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Flashcards in Gene Expression Deck (87):
1

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

Gene expression

2

What are the two classification of genes?

-housekeeping
-regulated

3

Housekeeping genes

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

4

Regulated genes

-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

5

What is the main site of gene control in prokaryotes?

Transcription

6

Gene regulation in eukaryotes

1.transcriptional
2. Post-transcription
3. Translation
4. Post translation

7

What is rresponsible for sophisticated gene regulation control in eukaryotes?

Nucleus separation

8

Regulatory molecules

1. Depressors
2. Activators

9

Regulatory molecules that suppress the transcription of a gene?

Repressors

10

Regulatory molecules that increase the transcription of a gene

Activators

11

Types of operons

1. Repressible
2. Inducible

12

Repressible operon

Transcription is usually on but can be inhibited

13

Inducible operon

Transcription is usually off by can be stimulated

14

What is the preferred carbon source for E. coli?

Glucose

15

Can E coli use other sugars?

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

16

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

-glucose is absent
-another sugar is present (lactose)

17

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

Off

18

What is the repressor protein encoded by?

Lacl gene

19

Repressor protein for the lac operon when glucose only is present

-encoded by lacl gene
-always present and bound to the operator
-blocks RNA polymerase

20

Adenyly cyclase when the lac operon is off

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

21

Lac operon when lactose is present

Its on

22

When the lac operon is on and glucose is absent

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

23

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

RNA polymerase

24

If the lac operon is on and lactose is present

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

25

When lactose is present, what is produced?

Allolactose

26

Lac operon when both glucose and lactose are present

Off

27

when lactose is present and the lac operon is off

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

28

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

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

29

Why do eukaryotes have 5 different levels of transcription?

We are more complex and need more cell types

30

What is regulation of transcription controlled by in eukaryotes?

Regulatory sequences of DNA

31

What are the regulatory sequences of DNA in eukaryotic transcription control

-usually embedded in the noncoding regions of the genome
-cis-acting
-interacts with trans acting regulators

32

Where are the regulatory sequences of DNA imbedded in?

Noncoding regions of the genome

33

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

Cis-acting

34

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

They influence expression of genes only on the same chromosome

35

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

Trans-acting regulators

36

Trans-acting regulator

-transcription factors
-they are proteins
-transcription not possible without this

37

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

-Zinc finger
-leucine zipper
-helix-turn-helix in the protein

38

DNA sequences that increase the rate of initiation of transcription

Enhancers

39

Where are enhancers typically located>?

On the same chromosome

40

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

-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

How do the enhancers act?

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

42

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

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

43

Transcription factors

- =trans-acting molecules
-DNA binding domain
-activation domain

44

Activation domain

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

45

What is PEPCK gene expression induced by?

Cortisol

46

Steroid hormone that diffuses into hepatocyte

Cortisol

47

What binds to intracellular receptors in PEPCK gene?

Cortisol

48

What does the cortisol-receptor complex enter?

Nucleus

49

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

Glucocorticoid response element (GRE)

50

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

PEPCK transcription is induced

51

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

Tissue specific ISO forms or proteins

52

What percentage of genes in humans undergo alternative splicing

60% of the ~25,000

53

Topomyosin

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

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

mRNA editing

55

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

Is deaminated to U, changing the sense codon to a nonsense or stop codon
-mRNA editing
-results in a shorter protein apo-B48

56

Apo B-100

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

57

Mechanism of reducing gene expression

RNA interface (RNAi)

58

What are the mechanisms of reducing gene expression (RNAi)

-repressing translation
-increasing the degradation of specific mRNAs

59

RNAi is a fundamental role in what

Cell proliferation, differentiation, and apoptosis

60

What is RNAi widely used for?

A tool in research

61

Therapeutic potential of RNAi

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

62

1st clinical trial of RNAi-based therapy

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

63

What is neovascular AMD triggered by?

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

SiRNA for VEGF

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

65

What is RNAi mediated by?

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

66

What does miRNA act as?

Guide strand to target specific mRNAS that contain the complementary sequence

67

RISC-RNA-induced silencing complex

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

68

Double stranded short interfering RNAs (siRNAs)

Introduced into a cell from exogenous sources can also trigger RNAi

69

Phosphorylation of eIF2

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

70

What is phosphorylation catalyzed by?

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

Post translational control: modifications of the polypeptide chain

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

72

Trimming

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

73

Covalent attachment

Phosphorylation, glycosylation, hydroxylation, others

74

Protein folding

Directed by chaperones

75

Protein degradation

By ubiquination

76

Loosely packed accessibly for transcription

Euchromatin

77

Tightly packed, inaccessible

Heterchromatin

78

Regions in DNA rich in CG that are prone to modifications

CpG islands

79

Epigentics regulation: modifications of DNA

-histones
-DNA

80

Methylation of DAN and histones

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

81

Histone acetylation

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

82

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

Transposons (Tns)

83

What is the movement of the transposons mediated by?

Transposase, an enzyme encoded by the Tn itself

84

Direct movement of transposons

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

85

Replication movement of transposons

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

86

What has transposition contributed to?

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

87

What diseases is transpostion associated with?

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