Genetics Exam 4 Flashcards
What is Hardy-Weinburg all about?
about frequencies
-when talking about population genetics, we are interested in the prevalence of a particular allele or genotype in a population
Hardy-Weinburg Principle
frequencies of alleles and genotypes in a population will remain constant over time in the absence of other evolutionary influences
Frequency of the dominant allele
p
Frequency of the recessive allele
q
the sum of all possible outcomes must…
equal 1
p+q=1
p^2+2pq+q^2=1
frequency of the homozygous dominant genotype
p^2
frequency of the heterozygous genotype
2pq
frequency of the homozygous recessive genotype
q^2
the key to hardy-weinburg problems is in..
the homozygous recessive individuals!
Solving Hardy-Weinburg problems
- Assign the alleles
- Calculate q taking the SQUARE ROOT of the number of homozygous recessive individuals
- Calculate p
- Use p and q to calculate the other genotype frequencies
Evolution
the sum total of the genetically inherited changes in individuals who are members of a population’s gene pool
-a change in frequencies of alleles in the gene pool of a population
microevolution
evolution over a short period of time
Effects of evolution
effects of evolution are felt by individuals, but it is the population as a whole that actually evolves
Populations evolve, not individuals!
Hardy-weinberg principles/ assumptions
- No mutation (no new alleles added to gene pool)
- No migration (no gene flow)
- Large population (no genetic drift)
- Random mating (easiest one to violate) (no sexual selection)
- No natural selection (all traits equally fit)
ALL of them must be held to be in Hardy-Weinberg equillibrium
Gene pools
collection of all alleles in population
usually about one gene & one phenotype
Population
a group of breeding individuals of same species living in an area
- variation between individuals
- more fit individuals will survive and pass on their traits
Phenotype frequency
of individuals with particular phenotype divided by total # of individuals in population
Allele frequency
# of alleles in question divided by total # of alleles simplify and make one allele dominant and one the recessive
genotype frequency
how many of each separate genotype there are
p^2 2pq q^2
Hardy Weinberg logic
if you know the frequency of one allele you know the frequency of the other
Hardy Weinberg predicts
equilibrium can be reached in 1 generation
- dominant and recessive alleles behave similarly
- allele frequency does not change over generations
- genotype frequency stabilizes in 1 generation after random mating
genetic drift
unpredictable chance fluctuations in allele frequency
-especially happens in small populations where alleles can be lost or fixed
Flavors of genetic drift
bottleneck effect and
founder effect
More pronounced in smaller populations
bottleneck effect
A large genetically diverse population becomes a large less genetically diverse population because of some bottleneck
founder effect
a few alleles go to a new island where the allele frequency of h went up from 0.05 to 0.33 because there is a smaller population with less alleles
(a few individuals start a new population with different allele frequency than original)
assortative mating
occurs when individuals do not mate randomly
positive assortative mating
when individuals are more likely to mate due to similar phenotypic characteristics
negative assortative mating
when individuals with dissimilar phenotypes mate preferentially
inbreeding
non-random mating can lead to inbreeding which increases the number of individuals homozygous for deleterious genes
inbreeding is the…
production of offspring by individuals related by descent
inbreeding depression
reduced reproduction and survival (reproductive fitness) due to inbreeding
the inbreeding coefficient (F)
For an individual, F refers to how closely related its parents are
- when parents are unrelated, offspring F=0
- when inbreeding is complete, F=1
biggest force in changing allele frequency
natural selection
why don’t unfit alleles disappear from a population?
the rate of disappearance of an allele depends on the strength of selection against it
One reason why recessive disease alleles persist..
