BIO 202 Flashcards
1
Q
Pattern of recessive traits recovery
A
1/4
2
Q
Mono hybrid cross-ratio
A
3:1
3
Q
large sample increase or decrease variability
A
reduce
4
Q
why use testcross
A
to see if theres a recessive trait
5
Q
haploinsufficient
A
one functional copy of gene is enough to have normal function
6
Q
What causes Cystic fibrosis and ratios of carrier parents
A
- mutations in the CFTR gene
- recessive
- carriers parents = 1/4 of having a child with CF
7
Q
dihybrid cross (explain and ratio)
A
ration: 9:3:3:1
- Rr/Yy
RY Ry rY Ry x RY Ry rY R
- must be on separate chromosome
8
Q
can u get recombiannt progeny if gene A and B are on the same chromosome
A
no
9
Q
what does dihybrid testcross get you?
A
equal numbers of parental and recombinant progeny (1/4 , 1/4 parental, 1/4 1/4 recombiannt)
1:1:1:1 ratio
10
Q
Chi-square test formula and confidence level
A
X^2 = ∑(O-E)^2/E
p < 0.05 (95 confidence)
11
Q
when does crossover happen in meiosis
A
after DNA replication
12
Q
could there be multiple crossovers in a single meiosis?
A
yes
13
Q
How do we calculate recombinant frequency
A
(#recombinants)/total progeny for every combination
Ex: 151 and 154 out of 2939 progeny have recombinant genotype
- (151+154)/2839 x100 = 10.7% = 10.7 m.u
14
Q
what are SSLP
A
simple sequence lentgh polymorphism
- repetiitve DNA (short, simple DNA sequences)
- not associated with gene function)
- can determine crime, fingerprint
15
Q
haplotype
A
Physical grouping of genomic variants (or polymorphisms) that tend to be inherited
together, as a single group
16
Q
What gene is eliminated in CF patients.
A
loss of Phe508
17
Q
People who lived up in teh mountain shad a special gene to them. what was it and what did it do
A
EPAS1 regulated the number of red blood cells that our bodies produce in response to the level of oxygen in our tissues
18
Q
Relation between drugs and SNP?
A
- Can see if there are certain SNP that are overrepresented
- Can help determine if there are gene variants are present in future patients to assess possible future treatment or
not (can be quite painful)
19
Q
what is haploinsufficiency?
A
you need 2 wild type copies for a protein function
20
Q
What is dominant negative and give an example
A
example: p-53 in cancer
- need 2 normal copies
- 1 mutant gene could allow thing to assemble but there would be loss of function
21
Q
difference between incomplete and partial dominance
A
incomplete: the heterozygous phenotype is a blend or mixture of the two homozygous phenotypes.
partial: shows a phenotype closer to one of the homozygous phenotypes. (will be closer to the dominant, not a perfect blend of both)
22
Q
what is co-dominance and example
A
blood type (AB is co)
both alleles as a phenotype are expressed/detected
23
Q
define recessive lethal. Is it the same as synthetic?
A
NO!
recessive= having both alleles means death (cant happen in haploid organism because instant death)
- maintained as heterozygotes in our genome
- can be dominant or recessive
24
Q
what is auxotrophs. can we identify what genes they are missing
A
Organisms that lost the ability
to synthesize certain substances required for their growth
- yes, we can add random amino acids or nutrients to see what sprks their growth until we find it
25
what is conditional alleles give an example
phenotype depends on external factors
- Tyrosine kinase is an enzyme that is
responsible for black pigment, and is
active at lower temperatures
- Black pigment is produced as lower
temperatures
- higher temp = lethal
26
Define penetrance
The percentage of individuals with a given allele who exhibit the phenotype of that allele (even if you have the mutation, phenotype may be obvious or not)
27
define expressivity
veryone is affected, but the degree to which a given allele is expressed at the
phenotypic level is different (ie: the intensity of the phenotype)
28
Define and give example of variable penetrance
Some develop the phenotype, some don’t
ex:
BRAC2 mutation is a predisposition to breast, ovarian, and pancreatic cancers, but not everyone with the mutation develops the mutation due to external factors:
- Environment
- Interacting genes
- Subtlety of mutant phenotype (difficult to diagnose)
29
what is the complementation test?
for recessive mutation we can use this
- cross two pure bread mutants
- if it appears wild type: different genes
- if it appears mutant: same gene
30
how can we see if mutation is on one or different genes?
complementation test with 3 mutations that make it look white
- %, & and $
- % and $ did not complement and resulted in white (so on the same gene)
- % and & = complement (bleu)
- $ and & = complement (bleu)
31
what does a 9:7 ratio mean
that two different genes are on the sam pathway
- could also mean that there's an interaction between regulatory gene and target gene
32
what is recessive epistasis. what ratio results of this?
-mutation of one gene
affects the phenotype controlled by another
-
- 9:3:4 (9 = bleu flower, 4, white flower, 3 pink)
33
what is a suppressor
Suppressor is a mutant allele of a gene that reverses the effects of an
original mutation
34
what is a modifier?
Second mutation that changes the
degree of expression of a mutated gene (phenotype)
35
define synthetic lethal
Mutations in two genes, each often has a weak mutant phenotype, resulting in lethality (when both are together)
36
what is an indel
Insertion or deletion even of nucleotides
37
what is a micosatellite
Repeats in nucleotides (with variation in the #repeats across individuals)
38
what is a SNP
(single nucleotide polymorphisms): Nucleotide positions that vary in which nucleotide they are.
