Midterm 4 Flashcards
what is limited and has competition
RESOURCES–> resources are limited; there is competition for those resources
what changes over time?
the distribution of alleles and genotype changes over time
Population genetics aim to …
make quantitative predictions and provide mathematical insights into the dynamics of allele frequencies and genotype frequencies in populations
what is a population
group of organisms of the same species living in the same geographical area
what is a gene pool
all alleles in population
genotype frequency
proportion of individuals in a population with a specific genotype
allele frequency
proportion of alleles in a population
genotype frequency does NOT equal
allele frequency
when does allele frequency equal genotype frequencies?
Bacteria
There is no homozygous or heterozygous
One allele for each gene
X-linked gene
Homozygous
one gene has how many alleles
one gene haas 2 alleles
p and q are what ??
shorthand notation for allele frequencies
what is the Hardy-Weinberg Equation?
p^2+2pq+ q^2= (p+q)^2=1
from generation to generation what doesnt change
allele frequencies and genotype frequencies
what are the hardy Weinberg conditions
- migration in/out is absent (no gene flow)
- Large population (no genetic drift)
- No mutations
- Equivalent viability and fertility (no selection)
- Mating is random
- Same allelic frequencies in men and women
hardy weinberg conditions are rarely…
rarely met but helps us learn why allele frequencies change –> often met “close enough” mating is random for most genes
what is p^2
AA genotype frequency
what is 2pq
Aa genotype frequency
what is q^2
aa genotype frequency
what does the p and q in this relate too –> (p+q)^2
p is the A frequency
q is the a frequency
what will all genotype and allele frequencies add up too
always add up to 1 whether or not the population is in HW
if we know genotype frequencies in a population, when can we calculate corresponding allele frequencies?
a) if population is in HWE
b) if we know allele frequency of one of the allele
c) if population is not in HW equilibrium
D) any of the above
D) any of the above
if we know GF’s in a population, then we can always ….
calculate AF’s whether or not the population is in HW equilibrium
if we know Af;s we can only calculate…
GF’s if the population is in HW equilibrium and autosomal locus has two alleles
If we have X-linked recessive a allele, genotype frequencies among males are the same as allele frequencies:
Frequency of XAY males = p
Frequency of XaY males = q
forces that can cause deviation from HW ratios
- gene flow (migration)
- genetic drift (small population)
- Muations
- Selection
- Inbreeding
- Different allelic frequencies in males and females
Which of these forces does not
contribute to Evolution?
1. Gene flow
2. Genetic drift
3. Mutations
4. Selection
5. Inbreeding
6. All contribute
6- all contribute
evolution=
long lasting changes in the gene pool due to natural selection and other forces ( mutation, drift)
Gene flow example
migration example is gene flow between human subspecies –> Neandetals which caused 2% of DNA in europeans and east asians from Neandertals alleles that are potentially adaptive
genetic drift?
random events that can result in very good dominant allele being eliminated from the population
the vast majority of good alleles/genes that arose during our evolution …
did not end up in our gene pool
two types of genetic drift
bottleneck effect and founders effect
example of bottle neck effect
northern elephant seal population
Hunted to near extinction
* Population decreased to 20 individuals in 1800’s.
* Those 20 repopulated so today’s population is
~30,000
* Very low level of genetic variation
founders effect
when smalll group from population migrate to form new population
example of founders effect in human population
–> Old Order Amish populations are derived from a few dozen colonists who escaped religious persecution in Germany in 1719 to
settle in Pennsylvania.
* The community is closed.
* Allele and genetic disease frequencies in Amish are significantly different from the German ancestral and the surrounding local populations.
a random mutation is …
far more likely to harm the function of a protein than to enhance it
if mutations was the only force operating on the gene pool, then eventually
most alleles would become nonfunctional
how many bad (lethal) recessive mutations an average person carries?
1-2
Humans carry on average one to two mutations that, if inherited from both parents, can cause…
severe genetic disorders or death before reaching
reproductive age
Natural selection
more organisms are produces each generation than can survive and reproduce
Organisms differ in their ability to compete, based
(in part) on their genotype
*Hence, genotypes that promote
survival/reproduction are favored, and are more likely to contribute alleles to the next generation’s gene pool
forces that keep bad alleles in gene pools despite natural selection
- delayed age of disease onset
- slow selection against recessive alleles
- mutation selection equilibrium
- heterozygote superiority
in haploid organisms selection is ____-
efficiennt
why are haploid organism’s selection efficient
No recessive/dominant alleles means that a very weak selective advantage can quickly lead to a favored allele becoming fixed
In diploids, selection for/against
recessive alleles is
inefficient
why are diploids, selection for/against
recessive alleles is inefficient
Rare disease-causing recessive alleles
persist in the population in heterozygote carriers, even if they are lethal when homozygous
disease incident?
