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Ch.17 Transcription and Translation (Exam 3)
Terms in this set (138)
strand that is read by RNA polymerase
non-template strand whose sequence matches the sequence of the RNA that is transcribe from the template strand and codes for a polypeptide
(bacteria) detachable protein subunit that binds to bacterial RNA polymerase before transcription can begin
holoenzyme; core enzyme
Bacterial RNA polymerase and sigma form a ___, which consists of a(n) ___ (RNA polymerase, in this case), which contains the active site for catalysis, and other required proteins.
sections of DNA that promote the start of transcription in bacteria and viruses
Pribnow found that promoters in bacteria and viruses were 40-50 base pairs long and had a series of bases identical or similar to TATAAT. This six-base-pair sequence is now known as the ___, because it centered about 10 bases upstream from the point where bacterial RNA polymerase starts transcription.
DNA that is located in the direction RNA polymerase moves during transcription is said to be ___ from the point of reference; DNA located in the opposite direction is said to be ___.
(bacteria) ___, and not RNA polymerase, makes the initial contact with DNA of the promoter. This bond determines where and in which direction RNA polymerase will start synthesizing RNA.
RNA pol II
the only polymerase that transcribes protein-coding genes in eukaryotes
Most eukaryotic promoters include a sequence called the ___, centered about 30 base pairs upstream of the transcription start site, and other important sequences that vary more widely.
basal transcription factors
Instead of using a sigma protein, eukaryotic RNA polymerases recognize promoters using a group of proteins called ___; these assemble at the promoter, followed by RNA polymerase.
poly(A) signal; polymerase
Termination of eukaryotic protein-coding genes involves a short sequence called the ___. Soon after the signal is transcribed, the RNA is cut by an enzyme downstream of this signal as the ___ continues to transcribe the DNA template.
___ end transcription at a distinct site for each gene, but in ___, transcription ends variable distances from the poly(A) signal.
the initial product of eukaryotic transcription
the primary transcript for protein-coding genes in eukaryotes
Transcription ___ depends on interactions between proteins associated with RNA polymerase and a promotor sequence in DNA
sigma protein; promoter; basal transcription factors; RNA polymerase
In bacteria, ___ binds to RNA polymerase and contacts the ___. In eukaryotes, ___ bind to the promoter and recruit ___.
During transcription ___, ribonucleoside triphosphates are the substrate for a polymerization reaction catalyzed by RNA polymerase. The enzyme adds ribonucleotides that are complementary to the template strand in DNA.
RNA polymerase; DNA template
Transcription ends in bacteria when a termination signal at the end of the gene is transcribed, leading to the disassociation of ___ and the ___.
sections of genes that are not represented in the final RNA product
sections of genes that are represented in the final RNA product
During transcription, introns are removed from a growing RNA strand by a process known as ___.
small nuclear RNAs (snRNAs); small nuclear ribonucleoproteins (snRNPs)
Splicing of primary transcripts is catalyzed by RNAs called ___ working with a complex of proteins. These proteins-plus-RNA macromolecular machines are known as ___.
snRNPs; spliceosome; lariat; phosphodiester linkage; pre-mRNA
1. ___ bind to the 5' exon-intron boundary, which is marked by the bases GU, and to a key adenine ribonucleotide near the end of the intron.
2. Other snRNPs arrive to form a multipart complex called a ___.
3. The intron forms a loop plus a single-stranded stem (a[n] ___) with the adenine at its connecting point.
4. Once the lariat is cut out, a ___ links the exons on either side, producing a continuous coding sequence--the ___.
As soon as the 5' end of a eukaryotic pre-mRNA emerges from RNA polymerase, enzymes add a structure called the ___, which consists of a modified guanine (7-methylguanylate) nucleotide with three phosphate groups.
An enzyme cleaves the 3' end of the pre-mRNA downstream of the poly(a) signal. Another enzyme adds a long row of 100-250 adenine nucleotides that are not encoded on the DNA template strand. This string of adenines is known as the ___.
