Mutations and Repair

genome

the complete set of genes or genetic materital present in a cell or organism

exome

all of the exons within a genome

Transcriptome

the sum total of all the messenger RNA molecules expressed from the genes of an organism, coding and non-coding

proteome

entire set of proteins that are or can be expressed

transposons

(jumping genes) short strands of DNA capable of moving from one location to another within a cell's genetic material

mismatch mutation

a base-pairing error in DNA

insertion mutation

one or more nucleotides are added into a sequence

deletion mutation

part of a DNA sequence is lost

spontaneous mutation

a random change in DNA that occurs without an external cause

induced mutation

caused by exposure to exogenous mutagenic factors

deamination

the removal of an amino group from an amino acid or another compound

aneuploidy

abnormal number of chromosomes in a cell

translocation

a piece of one chromosome breaks off and attaches to another chromosome

duplication

a DNA segment in a chromosome which is a copy of another segment

inversion

chromosome breaks off and reattatches to the same chromosome in a different orientation

germline mutation

a change in the DNA sequence that occurs in the reproductive cells

somatic mutation

a change in the DNA sequence that occurs in a body cell (somatic cell) after fertilization

substitution mutation

a type of mutation in which one nucleotide is replaced by another nucleotide

silent mutation

a single nucleotide is changed but the codon still codes for the same amino acid

nonsense mutation

a single nucleotide is changed converting the codon to a stop codon

missense mutation

a base pair substitution that results in a codon for a different protein

frameshift mutation

mutation that shifts the "reading" frame of the genetic message by inserting or deleting a nucleotide

loss of function mutation

eliminates or reduces the function of a gene

gain of function mutation

enhances or gives new function to a gene

neutral mutation

change is dna sequence that has no effect on survival or reproduction

influence of mutation in promotor region

may increase or decrease rate of transcription

influence of mutation in regulatory/operator region

disrupts the ability of a gene to be properly regulated

influence of mutation in untranslated regions (mRNA)

may alter mRNA stability of ability for it to be translated

influence of mutation in splice recognition sequence

may alter the ability of pre-mRNA to be properly spliced

deamination can change a cytosine to a

uracil

thymine-guanine wobble

carbonyl ends of T and G switching with amino of the other

mismatches are usually due to

slippage

most mutations are repaid but mutations that are not repaired require ___________ ___________ to replicate past the error such as ___________ ___________ ___________

unique polymerase, translesion DNA polymerase

Unique DNA sequences

non-repetitive, 1 to a few times in the genome, structural and intergenic areas

moderately repetitive

repeats hundreds to thousands of times, genes for rRNA, histones, regulatory regions, transposons

highly repetitive

tens of thousands to millions of times, relatively short, telomeres

origins of replication

initiate DNA replication

centromere

role in segregation of chromosomes, recognized by kinetochore proteins

telomeres

at the ends of chromosomes, role in replication and chromosome stability

different types of DNA repair mechanisms exist to recognize different types of ___________

damage

direct repair

DNA repair in which modified bases are changed back into their original structures without removing them

base excision repair

DNA repair that first excises modified bases and then replaces the entire nucleotide

nucleotide excision repair

A repair system that removes and then correctly replaces a damaged segment of DNA using the undamaged strand as a guide.

mismatch repair

repair enzymes correct errors in base pairing

homologous recombination repair

error ftee repair process that uses a sister chromatid to fix double strand breaks

Non-homologous end joining (NHEJ)

Method for repairing double-strand breaks by joining nonhomologous DNA ends in a process that does not conserve the original sequence, error prone

depurination

the loss of a purine base ( A and G) from a nucleotide

deamination

an amino group is lost from a nucelotide

tautomeric shift

a spontaneous mutation that involves a temporary change from T to G that alters base pairing

UV causes ____________ ____________

thymine dimers

ionizing radiation causes

double strand break

example of direct repair

UV - thymine dimers - photolyase cleaves bond

example of base excision repair

spontaneous deamination - remove and replace base

Uvr A and B ____________ damage, Uvr C ____________ it, and this is an example of ____________

recognizes, fixes, nucleotide excision repair

mismatch repair

recognizes errors in base pairing

translesion synthesis

when polymerase can still replicate mutated DNA

ROS damage

reactive oxidative species damage

PHAs

polycyclic aromatic hydrocarbons can damage DNA through adducts and oxidative stress