q^2
fraction of disease alleles in patients?
q
fraction of disease alleles in carries?
p
the rarer the recessive disease….
the greater the % of alleles that are in carries
alleles in carries are …
hidden from selection
function of selection and new mutations
selection = eliminates harmful alleles
new mutation = generate harmful new alleles
describe the relationship between selection and new mutations
These forces push the population out of HW equilibrium, but they push in OPPOSITE directions
Over time, an equilibrium is reached where allele frequencies are stable - new alleles are removed by selection at the same rate they are created by
mutation
bad alleles are a …
stable part of the gene pool
Malaria
A serious, infectious disease
(~300 million annual cases; ~1 million deaths)
* Flu-like symptoms, anemia, jaundice
->kidney failure, coma, death
* Caused by infection with the parasite Plasmodium
* Transmitted by mosquito bites
* Kills Red Blood Cells and releases toxins into bloodstream
Sickle Cell Anemia
-Autosomal recessive, incidence 1/500 among AA
* Gain-of-function mutation in the gene encoding the b chain of
hemoglobin → causes Hb aggregation which in turn
deforms red blood cells (RBCs)
* Sporadic vessel clotting causes acute pain, organ failure
* Shorter half-life of RBCs causes anemia
Heterozygote Superiority
(or advantage)
Homozygous normal (SS)
* Reduced survival because of Malaria
Homozygous recessive (ss)
* Reduced survival because of Sickle cell anemia
Heterozygous carrier (Ss)
* Survival and reproductive advantage
result of slow selection against recessive alleles
most disease causing recessive alleles are in carriers, not patients
result of mutation-selection equilibrium
Result: disease-causing alleles are a stable part of our gene pool –> we’re all genetically defective
result of heterozygote superiority
Result: “bad” alleles may be good in some contexts
inbreeding affect on individual
Increases the risk of having a
kid homozygous for a rare recessive allele
inbreeding affect on population
Results in an excess of
homozygotes compared with random
mating
how to check for HWE
If a population is in HW equil., then genotype and allele freqs. should be related as follows:
AFs should correctly predict GFs
Freq (AA) = p2
Freq (aa) = q2
Freq (Aa) = 2pq
complex or quantitative trait is a
measurable phenotype that depends on the cumulative actions of many genes and the environmnent
multiple additive genes can give rise to …
continuous variation
With lots of additive genes it starts to look like a…
normal distribution
what are the properties of quantitative traits
- polygenic
- multifactoral
polygenic?
variation is caused by the combined effects of multiple genes
multifactorial?
variation is caused by the combined effects of genes and environments
When considering an additive trait, the
larger the number of genes controlling
the trait, the _____ the number of
phenotypes
A. Larger
B. Smaller
C. Same
A) larger
examples of quantitative/complex traits
height
weight
blood pressure
eye color
personality
heart disease
diabetes
alzheimers disease
quantitative traits fit what??
normal distribution
threshold trait examples?
autism, most birth defects
heart disease, diabetes, alzeihmer’s disease,
threshold traits are …..!
multifactorial (environment matters
Threshold traits description
traits that are all or none, but appear to be influenced by multiple genes and the environment.–> think diabetes bc you have diabetes only if your blood in your sugar reaches a certain threshold
phenotypic variance is a…
sum of environmental variance (Ve) and genetic variance (Vg)
Environmental variance?
Ve= the portion
of phenotypic variance that is due to
differences in the environments to which the individuals have been exposed.
broad sense heritabilty?
H^2 is between 0 and 1 and is proportion of the total variance of a trait that is caused by genetic variation
equation for H^2
H^2= Vg/ (Vg +Ve)
H^2 is also known as
broad sense heritability
how to asses environmental variance in human population
Comparisons of variability between
identical twins can be used to estimate
heritability
identical twins arise from
the splitting of a single fertilized egg –. clones –> all alleles identical
If there is variation in a trait between two identical twins,
then that variation must have been caused by environmental,
not genetic factors
example of variation due to environment in identical twins
Fingerprints differ between
identical twins -> Variation in
fingerprints is due to environment
Little variation in a trait (e.g height) between identical twins - the cause is genetic?
Not necessarily, because identical twins
are usually raised in a very similar
environment
Little variation in a trait (e.g height) between identical twins - Solutions?
Solution 1: Compare to fraternal twins.