With the addition of a cap and tail and completion of splicing, processing of the pre-mRNA is complete. The product is ___.
untranslated regions (UTRs)
In the mature RNA molecule, the coding sequence for the polypeptide is flanked by sequences that are not destined to be translated. These 5' and 3' ___ help stabilize the mature RNA and regulate its translation.
Caps and tails on eukaryotic mRNAs protect mRNAs from degradation by ___--enzymes that degrade RNA--and enhance the efficiency of translation.
5' cap; poly(A) tail
Enzymes add a ___ and a ___ to spliced transcripts, producing a mature mRNA that is ready to be translated.
a general term for any of the modifications, such as splicing or 5' cap/3' poly(A) tail addition, needed to convert a primary transcript into a mature RNA
Transcription and translation occur simultaneously in ___.
Ribosomes are the site of ___.
During translation, multiple ribosomes attach to each mRNA, forming a ___.
Transcription and translation can occur concurrently in bacteria because there is no ___ to separate the two processes.
In eukaryotes, primary transcripts are processed in the ___ to produce a mature mRNA, which is then exported to the ___.
transfer RNA (tRNA)
transfers amino acids from the RNA to a growing polypeptide; act as the interpreter during translation
a set of three ribonucleotides on the tRNA that form complementary base pairs with an mRNA codon
amino acid attachment; anticodon
Secondary Structure of tRNA
3' end: CCA sequence that offers a site for ___
5' end: triplet on a loop that can serve as a(n) ___
tRNA tertiary structure; maintains a precise physical distance between the anticodon and the amino acid, which is important for positioning the anticodon and amino acid within the ribosome
ATP; aminoacyl-tRNA synthetases; charging; aminoacyl-tRNa synthetase; tRNAs
Steps for amino acid linkage to tRNA:
1. ___ is required
2. enzymes called ___ catalyze the addition of amino acids to tRNAs--what biologists call "___" a tRNA
3. for each of the 20 major amino acids, there is a different ___ and one or more ___.
amino acid; tRNA
Each aminoacyl-tRNA synthetase has a binding site for a particular ___ and a particular ___.
the combination of a tRNA molecule convalently linked to an amino acid
Many amino acids are specified by more than one codon.
first; second; third
Codons for the same amino acid tend to have the same nucleotides at the ___ and ___ positions but a different nucleotide at the ___ position.
(Crick) Inside the ribosome, certain bases in the third position of tRNA anticodons can bind to bases in the third position of a codon in a manner that does not match Watson-Crick base pairing. If so, this would allow a limited flexibility in base-pairing. According to this idea, particular nonstandard base pairs--such as G-U--are acceptable in the third position of a codon and do not change the amino acid that the codon specifies. This allows just 40 or so tRNAs to bind to all 61 mRNA codons.
anticodon aminoacyl tRNA; peptide bond; ribosome
The translation of each mRNA codon begins when the ___ of a(n) ___ binds to the codon. Translation of a codon is complete when a ___ forms between the tRNA's amino acid and the growing polypeptide chain. Both of these events take place inside a ___.
mRNA; peptide-bond formation
In a ribosome, the small subunit holds the ___ in place during translation; the large subunit is where ___ takes place.
During protein synthesis, 3 distinct ___ are lined up inside the ribosome, bound to their corresponding ___ codons.
A; P; E
The ribosome is a macromolecular machine that synthesizes proteins in a 3-step sequence:
1. An aminoacyl tRNA diffuses into the ___ site; if its anticodon matches a codon in mRNA, it stays in the ribosome.
2. A peptide bond forms between the amino acid and the growing polypeptide, which was held by a tRNA in the ___ site.
3. The ribosome moves down the mRNA by one codon, and all three tRNAs move one position within the ribosome. The tRNA in the ___ site exits.
