Exam 2 Flashcards
(144 cards)
0
Q
Multifactorial traits are also called…
Multifactorial diseases are also called…
A
Quantitative traits; Complex diseases
1
Q
Define Penetrance
A
Risk of being affected when you have a risk increasing gene
2
Q
What is an isoform?
A
different versions/forms of a protein that may be produced from the same gene due to alternative splicing, alternative promotors
3
Q
Phenocopies occur due to…
A
non genetic factors alone
4
Q
Hemochromatosis risk is a…
A
functional polymorphism of the HFE gene
5
Q
Risk for a disease can be ________ despite the disease being a _________ trait.
A
continuous; threshold
6
Q
What is VARIANCE? How is it calculated?
A
S^2: how far distribution spreads from the mean
Calculated by finding the average squared distance from the mean:
1) Subtract individual scores from the mean
2) Square each of the differences
3) Sum the squared differences and divide by n-1
7
Q
What is STANDARD DEVIATION? How is it calculated?
A
S; square root of the variance
8
Q
What percentage is included in 1SDs, 2SDs, and 3SDs of the mean?
A
1SD=66%
2SD=95%
3SD=99%
9
Q
What is the range of the correlation coefficient? What does it mean if it is zero?
A
-1 to +1; 0=no correlation
10
Q
What does regression allow you to do?
A
Predict the value of one variable given the value of the other
11
Q
In a line of best fit, the slope represents…
A
The value of the regression coefficient.
12
Q
Define all of the following: Vp Vg Ve Vge Va Vd Vi
A
Vp = variance due to population Vg = variance due to genetic factors Ve = variance due to environmental factors Vge = variance due to interactions between genetic and environmental factors Va = additive genetic variance (how much offspring resemble parents) Vd = genetic variance due to dominant alleles Vi = variance due to interactions between gene alleles (like epistasis)
13
Q
How do you calculate Vp?
A
Vp=Vg+Ve+Vge
14
Q
How do you calculate Vg?
A
Vg=Va+Vd+Vi
15
Q
What are all the variables that contribute to Vp?
A
Vp=Va+Vd+Vi+Ve+Vge
16
Q
What is broad sense heritability and how is it calculated? What is its range?
A
H^2; Portion of population variance due to ALL genetic factors;
Calculated using Va, Vg, Vi
Formula: Vg/Vp = (Va+Vg+Vi)/Vp
Range: 0 to 1
17
Q
What is narrow sense heritability? How is it measured? What is its range? What is another thing that this equals?
A
h^2; Proportion of variance due to ADDITIVE genetic factors (Va);
Formula: Va/Vp
Range: 0 to 1
Also equals the REGRESSION COEFFICIENT when (uparents, uoffspring)
18
Q
What does it mean if Va is low?
A
Offspring do not resemble parents; other factors (like food) must contribute more heavily to phenotype
19
Q
Va give you a…
A
Nice, normal distribution
20
Q
You can study genetically identical twins to eliminate _______ meaning that all variability is due to _______.
A
genetic variance (Vg); all variability is due to nongenetic factors (Vp=Ve)
21
Q
How do you calculate broad sense heritability for the F2 generation?
A
Vg/Vp=(VF2-VF1)/VF2
Because VF2=Vg+Ve
and VF1=Ve
Vg+Ve-Ve/)(Vg+Ve)=Vg/(Vg+Ve)=Vg/Vp
22
Q
Using MZ and DZ twins, how to you calculate broad sense heritability?
A
H^2=2(rMZ-rDZ)
Where r represents the correlation coefficient between the twins PHENOTYPES
23
Q
What is a selection differential? What symbol is used to represent it?
A
Difference between mean phenotype of the individuals chosen for breeding versus the total population’s mean
= Mean(parents)-Mean(population)
Symbol=S
24
How do you calculate response to selection? How is this used to calculate the new mean of the population?
R=h^2xS
where R=response to selection, S=selection differential
Long Form: R=(2(rMZ-rDZ))(Mean(parents)-Mean(population))
New Mean=Original Mean+Response to selection
New Mean=Original Mean+(h^2)(breeder's means - population mean)
25
What limits the phenotypes produced by selective breeding?
