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Molecular 3rd pt. 2 > 02: Transcription > Flashcards

02: Transcription Flashcards

1
Q

does DNA direct the synthesis of proteins directly

A

no

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2
Q

what is RNA to protein

A

translation

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3
Q

what is DNA to RNA

A

transcription

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4
Q

what is the central dogma

A

dna-rna-protein

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5
Q

true/false proteins are always the final product

A
  • false
  • sometimes it stops at RNA
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6
Q

are exons normally long or short compared to introns

A
  • exons= short
  • introns= long
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7
Q

true/false genes can be transcribed and translated with different efficiencies

A

true

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8
Q

what is one of the central problems in producing proteins from info in genomes

A
  • most steps depend on conventional nucleic acid base pairing
  • which is only modestly accurate
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9
Q

true/false info in DNA is written exactly the same as RNA

A
  • false
  • theyre very similar but not exactly the same
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10
Q

true/false RNA is a linear polymer made of four different types of nucleotide subunits linked together by phosphodiester bonds

A

true

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11
Q

how does RNA differ chemically from DNA

A
  1. nucleotides in RNA are ribonucleotides (have ribose instead of deoxyribose)
  2. RNA has U instead of T
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12
Q

true/false DNA and RNA differ dramatically in overall structure

A

true

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13
Q

is RNA single or double stranded

A

single

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14
Q

describe the steps in transcription

A
  • a small portion of DNA is opened and unwinded
  • the sequence of RNA is based on complementary base pairing with one of the DNA strands
  • when an incoming ribonucleotide is matched well with a nucleotide, they are enzymatically covalently linked
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15
Q

how does transcription differ from DNA replication

A
  • RNA does not remain H bonded to the DNA template, instead it is displaced after the ribonucleotide is added, allowing the DNA double helix to return
  • RNA molecules are single stranded, and much shorter
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16
Q

what enzymes perform transcription

A

RNA polymerases

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17
Q

what do RNA polymerases do in transcription

A

catalyze the formation of the phosphodiester bonds between nucleotides to form a linear chain

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18
Q

what allows an RNA molecule to form a 3d structure

A
  • its ability to complementary bind with itself
  • also nonconventional base pairing interactions
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19
Q

how does RNA polymerase perform transcription

A
  • moves stepwise along the DNA
  • unwinds the helix just ahead of its active site
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20
Q

what are involved in the reaction of extended the RNA strand

A
  • ribonucleoside triphosphates
  • by hydrolysis of their high-energy bonds, they get added to the chain
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21
Q

why can many RNA copies can be made from the same gene in a relatively short time

A

because RNA is almost immediately separated from the DNA strand (quick turnover time)

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22
Q

what are the key differences between RNA polymerase and DNA polymerase

A
  • RNA polymerase catalyzes the linkage of ribonucleotides, not deoxyribonucleotide
  • RNA polymerases can start an RNA chain without a primer
  • RNA polymerases are processive (the same RNA polymerase that begins an RNA molecule must finish it without dissociating from the DNA template)
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23
Q

why does RNA polymerase need a primer

A

cause it doesn’t have to be as accurate as dna replication

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24
Q

describe the RNA polymerase proofreading capability

A
  • polymerase can back up
  • the active site of the enzyme can perform an excision reaction that resembles the reverse of the polymerization reaction (except that a water molecule replaces the pyrophosphate and a nucleoside monophosphate is released)
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25
Q

true/false the structure of DNA and RNA polymerases are similar

A

false

26
Q

what do mRNAs stand for and what do they do

A
  • messenger RNAs
  • code for proteins
27
Q

what do rRNAs stand for and what do they do

A
  • ribosomal RNAs
  • form the basic structure of the ribosome and catalyze protein synthesis
28
Q

what do tRNAs stand for and what do they do

A
  • transfer RNAs
  • central to protein synthesis as the adaptors between mRNA and AA
  • serve as the adaptors that select amino acids and hold them in place on a ribosome for incorporation into protein
29
Q

what do snRNAs stand for and what do they do

A
  • small nuclear RNA
  • function in a variety of nuclear processes,
  • direct the splicing of pre-mRNA to form mRNA
30
Q

what do snoRNAs stand for and what do they do

A
  • Small nucleolar RNAs
  • help to process and chemically modify rRNAs
31
Q

what do lncRNAs stand for and what do they do

A
  • Long noncoding RNAs
  • not all of which appear to have a function; some serve as scaffolds and regulate diverse cell processes, including X-chromosome inactivation
32
Q

what do miRNAs stand for and what do they do

A
  • MicroRNAs
  • regulate gene expression by blocking translation of specific mRNAs and causing their degradation
33
Q

what do siRNAs stand for and what do they do

A
  • Small interfering RNAs
  • turn off gene expression by directing the degradation of selective mRNAs and helping to establish repressive chromatin structures
34
Q

what do piRNAs stand for and what do they do

A
  • Piwi-interacting RNAs
  • bind to piwi proteins and protect the germ line from transposable elements
35
Q

Each transcribed segment of DNA is called what

A

a transcription unit

36
Q

In eukaryotes, a transcription unit typically carries the information of how many genes