heterozygous advantage…sickle cell anemia
being a carrier or diseased makes you resistant to malaria
many possible causes of microevolution
- Mutation
- Natural selection
- Genetic drift
- Gene Flow (migration)
- Nonrandom mating
mutation
produce genetic variation
-new mutations that increase fitness rapidly spread through population
natural selection
selects for traits that increase fitness
-success in reproduction based on heritable traits results in selected alleles being passed to relatively more offspring (Darwinian inheritance)
Cause ADAPTATIONS of populations
fitness
increased reproduction
genetic drift is…
change in the gene pool due to sudden population shrinkage
changes in allele frequencies due to CHANCE ALONE
gene flow
(migration)
genetic exchange due to the migration of fertile individuals or gametes between populations
non-random mating
mates are chosen on the basis of the best traits
resistance to antibacterial soap
the original mutation was a RANDOM event
-not caused by the environment (already present when antibacterial soap was introduced)
-BUT environment influenced who survived
(example of directional selection)
directional selection
favors individuals at ONE extreme of phenotypic range
-most common during times of environmental change or when moving to new habitats
disruptive selection
favors extremes at BOTH extremes over intermediate phenotypes
-occurs when environmental change favors extreme phenotype
stabilizing selection
favors intermediate over extreme phenotypes
-reduces variation and maintains the current average
heterozygous advantage
disease alleles can persist
Huntingtons
there are also late onset diseases such as Huntingtons that do not change reproductive success and so don’t change fitness (not heterozygous advantage-just no impact on fitness)
Neutral theory of evolution
at the molecular level, most changes and most variation within and between species is NOT caused by natural selection it is RANDOM
like genetic drift
genetic drift
=random changes in allele frequencies
- ALL finite populations experience random changes: these lead to changes that are not due to natural selection
- not all individuals contribute equally to next generation (due to chance, not differential reproduction)
- genetic changes due to drift are NOT directional or predictable
bottleneck examples
typically result from environmental events like earthquakes, floods, fires, droughts or human activities like genocide or hunting
outbreeding
taking most diverse and breeding back with species
Phylogeny
the sequence of events involved in the evolutionary development of a biological entity (such as a species)
phylogenetic tree
a diagram that describes the phylogeny of a species
classic phylogenetic trees vs. modern ones
classic phylogenetic analysis uses morphological features and now we use DNA sequence (molecular data) to construct phylogenies
outgroup
helps us estimate the position of the root with an out group which is a set of species that are definitely distant from all the species of interest
Domains of life
Bacteria, Archaea, & Eukaryotes
tree of life is rootless
principle of parsimony
the preferred hypothesis is the simplest one (assumes that a new trait only arose once)
horizontal gene transfer
an organism incorporates genetic material from another organism without being the offspring of that organism.
-common in bacteria today & was prevalent during the early stages of evolution
Mitochondria and chloroplasts arose from horizontal gene transfer
topology
refers to the general pattern of branching within the tree
how do we talk about similar genes in different species?
when there is a high sequence similarity between genes, there is likely an evolutionary relationship between them
BLAST searches
low e value means a homologous gene with high sequence similarity
homologous genes
two genes are derived from the same ancestral gene
two sub terms of homologous
- orthologous genes
2. paralogous genes
orthologous genes (orthologs)
homologous genes that arose by a speciation event (ex: two homologous genes in two different organisms are orthologs)
one key mechanism that has made eukaryotic genomes more complex than bacteria is duplication…
take what you have in a simpler organism, and make copies of this gene (creates paralogs)
paralogous genes (paralogs)
homologous genes in that arose by gene duplication
ex: Hox genes
different parts of genomes (or genes) evolve at different rates
- each region has a different effect on organism’s fitness
- intron sequences likely to diverge more over time (neutral, no selective pressure)
recombinant DNA technology
isolating and manipulating DNA by combining DNA from two different sources
What principle of biology makes it possible to express a gene from one species in a different species?
like in humans from bacteria … the universality of the genetic code!
What are the steps to gene cloning?
- isolate the gene of interest from cells
- digest gene of interest and cloning vector with the same restriction enzymes
- mix and bind together the foreign and plasmid DNA
- introduce the plasmid into bacterial cells through transformation
- select for transformed cells
- produce recombinant protein and experiment
how do we isolate gene of interest?
a needle in a haystack problem solved with Polymerase Chain Reaction (PCR) by designing primers that are going to specifically amplify just to the gene we want –> we know sequence of gene that we want
what is meant by the term vector?
a vehicle to carry recombinant DNA molecules into host cells where independent replication occurs
Most common: plasmids, bacteriophages, & cosmids
plasmids
- bacterial DNA independent of normal circular chromosome
- replicated by bacteria
- can be made to carry any piece of DNA
essential features of cloning vector or plasmid
- multiple cloning sites (MCS) series of unique restriction sites
- Antibiotic resistance gene (such as amp) allows selection of cells with the plasmid
- ORI (origin of replication) for bacteria allows plasmid to be replicated in bacteria
Digest gene and cloning vector with SAME restriction enzyme
restriction enzymes bind to specific palindromic DNA sequences and cut DNA at two defined places
very sequence specific & cuts on both strands for a double strand break
Sticky ends
hydrogen bonding sites are exposed
-allow for reattachment with another DNA with same single stranded nucleotides (complementary sticky ends)
whats the problem with using only one RE?
plasmid reclosing or a chance of gene going in backwards or upside down so we should use different enzymes to create directionality
with different sticky ends on each side, gene inserts into plasmid…
in one orientation!!
still digest gene and cloning vector with the same set of restriction enzymes, but use 2
How do we bind together foreign and plasmid DNA?