Genes becomes fixed (exist at 100% frequency) because the environment might select against a very extreme version of the trait.
At this point, there is no more additive genetics inheritance (h^2=0)...which means R=(h^2)(S)=0
26
Heritability tells you...not...
Heritability tells you what FRACTION of the VARIANCE is due to genetic factors, NOT THE DEGREE to which a trait is determined by genetic factors.d
27
Heritability is specific to a particular ______ and ______.
Population and Environment
28
Heritability never applies to _____
Individuals
29
Define INBRED vs OUTBRED
Inbred: Genetically identical (Vg=0)
Outbred: Genetically non-identical (Vg is not 0)
30
What formula is used to estimate the number of genes that influence a trait?
(1/4)^n
| where n is # of genes
31
Which of these is not like the others? (in regard to genes involved)
"more than 3" "at least 4" "3 or more"
"3 or more" because it includes 3 as a possible answer
32
Which is more detailed: GWAS or QTL?
QTL is a more detailed analysis that allow you to identify genes that influence a trait or disease
33
Two ways to identify QTLs:
Linkage Study: within family approach
| Association Study: between groups approach (case vs control group)
34
What is a GWAS?
genome wide association study; uses markers from all over the genome
35
What has 100% penetrance?
single-gene disorders
36
Incomplete dominance= ______
| Codominance= ________
Blending; spots
37
Explain how types of dominance can be different at different levels of analysis.
Incomplete dominance at cellular level (Aa produces lower level of a protein per cell), BUT recessive at clinical level (must have aa to express the disease, as Aa still makes enough of the protein to be functional).
38
What is the difference between dominant and recessive epistasis?
Dominant Epistasis: requires only one (heterozygous expression of) epistatic gene to cover expression of hypostatic gene -- Example: Corn kernel color
Recessive Epistasis: requires homozygous expression of epistatic gene to cover expression of hypostatic gene -- Example: Coat color in retrievers
39
What type of epistasis is blood type?
Recessive Epistasis
40
What genotype(s) yields the BOMBAY PHENOTYPE in blood?
hh with any combination of I alleles (can be IA_, IB_, or ii)...because compound H (dominant) is needed to bind to the terminal sugar that produces type A or B or O (non-bombay)...However, blood type is an example of recessive epistasis because two hh alleles is needed to cover the expression of the hypostatic gene (IA, IB, or ii)
41
What is duplicate recessive epistasis? What is an example of this?
Both genes capable of being epistatic gene if either one occurs in homozygous recessive form; a certain type of albinism (can be missing gene for tyrosine transporter gene or missing gene for enzyme tyrosinase, which makes melanin from tyrosine)...you need both to have pigment in your skin.
Both aaB_ and A_bb produce albinism
42
What is an allelic disorder?
Different mutations in the same gene produce different phenotypes.
Example: mutations in grown factor 2 receptor gene cause 3 different syndromes
43
What is pleiotropy? Give an example.
One gene influences multiple traits.
| Example: same gene that gives siamese cats their coat color makes them have crossed eyes
44
Differentiate between SEX LIMITED and SEX INFLUENCED characteristics.
Sex Limited: Only appear in one sex (zero penetrance in one sex)
Sex Influenced: Appear in one sex more than the other
45
What is cytoplasmic inheritance?
Must come from mom, because a zygote gets all of its cytoplasm from mom...remember, dad ONLY CONTRIBUTES DNA (this is why the sperm is so tiny compared to the egg, as the sperm only has DNA and none of the organelles)
46
Define MATERNAL EFFECT genes.
A gene whose products are required for very early development of the embryo, such as the establishment of overall polarity of the embryo. These "maternal cells" disappear from the zygote after they assert their effects.
*Mutant genes not necessarily found in the offspring; only in the mother
47
Define MATERNALLY imprinted.
Maternally derived copy of gene is silenced; Paternally derived copy is active
48
What are the two types of UNIPARENTAL DISOMY? Define them.
