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Biochemistry > Exam 2 Lecture 17 > Flashcards

Exam 2 Lecture 17 Flashcards

1
Q

How many types of RNA polymerases do eukaryotes have?

A

3

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2
Q

What is required for initiation in eukaryotes?

A

Transcription factors

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3
Q

What increases protein levels?

A

Transcription and protein synthesis

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4
Q

What decreases protein levels?

A

Degradation

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5
Q

What are some highlights of DNA replication?

A
  1. Uses DNA helicase, polymerase, and ligase
  2. Occurs in the S phase
  3. Occurs on both DNA strands
  4. RNA primer needed
  5. Entire genome is copied
  6. Produces DNA molecules that stay within the nucleus and do not get degraded
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6
Q

What are some highlights of gene transcription?

A
  1. Makes RNA from DNA template
  2. Uses DNA helicase, RNA polymerase
  3. Occurs in G1 and G2 phases of the cell cycle
  4. Occurs along one strand of DNA (template strand)
  5. No primer required
  6. Is a need driven process so only individual genes are copied
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7
Q

What is the main difference between prokaryote and eukaryote transcription?

A

Prokaryotes have continuous transcription and translation since they have no membrane bound organelles and no nucleus unlike eukaryotes

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8
Q

What are the 3 RNA polymerases in eukaryotes?

A

I: transcribes rRNA genes
II: transcribes the protein-encoding genes to produce mRNA
III: transcribes the genes for tRNAs and other small RNAs

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9
Q

What does the initiation complex consist of?

A

TATA binding protein (TBP) and other co-activating TBP-associated factors (TAFs)

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10
Q

What does the initiation complex do?

A

It recruits RNA polymerase II and other cofactor proteins like TFIIB, TFIIF, TFIIE, and TFIIH → TFII refers to transcription factors for RNAPII

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11
Q

Specific transcription factors can serve as what?

A

Activators or repressors/silencers and bind to the transcription activator complex and specific DNA enhancer regions

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12
Q

How many TF genes do humans have?

A

1700-1900 TF genes with lots of mechanisms for regulation

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13
Q

What is the function of RNA polymerase?

A

It encases the whole DNA molecule and adds NTPs depending on where it’s at and the sequence (DNA is in an alpha helix and only unwinds in the complex/transcription bubble)

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14
Q

What does the core part of Pol II do?

A

It unwinds DNA, builds RNA, and proofreads

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15
Q

Where are the sites of phosphorylation in RNA polymerase II?

A

The C terminus that has repeats of the sequence PTSPSYS

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16
Q

What is the first step in the pre-initiation complex in eukaryotic transcription?

A

TFIID + TFIIA +TFIIB = DAB complex

in which TFIID (TATA binding protein) bends the DNA and enables the other two factors, TFIIA and TFIIB, to bind

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17
Q

What is the second step in the formation of the pre-initiation complex?

A

RNA pol II and TFIIF bind in which TFIIF recruits RNAPII

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18
Q

What is the third step in the formation of the pre-initiation complex?

A

Multiple other general TFs bind

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19
Q

What is the final step in the formation of the pre-initiation complex?

A

TFIIH binds to the complex (the last to bind) and aids in transcription initiation

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20
Q

What are the three activities/mechanisms of TFIIH that is important for the start of transcription?

A

helicase, ATPase, and kinase

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21
Q

The final pre-initiation complex has how many polypeptides/proteins?

A

27

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22
Q

What are the steps of transcription once it is initiated by actions of TFIIH subunits?

A
  1. Phosphorylation of RNAPII by CDK7/cyclin H
  2. XPB helicase unwinds DNA (ATP dependent) and melts 1 DNA turn (opens up DNA a little) to generate the transcription bubble
  3. Allows RNAPII to initiate RNA synthesis
  4. RNAPII stalls after 10-13 units of RNA are synthesized
  5. XPB melts more dsDNA and RNAPII progresses along
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23
Q

What does the DAB complex consist of?

A

TFIID, TFIIA, and TFIIB

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24
Q

The DAB complex remains where after transcription?

A

It remains at the promoter (beginning) to initiate another round of transcription

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25
Q

Where do activators bind and what do they do?

A

Activators bind to enhancer regions and they increase transcription rate

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26
Q

Where do repressors bind to and what do they do?

A

They bind to silencer regions and decrease transcription rate

27
Q

What is the importance of having multiple TFs assemble at one promoter region?

A

Regulating the expression of the specific TFs allows an organism to control a large number of genes by a particular TF

28
Q

What do coactivators do?

A

They are “adapter” molecules that can integrate signals from activators and also possibly repressors

29
Q

How short is the DNA that is targeted by DNA binding motifs?

A

6-8 bp

30
Q

What are complex promoters?

A

They provide additional regulation for enhancing or repressing transcription → accelerates and provides specialized regulation

31
Q

What is the importance of the distal promoter?

A

It can regulate multiple transcription start sites and is needed to initiate transcription

32
Q

What are 2 examples of DNA response elements?

A
  1. SRE (sterol response element)
  2. CRE (cAMP response element) → activates PKA and target of PKA is CREB which can bind to CRE response binding → Gq activation is linked to transcription
33
Q

What is the example involving the LDL receptor gene?

A

SREBP-1A moves to the nucleus when cholesterol levels are low and binds SRE via HLH motifs → recruits CBP which couples chromatin remodeling to transcription factor recognition (HAT) activity → Sb1 binds GC boxes via Zn fingers

34
Q

What are some examples of transcription factor specificity in DNA recognition (aka modularity)?

