Midterm 3 Flashcards
1
Q
What are the 3 ways eukaryotic gene regulation differs from bacterial regulation?
A
- Each structural gene has its own promoter, and is transcribed separately
- DNA must unwind from the histone proteins before transcription
- Transcription and translation are separated in time and space.
2
Q
T/F changes in chromatin structure affect the expression of genes.
A
True
3
Q
What is histone modification?
A
Addition of methyl groups
(can cause condensation or relaxation of chromatin, depending on location of methyl groups)
OR
Addition of acetyl groups to histone proteins
(typically causes relaxation)
4
Q
What is another word for the addition of methyl groups
A
Acetylation
5
Q
Acetylation is associated with gene expression
A
True
6
Q
What are the steps to acetylation?
A
- The chromatin remodeling complex binds to DNA
- This repositions nucleosomes, exposing a transcription factor binding site
- Transcription factors and RNA polymerase bind to DNA and initiate transcription.
7
Q
How does acetylation lead to gene expression?
A
- charged tails of histone interact with - charged DNA molecule
- Acetylation of these tails weakens these interactions and permits transcription factors to bind to DNA
(Transcription factors activate gene expression)
8
Q
What is an example of acetylation in the real world?
A
In the flower Arabidopsis, two genes interact (FLC & FLD)
FLC: Makes protein that binds to DNA and turns off flowering
FLD: protein that removes acetyl groups from histone protein surrounding FLC gene. Thus FLC is compacted densely and will not transcribe.
SOOO.. In acetylation FLC is repressed therefore it cannot shut off flowering and flowering occurs.
9
Q
Chromatin remodeling plays a very important role in gene expression!!!
A
TRUE
10
Q
What complexes bind directly to DNA sites and reposition nucleosomes by remodeling chromatin?
A
Chromatin-remodeling complexes.
11
Q
What is DNA methylation also referred to?
A
CpG island
12
Q
What occurs during DNA methylation?
A
DNA methylates cytosine bases adjacent to guanine nucleotides.
This represses transcription until it is removed.
13
Q
What is the role of transcriptional activators and coactivators in gene expression?
A
They stimulate and stabilize the basal transcription apparatus at the core promoter
14
Q
What happens with the GAL system in yeast?
A
- GAL4 protein binds to DNA called upstream activation sequence, this activates gene expression of genes involved in galactose metabolism
- GAL80 binds to GAL4 to stop it from doing its job.
- Galactose allows GAL3 protein to bind to GAL80 to stop it from stopping GAL4
- This allows GAL4 to interact and activate gene expression
15
Q
What are transcriptional repressors and what do they do?
A
They stop transcription from occurring by binding to silencers
16
Q
What are the roles of enhancers and insulators?
A
Enhancers: DNA sequence stimulating transcription from a distance away from promoter
Insulators: DNA sequence that blocks or insulates the effect of enhancers
- Insulators prevent the enhancers from doing something they aren’t supposed to
(insulator + binding protein)
17
Q
What performs coordinated gene regulation and why:
A
Response elements when they want multiple sites to be turned on at the same time
(upstream of start sites that are to be turned on in response to the same element)
18
Q
How can gene regulation be regulated after transcription?
A
RNA splicing
Example in drosophila
( Female functional Sxl gene leads to correct and functional splicing and Tra protein so female flies produced
whereas in man Sxl protein is infunctional so splicing is not the same so Tra not produced and fly is male)
19
Q
What are 3 mechanisms of gene regulation caused by RNA interference?
A
- RNA Cleavage
- Inhibition of translation
- Transcriptional silencing: altering chromatin structure
20
Q
What happens in RNA cleavage?
A
- double stranded RNA is cleaved by the enzyme dicer to produce small interfering RNAs (siRNAs)
- siRNAs combine with RISC complex and pair with complementary sequences
- complex leaves mRNA therefore degradation occurs
21
Q
What happens in inhibition of translation?
A
- Single RNA molecular cleaved by dicer, these are microRNAs.
- mirRNAs combine with RISC but pair imperfectly.
- Not cut but inhibited.
22
Q
Operons uncommon in eukaryotic expression
A
true
23
Q
Initiation of transcription is relatively complex in eukaryotes
A
true
24
Q
What is epigenetics?