Heterodisomy: a pair of NON-IDENTICAL CHROMOSOMES are inherited from one parent
- Meiosis 1 error
- If any genes on chromosome are imprinted, child will have either 0 or 2 active copies
Isodisomy: a SINGLE CHROMOSOME from one parent is duplicated and both copies are inherited
- Meiosis 2 error
- Can cause expression of recessive genes
49
What is GENETIC ANTICIPATION? What causes it?
each subsequent generation is affected more severely.
CAUSE: expansion of trinucleotide repeat sequences, which expand during meiosis
NOTE: as repeat expands (gets LONGER), there is LESS ACTIVITY in the gene
50
Define INCOMPLETE PENETRANCE.
The expected phenotype of a particular genotype is not expressed because of extra factors like environmental factors and effects of other genes
51
Differentiate between the EPIstatic and HYPOstaic gene.
Epistatic gene expression has the ability to cover expression of the hypostatic gene
52
When given a cross concerning two different characteristics (like hair color and hair texture), what is a good way to approach the problem?
Figure out the inheritance of each characteristic separately.
53
What ratio is usually associated with the presence of recessive lethal gene?
2:1
Example: The ratio of yellow:gray was found to be 2:1 --> We conclude that YY (yellow,yellow) is lethal
54
What ratio is associated for a trait that come from a cross between two heterozygous parents?
3:1
| Where the trait that is more common is the dominant allele
55
What tests can be carried out to test if a particular trait is recessive lethal? How about to test that (y) is recessive to (Y)?
If YY (yellow) is recessive lethal and is dominant to gray (y) then...
(Yellow)x(Yellow) --always--> 2/3 yellow, 1/3 gray
(Gray)x(Gray) --always--> ONLY gray
56
If your phenotype ratios are given out of 16, this is a hint that...
You are dealing with two alleles (even if there is only one trait)
57
How many replication forks in E. Coli?
| How many in human DNA?
2; MANY
58
Exonuclease activity goes in what direction?
3'--->5'
59
How many de novo mutations are there per child?
30-35
60
Differentiate between:
| Conservative, Dispersive, and Semiconservative Replication
Conservative: original DNA molecules STAY INTACT
Dispersive: original DNA gets FRAGMENTED and randomly recombined (like a mosaic)
Semiconservative: New DNA has ONE NEW strand and ONE OLD strand
61
Differentiate between the experiments by Messelson & Stahl and those by Taylor.
Messelson & Stahl:
Grew E. Coli in 15N (heavy) and then 14N
*Old DNA was heavy
Taylor:
First Round of Replication: Grew root bean tips in regular growth medium and then 3H (radioactive tritium)
Second Round: Back to regular growth medium
*Newly synthesized DNA was radioactive
62
What did Taylor use to dissolve spindle fibers? Why did he do this?
Colchisine
63
Theta replication occurs in...
organisms with circular chromosomes...like bacteria
64
In theta replication, how many origins of replication are there?
1
65
In theta replication, describe the direction in which replication occurs.
BOTH directions
66
In which type of replication are Ter and Tus sites used? What is their purpose?
Theta replication; Tus binds to Ter at one of the replication forks and the other fork comes to meet it
67
What is used to separate the two DNA molecules in theta replication?
Topoisomerase II -- makes a double stranded break
68
Rolling circle replications occurs in...
viruses and plasmids
69
What are the products of rolling circle replication?
Initially, 2 DNA molecules...but rolling circle replication can replete over and over again without stopping
70
In rolling circle replication, what strand is used as the template?
Inner strand
71
The OH is on the ___ Carbon; the PO4 is on the ___ Carbon
3' OH
| 5' PO4
72
In rolling circle replication, new nucleotides are added to the ____ end of the _____ (outer/inner) strand.
New nucleotides added to 3' end of OUTER strand
73
In rolling circle replication, the ____ end of the outer strand is pushed off.
5' is pushed off and used as a template to synthesize a new "inner" strand
74
What is GYRASE? What does it do?
Gyrase is a type of TOPOISOMERASE; its breaks the DNA strand outside the open region to relieve tension and allow the helix to open further
75
How do 4-quinoline antibiotics kill bacteria?
Inhibit gyrase...which then inhibits DNA from opening (and thus replicating) by inhibiting gyrase's ability to relieve tension in the DNA.
