Exam 3 genetics Flashcards
What is Transduction in phage genetics?
During replication, the phage accidentally takes in a piece of the bacterial genome and puts it in another cell.
What is the Lytic cycle in phage replication?
When a phage injects its DNA into a host cell (which circularizes to protect it from degradation) and uses host cell machinery to replicate the phage chromosome. The host cell’s DNA breaks down.
-Transcription and translation produces new phage components, which are assembled into phage progeny.
-Progeny phage are released by lysis from host bacterial cell
What is the Lysogenic cycle in phage replication?
When a phage has injected its DNA into a host cell.
-The phage chromosome circularizes and does crossing over to integrate into the host chromosome.
-Multiple cell divisions helps to copy the prophage into multiple cells
-The prophage excises itself from the host chromosome, and the lytic cycle usually follows
What is a prophage?
A bacteriophage genome integrated into the host’s chromosome or exists as an exchromosomal plasmid inside the cell
When would you find clear media that you’ve cultured bacteria in?
If there were phages present, the cells would be lysed and the media would be clear
How do you calculate titer? (phage concentration aka plaque forming units)
(Number of plaques)*(Dilution)/(volume=usually 0.1mL)
What is MOI?
Multiplicity of Infection
-The average number of phage particles that infect a single bacterial cell
-Can be low or high depending on intent of experiment
When would you use a low MOI?
(<1 phage per cell)
-Assess genotype and phenotype of an individual phage
-Score viral genotypes
-Assess distance between genes
When would you use a high MOI
(>2 phage per cell)
-Used for phage crossing and recombination
-Complementation testing
How do you calculate distance between two genes?
-Add frequencies of recombinant genotypes together, divide by total
What is Cotransduction?
Transferring 2 or more genes together using a phage from one bacterium to another
What is Cotransduction frequency?
-Depends on distance btwn two genes (happens more often when genes are closer together)
-Also depends on chance of genes being separated by a crossover event in the recipient cell
What is genetic fine structure?
The idea that there exist components that make up genes (the many base pairs)
How do you test for complementation between two mutations in different viruses?
-Do one infection at high MOI (want 2 viruses in the same cell)
-phenotype Mutant = mutations on same gene
-phenotype WT= mutations on different genes
How do you test for recombination between two viruses?
-Infect cells with high MOI (induces recombination btwn viruses)
-Do a second infection at low MOI (so we can phenotype and genotype the virus)
What is Transformation in phage genetics?
DNA uptake from environment
-Crossover of environmentally acquired DNA with recipient chromosome leads to a transformant cell
What did Esther Lederberg contribute to science?
Discovered F+ fertility factor, lambda phage, replica plating, and genetic mechanisms of specialized transduction
-Her work was overshadowed by her husband
What are other names for quantitative traits?
Polygenic traits or continuous traits
How are quantitative traits determined?
Environmental and genetic factors
How to calculate Vp for F2 populations?
Vp= VG+VE
What is the VG of F1 progeny of two true breeding homozygous lines?
VG=0 (all genetically identical)
What is the Vp of F1 progeny of two true breeding homozygous lines?
Vp=VE
How can you calculate VG?
(Vp of F2) - (Vp of F1)
How to calculate heritability? (H^2)
((Vp of F2) - (Vp of F1))/(Vp of F2)
or
VG/Vp
-If close to 1, theres a lot of genetic variance! (less environmental)
-If 0, the parental phenotypes have no influence on the child’s phenotype (all environmental)
What is heritability?
How much of the trait is determined genetically
-Midparent phenotype= average of mother and father phenotypes
-If Midparent phenotype and child phenotype are the same, there is no environmental influence
How do heritability and selection interact?
Selection does not alter offspring phenotypes if the trait is NOT HERITABLE
-If heritability is close to 1, the mean will move dramatically between generations
What is QTL Mapping?
Can be used to determine the genetic basis of continuous traits by comparing the observed and expected allele frequencies between classified phenotypes.
-Normally preformed with a backcross btw F1 and homozygous recessive parent
How do you calculate the distance between a marker and a QTL?
number of recombinants/total progeny
What are assumptions of the Hardy-Weinberg equilibrium?
-Infinitely large population
-Non-overlapping generations
-Randomly mating populations
also
-No mutation, selection, or migration
What does “Infinitely large population” mean for HWE?
In a small population, you lose genetic variation (bc of genetic drift affecting allele frequencies)
What does “Non-overlapping generations” mean for HWE?
-No mixing between generations
-Complete turnover at each generation
-One generation dies before the next generation is born
What does “randomly mating populations” for HWE?
-The genotype of an individual doesn’t influence the genotype of its chosen mate.
-Probability for a pair only depends on their frequency in the population
-
What is the equation for how allele frequency determines genotype frequency in the next generation (under HWE)?