The protein that is being synthesized grows by one amino acid each time this 3-step sequence repeats.
ribosome binding site (Shine-Dalgarno sequence); initiation factors
In bacteria, translation begins when a section of rRNA in a small ribosomal subunit binds to a complementary sequence on an mRNA. The mRNA region is called the ___. ___ help in preparing the ribosome for translation, including binding the first aminoacyl tRNA to the ribosome.
___ proceeds when an aminoacyl tRNA binds to the codon in the A site by complementary base pairing between the anticodon and codon.
When both the P site and A site are occupied by tRNAs, the amino acids on the tRNAs are in the ribosome's ___ site. This is where peptide-bond formation occurs.
Protein synthesis is catalyzed by ___.
The ribosome is a(n) ___, not a protein-based enzyme.
Translocation occurs when proteins called ___ help move the ribosome relative to the mRNA so that translation occurs in the 5'-->3' direction.
Translocation is an energy-demanding event that requires GTP.
Process that moves the uncharged RNA into the E site; moves the tRNA containing the growing polypeptide into the P site; and opens the A site and exposes a new mRNA codon. The empty tRNA that finds itself in the E site is ejected into the cytosol.
E; P; A; mRNA; cytosol
Translocation is a process that moves the uncharged RNA into the ___ site; moves the tRNA containing the growing polypeptide into the ___ site; and opens the ___ site and exposes a new ___ codon. The empty tRNA that finds itself in the E site is ejected into the ___.
There are three steps in ___:
1. arrival of aminoacyl tRNA
2. peptide-bond formation
aminoacyl tRNA; peptide-bond; translocation
There are three steps in elongation:
1. arrival of ___
2. ___ formation
When the translocation ribosome reaches one of the stop codons, a protein called a(n) ___ recognizes the stop codon and fills the A site.
When a release factor occupies the A site, the protein's active site catalyzes the ___ of the bond that links the tRNA in the P site to the polypeptide chain. This reaction frees the polypeptide.
In termination, the newly synthesize polypeptide and uncharged tRNAs are released from the ribosome, the ribosome separates from the mRNA, and the two ribosomal ___ dissociate.
Although protein folding can occur spontaneously, it is frequently speeded up by proteins called ___.
___ begins when:
1. the ribosome binding site on an mRNA binds to an rRNA sequence in the small ribosomal unit
2. the initiator aminoacyl tRNA binds to the start codon in the mRNA
3. the large subunit of the ribosome attached to the small subunit to complete the ribosome
___ occurs when:
1. an appropriate aminoacyl tRNA enters the A site
2. a peptide bond forms between the amino acid held by that tRNA in the A site and the polypeptide held by the tRNA in the P site
3. the ribosome moves down the mRNA one codon.
___ ends when the ribosome reaches a stop codon.
folding; sugar; lipid; phosphate groups
Completed proteins are modified by ___ and, in many cases, addition of ___, ___, or ___.
___ binds to specific site in DNA with help of other proteins; catalyzes production of an RNA molecule.
The base sequence of the RNA produced is complementary to the base sequence of the DNA ___ strand.
During RNA processing, ___ are removed (spliced out) and the ends of the remaining RNA receive a cap and tail.
Inside ribosomes, mRNAs are translated to proteins via intermediary molecules called ___.
the site of DNA where the RNA polymerase must bind to initiate transcription
The ___ is the regulatory region of a protein-coding gene at which RNA polymerase must bind to initiate transcription—it is not transcribed into the RNA.
Base pairing between the DNA ___ strand and the RNA ___ determines which base is to be added to an RNA strand during transcription.
A gene has two main parts: a regulatory region, containing a(n) ___, and a(n) ___ region, which contains the coding information for a protein product.
initiation; elongation; termination
3 phases of prokaryotic and eukaryotic transcription: (1) ___ (2) ___ (3) ___
RNA polymerase II
In eukaryotes, the enzyme ___ is responsible for transcribing protein-coded genes.
In the ___ phase of transcription, the RNA polymerase begins to travel in the 5'-->3' direction along the template strand, catalyzing the addition of complementary ___.
