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[OS 201] 3rd Exam > Trans - Regulation of Gene Expression > Flashcards

Trans - Regulation of Gene Expression Flashcards

2
Q

Importance of regulation of gene expression (3), give examples of each

A
  1. adaptation to environmental changes –> ex. memory B cell antibody production during immune response
  2. development –> ex. pluripotential stem cells
  3. differentiation of cells –> ex. specific proteins for specific cell function
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3
Q

Levels of eukaryotic gene regulation (6)

A
  1. epigenetic control
  2. transcriptional control
  3. post-transcriptional control
  4. RNA transport control
  5. Translational control
  6. Post-translational control
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4
Q

Heterochromatin vs Euchromatin

A
  1. heterochromatin –> dense, transcriptionally silent, tightly packed, inaccessible to polymerases and other enzymes
  2. euchromatin –> loosely packed and active in gene transcription
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5
Q

Define differential gene expression

A

Some genes are expressed while others are repressed

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6
Q

a) structure and b) significance of telomeres

A

a) complexes of DNA and proteins at the end of chromosomes
b) maintain structural integrity, prevent attack by nucleases, allow repair systems to differentiate between ends and breaks

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7
Q

Mechanisms to increase/decrease access to DNA sequence (2)

A
  1. gene regulatory proteins

2. RNA polymerases

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8
Q

Mechanisms to alter chromatin structure (2)

A
  1. cytidine methylation

2. histone methylation

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9
Q

Old and new concepts related to genetic switches

A

Old: “loss” of genesNew: genes can be turned “on” or “off”

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10
Q

Principle of DNA methylation

A

[1] Silencing genes to reduce unnecessary gene expression

[2] Methylation of CG dinucleotide (CpG) in promoter causes silencing of genes

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11
Q

Principle of DNA methylation

A

[1] Silencing genes to reduce unnecessary gene expression

[2] Methylation of CG dinucleotide (CpG) in promoter causes silencing of genes

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12
Q

CpG

A

Cytosine-phosphate-guanine

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13
Q

Characteristic of promoter region related to methylation

A

10-20x more CpG dinucleotides –> more affected by methylation

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14
Q

Effect of methylation on promoter

A

[1] High methylation / hypermethylation –> transcriptionally silent
[2] Low methylation / hypomethylation –> transcriptionally active

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15
Q

Other effects of methylation

A

Prevent binding of regulatory factors by stearic hindrance

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16
Q

Mediators of methylation

A

MeCP1 and MeCP2 (Methylated CpG binding proteins 1 & 2)

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17
Q

Fragile X syndrome

A

Mental retardation caused by expansion of CGG at 5’ UTR of FMR1 gene –> increased methylation causing silencing of FMR and brain-specific mRNA during development

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18
Q

Histones

A

Order DNA into nucleosomes, (+) charged due to high lysine and arginine content –> form ionic bonds with (-) charged DNA

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19
Q

Principle of histone acetylation

A

Acetyl groups attached to lysine in histone, forming tails that protrude from the nucleosome –> repulsion between tails causes more open DNA structure

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20
Q

Effect of histone acetylation

A

More acetylation –> more open DNA structure –> more accessible for transcription

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21
Q

Histone aminotransferases - function?

A

Eliminate positive charge on lysine, decreasing interaction of histone and negative DNA

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22
Q

Histone deacetylases - function?

A

Restore positive charge of lysine, increasing interaction of histone and negative DNA

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23
Q

Relationship between DNA methylation and histone acetylation

A

Reciprocal –> when DNA is methylated, histone is deacetylated, and vice versa

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24
Q

Sites of histone methylation to hinder transcription

A

Histone H3 lysine 9, 27

Histone H4 lysine 2

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25
Q

Sites of histone methylation to enhance transcription

A

Histone H3 lysine 4, 27, 36

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26
Q

Effect of histone methylation

A

Activate or deactivate DNA, depending on methylation site

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27
Q

Ubiquitin - function?

