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block 3 biochemistry > Transcription > Flashcards

Transcription Flashcards

1
Q

Transcription:
General Features of Transcription:

Description of RNA polymerase action: It begins transcription without a ‘______. RNA polymerase reads the template strand from _________.

A

‘primer’

3’ to 5’

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2
Q

Transcription:
General Features of Transcription:

RNA polymerase synthesizes the RNA transcript _____ using ribonucleotides (NTPs) and it recognizes transcription termination signals. It makes a _______ chain.

A

5’ to 3’

ribonucleotide

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3
Q

Transcription:
General Features of Transcription:

Transcription begins with RNA polymerase identifying a ______. It interacts with the DNA template strand. RNA polymerase initiates synthesis of a ______. Transcription ends when a termination signal is reached.

A

gene’s promoter region

complementary, antiparallel RNA transcript

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4
Q

Transcription:
General Features of Transcription:

By convention, genes are described by the sequence of the coding strand, however, the ____ strand is actually the strand read during synthesis. The DNA coding strand base sequence is identical to the RNA transcript sequence, except RNA has uracil instead of thymine.

A

template

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5
Q

Transcription:
General Features of Transcription:

Base sequences (in the DNA) are numbered by giving the first base a +1 designation with +2, +3, etc. in the __ direction (downstream to the right). The upstream DNA bases to the left, in the __ direction, are designated -1, -2, -3, etc.

A

3’

5’

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6
Q

Flow of Genetic Information:

Using the ______, given any one of the strands (coding, template, or mRNA) you should be able to determine the other two strands (paying careful attention to the orientation).

A

Watson-Crick base pairing

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7
Q

Prokaryotic RNA Polymerase:

_____ + _______= holoenzyme

A

Core enzyme + sigma factor = holoenzyme

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8
Q

Prokaryotic RNA Polymerase:

The core enzyme has 4 subunits:

A

2 alpha subunits, 1 beta subunit, and 1 beta-prime subunit

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9
Q

Prokaryotic RNA Polymerase:

The core enzyme has RNA polymerase activity. The sigma factor is required to _________.

A

recognize and bind promoter sequences

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10
Q

Prokaryotic RNA Polymerase:

Sigma factor: There are different sigma factors that recognize different types of promoter sequences. It recruits the ______ to the DNA promoter. The sigma factor dissociates from the core enzyme after __________.

A

core enzyme

transcription begins

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11
Q

Prokaryotic RNA Synthesis:

Initiation of transcription: Scanning and recognition of promoter sequence cues by the holoenzyme trigger transcription initiation. Promoters contain two consensus sequences that are recognized by the sigma factor and they are the ________ and __________. Sequences within the prokaryotic promoter region that are recognized by the RNA polymerase holoenzyme.

A

TATA box and -35 sequence

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12
Q

Prokaryotic RNA Synthesis:

TATA box: The TATA box is a consensus sequence of 6 nucleotides (TATAAT), sometimes called the _____. It is 7 nucleotides ____ from the +1 transcriptional start site (-7).

A

Pribnow box

upstream

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13
Q

Prokaryotic RNA Synthesis:

The _____ is a second consensus sequence (TTGACA). The ___ bases upstream start at the +1 start site.

A

35 sequence

-35

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14
Q

Prokaryotic RNA Synthesis:

_____ is the when transcription beings at the +1 transcriptional start site. The sigma factor is released and the core enzyme continues. It is generated from 5’ to 3’. ________ creates a temporary ‘melt’ between the double stranded DNA forming the transcription bubble. Supercoils may be relieved by the action of topoisomerases.

A

Elongation

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15
Q

Prokaryotic RNA Synthesis:

Net reaction is the addition of a _______ to the growing RNA chain and the release of _______ which is further cleaved by pyrophosphatase from nucleotides. It is an irreversible coupled reaction. There are 2 high energy bonds cleaved.

A

ribonucleotide

pyrophosphate

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16
Q

Termination of Prokaryotic RNA synthesis:

There are 2 termination mechanisms:

A

Rho dependent and Rho independent.

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17
Q

Termination of Prokaryotic RNA synthesis:

The ________ requires an additional protein. The rho factor displaces the DNA template strand from RNA polymerase.

A

Rho-dependent termination

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18
Q

Termination of Prokaryotic RNA synthesis:

The ______ requires a G-C rich stem loop followed by a poly-U stretch. It causes RNA polymerase to dissociate.

