Chapter 13 - Transcription Flashcards by Elisa Soto

Which of the following is true of RNA compared to DNA?
A. RNA and DNA use the same four bases.
B. RNA lacks the hydroxyl group on the 2’- carbon atom of its sugar component that DNA has.
C. Both RNA and DNA are primarily double stranded.
D. RNA molecules are more variable in their secondary structures than DNA molecules.
E. RNA is more stable than DNA

D. RNA molecules are more variable in their secondary structures than DNA molecules.

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Which of the following statements is NOT correct about the process of transcription?
A. Transcription of a given gene takes place on only one of the two DNA strands.
B. During transcription the RNA molecule is synthesized in the 3’ to 5’ direction.
C. During transcription the RNA molecule that is synthesized is anti-parallel and complementary to the template DNA strand.
D. The start site and direction of transcription are determined by a region of the nontemplate DNA strand known as the promoter.

B. During transcription the RNA molecule is synthesized in the 3’ to 5’ direction.

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What would the likely result be if a specific sigma subunit were mutated?
A. Nothing would result: sigma is not essential.
B. RNA polymerase would still bind at specific sites, but elongation would fail.
C. RNA polymerase would fail to initiate transcription at the promoter specific to the sigma subunit.
D. The core enzyme would not be stable.

C. RNA polymerase would fail to initiate transcription at the promoter specific to the sigma subunit.

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A mutation in the promoter of an E. coli gene that makes the − 10 region a closer match to the consensus would be expected to:
A. be an “up” mutation.
B. be a “down” mutation.
C. improve the binding of RNA polymerase holoenzyme to the promoter.
D. both a and c.
E. both b and c.

D. both a and c.

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In rho-dependent transcription termination, the rho factor binds to ___________.

RNA (usually mRNA)

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Early in the history of life, RNA probably served both as the original ___ material and as biological ___.

genetic; catalysts

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Which class of RNA is correctly paired with its function?

a. Small nuclear RNA (snRNA): processes rRNA
b. Transfer RNA (tRNA): attaches to an amino acid
c. MicroRNA (miRNA): carries information for the amino acid sequence of a protein
d. Ribosomal RNA (rRNA): carries out RNA interference

b. Transfer RNA (tRNA): attaches to an amino acid

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Which of the following phrases does not describe a function of the promoter?

a. Serves as the sequence to which the transcription apparatus binds
b. Determines the first nucleotide that is transcribed into RNA
c. Determines which DNA strand is the template
d. Signals where transcription ends

d. Signals where transcription ends

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What is the difference between the template strand and the nontemplate strand?

The template strand is the DNA strand that is copied into an RNA molecule, whereas the nontemplate strand is not copied.

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What is the function of the sigma factor?

The sigma factor specifies the binding of RNA polymerase to the correct promoter.

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The __ (__ enzyme + __ factor) binds to the −10 consensus sequence found in most bacterial ___.

holoenzyme; core; sigma; promoters

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What characteristics are most commonly found in rho-independent terminators?

Inverted repeats followed by a string of adenine nucleotides.

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The initiation of transcription in eukaryotes requires modification of___ structure so that DNA is ___ to the transcription machinery.

chromatin; accessible

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What is the difference between the core promoter and the regulatory promoter?

a. Only the core promoter has consensus sequences.
b. The regulatory promoter is farther upstream of the gene.
c. Transcription factors bind only to the core promoter and not to the regulatory promoter.
d. Both b and c.

b. The regulatory promoter is farther upstream of the gene.

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Transcription in eukaryotes is initiated when the ___ ___ ___ — consisting of RNA polymerase, general ___ ___, and a ___ — assembles on the __ __ and the DNA becomes an ___ complex.

basal transcription apparatus; transcription factors; mediator; core promoter; open

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TFIID binds to the __ box and helps to center the __ __ over the transcription start site.

TATA; RNA polymerase

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The processes of RNA polymerase II termination in eukaryotes and rho-dependent termination in bacteria are similar: Both use a __ that binds to __ and moves toward __ __.

They differ in that __ does not degrade the RNA, whereas (an __) does.

protein; RNA; RNA poly

rho; Rat1;

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RNA is less chemically stable than DNA for what two reasons?

(1) Steric hinderance due to 2’OH; (2) The ubiquitous nature of RNAses.

