Genetics Test 3

studied byStudied by 129 people
5.0(1)
Get a hint
Hint

Why regulate gene expression?

1 / 170

flashcard set

Earn XP

Description and Tags

171 Terms

1

Why regulate gene expression?

  1. Respond to environmental conditions

  2. Express genes appropriate to developmental stages of life cycle

  3. Express genes appropriate to cell type

New cards
2

Transcriptional Regulation in Eukaryotes

  1. Regulatory Transcription factors

  2. Chromatin / Histone Modifications

  3. DNA methylation

New cards
3

General transcription factors

  • required for binding of RNA pol to core promoter and progression to elongation stage

  • necessary for basal transcription

  • Recall TFIID, TFIIH, etc.

New cards
4

Regulatory transcription factors

  • regulate the rate of transcription of target genes

  • influence ability of RNA pol to begin transcription of a particular gene

  • **2-3% of human genes encode transcription factors

New cards
5

regulatory transcription factors recognize

cis regulatory elements near the core promoter

New cards
6

regulatory TF’s: activators

proteins with DNA-binding motifs

New cards
7

regulatory elements (control elements / regulatory sequences): enhancers

  • most upstream of promoter, within few hundred bps

  • many orientation-independent

New cards
8

______ bind ________ and up-regulate gene expression

activators, enhancers

New cards
9

regulatory TF’s: repressor

proteins with DNA-binding motifs

(repressor binds silencer)

New cards
10

regulatory elements (control elements, regulatory sequences): silencers

  • most upstream of promoter within a few hundred bps

  • many-orientation dependent

  • repressor - silencer

New cards
11

_____ binds ______ and down regulates expression

repressors, silencers

New cards
12

Structural features of regulatory TFs

-Regulatory TF’s contain motifs that contribute to their activity

  • DNA binding domain

  • binding site for effector molecules

  • dimerization domains

New cards
13

mechanism of action

most regulatory TFs don’t bind directly to RNA poymerase

New cards
14

1) Interact with TFIID

  • Transcription activation occurs when activator complex recruits TFIID

  • Transcription repression occurs when repressor inhibits binding of TFIID to core promoter

New cards
15

2) Interact with mediator

  • Activation: activator protein + mediator, phosphorylation of C-terminal domain of RNA pol enhanced, GTFs released and RNA poly proceeds to elongation

  • Repression: repressor protein + mediator, prevents phosphorylation of C-terminal domain of RNA pol, inhibits switch to elongation stage

New cards
16

steroid hormones

produced by endocrine glands, secreted into the bloodstream, diffuse into cells

New cards
17

steroid receptors

regulatory TFs that respond to steroid hormones

New cards
18

GRE (Glucocorticoid Response Elements)

Enhancers where steroid receptors bind (near dozens of different genes)

New cards
19

responding to extracellular signals

  • most signaling molecules can’t enter cells

  • detected at surface, message relayed to TF’s inside the cell]

  • ex. G-coupled protein receptors (cAMP levels)

New cards
20

Cyclic AMP Response Element Binding protein (CREB)

activator - activated by increased cAMP levels and phosphorylation

New cards
21

Cyclic AMP Response Element (CRE)

enhancer

New cards
22

gene body

A region DNA whose nucleotide sequence encodes for a transcribed RNA and for those that go on to be translated to protein it typically contains exons and introns that will
be used to create primary RNA transcript

New cards
23

5’ UTR

A region of DNA/RNA from the 5’ end to the position of the first codon used in translation initiation (post-transcriptional control)

New cards
24

3’ UTR

A region of DNA/RNA from the 3’ end to the position of the last codon near the termination of transcription and used in translation for stability (post-transcriptional control)

New cards
25

Enhancer

A region or site of DNA to which transcription factor and co-activator binding occurs and regulates promoter availability

New cards
26

silencer

A region of DNA that binds negative regulatory elements for transcription suppression

New cards
27

promoter

A region of DNA on which transcription machinery assembles including RNA polymerase

New cards
28

insulators

A region of DNA that binds proteins to help define chromatin domains and protect genes from inappropriate signals, in human this is a CTCF binding site

New cards
29

Chromatine Structure

  • DNA is condensed/compact

  • several levels of compaction

  • space constraints

  • organization of chromosomes into domains

  • affects access to transcription machinery

New cards
30

chromatin

DNA plus associated proteins

New cards
31

chromatin structure is

dynamic

New cards
32

DNA wraps around

histone proteins (nucleosome)