If variation in a trait between fraternal
twins is greater than variation between
identical twins
–> that additional variation is presumed to
be due to genetic differences
Solution 2: Use reared apart identical
twins and compare to random people
Fraternal twins have ________ _________,
while most identical twins share______
Fraternal twins have separate placentas, while most identical twins share placenta
Which of the following is TRUE about
twin studies?
A. Differences between identical twins can be
due to genes or the environment
B. Differences between fraternal twins are due
to the environment only
C. If there is a genetic component to a trait, you
would expect more variation between
identical than fraternal twins
D. If a trait has a heritability near 0, identical
twins reared apart from each other will
vary as much as two random people
D. If a trait has a heritability near 0, identical
twins reared apart from each other will
vary as much as two random people
*H2 near 1.0 –>
identical twins will have the
same value for the trait, even if they are reared apart*
H2 near 0 –>
identical twins reared apart
from each other are no more likely to have the same value for the trait than any two random people
Vaccines do not cause….!
autism
why are the genetics of autism complex?
identical twins reared apart
from each other are no more likely to have the same value for the trait than any two random people
PROBABLY both since many gene sare implicated in autism (some epistatic) but environment also plays a role
concordance?
is the likelihood that a pair of individuals will share a trait or characteristic if one of them does.
autism and concordance?
A 1977 study found 82% concordance in identical twins vs. 10% in fraternal twins.
Do organismal clones ever occur naturally?
bacteria
twins
plants
mitosis
explain the cloning the vertebrate from somatic cells
too cell and put UV radiation on it, then they inserted an intestinal cell of a baby frog and it became a cloned frog
cloning the first mammal pathway
take egg donor (black sheep) and remove nucleous from the egg, then add the mamary cells from white sheep and combine. The blastocyst is then placed in uterus of a surrogate EWe and DOLLY IS BORN
what is the result of cloning the first mammal
result is a genitally identical copy sheep
what is the only other way (other than cloning ) where mammals have the same exact genotype
identical twins
epigenetics?
is the study of heritable phenotype changes that do not involve alteration in the DNA sequence
why did the clone of the cat Rainbow result in a copy cat with diffent fur color
Even though two cats are genetically identical,
epigenetic process called X-inactivation causes
random orange making gene gene inactivation
during development
What causes rainbow fur color in calico Cats
x-inactivation
can make cats have rainbow color?
no, and yes in very rare instance
when was the first primate cloned
2018
Ethical issues with reproducing cloning of humans
Dozens of cloned embryos must be created and
placed into surrogate mothers to produce a single
live birth
* Dying, stillborn and deformed babies frequent
* Even those who have lived a long time (such as
Dolly) have a some of serious health problems
* It would diminish the sense of the uniqueness of an
individual
has reproductive cloning of human happened yet?
no
what is reproductive cloning
cloning to make a baby
Embryonic Stem Cells
(ES Cells) hold ….
a great
potential for treating
disease
ES cells have the theoretical. potential to …
differentiate into any
cell in the body (->
they are pluripotent)
Some merits of therapeutic cloning
- Rebuild the pancreas of
someone with type-I diabetes - Replace dead neurons in
patients with spinal cord
injuries - Replace failed heart muscle
etc. - If patients are treated with
stem cells derived from their
own tissue, immune rejection
will be less likely
ethical issues with therapeutic cloning of humans
- Therapeutic cloning, while offering the potential for
treating humans suffering from disease or injury,
would require the destruction of very early human
embryos in the test tube. - Opponents argue that using this technique to
collect embryonic stem cells is wrong, regardless
of whether such cells are used to benefit sick or
injured people
DNA cloning synonym
molecular cloning
DNA cloning is…
is a molecular biology technique
that makes many identical copies of a piece of
DNA, such as a gene
DNA cloning greatly aids…
further study of that gene,
and its use in diagnosis or treatment
DNA cloning steps
- A target gene is inserted into a circular piece of DNA
called a plasmid (Ligation). - The plasmid is introduced into bacteria via a
transformation, and bacteria carrying the plasmid
are selected using antibiotics. - Bacteria with the correct plasmid are used to make
more plasmid DNA
restriction site?
