Midterm 3 Flashcards
which statement accurately describes chromosomes, chromatids, and alleles?
chromosomes contain DNA, chromatids are replicated chromosomes, and alleles are gene variants
homologous chromosomes consist of what?
one mom and one dad chromsome
2 chromatids mean what
2 sister chromatids that come from the same parent
three principles of Linked Genes and Mapping
- Independent assortement of homologous chromosomes during meiosis
- Genes can be close to each other on a chromosome
- meiotic recombination between homologous chromosomes can swap alleles
AKKA independent assortment, syntenic genes, and recpmbination
ratio for independently assorted alleles/ chromomomes (when genes on diff chromosomes)
1:1:1:1
when do genes undergo indepenedent assortment
when the genes are on different chromosomes
Genes A, B, C are located on different autosomes. If I have a plant with the genotype AaBbCc, which resulted
from crossing ABC x abc, how many different gametes
will be formed by AaBbCc plant?
8
Each gene occurs at a specific site, or ….
LOCUS on a chromosomes
genes located on the same chromosome are called
syntenic
humans have __ pairs of homoglous chromsomes, but _______ genes
23; 20,000
describe the phenotype/genotype of the normal wild type of thomsas morgans linkage using flies
red eyes (pr+) and full wings (vg+)
describe the phenotype: genotype of the homozygous recessive genotype of thomsas morgans linkage using flies
purple eyes (pr), Vestigial wing (vr)
in the Fly gene nomenclature what does + mean
wild type akak vg+ = normal
what will be the phenotype of the flies resulted from the cross of. a pr+ vg+ and a pr vg
red eye, full wing
Thomas Morgan Crossed F1 flies to flies with
homozygous recessive phenotype (Test Cross) results?? and analysis of them ??
pr+ vg+= 1339
pr+ vg= 151
pr vg+= 154
pr vg= 1195
–> meaning that results confirm hypothesis that two genes DO NOT always assort independently. since there was no 1:1:1:1
recombination =?
crossing over
non parental chromosomes are the result of
recombination
what is recombination
physical exchange of segments between homologous chromosomes
how often does recombination occue
about 1-3 times/ chromosome on average
when does recombination occurs
synapsis of meiotic prophase 1 –> when synaptonemal complex is formed
chiasma=
cross-chaped configuration caused by breakage and rejoining of chromatids
recommbination machinery?
proteins catalyzed by enzymes
what is the result of recombination
greatly increases the numbers of possible genotypes BY ENABLING MORE LOCI TO ASSORT INDEPENDENTLY
what does recombination enable
genetic mapping think recombination %
recombination results in what types of gametes ?
gametes with combinations of alleles that were not present in parents
recombination frequency
is a measure of how linked are two genes
If I have a plant with the genotype PpLl, which resulted
from crossing PPLL x ppll, what are the recombinant
gametes formed by the PpLl plant?
Pl and pL
In the extreme case of complete genetic linkage between two genes what does it look like
they are so close together on the same chromosome (syntenic) that they are practically always inherited together, with almost no recombination events occurring between them
implications of gentic linkage
linkage is a real concern for many selective breeding experiments –> linked to cancer and linked to deafness
what happens when syntenic genes are NOT very close to each other in genetic linkage
incomplete genetic linkage where parental gametes are significantly more frequent and nonparental gametes significantly less frequent than predicted by independent assortment
explain how recombination can break apart linked apart linked alleles
Recombination can separate these alleles and shuffle them into new combinations. –> Recombination doesn’t inherently “sort out bad genes,” but it does create genetic diversity, which can lead to a combination of traits that may be beneficial or harmful depending on the environment.
implications of recomponation in humans
more combinatorics–> more gentic and phenotypic diversity
Assume that in any person we can find ___ loci
for which they are …
700; heterozygous, and which assort independently
the # of genetically distinct gametes any
person can make is….
> # of atoms in the universe
a test cross can be used to measure …
recombination frequency
recombination frequency is equivalent to the
frequency of recombination alleles
What is the maximum recombination
frequency?
If genes are very far apart on the same
chromosome, at what frequency will they
recombine?