  • 146 bps DNA in wrap

  • linker DNA more accessible

New cards
33

core histones (octamer)

2* H2A, H2B, H3, H4

New cards
34

linker histone

H1

New cards
35

histones

  • basic(positively charged) proteins

  • contain many Lys and Arg

  • bind to phosphate in DNA backbone

New cards
36

Histone structure

  • globular domain

  • flexible, charged ‘tail’

New cards
37

nucleosomes associate to form a

30 nm fiber - histone H1 involved

  • structure still not fully elucidated

New cards
38

chromatin remodeling

chromatin structure is dynamic, and influences levels of gene expression

New cards
39

ATP-dependent chromatin remodeling can alter

chromatin structure

  • small local changes or large-scale

  • multiprotein complexes move or modify nucleosomes

  • this changes compaction level and accessibility to transcription

New cards
40

histone modifications can alter

transcription levels

New cards
41

acetylation

looser wrap

New cards
42

methylation

tighter wrap

New cards
43

histone code

histone modifications occur in patterns that are recognized by proteins

  • pattern of modifications provide binding sites for proteins that specify alterations to be made to chromatin structure

New cards
44

histone variants

  • human genome contains over 70 histone genes

  • most encode standard histones

  • few have accumulated mutations

New cards
45

nucleosome-free regions (NFR)

  • found at the beginning and end of many genes

  • less regularly distributed elsewhere

New cards
46

tightly packed nucleosome

inaccessible protein

New cards
47

caveats to protein accessibility

epigenetic modifications and methylation/acetylation

New cards
48

DNA methylation

silences gene expression

New cards
49

DNA methylation enzyme

DNA methyltransferase

New cards
50

DNA can be

methylated on cytosine

  • CpG islands near promoters of many genes

New cards
51

methylation of CpG islands

silences gene expression

  • methylation influences TF binding

  • methyl-CpG-binding proteins recruit factors that increase chromatin compaction

New cards
52

housekeeping genes

  • expressed in most cell types

  • CpG islands unmethylated

New cards
53

tissue-specific genes

  • CpG islands unmethylated in tissues where expression is needed

  • CpG islands methylated in non-target tissues

New cards
54

Transcriptional silencing by methylation

a. methylation inhibits the binding of an activator protein

b. Methyl-CpG-binding protein recruits proteins that close chromatin structure

New cards
55

DNA methylation is

heritable

  • Methylated DNA sequences are inherited during cell division

  • de novo methylation is infrequent, highly regulated

  • genomic imprinting, epigenetics

New cards
56

combinatorial control

multiple factors can contribute to regulation of one single gene

New cards
57

activator and repressor activity can be modulated

effectors, protein-protein interactions, covalent modification

New cards
58

regulatory proteins can alter

nucleosomes near the promoter

New cards
59

DNA methylation inhibits transcription by

preventing binding of the activator and recruiting proteins that compact chromatin

New cards
60

Transcriptional regulation of gene expression

  • regulatory TFs

  • DNA methylation

  • nucleosome location/composition

New cards
61

Translational regulation of gene expression

  • small non-coding RNA

  • RNA stability

  • feedback inhibition

  • covalent modifications

New cards
62

Histone acetyltransferases are directly involved in which of the following?

chemical modification of histones

New cards
63

Transcription factors are proteins that influence the ability of the RNA polymerase to transcribe a gene.

true

New cards
64

Activator proteins bind to silencer sequences and repressor proteins bind to enhancer sequences.

false

New cards
65

A heterodimer occurs when two identical transcription factors interact on a sequence of DNA.

false

New cards
66

A repressor protein would enhance the ability of TFIID to bind to the TATA box of the promoter.

False

New cards
67

Steroid hormones are an example of an effector which regulates regulatory transcription factor activity.

True

New cards
68

DNA that contains actively transcribed genes would most likely contain chromatin in the closed configuration.

False

New cards
69

Nucleosome location may be changed by a process called ATP-dependent chromatin remodeling.

True

New cards
70

DNA methylation usually activates gene expression.

False - it inhibits it

New cards
71

Which of the following is the most likely location of an insulator sequence?

Between two genes

New cards
72

What general transcription factor is most often affected by regulatory transcription factors?

TFIID

New cards
73

CpG islands are associated with which of the following?

DNA methylation

New cards
74

Housekeeping genes are unmethylated and active in most cells

true

New cards
75

A particular cell contains all of the standard histones but lacks several histone variants. Which of the following MAY be true of this cell?

