Mol Bol Flashcards
3´–OH terminus
The end of a polynucleotide that terminates with a hydroxyl group attached to the 3´-carbon of the sugar.
5´–P terminus
The end of a polynucleotide that terminates with a mono-, di- or triphosphate attached to the 5´-carbon of the sugar.
β-N-glycosidic bond
The linkage between the base and sugar of a nucleotide.
adenine
A purine base found in DNA and RNA.
A-form
A structural configuration of the double helix, present but not common in cellular DNA.
antiparallel
Refers to the arrangement of polynucleotides in the double helix, these running in opposite directions.
base pairing
The attachment of one polynucleotide to another, or one part of a polynucleotide to another part of the same polynucleotide, by base pairs.
B-form
The commonest structural conformation of the DNA double helix in living cells.
complementary
Refers to two nucleotides or nucleotide sequences that are able to base-pair with one another.
cytosine
One of the pyrimidine bases found in DNA and RNA.
guanine
One of the pyrimidine bases found in DNA and RNA.
hydrogen bond
A weak electrostatic attraction between an electronegative atom such as oxygen or nitrogen and a hydrogen atom attached to a second electronegative atom.
major groove
The larger of the two grooves that spiral around the surface of the B-form of DNA.
minor groove
The smaller of the two grooves that spiral around the surface of the B-form of DNA.
monomer
One of the structural units that are joined together to form a polymer.
nucleoside
A purine or pyrimidine base attached to a five-carbon sugar.
nucleotide
A purine or pyrimidine base attached to a five-carbon sugar, to which a mono-, di-, or triphosphate is also attached. The monomeric unit of DNA and RNA.
pentose
A sugar comprising five carbon atoms.
phosphodiester bond
The chemical link between adjacent nucleotides in a polynucleotide.
polymer
A compound made up of a long chain of identical or similar units
polynucleotide
A single-stranded DNA or RNA molecule.
purine
One of the two types of nitrogenous base found in nucleotides.
pyrimidine
One of the two types of nitrogenous base found in nucleotides.
thymine
One of the pyrimidine bases found in DNA.
Z-DNA
A conformation of DNA in which the two polynucleotides are wound into a left-handed helix.
complex multigene family
A type of multigene family in which the genes have similar nucleotide sequences, but are sufficiently different to code for proteins with distinctive properties.
discontinuous gene
A gene that is split into exons and introns.
exon
A coding region within a discontinuous gene.
intergenic DNA
The regions of a genome that do not contain genes.
intron
A noncoding region within a discontinuous gene
kilobase pair (kb)
1000 base pairs.
megabase pair (Mb)
1000 kb; 1,000,000 bp.
molecular clock
A device based on the inferred mutation rate that enables times to be assigned to the branch points in a gene tree.
multigene family
A group of genes, clustered or dispersed, with related nucleotide sequences.
pseudogene
An inactivated and hence non-functional copy of a gene.
simple multigene family
A multigene family in which all of the genes are the same.
tandem array
A set of identical or very similar genes that are arranged one after the other in a group.
buoyant density
The density possessed by a molecule or particle when suspended in an aqueous salt or sugar solution.
conservative replication
A hypothetical mode of DNA replication in which one daughter double helix is made up of the two parental polynucleotides and the other is made up of two newly synthesized polynucleotides.
dispersive replication
A hypothetical mode of DNA replication in which both polynucleotides of each daughter double helix are made up partly of parental DNA and partly of newly synthesized DNA.
DNA topoisomerase
An enzyme that introduces or removes turns from the double helix by breakage and reunion of one or both polynucleotides.
plectonemic
Refers to a helix whose strands can only be separated by unwinding.
semiconservative replication
The mode of DNA replication in which each daughter double helix is made up of one polynucleotide from the parent and one newly synthesized polynucleotide.
type I topoisomerase
A topoisomerase that makes a single-stranded break in a double-stranded DNA molecule.
type II topoisomerase
A topoisomerase that makes a double-stranded break in a double-stranded DNA molecule.
3´→5´ exonuclease
An enzyme that sequentially removes nucleotides in the 3´→5´ direction from the end of a nucleic acid molecule.
