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Biochemistry > Exam 2: Gene Expression > Flashcards

Exam 2: Gene Expression Flashcards

1
Q

What controls gene transcription?

A

Cis and trans-regulatory elements

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2
Q

List some cis-acting elements:

A

DNA sequences, promoters, enhancers, silencers; usually consensus sequences that proteins (transcription factors) bind to

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3
Q

List some trans-acting elements:

A

Transcription factors such as regulatory proteins that bind to cis (DNA) elements

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4
Q

Which two elements exist to regulate gene transcription?

A

DNA binding proteins (trans) and DNA sequence elements (cis)
*they sequence specific/non-specific binding

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5
Q

T/F: Most DNA-protein interactions are weak, non-covalent, readily reversible bonds

A

True; important for regulation

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6
Q

Do many DNA binding proteins have specificity + affinity for multiple sequences?

A

Yes

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7
Q

How do DNA binding proteins increase specificity?

A

They contact several DNA bases

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8
Q

How do DNA binding proteins organize functional domains?

A

Sequence-specific DNA binding proteins have a modular
organization of functional domains

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9
Q

What are the regulatory DNA sites in bacteria called?

A

Operators (O) that control genes at an operon

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10
Q

How are bacteria operators (O) bound?

A

By repressors that block RNA polymerase from binding to the operator

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11
Q

How are prokaryotic genes negatively regulated?

A

Via a ligand-activated repressor

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12
Q

Which repressor controls Lactose (Lac) Operon?

A

Ligand-inactivated repressor

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13
Q

Regulatory mechanism to ensure optimal substrate use

A

Catabolite repression

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14
Q

What is an example of catabolite repression in lac operon?

A

Optimal transcription is achieved when lactose is present and glucose is low

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15
Q

When is cAMP high?

A

When glucose is low

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16
Q

How is optimal transcription achieved in lac operon?

A

By using a regulatory protein (CRP) which binds to cAMP and becomes ligand-activated

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17
Q

How can we get maximal expression of lac operon genes?

A

CRP must be bound to the CRP site AND the lac repressor must not be bound to the lac operator

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18
Q

How can we access gene promoters since condensed chromatin is transcriptionally silent?

A

Via chromatin remodeling
*opening up the tight chromatin structure

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19
Q

How is chromatin remodeled to allow transcription?

A

Acetylation and methylation of core histones. Acetylation of lysines by histone acetyltransferases (HATs): reduces positive charge of lysine residues and decreases the affinity of histones for DNA

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20
Q

Which 3 classes of proteins are recruited by RNA Pol via transcription by RNA pol II?

A
  • Basal transcription factors
  • DNA-binding transactivators
  • Co-activators + repressors– involved in protein: protein binding
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21
Q

What represses most eukaryotic gene expression?

A

Condensed chromatin structure

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22
Q

What requires local remodeling of chromatin to relieve expression?

A

Active transcription

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23
Q

What do histone deacetylases (HDAC’s) do?

A

Remove acetyl groups from histones

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24
Q

What do histone acetyltransferases (HAT’s) do?