A
Variation in a phenotype that is not caused by differences in the DNA sequence
- often caused by changes to chromatin some of which are heritable
25
What is DNA methylation?
Addition of methyl groups to nucleotide bases (often C)
- most often causes gene silencing
- can be maintained during DNA replication and transfer from parent to progeny
26
DNA methylation and honeybees
- Queen (fertile) and workers (sterile) are both female
Royal jelly, fed to larvae, silence a methyltransferase, prevents methylation (induces fertility)
- this activates embryo into queen.
-regular bee food allows methylation. --> genes repressed, therefore worker bee!
27
Histone modifications can lead to epigenetic changes.
-More than 100 different modifications.
-Some can be maintained during DNA replication.
Perhaps the marks on original histones could be used to mark new ones?
28
Epigenetics effects RNA molecules
True
29
What is X inactivation?
One of the 2X chromosomes is turned off. Xist silences the chromosome. Different Xs are inactivated in different cells.
Tortoise shell cat: different follicles are different x inactivation
30
What is an interaction between two alleles that can lead to a heritable change in expression of one alleles?
Paramutation
| -wild type silencing in heterozygous individuals
31
What is behavioral epigenetics?
Life experiences early on in life that have long lasting effects on behaviors.
- epigenetic changes can be induced by:
1. maternal behavior
2. early stress
3. abuse
4. diets
5. environmental chemicals
32
Genomic imprinting is:
the idea that different genes are imprinted in egg v sperm cells.
(mom wants to slow development so speedy development genes are imprinted,
dad wants to speed up development so slow development genes are imprinted)
33
What is the difference between discontinuous (qualitative) traits and continuous (quantitative) traits?
discontinuous (qualitative) traits possess only a few phenotypes
continuous (quantitative) traits vary along a scale of measurement with many overlapping phenoytpes
34
What is an example of qualitative traits?
short, or tall
35
What is an example of quantitative trait?
human height
36
Something important to remember***
Just because you can use a number to value a particular trait, doesn’t mean it’s quantitative in the sense we’re using it
37
What are characteristics of quantitative traits?
−Exhibit complex relationship between genotype and phenotype
−May be influenced by multiple genes (polygenic)−May be influenced by environment
−Phenotypic ranges may overlap
−Cannot use standard methods to analyze
38
What are the types of quantitative characteristics?
- Meristic
| - Threshold
39
What are meristic characteristics?
−Determined by multiple genetic and environmental factors, and can be measured in whole numbers.
−Animal litter size.
40
What are threshold characteristics?
−Measured by presence or absence
| −Susceptibility to disease
41
T/F Quantitative Characteristics Vary Continuously and Many Are Influenced by Alleles at Multiple Loci
TRUE*** KNOW THIS
42
What is meant by polygenic inheritance?
- Refers to quantitative characteristics controlled by cumulative effects of many genes.
- Each character still follows Mendel’s rules.
- May be influenced by environmental factors.
43
How can you calculate the amount of genes that control variation in a trait?
```
(1/4)n = number of individuals in the F2 progeny that resemble each of the homozygous parents
–n = number of loci with a segregating pair of alleles that affects the characteristic
```
44
What does it mean when two characteristics are correlated?
a change in one characteristic is likely to be associated with a change in the other.
45
What does a correlation coefficient measure?
the strength of their association
- ranges from -1 to 1
- negative values mean that as one trait increases, the other tends to decrease (inverse correlation)
- positive values mean that as one trait increases, so does the other (positive correlation)
- 0 means there is no correlation between the two traits
46
positive correlation
/ as one increases, the other will follow
47
negative correlation
\ inverse association between variables
48
correlation of zero
----
49
regression line best fits all the points on the graph.
true ;)
| regression coefficient represents the slope of the regression line
50
An individual’s phenotypic value equals the average, plus differences caused by genetic and environmental factors.
How would this be mathematically represented?
P = P + g + e
51
Define heritability:
how much of the variation in a trait is genetic
52
The amount of variation in a trait is the sum of genetic and environmental variation,
How would this be formulated mathematically?
Vp = Vg + Ve
53
In a cross between homozygous recessive and dominant, the f1's are genetically identical. Therefore any variation must be.....
environmental.
Vg= 0
Vp = 0 + Ve
54
In a cross between homozygous recessive and dominant, the f1's are genetically identical. But the f2s vary genetically.