A short DNA sequence
that can be cleaved by a restriction enzyme
vector
a carrier for recombinant DNA
characteristics of vectors
- Typically small (<10 Kbp) extrachromosomal
element such as a plasmid or a phage - Has restriction enzyme site and selection
marker (antibiotic resistance gene)
DNA ligase catalyzes
phosphodiester
bond formation between a free 3’ OH
and a free 5’ PO
Since the same sticky ends are on ‘both
sides’ of the vector and insert,
the insert
can ligate into the vector in either of two
orientations
How many different ligation
products besides desired will be isolated after transformation?
greater than 3
example application of DNA cloning
insulin production for diabetic patients + mRNA vaccines against COVID 19 you need to first clone the viral gene
4 applications of gene cloning -general
- Biopharmaceuticals (Insulin, human growth
hormones, mRNA vaccines etc.) - Gene analysis for basic research (to study gene
function, need to clone it first) - Gene therapy (fixed copy of a gene)
- Every molecular biology lab uses DNA cloning
How to understand the genetic basis of the trait or disease
step 1- map the genes responsible fro trait/disease
step 2 - clone the canidate gene
step 3- understand the function of the gene using model organisms (create a gene knowck out or a transgene)
step 4- designa drug or use gene editing to cure a genetic disease
positional cloning :
map the gene first then clone
HOw to map human genes
Linkage Analysis
Genome Wide Association Studies
Whole Genome or Exome Sequencing
Linkage analysis is based on
co-inheritance
of disease genes and neighboring regions
A genetic marker is a
DNA sequence with a known
physical location on a chromosome, a “landmark”
DNA segments close to each other on a
chromosome tend to be
inherited together (linkage)
Genetic marker that is close to the gene will be…
`inherited together with the gene because of linkage
Genetic markers ______ between individuals to the extend that …
Genetic markers VARY between individuals to the
extent that they can be used to find a nearby gene
causing a certain disease or trait within a family.
LOD score is a
statistical estimate
whether a disease
gene and a marker,
are likely to be
located near each
other on a
chromosome.
LOD score >3 means that
marker and gene are likely
linked, and gene is mapped
GWAS (Genome-Wide Association Studies) are also
based on
co-inheritance of disease genes and
neighboring genetic markers (or polymorphisms) but
has much higher resolution
GWAS is especially powerful for identifying
genes responsible for complex traits
WGS or WES (Whole-Genome or WholeExome Sequencing) of patients is increasingly used to identify
gene mutations responsible for rare diseases
what is the caveat of WGS or WES
very expensive, price of DNA sequencing goes down every tear
How to clone a human genes
look at human genome take gene of interest and isolate from genome then insert that gene into plasmis and then that plasmid is inserted into bacterial population generating clones of this gene
why is it easy to clone a human gene now
because
we know entire human
genome sequence
–> Before 2003 when
human genome was
completed scientists
had to use sophisticated
method such as
screening DNA
libraries to clone
human genes
Many human disease genes were mapped & cloned using
positional cloning
How to study gene function once you
identified and cloned the gene?
- Create gene knock-out in a model organism
OR
Use transgenic technology to create transgenic
model organism
* Express recombinant protein (Insulin)
* Reveals properties of the gene
* Reveals where & when the gene is active
what is a gene knock-out
removing gene from the organism and see what happens –> reveals the purpose of the gene
what is transgenic technoloy
introducing foreign gene to the organism this reveals the properties of the gene and where and when the gene is activated
what can transgenic technology express/reveal
-express recombinant protein (insulin)
- reveal properties of the gene
-reveals where and when the gene is active
To create knock out mouse scientists first create
mouse embryonic stem cells harboring desired gene mutation (knock out)
what is a knock out mouse
A knockout mouse is a genetically engineered mouse in which one or more specific genes have been “knocked out” or intentionally inactivated, making them nonfunctional.
Since knock out mouse technology was developed in 1980…
thousands of human genes were knoched out in mice
Steps to create knock mouse
-target ES cells are injected into blastocysts which are implanted into foster mothers which give birth to chimeric mice –> mating between chimeric mouse and normal mouse create knock out
The phenotype of a knock out mouse reveals
the purpose of the unmated gene
Introducing foreign genes into genomes creates…
transgenic organisms
introduced gene into forign genome is called…
transgene
expression vectors are …
specialized cloning vectors that contain regulartory sequences so that inserted trangenes will be expressed in the target organism
ex example of a typical expression vector is …
E coli where we see an E.coli expression vector with
the human insulin
cDNA inserted into the
cloning site
Expression vector is a
vector with a
promoter
to direct expression of
insert in a particular
host organism
What was the first human gene to be expressed in E coli
an insulin gene
the bacterially expressed human insulin can be given to
diabetic patients
the bacterially expressed human insulin is better and …
cheaper than getting insulin from pigs (where it used to come from)
some exampled of using genetic engineering for protein therapy
recombinat Human Insulin for treating Type 1 Diabetes
Recombinant Human Factor V111 for treating Hemophillia A
Recombinat Growth Hormone for treating dwarfism
where did human factor V111 come from before expression vectors
donated blood
where did growth hormone come from before expression vector
cadavers
Animal transgenes typically ….
