Gene, Genome, Chromosome Structure

dsDNA

genes encoded on both strands, though usually not simultaneously; viruses and cells

ssDNA

single stranded DNA; viruses

ssRNA (positive strand)

all genes coded on the same strand, strand with protein coding sequences (same sequence as mRNA); viruses

ssRNA (negative strand)

all genes coded on the same strand, reverse compliment of mRNA strand; viruses

dsRNA

double stranded RNA

RNA viruses

RNA ←→ RNA

(-) RNA , influenza, ebloa

dsRNA, reto, rota

(+) RNA, hep.C, SARS

Reverse-transcribing viruses

RNA ←→DNA

make DNA from RNA template

(+) RNA, HIV, retro

dsRNA, hep. B

DNA viruses

DNA ←→ DNA

ssDNA, parvo

dsDNA, herpes

Haploid genome sizes

1 copy of each chromosome

bacteria, birds, mammals, flowering plants

mil → billion

Chromosome toplogy

Prokaryotes: circular sometimes linear

Unicellular eukaryotes: linear

Multicellular prokaryotes: linear

Plasmids

Prokaryotes: more frequent

Unicellular eukaryotes: less frequent

Multicellular prokaryotes: less frequent

Ploidy

Prokaryotes: haploid

Unicellular eukaryotes: variable

Multicellular prokaryotes: variable

Protein coding content

Prokaryotes: about 80%

Unicellular eukaryotes: 50-80%

Multicellular prokaryotes: usually <<50%

Introns

Prokaryotes: rare

Unicellular eukaryotes: sometimes

Multicellular prokaryotes: common

Prokaryotes and unicellular eukaryotes

compact genomes typical in microbes

DNA transposons, LTR retrotransposons

½ human genome, <5% typical bacteria genome

Transposons

jumping genes considered to be molecular parasites/selfish DNA

move within or between genes

cut and paste/copy and paste

used as research tools

Protein coding genes

1.5%

Introns

25.9%

Eukaryotic gene structure

leader, exons, introns, trailer

Leader

5’ UTR

Trailer

3’UTR

UTR

untranslated region

Prokaryotic gene structure

both polycistronic and monocistronic mRNA

polycistronic

multiple proteins coded on single mRNA, multiple start and stop codons

Histone core

protein complexes

nucleosome

DNA and protein

Histones

composed of 8 individual polypeptides: 2 copies each of 4 distinct proteins: H2A, H2B, H3, H4 must be removed for transcription to occur

Histone H1

facilitates higher-order compaction and generally repress transcription

Histone tails

contribute to the formation of higher-order chromatic structure and regulation of transcription

Prokaryotes don’t have histones

histone-like proteins that perform analogous functions

DNA supercoiling

also important DNA composition

Relaxed RNA

more energetically favorable amount of twist

Supercoiling

induced positively by transcription and RNA replication

Supercoiling caused by transcription

underwound DNA

overwound DNA

underwound DNA

negative, right-supercoils

overwound

positive, left-handed supercoils

Segments of chromosomes

fixed in place by scaffold proteins and negatively supercoiled to keep them compact and organized

Topoisomerase

cut and re-ligate DNA to add or remove supercoils, bring DNA to relaxed state from supercoiled and vice-versa