To be considered a SNP, the nucleotide position must be variable (“polymorphic”)
39
what is a specific haplotype
Typically reflects a unique combination of variants that reside
near each other on a chromosome
40
Name the 4 Emergent Population Genetic Level Forces (to cause evolutionary change
1. mutation
2. migration
3. selection
4. change (genetic drift)
41
For a gene with 2 alleles what is the sum of frequencies?
For a gene with two alleles, A and a:
the frequency genotypes AA, Aa and aa can be denoted:
- fAA, fAa, faa
- The sum of fAA + fAa + faa = 1.0
42
what are two symbols for frequency of one allele? name some equations
p and q
p + q = 1
q = 1-p
P = f(AA) + 1/2 f(Aa)
AF = Homozygous + 1/2 Heterozygous
43
define Ploidy
How many sets of chromosomes something has (n)
44
What can allele, genotype, haplotype frequencies be used for?
to characterize the genetic composition of
populations
45
when does evolution occur?
when allele, genotype, and haplotype frequencies change
46
Hardy-Weinberg theory helps us calculate what?
genotype frequencies in populations
47
DNA fingerprinting and hardy weinberg?
- Assuming Hardy-Weinberg principles and then calculating
probability that the DNA match occurs simply by chance alone
- google doc
48
When there is random mating what are the frequencies?
AA: p^2
Aa: pq
aa: q^2
p^2 + 2pq + q^2 = 1
49
what does identical by descent mean?
Inbreeding increases the probability that two alleles at a locus will be copies of an allele present in an ancestor
50
what is inbreeding coefficient and the equations that come with it?
F quantifies the overall probability that the two alleles inherited by a given individual will be
identical by descent
1. F = (1/2)^n
2. f the parent A is also inbred:
F = (1/2)^n *(1+F_A)
51
What If There is More than One Common Ancestor (Full Sibling Mating)?
F = (1/2)^n + (1/2)^m
52
what do you observe in population that switches over to inbreeding from random mating
more homozygous, less heterozygous
- Inbreeding has no effect on allelic frequencies, but does affect genotype frequencies
53
what is inbred depression
Inbreeding depression (reduction in the viability of inbred individuals) occurs because most deleterious (harmful)
conditions require two copies of the mutation to be expressed
- can lead to smaller population, lower reprduction and higher mortality
54
describe mutations
- event rates are relatively low
- doesn't cause much change in allele frequencies
55
describe genetic drift
- Losing alleles due to chance
- Individual populations lose genetic diversity and
populations diverge from one another
- normally occurs in small populations
56
describe migration
- Introduces new genes into the gene pool from somewhere else
- can be uni (like mutations introduce alleles into a population) or bidirectional (keeps population from diverging from one another)
57
what is bottleneck event
dont expect the same porptions as previous large populations
58
Determine the Average Population Fitness equation
Wavg = f(AA)*w(AA) + f(Aa)*w(Aa) + f(aa)*w(aa)
59
Determine the Frequency of the Genotype After Selection
w(AA)*f(AA)/Wavg
60
Determine the Frequency of the Alelle After Selection
q = f(aa) + 1/2*f(Aa)
61
Name the twp types of selection possible.
- Directional selection: Where there’s a real advantage to one form that carries as homozygous for the alleles in question
- Balancing selection can also occur in nature: Maintains variability of alleles with heterozygous advantage
62
what is the ration for GENOTYPE of a heterozygous x heterozygous cross?
1:2:1 (YY, Yy, yy)
63
Why is it that the recessive and deleterious diseases haven’t been driven out already by natural selection?
Mutation (consistently introducing these new alleles)
64
what is a selective sweep
- reduces diversity
- specific allele (a variant form of a gene) increases rapidly in frequency in a population due to positive natural selection
- leaves trace of past events
65
Difference between simple and complex traits
simple: discrete expression (white/purple, long/short)
- Population variation controlled by one/two genes
complex: many genes and many environmental effects influence trait expression and variation (ex: population variation) (bell-shaped distribution= height)
66
what are the two types of complex traits
1. continuous
- Body size, running speed
- All individuals present the trait in some way
2. threshold
- Increasing genetic/environmental liability to a certain
threshold (and then the individuals present the trait)
- cancers, heart disease
67
What is phenotypic variance of a trait
How much is due to differences in the environment that individuals experience and how much is due to genetic differences among individuals
68
Equation for broad sense heritability and meaning of it being high or low.
H^2 = Vg/Vx
Vx= Vg+Ve
low: no correlation
high: traiy affected by both genes and envirnment
69
what is GWAS
- Using molecular markers to infer the presence and affects of genes that influence genetic variance
- Using association between SNPs and disease to
detect genes that influence complex diseases
70
describe QLT mapping
- Co-segregation (co-inheritance) of phenotypes and marker alleles (usually SNPs)
- locate the region of the genome where a gene with influence on the phenotype resides
71
define Autopolyploids
An individual that has multiple chromosome sets originating from within one species
72
define Allopolyploids
An individual that has multiple chromosome sets originating from two or more different species (ie: hybrids
73
define aneuploidy
Not a whole full set (extra/missing individual chromosomes) (not a multiple of n)
74
how dow e calculate P(euploid)
P(euploid)= (0.5) ^(n-1) (n being how many chromosome sets we have)
75
are triploids sterile? how can they be made
yes, cross a 4n (forms diploid gamete = 2n) with a 2n (forms haploid gamete 1n) 1n+2n = 3n
76
how do we form tetraploid
used colchicine to disrupt microtubules to keep the replicated chromosome
77
what is dispermy
2 chromosome from sperm and 1 from egg
78
example of allopolyploid
- Crossing a cabbage (2n) with a radish (2n)
- Somewhere along the line, there was spontaneous doubling of the chromosomes (4n)
- results in amphidiploid (a hybrid with four pairs of chromosomes, two different kinds)
- if amphidiploid mixed back with parent it makes sterile children cannot mix again
79
name 5 types of trisomies
- XXX (normal)
- XXY (Klinefelter syndrome (still normal, just different characteristics)
- Trisomy 21: Down syndrome
- Trisomy 13,18: Non-viable, die in infancy
- All others: Non-viable, die in utero
80
name an example of viable monosomy and what it is
XO (instead of XY or XX) : Turner syndrome
81
what is the gene dosage hypothesis
refers to the idea that the amount of genetic material (the "dosage") present in an organism directly influences its traits and characteristics
82
what is non-disjunction and when can it occur
- Failure of chromosomes to properly segregate during anaphase
- If occurs in meiosis I, results in 100% aneuploid gametes
- If occurs in meiosis II, results in only 50% aneuploid
gametes
83
what is Cri-du-Chat Syndrome
Part of chromosome #5 is missing (chromosomal deletion of 17 genes) resulting in a diseased phenotype
this means:
- 1 or more of these 17 genes is required for development
- None of the 17 genes are haplosufficient
84
how can chromosomal deletion occur and give an example.