A
  • one
  • therefore codes for either a single RNA molecule or a single protein
37
Q

In bacteria, a transcription unit typically carries the information of how many genes

A
  • multiple distinct proteins
  • they usually have a set of adjacent genes transcribed as a unit
38
Q

most of RNA in cells is what kind

A

rRNA

39
Q

describe the transcription cycle of bacterial RNA polymerase

A
  1. RNA polymerase holoenzyme assembles (polymerase an a sigma) and locates a promoter DNA sequence
  2. The polymerase unwinds the DNA at the spot to start transcription
  3. abortive initiation occurs. basically short unproductive transcripts are released over and over until it can reach step 4
  4. once RNA polymerase has managed to synthesize about 10 nucleotides of RNA, it breaks its interactions with the promoter DNA and releases a sigma factor
  5. polymerase tightens around the DNA and shifts to the elongation mode of RNA synthesis, moving along the DNA
  6. elongates until it hits a termination signal, typically making it form a hairpin
40
Q

what is the main point at which the cell regulates which proteins are to be produced and at what rate

A

initiation of transcription

41
Q

what does the sigma factor do for bacteria transcription

A

assists the core polymerase in reading the signals in the DNA that tell it where to begin transcribing

42
Q

what is included in the RNA polymerase holoenzyme

A
  • rna polymerase
  • sigma factor
43
Q

how is the unwound transcription bubble stabilized

A

by the binding of the sigma factor to the unpaired bases on one of the exposed strands (the other strand will be the template)

44
Q

explain the abortive initiation concept

A
  • The first 10 or so nucleotides of RNA are synthesized using a “scrunching” mechanism
  • RNA polymerase remains bound to the promoter and pulls the upstream DNA into its active site, thereby expanding the transcription bubble.
  • this process creates considerable stress, and the short RNAs are often released, thereby relieving the stress and forcing the polymerase, which remains in place, to begin synthesis over again
45
Q

how do termination signals in the DNA stop the elongating polymerase

A
  • a termination signal consists of a string of A-T nucleotide pairs preceded by a twofold symmetric DNA sequence, which, when transcribed into RNA, folds into a “hairpin” structure
  • As the polymerase transcribes across a terminator, the formation of the hairpin helps release the RNA transcript, which is held in place by relatively weak A-T and U-A base pairs
46
Q

what is a consensus nucleotide sequence

A

derived by comparing many sequences with the same basic function and tallying up the most common nucleotides found at each position

47
Q

how many types of RNA polymerase are there in bacteria

A

1

48
Q

how many types of RNA polymerase are there in eukaryotes

A

3

49
Q

what rna polymerases are there in eukaryotes

A
  • RNA polymerase I
  • RNA polymerase II
  • RNA polymerase III
50
Q

what genes does RNA polymerase I transcribe

A

rRNA genes

51
Q

what genes does RNA polymerase II transcribe

A
  • All protein-coding genes
  • snoRNA genes
  • miRNA genes
  • siRNA genes
  • lncRNA genes
  • most snRNA genes
52
Q

what genes does RNA polymerase III transcribe

A
  • tRNA genes
  • rRNA genes
  • some snRNA genes
  • genes for other small RNAs
53
Q

what is the difference between the diff rna polymerases

A

code for diff genes

54
Q

which eukaryotic rna polymerase is most like the bacterial one

A

rna polymerase II

55
Q

what are 2 key differences in how bacterial and eukaryotic rna polymerases work

A
  1. While bacterial RNA polymerase requires only a single transcription- initiation factor (σ) to begin transcription, eukaryotic RNA polymerases require many such factors, collectively called the general transcription factors
  2. Eukaryotic transcription initiation must take place on DNA that is packaged into nucleosomes and higher-order forms of chromatin structure, features that are absent from bacterial chromosomes.
56
Q

what do the general transcription factors help to do

A
  • help to position eukaryotic RNA polymerase correctly at the promoter
  • aid in pulling apart the two strands of DNA to allow transcription to begin
  • and release RNA polymerase from the promoter to start its elongation mode
57
Q

describe how the general transcription factors do their thing

A
  • Many promoters contain a DNA sequence called the TATA box, which, in humans, is located about 30 nucleotides away from the site at which transcription is initiated.
  • Through its subunit TBP, TFIID recognizes and binds the TATA box, which then enables the adjacent binding of TFIIB and TFIIA
  • the RNA polymerase and the rest of the general transcription factors assemble at the promoter.
  • TFIIH then uses energy from ATP hydrolysis to pry apart the DNA double helix at the transcription start point, locally exposing the template strand.
  • TFIIH also phosphorylates the long C-terminal polypeptide tail of RNA polymerase II, also called the C-terminal domain (CTD).
  • This causes the polymerase to be released from the general factors and begin the elongation phase of transcription.
58
Q

what happens to the general transcription factors once rna polymerase begins transcribing

A
  • TFIID remains bound at the promoter
  • most of the other general transcription factors are released
59
Q

what does TBP stand for

A

TATA-binding protein

60
Q

true/false -30 the one site that signals the start of transcription

A
  • false
  • but for many polymerase II promoters it is the most important
61
Q
A

Molecular 3rd pt. 2 (5 decks)

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