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Biochem BLOCK 3 > Gene Expression > Flashcards

Gene Expression Flashcards

1
Q

A multi step process that ultimately results in the production of a functional gene product (either ribonucleotide acid or a protein)

A

Gene expression

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2
Q

What are the two classification of genes?

A
  • housekeeping

- regulated

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3
Q

Housekeeping genes

A
  • involved in basic cellular functions that are requires regardless of the cell type or environmental cues
  • constitutively expressed and not regulated
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4
Q

Regulated genes

A
  • required only in certain cells types and/or only under certain conditions
  • subject to various control mechanisms that determine if and when these genes will be expressed
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5
Q

What is the main site of gene control in prokaryotes?

A

Transcription

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6
Q

Gene regulation in eukaryotes

A
  1. transcriptional
  2. Post-transcription
  3. Translation
  4. Post translation
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7
Q

What is rresponsible for sophisticated gene regulation control in eukaryotes?

A

Nucleus separation

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8
Q

Regulatory molecules

A
  1. Depressors

2. Activators

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9
Q

Regulatory molecules that suppress the transcription of a gene?

A

Repressors

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10
Q

Regulatory molecules that increase the transcription of a gene

A

Activators

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11
Q

Types of operons

A
  1. Repressible

2. Inducible

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12
Q

Repressible operon

A

Transcription is usually on but can be inhibited

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13
Q

Inducible operon

A

Transcription is usually off by can be stimulated

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14
Q

What is the preferred carbon source for E. coli?

A

Glucose

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15
Q

Can E coli use other sugars?

A

Yes, however, this requires more enzymes (and energy) so E. coli only produces the enzymes to use other sugars if glucose is absent and another sugar is present

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16
Q

When does E coli produce the enzymes to use other sugars?

A
  • glucose is absent

- another sugar is present (lactose)

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17
Q

Is the lac operon off or on when only glucose is present?

A

Off

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18
Q

What is the repressor protein encoded by?

A

Lacl gene

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19
Q

Repressor protein for the lac operon when glucose only is present

A
  • encoded by lacl gene
  • always present and bound to the operator
  • blocks RNA polymerase
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20
Q

Adenyly cyclase when the lac operon is off

A
  • Glucose present

- glucose inhibits adenyly cyclase, no cAMP, cannot form CAP/cAMP complex, cannot initiate transcription

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21
Q

Lac operon when lactose is present

A

Its on

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22
Q

When the lac operon is on and glucose is absent

A

Adenyly cyclase makes cAMP, CAP/cAMP complex forms, binds to CAP binding site, RNA polymerase can efficiently initiate transcription

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23
Q

When glucose is absent and the lac operon is on, what can efficiently initiate transcription?

A

RNA polymerase

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24
Q

If the lac operon is on and lactose is present

A

A small amount of allolactose is produced that binds to the repressor, and prevents it from binding to the operator

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25
Q

When lactose is present, what is produced?

A

Allolactose

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26
Q

Lac operon when both glucose and lactose are present

A

Off

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27
Q

when lactose is present and the lac operon is off

A

A small amount of allolactose is produced that binds to the repressor and prevents it from binding to the operator

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28
Q

Transcription when lac operon is off in the presence of lactose and glucose

A

Although the repressor is inactive, the transcription can not be initiated because the CAP site is empty

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29
Q

Why do eukaryotes have 5 different levels of transcription?

A

We are more complex and need more cell types

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30
Q

What is regulation of transcription controlled by in eukaryotes?

A

Regulatory sequences of DNA

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31
Q

What are the regulatory sequences of DNA in eukaryotic transcription control

A
  • usually embedded in the noncoding regions of the genome
  • cis-acting
  • interacts with trans acting regulators
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32
Q

Where are the regulatory sequences of DNA imbedded in?

A

Noncoding regions of the genome

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33
Q

What are these regulatroy sequences of DNA that are embedded in the noncoding region of the genome called?

A

Cis-acting

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34
Q

Why are the regulatory sequences of DNA that are embedded in the noncoding regions of the genome called cis-acting

A

They influence expression of genes only on the same chromosome

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35
Q

What are the cis-acting DNA regulatory sequences capable of interacting with?

A

Trans-acting regulators

36
Q

Trans-acting regulator

A
  • transcription factors
  • they are proteins
  • transcription not possible without this
37
Q

How is binding of the trans-acting regulators (TF) to DNA achieved?

A
  • Zinc finger
  • leucine zipper
  • helix-turn-helix in the protein
38
Q

DNA sequences that increase the rate of initiation of transcription

39
Q

Where are enhancers typically located>?

A

On the same chromosome

40
Q

Where on the chromosome is the enhancer in comparison to the gene?

A
  • Can be close to the gene they are controlling or thousands of base pairs away
  • can be located upstream, downstream, or even within intron regions or other chromosomes
41
Q

How do the enhancers act?

A

In a tissue specific manner if the DNA binding proteins (transcription factors) are only present in certain tissues

42
Q

How can the enhancers be brought closer to where they need to be?

A

Can be brought close to the basal promoter by bending o the DNA molecule

43
Q

Transcription factors

A
  • =trans-acting molecules
  • DNA binding domain
  • activation domain
44
Q

Activation domain

A
  • transcription factors
  • bind to other transcription factors, interact with RNA polymerase II to stabilize formation of the invitation complex, recruit chromatin modifying proteins
45
Q

What is PEPCK gene expression induced by?