1=p^2+2pq+q^2
In HWE, alleles at low frequency are mostly found in heterozygotes or homozygotes?
heterozygotes
What are violations of HWE?
-Migration (introduces new allele frequencies and genotypic frequencies of both populations)
-Assortative mating (non-random)(certain genotype individuals attracted to certain other genotype individuals)
-Inbreeding (non-random) (increases likelihood of homozygotes for alleles that are rare in the population at large)
-Mutation (creates new alleles to alter allele frequency)
What is the probability of mutation in humans per site, per generation?
10^ -8
What is natural selection?
-Individuals with genotypes that make them better suited to their environments than their peers are more likely to transmit their gametes to the next generation
-Selection on existing genetic variation
What are the two main sources of genetic variation?
mutations and recombination
What is evolution?
descent with modification and change in allele frequencies over time
What is genetic fitness?
Differential ability for individuals to survive and reproduce in a particular environment
How do you calculate the selection coefficient?
1-(fitness)
How do you calculate frequency after selection?
fitness*genotypic frequency
How do you calculate the allele frequency in the next generation of offspring after a selection has happened?
((fitnessgenotypic freq)+(0.5previous allele frequency))/((fitness*genotypic freq)+(previous allele frequency))
What is the fitness of a most favored genotype?
1
What is the fitness of a least favored genotype?
<1
What is the founder effect?
-A type of population bottleneck and genetic drift where a small population is established from a larger population (via chance)
-Allele frequencies in this population will differ from original populations
What is a population/genetic bottleneck?
When a relatively large population is reduced by a catastrophic event
–Allele frequencies in this population will differ from original populations
Will small or large populations experience more dramatic changes in allele frequency due to genetic drift?
small populations
What is directional selection?
When a specific phenotype is favored and natural selection acts to shift allele frequency in that direction
What is balancing selection?
When multiple alleles are maintained in a population at high frequencies
What is the study of molecular evolution?
Using comparisons of DNA variability within and between species to make inferences about evolutionary relationships and past evolutionary processes
Why do proteins have differing evolutionary constraints in their sequences?
Higher evolutionary constraints (less mutations to a gene that show up in living things) indicate that a protein is vital to function and mutations are usually detrimental to it
How does redundancy of genetic code create the possibility of silent mutations?
The third position of a codon is variable and usually will code for the same amino acid if a mutation happens to that 3rd nucleotide
What is negative selection?
When the ratio of non-synonymous/synonymous mutations is HIGHER within a species
What is positive selection?
When the ratio of non-synonymous/synonymous mutations is HIGHER BETWEEN species
What is speciation?
Reproductive isolation which may result from morphological, behavioral, or geographic conditions that prevents interbreeding btwn populations
What is allopatric speciation?
Geographical isolation causing speciation
What is sympatric speciation?
Reproductive isolation causing speciation
where on the deoxyribose molecule does each new nucleotide bind in a sugar-phosphate backbone?
the 3’ -OH
How can you tell when genetic material of a virus is single or double stranded (given % nucleotide data?)
If A and U are not the same percentage, the genetic material of the virus is single stranded
Is DNA right or left handed?
right
Is DNA parallel or antiparallel?
antiparallel
Where do sequence specific DNA binding proteins bind?
In the major groove of DNA
Where do non-specific DNA binding proteins bind?
To the sugar phosphate backbone
What type of supercoiling facilitates helix opening?
negative
What type of supercoiling hinders helix opening?
positive
What are the three essential features of genetic material?
-Sufficient info capacity
-Ability to replicate
-Ability to mutate
What end of DNA are nucleotides added to?
3’
What direction is replication?
5’-3’
What does DNA polymerase require?
-DNA template
-dNTPs
-3’ OH primer
What are functions of DNA pol1
PRIMER REMOVAL AND GAP FILLING
-5’-3’ polymerization
-3’-5’ exonuclease proofreading
-5’-3’ exonuclease primer removal
What are functions of DNA pol2
DNA REPAIR
-5’-3’ polymerization
-3’-5’ exonuclease proofreading
What are functions of DNA pol3
DNA SYNTHESIS
-5’-3’ polymerization
-3’-5’ exonuclease proofreading
WHat are the fucntion of telomeres?
-Repeated DNA sequences at teh end of eukaryotic chromosomes
-Telomere binding proteins TRF1 TRF2 WRN
What is the structure and function of telomerase
RNA Component: serves as a template for telomere elongation
Protein component: catalyzes addition of nucleotides 5’-3’
-Makes DNA copy of RNA (reverse transcriptase)
What is Telomerase?
An RNA dependant DNA POLYMERASE
What are the steps to telomere elongation?
- Telomerase extends ss DNA template of lagging strand
- DNA pol synthesizes primers and okazaki fragments
3.Primer is removed and ligation of DNA fragments
What type of cells have higher telomerase activity?
cells with higher prolifertaion
