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MCAT Nucleic Acids, DNA, and RNA > Transcription > Flashcards

Transcription Flashcards

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1
Q

What are the 3 primary types of RNA?

A

mRNA (messenger)
tRNA (transfer)
rRNA (ribosomal)

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2
Q

What is hnRNA?

A

heterogenous nuclear RNA: this is an immature precursor to mRNA, as this is the first RNA transcribed from DNA. Processing events like splicing and addition of cap and tail are required for hnRNA to become mature mRNA

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3
Q

What type of cell is hnRNA found?

A

eukaryotes, not prokaryotes (because prokaryotic RNA does not have to undergo processing)

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4
Q

What are the 2 major types of noncoding RNA?

A

rRNA and tRNA

referred to as noncoding because it is functional RNA that is not translated into a protein

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5
Q

What is tRNA?

A
  • responsible for translating the genetic code

- carries AA from the cytoplasm to the ribosome to be added to a growing protein

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6
Q

catalytic ribosomes are called _____

A

ribozymes (or ribonucleic acid enzymes)

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7
Q

What are snRNA?

A

small nuclear RNA: they associate with proteins to form small nuclear ribonucleic particle complexes in the spliceosome

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8
Q

What is miRNA and siRNA?

A

microRNA and small interfering RNA: they function in post transcriptional regulation of gene expression by binding to parts of mRNA, so that part of mRNA won’t end up being translated

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9
Q

Name 3 major differences that transcription has to DNA replication does not.

A

transcription has a stop site (is not the same as a stop codon), does not require a primer, and does not require proofreading mechanism

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10
Q

Whats the difference between a stop site and a stop codon?

A

a stop site refers to the place on the DNA that tells transcription to stop
a stop codon refers to the place on the mRNA that tells translation to stop

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11
Q

What is the function of the sigma factor (in prokaryotes) and TFII-B (in eukaryotes) on the holoenzyme?

A

functions as a little arm to hold the RNA Polymerase onto the DNA, preventing it from falling off during transcription.

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12
Q

The sequence of nucleotides on a chromosome that activates RNA polymerase to begin the process of transcription is called the _____

A

promoter

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13
Q

The point where RNA polymerization actually starts is called the _________

A

start site

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14
Q

What is the promoter?

A

the binding site for RNA Polymerase

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15
Q

What marks the beginning of transcription?

A

when the RNA Polymerase binds to the start site (NOT when RNA Polymerase binds to the promoter)

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16
Q

What is the SV 40 Poly A sequence?

A
  • a very common stop site sequence found in eukaryotes

- these sequences have a very poor affinity for RNA Polymerase, which causes RNA to fall off and stop transcription)

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17
Q

What is the strand called that is read by the RNA Polymerase?

A

the template strand, aka the noncoding strand or antisense strand

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18
Q

What is the DNA strand called that is complementary to the DNA template strand?

A

the coding strand, aka the sense strand

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19
Q

Is the transcribed mRNA complementary to the template strand or the coding strand?

A

it is complementary to the template/antisense strand

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20
Q

The term upstream and downstream for transcription is in reference to the template strand or the coding strand?

A

the coding strand

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21
Q

Upstream means toward the ___ end of the coding strand

A

5’

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22
Q

Downstream means toward the ___ end of the coding strand

A

3’

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23
Q

Upstream means toward the ____ end of the template strand

A

5’

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24
Q

Downstream means toward the ____ end of the template strand

A

3’

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25
Q

It is customary to say that transcription starts at a point and proceeds ______, which means toward the 3’ end of the coding strand

A

downstream

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26
Q

It is customary to say that transcription starts at a point and proceeds ______, which means toward the 3’ end of the coding strand

A

downstream

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27
Q

_____ is the primary regulatory point for translation

A

transcription

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28
Q

Distinguish between strong and weak promoters

A
  • strong promoters have a high affinity for RNA Pol, which means RNA Pol can bind better and transcription can happen faster and more RNA can be produced
  • weak promoters have a low affinity for RNA Pol, resulting in less RNA being produced
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29
Q

How is strength of a promoter determined in an individual?

A

determined by genetics

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30
Q

How do DNA binding proteins help regulate transcription?

A

DNA binding proteins bind to operator sequences (aka regulatory regions) on DNA to control whether or not transcription occurs. If it prevents transcription, it is a repressor protein. If it promotes transcription, it is an enhancer protein.

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31
Q

What are operator sequences on DNA?

A

these are regulatory regions to which DNA binding proteins bind to prevent or promote transcription

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32
Q

What is the lac operon?