intermediate segment is cut out and lost
1. incorrect breakage and rejoining
2. incorrect crossover between repetitive DNA during meiosis
ex: Williams Syndrome Deletion
85
explain Williams Syndrome Deletion
1.5-Mb deletion on one homolog of chromosome 7, specifically at band 7q11.23
1. two repeptivtive sequences will form an unequal crossover
- leads to 1 deletion and 1 duplicated chromosome
86
how can duplications occur (2)
- results from breakage and rejoining but rejoining with incorrect chromosome
- results from crossing over between repetitive DNA
87
name 2 ways chromosomal Rearrangements: Inversions can occur and the difference between including or not the centromere
- results from breakage, flipping and misrepair
- Results from the misalignment of homologous
- can be paracentric (doesn’t include the centromere) or
pericentric (does include the centromere) inversions.
88
name 3 different breakpoints ways/conseuqneces
1. Breakpoints between genes: No genes are disrupted
2. one breakpoint point within genes: Split gene is
disrupted
3. Breakpoints within two genes, resulting in fused genes (eg: A and D are now fused): Gene fusion
89
when does combination occur
during meosis I (crossing over of homologous chromosomes)
90
consequences (germline) of inversion
- during meiosis in order to line up properly with its homolog, part of the chromosome has to loop out (formation of an inversion loop)
91
what happens to crossing over with paracentric inversion
- eterozygote, the result is a dicentric chromosome (a chromosome connected by two centromeres)
- can lead to deletions: The chromosomes try to segregate, but the dicentric chromosome breaks randomly and a chromatid (that wasn’t attached) is lost
SUMMARY:
Crossing over in a paracentric inversion heterozygote —>
Dicentric chromosome —> Breakage —> Loss of acentric fragment --> dicentric bridge breaks randomly and products with major deletions
- acentric : no centrosome
- dicentric: has it
92
Clinical Consequences In Chromosomal Inversion Adult
- decreased fertility
- when germ cells undergo meiosis (as shown above), only 2/4 gamete are viable (the non-recombinant products)
93
Chromosomal Translocations explanation and consequences
- no gain/loss of genetic material
- can occur due to breakage or disrepair or cross over
- as long as break didn’t disrupt any haploinsufficient
genes, not many consequences somatically
94
name two segregation patterns in a reciprocal-translocation heterozygote
1. Adjacent segregation pattern: N1 and T2 migrate together (bad both incomplete)
2. Alternate segregation pattern: N1 and N2 migrate together (both good one normal one translocation making them viable)
95
Robertsonian Translocations what is it
- involve any of the acrocentric (one chromosomal arm is much shorter than the other due to positioning of the centromere)
- chromosomes: 13, 14, 15, 21, 22
- long ones bind = survive
- long and short bind = survive
- short and short = get lost because not haplosufficient
96
explain Grape-Colour Genetics in relation with transposable element insertions are associated with changes in grape colour
- insert LTR retroelement = LOF of green pigment because insertion in regulatory region
- recombination LTR: leaving only a small insertion behind
- This insertion is enough to not allow pigment to be expressed at a normal level (resulting in red colour, an intermediate)
97
what traits can we map on chromosome 9
- Colour
- Shrunken
- Bronze
- Waxy
chromosome 9; recognizable with its distinct knob at the end
98
difference between embryo and endosperm
- Endosperm (made up of many cells); where we see the traits; fertilized by sperm cell (n) and central cell (2n)
- Embryo; what’s growing inside; fertilized by sperm cell (n) and egg cell (n)
99
explain hypothesis where C1 allele is lost in some cells of the developing endosperm, no longer blocks C function (corn)
loss of C1 alleles is caused by chromosome breakage
- done on chromosome 9
100
are breakage random? do they always happen at the same place? what is needed? (corn)
no, they always happen at the breakpoint (Ds = dissociation locus)
- also, Ac locus is also needed on other chromosome
101
what does it mean for alleles if breakage occurs or not (at breakpoint) (corn)
- break doesn’t occur, wild type alleles are present
- breakage occurs, you’ve lost the wild type alleles and recovers recessive mutant phenotype
102
are Ds and Ac mobile? to the same degree?
Yes both are mobile.
NO:
1. Ds requires Ac to “jump out” (ie: transpose); Non- autonomous
2. Ac jumps out on its own; autonomous (encodes it’s own transposition machinery)
103
what does different spots in kernel mean about when they get activated
earlier activation results in a larger spot, while later activation results in a smaller spot.
