genetics exam 3

Randomly (Darwin)

Darwin: genetic variation occurs by chance; natural selection then results in better-adapted organisms.

Replica plating

Transfer bacteria to a new plate with velvet; keeps the pattern of the colonies on the plate.

Selection (Lederberg experiment)

Resistance to phage T1.

Contains phage T1

Label for the selective-medium replica plate; resistant colonies grew here and on the non-selective plates.

Mutations did not occur because the cell needed them

Resistant mutations were there before any contact with the selective medium (phage T1); the mutation did not arise because of selection.

Mutation

Any heritable change in the genetic material.

Transitions (3rd codon position)

Rarely change the amino acid; pyrimidine to pyrimidine never changes a codon; purine to purine only changes 2 codons (ile/met, trp/stop).

Never (3rd position pyrimidine to pyrimidine)

A pyrimidine to pyrimidine change at the 3rd codon position never changes the code.

Transversions (genetic code)

Change 7 codons; more potentially detrimental, more likely purged by selection, more likely to result in a different amino acid.

Intragenic suppressor

A second suppressor mutation within the same gene/protein that restores function lost by the first mutation.

Intergenic suppressor

A second mutation in a different gene that restores the phenotype (redundant function, common pathway, multimeric protein, or transcription factor examples).

Cannot (somatic mutations)

Somatic mutations cannot be passed on to future generations.

Genetic mosaic

An individual who has somatic regions that are genotypically different from each other.

Transition

Purine changes to a different purine; pyrimidine changes to a different pyrimidine (4 possible changes; observed more frequently).

Transversion

Purine and pyrimidine are interchanged (8 possible changes).

Apurinic or abasic (AP) site

The bond between the base and sugar is broken; extremely common spontaneous mutation (~10,000 per human cell per day).

Not detected by repair mechanisms (5-methylcytosine deamination)

Deaminated methylcytosine becomes thymine, causing CG to AT; repair mechanisms do not detect it (BAD!).

FMR1

Gene lost in Fragile X syndrome (loss of function); thought to transport mRNAs; expressed in brain, testes and ovaries.

Normal (Fragile X)

6-50 CGG repeats.

Premutation (Fragile X)

50-200 CGG repeats.

Affected (Fragile X)

More than 200 CGG repeats.

Insertion (strand slippage)

Newly synthesized strand slips (nucleotide loops out on the new strand).

Deletion (strand slippage)

Template strand slips (nucleotide loops out on the old strand).

TNRE (TriNucleotide Repeat Expansion)

Triplet repeat sequences are prone to changes in copy number during replication (strand slippage).

Anticipation

Some disorders progressively worsen and/or appear earlier in future generations.

Dynamic mutation

Another name for anticipation.

Mutagens

Substances that induce mutations; they bias the types of mutations according to the type of DNA damage they produce.

Alkylating agents

Donate an alkyl group to amino or keto groups in nucleotides to alter base-pairing affinity (examples: mustard gas, EMS).

Ethyl methane sulfonate (EMS)

Alkylating agent used for random mutagenesis.

Prevents potential hydrogen bond

What the added ethyl group on O6-ethylguanine does, which alters base pairing (CG to TA).

5-bromouracil

Base analog that can pair with adenine or guanine; used as cancer chemotherapy.

Frameshift mutations

Often caused by intercalating agents (proflavin, ethidium bromide), which insert themselves into DNA and distort the molecule.

Pyrimidine dimers

Created when UV light is absorbed; distort DNA so errors tend to be introduced during replication.

Reactive Oxygen Species (ROS)

Reactive forms of oxygen; oxidative damage causes transversions (G pairs with A; GC to TA).

Ionizing radiation

X rays, gamma rays and cosmic rays; eject electrons from atoms, damage bases, break phosphodiester bonds, cause chromosomal aberrations.

Free radicals and ROS

Generated by ionizing radiation; cause indirect DNA damage (single or double strand breaks) leading to mutation.

Ames test

Biological assay to assess the mutagenic potential of chemical compounds, using his- auxotrophic Salmonella typhimurium.

Revertants (his+)

Bacteria that reverted from his- to his+ in the Ames test; the number of revertants measures the severity of the mutagen.

Liver extracts (Ames test)

Added to simulate the effect of metabolism, since some compounds are not mutagenic themselves but their metabolic products are.

Photoreactivation repair

Direct repair that removes thymine dimers caused by UV light.

DNA photolyase

Enzyme involved in photoreactivation repair.

Alkyltransferase

Repairs alkylation damage; the enzyme catalyzes transfer of the alkyl group to itself.

MutS

Mismatch repair protein that binds to the mismatch.

MutH

Mismatch repair protein that binds to hemimethylated GATC.

MutL

Mismatch repair protein that binds to MutS and MutH.

One cut (MutH)

MutH makes one cut on the non-methylated DNA strand.

DNA polymerase (mismatch repair)

Synthesizes DNA to fill in after the strand is degraded.