integrate into the genome
what are the type types of transgenesis
random transgenesis
targeted transgenesis
what is random transgenesis
–> transgenes integrate into random locations of the genome
-no homology between the introduced DNA and the site of insertion required
What is targeted transgenesis
-transgenes intregrate into specific landing sites
-requires extensive homology between the introduced DNA and the site of insertion in the genome
How are transgenes introduced into animal model organisms?
via needle injection, electroporation or viral infection
Transgenes reveal the …
properties of the gene
eyeless or Pax-6 is a …
conserved gene which is essential for eye development in flies, mice and human
expression of mouse eyeless in Drosophila induced…
ectopic eye development in legs and antennae
the experiments surrounding the eyeless gene suggest that
eyeless gene is a master control gene for eye developement in all animals
Reporter Transgenes are used to investigate
gene regulation
Regulatory sequences for a gene of interest are fused
to the reporter gene, which will then be expressed in the pattern dictated by the regulatory sequences
how can you visualize the reporter gene expressiion–>
β-galactosidase from E. coli -> blue precipitate with X-Gal
Green Fluorescent Protein (GFP) from jellyfish*
Red Fluorescent Protein (RFP) from sea anemones*
Reporter transgenes reveal
where and when genes are active
CRISPR/ Cas 9 has the ability to…
change or edit the DNA of organisms (delete, insert, replace parts of DNA)
Bacteria has a …
immune defense system against phages
CRISPR is a
bacterial immune system that recognizes and cuts the DNA of an invading bacteriophage
CRISPR stand for
clustered regularly interspaced Short Palindromic repeats in the bacterial genome
Scientists immediately suspected that these spacers in CRISPR are used by
bacteria to recognize invading phage viruses that bacteria has “seen” before
SPacers are
unique sequences that were acquired from invading phage viruses
CRISPR repeats …
transcribe into pre-crRNA and cut into short
crRNAs
CRISPR locus also expresses
a tracrRNA and a DNA cutting enzyme called Cas
Bacteria uses CRISPR to recognize
invading phage viruses that bacteria has “seen” before
Charpentier and Doudna hypothesized that if you mix together….
Cas9 and crRNA it can be used as programable DNA cutter.
CRISPR allows scientists to
cut DNA at any gene or specific location of the genome of choice
Main advantage of CRISPR/CAS9 over restriction enzyme
Restriction enzyme can only cut that sequence that occurs every 2000 base pairs
CRISPR= You can cut any sequence you want almost anywhere you want –> Can also introduce any DNA modification of choice (deletion, insertion, replacement)
Can rewrite sequences
With CRISPR you can introduce any
DNA modification of choice
(deletion, insertion, replacement)
CLassic Knock out technology in mouse ES cells is very
inefficient –> For many loci you have to screen 1000s of clones to
get one clone with targeted mutation!
For CRISPR/Cas9 it is common to have what percent efficiency
90%
CRISPR/Cas9 system is easy to use bc to cut DNA at specific genome location you just need
short complementary crRNA
CRISPR/Cas9 editing is more
efficient, easier to use and is also faster in generating knock-out mice
ES cell targeting takes how long for a knock out mouse
1 year
CRISPR takes how long for knock out mouse
1-2 months
Why CRISPR/Cas9 revolutionized biology?
We could already introduce mutations
before
A.CRISPR/Cas9 is more efficient and is
easy to use
B. CRISPR/Cas9 is safer to use
C.Because they gave a Nobel prize for it
D.CRISPR/Cas9 does not have off-targets
(cutting in the wrong place)
A.CRISPR/Cas9 is more efficient and is
easy to use
With CRISPR we can swap DNA between species -> CRISPR technology enables what type of studies
evolution studies think serpentized mouse
CRISPR enables genome editing in ___________ in which it was simply not possible before
exotic animals
Crisper also benefits ….
AGRICULTURE ex–> leaver pics, no browning mushrooms, and improved crops
How CRISPR-based sickle cell treatment
works?
hematopoeitic Stem Clls removed from patient –> crispr-cas 9 repairs mutant B globin gene and reinfusion of edited cells and engraftment in bone marrow
Human heritable gene editing has been
performed by
Jiankui He –> for HIV
why was the human heritable gene preformed by Jiankui He unethical?
A. There are other ways to prevent HIV transfer
during IVF (e.g., wash sperm)
B. Mosaic embryos won’t prevent HIV enterance
C. Potential off-target mutations
D. Mother was given a misleading consent form