104
name the two classes of transposable elements
- Class 1: Retrotransposons (eukaryotes)
- Class 2: DNA transposons (prokaryotes and eukaryotes)
105
which class does Ac and Ds belong to of transposable elements
DNA transposons
- each has a transposes version specific for its own family
106
explain process of class 2 tranposons getting cleaved and by who (corn)
-Ac and Ds have enzyme in the middle of them that catalyses reaction
- two end of inverted repeats of each other
- Transposase binds to repeats, cleavage event, breakage releases intervening sequence
- insertion into target protein
107
explain how class 2 retrotransposons occur, form and give examples
- similar to retrovirus
- Have LTRs
- Have pol gene; replicates viral genome
- Have env gene; viral envelope needed for the cell to produce more virus
- Have gag gene; protein antigen on viral coat
TE: have everything except env
- EX: LINE (long interspersed element) is a retrotransposon found in the human genome or SINE
108
Can retrotransposon move through an RNA intermediate? if yes, how?
yes
- this transposition is mediated by reverse transcriptase (encoded by pol gene) NOT THE TRANSPOSASE
- copy-paste mechanism
- Makes a double stranded transposon genome that goes back into the nucleus and with LTRs can insert into the genome
109
where are TE located
- in introns or intergenic regions
- low risk of potential harmful effects because its in between cells (because it isn't in ORF which would be lethal = selection for fitness and viability)
110
are genomes with more TE bigger or smaller why.
bigger: larger the genome, the larger the percentage of transposable elements
111
what happens if TE is introduced in exons instead of introns
many disease mutations :
- could disrupt slipcing:
insertion of an AluYa5 element in a patient with Dent disease (a rare genetic kidney disorder) interrupts an exonic splicing enhancer, resulting in skipping of an exon 11 producing a stop codon in exon 12
112
how are TE associated with cancers
- their mobility can destabilization of the genome causing tumour formations
- this is why they're highly regulated and cells have mechanism to repress them
113
is TE mobility always bad? (moths)
NO! can be an positive adaptive change:
- Dark pigmentation is caused by TE insertion into a gene in moths
- this is beneficial for them
114
discuss drosophila P-elements
- class 2
p-elemnts are TE
- discovered mating lab and wild caught flies
- lab female x wild male
- F1 could not produce any offspring due to mutations and non-disjunction
RECIPROCAL CROSS:
- lab male x female will
- they were fine suggest that there's a mechanism that blocks transposon mobility
- key is the female germ line
- p-element from male moves and infers female germline
- this is silences if the female is wild-caught
115
how many spontaneous mutations are due to TE of LINE or SINE
1/600
116
explain TE in c.elegans and work and discuss experiment they did (somatic vs germline)
- C elegans also have TE
- Tc1 element: An autonomous DNA transposon (class 2
- Tc1 elements transpose in somatic cells but not
germline cells meaning the germline contains some sort of silencing machine that represses tc1 mobility
117
how can we find TE
if we knock out a gene involved in repressing TE mobility, then TE will be able to move
- Figuring out which gene is mutate in such a train will identify a part of the cellular machine that represses TE
mobility
118
discuss a time where TE mobility was good. (not moths)
c elengans for twitching
- Tc1 insertion in the unc-22 gene (disrupting it)
- If the Tc1 mobilizes/jumps; the worm can move smoothly
119
what type of genes are involved in blocking Tc1 mobility.
RNAi silencing
120
describe RNAi silencing pathway
- derived from dsRNA precursors
- Once fully processed, miRNAs bind to RISC complex
- RISC complex has a single nucleotide (miRNA) strand that targets RISC destruction complex to the transcript it is programmed to silence
- cause degradation via deadenylation or block translation
- this processes also includes dicer which does the cleaving
121
difference between endogenous and foreign gene.
- miRNA: endogenous gene
- siRNA: foreign gene (transgene, virus, TE)
122
describe the process of dicer/RISC complex (end part)
- Tc inserted normally in the genome (not next to any cellular
genes), the TIRs are not transcribed (only the transposase gene)
- Tc directly adjacent to a cellular gene and the cellular gene gets
transcribed, the TE and it’s TIR’s are transcribed
- complementary
stem loop forms between the TIR’s of the mRNA transcript
- Dicer recognized the stem loop, chops it up and programs it into the RISC complex
- RISC complex can now find any transposase transcript in the genome and target it for degradation
123
what are piRNA. explain mechanism.
- repress transposon mobility in germ line of Drosophila
- blocks the transcripts coming from the TE
- are NOT derived from dsRNA precursors
- Like siRNAs, piRNAs are short single-stranded RNAs that interact with a protein complex that destroys complementary target mRNAs
124
what does pi-cluster mean
- Pi-cluster: RNAs that participate in destruction complex are made here (the programmed transcripts)
125
explain what piwi-argonaute is and what mechanism it belongs to
- piRNA
- Piwi-Argonaute is programmed with sequence information and destroys mRNAs
126
explain Three Different Scenarios for TEs Mobility (active/inactice area?)