A

Marks defective protein for destruction

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28
Q

Effects of histone ubiquitination

A

[1] disruption and spreading of chromatin allowing binding of transcription proteins;
[2] binding of effector proteins for other regulatory processes;
[3] allows other histone modifications to occur

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29
Q

Principle of histone ubiquitination

A

Attachment of ubiquitin to histone in order to modulate gene expression

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30
Q

Histone ubiquitination is required for these specific regulatory processes

A

di- and tri- methylation of H3 lysine 4 and lysine 79

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31
Q

Effects of histone phosphorylation

A

[1] chromatin condensation during mitosis;

[2] unknown effect on gene regulation

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32
Q

Modulator of histone ubiquitination

A

Ubiquitine proteases (mediate reversible process of ubiquitination)

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33
Q

Site of histone phosphorylation for chromatin condensation

A

H3 serine 10 and serine 28

34
Q

Gene regulation at level of DNA - other types (5)?

A

[1] gene deletion (ex. RBCs);
[2] gene duplication;
[3] gene amplification;
[4] DNA rearrangement (ex. antigen recognition);
[5] chemical modification of DNA (ex. methylated globin genes)

35
Q

Tumor suppressor genes - significance?

A

important in cell cycle & control of cell division –> prevent changes in methylation (mutation can lead to cancer)

36
Q

Trans acting factors - characteristics [4]?

A

[1] proteins with 2 binding domains –> DNA binding domain, transcription activation domain;
[2] coded by distant genes;
[3] migrate to site of action;
[4] bind to cis acting elements

37
Q

Trans-acting factors - function?

A

Transcriptional activators / transcription factors

38
Q

How can trans-acting factors control gene expression [4]?

A

[1] expression of factors in a specific type of tissue;
[2] expression of factors at a specific time of development;
[3] may be required for protein modification;
[4] may be activated by ligand binding

39
Q

Trans-acting factors interact with cis-acting elements through:______ [4]

A

[1] Helix-turn-helix,
[2] Helix-loop-helix;
[3] zinc finger;
[4] leucine zipper

40
Q

Trans acting factors - significance in transcription

A

RNA polymerase II cannot initiate transcription alone; it needs transcription factors!

41
Q

Cis-acting elements - characteristics [3]

A

[1] DNA sequences close to a gene that are required for gene expression;
[2] lie on the same strand as the gene being transcribed;
[3] bind to trans-acting factors

42
Q

Cis-acting elements - features [6]

A 
[1] promoters; 
[2] enhancers; 
[3] terminators; 
[4] silencers; 
[5] insulators; 
[6] response elements
43
Q

Promoters

A

[1] located upstream of the start point;

[2] determine if transcription begins, and/or where transcription begins

44
Q

Main mechanisms of transcriptional control

A

Through action of trans-acting factors (transcription factors) and cis-acting factors (promoters, terminators, enhancers, silencers, insulators, response elements, etc.)

45
Q

Examples of promoters

A

TATA box, Initiator (Inr)

46
Q

Promoter-proximal elements

A

Upstream to promoter; tightens control; helps promoter do its job

47
Q

Examples of promoter-proximal elements

A

CAAT box, GC box

48
Q

Terminators

A

Downstream of coding segment, recognized by RNA polymerase as a signal to stop transcription –> stop codon (UAA, UAG, UGA)

49
Q

Enhancer

A

Greatly enhances transcription by increasing rate of initiation of transcription by RNA polymerase II; varied location

50
Q

Silencer

A

DNA sequence that helps reduce or shut off the expression of a nearby gene; binding to trans-acting factors causes repression of gene expression

51
Q

Location of insulators [2]

A

[1] between enhancer and promoter of adjacent genes;

[2] between silencer and promoter of adjacent genes

52
Q

Insulator

A

DNA sequence that prevents a gene from being influenced by activation or repression of its neighbors

53
Q

Factors conferring specificity of tissue gene regulation [2]