50% –> Remember, Crossovers occurs in the 4-strand stage of meiosis I, and involve only two of the four chromatids.
*Thus any single crossover event creates two recombinant (non parental)
chromatids, while leaving the other two in the parental configuration
crossing over occurs in the ____ and only involves
4- strand stage of meiosis one; only involves two if the four chromatids
in any single crossover event it creates –>
two recombinat chromatids while leaving the other two in the parental configuration
you can detect genetic linkage by using a
chi-squared test
independent assortment is what type of hypotheisis in chi-squared
null hypotheis
Based on the chi-square value of 19.6
can you reject your null hypothesis?
Yes, the genes are likely linked –> remember the null hypothesis is independent assortment so If the chi-square value is high enough to give a p-value less than 0.05, we reject the null hypothesis. A chi-square value of 19.6, with 1 degree of freedom, corresponds to a p-value well below 0.05, so you can reject the null hypothesis and conclude that the genes are likely linked.
A chi-squared test can be completed by
following five simple steps:
A. Identify hypotheses (null versus alternative)
B. Construct a table of frequencies (observed versus
expected)
C. Apply the chi-squared formula
D. Determine the degree of freedom (df)
E. Identify the p value (should be <0.05)
The probability of crossing over
between two genes (or loci) is
roughly proportional to their distance
apart on the chromosome.
Genetic Linkage Mapping
is based
on recombination
frequency between genes
Alfred H. STurtevant did what?
” the linear arrangement of sex-linked factors in Drosophilia, as shown by their mode of association” –> mapping genes by recombination frequency
alfred H. Stustevant worked on gene mapping when he was ..
an undergraduate in the T.H. Morgan’s Lab
describe graph relationship between distance and recombination frequency
positive exponential graph –> steadily increases and then kinda horizontals off–>
as the distance between two alleles grows the …
recombination frequency grows
1% recombination =
1 centiMorgan (cM)= 1 map unit. (m.u.) which is about 1 million base pair
lets say that the Recombination frequency
between vg and pr alleles is
10.7% this means how many centimorgans are the alleles apart
10.7 centiMorgans
Linked genes exhibit …
less than 50 % recombination meaing that they are less than 50 cM apart
how long is the human chromosome 9
about 200 cM
relate trisomy 21 to recombination
Reason why trisomy 21 is okay is bc chromosome 21 is VERY short so recombination isn’t that often → does not contain many genes
what is the recombination frequency between A and B based off of this data: AB/ab x ab/ab: 39% AB; 11% Ab; 11% aB; 39% ab
look fore recombinant alleles and then add them together to get ther recombination frequency –> 22%
Double-crossovers cause an
under-estimation of the
distance between two loci.
In a genetic mapping experiment, double
crossovers between two loci can affect the
calculated genetic distance. How do double
crossovers impact the observed genetic distance
between these loci?
They decrease the observed genetic distance.
what simplification to recombination have we made that underestimates the obsrved genetic distance
assumed that crossovers are equally likely to occur all along the chromosome–> when recombination haas hotspots and cold spots
true or false: crossovers are equally likely to
occur all along the chromosome
FALSe–> recombination has hotspots and cold spots
recombination frequency can be affected by
biological factors such as
- sex –> females have more recombination then men
- temperature
in our bodies, harmless bacterial cells can outnumber our own cells by
10:1 ratio
antibiotics are arguably the …
most important discovery in medicine in 20th century
1928?
discovered penicillin
1945?
nobel proze for penecilin
How can pathogens acquire antibiotic resistance?
through lateral gene transfer
harmless bacterial cells in our organism might be ///
actually important and play important role in obesity, allergies, metabolic diseases, type 2 diabetes
bacteria have what type of chromosomes
circular chromosomes
3 descriptive word of bacteria
prokaryotic
unicellular
haploid
bacterial cells are …
HAPLOID`
What do bacterial cells NOT HAVE (two things) and have (one thing)
no homozygous or heterozygous alleles
NO meiosis
BUT THEY HAVE RECOMBINATION
what does lac+ mean
means a WT allele that can grow a medium containing lactose instead of glucose
what does lac- means
mutain strain that cannot grow on lactose media
which one is the mutant strain lac + or lac -
lac -
lac - has the inability to …
METABOLIZE (process ) lactose so t has no sugar to grow
Two strains of E. coli, lac⁺ (can metabolize
lactose) and lac⁻ (cannot metabolize lactose),
are grown on media with and without lactose.
