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Bio 131 > Final Unit: Gene Expression > Flashcards

Final Unit: Gene Expression Flashcards

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
Q

What is the end result of acetylation?

A

Decondensed chromatin –> allow gene expression

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26
Q

Which enzyme facilitates de-acetylation of histones?

A

Histone deacetylases (HDACs)

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27
Q

What does HDAC remove? What is the effect of this?

A

Removes the acetyl groups from histones which therefore reverses the effects of acetylation

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28
Q

What is the end result of de-acetylation?

A

Chromatin condenses –> transcription repressed

29
Q

Which enzyme facilitates histone methylation?

A

DNA methyltransferase

30
Q

What does DNA methyltransferase do?

A

Adds methyl groups to cytosine residues of DNA

31
Q

What is the end result of histone methylation?

A

Transcription repression

32
Q

What is epigenetic inheritance?

A

Patterns of inheritance not due to differences in gene sequences

33
Q

What two patterns do daughter cells inherit?

A
  1. Patterns of histone modification
  2. Patterns of gene expression
34
Q

What happens to chromatin modifications at fertilization?

A

Reprogramming resets the chromatin modifications

35
Q

What are the three requirements for the initiation of transcription?

A
  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
Q

What are transcription factors?

A

Proteins that causes genes to be turned on or off

37
Q

What is another name for basal transcription factors?

A

General transcription factors

38
Q

What do basal transcription factors bind to?

A

DNA

39
Q

What do regulatory transcription factors bind to?

A

Enhancers

40
Q

What are the three components of eukaryotic promoters?

A
  1. TATA box
  2. Transcriptional start site
  3. Regulator/response elements
41
Q

What are the two components of low level basal transcription?

A

TATA box and transcriptional start site

42
Q

What is the main component of activated transcription?

A

Regulatory elements

43
Q

What is the TATA box’s sequence of bases?

A

5’ TATAAAA 3’

44
Q

What is the role of the TATA box?

A

Determine the starting point for transcription

45
Q

Where does transcription begin?

A

At the transcriptional start site

46
Q

The transcriptional start site and TATA box form the ___

A

Core promoter

47
Q

What are regulatory/response elements?

A

DNA sequences that are recognized by regulatory proteins that control initiation of transcription

48
Q

What are three examples of regulatory elements?

A

Enhancers, silencers, promoter-proximal elements

49
Q

Where are promoter-proximal elements located?

A

Just upstream of the promoter and the transcription start site

50
Q

What do enhancers bind?

A

Specific transcription factors called activators

51
Q

What do silencers bind?

A

Specific proteins called repressors to inhibit transcription

52
Q

Do enhancers increase or decrease gene expression?

A

Increase

53
Q

Where can enhancers be located?

A

Upstream or downstream

54
Q

What are three differences between promoters and enhancers?

A
  1. Promoters are immediately upstream
  2. Promoters function in only one orientation
  3. Enhancers determine the rate and efficiency of transcription
55
Q

How do transcription factors recognize DNA?

A

The edges of an AT base pair and a GC base pair have different surface shapes

56
Q

Why do transcription factors bind to a specific enhancer?

A

Because of complementary interactions between base pairs and its amino acids

57
Q

Alternative splicing is regulated by proteins that … (2 things)

A
  1. Bind to the mRNAs in the nucleus
  2. Interact with the spliceosomes
58
Q

Frequency of alternative splicing increases with more _______

A

Biological complexity

59
Q

What is RNA interference?

A

Silencing of an endogenous gene caused by a complementary double-stranded RNA

60
Q

Which type of RNA is critical for RNA interference?

A

microRNA

61
Q

What does miRNA bind to?

A

The RISC protein complex

62
Q

What does the RISC protein complex with miRNA bind to?

A

Complementary sequences of mRNA

63
Q

What happens once the targeted mRNA is attached to the RISC complex with miRNA?

A

The target mRNA is degraded

64
Q

In response to viral infection, translation can be slowed or stopped by …

A

Phosphorylation of a certain ribosomal protein

65
Q

What are two differences in chromatin remodeling of bacteria vs eukaryotes?

A
  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
Q

What are three differences in transcription of bacteria vs eukaryotes?

A
  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
Q

What is one difference in RNA processing of bacteria vs eukaryotes?

A

There is no RNA processing in bacteria

68
Q

What is one difference in mRNA stability of bacteria vs eukaryotes?

A

Rare used in bacteria, commonly used in eukaryotes

Bio 131 (25 decks)

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