1 - Genes and Genomes

Function of nucleic acids

• Store, transmit (RNA) and express genetic information

• RNAs only carry one or a few genes

Nucleotide components

•Phosphate group, 5C sugar, nitrogenous base

• Purines - adenine and guanine

• Pyramidines - cytosine and thymine (uracil)

Differences between DNA and RNA

• Double vs single stranded

• Pentose sugar, bases

•Storage vs expression

Chargaffs rule

• Complimentary base pairing by hydrogen bonds, sequence of one strand determines the other

• G+C (3), A+T (2)

Gene vs genome

• Gene - unit of genetic information that occupies a specific location on a chromosome

• Genome - the entire genetic information of an organism, can be RNA (HIV) or DNA (e.coli)

• Extra genes may be carried on plasmids

Chromosomes

• Organise, store and transmit genetic information, are compact

• Compatible with DNA based processes like replication, transcription and recombination (ds to ss)

• Can be circular or linear

Bacterial genomes

• Usually single copy of circular dsDNA chromosome (haploid) packed in nucleoid but can be linerar or have multiple chromosomes

• Supercoiled for compaction, binding of small basic proteins (posotive) bends DNA

• No nuclear membrane means transcription and translation occur at the same time, unwind and project into cytoplasm to make contact with ribosomes

• Plasmids - extrachromosomal DNA, non essential genes, can integrate into chromosome or move from cell to cell

Prokaryotic gene structure

• Genes organised into operons (cluster of co-regulated genes)

• Polycistronic mRNA - several genes transcribed at once

• Enhancer and repressor mechanisms

• Non coding sequences only account for 12%

Pathogenicity islands

• Operons acquired via horizontal gene transfer

• Contain virulence factors - T3SS, toxins

• Present in pathogenic strains but not commensals e.g enteropathogenic e.coli

Eukaryotic genome

• Linear chromosomes, dsDNA, diploid, 23 pairs

• Centromere in the center of chromosome

• Telomeres at the ends, special sequences for chromosome stability, shortened by a few bases each time DNA is replicated

Chromatin

• Genetic material associated with histone proteins to form chromatin (repeating units of nucleosomes#)

• Compaction and organisation for processes

• 98% of genome is non coding, 50% repetitive sequences

Mitochondrial DNA

• Small amount, maternal inheritence

• 17k bp, ds circular molecule, 37 genes

• 10-20x higher mutation rate vs nuclear DNA

• Heteroplasmy - 2 or more mtDNA variations within the same cell

Repeated sequences in eukaryotic DNA

• Pseudogenes - defective duplicate copies of genuine genes which prevents them from being expressed, may be able to be transcribed but not translated

• Long interspersed nuclear elements - multiple copies of long sequences that make up moderately repetitive DNA

• Short interspersed nuclear elements - multiple copies of short sequences that make up much of highly repetitive DNA

• Sattelite DNA - long clusters of tandem repeats, highly repetitive DNA

Transcription

• Precursor mRNA synthesised by RNA polymerase

• Transcription factors bind to promoter

• Interons removed during splicing (spliceosome), alternative

• UTR’s at each end

• 5’ upstream, 3’ downstream

Gene expression

• One gene produces monocistronic mRNA (single protein per transcript)

• Transcript isoforms - mRNA of different lengths produced by alterantive initiation or termination sites, creates version of the same protein

• Bacteria - several genes transcribed under control of single promoter, plycistronic mRNA, many proteins

Epigenetic modification

• Reversible chemical modifications to DNA that do not alter sequence

• Regulate gene expression, influenced by environmental factors

• Methylation and histone modifications

Primary DNA database

• International nucleotide sequence database collaboration

• NCBI - national center for biotechnology information

• EMBL - european molecular biology laboratory 

• DDBJ - DNA data bank of Japan

Genome databases

• Ensembl, NCBI, UCSC (university of california santa crus)

• Genome browser - feautures drawn over linear track