Glycosylase

Removes altered bases from the DNA; specific for different altered bases; generates an AP site.

AP site

Site generated by glycosylases when an altered base is removed.

UvrA, UvrB

2 UvrA with UvrB scan the DNA for damage; UvrA leaves upon recognition of damage.

UvrC

Recruited after damage recognition; UvrBC cut 5' and 3' of damage on the damaged strand only.

Helicase (NER)

Removes the damaged segment (13 nucleotides total).

DNA polymerase I and ligase (NER)

Seal the gap in nucleotide excision repair.

Xeroderma pigmentosum

Lost the ability to undergo nucleotide excision repair.

Exchange between non-sister chromatids

Where the crossover occurs during recombination between homologous chromosomes in meiosis.

Alleles now in new combination

Result of crossing over: recombinant genotype.

Nicking (Holliday model)

Endonuclease nicking (single strand break); one strand on each homolog is cut by an endonuclease.

Holliday structure

Characteristic structure formed during genetic recombination.

Alignment of homologous chromosomes

First step of the Holliday model.

Strand invasion and ligation

Nicked strands invade the homologous chromatid and are covalently linked.

Holliday junction formation

Result of strand invasion and ligation in the Holliday model.

Branch migration

Lateral movement of the Holliday junction; heteroduplex DNA formation.

2nd nick, SAME strands as 1st nicks

Results in no observable recombination of "A" and "B".

2nd nick, OTHER strands as 1st nick

Results in alleles for "A" and "B" being recombined: "A" is now on the same chromosome as "b", and "B" is on the same chromosome as "a".

Double strand break (DSBR)

Starts the recombination.

Exonuclease (DSBR)

Produces single stranded DNA (ssDNA) tails, extended on the 3'-OH.

Strand invasion and D-loop formation

D-loop = Displacement loop.

Purple strands are templates for DNA synthesis

In the DSBR figure, the purple strands are the templates for DNA synthesis.

DNA polymerase (DSBR)

Synthesizes new DNA.

Endonuclease (DSBR)

Cuts and rejoins DNA to resolve Holliday junctions.

Negative regulation

ON until a repressor turns it OFF (transcriptional regulation by repressor proteins).

Repressor

Protein that binds DNA and reduces transcription.

Positive regulation

OFF until an activator turns it ON (regulation by activator proteins).

Activator

Protein that binds DNA and increases transcription.

Inducer

Small effector molecule that increases transcription: it either removes the repressor from DNA, or makes an activator bind to DNA.

Catabolic (degradative) pathways

Pathways that use inducible regulation (example: carbon source/sugar utilization).

Carbon source/sugar utilization

Example of a catabolic pathway regulated by inducible regulation (lac operon).

Corepressor

Small effector molecule that makes a repressor bind to DNA, turning transcription OFF (repressible regulation).

Inhibitor

Small effector molecule that removes an activator from DNA, turning transcription OFF (repressible regulation).

Anabolic (biosynthetic) pathways

Pathways that use repressible regulation (example: amino acid synthesis).

Amino acid synthesis

Example of an anabolic pathway regulated by repressible regulation (trp operon).

Operon

A set of genes that are linked (adjacent) on the chromosome, transcribed as a unit, coordinately regulated, and usually encode proteins with a common function.

One promoter (operon)

An operon has one promoter and one mRNA for all of its genes.

lacZ

Gene for beta-galactosidase, which breaks down lactose into glucose and galactose.

lacY

Gene for lactose permease, which transports lactose into the cell.

lacA

Gene for transacetylase, which may act as a detoxifying enzyme by acetylating non-metabolizable sugars to prevent their re-entry into the cell.

Cis-acting regulatory elements

DNA sequences that control the expression of genes they are physically next to (adjacent/linked).

lacP

Promoter; DNA sequence bound by RNAP.

lacO

Operator; DNA sequence bound by the Lac repressor.

Trans-acting regulatory proteins/factors

Proteins made in the cell that can diffuse to the lac operon and bind the regulatory DNA sequences.

LacI

Lac repressor; binds to the operator (lacO).

Not part of the lac operon!

The lacI gene (which encodes the Lac repressor) is not part of the lac operon.

RNAP

RNA polymerase; binds to the promoter (lacP).

Conformational change (Lac repressor)

Lactose/allolactose binding at the inducer site changes the 3D shape of LacI, so the repressor loses the ability to bind the operator DNA.

No lactose present

Repressor binds to the operator and shuts off transcription.

Lactose present

Repressor binds to lactose, cannot bind the operator, and transcription may proceed.

Repressor does not completely inhibit transcription

So very small amounts of the lac operon proteins are made (this lets the cell detect lactose).

Repressor (lacI- mutation)

Loss-of-function mutation in lacI; repressor has lost the ability to bind the operator.

Cannot repress

With lacI-, the repressor cannot repress the operon.

Constitutive

Always on, even with no lactose (seen in lacI- and lacOc mutants).