1. TE is inserted into an inactive area; not transcribed in the first place
2. inserted into active: gets transcribed, BUT is present in pi-cluster so gets degrades by Piwi argonauts
3. inserted into active: gets transcribed, NOT yet inserted into pi- cluster can be mobile
127
explain piRNA in male/female lab/wild type
- piRNAs are present in P-strain (wild caught) but not M strain (lab strain)
P-female x M-male: F1 are fertile
- P-female chromosome has P-elements in her pi cluster (piRNAs in her eggs that block transposition in the germline of the embryo)
128
what gene I sable to repress TE activity. explain mechanism in drosophila
p53 (plays a role in repressing TE mobility)
- TAHRE is the retrotransposon in drosophila
- little TE transcripts when p53 is rescued (due to p53’s silencing)
- a lot of TE transcript when p53 is mutant
- Human p53 corrects disregulated transposon activity in p53- flies, but p53 variants commonly seen in cancer patients do not
- cancer alleles don’t block TE mobility
129
where do most mutations occur
somatic cells
130
can mutations be inherited
- mutations that occur in the formation of gametes can be inherited
- In 50% of the offspring, they carry the mutation
131
describe 3 categories of mutations
- Chromosomal mutations: Gain or loss of all or part of a chromosome (deletion; duplication; inversion;
translocation)
- Insertional mutations: Insertion of large regions of DNA (TEs)
- Point mutations: Changes in a single nucleotide or addition/deletion of one or more nucleotides (as long as
they are small)
132
2 groups of point mutations
1. Base substitutions
- Transition: Purine—> Purine; Pyrimidine —> Pyrimidine
- Transversion: Pyrimidine —> Purine; Purine—> Pyrimidine
2. Base additions and deletions (indels)
133
The Consequences of Point Mutations in ORF
1. Synonymous Mutations
- Silent mutations (sequence change
but not the amino acid it encodes)
2. Non-synonymous Mutations
- Missense mutations (sequence change of a codon to one that codes for a different amino acid)
- Can be conservative (amino acid similar) or non-conservative (chemically different amino acid)
3. Nonsense Mutations
- Change the sequence of a codon to one that stops translation (stop codon; UAA; UGA; UAG) - Effect depends on distance from 3’ end of the ORF
- Can trigger nonsense-mediated decay (NMD) which degrades the mRNA
4. Frameshift mutations
- Caused by an insertion or deletion
- Changes the reading frame for all codons downstream of the mutation
134
discuss Point Mutations Different Effects; Depending on Their Location and Type of Mutation
1. LOF (partially or completely lost)
- Hypomorphic: Weak/partial —> retains some function or produced at reduced level
- Null: Protein is non-functional or not produced
ex: p53 mutations eliminate function
2. GOF: (gene function increased)
- Hypermorphic: protein is hyperactive
- Ectopic: More protein is made in wrong time/place - Neomorphic: Protein gains new function
ex: mutation in ras gene make them constitutively active
135
discuss example of Sequences in Non-Coding Regions can be Important for Gene Function
Mutations in non-coding regions can disrupt:
- Transcription - Splicing
- Stability
- Translation
- function
- if mutation in promoters or enhance = compromises ability of the gene to be expresses
136
why can point mutation affect splicing
Can make new splice sites or eliminate existing splice sites
137
explain how Same Mutation and Different Prognoses
- can have additional mutation correlated, worsening the situation
- PBRM1 gene has BAP1 which creates stop codon = terrible
138
difference between northern and western blots
- Northern blots look for RNA
- Western blots are looking at protein
139
what is Electrophoretic mobility and what does it depend upon
- position on a gel
- reflect size, and band intensity reflects the amount present
140
can mutations be Spontaneous or Induced
both:
- Spontaneous: Occur naturally, arise in all cells (due to errors in DNA replication and chemical changes in the DNA)
- Induced: Caused by exposure to ionizing radiation, mutagenic chemicals, etc, which increase the rate at which mutations occur
141
how many mutations do we carry in our DNA
100-200 new mutations in our DNA
142
discuss errors in base pairing and give example
- no prrmfreadin : mismatch
- relevant during replication because conversion between tautomers happen all the time
- BUT if polymeriase adds complementary nucleotides, its bad
EX: If Guanine is in its enol form, DNA Pol. adds a T instead of a C (because that is the complementary pairing to the enol guanine)
143
what is a tautomer
- isomers that differ in the positions of their atoms and in the bonds between the forms; the forms are in equilibrium
144
difference between incorporate terror and replicated error
- Incorporated error: can still be repaired (G reverts to its normal form, and mis-match it recognized and repaired)
- Replicated error: permanent
145
how do spontaneous mutation occur
- Strand slippage during DNA replication leads to indels
2 ways of insertions/deletion:
- Newly synthesized strand looping out causes
insertions
- Template strand looping out causes deletions
146
give an example of slippage
- Trinucleotide repeat disorders (expansion of
of repeated sequence) (prone to slippage)
- If they loop out; they get duplicated or deleted
- high # of repeats (n) = high slippage = more expansion (more n)
147
explain fragile x syndrome
- Trinucleotide repeat expansion in non-coding region of the FMR1 gene
- Normal: <45 repeats of CGG
- > 200 repeats = methylation occurs and gene no longer transcribed
148
explain Huntington disease
- Trinucleotide repeat expansion in coding region of the HTT gene
- >40 repeats the mutation is severe
- genetic anticipation; gets more severe with each new generation)
- More expanded repeats means a more severe allele
149
3 things that can cause spontaneous chemical changes to DNA
1. Deamination of cytosine: Structure becomes identical to uracil (and thus binds to A)
2. Depurination: Nucleotide loses its nitrogenous base and left with apurinic site (there is no base pairing
possible)
3. Oxidative damage: Causes by byproducts generated by mitochondria
150
explain induced mutations. explain the 3 mechanism
- Mutagens can induce misfiring or damage/non-recognition
1. Replace a base in the DNA (base analogs get incorporated instead; look like a DNA base)
2. Alter a base so that is mispairs with another base
3. Damage a base so that it can no longer base pair with any base
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what does UV light do
- Base damage
- UVB light can induce covalent interactions between adjacent pyrimidines
- If not repairs, this can block DNA replication
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what does radiation do
Cause breaks in the DNA; make the DNA very vulnerable to insertions/deletions/inversions/etc.