A

Rho-independent termination

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19
Q

Prokaryotic mRNA:

Prokaryotic mRNA can be ________ (one mRNA code can code for several proteins.) If the mRNA carries information from more than one gene, it is said to be _______ (cistron = gene). ________mRNA is characteristic of prokaryotes.

A

polycistronic

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20
Q

Prokaryotic mRNA:

If the mRNA carries information from just one gene, it is said to be ________ and is characteristic of eukaryotes.

A

monocistronic

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21
Q

Prokaryotic mRNA:

______ mRNAs often code for multiple enzymes in the same biosynthetic pathway. Eukaryotic mRNAs are ALWAYS _________.

A

Polycistronic

monocistronic

22
Q

Prokaryotic mRNA:

A polyribosome consists of several ribosomes simultaneously translating one messenger RNA (mRNA).
The _______ sequence is a ribosomal binding site in prokaryotic messenger RNA, generally located around 8 bases upstream of the start codon AUG. The RNA sequence helps recruit the ribosome to the messenger RNA (mRNA) to initiate protein synthesis by aligning the ribosome with the start codon. With ______, multiple enzymes can be expressed.

A

Shine-Dalgarno (SD)

23
Q

Inhibition of Prokaryotic RNA Synthesis:

______ is an antibiotic. It binds to prokaryotic RNA polyermase and prevents transcription intitionation/elongation. It is used to treat tuberculosis. ______ binds to RNA polymerase and changes its conformation so that it cannot initiate RNA synthesis. RNA polymerase from eukaryotic cells does not bind rifampin and RNA synthesis is unaffected.

A

Rifampin

24
Q

tRNA and rRNA synthesis:

Prokaryotic synthesis of tRNA and rRNA is similar to the model for eukaryotes, except in prokaryotes the same RNA polymerase produces _____________ types of RNA.

A

all

25
Q

Eukaryotic RNA Synthesis:

Remember, eukaryotic DNA is highly condensed (chromatin). To allow gene transcription the genes must be “exposed”. _______ is a less condensed form of chromatin and it is more accessible to RNA polymerases. ______of histone H1 causes the chromatin to revert to nucleosomes. It allows the DNA to “open up”.

A

Euchromatin

Acetylation

26
Q

Eukaryotic RNA Synthesis:

Another type of chromatin is _______. It appears to be more dense. DNA is relatively inaccessible due to its highly condensed structure.

DNA in _______is highly methylated. DNA methylation characteristics is the foundation of ________. It is important for how genes are regulated (i.e. phenotypes).

A

heterochromatin
heterochromatin
epigenetics

27
Q

Eukaryotic RNA Synthesis:
Eukaryotic RNA polymerases:
________: transcribes precursors to rRNA in the nucleolus.

A

RNA polymerase I

28
Q

Eukaryotic RNA Synthesis:
Eukaryotic RNA polymerases:
________: Transcribes the precursor to mRNA (hnRNA) in the nucleoplasm (some snRNAs as well).

A

RNA polymerase II

29
Q

Eukaryotic RNA Synthesis:
Eukaryotic RNA polymerases:
________: Transcribes tRNA precursors (also small rRNA 5S) and some snRNAs.

A

RNA polymerase III

30
Q

Transcription Initiation in Eukaryotes:

RNA polymerase II recognizes two consensus sequences: _____ and ________.

A

TATA Box and CAAT Box.

31
Q

Transcription Initiation in Eukaryotes:
The TATA box is also called the ______. It is similar to the prokaryotic TATA box. It has approximately 25 nucleotides upstream (-25).

A

Hogness box

32
Q

Transcription Initiation in Eukaryotes:

The CAAT box has approximately __ nucleotides upstream (-__).

A

70

33
Q

Transcription Initiation in Eukaryotes:

Elongation is essentially the same as__________.

A

prokaryotic RNA synthesis

34
Q

Transcription Initiation in Eukaryotes:

___________requires a signal not well understood in eukaryotes.

A

Termination

35
Q

Transcription Initiation in Eukaryotes:
rRNA Synthesis and Processing:
There are three rRNAs that are transcribed as a single large precursor (by ________ in the nucleolus). The individual RNAs are cleaved apart by RNases. Prokaryotic rRNA synthesis is the same as in eukaryotes.

