Genomes

Genome

The complete set of genetic material in an organism, defining its species

DNA

Deoxyribonucleic acid; the molecule that carries genetic information.

B-form DNA

The most common DNA form in cells; a right-handed double helix.

A-form DNA

A compact, right-handed form of DNA found in harsh environments, especially in some viruses and bacteria

Z-form DNA

A left-handed DNA helix that is transient and may play a role in gene regulation.

Holiday intermediates

Cross-shaped structures that form during homologous recombination in DNA.

Heteroduplex

DNA double helix composed of strands from different sources.

Cruciform

Cross-shaped DNA structures that form in palindromic sequences.

Catenanes

Interlinked circular DNA molecules formed during replication.

Hairpins

Single-stranded loops in DNA or RNA caused by base pairing within the strand.

5’ to 3’ orientation

Directionality of nucleic acid synthesis and structure.

RNA genomes

Genomes made of RNA, found in some viruses like Orthomyxoviridae.

Chromosome

A structure of DNA and proteins that contains genes; linear in eukaryotes, circular in prokaryotes.

Haploid

Having a single set of chromosomes.

Polyploid

Having more than two sets of chromosomes.

Endogenous Viral Elements (EVEs)

Viral sequences vertically transmitted into host genomes that can be inherited.

Prophage

A bacteriophage genome integrated into a bacterial chromosome.

Non-coding DNA

DNA that does not code for proteins; often regulatory or structural. In prokaryotes, only 15% of DNA

Plasmid

Small, circular DNA molecules separate from the chromosome; common in bacteria.

Mitochondrial DNA

Circular DNA found in mitochondria, inherited maternally in most species.

Chloroplast DNA

Circular DNA found in chloroplasts, involved in photosynthesis.

Nucleosome

DNA wrapped around histone proteins in eukaryotes for packaging.

Histones

Proteins that help condense DNA into chromatin.

Chromatin

The complex of DNA and proteins that forms chromosomes.

Hypernucleosome

Chromatin-like structure in archaea with different histone proteins.

Nucleoid

Non-membrane bound region in prokaryotes where DNA is located.

NAPs

Nucleoid-Associated Proteins that help package DNA in bacteria.

Topoisomerase

Enzyme that modifies DNA topology by relaxing or introducing supercoils.

Gyrase

A type of topoisomerase in bacteria that introduces negative supercoils.

Quinolones

Antibiotics that inhibit bacterial DNA gyrase and topoisomerase IV, ex. ciprofloxacin

Semiconservative replication

Each new DNA molecule consists of one old strand and one new strand.

oriC

Origin of replication in bacterial chromosomes.

DnaA

Protein that initiates replication by binding to oriC.

DnaBC

Helicase complex that unwinds DNA at the replication fork.

Replisome

Multiprotein complex that forms at each fork to carry out DNA replication.

Pol I

Bacterial DNA polymerase involved in repair and replacing RNA primers.

Pol II

synthesis, repair, and Pol III’s wingman

Pol III

Main DNA polymerase in bacteria for replication.

Pol B

aids in synthesis and repair

Pol γ

aids mitochondrial DNA replication and repair

Okazaki fragments

Short DNA fragments synthesized on the lagging strand.

MCM complex

Helicase complex in archaea and eukaryotes.

ORC

Origin Recognition Complex; marks replication origins in eukaryotes.

ter site

Termination sequence in bacterial DNA replication. Helicase traps

RTP and Tus

Protein that binds ter sites to stop DNA replication in bacteria.

NAPs common to bacteria

IHF, Fis, HU, and H-NS

prokaryote supercoiling

class I topos relax supercoiling while class II topos introduce supercoiling

eukaryote supercoiling

class I topos relax and introduce supercoils—class II topos relax supercoiling

GyrAB

prototypic class II topoisomerase—first described in E. coli

GyrA

subunit binds and cuts DNA

GyrB

ATPase, energizing GyrA, re-ligates coiled DNA

What does the replisome contain?

helicase complex, polymerase complex, and primase

Primase

protein that adds primers to parental strand

bacteria polymerase

Pol I, II, and III

archaea polymerase

Pol B and D

eukarya polymerase

α, δ, and ε