A

Acetylate lysine residues on histones

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25
T/F: HAT's turn gene transcription on and HDAC's turn it off?
True
26
Which chromatin remodeling are we primarily concerned with?
Acetylation
27
What does signal transduction do?
Regulates gene expression
28
How does vitamin D regulate gene expression?
Vitamin D3 (chemical) binds to the vitamin D receptor (protein)
29
What is the result of vitamin D receptor binding to vitamin D3?
Dimerzation with RXR (protein)
30
What does a trans element always prefer to bind to?
Its favorite cis-element
31
Does a vitamin D receptor (trans factor) have several or few domains?
Several
32
What is cholecalciferol?
Vitamin D3 (ligand)
33
Do transcription factors bind at specific DNA sequences?
Yes
34
DNA binding domains of transcription factors have ____?
Conserved motifs
35
How does the vitamin D receptor (VDR) regulate gene expression?
By interacting with different trans-acting factors. Depending on what it interacts with, it can activate or repress a gene
36
What is the result of vitamin D receptor regulation?
Increased expression of 1 gene and decreased expression of another in the same tissue
37
What is the result of DNA methylation regulation?
-Hypermethylation in promoter regions results in decreased expression -Hypomethylation of promoter regions results in increased expression
38
What is the result of translational repression regulation?
-Phosphorylate initiation factors inactivate them -Proteins binding to mRNA and initiation factors stop translation *this is very important in eukaryotes
39
What are 2 small, noncoding regulatory RNAs?
miRNA (micro RNA) and siRNA (small interfering RNA)
40
Which type of RNA is responsible for gene silencing?
siRNA (small interfering)
41
What is PCR (polymerase chain reaction)?
Biochemical process or method to amplify target DNA
42
What is the importance of primers in PCR?
They define the region that will be amplified and create millions of copies in a short timeframe
43
____ occurs using multiple repeated cycles (chain reaction) of DNA polymerase activity
PCR amplification
44
Can PCR-amplified DNA be seen?
Yes
45
How can PCR genotyping be applied to everyday stuff?
Identity testing: paternity, forensic science, violent crimes, missing persons
46
How is PCR used in paternity testing?
Genotyping
47
What is an example of a real-time PCR method?
5' exonuclease-based
48
The process by which a single stranded DNA or RNA molecule anneals (binds) to a complementary sequence:
Nucleic acid hybridization
49
Nucleic acid hybridization in SNP genotyping:
Synthetic probes are designed to be complementary to specific SNP sites. When the probe hybridizes with the target SNP sequence, it indicates that the sequence is present in the DNA sample
50
What is fluorescence function in SNP genotyping used for?
To visualize and quantify the presence of specific SNPs in the DNA sample
51
Fluorescence function in SNP genotyping:
Probes attached to fluorochromes emit light when hybridized with the target DNA sequence. The emitted light is captured by an optical scanner, and the resulting fluorescence pattern is analyzed to determine the genotype
52
RNA-guided/nuclease-mediated gene editing technique:
Crispr cas9 system
53
How does Crispr cas9 work?
1. using guide-RNA to find the exact mistake in DNA you want to fix 2. cutting the mistake out with Cas9 tool 3. once the DNA is cut, scientists can give the DNA new DNA to replace the old, incorrect one
54
What is used in the gene-targeted editing approach?
Guide-RNA which recruits Cas nuclease
55
How is Crispr Cas9 versatile?
Allows genetic manipulation across the central dogma (can take place in DNA, RNA, or proteins)
56
Single-stranded oligonucleotides with well-defined three-dimensional structures that bind to specific proteins
Aptamer drugs
57
In-vitro transcribed mRNAs are delivered to cells and translated into antigens or other proteins
mRNA's and mRNA vaccines
58
Give an example of an RNA-based therapeutic
COVID-19: mRNA vaccines targeting SARS-CoV-2 spike protein
59
How do mRNA vaccines work?
mRNA is packaged and delivered to antigen presenting cells (APCs)
60
Why are ddNTPs relevant to DNA sequencing?
They are like the period at the end of a sentence. They tell copying to stop so scientists know where to sequence DNA
61
What does ddNTP stand for?
Dideoxynucleoside triphosphates
62
What is DNA sequencing?
Process where scientists determine the exact order of the building blocks (nucleotides) in a strand of DNA
63
Which complex needs to bind to activate chromatin remodeling?
SWI/SNF
64
What does SWI/SNF do when it binds?
Removes positive charges from histone. This opens up promoter
65
Most proteins that regulate gene expression by binding to specific DNA sequences...
Have modular organization of distinct functional domains
66
Transcription at the lactose (lac) operon in maximal in bacteria when
Both cAMP and lactose levels are high *lac repressor off
67
A mechanism used to regulate expression of eukaryotic gene is
Protein-DNA interaction
68
Hypermethylated gene:
Lower expression
69
Hypomethylated gene:
Higher expression
70
What gives a CRISP Cas9 system target specificty?
Guide RNA
71
Which mechanism integrates NEW genetic info into gene targeted for editing?
Homology directed repair
72
How is DNA damaged by a CRISPR Cas9?
Nuclease activity
73
What recruits Cas9 to a target site?
RNA

Biochemistry (6 decks)

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