DNA and RNA: Structure and Function

May 14, 2004

Two Fundamental types of nucleic acids participate as genetic

molecules DNA: deoxyribonucleic acid

Found in the chromosome form in the cells nucleus

In mitochondria and chloroplast RNA: ribonucleic acid

Ribosomal Messanger Transfer

Outline

RNA and DNA Chemical Structures DNA Structural Elements RNA Structural Elements Cleavage of DNA and RNA by Nucleases Nucleic Acid-Protein Complexes

Outline

RNA and DNA Chemical Structures DNA Structural Elements RNA Structural Elements Cleavage of DNA and RNA by Nucleases Nucleic Acid-Protein Complexes

Components of Nucleotides

Nitrogenous bases A five-carbon carbohydrate One, two, or three phosphate group

RNA

DNA

Major Bases

Minor Bases

A five-carbon carbohydrate:Aldopentose

RNA DNA

A Nucleoside

Consists of a purine or pyrimidine base linked to a carbohydrate

Synthetic Nucleosides Treat for AIDS

Synthetic Nucleosides

Treat for AIDS

Purines and Pyrimidines with Physiological Activity (1)

Caffeine: a trimethylated derivative of the fundamental

purine ring Stimulates the cerebral cortex by inhibiting the

enzyme phophodiesterase, which is involved in cell-signaling processes.

Purines and Pyrimidines with Physiological Activity (2)

6-mercaptopurine (6-MP) Block the synthesis of nucleic acids Effective for treatment of leukemia

Purines and Pyrimidines with Physiological Activity (3)

Acyclovir Used in treatment of herpes viral infections Acts by inhibiting the DNA polymeraase of

herpes viral infections

Purines and Pyrimidines with Physiological Activity (4)

5-fluorouracil (5-FU) A potent inhibitor of DNA synthesis and used

in cancer treatment

Structures for Three Types of Nucleotides

Structures for Three Types of Nucleotides

ATP is the principal carrier of chemical energy in the cell.

ATP + H2O ADP + Pi + energy

GTP, cyclic AMP, and cyclic GMP are transient intermediates that send messages via signal transduction through cell membranes

Pi: HPO42-

Phosphodiester bonds linking mononucleotides into nucleic acids

Comparison of DNA from Different Species

RNA Molecules in E. coli

Nucleic acids Have acidic and basic regions H bond is important in nucleic acids folding

Hydrophilic

Hydrophobic

Outline

RNA and DNA Chemical Structures DNA Structural Elements RNA Structural Elements Cleavage of DNA and RNA by Nucleases Nucleic Acid-Protein Complexes

History Landmarks

The DNA Double Helix

The DNA Double Helix

Two right-handed, helical, polynucleotide chains are coiled around a common axis to form a double helix.

Antiparallel Deoxyribose and phosphatein on the outside of the

helix; hydrophobic purine and pyrimidine base on the inside of the helix

Is stabilized by two types of forces Hydrogen bonds Van der Waals and hydrophobic interactions

Hydrogen Bonding

A-DNA, B-DNA and Z-DNA A-DNA:

right-handed helix 11 bases per helix turn a greater diameter (26 )

B-DNA right-handed helix 10.5 bases per helix turn a diameter (20 )

Z-DNA left-handed helix 12 bases per helix turn a diameter (18 )

Physical and Biological Properties of Double Helix

By Watson and CrickNow our model for deoxyribonucleic acid is, in effect, a pair of templates, each of which is complementary to the other. We imagine that prior to duplication the hydrogen bonds are broken and the two chains unwind and separate. Each chain then acts as a template for the formation onto itself of a new companion chain, so that eventually we shall have two pairs of chains, where we only had one before. Moreover, the sequence of the pairs of bases will have been duplicated exactly.

Nature 171: 964-967, 1953.

