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Biochem Final > Transcription > Flashcards

Transcription Flashcards

1
Q

Transcription is the process where ____ is made using ___ as a ____.

A
  • RNA
  • DNA
  • template
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2
Q

RNA polymerization requires an enzyme called:

A

-RNA polymerase

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3
Q

RNA polymerase can start a chain without a ___, incorporates nucleotides into a growing chain in the ___ to __ direction using ___ bonds, and uses ___, ___, ___, and ___ as starting compounds.

A
  • primer
  • nucleotides
  • 5’ to 3’
  • phosphodiester
  • ATP, GTP, CTP, UTP
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4
Q

Cells have three main types of RNA-

what are the functions?

A

mRNA (carries message to be translated into protein), tRNA (carries amino acids to ribosomes for incorporation into protein), and rRNA (components of ribosomes).

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5
Q

In E. coli, all of the RNAs are made by:

A

a single RNA Polymerase.

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6
Q

E. coli RNA Polymerase has five distinct:

A

distinct polypeptide subunits.

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7
Q

Promoters in E. coli (___ ___ binding sites adjacent to genes) function with widely varying rates of efficiency - some stimulating ___ of transcription every ___ ___, others only one or twice per ___ ___.

A
  • RNA polymerase
  • initiation
  • few seconds
  • life cycle
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8
Q

One way for a promoter to control such events is via ___ in ___ sequences. E. coli genes have two conserved sequences- one at ___ relative to the transcription start site (___) and another at ___ relative to the transcription start site (___).

A
  • variation
  • conserved
  • -10
  • TATAAT
  • -35
  • TTGACA
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9
Q

The more closely a given promoter’s sequence matches the consensus sequence of the ___ sequence, the more ___ the promoter is at ___ transcription.

A
  • -10
  • active
  • initiating
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10
Q

Different ___ ___ (such as the one made during ___ ___) allow the cell to turn ___ sets of ___ with different sequences in the -10/-35 sequences as needs arise.

A
  • sigma factors
  • heat shock
  • on
  • genes
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11
Q

The strand of DNA being copied is known as the ___ ___. It runs ___ to ___, since the RNA is being made ___ to ___, _____ to it.

A
  • template strand
  • 3’ to 5’
  • 5’ to 3’
  • complementary
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12
Q

The strand of DNA that is NOT copied in transcription is called the ___ ___, since it has the ___ sequence as the ___ except for having ___ instead of ___.

A
  • coding strand
  • same
  • RNA
  • T
  • U
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13
Q

Transcription occurs under the ‘control’ of ___. The more strongly RNA Polymerase (in ___) binds to the ___, the more ___ are made of that particular gene.

A
  • promoters
  • prokaryotes
  • promotor
  • transcripts
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14
Q

The more transcripts are made, the ___ is referred to as being ‘___.’

A
  • promoter

- stronger

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15
Q

Transcription ___ occurs by both ___ ___ means (requires a ___ ___) and ___ ___ means (no extra ___ required). The factor independent method relies on formation of a ___ sequence of ___ base pairs immediately ahead of a stretch of ___.

A
  • termination
  • factor dependent
  • protein factor
  • factor independent
  • protein
  • duplex
  • GC
  • Us
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16
Q

The ___ destabilizes the ___-___-___ _____ complex and this is favored by the relatively weak ___ bonds of the ___ interactions.

A
  • duplex
  • RNA-DNA-RNA polymerase
  • hydrogen
  • U-A
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17
Q

The factor involved in factor dependent transcription termination in E. coli is called ___. It binds to the ___ end of an ___ being made and (using ___ energy) “climbs” the RNA until it reaches the ___ ___.

A
  • rho
  • 5’
  • RNA
  • ATP
  • RNA polymerase
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18
Q

There it destabilizes the ______ ___, favoring the release of the ___ ______ from the DNA and the ___ from the DNA, as well.

A
  • RNA/DNA complex
  • RNA polymerase
  • RNA
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19
Q

In prokaryotes, ___ are the most altered (___) RNAs. Modifications start with their being ___ from a larger RNA containing both ___ and ___.