76
What is the role of PRIMASE in bacterial DNA replication?
lays down RNA nucleotides as primer; provides 3' OH group
77
What is the role of DNA POLYMERASE III in bacterial DNA replication?
chains bases together & proofreads itself
78
What is the role of DNA POLYMERASE 1 in bacterial DNA replication?
kicks out RNA primers and replaces them with DNA nucleotides
79
What is the role of DNA LIGASE in bacterial DNA replication?
knits all fragments together
80
What is the role of ALPHA polymerase?
lays down RNA primer and a few DNA nucleotides
81
What is the role of DELTA polymerase?
replicates LAGGING strand
82
What is the role of EPSILON polymerase?
replicated LEADING strand
83
What is the function of Chromatin Assembly Factor 1 (CAF1)?
helps DNA assemble back into proper orientation around nucleosomes
84
What does RLF stand for? What is its role in replication? Does it work in eukaryotic or prokaryotic cells?
RLF=Replication Licensing Factor
Role: REQUIRED for replication to begin; keeps origins of replication from replicating twice; contains a HELICASE and GEMINIM
Works in EUKARYOTIC cells
85
What does RLF (Replication Licensing Factor) contain? What is the role of each of these?
Contains HELICASE and GEMINIM.
Geminim:
- Stays behind when RLF is released during replication
- prevents another RLF from binding to the DNA
- Degraded in G1 (so replication can occur in S phase)
86
When is RLF released from the DNA? What stays behind?
Release in replication. Leaves behind Geminim.
87
When RLF attaches to the origin of replication it...
unwinds just a little bit of the DNA (it's required for DNA replication to begin)
88
Where does geminim come from? What attaches it to the DNA?
RLF leaves it on the DNA when it leaves during replication
89
When is geminim degraded?
G1 (so that DNA replication can reoccur in S phase)
90
Differentiate between GYRASE and GEMINIM.
Gyrase: a type of topoisomerase that cuts the DNA to relieve tension so that it can open enough to replicate.
Geminim: Left of DNA when RLF leaves; prevents another RLF from binding to the DNA and replicating a second time; degraded in G1 so that replication can reoccur in S phase
91
Why do telomeres continually get shorter?
When DNA polymerase 1 removes the primer at the 5' end of the lagging strand, it cannot fill the place with a DNA nucleotide because it cannot see a 3' oxygen to hang the nucleotide on
92
What end of the DNA strand is NOT VISIBLE by the DNA polymerase 1? What does this mean for that DNA strand?
Cannot see 3' OH; DNA end (telomere) will not be replicated and will be chopped off...shortening telomere with each replication
93
What substance helps to replicate telomeres?
telomerase
94
What is Werner's Syndrome? What causes it?
Premature aging; defect in RecQ helicase (an enzyme necessary for telomere replication)
95
The RNA part of telomerase is complementary to the __-rich strand on the telomere.
G-rich
96
Telomere is rich in what type of nucleotide?
G
97
How many origins of replication are typically in archaea?
Most have 1 (some have 2)
98
How are archaea like bacteria in terms of their DNA and replication mechanisms?
single origin of replication (though some have two)
99
How are archaea like eukaryotes in terms of their DNA and replication mechanisms?
Multiple initiator proteins with similar amino acid sequences to those seen in eukaryotes
100
What is the equivalence of the start codon (AUG) in the mRNA? (U's change to T's in mRNA)
ATG
101
When numbering autosomes, which number (1 or 22) is the largest?
1 is largest
102
Two meaning of karotype:
1) Picture of chromosomes
| 2) An individual's chromosome status
103
What is included in an individuals written karotype?
a) total number of chromosomes
b) sex chromosomes
c) any abnormalities
```
Examples:
Normal Female = 46, XX
Normal Male = 46, XY
Male with Down's Syndrome = 47,XY,+21
Female with Turner's Syndrome = 45, X
```
104
```
Types of banding: (What area do each of these types stain?)
G-banding
R-banding
Q-banding
C-banding
```
G-banding: AT rich areas
R-banding: CG rich areas
Q-banding: AT rich areas
C-banding: dense (heterochromatin) areas
105
How does numbering on a chromosome work?
