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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
Q

T/F: HAT’s turn gene transcription on and HDAC’s turn it off?

A

True

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26
Q

Which chromatin remodeling are we primarily concerned with?

A

Acetylation

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27
Q

What does signal transduction do?

A

Regulates gene expression

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28
Q

How does vitamin D regulate gene expression?

A

Vitamin D3 (chemical) binds to the vitamin D receptor (protein)

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29
Q

What is the result of vitamin D receptor binding to vitamin D3?

A

Dimerzation with RXR (protein)

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30
Q

What does a trans element always prefer to bind to?

A

Its favorite cis-element

31
Q

Does a vitamin D receptor (trans factor) have several or few domains?

A

Several

32
Q

What is cholecalciferol?

A

Vitamin D3 (ligand)

33
Q

Do transcription factors bind at specific DNA sequences?

A

Yes

34
Q

DNA binding domains of transcription factors have ____?

A

Conserved motifs

35
Q

How does the vitamin D receptor (VDR) regulate gene expression?

A

By interacting with different trans-acting factors. Depending on what it interacts with, it can activate or repress a gene

36
Q

What is the result of vitamin D receptor regulation?

A

Increased expression of 1 gene and decreased expression of another in the same tissue

37
Q

What is the result of DNA methylation regulation?

A

-Hypermethylation in promoter regions results in decreased expression
-Hypomethylation of promoter regions results in increased expression

38
Q

What is the result of translational repression regulation?

A

-Phosphorylate initiation factors inactivate them
-Proteins binding to mRNA and initiation factors stop translation

*this is very important in eukaryotes

39
Q

What are 2 small, noncoding regulatory RNAs?

A

miRNA (micro RNA) and siRNA (small interfering RNA)

40
Q

Which type of RNA is responsible for gene silencing?

A

siRNA (small interfering)

41
Q

What is PCR (polymerase chain reaction)?

A

Biochemical process or method to amplify target DNA

42
Q

What is the importance of primers in PCR?

A

They define the region that will be amplified and create millions of copies in a short timeframe

43
Q

____ occurs using multiple repeated cycles (chain reaction) of DNA polymerase activity

A

PCR amplification

44
Q

Can PCR-amplified DNA be seen?

A

Yes

45
Q

How can PCR genotyping be applied to everyday stuff?

A

Identity testing: paternity, forensic science, violent crimes, missing persons

46
Q

How is PCR used in paternity testing?

A

Genotyping

47
Q

What is an example of a real-time PCR method?

A

5’ exonuclease-based

48
Q

The process by which a single stranded DNA or RNA molecule anneals (binds) to a complementary sequence:

A

Nucleic acid hybridization

49
Q

Nucleic acid hybridization in SNP genotyping:

A

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
Q

What is fluorescence function in SNP genotyping used for?

A

To visualize and quantify the presence of specific SNPs in the DNA sample

51
Q

Fluorescence function in SNP genotyping:

A

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
Q

RNA-guided/nuclease-mediated gene editing technique:

A

Crispr cas9 system

53
Q

How does Crispr cas9 work?

A
  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
Q

What is used in the gene-targeted editing approach?

A

Guide-RNA which recruits Cas nuclease

55
Q

How is Crispr Cas9 versatile?

A

Allows genetic manipulation across the central dogma (can take place in DNA, RNA, or proteins)

56
Q

Single-stranded oligonucleotides with well-defined three-dimensional structures that bind to specific proteins

A

Aptamer drugs

57
Q

In-vitro transcribed mRNAs are delivered to cells and translated into antigens or other proteins

A

mRNA’s and mRNA vaccines

58
Q

Give an example of an RNA-based therapeutic

A

COVID-19: mRNA vaccines targeting
SARS-CoV-2 spike protein

59
Q

How do mRNA vaccines work?

A

mRNA is packaged and
delivered to antigen
presenting cells (APCs)

60
Q

Why are ddNTPs relevant to DNA sequencing?

A

They are like the period at the end of a sentence. They tell copying to stop so scientists know where to sequence DNA

61
Q

What does ddNTP stand for?

A

Dideoxynucleoside triphosphates

62
Q

What is DNA sequencing?

A

Process where scientists determine the exact order of the building blocks (nucleotides) in a strand of DNA

63
Q

Which complex needs to bind to activate chromatin remodeling?

A

SWI/SNF

64
Q

What does SWI/SNF do when it binds?

A

Removes positive charges from histone. This opens up promoter

65
Q

Most proteins that regulate gene expression by binding to specific DNA sequences…

A

Have modular organization of distinct functional domains

66
Q

Transcription at the lactose (lac) operon in maximal in bacteria when

A

Both cAMP and lactose levels are high
*lac repressor off

67
Q

A mechanism used to regulate expression of eukaryotic gene is

A

Protein-DNA interaction

68
Q

Hypermethylated gene:

A

Lower expression

69
Q

Hypomethylated gene:

A

Higher expression

70
Q

What gives a CRISP Cas9 system target specificty?

A

Guide RNA

71
Q

Which mechanism integrates NEW genetic info into gene targeted for editing?

A

Homology directed repair

72
Q

How is DNA damaged by a CRISPR Cas9?

A

Nuclease activity

73
Q

What recruits Cas9 to a target site?

A

RNA

Biochemistry (6 decks)

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