A
  • tRNAs
  • processed
  • cleaved
  • tRNAs
  • rRNAs
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20
Q

___ ___ is a ribozyme (catalytic RNA) that cleaves the ___’ end of ___ from the larger RNA. ___ ___ catalyzes ___ of ___ from the larger molecule.

A
  • Ribonuclease P
  • 5’
  • tRNAs
  • Ribonuclease III
  • excision
  • rRNAs
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21
Q

Transcription and translation are targets of ___. In transcription,___ binds to the open ___ complex and ___ the movement of the ___, thus stopping ___.

A
  • antibiotics
  • rifampicin
  • promoter
  • inhibits
  • RNA polymerase
  • elongation
22
Q

___ ___ binds to DNA and also prevents the ___ of the transcription complex.

A
  • Actinomycin D

- movement

23
Q

Eukaryotes and prokaryotes differ significantly in the relationship between ___ and ___.

A
  • Transcription

- Translation

24
Q

Prokaryotes have no ___. In them, translation starts oftentimes ___ a message is being ___. There are no significant ___ to mRNAs in prokaryotes.

A
  • nucleus
  • WHILE
  • transcribed
  • modifications
25
Q

In eukaryotes, transcription and translation are ___ ___. Transcription occurs in the ___, whereas translation occurs in the ___.

A
  • spacially separated
  • nucleus
  • cytoplasm
26
Q

Eukaryotic mRNAs are modified at the ___ end (capping), the ___ end (___) and even in the ___ (___ and s___).

A
  • 5’
  • capping
  • 3’
  • polyadenylation
  • middle
  • editing and splicing
27
Q

Eukaryotes have 3 specialized RNA polymerases. They differ in their sensitivity to ___-___ (a ___ from some mushrooms).

A
  • alpha-amanitin

- poison

28
Q

RNA polymerase II (makes mRNAs) is the most ___. RNA polymerase III (makes ___ and ___ ___) has ___ sensitivity and RNA polymerase I (makes ___ ___) has ___ sensitivity.

A
  • sensitive
  • tRNAs and small rRNAs
  • moderate
  • large rRNAs
  • low
29
Q

Sequence elements affect transcription of eukaryotic genes. They include the ___ ___ (positioned approximately ___ to ___), and a ___ box and ___ box (___ to ___).

A
  • TATA box
  • -30 to -100
  • CAAT box
  • GC box
  • -40 and -150
30
Q

The promoters for each RNA polymerase are:

A

different in structure

31
Q

Enhancer sequence elements are DNA sequences that are:

A

bound by enhancer (transcription factor) proteins.

32
Q

Enhancer proteins act in this way to enhance transcription of genes located up to many thousands of base pairs ___ (___ __), ____ (__ ___ ) or even in the ___ of genes.

A
  • upstream (ahead of)
  • downstream (down from)
  • middle
33
Q

RNA Polymerase II in eukaryotes differs from RNA polymerase in E. coli in not binding to the ___ ___, but rather, it must bind to another ___ that binds to the ___ first.

A
  • DNA directly
  • protein
  • promoter
34
Q

In eukaryotes, rRNA is made by the action of ___ ___ ___. It is made as a ___ and then processed, like what occurs in prokaryotes.

A
  • RNA Polymerase I

- precursor

35
Q

tRNAs in eukaryotes are made by action of ___ ___ ___. Processing of them includes ___ of a ___ leader sequence and part of a ___ tail, as well as addition of a ___ sequence at the new ___ end. The amino acid gets attached to the ___ end of the tRNA.

A
  • RNA Polymerase III
  • removal
  • 5’
  • 3’
  • CCA
  • 3’
  • 3’
36
Q

Micro RNAs affect the amount of ___ ___ - note that the term ‘___ ___’ refers ultimately to the amount of ___ ___ made from a particular gene.

A
  • gene expression
  • gene expression
  • functional protein
37
Q

Micro RNAs and silencing RNAs are made as ___ ___ ___ that get processed ultimately to produce a ___ ___ ___ that is ___ to a target sequence in a given ___. When it binds to that sequence, it may result in either ___ of the mRNA or in ___ translation of the mRNA.