Therefore any variation must be due to...
genetic and environmental variation
55
What is broad sense heritability? (H2)
The proportion of the trait variation due to genetic variation
This is calculated by Vg/Vp
56
What are operons?
a set of co-expressed genes, controlled by the same regulatory elements
57
Are operons found in eukaryotes, prokaryotes, or both?
rare in eukaryotes, always in prokaryotes
58
Define structural genes:
encoding proteins, often with enzymatic activity
59
Define regulatory genes:
encoding products (ie. transcription factors) that interact with other sequences and affect the transcription and translation of these sequences
60
Define regulatory elements:
DNA sequences that also play a role in regulating gene expression (often binding sites for transcription factors)
61
How is transcription regulated?
DNA-binding proteins
| Proteins that regulate transcription of a gene by binding to a regulatory element that controls that gene
62
What is a set of co-expressed genes, controlled by the same regulatory elements
An operon
63
What is the DNA sequence encoding products that affect the operon function, but are not part of the operon
A regulator gene
64
How do we classify operons? (4 ways)
+ protein binding to DNA means gene is turned on
- protein binding to DNA means gene is turned off
- inducible environmental signal (effector) turns gene "on"
- repressible
environmental signal (effector) turns gene "off"
65
What happens in a negative inducible operon?
```
Protein binding to DNA prevents gene expression
Small molecule (inducer) prevents protein from binding DNA, allowing gene to be turned on
```
66
What happens in a negative repressible operon?
Protein binding to DNA prevents gene expression
| Needs a small molecule (co-repressor) to allow it to bind DNA and turn the gene “off”
67
What happens in a positive inducible operon?
Positive inducible operon
Protein binding to DNA turns gene “on”
Small molecule required to allow protein to bind
68
What happens in a positive repressible operon?
Positive repressible operon
Protein binding to DNA turns gene “on”
Small molecule prevents protein from binding
69
* ****JUST IMPORTANT INFORMATION
| - Completely memorize.
The lac operon of E. coli is...
```
A negative inducible operon
Lactose metabolism
Regulation of the lac operon
Inducer: allolactose
lacI: repressor encoding gene
lacP: operon promoter
lacO: operon operator
```
Structural genes
lacZ: encoding β-galactosidase
lacY: encoding permease
lacA: encoding transacetylase
The repression of the lac operon never completely shuts down transcription.
70
More important information about E. Coli
Identify mutations that alter gene expression. Either
Z or Y off when they should be on
Z or Y on when they should be off
Which allele (wild-type or mutant) is dominant?
Problem – bacteria are haploid – only 1 copy of each gene
Solution – Use extrachromosomal DNA (F’ plasmid) to bring in a second copy
71
What type of operon is the lac operon of e coli?
negative inducible operon
72
What is the inducer of the lac operon?
allolactose
73
lacI does what?
encodes for repressor protein
74
what is lacP
the promoter
75
what is lacO
the operator sequence that lacI binds to
76
What are the structural genes?
lacZ: encoding B-galactosidase
lacY: encoding permease
lacA: encoding transacetylase (not necessarily needed)
77
Which allele is dominant in e coli?
the wild type.
| We found this by using extrachromosomal DNA (F' plasmid) to bring in a second copy.
78
Z+ is dominant to Z-,
| why?
because we would essentially double the DNA, almost like across to see which would show up.
Therefore if you have the Z+ and the Z- and the Z+ shows up then we can assume that Z+ is dominant.
79
Oc is what?
A constitutively active staring, that causes expression of Z and Y even without induction.
80
FYI: If you see Oc then you can assume all plus signs.
TRUE
81
FYI Oc is dominant to O+
TRUE
82
FYI Oc (dominant allele) can only regulate the genes that are on the same strand as itself (cis acting)
TRUE
83
FYI lacI- is recessive to lacI+
TRUE
84
The dominant allele I+ can regulate genes on both strands (trans acting)
TRUE
85
Summary of mutants:
lacI acts in trans, constitutive allele recessive
| LacO acts in cis, constitutive allele dominant
86
Is is a super repressor, what does this mean?
Mutants prevent expression of Z and Y even in presence of lactose.