DNA ligase seals the nick in the backbone and creates a continuous molecule
how do we select for rare transformed cells (contain plasmid)
ampicillin kills bacteria
-plasmid contains an ampicillin resistance gene: AmpR
-AmpR codes for an enzyme that breaks down ampicillin
-cells with AmpR gene are resistant to ampicillin and can live in its presence
Non transformed will die and transformed will live
how can we be SURE the bacteria contain the gene of interest within the plasmid (not the parental plasmid) ?
lacZ screening
lacZ gene encodes the enzyme Beta-galactosidase: produces blue pigment when give precursor compound X-gal
If lacZ gene interrupted by insertion of gene of interest, Beta-galactosidase is not made so colonies are white
Only white have gene of interest
transgenic organism
an organism that contains DNA from another organism in its genome
gene replacement
cloned gene replaced chromosomal copy by homologous recombination
two types: gene knock out & gene knock in
gene knock out
chromosomal copy replaced with inactive mutant
gene knock in
copy replaced with different sequence
gene addition
cloned gene integrates at a different site: both copies (original and transgene) are present
which is harder to control?
gene addition because you don’t know where it will add in (random) could happen where it is tightly condensed and not be expressed or interrupt a gene
transgenic organism can be animals or plants
-animals usually used to produce proteins for humans (like insulin)
-genetically modified food plants generated to be more resistant, higher yield, etc
plants easier to generate (can do in dish) than a cow
uses of transgenic plants
- resistance to disease
- resistance to insects
- resistance to herbicides
biopharming
generating useful compounds for humans in other organisms
suppose you add a normal CTFR allele to a lung cell, how many copies will there be of the gene?
3!
two originals and one addition
somatic gene therapy
the delivery of therapeutic genes into living cells in an attempt to cure or treat a disease
- started as single-gene diseases
- cancer and heart disease
What do you need for somatic gene therapy
-gene(s) for disease must be identified and cloned
-access to defective cells (eg blood cells for leukemia)
-way to get normal gene into defective gene
last two are the hard parts
main difference between somatic and germ line gene therapy
in germ line gene therapy, the DNA change is made such that all cells of the organism will contain the change – in somatic cell therapy the change will be mosaic because we only target some cells
a heritable change
can happen for a transgenic animal but somatic cell therapy is not
mosaic
some cells have been altered to contain copy of normal gene; rest of cells are unchanged
reproductive (germ line) gene therapy
a heritable change
requires altering the genome of an embryo -like generating a knock in: defective gene replaced with normal gene
two approaches to somatic gene therapy
- in vitro (ex vivo) in cell cultures
- in vivo (viral approach)
in both cases you can use the virus
viral approach
- most common are retroviruses, adenoviruses and parvoviruses
- easy to encapsulate DNA within virus
- have high efficiency of transfer of DNA into cell
- disadvantage: can trigger immune response –> could be fatal but very efficient
nonviral approach
-liposomes, electroporation
-low efficiency of transfer of DNA, but no immune response mounted
less dangerous and less efficient
delivery issue to get DNA into cell
using a viral vector
- insert “good” copy of a gene into a virus
- introduce the virus into person’s cells directly in body or into stem cells dividing in a dish
- if into stem cells, insert the stem cells back into person’s body
- hope that the virus infects the cells and allows cells to produce good copy of whatever protein is not functioning properly
better gene therapy methods?
CRISPR-Cas
RNA interference
CRISPR-Cas
allows for gene editing by targeting specific sequences
- so far, has been successful in many kinds of cells in culture
- can target site of gene editing by the PAM sequence
- introduce guide RNA and replacement DNA sequence
- Homologous recombination occurs, removing mutated sequence, replacing with normal sequence
Anti-sense RNA and RNA interference (RNAi) approaches to gene therapy
- target mutated sequence with antisense or siRNA
- complementary RNA binds to mRNA for disease gene
- complex is degraded: no (or a lot less) mutant protein generated