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Secondary structures in ssRNA (hairpins and stems) are formed between ____ ____.

complimentary regions

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Secondary structures in RNA are important for ___ ___ (“___ dictates ____”).

biological function; structure; function

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rRNAs are an important part of ___ (which are the site of polypeptide synthesis).

ribosomes

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Classes of RNA: this one carries genetic info encoding the sequence of amino acids for a polypeptide out of the nucleus and into the ribosomes.

mRNA

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Classes of RNA: this one reads codons on RNA template/blueprint and brings the correct amino acid.

tRNA (transfer RNA)

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Classes of RNA: these are found in the nucleus and become associated with numerous proteins to form small nuclear ribonucleoproteins (snRNPs).

snRNA (small nuclear RNA)

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Classes of RNA: these are involved in processing rRNA in the nucleolus.

snoRNA (small nucleolar RNA)

Classes of RNA: this one is found in the cytoplasm; its function isn't fully understood.

scRNA (small cytoplasmic RNA)

Classes of RNA: these 2 are found in the cytoplasm - they either interfere with translation of mRNA, or they initiate degradation of mRNA (gene regulation)

miRNA (microRNA) and siRNA (small interfering RNA)

Transcription resembles DNA, but key differences include: 1. RNA molecules are much ____. 2. Transcription is highly regulated: specific __ are transcribed at specific ___ in specific ___ types. 3. In more complex eukaryotes, only a ___ portion of the genome is used for ____.

smaller genes; times; cell small; transcription

RNA synthesis occurs __ __ (meaning no primer), and requires 3 things: a DNA ___; a ___ (rNTPs); and ___ needed for transcription (i.e. RNA ___).

de Novo; template; substrate; protein (enzyme / polymerase)

A factor = ___; an element = ___; a transcript = ___.

protein; DNA; RNA

Electron microscopy of chromosomes involved in transcription revealed Christmas tree-like structures (or a bottle brush) of the RNA transcripts peeling away from the DNA 'trunk'. What does this suggest about RNA transcription?

Transcripts can be synthesized continuously and in succession.

The template strand is AKA ___ strand or the __ strand. The nontemplate strand is AKA ___ strand or the ___ strand.

nonsense; -- sense; +

Why is the nontemplate strand called the sense strand? Why is the template strand called the nonsense strand?

The sense strand reads almost exactly as the RNA (except T's are U's in RNA) due to the fact that it's collinear to the RNA strand. The nonsense strand is complimentary to the RNA; so it must be "translated" in order to determine the RNA sequence

Usually each gene is ___ from only one of the DNA strands; however, ___ strand can be used for transcription by ___ genes.

transcribed; either; different

The portion of the DNA that contains al of the sequences needed for transcription is called the ___ ___. There are 3 critical regions: (1) the ___; (2) the RNA ___ region; and (3) the ____. The ___ is usually upstream of the start site, and transcription proceeds ___ from it.

Transcription unit Promoter; coding; terminator promotor; downstream

The promoter is the __ part of the transcription unit. It determines which ___ ___ will be transcribed; it determines the __ site (which corresponds to the first __ of the RNA molecule); it's usually immediately ___ and ___ to the start site; and is not ____.

first. DNA strand; start; nucleotide; adjacent and upstream; transcribed.

The terminator portion of the transcription unit is usually part of the ____.

transcript.

RNA synthesis occurs _' to _'; however, it's important to remember that the _' carbon of new nucleotides are added to the _' end of the nascent RNA.

5' - 3'; 5'; 3'

Bacteria typically have __ RNA polymerase that is responsible for synthesis of ___, ___, and ___. It is a large ___ protein complex containing several ___. One exception is the RNA ___ which is needed for ___ replication.

1; mRNA, tRNA; rRNA. multimeric; polypeptides primer; DNA

Bacterial RNA polymerase consists of two main parts: a ___ enzyme and a ___ factor. The ___ enzyme's main function is ___ of the full RNA transcript. In addition, it has no ___ and will produce any RNA in vitro (resolved by the ___ factor). The enzyme consists of several subunits: 2 copies of __; one of __, one of __', and one of __ (the last of which is not essential for activity, but helps ___ the enzymatic complex).

core enzyme; sigma factor core; elongation. specificity; sigma alpha, beta, beta prime; omega; stabilize

The __ factor of bacterial RNA polymerase directs the ___ enzyme to the specific ___ (the 's' is for ____). Together, the __ factor and the __ enzyme form the __; however, the __ factor is only needed to bind the __ to the __ and will dissociate after the addition of the first few nucleotides (it will ___ synthesis if it does not dissociate).

