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M2M Unit I > Gene Expression, Mitosis, & Diseases > Flashcards

Gene Expression, Mitosis, & Diseases Flashcards

1
Q

What are the two main mechanisms used to control gene expression?

A

DNA control elements (cis) & transcriptional activators/suppressors (trans)

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2
Q

What is the TATA box on DNA?

A

A promoter that is a bit upstream of transcription start; determines site of transcription initiation and directs binding of RNA Pol II

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3
Q

What is a promoter proximal element?

A

Further upstream of start site of transcription than is the TATA box; helps regulate transcription & can be cell type specific

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4
Q

What is an enhancer?

A

An enhancer contains many control elements. It is very upstream or downstream to start site of transcription

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5
Q

Thalassemias, Hemophilia B-leyden, and Fragile X-Syndrome are associated with mutations in what?

A

DNA control elements

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6
Q

Describe Thalassemias

A

An anemia associated with slicing mutations of genes. Also due to mutations in betaglobin gene

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7
Q

Describe Hemophilia B-leyden

A

An X-linked clotting disorder in which only 1% of normal factor 9 is made

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8
Q

Describe Fragile X-Syndrome

A

An X-linked defect in a control element called efemar which controls a protein that transports mRNAs and synapes; frequent cause of mental retardation

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9
Q

Transcriptional activators are composed of which distinct functional domains?

A

DNA-binding domain, activation domain, flexible protein domain

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10
Q

DNA-Binding domains of transcriptional activators fall into which four classes?

A

Homeodomain structure, zinc-finger, basic leaucin zipper (bZIP), & helix-loop-helix

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11
Q

Describe craniosynostosis

A

A disease in which the cranial bones fuse prematurely. This is caused when a small defect in a homeodomain protein MSX2 causes it to bind DNA more tightly, resulting in a gain-of-function

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12
Q

A damage in the homeodomain protein MSX2 is associated with which abnormality?

A

Craniosynostosis

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13
Q

Describe Androgen Insensitivity Syndrome

A

A mutation in the DNA-binding or ligand binding domain of the androgen protein (zinc finger) causes the androgen receptor to be less responsive to androgen

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14
Q

Describe Waardenburg Syndrome Type II

A

~15% of cases result from a mutation in MITF gene - affects transcription of genes important in pigmentation and hearing

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15
Q

Which types of transcriptional activators can form dimers?

A

bZIP, helix-loop-helix, & zinc finger

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16
Q

What is the benefit of dimerizing transcriptional activators together?

A

Combinatorial Control! If each activator recognizes a specific DNA sequence, then combining multiple allows for more transcriptional control.

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17
Q

What is the function of activation domains of transcriptional activators?

A

To recruit coactivators and general transcription machinery

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18
Q

Describe the structure of chromatin

A

The fundamental repeating unit of chromatin is the nucleosome, which contains DNA wrapped around an octomer of histone proteins

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19
Q

Describe ATP-dependent chromatin remodelers

A

Using ATP hydrolysis, the histone-DNA contact is broke in order to slide the histone along the DNA to uncover an area of DNA.

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20
Q

What is the main site of post-translational histone modification?

A

Unstructured tails of histones

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21
Q

What do histone acetyl transferases (HATs) do?

A

They hyperacetylate histone lysine N-terminal tails, neutralizing the charge and allowing the chromatin to “open up” and make room for transcription.

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22
Q

What do histone deacetylases (HDACs) do?

A

HDACs deacetylate histone N-terminal tails to tight up chromatin and repress transcription

23
Q

Do activators or repressors recruit HATs? HDACs?

A

Activators recruit HATs and repressors recruit HDACs

24
Q

Describe Rubinstein-Taybi Syndrome

A

Results from CBP haploinsufficiency; CBP is a co-activator for transcription factors; has HAT activity; may affect transcription of multiple gene targets

25
Q

What is euchromatin?

A

Where genes reside; the more accessible form of chromatin

26
Q

What is heterochromatin?

