Gene mutation, DNA repair, and transposition & Chromosomal mutations: variation in number and arrangement (15&8)

mutation

An alteration in the nucleotide sequence of an organism’s genome; any base-pair change in any part of a DNA molecule

point mutation

A change of one base pair to another

missense mutation

A mutation that changes a codon to one coding for a different amino acid

nonsense mutation

A mutation that changes a codon to a stop codon, prematurely halting protein synthesis

silent mutation

A base pair change that does not result in any change to the amino acid sequence

neutral mutation

A mutation with no perceived significance or phenotypic effect

transition

A mutation where a pyrimidine replaces another pyrimidine or a purine replaces another purine

transversion

A mutation where a pyrimidine replaces a purine or vice versa

frameshift mutation

A mutation where the “reading frame” is altered by the loss/addition of a nucleotide(s)

suppressor mutation

A mutation that reverses or relieves the effects of a previous mutation

intragenic mutation

A suppressor mutation located within the same gene as the other mutation it suppresses

intergenic mutation

A suppressor mutation located elsewhere in the genome relative to the mutation it is suppressing

somatic mutation

non-heritable mutation occurring in non-germ cells

autosomal mutation

Inheritable mutation occuring on one of the autosomes; can be transmitted to offspring as gametes

X-linked mutation

Autosomal mutation located on the X chromosome

Y-linked mutation

Autosomal mutation located on the Y chromosome

spontaneous mutation

Change in the nucleotide sequence of genes that appears to occur “naturally” and is not induced by any mutagenic agent; extremely low mutation rate

mutation hotspots

DNA sequences that are highly susceptible to mutations

SNPs

A single-nucleotide pair variation in DNA that occurs in at least 1% of the population and can be used as a genetic marker

Luria-Delbruck fluctuation test

Experiment that proved that mutations arise randomly, even in the absence of selective pressure, and are inherited in a stable fashion

replication slippage

A phenomenon that occurs when DNA polymerase slips/stutters on the template strand during DNA replication, leading to insertions/deletions

tautomeric shift

A phenomenon where the covalent structure of a nitrogenous base is altered to allow it to bind with noncomplementary bases (such as A:C or T:G), potentially resulting in a point mutation

depurination

The loss of a purine in a double-stranded DNA molecule, resulting in a gap where DNA polymerase inserts a random nucleotide during DNA replication

deamination

A process where an amino group in A/C is converted to a ketone, converting C→U or A→hypoxanthine (which pairs with C), resulting in a G:C pair becoming an A:T pair (or vice versa) after replication

induced mutations

Mutations that result from the influence of external forces (natural/artificial mutagenic agents)

base analogs

Compounds that can substitute for nitrogenous bases during DNA synthesis and lead to transition mutations

Alkylating agents

mutagens that donate an alkyl group to nucleotides, altering base-pairing affinities and resulting in transition mutations

Intercalating agents

mutagens that wedge between base pairs and cause the DNA strands to unwind, leading to frameshift mutations

adduct-forming agents

Compounds that covalently bind to DNA, altering its conformation and interfering with replication/repair

pyrimidine dimers

Sets of two identical pyrimidines (usually thymine) caused by UV radiation, which distort the DNA and inhibit normal replication so that errors are introduced during replication

free radicals

Chemical species with one or more unpaired electrons formed by exposure to high-energy ionizing radiation, which can affect the DNA and produce a variety of chromosomal aberrations

trinucleotide repeat mutation

A type of mutation where a sequence of 3 nucleotides repeats multiple times in the DNA (ex. huntington’s disease)

mismatch repair

Mismatched bases are corrected by _____ _____

unmethylated

During mismatch repair, the repair enzymes identify mismatches on the ______ (newly-formed) strand

endonuclease

During mismatch repair, an _____ creates a nick in the sugar-phosphate backbone of the DNA

exonuclease

During mismatch repair, an _______ degrades the erroneous DNA segment before the gap is repaired by DNA polymerase and ligase

postreplication repair

______ ______ addresses gaps left in DNA after replication, typically caused by damaged sections of DNA that DNA polymerase “skips” over

homologous recombination

During postreplication repair, the undamaged segment from the donor strand replaces the gapped segment and is then filled by repair synthesis. This is an example of _____ _____

photoreactivation repair

thymine dimers from UV light exposure are enzymatically reversed through _____ ____

photoreactivation enzyme

______ ____ absorbs a photon of visible blue light to cleave the bonds between thymine dimers during photoreactivation repair

base excision repair

Mutations resulting from chemically-altered/abnormal bases (base analogs, alkylating agents, etc) are corrected through ____ ____ ____

DNA glycosylase

____ _______ recognizes and cuts out a damaged base during BER, then the gap is filled by DNA polymerase and ligase

nucleotide excision repair

UV-induced pyrimidine dimers and DNA adducts are repaired by ______ ______ ______

nucleotide excision repair

Process where a stretch of damaged DNA is removed and replaced by resynthesis using the undamaged strand as a template

transposable elements

DNA sequences that can move/transpose within/between chromosomes, inserting themselves into various locations within the genome