Which statement is correct?
A) Both lac⁺ and lac⁻ grow without lactose; only lac⁺
grows with lactose.
B) Only lac⁺ grows without lactose; both grow with
lactose.
C) Both grow with lactose; only lac⁻ grows without
lactose.
A) Both lac⁺ and lac⁻ grow without lactose; only
lac⁺ grows with lactose
what does leu + mean
a WT strain with ability to synthesize amino acid leucin
leu - means
a mutant strain that CANNOT synthesize aminoacid leucin
out of leu+ and leu- which is the mutant strain
leu-
leu - strain has the inability to…
inability to SYNTHESIZE (make a component)–> cant make amino acid leucin so it cannot grow
a bacteria has a genotype Lac-, leu+ met- cys-. which media it will grow on?
A. Lactose*, no leucin, methionine, cysteine
B. No lactose, no leucin, methionine, cysteine
C. No lactose, leucin, no methionine, cysteine
D. Lactose*, leucin, methionine, no cysteine
B. No lactose, no leucin, methionine, cysteine`
vertical vs lateral gene transfer
Vertical gene transfer = genetic material passing through a parent to its offspring during reproduction,
lateral (or horizontal) gene transfer involves the transfer of genetic material between organisms that are not direct descendants
lateral gene transfer is also known as
horizontal gene transfer
on average what percent of bacterial species genome has been acquired by LGT
less than 10% of genes
which genes ARE often transfered by LGT
antibiotic resistance genes
what are the types of lateral gene transfer
conjugation
transduction
transformation
what is the main way conjugation works
think PLASMID
what is the main way transduction works
think PHAGES
what is the main way in which transformation works
THINK free DNA
plasmids?
are circular DNA molecules that replicate independently of the bacterial chromosome
how are plasmids usually thought of as
selfish DNA elements that parasitize the host bacterium
what are feature of the most successful plasmids
plasmids that give the host something in return such as antibiotic resistance
when were plasmids discovered
in 1950s by Joshua Lederberg adn colleagues
who were the first to use plasmid in recombinant DNA
1973 Cohen Boyer and Berg
today how are plasmids used?
routinely used in genetic engineering as gene transfer vectors
F(fertility) factor plasmis is
a low-copy number plasmid 100kb in length and is present in 1-2 copies per cell
the F factor plasmid replicates …
once per cell cycle and segregates to both daughter cells in cell divison
F+ cells can transfer a copy of the F-factor plasmid to F–
cells by a process called
conjugation
Conjugation is a process in which
DNA is transferred from bacterial donor cell to a recipient cell
what mediated the F-Factor plasmid transfer
PILUS–> a tube like structue
what is pilus
a tube like structure formed between the cells, through which the plasmid DNA passes
The ~20 proteins that make up the pilus are encoded by
the F-factor
plasmid
F Factor plasmid replication and tranmission to F- cell are
COUPLED
Beside conjugation genes the F plasmid…
doesnot carry any other (resistance) genes
what are the only genes that the F plasmid carry
conjugation genes
once a bacterial cell has the plasmid F+ what can it do with it
the F-plasmids can recombine with other circular DNAs
what does integration mean when taking about F-plasmids
the F-plasmids can recombine with the baterial chromosome to become apart of the bacterial DNA
where does the F-factor recombination happen at on the bacterial chromosome
at the IS element
integrated F-plasmids form…
Hfr chromosomes
Hfr chromosomes can facilitate
transfer of pieces of chromosomal DNA–> make another cell lac + by giving its portion of the f-plasmid dna (i think through recombination but dont quote me on this )_
what are the two mechanisms where F-plamids can facilitate chromosomal DNA
1) Hfr gene transfer
2)F Factor excision
What is Hfr gene transfer
when a part of the F-factor sequence moves through the pilus, some bacterial genes go along for the ride
F-factor excision
when F-factor sequence seperates from Hfr chromosome s and carries a piece of chromosomal DNA –> f factor becomes plasmid again
the F factor plasmid found in the 1950s did not carry
antibiotic resistance genes
TRUE OR FALSE: Today, R plasmids containing antibiotic-resistance genes are often isolated
from resistant bacteria.