Replication of the DNA Double Helix

DNA during Denaturation and Renaturation

85-90 C for many DNA molecules

melting annealing

Melting Curves for DNA Molecules

Tertiary Forms of DNA

Less stable

Topoisomerases

Outline

RNA and DNA Chemical Structures DNA Structural Elements RNA Structural Elements Cleavage of DNA and RNA by Nucleases Nucleic Acid-Protein Complexes

RNA Structural Elements

Two fundamental differences in DNA and RNA RNA contains the carbohydrate ribose rather

than 2-deoxyribose. This makes RNA more susceptible to hydrolysis than DNA.

One of the major bases in RNA is uracil (U)instead of thymine (T) in DNA.

General Features of RNA Secondary and Tertiary Structure

Hairpin turns Right-handed double helixes:

similar to A-DNA Internal loops and bulges

tRNA Structure

74-93 nucleotides in a single chain

methylguanosine

dimethylguanosine

methylinosine

dihydrouridine

psedouridine

The Three-dimensional Structure of Yeast tRNA for Phenylalanine

Proposed Secondary Structure for E. coli 16S rRNA

Outline

RNA and DNA Chemical Structures DNA Structural Elements RNA Structural Elements Cleavage of DNA and RNA by Nucleases Nucleic Acid-Protein Complexes

Nucleases

Catalyze the hydrolysis of phosphodiesterbonds.

Deoxyribonucleases (DNases) and ribonucleases (RNases)

Exonucleases: catalyze the hydrolytic removal of terminal nucleotides

Exonucleases and Endonucleases

Exonucleases

Endonucleases

DNA Restriction Enzymes

Restriction endonucleases Was discovered in DNA molecules. Recognize specific base sequences in

double-strand DNA and catalyze hydrolytic cleavage of the two strands in or near that specific region.

DNA Restriction Enzymes

The enzyme consists of a three-letter abbreviation. EcoRI: the first restriction enzyme to be isolated

from E. coli (strain R)

A specific hexanucleotide sequence

5G-A-A-T-T-C3 5G + A-A-T-T-C33C-T-T-A-A-G5 3C-T-T-A-A G5

OH

OH

DNA Restriction Enzymes

It is unlikely that this set of fragments will be the same for any two different DNA molecules, so the fragmentation pattern is unique and can be considered a fingerprintof DNA substrate.

Outline

RNA and DNA Chemical Structures DNA Structural Elements RNA Structural Elements Cleavage of DNA and RNA by Nucleases Nucleic Acid-Protein Complexes

Nucleic Acid-Protein Complexes

Nucleoproteins Complexes of nucleic acids and proteins.

Viruses Stable, infective particles composed of nucleic

acid, either DNA or RNA, and protein subunits. Bacteriophage or phages

Viruses are specific for bacteria The majority of phages are DNA viruses

Viruses

X174: Infects E. coli DNA genome with relatively small, single-

stranded, circular molecules (5386 b) Tobacco mosaic virus (TMV)

Infects the leaves of the plant. RNA genome with single strand (6390 b)

Viruses Rous sarcoma: causes tumors. Human immunodeficiency

virus (HIV) : causes AIDSGp41 and gp121

Chromosomes Are packages composed of DNA and

protein in eukaryotic cells. The nucleoprotein complex in

eukaryotic cell nucleus is called chromatin.

Histones: are a family of small proteins that containing relatively large numbers of basic amino acid residues Arg and Lys.

Nucleosomes: are held together by ionic bonds between positively charged Arg nad Lys protein residues with the negatively charged phosphate groups in the DNA backbone.

snRNPs

Play a role in RNA processing. These active clusters composed of small

nuclear ribonucleic acids (snRNAs) and proteins are called small nuclear ribonucleoprotein particles (snRNPs)

RNA Processing Fig 11.25

Ribosomes

Supramolecules assemblies of RNA and protein that function as the intracellular sites for protein synthesis.

Ribosomes

Fig 12.1

Ribonucleases

Onconase: The frog enzyme

Exercises

10.1 10.3 10.4 10.5 10.8 10.9 10.11 10.12