87
trp operon is....
negative repressible
88
Define attenuation:
this affects the continuation of transcription, not its initiation
89
secondary structure (folding) of the mRNA molecule is influence by....
levels of tryptophan in the cell.
90
upstream of trp operon is..
5' UTR
91
when tryptophan level is high region 3 pairs with region 4 and transcription...
ends
92
when tryptophan is low,
RNA transcription will continue
93
which RNA molecules control the expression of gene expression?
- antisense RNA: RNA's that are complementary to mRNA
- riboswitches
- ribozymes: catalytic activity
94
Name and explain the 5 main evolutionary forces that can cause H-W disequilibrium.
- migration
- mutation
- non random mating
- genetic drift
- selection
95
In this population, which characteristic would respond BEST to selection?
The one with the highest narrow-sense heritability
96
Narrow-sense heritability is due to what type of genetic variance?
additive genes
97
Why does the response to selection often level off after many generations of selection?
Eventually, everyone is homozygous for the selected allele, plus there might be detrimental effects of having a phenotype too extreme.10.
98
Why is the relation between genotype and phenotype frequently complex for quantitative characteristics?
Because many genes can influence the phenotype, as can environmental factors.
99
Will a worker or queen bee have more copies of 5-methylcytosine in their DNA? Why?
Workers. Royal jelly fed to larvae meant to be queens silences methyltransferase Dnmt3 and prevents methylation of cytosine.
100
How do epigenetic traits differ from traditional genetic traits, such as the differences in color and shape of peas that Mendel studied?
Epigenetic traits are stably heritable phenotypes resulting from changes in chromosome without alterations in the DNA sequence
101
What is the genomic conflict hypothesis for the origin of genomic imprinting?
Imprinting grew out of a competition between males and females for maternal resources.
102
How is X inactivation an epigenetic phenotype?
An example of RNA molecules affecting the phenotypes produced by the chromosomes.
103
Where is DNA methylation usually found?
On the 5 position of cytosine.
104
Suppose a geneticist introduced a small interfering RNA (siRNA) that was complementary to the FLC mRNA in the provided figure. What would be the effect on the flowering of Arabidopsis?
siRNA would interfere with the transcription of FLC and would allow flowering of the Arabidopsis.
105
Discuss the role of alternative splicing in the control of sex differentiation in Drosophila?Discuss the role of alternative splicing in the control of sex differentiation in Drosophila?
n XX embryos, the Sxl gene produces a protein that splices Tra pre-mRNA so that Tra protein is made. With Tra-2 protein, the two direct female specific splicing of dsx pre-mRNA and the fly develops into a female.In XY the Sxl gene is not active and Tra pre-mRNA is spliced differently so that no functional Tra protein is made. Without the Tra protein, male-specific splicing of dsx pre-mRNA occurs and a male develops.
106
How do response elements bring about the coordinated expression of eukaryotic genes?
Response elements work within a genes promoter and can respond to environmental conditions to increase transcription. When the same element is in different genes, they get activate simultaneously by the same stimuli and create a coordinated response.
107
What is an insulator?
Insulators work to block enhancer elements.
108
How does an enhancer affect the transcription of distant genes?
Enhancers bind to transcription factors that can enhance the frequency of transcription for a gene.
109
How do transcriptional activator proteins and repressors affect the level of transcription of eukaryotic genes?
Activator proteins activate or co-activate transcription. Repressors block transcription.
110
How does DNA methylation affect transcription?
Methyl groups may prevent the binding of transcriptional factors – gene silencing.
111
How does histone acetylation affect chromatin structure and transcription?
Acetyl groups are attached to positively charged lysines in histone tails. This loosens chromatin structure and promotes initiation of transcription.
112
If negative is mutated all will be...
ON
113
if positive operon is mutated, all signals will be turned..
OFF
114
initially in a negative repressible operon the gene will be...
on when signal absent and off when signal present
115
initially in a negative inducible operon the gene will be...
off when signal absent and on when signal present
116
initially in a positive repressible operon the gene will be...
on when signal absent and off when signal present
117
initially in a positive inducible operon the gene will be
off when signal absent and on when signal present
118
initially in an INDUCIBLE operon the gene will be...
off when signal absent and on when signal present
119
initially in a REPRESSIBLE operon the gene will be
on when signal absent and off when signal present