5´→3´ exonuclease
An enzyme that sequentially removes nucleotides in the 5´→3´ direction from the end of a nucleic acid molecule
DNA polymerase III
The main DNA replicating enzyme of bacteria.
DNA polymerase α
The enzyme that primes DNA replication in eukaryotes.
DNA polymerase δ
The main eukaryotic DNA replicating enzyme.
DNA-dependent DNA polymerase
An enzyme that makes a DNA copy of a DNA template.
leading strand
The strand of the double helix which is copied in a continuous fashion during genome replication.
primase
The RNA polymerase enzyme that synthesizes RNA primers during bacterial DNA replication.
replication fork
replication fork
single-strand binding protein (SSB)
One of the proteins that attach to single-stranded DNA in the region of the replication fork, preventing base pairs forming between the two parent strands before they have been copied.
DNA ligase
An enzyme that synthesizes phosphodiester bonds as part of DNA replication, repair and recombination processes.
DNA polymerase I
The bacterial enzyme that completes synthesis of Okazaki fragments during genome replication.
FEN1
The ‘flap endonuclease’ involved in replication of the lagging strand in eukaryotes.
lagging strand
The strand of the double helix which is copied in a discontinuous fashion during genome replication.
Okazaki fragment
One of the short segments of RNA-primed DNA synthesized during replication of the lagging strand of the double helix.
telomerase
The enzyme that maintains the ends of eukaryotic chromosomes by synthesizing telomeric repeat sequences.
gamma-complex
A multisubunit bacterial protein that attaches and detaches DNA polymerase III during copying of the lagging strand.
helicase
An enzyme that breaks base pairs in a double-stranded DNA molecule.
origin of replication
A site on a DNA molecule where replication initiates.
prepriming complex
A protein complex including the DnaB helicase which initiates construction of a replication fork on a bacterial DNA molecule.
primosome
A protein complex including the DnaB helicase and primase involved in initiation of DNA replication in bacteria.
proliferating cell nuclear antigen (PCNA)
An accessory protein involved in DNA replication in eukaryotes, whose function is to hold DNA polymerase tightly to the DNA.
terminator sequence
One of several sequences on a bacterial genome involved in termination of genome replication.
Tus
The protein that binds to a bacterial terminator sequence and mediates termination of genome replication.
30 nm chromatin fiber.
A relatively unpacked form of chromatin consisting of a possibly helical array of nucleosomes in a fiber approximately 30 nm in diameter.beads-on-a-string
beads-on-a-string
An unpacked form of chromatin consisting of nucleosome beads on a string of DNA.
centromere
The constricted region of a chromosome that is the position at which the pair of chromatids are held together.
chromatid
The arm of a chromosome.
chromatin
The complex of DNA and histone proteins found in chromosomes.
chromatosome
A subcomponent of chromatin made up of a nucleosome core octamer with associated DNA and a linker histone.
constitutive heterochromatin
Chromatin that is permanently in a compact organization.
core octamer
The central component of a nucleosome, made up of two subunits each of histones H2A, H2B, H3 and H4, around which DNA is wound.
euchromatin
Regions of a eukaryotic chromosome that are relatively uncondensed, thought to contain active genes.
facultative heterochromatin
Chromatin that has a compact organization in some, but not all cells, thought to contain genes that are inactive in some cells or at some periods of the cell cycle.
heterochromatin
Chromatin that is relatively condensed and is thought to contain DNA that is not being transcribed.
histone
One of the basic proteins found in nucleosomes.
interphase
The period between cell divisions.
karyogram
The entire chromosome complement of a cell, with each chromosome described in terms of its appearance at metaphase.
5-bromouracil (5-bU)
A base analog that can cause mutations by replacing thymine in a DNA molecule.
(6–4) lesion
A dimer between two adjacent pyrimidine bases in a polynucleotide, formed by ultraviolet irradiation.
alkylating agent
A mutagen that acts by adding alkyl groups to nucleotide bases.