A

a regulatory region on DNA that is regulated by a repressor protein. In absence of lactose, the repressor protein is bound to the lac operon. In the presence of protein, lactose binds to the repressor protein, resulting it to fall off the regulatory region, allowing the RNA Pol to slide down from the promoter region to the start site, thus initiating transcription of the mRNA coding for the lactose protein

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33
Q

What is the holoenzyme?

A

refers to the complete enzyme of the RNA polymerase core enzyme and the sigma factor (or TFII-B for eukaryotes)

34
Q

What is the primary transcript in prokaryotes? What is the primary transcript in eukaryotes?

A 
prokaryotes = mRNA (does not need processing before translation)
eukaryotes = hnRNA (requires processing before turning into mRNA for translation)
35
Q

In eukaryotes, intervening sequences in hnRNA are called _____

A

introns

mnemonic: think introns intervene

36
Q

In eukaryotes, protein-coding regions of hnRNA are termed _____

A

exons

mnemonic: think exons are expressed

37
Q

splicing is mediated by the ___1___, a complex that contains over 100 proteins and 5 ___2___ molecules

A

1) spliceosome

2) snRNA (small nuclear RNA)

38
Q

After splicing, the hnRNA is modified by adding a ___ cap and a _____ tail

A

5’ cap

3’ poly-A tail

39
Q

What is the purpose/function of adding the cap and tail on an hnRNA?

A

The 5’ cap is essential for aligning the mRNA on the ribosome for translation, while both the 5’ cap and 3’ poly-A tail are important in preventing digestion of the mRNA by exonucleases that are free in the cell.

40
Q

What is differential splicing?

A

Refers to how hnRNA can be spliced in different ways by keeping and extracting certain desired extrons in addition to the extracting the introns. This ultimately means one hnRNA has the potential to produce multiple different polypeptides (all depending on how it is spliced).

41
Q

Distinguish between polycistronic mRNA and monocistronic mRNA

A 
polycistronic = multiple proteins can be made from one (mature) mRNA during translation
monocistronic = only one protein can be made from one (mature) mRNA during translation (note that an hnRNA can undergo differential splicing to produce different polypeptides, but mature mRNA can only yield one protein during translation)
42
Q

What are the different types of eukaryotic RNA polymerases and what does each RNA polymerase transcribe?

A

RNA Pol I: rRNA
RNA Pol II: hnRNA/mRNA
RNA Pol III: tRNA

43
Q

Where is the amino acid acceptor site (or AA binding site) on tRNA?

A

on the 3’ end

44
Q

What is the sequence on tRNA that is capable of interacting with the mRNA?

A

the anticodon loop

45
Q

If the codon on the mRNA is AUG, what will be the sequence found on the anticodon loop of tRNA? What AA will this tRNA carry?

A

UAC

This tRNA will carry methionine

46
Q

Nomenclature for tRNA: how would a tRNA for valine that is loaded with valine be named?

A

Val-tRNAVal

the Val written after the tRNA is a subscript

47
Q

What is the wobble hypothesis?

A

The first 2 codon-anticodon pairs obey normal Watson-Crick base pairing rules, but the third anticodon position (or the 5’ end of the anticodon) is more flexible and allows for nontraditional pairing.

48
Q

For wobble base pairing: If the third position in the anticodon of tRNA contains G, what base(s) can it possibly bind to on the mRNA?

A

C or U

49
Q

For wobble base pairing: If the third position in the anticodon of tRNA contains C, what base(s) can it possibly bind to on the mRNA?

A

G only

50
Q

For wobble base pairing: If the third position in the anticodon of tRNA contains A, what base(s) can it possibly bind to on the mRNA?

A

U only

51
Q

For wobble base pairing: If the third position in the anticodon of tRNA contains U, what base(s) can it possibly bind to on the mRNA?

A

A or G

52
Q

For wobble base pairing: If the third position in the anticodon of tRNA contains I (inosine), what base(s) can it possibly bind to on the mRNA?

A

A, U, or C

53
Q

For wobble base pairing, what bases on the anticodon are capable of wobble base pairing?

A

G, U, I

54
Q

What is the only base that cannot pair up with inosine according to the wobble base hypothesis?

A

G

55
Q

An adenine on tRNA can be converted into ____, which allows for more flexibility in wobble base pairing

A

inosine

56
Q

wobble base pairing occurs if there is ___, ___, or ___ at the 5’ end of the anticodon

A

G, U, or I

57
Q

How many high-energy phosphate bonds are hydrolyzed to provide the energy to attach an AA to its tRNA molecule?

A

2

58
Q

What is tRNA loading, aka AA activation?

