nucleotides composed of:

1. Pentose (C5) sugar, either ribose (RNA) or deoxyribose (DNA) 2. Nitrogen bases which belong to two chemical classes

 Purine bases (adenine and guanine): contain two fused heterocyclic rings

 Pyrimidine bases (thymine, cytosine, and uracil): contain a single six-membered heterocyclic ring

3. Phosphate group

Nucleotide

 Nucleoside: nitrogen base bonded to its C₅ sugar

 Nucleotide: nitrogen base attached to C₅ sugar by glycosidic linkage and bonded to a phosphate

o Major components of nucleic acids

o Key forms of chemical energy (e.g., ATP)

o Carriers of sugars in biosynthesis of polysaccharides

o Regulatory molecules for certain enzymes or metabolic events

Nucleotid e

PO₄

Nucleoside

O^- P O O^-

O^-

Ribose

Nitrogen base Pentose

Sugar Deoxyribose

Purines DNA

RNA

(A) (G)

Pyrimidines

(T) (U)

Primary Structure of nucleic acid

• Is a Sequence of nucleotides in a DNA or RNA molecule

-Oligonucleotide: small polymer contains only a few nucleotides -Polynucleotide: very large polymer contains thousand or

millions of nucleotides

- The polynucleotide chain (strand) has a sense of direction with

one end of the chain terminating in a 5’ phosphate group and the other in a 3’ hydroxyl group of growing Chain

- The sequence of bases in RNA and DNA is written in the 5’ to 3’ direction

- Two polynucleotide strands wrap around each other to form a DNA double helix

- The two strands are associated because particular bases always hydrogen bond to one another A pairs with T, and C pairs with G, producing base pairs

- RNA is usually a single polynucleotide strand

Base –pairing of nitrogen bases

Types of nucleic acid

1. DNA



-Double-stranded

molecules consisting of two complementary

polynucleotide chains running in opposite direction



- Strands held together by hydrogen bonds

Basepair

Types of nucleic acid

2. RNA

- Typically single-stranded - Demonstrates secondary

structure (folding back upon itself)

- Four classes: mRNAs, tRNAs, rRNAs, and small RNAs

Gene

 A particular nucleotide sequence that can instruct the formation of a

polypeptide is called a Gene

- Most DNA molecules consist of millions of base pairs and,

consequently, many genes

- These genes, many of which are

unique to the species, determine the structure of proteins and, thus, life’s structures and functions

Enzymes

 Enzymes are specialized macromolecules that speed up chemical reactions in cells

 They are characterized by the following fundamental properties:

1- They are Catalytic proteins( biological catalysts) that accelerate the rate of biological reactions by reducing the activation energy (energy required to reach the substrate to the transition state (high energy state)

2- enzymes can be denatured and precipitated with salts, solvents and other reagents.

3- Many enzymes require the presence of other compounds - cofactors - before their catalytic activity can be exerted.

- This entire active complex is referred to as the holoenzyme; i.e., apoenzyme (protein portion) plus the cofactor (coenzyme, Prosthetic

Apoenzyme + Cofactor = Holoenzyme

Enzymes

4- Increase the rate of chemical reaction without themselves being consuming or permanently altered by the reaction

5- Increase reaction rates without altering the chemical equilibrium between reactants and products Therefore : the enzyme must accelerate both forward and reverse reaction equally

6- Enzymes are usually very specific as to which reactions they catalyze and the substrates that are involved in these reactions.

Cofactors and coenzymes

- Some enzymes do not need any additional components to show full activity.

- Others require non-protein molecules called

cofactors

to be bound for activity

Cofactors



Cofactors

can be either:

• Inorganic (e.g., metal ions and iron-sulfur clusters)

• Organic compounds (e.g., flavin and heme). which can be either:

- Prosthetic groups, which are tightly bound to an enzyme and play critical function roles (e.g : heme, Zinc)

- Coenzymes, which are released from the enzyme's active site during the reaction, they called coenzymes because they work together with enzymes to enhance reaction rate.

* Coenzymes include NADH, NADPH and adenosine triphosphate.

* These molecules transfer chemical groups between enzymes.

Coenzymes



Coenzymes are small organic molecules that transport chemical groups from one enzyme to another



The chemical groups carried include the hydride ion (H-) carried by NAD or NADP+, the acetyl group

carried by coenzyme A



Coenzymes are usually regenerated and their

concentrations maintained at a steady level inside

the cell

Enzyme classification



EC 1 Oxidoreductases: catalyze oxidation/reduction reactions



EC 2 Transferases: transfer a functional group (e.g. a methyl or phosphate group)



EC 3 Hydrolases: catalyze the hydrolysis of various bonds



EC 4 Lyases: cleave various bonds by means other than hydrolysis and oxidation



EC 5 Isomerases: catalyze isomerization changes within a single molecule



EC 6 Ligases: join two molecules with covalent bonds

Many factors influence enzyme function

1. pH Enzymes in your stomach may prefer an acidic environment with a low pH while enzymes elsewhere may not.

2. Higher temperatures speed reactions -- to a point. Above 104 degrees fahreinheit, enzymes become denatured and can no longer catalyze reactions.

3. Higher concentrations of substrate also speed reactions until the solution reaches a saturation point .Past that point, the addition of substrate will not affect the velocity of the reaction.

4. Irreversible inhibition occurs when the inhibitor added denatures or destroys the enzyme.

Remember



Monomers

-Small molecules that are the building blocks of larger molecules

- Chemical elements bond in different combinations to form monomers



Polymers

- Larger molecules composed of bonded monomers



Macromolecules

- Larger molecules composed of covalently bonded polymers

References

 Gupta, K, (2008) Cell and Molecular biology (Third edition. Rastogi publication, Meerut, New Delhi. ISBN: 61-7133-617-8.

 Lodish, H., Berk, A., Zipursky, S. L., Matsudaire, P., Baltimore, D. and Darnell, J. (1999) Molecular cell biology (Fourth edition). Freeman company. ISBN: 0-7167-3136-3.

 Cooper, G.M.and Hausman, R.E. (2004) The cell a molecular approach (Third edition). Sinauer publication

 Campbell, Reece, Taylor , Simon, Dickey . BIOLOGY – Concepts &

Connections, Sixth Edition. 2009