DNA transposons

Mobile genetic elements that are excised from one location and inserted into another without going through an RNA intermediate stage; contain inverted terminal repeats (ITRs) and an ORF that codes for transposase enzyme; flanked by short direct repeats (DRs)

autonomous transposons

Transposons that code for a functional transposase enzyme and are able to transpose independently

non-autonomous transposons

Transposons that code for a non-functional transposase enzyme and require the presence of an autonomous transposon elsewhere in the genome for transposition

retrotransposons

Transposable elements that are copies by means of an RNA intermediate and inserted at other chromosomal sites; encode for enzymes required for transposition

integrase, reverse transcriptase

What are the enzymes required for retrotransposon transposition

LTR retrotransposons

retrotransposons that contain long terminal repeats on both ends

non-LTR retrotransposons

retrotransposons that do not contain long terminal repeats

transposition

1) Retrotransposon is transcribed to RNA and translated to reverse transcriptase and integrase

2) Reverse transcriptase creates a DNA copy from the RNA template

3) Integrase inserts the DNA copy into the genome

retroviruses

A type of virus that integrates its viral RNA into the host genome using reverse transcriptase; can become fixed in a species if integrated into the germline

aneuploidy

A condition where an organism gains/loses one or more chromosomes, but not an entire set (n)

monosomy

The loss of a single chromosome in a diploid genome, resulting in a chromosome number of 2n-1

haploinsufficiency

A condition where an organism has only one copy of a gene and dies because it is not sufficient

trisomy

The gain of a single chromosome in a dilpoid genome, resulting in a chromosome number of 2n+1

polyploidy

A condition in which a cell or individual has more than two complete haploid sets of chromosomes (multiple of n)

nondisjunction

A cell division error in which homologous chromosomes/sister chromatids fail to separate and migrate to opposite poles, resulting in chromosomal variation

autopolyploidy

A condition in which an organism has one or more extra sets of chromosomes that are identical to the parent species; contain a multiple of n chromosomes; results from the production of a diploid gamete or (rarely) from two sperm fertilizing one ovum

allopolyploidy

The combination of chromosome sets from different (but closely related) species as a result of hybridization; chromosomes are non-homologous and thus cannot synapse during meiosis

fertile amphidiploid

Fertile allopolyploid that results from a sterile hybrid undergoing chromosome doubling

translocations

Chromosomal alterations in which the locations of genes are altered within the genome (including exchanges and transfers)

deletion

A chromosomal mutation involving the loss of chromosomal material

terminal deletion

The deletion of an end region of a chromosome via a simple break

intercalary deletion

The deletion of an internal region of a chromosome via two breaks; the two halves of the chromosome are then reconnected

synapsis

The pairing and alignment of homologs during meiosis

deletion loop

During synapsis between a normal homolog and one with a large intercalary deletion, the unpaired region of the normal homolog mustfold outwards to form a ______ ____

duplication

A chromosomal aberration in which a segment of the chromosome is repeated; can result from misalignment and uneven crossing over

gene redundancy

The presence of several genes in an organism’s genome that all have variations of the same function

tandem duplication

An extra copy of a chromosomal segment is placed immediately next to the original segment

reverse tandem duplication

An extra copy of a chromosomal segment is reversed and placed immediately next to the original segment

Terminal tandem duplication

The terminal segment of a chromosome is duplicated and placed immediately next to the original

inversion

A chromosomal aberration in which a chromosomal segment is reversed, rearranging the linear gene sequence

pericentric inversion

Inversion in which a segment that includes the centromere is inverted

paracentric inversion

Inversion in which a segment that does not include the centromere is inverted

inversion heterozygotes

Organisms with one inverted chromosome and one non-inverted homolog

inversion loop

the two chromosomes of an inversion heterozygote can align and pair during meiosis by forming an _____ ______

paracentric inversion

Crossover involving a chromosome with a _____ _____ in an inversion loop will result in an acentric and a dicentric recombinant, both with insertions/deletions

pericentric inversion

Crossover involving a chromosome with a _____ _____ in an inversion loop will result in monocentric recombinants with insertions/deletions

translocation

A chromosomal mutation involving the movement of a chromosomal segment to a different location within the same chromosome

nonreciprocal intrachromosomal translocation

A chromosomal mutation involving the movement of a chromosomal segment to a new location in the genome

nonreciprocal interchromosomal translocation

A chromosomal mutation involving the movement of a chromosomal segment to a different chromosome

reciprocal interchromosomal translocation

The exchange / “swapping” of chromosomal segments between two different chromosomes

Robertson translocation

A translocation event that occurs when the very ends of two nonhomologous acrocentric chromosomes break off and translocate, forming a large metacentric chromosome from the two long “arms” of the acrocentric chromosomes and a small fragment that is lost

acrocentric

Chromosomes with a centromere close to one end, resulting in one “long arm” and one “short arm”

metacentric

Chromosomes with a centromere in the middle, forming two equal-length “arms”

fragile site

A heritable gap/region of the chromosome that is susceptible to chromosome breaks

shared synteny

The conservation of gene order and organization on a chromosome across different species; can indicate history of inversions/translocations