A

refers to loading an AA onto a tRNA molecule

59
Q

In prokaryotes: the large subunit of the ribosome is labeled __1__ while the small subunit is labeled __2__. Collectively, the ribosome is labeled __3___

A

1) 50S
2) 30S
3) 70S
mnemonic: all first numbers are odd. Prokaryotes are odd little creatures

60
Q

In eukaryotes: the large subunit of the ribosome is labeled __1__ while the small subunit is labeled __2__. Collectively, the ribosome is labeled __3___

A

1) 60S
2) 40S
3) 80S
mneumonic: all first numbers are even. Even for Eukaryotes

61
Q

How can you get 2 ATP equivalents (aka 2 high energy bonds) from one ATP molecule?

A

hydrolyze the ATP twice, resulting in AMP + 2 Pi

62
Q

Which hydrolysis reaction will drive peptide bond formation?

A

the hydrolysis between the tRNA molecule and the AA attached to it.

63
Q

Prokaryotic translation: initiation starts with the __1__ ribsosomal subunit binding to the mRNA with the help of some initiation proteins; then __2__ binds to this complex. The __3__ ribosomal subunit is then recruited and bound to the complex. Now translation can take place.

A

1) small
2) tRNA
3) large

64
Q

In prokaryotic translation, does the start codon AUG initiate translation whereever it appears?

A

No. It only initiates translation when it is preceded by a Shine-Dalgarno sequence (aka a ribosome binding site).

65
Q

Prokaryotic translation: elongation
Step 1: the first tRNA was bound to the ___ site during initiation, so the second tRNA enters the ___ site.
Step 2: _____ transferase breaks the bond between the AA and the first tRNA, and uses that energy to link the broken AA to the AA located on the second tRNA (sitting in the A site)
Step 3: ______ occurs, where the first tRNA in the P site moves to the ____ site, and the second tRNA in the A site is transferred from the A site to the P site.

A

Step 1: first binds to P site, second binds to A site
Step 2: peptidyl transferase
Step 3: translocation, first tRNA move from P to E site

66
Q

What’s the difference in translation initiation of eukaryotes compared to prokaryotes?

A
  • in eukaryotes, the tRNA binds first to the mRNA, and then binds to the small ribosomal subunit. Large ribosomal unit binds last
  • in prokaryotes, the small ribosomal subunit binds to mRNA first, and then tRNA binds to the complex. Large subunit binds last
67
Q

What is the major purpose of the E site, P site, and A site of the ribosome in translation?

A

E site = thought to help maintain the reading frame of the mRNA (disruption of the tRNA binding to the E site results in an increase of frameshift mutations in the resulting protein)
P site = growing protein is held here
A site = new AA is added here

68
Q

What enzyme is responsible for the translocation in the elongation step of translation?

A

translocase, aka Elongation factor G

69
Q

What signals termination during translation?

A

termination is triggered when the stop codon appears in the A site.

70
Q

What is bound to the A site after the stop codon of mRNA enters the A site? What does this cause peptidyl transferase to do?

A

a release factor, also called a terminating factor, (not a tRNA) enters the A site, which causes the peptidyl transferase to hydrolyze the bond between the last tRNA and the completed polypeptide.

71
Q

What simple equation can you use to calculate how much ATP energy is needed to make a peptide that is X AA long?

A

AA x 4 = #ATP needed to synthesize that protein

72
Q

How much ATP is used during translation of a peptide that is 50 AA long?

A

200

73
Q

Eukaryotes do not use the Shine-Dalgarno sequence like prokaryotes to initiate translation. What do they use instead to initiate translation?

A

5’ UTR sequences i.e. Kozak sequence

74
Q

Where does splicing occur in the cell?

A

in the nucleus

75
Q

What is cap-dependent translation?

A

refers to translation that can only start at the 5’ mRNA cap (hence this is only occurs with monocistronic mRNA; does not occur with polycistronic mRNA)

76
Q

What is cap-independent translation?

A

refers to translation that does not require starting at a 5’ cap of the mRNA molecule (some eukaryotes are capable of starting translation in the middle of their capped mRNA molecule)

77
Q

Post-translational modification: protein folding is aided by ______

A

chaperones

78
Q

Post-translational modification: name a few covalent modifications that happen to proteins

A

overall refers to adding covalent bonds between atoms, including covalently bonding particular substituents to a protein:

  • disulfide bridges
  • sulphation
  • acetylation
  • alkylation
  • formylation
  • glycosylation
  • phosphorylation
79
Q

Post-translational modification: processing refers to _____ of proteins so that they can become mature and functional

A

cleavage

80
Q

Enzyme precursors (that must undergo processing to become active enzymes) are called _____ or ____

A

zymogens or proenzymes

MCAT Nucleic Acids, DNA, and RNA (5 decks)

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