The cell will express different sets of genes than other cells in the same organism

New cards
76

The activity of some transcription factors can be regulated by covalent modifications.

True

New cards
77

nucleosome positioning

structure is fluid and can be changed by modifications, evictions, variants

New cards
78

schizophrenia and chromatin accessibility

  • Very few coding mutations discovered

  • must mutations are SNPs lying in non-coding regions

New cards
79

transposable elements

repetitive DNA

New cards
80

DNA transposases

enzymes that move discrete segments of DNA from one location in the genome to a new site

New cards
81

retrotransposons

use RNA instead of DNA

New cards
82

Tn5

bacterial cut and paste, inserts a fragment of DNA in a new location

  • altered to carry and insert two double stranded adaptors

New cards
83

what is epigenetics

  • changes in gene expression without change in DNA sequence

  • passed from cell to cell

  • can last lifetime of individual

  • not permanent over multiple generations

  • reversible

New cards
84

epigenetic inheritance

from parent to offspring

New cards
85

epigenetics deals with

the markings that are placed ‘on’ the genome

  • marks can be ON DNA itself (CpG islands)

  • marks can be on the histones

New cards
86

mechanisms of Epigenetic gene regulation

  • DNA methylation

  • Chromatin remodeling

  • Covalent histone modification

  • Localization of histone variant

New cards
87

HP1 and PTMs

specific proteins bind to them

New cards
88

PTM

post-translational modifications

New cards
89

HP1

  • binds methylated histones

  • pulls nucleosomes closer together

  • has a reader domain

New cards
90

role of heterochromatin

  • gene silencing

  • prevent transposable element movement

  • prevent viral proliferation

New cards
91

heterochromatin gene silencing

limit access to DNA-binding proteins

New cards
92

Heterochromatin prevents transposable element movement

  • random insertion in genes, can disrupt function

  • block movement of these DNA regions

New cards
93

Heterochromatin prevents viral proliferation

  • viral DNA integrated on genome

  • prevent viral activation/transcription

New cards
94

DNA methylation maintenance of heterochromatin after cell division

hemi-methylated DNA fully methylated via maintenance methylation

New cards
95

Histone modifications - maintenance of heterochromatin

histones recruit chromatin-modifying/remodeling enzymes to new histones/nucleosomes

New cards
96

DNA polymerase - maintenance of heterochromatin

recruits chromatin-modifying complexes

New cards
97

epigenetics and development

  • genetically programmed stages of development

  • many changes maintained by epigenetic regulation

New cards
98

genomic imprinting

  • occurs during gametogenesis

  • offspring expresses allele from one parent only

  • in germ cells, base imprint erased and reestablished based on sex of individual

New cards
99

X chromosome inactivation

  • occurs during embryonic development of female mammals

  • ‘count’ number of X chromosomes, silence all but 1

  • inactivation occurs at X inactivation center

  • dosage compensation

New cards
100

Before inactivation

  • Tsix expressed from both X chromosomes

  • expression stimulated by pluripotency factors

  • Tsix expression recruits DNA methyltransferase, silence Xist promoter

New cards

Explore top notes

note Note
studied byStudied by 12 people
... ago
5.0(1)
note Note
studied byStudied by 24 people
... ago
5.0(1)
note Note
studied byStudied by 20 people
... ago
5.0(1)
note Note
studied byStudied by 13 people
... ago
5.0(1)
note Note
studied byStudied by 295 people
... ago
5.0(11)
note Note
studied byStudied by 17 people
... ago
4.0(1)
note Note
studied byStudied by 123 people
... ago
5.0(2)
note Note
studied byStudied by 606 people
... ago
5.0(2)

Explore top flashcards

flashcards Flashcard (40)
studied byStudied by 3 people
... ago
5.0(1)
flashcards Flashcard (20)
studied byStudied by 6 people
... ago
5.0(1)
flashcards Flashcard (95)
studied byStudied by 9 people
... ago
5.0(2)
flashcards Flashcard (41)
studied byStudied by 15 people
... ago
5.0(1)
flashcards Flashcard (52)
studied byStudied by 12 people
... ago
5.0(1)
flashcards Flashcard (26)
studied byStudied by 5 people
... ago
5.0(1)
flashcards Flashcard (45)
studied byStudied by 1 person
... ago
5.0(1)
flashcards Flashcard (58)
studied byStudied by 32 people
... ago
5.0(6)
robot