sigma; core; promoter; specificity. sigma; core; holoenzyme; sigma; holoenzyme; promoter; block

Bacteria have many types of ___ factors. Their nomenclature is derived from its ___ ___. Each ___ factor recognizes a specific class of ____. For example, σ^__ (E. coli) binds to promoters for genes that are expressed during environmental stress, specifically heat (known as __ __ genes).

sigma. molecular mass sigma; promoter. 32; heat shock

Eukaryotes have 3 RNA polymerases: (1) __ which transcribes 3 of the 4 types of __. (2) __ which transcribes __-___, ---RNAs, and some --RNAs. (3) __ which transcribes -RNAs, one of the 4 types of -RNAs (a small one), and some --RNAs. Each RNA polymerase is a large multimeric enzymatic complex consisting of more than __ polypeptide subunits.

I; rRNA II; pre-mRNAs, snoRNAs; snRNAs III; tRNA; rRNA; snRNAs 12

The rate-limiting step in RNA synthesis is the interaction between the __ __ __ and the promoter (binding to the promoter and '__' the DNA for transcription).

basal transcription apparatus (holoenzyme); opening

The 3 stages of bacterial transcription are (1) ___ (assembly of the ___, and laying the 1st ___); (2) ___ (synthesis as the ___ enzyme translocates along the mRNA); and finally (3) ___ where the transcript ___ from the DNA template.

initiation; holoenzyme; nucleotide elongation; core termination; separates

Eukaryotic transcription is a dynamic process; different genes are transcribed at different ___; it mainly depends on the ___ of the ___ ___ ___ for the promoter. The DNA sequence of the promoter determines __ transcription will begin, which __ will be used; and the __ in which RNA polymerase will move.

rates; affinity; basal transcription apparatus where; strand; direction

Bacterial promoters share a few short, highly-___ DNA sequences called a __ __ (can be defined as the most commonly found ___ when a large number of promoters are examined side-by-side).

conserved; consensus sequences; nucleotide

Consensus sequence conventions: bases that occur with equal frequency are designated with a __; Y or R is where you'll find ___ or ___, respectively; and N designates no ___ base. Consensus sequences enabled scientists to find ___; they could ___ them to see how it impacted transcription.

slash; pYrimidines; puRines; No common base. promoters; mutate.

The -__ consensus sequence, also called the ___ Box, is the most ___ found sequence (TATAAT) in bacteria. The -__ consensus sequence (TTGACA) is another bacterial consensus sequence that plays a role in transcription. Variability in these sequence can effect ___ of transcription.

- 10; Pribnow; commonly - 35 efficiency

Most mutations of either the -__ or -__ consensus sequences lead to slower initiation; these are called __ __. In contrast, some mutations increase the rate of transcription; these are called __ __.

-10; -35; down mutations | up mutations

In general, mutations of the ___ to more closely match the -__ or -__ consensus sequences ___ the rate of transcription. This has been exploited by scientists: the ___ of plasmids have been engineered to more closely match the consensus sequence and ___ up testing.

promoter; -10; -35 promoters; speed

Pyrimidines are __ and __ (or __ in RNA); purines are __ or __.

C; T; U A; G

__ __ interacts with -10 or -35 consensus sequences and directs the RNA polymerase complex to an area covering -50 to +20, which overlaps the consensus sequence and part of the __ __ __. The act of binding the ___ to the promoter ___ the gene structure.

Sigma factor; ORF holoenzyme; alters

Some bacterial __ have an upstream element of A-T pairs located about -40 to -60. When present, they ___ the rate of transcription. This makes sense because the A-T pairs require less __ to ___.

promoters increase energy; separate

Determination of the template strand is dependent on the __ and __ of the consensus sequences. Changing the ___ of the consensus sequences (--10 or -35) alters the __ site, which, in turn, likely changes the +_ nucleotide used in RNA synthesis.

orientation; spacing location; start; +1

T or F: RNA polymerase unwinds DNA ahead of synthesis; and rewinds DNA behind it.

True!

T or F: RNA synthesis is much faster than DNA synthesis.

False! RNA synthesis is much slower than DNA synthesis

Unwinding /rewinding of DNA by RNA polymerase creates __ and __ __ ahead and behind that are relieved by ___.

positive; negative supercoils; topoisomerases

T or F: the sigma factor binds to the consensus sequence which gives RNA polymerase a 'target' to acquire.