153
explain Ames test
- test if chemical causes mutations
- take a bacteria that is unable to grow withtou histidine (auxotroph)
- feed it chemicals until you see that one makes it grow again
- that chemical caused a mutation in the genome of the bacteria a
154
problems with Ames test
- in humans, some chemicals can only be activated when they are metabolised
- originally may not do anything unless they are metabolized
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what is the better version of the Ames test after discussing the problem with it
- add liver enzymes to test chemicals that might become mutagenic only when metabolized
2 strains used:
- Strain 1 = His-transition mutant (point mutation)
- Strain 2 = His-frameshift mutant
- we see that strain 1 has more revertant rate = can infer that the mutagens causes point mutations
156
explain how we can predict is and ORF corresponds to a real gene
- look fro ORF (can codes transcribe without hitting stop codon too early)
- is ORF conserved? (means important sequence)
- look for cDNA: mRNA and the RT makes cDNA
- compare cDNA sequence to the predicted ORF
- If cDNA sequence matches the predicted ORF = means that at some point, the gene was turned on and its mRNA was made in the cell
157
what is EST
Expressed Sequence Tag is a cDNA that has - not been completely sequences
158
how can use codon bias to check if and ORD was part of a real gene
- this codon preference reflect relative tRNA abundance and can be a signature of an ORF that’s part of a real gene
- If a predicted gene uses a common codon; hint that it might be part of a real gene
159
explain difference between comparing within organism , individuals of same species, between organism.
- within an organism: identify gene families and gene duplications
- individuals of the same species: identify differences associated with phenotypes or disease
- between organisms: different types of genes and their arrangement in the genome and to infer information about genome structure and evolutionary processes
160
does mutations aossicated with disease affect coding or non coding regions of genes
coding
161
discuss further comparing Sequences Within a Species
- reveals families and related genes
- Related genes within an organism that encode proteins of similar amino acid sequence
- Can contain 2 to >100 members (called PARALOGS)—> In the same genome (beta tubulin vs. alpha tubulin)
- Members can be functionally redundant or have independent functions
- Can arise through gene duplication during evolution
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how do we identify diseased genes. do we take the whole genome?
no, we look at exome
- contains all the protein-coding genes (non-coding region not included)
- more cost efficient this way
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what is synteny. give example
The conserved order of genes between the two genomes
- 99% of mouse genes have a homolog in the human genome
- Overall genome organization, including the relative order of genes and non-coding regions, is also highly
conserved
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difference between orthologs and paralogs
- Orthologs: Homologous genes at the same genetic locus in different species, evolutionary inherited from a common ancestor (frog A, human A, mouse A)
- Paralogs: Homologous genes at different loci in the same species, having arisen from gene duplication (mouse A and mouse B)
165
what is uni-parental disomy. discuss consequences
getting 2 copies of chromosome form 1 parent
- Non-disjunction; two copies in one gamete; gives rise to a trisomic zygote
- Randomly, one of the extra chromosomes get lost (trisomy rescue) —> reversion to disomic
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why does every cell in our body have the same DNA sequence
- they all get made by blastocyst which differentiate into different cells of our body (muscle, neurons..)
- What makes each cell type unique is largely determined by the expression of specific subsets of tissue-specific genes (mostly controlled at the level of transcription)
167
discuss gene expression in prokaryotes
- dna is nacked (not wrapped in histones)
- transcription initiation is a main regulator process
- Many prokaryotic metabolic genes involved in the same process (eg: same metabolic pathway) are organized into operons
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what are operons
one transcript unit coding for multiple proteins under a single promoter
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name 2 promoter sequences in prokaryotic genes + start codon
- TTGACAT: -35
- TATAAT: -10
- - ATG start codon (Met)
- Upstream is +1 nucleotide (first one incorporated into mRNA), transcription start site
- Everything between +1 and ATG: 5’ UTR
- Promoter: Where regulation takes place
170
Discuss RNA polymerase in prokaryotes
- RNA polymerase binds to -35 and -10 promoting paper position of holoenzyme (mili-subunit)
- RNA polymerase easily binds the promoter; default state of genes is “ON” (a bit...)
- Sigma factor finds sequences relatively easily since no other proteins associate with the DNA
171
DNA binding proteins can activate or repress gene when? where? what?
- depending on where they bind
- operator: binding sites for suppressor genes
- activating bringing site = positive regulation
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describe allosteric regulations and what they bind to in activator or repressors.
- Allosteric site in the protein binds to an effector;
ACTIVATOR:
- no effector = gene off
- effector = gene on
REPRESSOR
- no effector = gene off
- effector geen on
- Effectors: Sugars, amino acids, small chemicals, sometimes other proteins
- Effector is called an “inducer” if its presence leads to increased expression; effector can turn on an activator or also turn off a repressor
173
discuss the enzymes and regulatory components of la operon
- Bacteria want to metabolism lactose into glucose
Enzymes:
- LacY (permeate) —> Pumps lactose in
- LacZ (B-gal) —> Breaks it down
Regulatory components:
- Repressor protein (LacI) —> Not part of operon - LacO (operator)
- LacP (promoter)
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describe lac operon and how it works
- inducible: lactose will turn on expression of lac operon
- repressor: protein block RNA polymerase
- lactose binds the repressors allosteric site to allow RNA polymerase to transcribe
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how can we uncover the regulatory mechanism of lac operon using chemical in the lab?