A
  1. LMO2 binds a chromatin looping factor, bridges DNA binding proteins and stabilizes the bHLH heterodimer
  2. LDB1-LID folds on binding
  3. GATA1-NF binds DNA weakly and/or mediates protein binding
  4. Arg sidechains bind AT-rich minor groove
  5. Helices bind major grooves
  6. Basic domains fold on binding DNA
  7. bHLH subunits bind different half sites
35
Q

What are components of a distal promoter?

A

GATA site and E-box

36
Q

What percent of human genes have a TATA box in their proximal promoter?

A

10-24%

37
Q

How does TBP bind to the core promoter of genes that don’t have a TATA box?

A

TBP is loaded onto “compatible” (presumably AT rich regions) DNA by the 18 transcription accessory factors (TAFs) which are the other components of TFIID → the combined energy from weak DNA binding by TBP and strong DNA binding by the TAFs and TAF associated TFs make the interaction of TBP with the DNA sufficiently strong to cause the kink in the DNA

38
Q

What are nucleosomes?

A

They are DNA wound on nucleosomes like beads on a string

39
Q

What is the importance of chromatin remodeling?

A

A human cell contains (2 meters = 6 ft) of DNA so organization into chromatin enables the DNA to fit into a cell nucleus with a diameter of 6 micrometers

40
Q

Chromatin is as important/powerful as the preinitiation complex assembly for what?

A

Transcriptional control

41
Q

What is the difference between heterochromatin and euchromatin?

A

Heterochromatin has a condensed chromatin structure and is inactive for transcription. Euchromatin has a more relaxed chromatin structure and is active for transcription. → can activate or repress transcription

42
Q

The organization of DNA into chromatin and positioning of nucleosomes regulates protein access for what processes?

A

DNA replication, repair, recombination, and transcription → all processes that are dependent on having accessible DNA

43
Q

What is the histone code?

A

Patterns of histone covalent modification that alters higher order structure and recruits effector proteins to determine DNA transcription

44
Q

What are some examples of covalent modifications on histones by histone modifying enzymes?

A
  1. Methylation (lysine and arginine)
  2. Acetylation (lysine) using HATs and HDACs
  3. Phosphorylation (serine)
45
Q

Where does post-translational modification of histones occur?

A
  1. histone tails: unstructured in the context of one nucleosome and participate in higher order organization
  2. structured regions of the histone core
46
Q

What is the function of post-translational modification of histones?

A
  1. alter electrostatic interactions and loosen the nucleosome structure
  2. alter histone-DNA or histone-histone interactions within the core
  3. create binding sites to recruit proteins
47
Q

What are found in TFs and nucleosome-remodeling enzymes?

A
  1. Bromodomains that recognize acetyl-lysine

2. Chromodomains that recognize methyl-lysine

48
Q

What are ATP dependent nucleosome remodeling factors (ADNR)?

A

They catalyze the sliding of the nucleosome along the DNA to reorganize the position of nucleosomes and are thought to weaken histone-DNA contacts and generate access to DNA for interacting proteins (an example is Swi2/Snf2 superfamily)

49
Q

What works in concert?

A

Chromatin remodeling and post-translational modifications

50
Q

What happens when HDAC closes up?

A

Represses gene transcription

51
Q

Nucleosome mobility is regulated by what?

A

ADNRs and covalent histone modifications

52
Q

Activation of nucleosome mobility involves what?

A

Histone modification that weakens histone-DNA contacts such as acetylation by HATs → will increase nucleosome molbility/sliding

53
Q

Repression of nucleosome mobility involves what?

A

Histone modifications that restore contacts such as deacetylation by HDACs → decreased mobility

54
Q

If adding or acetylating…

A

structure opens up → transcription is activated

55
Q

If removing group…

A

structure closes up → transcription is repressed

56
Q

What is the importance of cytosine methylation at sequences CpG

A

It correlates with gene inactivation and is thought to be caused by proteins that recognize methylated cytosine through methyl-CpG-binding domain (MBD) which only recognizes methylated CpG

57
Q

What do MBD containing proteins do?

A

They recruit HDACs and block TFs from binding

58
Q

What is the disease relevance of DNA methylation?

A

In some cancers, DNA methylation is found in promoters of tumor suppressor genes → an example of an inhibitor of DNA methyltransferase is to treat leukemia

59
Q

If bound to a methylated cytosine, what can happen?

A

Gene transcription can be repressed

60
Q

RNA pol II has multiple subunits that do what?

A

Bind to DNA and perform the steps for transcription of unwinding, synthesizing RNA from a template, and proofreading

61
Q

What transcription factors are needed to position RNAPII?

A

Core transcription factors such as TFII and TBP and specialized TFs for specific genes

62
Q

How do transcription factors regulate transcription through multiple interactions by their structure?

A
  1. Some TFs bind promoter and enhancer response elements of DNA
  2. TFs can bind other coactivating TFs, proteins that modify histones/chromatin, or RNA polymerase
  3. Some TFs are activated by signaling molecules like steroid hormones
63
Q

How is TF specificity achieved?

A

By modularity

64
Q

How does chromatin remodeling play a role in transcriptional control by regulating the accessibility of condensed DNA to proteins?

A
  1. Histone modification by HATs and HDACs
  2. ADNRs alter nucleosome sliding
  3. DNA methylation plays a role in repressing transcription by forming a binding site for methyl-CpG domains that block TFs from binding DNA

Biochemistry (18 decks)

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