False! The sigma factor and core RNA polymerase first form the holoenzyme, then they bind to the consensus sequence.

Bacterial RNA transcription is initiated when the ___ binds to the ___.

holoenzyme; promoter

Bacterial transcription ends when RNA synthesis passes the ___ sequence (part of transcription). 4 things occur (no sp. order): (1) RNA synthesis ___; (2) RNA is released from ___ ___; (3) RNA is released from the __ __; (4) RNA polymerase releases from the ___ __.

termination stops; RNA polymerase; template strand; template strand

What are the 2 types of bacterial terminators?

Rho-dependent and Rho-independent.

What is needed to terminate synthesis in rho-independent termination?

Rho-independent requires two elemental features: an inverted repeat to form a hairpin (slows synthesis); and a series of A's on the template) to facilitate dissociation (A-U bond is the least stable / easiest to dissociate).

3 things are needed to terminate synthesis in rho-dependent termination: (1) __ factor; (2) a __ (slows synthesis); and (3) a sequence __ of the terminator with minimal __ structure to facilitate binding of __ factor. __ factor has helicase activity. It binds to __ RNA, then moves towards the 3' end while unwinding it from DNA.

rho; hairpin; upstream; secondary; rho Rho; unstructured

Bacteria have __ RNA polymerase(s); eukaryotes have __.

1; 3

Initiation of transcription is more complicated in eukaryotes due to the fact that DNA is ___ with ___ and highly ___. Chromatin must be __ to allow RNA polymerase to initiate. Changes in chromatin ___ are facilitated by several ___ (two main ones are ___ and ___-___ proteins).

complexed; histones; condensed relaxed; confirmation; proteins/factors; acetyltransferases; chromatin-remodeling proteins

Acetyltransferases facilitate initiation of transcription in eukaryotes by adding __ goups to ___ and ___. This ___ the ___ charge of the aa's which destabilizes the structure of the ___.

acetyl; lysine; arginine. neutralizes; positive; nucleosome

___-___ proteins help move nucleosomes away from promoters to facilitate initiation of transcription in eukaryotes.

chromatin-remodeling

Aside from ___ structure, initiation of transcription in eukaryotes is further complicated by numerous ___ ___ that interact with RNA polymerase, plus two classes of ___ sequences: a wide variety of ___ sequences, and ___ which are unique to eukaryotes.

chromatin; transcription factors; regulatory; promoter; enhancers

Eukaryotic promoters are usually upstream and adjacent to the ___ it regulates (start site); the exception is promoters for RNA polymerase ___ which are located ___ within the ___ itself. On the other hand, ___ (unique to eukaryotes) can be ___, ___, ___'s of bases away, or even within an ____.

gene; III; downstream; gene enhancers; upstream; downstream; 1000's; intron.

In bacteria, ___ factors recognize specific promotors. In eukaryotes, ___ transcription factors recognize promoters, and they "attract" the appropriate ___ ___, which forms the ___ ___ ___ with other __ __ (somewhat analogous to the holoenzyme).

sigma; general; RNA polymerase; basal transcription apparatus; transcription factors

___ ___ (a type of TF), together with another factor, bind to specific DNA sequences in eukaryotic cells and control the ___ of transcription by stimulating ____ assembly of the ___ ___ ___ thereby stimulating faster transcription.

Transcription activator; rate; faster; basal transcription apparatus

The promoter for RNA polymerase II has two parts: a ___ promoter which labels the 'parking spot for the ___ ___ ___; and a ___ promoter where transcription activator proteins bind. Both are located __ of the transcription start site, but the ___ promoter is further ___.

core; basal transcription apparatus; regulatory upstream; regulatory; upstream

RNA polymerase __ transcribes genes that encode ___ (i.e., they transcribe __-_RNAs).

II; proteins; pre-mRNAs

RNA poly II is found in ___. The core promoter for RNA poly. II has several consensus sequences, but the most common is the ___ Box (TATAAA). (located -25 to -35). Mutations alter ___ of transcription, and moving them changes the __ __ __ (which, in turn, likely changes the +_ nucleotide).

Eukaryotes TATA TATA; efficiency; transcription start site; +1

Regulatory promoters for RNA polymerases are used in different combinations - why?

Different combinations are required for different genes.