- used mutagenesis: treat E.coli with chemical mutagens
- measure B-Gal and/or Lac permease activity in presence and absence of a synthetic inducer (IPTG) —> Looks like lactose
- Selected mutant strains where one or both of these activities was altered
176
describe 3 classes of Jacob and Monod’s Lac Mutants (synthetic lactose experiment)
1. structural gene mutations (affect function of only one gene cannot function)
2. uninducile (cannot make LacY or LacZ in presence of IPTG = failure to activate any of them)
3. constitutive mutants (makes both LacY or LacZ in presence of IPTG= cannot turn them off)
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explain partial diploids in IPTG experiment replacing lactose
- "partial diploid" bacteria containing a plasmid with an extra copy of the lac operon (diploid lac operon)
- second copy of lac operon is often carried on a plasmid
- test for domincane/ recessiveness
- helps us determine cis/trans:
Cis: Mutation only affect transcription of genes on same DNA molecule (often a regulatory element)
- Trans: Mutation can also affect transcription of genes on the other DNA molecule (on other copy)
178
explain lac operon regulations (p-mutations) and cis/trans
p-mutation results in failure to activate gene expression ( indelibility of both B-Gal and
Permease)
- P+Z+Y+/F’P-Z-Y-: original has inducible promoter, but mutant makes it loose that ability (P-) = cannot act in trans
- P- acts in cis
-
P-Z+Y+/F’P+Z-Y-: original had P- but promoter was able to restore its ability making It act in cis
-
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DISCUSS LAC OPERON REGULATIONS: O MUTATIONS (operator)
O- = Oc (constitutive): Both B-Gal and Permease
are constitutively active
- repressor portion can't bind (can't be turned off)
- Oc/Z-/Y- doesn’t affect regulation of O+Z+Y+; inducible
- o mutations only works in cis WTF WHY
180
discuss Lac Operon Regulation: I- Mutations
- similar to O (always on)
- Won’t make functional repressor protein; genes expressed even in absence of lactose
- +/Z-Y- and F’I-/Z+Y: Inducible: Repressor from I+ will be made and will bind to the operator on I-/Z+/Y+
- I doesn’t have to be on the same DNA molecule, can act in trans (a diffusible molecule)
181
how to solve questions about lac operon mutations...
- First check Z and Y
- Second check promoter
- Third check O
- Fourth check I
182
discuss Lac Operon Regulation: I^S Mutations “Super-Repressor”
- always reposed no matter what (even if wild type I is present)
- Mutating the allosteric site of LacI, repressor can’t bind lactose to be turned off
- I^S is different from I-; it cannot be complemented by I+ (ie: it’s dominant to I+)
183
What would be the phenotype for the following lac operon partial diploid?
I+ P+ O+ Z- Y+/F’I+ P- Oc Z+ Y-
- Z is uninducible (Z- and P-)
- Y is inducible (left chromosome is completely functional for Y+
184
explain when lac operon is under positive regulation (CAP and cAMP)
bacteria likes glucose > lactose (doesn't ned to break it down less wasteful)
- glucose regulates cAMP levels (high glucose means cAMP inhibited)
- cAMP: allosteric regulates of CAP (coded by crp gene and Called Catabolite activator protein)
- no cAMP= no DNA binding
- CAP-cAMP binds promoter just upstream of RNA Pol.
- Facilitates RNA Pol. binding to the promoter to increase transcription
185
explain all 3 scenarios of lac operator regulation (glucose absent, lactose present....)
1. Glucose present; no lactose (low cAMP inactive CAP = no activation)
- repression = no lac mRNA produced
2. Glucose present; lactose present
-glucose present = (low cAMP inactive CAP = no activation)
- HOWEVER no repression because lactose is present
- Very little lac mRNA produced
3. Glucose absent; lactose present
- high cAMP active CAP = activation
- no repression
- Abundant lac mRNA
186
what is the default state of transcription for bacterias and eukaryote
- Default bacterial state is on (a bit)
- Default eukaryotic state is off (completely)
- Bacterial have simple group of proteins; repressor, activator, CAP
- Eukaryotes have many components to transcription
187
whats an enhanceosome
Sum of proteins + enhancers + folding; allows enhancer to be close to promoter
188
discus transcription Initiation (cis-acting or trans-acting proteins? DNA sequence?
1. Cis-acting DNA sequences
- Core promoter
- Promoter-proximal elements - Enhancers/silencers
2. Trans-acting Proteins
- General transcription factors
- Common transcription factors
- Cell/tissue-specific transcription factors
- Transcription co-factors; cofactors have no DNA binding domains and thus depend on those of a transcription factor
189
does transcription need enhancer sequences. describe these sequences
yes
- Distance-independent cis-acting DNA sequences
- can be far or close or in introns
- Bind DNA in a sequence-specific manner through DNA-binding domain
190
what are some influences of transcription
- Interacting with transcription apparatus (directly or indirectly)
- Influence chromatin structure opening/closing (directly or indirectly
191
what mutation is associated with OPN1-LW gene - explain skewed / 50/50
red-green blindness (check notes)
192
what x -linked disease is only seen in heterozygous female
rett syndrome (only mut/+ females are viable)
193
what is methylation of DMNT associated with
occurs on cytosine of CpG
194
is dna methylation inheritable
yes
195
what do DMNT have high affinity for
hemimethylated sites (only one is methyl) goes in and fixes it
196
describe IGf2 mutations
- dominant
- heterozygous things born small, only if got mutation from father
197
describe silences alleles and how it occurs
- if you get silenced allele it doesn't matter if its mutated or not
- occurs through methylation to the "imprinted" or silenced gene
198
whats an example of ICR (imprinting control region)
-CpG island
199
describe IRC methylation in father mother
father: only sex-specififc methylation of ICR: methylation prevents CTCF binding: methylation of H19 and enhancer turns on Igf2 gene
mother: non-methylation: allows CTCF to bind (acts as a insulator) regulates H19 and does NOT turn on IGf2
200
what is mono-allelic inheritance
- as if there's only one copy in the cell
- silneced/mutant gene is mutant: nothing happens
- normal one gets mutated: does matter
201
mechanic leading to a disorder associated with an imprinted gene
1. mutations affecting non-imprinted gene
2. epimuttaions ( histone tail or DNA methylation)
3. uniparental disomy ( non-disjunction , robersonian carrier..)
