Chapter 1

DNA Structure & Gene Expression

1. Structure of DNA, RNA, and polypeptides• DNA & RNA are long polymers of nucleotides

- nitrogenous bases – purines, pyrimidines

- differences between DNA & RNA

- difference between nucleoside and nucleotide

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• Polypeptides are long polymers of amino acids

- structure of amino acids – charged polar (basic and acidic), uncharged polar, and nonpolar (hydrophobic).

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2. Chemical bonds and structure: Primary linear structure of DNA, RNA, and proteins is held by strong covalent bonds while weaker noncovalent bonds (hydrogen, ionic, Van der Waals’, and hydrophobic forces) are responsible for intermolecular associations in the secondary, tertiary, and in some cases (proteins) quaternary structure of the molecule.

3. DNA structure and its replication:

• DNA is an antiparallel double helix

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• Intramolecular hydrogen bonding permits RNA-DNA duplexes and double-stranded RNA formation. Such structure formations are relevant in regulating gene expression.

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• DNA replication is semi-conservative

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• DNA replication in mammalian cells requires several enzymes and other proteins: Topoisomerases, helicases, DNA-directed DNA polymerase, RNA-directed DNA polymerases (reverse transcriptase) such as that present in telomerase (used to replicates ends of chromosomes). See Box 1.2 (page 12).

• Viral genomes are frequently maintained by RNA replication.

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4. RNA transcription & gene expression:

• DNA RNA Protein (in most cases)

• Only a small fraction is expressed to give proteins or just RNA.

• For any gene, there is a sense strand (like the RNA transcript) and a template strand (antisense strand).

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• Eukaryotic gene expression requires cis-acting regulatory elements (DNA sequences such as promoters, 5’ UTR, 3’UTR, enhnacers, silencers) and transacting transcription factors (proteins such as activators and repressors of gene expression.

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• Housekeeping genes (such as those encoding histones and ribosomal proteins) are constitutively expressed in all cell types.

• Tissue-specific genes are spatially regulated while developmentally regulated genes are spatially regulated.

• Transcriptionally inactive chromatin is characterized by being heterochromatic (highly condensed), is tightly bound to H1 histones, and is replicated in late S phase.

• Transcriptionally active chromatin is euchromatic (open conformation), replicated early in S phase, weak binding to H1 histone, and has extensive acetylation of the histones H2A, H2B, H3, and H4).

5. RNA processing:• RNA splicing (spliceosome)• Capping by 7-methylguanosine at 5’ end• Polyadenylation : for mRNA the sequence

AAUAAA at 3’ end is a polyadenylation signal and cleavage occurs 15-30 nucleotides downstream from such signal. Poly(A) polymerase then adds about 200 adenylate residues forming a poly(A) tail.

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6. Translation, post-transcriptional processing and protein structure:

• 5’UTR and 3’UTR regions of the mRNA are not translated.

• The genetic code is degenerate (wobble hypothesis at the third base position of codons) and not quite universal.

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• Post-translational modification include chemical modifications of some amino acids and polypeptide cleavage.

- By adding carbohydrate groups (N-glycosylation & O-glycosylation)

- By addition of lipid groups (glycosylphosphatidyl inositol)

- Postranslational cleavage e.g. insulin.

- Protein secretion and intracellular export.

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