3' hydroxyl; covalent
(Elongation) As in DNA synthesis, new ribonucleotides are added to the ___ group of the growing RNA strand being synthesized. If the incoming nucleotide pairs properly with the next base in the template DNA, the RNA polymerase catalyzes the formation of a(n) ___ bond. As a result, the RNA chain is elongated.
termination; transcription termination signals
Transcription ends with the ___ phase. The RNA polymerase proceeds along the length of the gene. As the polymerase travels, the RNA dissociates from the DNA, and the DNA re-forms a double helix. Sequences at the end of the gene called ___ direct the polymerase to end transcription. The RNA, DNA, and polymerase then dissociate from one another. The RNA polymerase is free to transcribe other genes in the cell.
(1) 5'—>3' (2) 3'—>5'
During transcription, in which direction is (1) RNA synthesized and in which direction is (2) the DNA template "read"?
Because ribonucleoside triphosphates have three negatively charged phosphates close together, they have ___ potential energy, which is released during polymerization, making RNA synthesis spontaneous (ΔG<0) in cells.
Ribonucleoside triphosphates have high potential energy, making the RNA polymerization reaction ___ (endergonic/exergonic).
The promoter is ___ (upstream/downstream) of the DNA to be transcribed.
sequence in DNA that brings RNA polymerase near the site for transcription
Nucleotides are added to the ___ end of the growing RNA molecule.
RNA polymerase II
In eukaryotes there are several different types of RNA polymerase. Which type is involved in transcription of mRNA for a globin protein?
RNA polymerase II; I; III
Death cap mushrooms produce a substance called alpha-amanitin. Alpha-amanitin efficiently blocks synthesis of mRNA, but not of tRNA or rRNA in eukaryotic organisms. This is possible because alpha-amanitin efficiently interferes with the action of ___, but not ___ or ___.
transcription factors; promoter
In eukaryotic cells, transcription cannot begin until several ___ have bound to the ___.
sigma; RNA polymerase
David Pribnow studied the base sequences of promoters in bacteria and bacterial viruses. He found two conserved regions in these promoters (the -10 box and the -35 box). These two regions of the promoter bind the ___ subunit that is associated with ___.
sigma; promoter region
The binding of ___ to the ___ is central to the initiation of transcription in prokaryotes.
(Bacteria) During elongation, ___ has three prominent channels, or grooves. These channels provide sites for all of the following:
(1) a site for the entry of ribonucleoside triphosphates
(2) a site for the growing RNA strand
(3) a site for the double-stranded DNA molecule
3, 1, 2, 5, 4
Put the following events of transcription in chronological order.
1. Sigma binds to the promoter region.
2. The double helix of DNA is unwound, breaking hydrogen bonds between complementary strands.
3. Sigma binds to RNA polymerase.
4. Sigma is released.
5. Transcription begins.
complementary base pairing; RNA transcript; RNA polymerase
How are RNA hairpin turns related to termination in E. coli? The turns are formed from ___ and cause separation of the ___ and ___.
a polyadenylation signal or poly(A)
___ is responsible for termination of transcription in eukaryotic protein-coding genes.
The 5' cap consists of a modified ___.
During RNA processing a(n) _____ is added to the 3' end of the RNA.
Spliceosomes are composed of _____.
The RNA segments joined to one another by spliceosomes are _____.
cytoplasm (Ribosomes, the sites of translation, are found in the cytoplasm.)
Translation occurs in the _____.
The 5' cap and the 3' poly(A) tail of eukaryotic mRNAs are important for initiating ___ and extending the ___ of the mRNA.
In eukaryotes, when mature mRNA is hybridized to complementary DNA, ___ loop out as single-stranded regions of ___.
During mRNA splicing, ___ that make up the ___ recognize and remove introns.
Ribozymes may function in RNA ___.
an RNA with catalytic activity
The 5'cap and poly-A tail protect the mRNA from being digested by ___.
What kind of regulation removes the introns, making the mRNA smaller than the length of the DNA it codes for?