AP (apurinic/apyrimidinic) site
A position in a DNA molecule where the base component of the nucleotide is missing.
base analog
A compound whose structural similarity to one of the bases in DNA enables it to act as a mutagen.
baseless site
A position in a DNA molecule where the base component of the nucleotide is missing.
cyclobutyl dimer
A dimer between two adjacent pyrimidine bases in a polynucleotide, formed by ultraviolet irradiation.
deaminating agent
A mutagen that acts by removing amino groups from nucleotide bases.
ethidium bromide
A type of intercalating agent that causes mutations by inserting between adjacent base pairs in a double-stranded DNA molecule.
ethylmethane sulfonate (EMS)
A mutagen that acts by adding alkyl groups to nucleotide bases.
intercalating agent
A compound that can enter the space between adjacent base pairs of a double-stranded DNA molecule, often causing mutations.
mismatch
A position in a double-stranded DNA molecule where base-pairing does not occur because the nucleotides are not complementary; in particular, a non-base-paired position resulting from an error in replication.
mutagen
A chemical or physical agent that can cause a mutation in a DNA molecule.
mutation
An alteration in the nucleotide sequence of a DNA molecule.
photoproduct
A modified nucleotide resulting from treatment of DNA with ultraviolet radiation
tautomers
Structural isomers that are in dynamic equilibrium.
Ada enzyme
An Escherichia coli enzyme that is involved in the direct repair of alkylation mutations.
AP endonuclease
AP endonuclease
direct repair
A DNA repair system that acts directly on a damaged nucleotide.
DNA glycosylase
An enzyme that cleaves the \beta-N-glycosidic bond between a base and the sugar component of a nucleotide as part of the base excision and mismatch repair processes.
DNA photolyase
A bacterial enzyme involved in repair of base dimers.
DNA repair
The biochemical processes that correct mutations arising from replication errors and the effects of mutagenic agents.
excision repair
A DNA repair process that corrects various types of DNA damage by excising and resynthesizing a region of polynucleotide.
MGMT (O6-methylguanine-DNA methyltransferase)
An enzyme involved in the direct repair of alkylation mutations.
mismatch repair
A DNA repair process that corrects mismatched nucleotide pairs by replacing the incorrect nucleotide in the daughter polynucleotide.
nonhomologous end-joining (NHEJ)
Another name for the double-strand break repair process.
deletion mutation
A mutation resulting from deletion of one or more base pairs from a DNA sequence.
frameshift mutation
A mutation resulting from insertion or deletion of a group of base pairs that is not a multiple of three and which therefore changes the frame in which translation occurs.
insertion mutation
A mutation that arises by insertion of one or more base pairs into a DNA sequence.
inversion
A mutation which involve excision of a portion of a DNA molecule followed by its reinsertion at the same position but in the reverse orientation.
nonsense mutation
An alteration in a nucleotide sequence that changes a triplet coding for an amino acid into a termination codon.
nonsynonymous mutation
A mutation that converts a codon for one amino acid into a codon for a second amino acid.
point mutation
A mutation that results from a single base pair change in a DNA molecule.
readthrough mutation
A mutation that changes a termination codon into a codon specifying an amino acid, and hence results in readthrough of the termination codon.
second site reversion
second site reversion
silent mutation
A change in a DNA sequence that has no effect on the expression or functioning of any gene or gene product.
synonymous mutation
A mutation that changes a codon into a second codon that specifies the same amino acid.
A mutation that changes a codon into a second codon that specifies the same amino acid.
A point mutation that replaces a purine with another purine, or a pyrimidine with another pyrimidine.
transversion
A point mutation that involves a purine being replaced by a pyrimidine, or vice versa.
aneuploid
A diploid chromosome set that is missing one chromosome.
carrier
An individual who has one normal and one defective allele for a gene responsible for an inherited disease, but does not suffer from the disease because the effect of the defective allele is masked by the presence of the unmutated gene.
haploinsufficiency
The situation where inactivation of one of a pair of gene results in a change in the phenotype of the mutant organism.
monosomy
The presence of a single copy of a pair of chromosomes in a nucleus that is otherwise diploid.
Philadelphia chromosome
An abnormal chromosome resulting from a translocation between human chromosomes 9 and 22, a common cause of chronic myeloid leukaemia.
trisomy
The presence of three copies of a chromosome in a nucleus that is otherwise diploid.