202
mitochondrial diseases diff in genes
987: come from mendelian fashion
13: come from the maternal/cytoplasmic fashion
203
what is neurospora
follows rules
poky: motherly inherited
ad gene: follows mendelian and is inherited independently to the mother one
204
explain heteroplasty in mtDNA mutations
- mtDNA is more likely to have mutations because they have more frequent DNA replication + no DNA repair mechanism
- spontaneous mtDNA leads to 2 distinct mt populations within a single cell
205
what happens if your mom is heteroplasmic mutated. like what does it mean for child
- means that mother has both affectes and unaffected mitochondria
- has a possibility of being normal due to random segregation
206
what were Heidelberg screens used for
- mutations disrupting early embryonic pattern
- did forwards genetics to see what genes were involved for organizing drosophila
207
what is the order of the genes (5 groups): cascade of TF that regulate drosophila
1. Egg-polarity event (maternally loaded)
2. gap genes
3. pair-rule gene
4. segment Polarity gene
5. homeotic genes
208
what is bicoid and what does it do
- lack anterior segments
- code for anterior things like head
- diffuse towards posterior to create a concentration gradient providing info about distances relative to anterior position
- hunchback is in the anterior and nanos will inhibits translation of hunchback
209
name eve proteins and what they do
- giant (expressed in front of gene)
- kruppel (expressed in back)
- both act as repressors
- hunchback proteins + bicoid : high levels act as activator (middle of protein)
210
discuss segment polarity and what it encodes for
- encode components of two cell-cell signalling pathways : hedgehog and wingless
211
give example of homeotic mutations
- Ubx: second third and set of wings in place of halters
- Antp: legs instead of antenna
212
humoral vs cellular immunity
- humo: production and secretions of B cells
- production of T cells (bind to antigen found on surface of their own body)
213
adaptive vs innate immunity
- adapt:antigen specific defense (T and B cells)
- Innate: quicker and non-specific (macrophages and neutrophils)
214
vaccines
use RNA vaccines using host cell to produce antigens which is must faster
215
light chains types and segments
kappa and lambda (cant be kappa/lamda)
- segments V, J and C
- binds to antigen
216
heavy chains types and segments
alpha, gamma, delta, mu, epsilon
- V, J, D and C
0 doest bind antigen specifically
217
describe somatic recombination
RAG1 RAG2 and DNA repair enzymes will dsDNA break and join random V and J producing DNA found in mature B cell
218
common inherited cancers
hereditary breast/ovarian: BRCA1 and BRCA2
LI-fraumeni: p53 gene
Retinoblastoma: RB1 gene
Familial andenomatous polyposis: APC gene
219
how is v-src hyperactivated
c terminus is deleted thus the kinase can no longer be regulated
220
what single point mutations can drive Ras to tumorgensis
Gly-Val
221
explain CML
fusion of chromosome 9 and 22 (philedelphia chromosome))
- BRC and Abl: BRC will hyperactive kinase (Abl) activity
222
which chromosome is often partially deleted in chromosomal actity found in retinoblastoma
chromosome 13
223
whats RB1
- 1st tumor supressor gene
224
are oncogenes and TSG both inherited
no, oncogene
yes , TSG
225
p53
dominant negative (explain)
226
HPV
DNA tumour virus (binds and inactivates TSG and promotes environment favourable for virsu)
227
loss of TSG p53 causes what
malignant tumour
228
activation of oncogene Ras causes what
benign tumour
229
whats PD-1 and how do cancers use it
it is a receptor for T cells
- T cells are inactivated when a ligand binds to their PD-1 receptor to avoid hyperactivity (we stop it when we don't need it)
- cancers were able to suppress T-cell functions by expressiong PD-1 ligand (inhibits T cells which attack foreign things)
230
which chromosome has the receptors for the measles virus
chromosome 1
- also measles cannot infect rodents they don't have the receptors for it
- some humans
231
explain how viral genomes are derives (2) AND EXPLAIN
1. derived from Adenovirus (DNA)
- infects all cells even non-dividing ones
- vector not integrated in genome
- transgene diluted and lost (not permanent)
2. derived from retrovirus
- infect dividing cells (HIV can infect without cell division)
- trasngene and vector will be incorporated ( permanent )
232
describe ADA-SCID
autonomous immune disease
- deoxyadenosime accumulates in your T-lymphocytes and kills them
- treatment : bone marrow transplants
- T-lymphocytes = responsible for stimulation of your B lymphocytes (antigen production)
233
what is the mutation that causes 5% of RP
RPE65 gene
234
Retinis pigmentosa
RP cells in the retina break over time causing tunnel vision
235
how to solve RP
- make vector from functional RPE65 gene into RPE with mutations to compensate
236
CRISP
uses RNA molecule that corresponds to target DNA sequence
- just change crRNA to target different things
- increasing expression of w+ copy, will changing the original mutant to a w+
237
explain how iPS works and example
induced pluripotent stem cells
-overexpressionf o 4 TF: Oct3/4, Sox2, c-Myc, Klf-4 in fibroblast is sufficient to reprogram the cells to beep,e pluripotent stem cells
- dont have to worry about immune response