true
R plasmids evolved from the F-factor plasmid BUT
but they
carry antibiotic-resistance genes (sometimes >1)
what is an example of darwinian evolution
A rare variant (F-factor that obtained resistance
gene) became common due to selective pressure…
Can bacteria be diploid?
yes, for certain genes
ex: f factor excission–> In this case, after receiving the F’ plasmid with chromosomal DNA, the recipient bacterium can have two copies of certain genes—one copy on the chromosome and one on the plasmid. This is diploid-like, but it’s not the same as true diploidy in eukaryotes, where two copies of each gene exist in each cell’s chromosomal set.
Transduction
when bacterial DNA is transferred from one bacterial cell to another by a phage
how may the transferred DNA in transduction be intergated
by recombination –> rare
Phage life cyle (transduction
- Injection of DNA by phage
- takeover of bacterial cell; production of phage proteins; replication of phage DNA
3: DNA packaged into pahe;assembly of phage particle
4: lysis –> phages released into environment
most phage particles carry what DNA
only phage DNA occassional phage particles carry bacterial DNA
Bacterial Transformation in the lab step by step
- uptake of DNA by compentent bacteria
- DNA may be integrated into genome or exists as a plasmids
What are the DNA containing organelles
chloroplasts and mitochondria
chloroplats location and function
found in plants and algae
capture sunlight energy (photosynthesis)
Mitochondira function
powerhouse of the cell
generate enegry from breaking down lipids and carbs
UNIparental inheritance of leaf color is explained by …
maternal inheritance of chloroplast DNA
Homoplasmic
all copies of genes are the same
Heteroplasmic
mixture of alleles
Homoplasmic cells can give rise to
homoplasmic cells
heteroplasmic cells can give rise to
homo OR heteroplasmic gametes
homoplasmic or heteroplasmic comes from where
THE MOTHER
what types of progeny will result from a fertilization of a homoplasmic mutant female plant by pollen from heteroplasmic mutant plant
only homoplasmic mutants
What makes organellar inheritance different from nuclear inheritance?
- can be uniparental (only get from one parent)
- Multiple organelles in each cell
- Each chloroplasts/ mitochondria has multiple copies of organellar genome
- Traits controlled by organellar DNA can be influenced by nuclear genes (EPISTASIS)
how is the organelle genome packaged?
into nucleoids containing multiple copies of DNA
the mutant allele can eventually become….
homoplasmic
After fertilization the zygote retains what from the mother
mitochondira
true or false: The inheritance patterns of x-linked genes and mitochondrial genes are the same.
false
true or false: Reciprocal crosses can reveal uniparental inheritance.
true
true or false: Homoplasmy means that a cell’s mitochondrial DNA is all identical.
true
true or false: A heteroplasmic cell can yield a homoplasmic daughter cell.
true
Mitochondiral DNA inheritance in mammals
uniparental –> maternal
implications of mitochondria DNA inheritance
- human genetic disease due to mtDNA mutations are maternally inherited
- Can examine maternal genealogies of a human population
(simpler than nuclear DNA – no Dad, no recombination, higher mutation rate
means more distinct alleles – can ID grandmas)
-> Example: Native American origin from populations in Siberia
some mitochondrial proteins are encoded in the
nucleus
Mutations in mitochondrial DNA can lead to
pleiotropic diseases
LHON, a mitochondrial disease,….
is partially penetrant.