46
Q

Steroid hormone that diffuses into hepatocyte

47
Q

What binds to intracellular receptors in PEPCK gene?

48
Q

What does the cortisol-receptor complex enter?

49
Q

Once in the nucleus, what does the cortisol-receptor complex bind to?

A

Glucocorticoid response element (GRE)

50
Q

What happens after cortisol-receptor complex binds to the glucocorticoid response element (GRE)

A

PEPCK transcription is induced

51
Q

What can be made by the same pre-mRNA by the use of alternative splice sites

A

Tissue specific ISO forms or proteins

52
Q

What percentage of genes in humans undergo alternative splicing

A

60% of the ~25,000

53
Q

Topomyosin

A

Actin filament-binding proteins, interaction with the cytoskeleton in most cells, and the contractile apparatus of muscle cells, undergoes tissue specific alternative splicing to produce multiple isoforms of the protein

54
Q

Additional posttranscriptional modification in which a base in the mRNA is altered

A

mRNA editing

55
Q

the C residue in the CAA codon for glutamine in the intestine only

A

Is deaminated to U, changing the sense codon to a nonsense or stop codon

  • mRNA editing
  • results in a shorter protein apo-B48
56
Q

Apo B-100

A

In the liver, fulllength, is made and incorporated into VLDL

57
Q

Mechanism of reducing gene expression

A

RNA interface (RNAi)

58
Q

What are the mechanisms of reducing gene expression (RNAi)

A
  • repressing translation

- increasing the degradation of specific mRNAs

59
Q

RNAi is a fundamental role in what

A

Cell proliferation, differentiation, and apoptosis

60
Q

What is RNAi widely used for?

A

A tool in research

61
Q

Therapeutic potential of RNAi

A

Huge therapeutic potential: currently more than 20 are in clinical trials for various diseases

62
Q

1st clinical trial of RNAi-based therapy

A

Involved patients with the neovascular form of ARMD, a leading form of adult blindness

63
Q

What is neovascular AMD triggered by?

A

Overproduction of vascular endothelial growth factor (VEGF), leading to the sprouting of excess blood vessels behind the retina. The vessels leak, clouding and often entirely destroying vision (wet)

64
Q

SiRNA for VEGF

A

An siRNA designed to target the mRNA of VEGF and promote its degradation went to clinical trials
-FIRST APPROVED FOR CLINICAL TRIALS

65
Q

What is RNAi mediated by?

A

Very short RNA (~20-22bp) called microRNA (miRNA)

66
Q

What does miRNA act as?

A

Guide strand to target specific mRNAS that contain the complementary sequence

67
Q

RISC-RNA-induced silencing complex

A

Together with this protein complex, expression of the gene is reduced by the cleaving of RNA (degradation) and/or physically blocking translation

68
Q

Double stranded short interfering RNAs (siRNAs)

A

Introduced into a cell from exogenous sources can also trigger RNAi

69
Q

Phosphorylation of eIF2

A

Inhibits its function by inhibited GDP-GTP exchange and so inhibits translation at the initiation step

70
Q

What is phosphorylation catalyzed by?

A

Kinases that are activated in response to environmental conditions

  • AA starvation
  • heme deficiency in erythroblasts
  • presence of double stranded RNA 9signaling viral infection)
  • accumulation of misfolded proteins in the rough ER
71
Q

Post translational control: modifications of the polypeptide chain

A
  1. Trimming
  2. Covalent attachment
  3. Protein folding
  4. protein degradation
72
Q

Trimming

A

Initially synthesized as large precursors many proteins undergo cleavage to become functionally active (protein digestion enzymes)

73
Q

Covalent attachment

A

Phosphorylation, glycosylation, hydroxylation, others

74
Q

Protein folding

A

Directed by chaperones

75
Q

Protein degradation

A

By ubiquination

76
Q

Loosely packed accessibly for transcription

A

Euchromatin

77
Q

Tightly packed, inaccessible

A

Heterchromatin

78
Q

Regions in DNA rich in CG that are prone to modifications

A

CpG islands

79
Q

Epigentics regulation: modifications of DNA

A
  • histones

- DNA

80
Q

Methylation of DAN and histones

A

Causes nucleosomes to pack tightly together. Transcription factors cannot bind the DNA, and genes are not expressed

81
Q

Histone acetylation

A

Results in loose packing of nucleosomes. Transcription factors can bind the DNA and genes are expressed

82
Q

Mobile segments of DNA that move in a random manner from one site to another on the same or a different chromosome

A

Transposons (Tns)

83
Q

What is the movement of the transposons mediated by?

A

Transposase, an enzyme encoded by the Tn itself

84
Q

Direct movement of transposons

A

Transposon cuts out and then inserts the Tn at a new site

85
Q

Replication movement of transposons

A

Tn is copied and the copy inserted elsewhere while the original remains in place

86
Q

What has transposition contributed to?

A

The structural variation in the genome but it also associated with diseases

87
Q

What diseases is transpostion associated with?

A
  • rare cases of hemophilia A
  • Duchenne muscular dystrophy
  • antibiotic resistance in bacteria is party due to this phenomena

Biochem BLOCK 3 (12 decks)

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