A

RNA polymerase I

36
Q

Transcription Initiation in Eukaryotes:
tRNA Synthesis and Processing:
_________ is in the nucleoplasm and it is responsible for the removal of intron loops, trimming the 5’ and 3’ ends, base modifications, and adding the 3’-CCA sequence.

A

RNA polymerase III

37
Q

Transcription Initiation in Eukaryotes:

Eukaryotic mRNA synthesis is spatially and temporally separated from translation:

A

Transcription in the nucleus

Transcription in the cytoplasm

38
Q

Transcription Initiation in Eukaryotes:

Eukaryotic mRNAs are extensively processed (_____ to _____). Prokaryotic mRNAs begin translation before transcription finishes.

A

hnRNA to mRNA

39
Q

Major Differences of Prokaryotic RNA Synthesis and Eukaryotic RNA Synthesis:

_________has promoter regions, 5’ to 3’ UTRs, and a coding region

________ has a 3’ terminus and 5’ terminus. Extrons and introns in eukaryotes. Introns have to be removed.

A
  1. Prokaryotic RNA Synthesis

2. Eukaryotic RNA Synthesis

40
Q

Eukaryotic mRNA:

5’-capping is the addition of a 7-_________to the 5’ end of the mRNA 5’ to 5’ linkage. It serves as a ribosome recognition signal and stabilizes mRNA. It protects from _____________.

A

methylguanosine

nuclease degradation

41
Q

Eukaryotic mRNA:

________ has the 3’ terminus and it contains a polyadenylation signal. It has a special enzyme (_____) adds a variable stretch of adenine residues (40-200).

A

3’-poly-A tail

poly-A-polymerase

42
Q

Eukaryotic mRNA:

It serves as a signal for transport out of the nucleus, and it stabilizes the mRNA from a nuclease attack. The _______ is not encoded in the gene. But the _______ sequence is encoded, but the additional A’s are not.

A

3’-poly-A terminus

SIGNAL

43
Q

Eukaryotic mRNA:

Intervening sequences are called ______.
Expressed sequences are called _______.
The removal of ______must be removed from the coding region for proper translation.

A

introns
extrons
introns

44
Q

Eukaryotic mRNA:

_____ is the removal of introns and the joining of extrons by snRNPs.

A

Splicing

45
Q

Eukaryotic mRNA:
snRNPs are composed of _____ and a group of ______. The snRNPs combined with the primary transcript form the _______. This is the molecular machine that performs the splicing reaction.

A

snRNAs and a group of proteins

spliceosome

46
Q

Eukaryotic mRNA:

What is the molecular machine that performs the splicing reaction?

A

SPLICEOSOME

The splice sites have very specific sequences (mutations at these sites can cause incorrect splicing).

47
Q

Eukaryotic mRNA:
Exons are joined together during splicing to form _____.

The ______ is the excised intron.

A

mature mRNA

Lariat

48
Q

Eukaryotic mRNA:
Eukaryotes may contain between _______ intron sequences! There are certain hnRNAs may undergo alternative splicing which is joining together of different exons to form different mRNAs.

A

0 and 50

49
Q

Eukaryotic mRNA:
__________ permits the production of proteins with some common domains, but the over-all function of the protein is different. (Plants do a lot of it -biotechnology. Lariats might play a role post-transcriptionally.

A

Alternative splicing

50
Q

Clinical Correlation:
_____________is an autoimmune disease and some patients produce antibodies that recognize host proteins, including snRNPs. Some can produce antibodies that recognize nucleic acids, i.e. anti-dsDNA (a test called antinuclear antibody panel is performed in suspected cases of Lupus.) It is often observed in late-teen females.

A

Systemic Lupus Erythematosus

51
Q

Eukaryotic mRNA Processing Summary:

A
  1. Processing events
  2. 5’ capping
  3. 3’-poly-adenylation
  4. Splicing
  5. After all processing events are complete, mature mRNA is transported to the cytoplasm.
52
Q

Clinical Correlation:
Mushroom Poisoning

  1. _______ accounts for 95% of all mushroom fatalities. 2. ______is the death cap mushroom.
  2. _______ is a toxin and it binds to RNA polymerase II which inhibits mRNA synthesis.
A
  1. Genus Amanita
  2. Amanita phalloides
  3. Alpha-amanitin

block 3 biochemistry (4 decks)

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