Mitochondrial Function depends on what
NUCLEAR AND mitochondrial encoded genes
leigh syndrome symptoms
a severe neurological disorder –>
Symptoms: worsening mental and motor functions, typically results in death by early infancy
what can cause leigh syndrome
mutation in more than 75 genes
what do all mutations taht cause leigh syndrome have in common?
all mutations affect mitochondrial oxidative phosphorylation
describe the gene ratio of the leigh syndrome genes
- ~75% of the genes are nuclear – both autosomal and X-linked
- ~25% of cases – mutations are in mitochondrial genes
Method 1 of Embryo Repair -IVF
take parents embryo(where mitochondria are unhealthy) remove parents nucleus and insert into donor embryo(where nucleases have been destroyed and mitochondria are healthy)
is method one of IVF approved or not in the us and in the uk?
An IVF Approach for Mitochondrial Disease was approved in the UK in 2015
Not legal in the US
Method 2: Egg repair IVF
mother egg has unhealthy mitochondria so mothers nucleaur is removed an place in a donors egg where nucleus has been destroyed and mitochondria is healthy
is method 2 IVF approved or not in UK and US
An IVF Approach for Mitochondrial Disease was approved in the UK in 2015
Not legal in the US
WHat is development
is the process by which a zygote matures into an adult
through development an organisms genotyope is expressed as a
phenotype
process of development is controlled by
developmental genes
what type of disease results from mutations in developmental genes
congenitial disorders
what has remarkable similarities between different animals
development
what are some model organisms used in developmental genetics
drosophilar, zebrafish, mouse
what is the best model organism
fruit flys- drosophila
how long is the life cycle of drosophilia
short –> 10 days –> with embryogenesis taking
place via a series of rapid,
genetically controlled
changes
drosophila development is a paradigm for
animal development
what type of segmentation does drosophila have – and how many of each
a typical segmentation with eight abdominal and three thoracic segments clearly visible
describe Genetic screenings old version
add mutagen to fly so that P0 will have gametes with random mutations
look for abnormal phenotypes in F1 and F2 progeny
Map genes
WHat is the problem with genetic screenings old version
most mutations result in lethality and no adult flies
Landmark screens in Drosophila led to
the identification of the basic toolkit of genes required for establishing the embryonic body plan
describe the modern version of genetic screening
- add mutagen to P0
- P0 will have gametes with random mutations
- look for abnormal phenotypes in EMBRYO and LARVAE on F1 and F2 progeny
- Map genes
describe F1 screening and dominant mutations
Dominant mutations are rare, but easy
to observe in a F1 screen
* + = WT
how many round of mutations are required to identify recessive mutations
THREE
loss of function mutations are common and usually …
recessive
screenings are ….
TIME CONSUMINg lots of crosses
what is the modern genetic screening known as
Heidelberg screening
the phenotype of the mutated gene reveals the …
purposed of the unmutated gene
what are coordinate genes
defines axis of embryo
what do mutations in coordinate genes look like and what is it called
bicoid
mutations result in the loss of segments and mirror image duplications of other segments
what are gap genes
defines broad region of the embryo
what are the types of gap gene mutatations
Kruppel
Hunchback
Knirps
what do mutations in gap genes do
mutations result in the loss of contiguous sets of segments –> missing genes
what is the pair rule gene
defines segments of the embryo
what is a result of a mutation in the pair rule gene
loss of alternate parasegments
what are the types of pair rule gene mutations
even skipped, odd-skipped
what is the segment polarity gene
defines anterior and posterior regions of individual segments
what do mutations in segment polarity gene cause
defects within anterior or posterior regions of each segment
what are the types of mutations in segment polarity genes
gooseberry
hedgehog
Virtually all genes discovered in Heidelbergs screens were
transcription and signal molecules
Embryonic patterning genes are highly –>
CONSERVED
hh gene in vertebrates is called
sonic hedgehod (Shh)
Disrupting hedgehog activity results in
severe embryonic defects like cyclopia, holoprosencephaly, limb malformations and cancer
Heidelberg Drosophila screen identified
600 mutants but only 120 genes?
Because many mutations cause by the different genes
Mutations in Shh limb enhancer played
important role in
evolution of limblines in snakes
Homeotic genes specify the…
anatomical identity of segments
example of homeotic genes:
- Different genes turned on in
different segments. - Mutations in a homeotic gene
causes transformation of one
body segment into another - The Hox genes are
conserved (similar) in all
animals from insects to
humans
