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Bio 131 > Final Unit: Gene Expression > Flashcards

Final Unit: Gene Expression Flashcards

(68 cards)

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1
Q

What is gene regulation?

A

The ability of cells to control their level of gene expression

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2
Q

Prokaryotes and eukaryotes can control level of gene expression at the levels of …

A

Transcription, Translation, Post-translation

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3
Q

What are three additional levels of control are unique to eukaryotes?

A
  1. Chromatin remodeling
  2. RNA processing
  3. Regulation of mRNA life span or stability
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4
Q

What helps DNA condense into such a small size?

A

Nucleosomes

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5
Q

What are nucleosomes and how are they produced?

A

Smallest structural component of chromatin

DNA wraps around histones

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6
Q

After the nucleosome is formed, what is next?

A

The nucleosomes get formed into a 30 nm fiber

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7
Q

What happens to the fiber of nucleosomes?

A

It is looped into place within the nuclear matrix

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8
Q

What is chromatin remodeling?

A

When DNA near the promoter is released from tight interactions with proteins

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9
Q

Is DNA unaccessible when the chromatin is condensed or decondensed?

A

Condensed

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10
Q

What is chromatin?

A

A complex of DNA and proteins

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11
Q

What is euchromatin?

A

Lightly stained, more open (decondensed) chromatin

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12
Q

What is heterochromatin?

A

Darkly stained, more closed (condensed) chromatin

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13
Q

Which type of chromatin contains the majority of eukaryotic genes?

A

Euchromatin

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14
Q

Which type of chromatin is associated with low gene transcription?

A

Heterochromatin

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15
Q

In preparation for transcription, nucleosomes are altered by what?

A

Multiprotein complexes

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16
Q

What are the two types of chromatin remodeling?

A
  1. Local histone mobilization
  2. Histone modifications
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17
Q

In local histone mobilization, what do chromatin remodeling complexes use to reshape chromatin?

A

ATP

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18
Q

What are the four mechanisms for local histone mobilization?

A
  1. Unwrapping
  2. Sliding
  3. Ejection
  4. Dimer exchange
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19
Q

What are the three mechanisms that histone modifications use?

A
  1. Acetylation
  2. De-acetylation
  3. Methylation
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20
Q

What is the histone code hypothesis?

A

Particular combinations of histone modifications set the state of chromatin condensation for a gene

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21
Q

Which enzyme facilitates acetylation of histones?

A

Histone acetyl transferases (HATs)

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22
Q

What does HAT add? To where?

A

Negatively charged acetyl groups to the positively charged lysine residues in histones

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23
Q

What is the effect of histone acetylation?

A

Neutralizing a histone’s positive charge

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24
Q

What two things does histone acetylation weaken?

A
  1. Weakens histone-DNA interactions
  2. Weakens nucleosome-nucleosome interactions
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25
What is the end result of acetylation?
Decondensed chromatin --> allow gene expression
26
Which enzyme facilitates de-acetylation of histones?
Histone deacetylases (HDACs)
27
What does HDAC remove? What is the effect of this?
Removes the acetyl groups from histones which therefore reverses the effects of acetylation
28
What is the end result of de-acetylation?
Chromatin condenses --> transcription repressed
29
Which enzyme facilitates histone methylation?
DNA methyltransferase
30
What does DNA methyltransferase do?
Adds methyl groups to cytosine residues of DNA
31
What is the end result of histone methylation?
Transcription repression
32
What is epigenetic inheritance?
Patterns of inheritance not due to differences in gene sequences
33
What two patterns do daughter cells inherit?
1. Patterns of histone modification 2. Patterns of gene expression
34
What happens to chromatin modifications at fertilization?
Reprogramming resets the chromatin modifications
35
What are the three requirements for the initiation of transcription?
1. Unwinding of DNA 2. Basal trancription factors at all gene promoters 3. All eukaryotic promoters are bound by the TATA-binding protein (TBP)
36
What are transcription factors?
Proteins that causes genes to be turned on or off
37
What is another name for basal transcription factors?
General transcription factors
38
What do basal transcription factors bind to?
DNA
39
What do regulatory transcription factors bind to?
Enhancers
40
What are the three components of eukaryotic promoters?
1. TATA box 2. Transcriptional start site 3. Regulator/response elements
41
What are the two components of low level basal transcription?
TATA box and transcriptional start site
42
What is the main component of activated transcription?
Regulatory elements
43
What is the TATA box's sequence of bases?
5' TATAAAA 3'
44
What is the role of the TATA box?
Determine the starting point for transcription
45
Where does transcription begin?
At the transcriptional start site
46
The transcriptional start site and TATA box form the ___
Core promoter
47
What are regulatory/response elements?
DNA sequences that are recognized by regulatory proteins that control initiation of transcription
48
What are three examples of regulatory elements?
Enhancers, silencers, promoter-proximal elements
49
Where are promoter-proximal elements located?
Just upstream of the promoter and the transcription start site
50
What do enhancers bind?
Specific transcription factors called activators
51
What do silencers bind?
Specific proteins called repressors to inhibit transcription
52
Do enhancers increase or decrease gene expression?
Increase
53
Where can enhancers be located?
Upstream or downstream
54
What are three differences between promoters and enhancers?
1. Promoters are immediately upstream 2. Promoters function in only one orientation 3. Enhancers determine the rate and efficiency of transcription
55
How do transcription factors recognize DNA?
The edges of an AT base pair and a GC base pair have different surface shapes
56
Why do transcription factors bind to a specific enhancer?
Because of complementary interactions between base pairs and its amino acids
57
Alternative splicing is regulated by proteins that ... (2 things)
1. Bind to the mRNAs in the nucleus 2. Interact with the spliceosomes
58
Frequency of alternative splicing increases with more _______
Biological complexity
59
What is RNA interference?
Silencing of an endogenous gene caused by a complementary double-stranded RNA
60
Which type of RNA is critical for RNA interference?
microRNA
61
What does miRNA bind to?
The RISC protein complex
62
What does the RISC protein complex with miRNA bind to?
Complementary sequences of mRNA
63
What happens once the targeted mRNA is attached to the RISC complex with miRNA?
The target mRNA is degraded
64
In response to viral infection, translation can be slowed or stopped by ...
Phosphorylation of a certain ribosomal protein
65
What are two differences in chromatin remodeling of bacteria vs eukaryotes?
1. Bacteria has limited packaging of DNA whereas Eukaryotes have extensive packaging of DNA 2. Chromatin must be decondensed for transcription to begin in eukaryotes, whereas remodeling is not a major issue in bacteria
66
What are three differences in transcription of bacteria vs eukaryotes?
1. In eukaryotes, positive and negative control by regulatory proteins acts close to and far from the promoter. On the other hand, that only happens close to the promoter in bacteria. 2. Bacteria needs sigma to interact with the promoter, whereas eukaryotes need a large set of basal transcription factors 3. Eukaryotes need a mediator
67
What is one difference in RNA processing of bacteria vs eukaryotes?
There is no RNA processing in bacteria
68
What is one difference in mRNA stability of bacteria vs eukaryotes?
Rare used in bacteria, commonly used in eukaryotes

Bio 131 (25 decks)

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