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MS Physiology - Block 1 > Chapter 4 > Flashcards

Chapter 4 Flashcards

1
Q

Gene information flows from ___ to ___:

A

DNA to protein

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2
Q

What is packed DNA called?

A

Chromatin

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3
Q

What exactly are transcription factors?

A

Proteins that can bind to specific DNA sites and regulate the rate of transcription

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4
Q

What determines the initiation site of transcription?

A

Promoter

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5
Q

The two types of elements that regulate transcription are?

A

Positive and negative regulatory elements

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6
Q

What are locus control regions?

A

A dominant, positive acting cis-element that regulates several genes within a chromosomal domain

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7
Q

What are boundary elements?

A

“Insulate” genes from neighboring regulatory elements so that there is some distiguishment between each gene domain

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8
Q

How are transcription factors grouped into classified families?

A

Based on their tertiary structure

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9
Q

How are coactivators and corepressors different from transcription factors?

A

They don’t directly bind to DNA

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10
Q

How can the rate of transcription increase/decrease exponentially?

A

By transcription factors working in combination with each other.

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11
Q

What are the three ways transcriptional repressors act?

A
  1. Competition for DNA-binding sites
  2. Binding (inhibiting) activating-transcription factors
  3. Active repression (binding to a silencer DNA sequence
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12
Q

How is the activity of transcriptional factors regulated?

A

Post-translational modifications

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13
Q

Are all transcription factors expressed in every cell?

A

No. It is tissue specific

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14
Q

How does cAMP regulate transcription?

A

Through the transcription factors CREB and CBP

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15
Q

How do RTK’s (receptor tyrosine kinases) regulate transcription?

A

Through a Ras-dependent cascade of protein kinases

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16
Q

How can tyrosine-kinase associated receptors regulate transcription?

A

Through the JAK-STAT pathway

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17
Q

What is special about nuclear receptors in relation to transcription?

A

They can directly regulate transcription!

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18
Q

External physiological stimuli can regulate transcription. Give an example of one such stimuli.

A

Low O2 levels

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19
Q

How many forms does chromatin exist in?

A

2

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20
Q

What influences gene expression in the long-term?

A

Chromatin modifications

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21
Q

What happens when you methylate DNA?

A

Gene inactivation

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22
Q

Alternative splicing generates?

A

Diversity from single gene transcripts

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23
Q

What controls mRNA stability? (2)

A
  1. Regulatory elements in the 3’ untranslated region

2. RNA interference (siRNA, miRNA)

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24
Q

What is the sequence of the poly-A tail?

A

5’-AATAAA-3’

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25
Q

What is the 5’ flanking region?

A

The region of DNA that is directly adjacent to and upstream of the transcription initiation site.

26
Q

What is the 3’ flanking region?

A

The region of DNA that is directly adjacent to and downstream of the transcription termination site

27
Q

Are the 5’ and 3’ flanking regions transcribed into RNA?

A

No.

28
Q

What is located in the 5’ and 3’ flanking regions?

A

DNA regulatory elements

29
Q

What is the “cap site”?

A

The site where transcription begins.

30
Q

What is the sequence of the “cap site”?

A

5’-ACTT(T/C)TG-3’

31
Q

What is heterogeneous nuclear RNA?

A

The primary transcript; or, the transcript of RNA that has not be processed (spliced and protected) yet.

32
Q

What is hnRNA?

A

Heterogeneous nuclear RNA

33
Q

What is the difference between hnRNA and mRNA?

A

hnRNA has not been processed and mRNA does not have introns.

34
Q

What exactly is the 5’ cap consisted of on mRNA?

A

A methyl group

35
Q

What does mRNA stand for?

A

Mature RNA (that has been processed)

36
Q

Why is the 5’ cap on mRNA required?

A

For mRNA to be able to be exported out of the nucleus and into the cytoplasm.

37
Q

What are the 4 steps of RNA processing?

A
  1. Removal of introns (pre-mRNA splicing)
  2. Addition of 5’ methyl cap
  3. Cleavage of RNA 20 nucleotides downstream from polyadenylation signal
  4. Addition of 100-200 adenine bases to the site of cleavage to form the poly-A tail
38
Q

What is the start codon amino acid and its sequence??

A

Methionine (AUG)

39
Q

What are the three stop codon sequences?

A

UAA, UAG, UGA

40
Q

Which side of the mRNA transcript provides the N-terminus of the protein?

A

5’-end

41
Q

Which side of the mRNA transcript provides the C-terminus of the protein?

A

3’-end

42
Q

How many subunits does a histone consist of?

A

8 subunits

43
Q

Difference between nucleosome and histone?

A

Nucleosome = Histone + H1

44
Q

What is H1?

A

A linker histone that associates DNA to the histone octamer

45
Q

What are the names of the histone subunits?

A

H2A, H2B, H3, H4. There are 2 of each subunit for a total of 8 subunits

46
Q

What are HATs?

A

Histone acetyltransferases

47
Q

What are HDACs?

A

Histone deacyteltransferases

48
Q

DNA is ____-charged:

A

negatively. (due to negative phosphate groups)

49
Q

Histones are ____-charged:

A

positively. (due to positive lysine residues near the N-terminus of the histone)

50
Q

Difference between cis and trans-elements on DNA

A

Cis: Located on the same molecule of DNA that it transcribes.

Trans: Can be located a far distance away

51
Q

What enzyme is responsible for transcription?

A

RNA polymerase

52
Q

How many types of RNA polymerase are there?

A

3 types

53
Q

List the roles of each of the different RNA polymerases:

A

RNA poly I: Transcribes rRNA
RNA poly II: Transcribes mRNA
RNA poly III: Transcribes tRNA and small nuclear RNA

54
Q

What does small nuclear RNA do?

A

RNA processing from hnRNA to mRNA

55
Q

What is another term for basal transcriptional machinery?

A

RNA polymerase holoenzyme; or preinitiation complex

56
Q

What is unique about the binding of RNA polymerase II to DNA?

A

It can’t bind to DNA by itself!

57
Q

How many transcription factors does RNA polymerase II require to bind to DNA and initiate transcription?

A

6:

TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH

58
Q

What is the gene promoter?

A

Where the RNA polymerase (and its respective transcriptional machinery) bind to DNA that is directly upstream from the gene of interest

59
Q

What is the order in which the 6 transcription factors bind to RNA polymerase II?

A

TFIID (binds to DNA first) –> TFIIA –> TFIIB (also binds to DNA) –> TFIIF + RNA poly II complex –> TFIIE –> TFIIH

60
Q

What is unique about TFIID?

A

It contains TATA-binding proteins and TBP-associated factors that recognizes the TATA “box”, the site of initiation.

MS Physiology - Block 1 (12 decks)

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