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Chapter 13 Flashcards

1
Q

Toxin ⍺-Amanitin

A

is a potent inhibitor of RNA polymerase II

  • ⍺-Amanitin binds to RNA polymerase and jams the moving parts
    of the enzyme, interfering with its ability to move along DNA
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2
Q

The Primary
Structure of RNA

A

Single stranded

Ribose sugar

Has uracil rather than thymine

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3
Q

The Secondary Structure of RNA

A

forms by folding

connects by complementary regions

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4
Q

The structures of DNA and RNA compared:Composed of nucleotides

A

Y,N

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5
Q

The structures of DNA and RNA compared: Type of sugar

A

Deoxyribosoe, ribose

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6
Q

The structures of DNA and RNA compared: Presense of 2’OH

A

N,Y

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7
Q

The structures of DNA and RNA compared: Bases

A

A G C T
A G C U

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8
Q

The structures of DNA and RNA compared: Nucleotides joined by
phosphodiester bonds

A

Y,Y

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9
Q

The structures of DNA and RNA compared: Double or single stranded

A

d,s

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10
Q

The structures of DNA and RNA compared: secondary structure

A

double helix, many types

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11
Q

The structures of DNA and RNA compared: stability

A

stable, easily degraded

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12
Q

Ribosomal RNA: rRNA

A

– Make up the ribosome, the site of protein assembly

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13
Q

Messenger RNA: mRNA

A

– Carries coding instructions for a polypeptide chain from
DNA to a ribosome.

– After attaching to ribosome, an mRNA specifies the
sequence of the amino acids in a polypeptide chain and
provides a template.

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14
Q

pre-messenger RNAs
(pre-mRNAs)

A

– Large precursor molecules are the immediate products of transcription
in eukaryotic cells.

– Pre-mRNAs are modified before becoming mRNA and
exiting nucleus for translation into protein

Bacterial cells do not possess pre-mRNAs – in
these cells, transcription takes place concurrently
with translation.

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15
Q

Transfer RNA: tRNA

A

– Serves as the link between the coding sequence of
nucleotides in an mRNA molecule and the amino
acid sequence of a polypeptide chain.

– Each tRNA attaches to one particular type of amino
acid and helps incorporate that into the chain.

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16
Q

Small nuclear RNAs: snRNAs

A

– Found in the nuclei of eukaryotic cells
– Combine with small protein subunits to form small
nuclear ribonucleoproteins (snRNPs, ‘snurps’)
– Some participate in the processing of RNA, converting pre-mRNA into mRNA.

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17
Q

Small nucleolar RNAs: snoRNAs

A

–Take part in the processing of RNA

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18
Q

MicroRNAs: miRNAs

A

Very small and abundant RNA molecules found in the
cytoplasm of eukaryotic cells

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19
Q

– Small interfering RNAs: siRNAs

A

These carry out RNA interference (RNAi)

RNAi - process in which
small RNA molecules help
trigger the degradation of
mRNA or inhibit its translation
into protein.

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20
Q

Piwi-interacting RNAs: piRNAs

A
  • Found in mammalian testes
  • Similar to miRNAs and siRNAs
    – Role in suppressing the expression of transposable elements
    (DNA sequence that can change it’s position) in reproductive
    cells.
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21
Q

Long noncoding RNAS (IncRNAs)

A
  • Found in Eukaryotes
  • Relatively long RNA molecules
  • Provide a variety of functions, including
    regulation of gene expression
22
Q

CRISPR RNAs (crRNAs)

A
  • Assist in the destruction of foreign DNA molecules
  • Found in prokaryotic cells
23
Q

Transcription Is the Synthesis of an RNA
Molecule from a DNA template

A

Unlike DNA replication, where all nucleotides
are copied, only parts of the DNA molecule are
transcribed into RNA.

Transcription is a highly selective process:
individual genes are transcribed only as their products
are needed.

24
Q

Transcription requires three major components:

A
  1. A DNA template
  2. The raw materials (ribonucleotide
    triphosphates) to build a new RNA molecule.
  3. The transcription apparatus (consists of
    proteins necessary for catalyzing synthesis of
    RNA)
25
Template strand (nucleotide strand used for transcription) vs. Nontemplate strand (not usually transcribed)
Thus, within a gene, only one of the nucleotide strands is normally transcribed into RNA
26
Transcription Unit –
stretch of DNA that encodes an RNA molecule and the sequences needed for its transcription. Included within a transcription unit are three critical regions: * A promoter * RNA-coding sequence * Terminator
27
Promoter
– DNA sequence that the transcription apparatus recognizes and binds
28
RNA-coding Sequence –
sequence of DNA nucleotides that is copied into an RNA molecule
29
Terminator
– sequence of nucleotides that signals where transcription ends.
30
The Transcription Apparatus
RNA polymerase carries out all the required steps for transcription. RNA polymerase actions are enhanced by a number of accessory proteins that join and leave the polymerase at different stages.
31
Eukaryotic RNA Polymerases
Most Eukaryotic cells possess three distinct types of RNA polymerase, each responsible for transcribing a different class of RNA RNA polymerase I – transcribes rRNA RNA polymerase II – transcribes pre-mRNAs, snoRNAs, some miRNAs, and some snRNAs RNA polymerase III – transcribes other small RNA molecules (tRNAs, small rRNAs, some miRNAs, and some snRNAs
32
Bacterial Transcription Initiation
– transcription apparatus assembles on the promoter and begins synthesis of RNA
33
Bacterial Transcription Elongation
– DNA is threaded through RNA polymerase and the polymerase unwinds the DNA, adding new nucleotides(to the 3’ end of the growing strand
34
Bacterial Transcription Termination
– recognition of the end of transcription and separation of the RNA molecule from the DNA template
35
Initiation comprises all necessary steps to begin RNA synthesis:
1.Promoter recognition 2.Formation of a transcription bubble 3.Creation of the first bonds between rNTPs 4.Escape of the transcription apparatus from the promoter
36
Consensus sequences
sequences that possess considerable similarity. Consensus sequences usually imply an important function!
37
Almost all bacterial promoters have –10 consensus sequence (~10 bp upstream of the start site) sometimes called the
Pribnow box: – 5' TATAAT 3' – 3' ATATTA 5' Also common: –35 consensus sequence: TTGACA
38
Initiation
– Initial RNA synthesis: no primer is required. – The location of the consensus sequence determines the position of the start site.
39
Elongation
– RNA elongation is carried out by RNA polymerase. – RNA polymerase does have the ability to do some backtracking and proofreading as well
40
Termination
– Transcription stops after the terminator region has been transcribed.
41
There are two types of terminators:
* Rho-dependent: requires an ancillary protein rho factor (⍴) It detaches due to helicase unzipping, want DNA and RNA to seperate * Rho-independent:: also referred to as intrinsic terminators, are able to cause termination without rho. Hairpin structure formed by inverted repeats, followed by a string of uracils
42
Which of the following phrases does not describe a function of the promoter?
Signals where transcription ends
43
Eukaryotic Transcription and Bacterial Transcription Differences
Eukaryotic cells possess three different RNA Polymerases – Each recognizes a different promotor * Promoter recognition and initiation are also different! – Many accessory proteins take part in the binding of eukaryotic RNA polymerases to DNA templates – Different types of promoters require different proteins! * Chromatin structure in eukaryotes needs to be modified before transcription can begin. A more open configuration is required for the machinery access to begin transcription!
44
Termination: The three RNA polymerases use different mechanisms for termination
– RNA polymerase I: Requires a terminator factor similar to rho factor (unlike rho, this termination factor binds to a DNA sequence downstream of the terminator) – RNA polymerase II: Does not occur at specific sequences (will look at more detail in Ch. 14) – RNA polymerase III: Ends transcription after transcribing a terminator sequence that produces a string of uracil nucleotides in the RNA molecule. Recent research suggests that secondary structures (hairpin, etc) are necessary
45
Eukaryotic Transcription and Bacterial Transcription Differences Initiation:
– Transcription in eukaryotes is initiated through the assembly of the transcription machinery on the promoter
46
Eukaryotic RNA Polymerases
Most Eukaryotic cells possess three distinct types of RNA polymerase, each responsible for transcribing a different class of RNA. RNA polymerase I – transcribes rRNA RNA polymerase II – transcribes pre-mRNAs, snoRNAs, some miRNAs, and some snRNAs RNA polymerase III – transcribes other small RNA molecules (tRNAs, small rRNAs, some miRNAs, and some snRNAs)
47
Polymerase I and III Promoters
RNA polymerase I and RNA polymerase III each recognize promoters that are distinct from those recognized by RNA polymerase II. Promoters for small rRNA and tRNA genes, transcribed by RNA polymerase III, contain internal promoters that are downstream of the start site and are transcribed into the RNA
48
Regulatory promoter
: located immediately upstream of the core promoter. Variety of different consensus sequences may be found in the regulatory promoters.
49
enhancers
Transcription activator proteins may also regulate transcription by binding to more distant sequences
50
Eukaryotic Promoters
Promoters recognized by RNA polymerase II – which transcribes the genes that encode proteins. – Core promoter is located immediately upstream of the gene, (the site where basal transcription apparatus binds). – TATA box TATAAAA – one of the most common promoter sequences ( –25 to –30 bp), bound by transcription factors
51
Transcriptional activator proteins
– another class of accessory proteins, bind specific DNA sequences and bring about higher levels of transcriptions by stimulating assembly of basal transcription apparatus at the start site. TATA box gets it started and box helps assemble apparatus
52
One class of accessory proteins comprises general transcription factors, which along with RNA polymerase form the
basal transcription apparatus group of proteins that assemble near transcription start site and initiates minimal levels of transcription.

Genetics (19 decks)

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