genetics exam 5

Gene mutations and DNA repair

Somatic mutations

arises in somatic (body cells)

Germ-line mutations

arises in germ line cells → gametes

gene mutation

small DNA lesion that affects single gene

chromosome mutation

large scale genetic alteration

base substitutions

single base pair of DNA is altered

Transition

purine for purine (adenine for guanine)

pyridines for pyridines (cytosine, thymine or uracil)

Transversion

purine for pyrimidines

insertions (indels)

additions of nucleotides

deletions (indels)

removal of nucleotides

frameshift mutations

indels that alter the reading frame

drastic effects

expanding nucleotide repeats

repeated sequences increase across genertaions

Huntingtons disease

forward mutation

wild type to mutant

reverse mutation

mutant to wild type

missense

different amino acid

nonsense

premature stop codon

silent

same amino acid

loss of function

reduced / absent function (recessive)

gain of function

new / abnormal function (dominant)

lethal

causes death

suppressor mutations

masks effects of another mutation

intragenic or intergenic

intragenic

same gene

intergenic

different gene

spontaneous mutations

occur naturally from replication errors / chemical changes

induced mutations

caused by environmental agents (chemicals/radiation)

tautomeric shifts

mispairing in replication from rearranging protons and electrons

wobble base pairing

non complementary base pairing due to wobble position

strand slippage

DNA poly encounters short tandem repeats

• Newly made strand loops out → insertion

• Template loops out → deletions

replicated errors become BLANK mutations if not repaired

permanent

Depurination

Chemical change that is the loss of a purine base

may lead to substitution

deamination

chemical change that is the removal of amino group

base alteration

base analogs

chemical mutagen → incorrect pairing

alkylating agents and oxidizing agents

chemical mutagens that alter base structure

common in cancer therapy

intercalating agents

insert between bases

common in cancer therapy

UV radiation

pyrimidine dimers that distorts DNA and block DNA poly
blocks replication

SOS repair pathway but may have errors

Ames test

uses bacteria to test if a chemical is mutagenic / cause DNA mutations

mutagenic → carcinogenic potential

Transposable elements

mobile DNA sequences that cause mutations

DNA transposons

cut and paste

• Removed and pasted somewhere new 

• Usually does not increase genome size

Retrotransposons

RNA intermediate

• Transcribed into RNA, then back into DNA

• Make genome size larger

Replicative mechanisms

copy stays + new copy inserted

Non replicative mechanisms

moves location

flanking direct repeats

short identical sequences of DNA

not part of the mobile element itself

terminal inverted repeats

short complementary DNA

recognition site for enzymes

DNA repair types

mismatch repair

fixes replication erros and strand slippage

direct repair

restores original DNA sequences (pryimidine dimers)

does not replace altered nucleotides

Base excision repair

removes damaged base → replaces nucleotides

DNA glycosylases

Nucleotide-excision repair

removes bulky lesions

double stranded break repair

• Homologous recombination (accurate) and uses sister chromatids

• Nonhomologous end joining (error-prone) and uses insertions/deletions (indels)

Translesion polymerase

bypass DNA damage, allowing for errors

Molecular Biotechnology and Omits

Chapter 19

Restriction enzymes

cut DNA at specific palindromic sequecnes

naturally in bacteria

sticky ends

cohesive ends

DNA fragments with short, single-stranded unpaired overhangs

created by staggered cuts

easily pair with complementary sequences

blunt ends

even lengths DNA fragments

no overhangs and created by straight cuts

gel electrophoresis

separates DNA by size and electrical charge

smallest size travels farthest

Probes

identify specific sequences that are complementary

can be RNA or DNA

Southern blotting

DNA

Northern blotting

RNA

Western blotting

protein

Plasmid Vectors

carry and insert foreign DNA using restriction enzymes

shuttle vector

no promoter system, no intermediates

expression vector

promoters and terminators

library

random fragments in plasmids

blue white screening

rapid molecular cloning technique to find bacteria that contain recombination plasmids

successful clones (white colonies)

unsuccessful ones (blue colonies)

PCR

polymerase chain reaction

amplifies DNA

PCR denaturation

heat is turned up and strands separate

PCR annealing

primers bind and temp is lowered

PCR extension

DNA polymerase makes new DNA strands

RT PCR

converts RNA to DNA before amplification to detect RNA viruses

Sanger sequencing

uses ddNTPS to terminate strands

Next gen sequencing

faster, parallel sequencing

ddNTP

lacks a 3’-OH group and terminates DNA synthesis

shotgun sequencing

laboratory method used to determine the entire sequence of an organism's DNA by breaking it into random, smaller fragments

DNA fingerprinting

uses STRS (short tandem repeats) by PCR for identification

CRISPR-Cas

edits DNA at specific sites

uses guide RNA + Cas9 nuclease

Cancer Genetics

Chapter 23

tumor

abnormal cell proliferation

benign

localized and noncancerous

malignant

invasive and cancerous

metastasis

spread to other tissues

cancer caused by the accumulation of BLANK

mutatuions

oncogenes

“mutated”

gain of function

dominant

proto-oncogenes

“wild type / normal”

tumor suppressors

loss of function and recessive

require both alleles mutated

Cell cycle

• Controlled by CDKs, cyclins, checkpoints (G1/S, G2/M)

communication of cells

• Signal transduction pathways (e.g., Ras) regulate growth

DNA repair

if defective increase mutation accumulation

telomerase regulation

Reactivation → unlimited division

vascularization

• Tumors stimulate blood vessel growth

mircoRNAs

• Regulate gene expression; misregulation → cancer

Epigenomic influences

• Methylation changes alter gene expression

time and progression

• Cancer develops through multiple mutations (clonal evolution)

Genome stability

• Chromosomal abnormalities common

infections

• Viruses can trigger cancer (e.g., HPV)

Quantitative/Population/Evolution

Chapter 24/25/26

Quantitative characteristics

traits that are controlled my multiple genes

bell curved and influenced by environment

heritability

Broad-sense: total genetic variance / phenotypic variance

Narrow-sense: additive genetic variance / phenotypic variance

• Range: 0–1

• Population-specific

QTL Quantitative Trait Loci (eQTLs)

chromosomal regions affecting traits

GWAS Genome-Wide Association Studies

studies that identify genes linked to traits using markers

natural selection

differential reproduction