A

The part of chromatin that is always repressed because the DNA is inaccessible (found at centromeres, telomeres, and some internal chromosome positions)

27
Q

What is the difference between constitutive heterochromatin and facultative heterochromatin

A

Constitutive heterochromatin is permanently heterochromatin and contains satellite DNA. Facultative heterochromatin can change to euchromatin, depending on cell type or developmental stage, and is enriched in LINE sequences.

28
Q

What are the three domains of nuclear receptors?

A

Variable region, DNA-binding domain, Hormone-binding domain

29
Q

Estrogen induces transcriptional (activation/repression) through ER by causing its _________.

A

Activation; Dimerization

30
Q

How does Tamoxifen antagonize estrogen?

A

It binds to ER and prevents recruitment of HAT co-factors

31
Q

What are some ways we regulate the trans-acting factors themselves? (#5)

A
  1. Controlling protein conformation by binding a ligand
  2. Regulating entry into nucleus
  3. Regulating amount of transcription factor in the cell
  4. Regulating binding to DNA
  5. Phosphorylation of DNA-binding protein alters properties
32
Q

How do Id proteins negatively regulate DNA binding of bHLH proteins?

A

Heterodimerizing through their HLH domains but preventing DNA binding due to their lack of a basic domain

33
Q

What is the culprit protein of Alzheimer’s?

A

Amyloid beta42

34
Q

What is responsible for extracellular cleavage of beta-amyloid precursor protein (APP)?

A

alpha-secretase or beta-secretase

35
Q

What is responsible for transmembrane cleavage of beta-amyloid precursor protein (APP)?

A

gamma-secretase

36
Q

What is the phenotype of a gene defect of beta-amyloid precursor protein mutations on chromosome ____?

A

Increased production of beta-amyloid proteins of beta-amyloid protein 42; 21

37
Q

What is the phenotype of a gene defect of apolipoprotein E4 polymorphism on chromosome ____?

A

Increased density of beta-amyloid plaques and vascular deposits; 19

38
Q

What is the phenotype of a gene defect of Presenilin 1 mutations of chromosome ____?

A

Increased production of beta-amyloid protein 42; 14

39
Q

What is the phenotype of a gene defect of Presenilin 2 mutations of chromosome ____?

A

Increased production of beta-amyloid protein 42; 1

40
Q

What are three medications used to help treat Alzheimer’s symptoms?

A

NSAIDs, memantine, donepezil

41
Q

Prion protein is the product of which chromosomal gene?

A

PRNP

42
Q

PrP(c) is the normal prion protein. Which is the diseased protein?

A

PrP(Sc)

43
Q

What is the annual incidence of Prion disease?

A

~300

44
Q

CDK needs to be bound to what for it to be activated?

A

Cyclin

45
Q

RB (retinoblastoma protein) is an ____________ of the cell cycle. It is inhibited by ________________.

A

inhibitor; CDK phosphorylation

46
Q

What is RB attached to when it is active, and releases when it is phosphorylated by CDK?

A

E2F (transcription factor)

47
Q

What are the two classes of CDIs (CDK inhibitors)?

A

Ink4 (p15, p16, p18, p19) & Cip/Kip (p21, p27, p57_

48
Q

Which CDI is frequently mutated in cancer?

A

p21

49
Q

Ink4 family of CDIs is specific to kinases that bind to _________.

A

cycD family

50
Q

Cip/Kip CDIs are specific to kinases that bind to __________.

A

Cyc A, B, C, D, E families (non-specific)

51
Q

What does APC (anaphase promotion complex) do?

A

Inactivates Cdk

52
Q

Rad17 binds directly to DNA damage and induces what else?

A

ATM & ATR, which activate p53 and p21 which inhibit CDK and halt cell cycle.

53
Q

Name two pathways to repair DNA double strand breaks

A

Non-homologous end joining (NHEJ) and homologous recombination (HR)

54
Q

How does NHEJ work?

A

With recognition of the DS break by Ku -> Ku recruits DNA-PKcs -> nuclease removes damaged DNA and polymerase fills gap -> ligase restores phosphodiester backbone on both strands

M2M Unit I (4 decks)

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