Most transcription factors are ___, but some are also ___ (and ___ the rate of transcription).

activators; inhibitors; slow

Regulation of transcription is accomplished by the type of ___ ___ that binds to the ___ promoter.

transcription factor; regulatory

Different ___ are used for RNA poly __ and __ than are used for RNA poly __; and __ for RNA poly __ are downstream - they are part of the transcript. Additionally, RNA poly __ and __ use different general __ __.

promoters; I; III; II promoters; III I; III; transcription factors.

General transcription factors are named TFxx𝛼, where xx = __ __ that corresponds to its __ __, and 𝛼 = a __ __. For RNA polymerase II, there there are 6 major players: __, __, __, __, __, __. TF--- has the lead role. TF--- stabilizes the interaction between TBP and the DNA. TF--- helps TBP with recognition of the start site. TF--- has helicase activity.

roman numeral; RNA polymerase; capital letter. TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH TFIID TFIIA. TFIIB. TFIIH

TF--- is a complex of at least __ different polypeptides; one of which is the __ __ __ __ (TBP). The TBP moves along the __ of the helix in search of the __ box. Once found, TBP binds to the __ box and bends the DNA which begins to __ the helix by breaking __ __.

TFIID; 9; TATA Box Binding protein (TBP) groves; TATA. TATA; unwind; H bonds

TBP-associated factors join TBP to form ___ (__ polypeptides total). However, preceding this step is the assembly of the ___ ___ ___ which consists of 3 main parts: __ __ __; various __ __ __; and a ___.

TFIID; 9 basal transcription apparatus; RNA poly II; general transcription factors; mediator

T or F: Transcription starts once the basal transcription apparatus binds to the core promoter.

False: transcription requires activation by a transcription activator protein.

Big picture: TBP + TF--- bind to the __ promoter and guide the preassembled __ __ __ to the __ promoter. Next, a __ __ binds to the __ promoter or to an ___ seq.; if it binds to the __ promoter, it interacts with the ___ via a ___; if it binds to an __, it interacts with the ___ directly. In the latter case, DNA ___ to enable direct interaction, which is why an __ can be located ___ on the DNA molecule.

TFIID; core; basal transcription apparatus; core. transcription activator, regulatory; enhancer regulatory; mediator; coactivator enhancer; mediator. loops; enhancer; anywhere

___ sequences are more flexible than regulatory promoters; they can be located ___ on the gene or even ___ - not so with regulatory promoters.

Enhancer; anywhere; inverted

For RNA poly. II, termination seems ___; it can take place at many sites over __'s of bases. Although weird, it's not critical since the _' end of the transcript is ___ at a specific site by ___ (an endonuclease that is similar to __ factor in bacteria). It moves in a _' to _' direction while ___ the remaining transcript.

random; 1000's 3'; cleaved; Rat1; rho 5' to 3'; degrading

The TATA-binding protein (TBP) binds to the TATA box sequence in eukaryotic promoters. What is its function in transcriptional initiation? A. It blocks access of RNA polymerase to the promoter, until removed by general transcription factors. B. It is the subunit of prokaryotic RNA polymerase that is required to recognize promoters. C. It modifies histones so that nucleosomes can be removed from DNA for transcription. D. It bends and partly unwinds DNA at a promoter. E. It creates a phosphodiester bond between the nucleotides.

D. It bends and partly unwinds DNA at a promoter.

In eukaryotes, transcriptional activator proteins do all of the following EXCEPT: A. form part of the RNA polymerase II holoenzyme. B. bind either the regulatory promoter or enhancer of a gene. C. modify chromatin to make it more open and accessible. D. increase the rate at which transcription is initiated by RNA polymerase II.

A. form part of the RNA polymerase II holoenzyme.

``` In eukaryotes, which RNA polymerase transcribes the genes that encode proteins? A. RNA polymerase I B. RNA polymerase II C. RNA polymerase III D. RNA polymerase IV E. RNA polymerase V ```

B. RNA polymerase II

An in vitro transcription system that contains a bacterial gene does not initiate transcription. What is one possible problem? A. Histones that were on the DNA when it was isolated from E. coli are blocking access to the template. B. There is a mutation in the inverted repeat sequence that prevents a hairpin secondary structure from forming. C. There is a mutation at –10, where a promoter consensus sequence is located. D. Rho factor has not been added. E. TATA-binding protein (TBP) has not been added.

C. There is a mutation at –10, where a promoter consensus sequence is located.