A
  • double stranded RNAs
  • single stranded stranded RNA
  • complementary
  • mRNA
  • degradation
  • inhibiting
38
Q

RNA editing occurs when a base in an ___ is altered. An example is the ___/___ system in our bodies. apoB100 codes for a ___ ___ protein. An enzyme can recognize a ___ codon inside of the ___ and ___ the C to make it a U. That makes ___

A
  • mRNA
  • apoB100/apoB48
  • 100 kilodalton
  • CAA
  • mRNA
  • deaminate
  • UAA
39
Q

UAA is a stop codon and stops ___, making a ___ ___ protein instead. Thus, the same ___ can make two different proteins.

A
  • translation
  • 48 kilodalton
  • mRNA
40
Q

Transcription factors are proteins that bind to specific sequences in ___ and affect transcription of the ___ near them. Specifically, they bind to ___ ___.

A
  • DNA
  • genes
  • sequence elements
41
Q

Eukaryotic mRNAs are significantly modified. At the ___ end, a cap is added in the form of a ___ ___ that is attached in a ___ to ___ linkage to the ___ base of the transcript. This linkage is important for ___, performs a role in ___, and protects against ___ ___.

A
  • 5’
  • modified GTP
  • 5’ to 5’
  • first
  • recognition
  • translation
  • exonuclease degradation
42
Q

At the ___ end of eukaryotic mRNAs, a long sequence of ___ is added. This too plays a role in ___ and also provides a “buffer” against ___ ___. The longer the sequence of poly-A, the longer a transcript tends to ___.

A
  • 3’
  • As
  • translation
  • exonuclease degradation
  • poly-A
  • exist
43
Q

___ is another modification that happens to eukaryotic mRNAs. Splicing also occurs to ___ and ___ in eukaryotes.

A
  • Splicing
  • tRNAs
  • rRNAs
44
Q

Splicing involves removal of ___ ___ from RNA followed by ___ of ends. The removed sequences are called ___. The segments that make it into the final RNA are called ___.

A
  • internal sequences
  • joining
  • introns
  • exons
45
Q

The only sequences common to all spliced RNAs are a ___ ___ at the ___ end of the intron and an ___ at the ___ end of the intron. A third sequence - an ___ residue surrounded by ___ also is common.

A
  • GU sequence
  • 5’
  • AG
  • 3’
  • A
  • pyrimidines
46
Q

Protein/RNA complexes called ___ mediate the ___ process in higher eukaryotes. ___ contain small ___ ___ (___) and ___.

A
  • snRNPs
  • splicing
  • snRNPs
  • nuclear RNAs (snRNAs)
  • proteins
47
Q

In splicing, the ___ of the A residue attacks the ___ of the phosphodiester bond at the ___ end of the intron, creating a 5’-2’ bond (part of the ___ structure). Attack by the released 3’ end of the ___ on the 3’ end of the intron joins the two exon ends and releases the intron as a ___.

A
  • hydroxyl
  • phosphate
  • 5’
  • lariat
  • Attack
  • exon
  • 3’
  • lariat
48
Q

In splicing, the ___ ___ forms base pairing with the ___ end of the ___ ___.

A
  • U1 snRNA
  • 5’
  • intron sequence
49
Q

In splicing, the ___ ___ forms base pairs with the ___-___ region in the ___ and with the ___ of ___. Pairing with the intron forces outwards the ‘___’ residue that attacks the ___.

A
  • U2 snRNA
  • pyrimidine-rich
  • intron
  • snRNA
  • U6
  • ‘A’
  • phosphate
50
Q

Transcription factors assist ___ ___ __ in binding. For genes with a ___ ___, the transcription factor ___ binds first. It contains a subunit called ___ (___ ___ ___) that recognizes and binds to the ___ sequence.

A
  • RNA polymerase II
  • TATA box
  • TFIID
  • TBP (TATA binding protein)
  • TATA

Biochem Final (5 decks)

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