Smallest numbers near the centromere (beginning as 11.1) and increasing as you move towards the telomeres
106
Define aneuploidy.
having ANY ABNORMAL number of chromosomes
107
Define euploidy.
Having THE NORMAL number of chromosomes
108
Define polyploidy. What are some types of this?
Having 1+ FULL SETS of extra chromosomes; haploid, diploid, triploid, tetraploid
109
Define aneusomy. What are some examples?
Having ANY ABNORMAL number of a SPECIFIC CHROMOSOME; nulsomy, monosomy, disomy, trisomy
110
What is a partial aneusomy?
deletions or duplications that include a large enough portion of the chromosome
111
Nondysjunction in somatic cells leads to...
mosaicism
112
Why are trisomies desirable in plants?
more chromosomes=larger plants, larger fruit
| Infertile= fewer seeds
113
NDJ in meiosis 1 leads to...
two trisomic gametes, 2 monosomic gametes
114
NDJ in meiosis 2 leads to...
1 trisomic gamete
1 monosomic gamete
2 normal diploid gametes
115
Differentiate between AUTO and ALLOpolyploidy.
Autopolyploidy: all chromosomescome from same species
Allopolyploidy: chromosomes come from 2 different species
116
Do autopolyploids produce unbalances gametes?
Yes
117
What are the three mechanisms of autopolyploidy?
1) NDJ of all chromosomes during MITOSIS in a 2n embryo --> creates an autotetraploid
2) NDJ of all chromosomes during MEIOSIS, which produces a diploid gamete that fuzes with a regular haploid gamete --> creates an autotriploid
3) Cross between an autotetraploid (produces 2n gametes) and a diploid (produces 1n gametes) --> Creates autotriploids
118
Define PSEUDOdominance.
individual loses the dominant allele and thus recessive allele is expressed
119
Define haploinsufficiency.
Losing one copy of the gene caused an abnormal phenotype because one working copy cannot make enough of the protein on its own
120
Define constitutive gene.
Always on; "housekeeping genes"
121
Where do promotor sequences often occur in bacterial genes?
-10 and -35 (from the transcription start site)
122
Upstream =
| Downstream =
```
Upstream = comes BEFORE
Downstream = AFTER
```
123
Where do sigma factors bind? What do they allow to then bind to them?
To the promotor; RNA polymerase
124
How do repressor proteins assert their effects in prokaryotes?
decrease binding of sigma factors --> decrease binding of RNA Polymerase --> Decrease transcription
125
Transcription factors can help ______s bind to ______s.
enhancers bind to promotors
126
Transcription factors directly bind to the ______.
Enhancer
127
Where does the repressor bind?
To the OPERATOR
128
Where does RNA Polymerase bind?
To the PROMOTOR
129
What kind of operon is lac?
Negative inducible operon
130
What kind of operon is trp?
Negative repressible operon
131
How does tryptophan function in the trp operon?
Tryptophan acts as a corepressor (activate the repressor)
132
How does lactose function within the lac operon?
lactose turns into allactose, which acts to inactivate the repressor and TURN ON the operon
133
The _____ operon is constitutive.
lac
134
LacI makes...
the repressor
135
What is a partial diploid cell?
cells that have taken up a plasmid that contains its own copy of an operon (like the lac operon)
136
What is a superrepressor?
Cannot be inactivated EVER --> ALWAYS repressing
Dominant to I+
137
When glucose is HIGH, cAMP is _____.
LOW
138
cAMP binds to ______. What does this do?
cAMP binds to CRP (activator). CRP is activated --> transcription is initiated
139
What portion of the trp operon contains the regions associated with attenuation?
trpL
140
When tryptophan is HIGH, what regions bind? What happens to transcription?
3 binds to 4; this BLOCKS transcription
141
What happens with tryptophan is LOW? What happens to transcription?
Ribosome stalls on region 1; Regions 2 and 3 bind; transcription is not blocked and is allowed to continue
142
How do riboswitches work?
Turned OFF by presence of regulatory molecules --> makes them fold up tightly and conceal ribosome binding sites
143
In end-product inhibition, to what does the end-product bind? What is the effect?
The ribozyme; caused mRNA to cleave itself