A

[1] presence or absence of transcription factors;

[2] use of alternative promoters for a single gene

54
Q

Transcription factors may be activated by: ____ [2]

A

[1] environmental stimuli (ex. Heat shock TF);

[2] signals from other cells (ex. hormones, growth factors)

55
Q

Response elements

A

DNA sequence that allows specific stimuli (e.g. hormones, cAMP, IGF-1) to control gene expression

56
Q

Mechanisms in post-translational control [3]

A

[1] alternative splicing;
[2] alternative polyadenylation;
[3] RNA editing

57
Q

Significance of alternative promoters

A

A single gene may have different promoters at different exons, in order to express different isoforms of the gene in different tissues (ex. Human Dystrophin Gene)

58
Q

Alternative splicing

A

Production of multiple related proteins (isoforms) from a single gene; different exon and intron combinations from the same gene

59
Q

Alternative polyadenylation vs alternative promoter

A

[1] alternative promoter –> different start, same stop;

[2] alternative polyadenylation –> same start, different stop

60
Q

Alternative polyadenylation

A

Variation in the location of the poly-A-tail produce different proteins from the same gene

61
Q

RNA editing

A

Insertion, deletion, substitution of nucleotides to create protein variations (similar to missense, nonsense, and framerate mutations) –> ex. ApoB100 & ApoB48

62
Q

Gene - historical definition

A

Region of the genome that segregates as a single unit during meiosis and gives rise to a definable phenotypic trait (ex. red eyes vs white eyes)

63
Q

Gene - molecular definition

A

Stretch of DNA transcribed into RNA, coding for a single polypeptide chain

64
Q

Gene - modern definition

A

DNA sequence that is transcribed as a single unit and encodes one set of closely related polypeptide chains

65
Q

RNA Transport Control

A

Nucleases may degrade mRNA as it travels from nucleus to cytoplasm

66
Q

What determines half-life of mRNA

A

Sequences at the 3’-end (poly-A-tail)

67
Q

Mechansims of translational control [2]

A

[1] bidning of protein factors to response elements in mRNA;
[2] phosphorylation of initiation factors

68
Q

Fates of unfolded proteins after emerging from ribosome [3]

A

[1] correctly folded without help;
[2] correctly folded with help from molecular chaperone;
[3] cannot be correctly folded, digested by proteasome

69
Q

Significance of short mRNA half-life

A

Constant transcription is needed to maintain protein levels

70
Q

Why is it important to correctly fold proteins?

A

Incorrectly folded proteins may form clumps, precipitate, and damage cells

71
Q

Molecular chaperones

A

HSP70 and HSP60-like proteins that aid in folding newly synthesized proteins

72
Q

Alzheimer’s disease

A

Accumulation of misfolded protein amyloid beta in the brain parenchyma & blood vessels

73
Q

Creutzfeldt-Jakob disease

A

Results from a change in configuration (alpha helix to beta sheet) in PrP^c due to infection by prions –> formation of insoluble aggregates of fibrils in the brain

74
Q

Huntington’s disease

A

Amplification of CAG codon (glutamine) results in abnormal translation of mRNA protein to huntingtin with abnormal repeats –> aggregation of glutamine –> neurodegenerative disorder

75
Q

Role of ubiquitin in post-translational control

A

Misfolded proteins are marked for degeneration by ubiquitin

76
Q

Proto-oncogene

A

Normal gene that can become an oncogene due to mutations or increased expression

77
Q

Oncogene

A

Protein-encoding gene which, when deregulated, participates in the onset and development of cancer

78
Q

Causes of cancer [6]

A 
[1] Viruses; 
[2] tobacco smoke; 
[3] food; 
[4] radiation; 
[5] chemicals; 
[6] pollution
79
Q

Tumor supressor gene

A

Also called anti-oncogenes; protects a cell from mutating into a cancer cell

[OS 201] 3rd Exam (10 decks)

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