There should be a strong positive correlation between the rate of protein synthesis and the number of ___.
Ribosomes can attach to prokaryotic messenger RNA before ___ is complete.
amino acid; tRNAs
An aminoacyl tRNA synthetase enzyme recognizes one [a] and the set of [b] that are coupled to that [a].
A particular triplet of bases in the coding sequence of DNA is AAA. The anticodon on the tRNA that binds the mRNA codon is _____.
anticodon (on tRNA); amino acids
Accuracy in the translation of mRNA into the primary structure of a polypeptide depends on specificity in the binding of the ___ to the codon and the attachment of ___ to tRNAs
amino acid; translation
The anticodon of a properly formed aminoacyl tRNA ensures that the correct ___ is added during ___.
If the DNA code for a particular amino acid is 5'AGT3', then the anticodon on the tRNA would be _____.
amino acid attachment site
On the 3' end of a tRNA, there is a(n) ___.
hydrogen bonding between base pairs
What type of bonding is responsible for maintaining the clover shape of a tRNA molecule?
mRNA, tRNA, ribosomes, and GTP are the molecules directly involved in ___.
ribosome; tRNA; peptide bond
The central paradigm of biochemistry holds that information flows from DNA to RNA to protein. The process of making protein from the mRNA is called translation. Translation is carried out by the [a], which binds to the mRNA and binds [b], which recognizes the codons on the mRNA and brings the appropriate amino acid with it. The [a] forms the [c] between the new amino acid and the growing peptide chain.
aminoacyl tRNA synthetase
Amino acids are attached to tRNA by enzymes called ___.
The process, performed by the ribosome, of reading mRNA and synthesizing a protein is called ___.
protein and ribosomal RNA (rRNA)
A ribosome is a large complex of ___.
In this step, two subunits of the ribosome associate with the mRNA. The ribosome translates the code of nucleotides in the mRNA into the sequence of amino acids in a protein.
initiation, elongation, termination
three stages of translation
a tRNA attached to a specific amino acid
initiation; 5' cap; start codon; anticodon; hydrogen bonds; methionine
The ___ stage begins when an mRNA molecule and the small subunit of the ribosome associate. In eukaryotes, the small subunit binds to a chemical group on the mRNA called the ___. It then slides to the first AUG sequence, which is the ___ in the mRNA. Next, an aminoacyl tRNA binds to the AUG subunit. This aminoacyl tRNA contains a complementary triplet--the ___--that forms ___ with the bases in the start codon. The start codon codes for ___, abbreviated at Met. The large ribosomal subunit then joins the complex, completing this stage of translation.
elongation; P site; A site; E site; peptide bond; translocation
The ribosome builds the protein during the [a] stage. An aminoacyl tRNA occupies the middle position, called the ___. The tRNA at this site holds the growing polypeptide chain. The ___ holds new aminoacyl tRNAs that enter the ribosome. At the ___, the ribosome ejects the used tRNA, which no longer holds an amino acid. [a] begins when a new aminoacyl tRNA enters the A site. To remain in the A site, this tRNA's anticodon must be complementary to the opposing codon in the mRNA.
The large ribosomal subunit catalyzes a reaction in which the two adjacent amino acids form a covalent bond called a ___. At the same time, in the P site, the bond between the tRNA and its amino acid breaks.
In a process called ___, the ribosome slides one codon down the mRNA, in the 5' to 3' direction. The first tRNA is ejected from the E site into the cytoplasm. The tRNA holding the peptide chain is now in the P site. The cycle of [a] repeats for each of the codons in the mRNA molecule.
termination; release factors
The last stage of translation is called ___. In the cell, there is no tRNA that has an anticodon complementary to the stop codon. Instead, proteins called ___ enter the A site, recognize the stop codons, and catalyze a reaction in which the polypeptide is cleaved from the adjacent tRNA. The mRNA and the two ribosomal subunits dissociate.
the process by which the ribosome slides down the mRNA so a new cycle of elongation can begin
(How does the bacterial ribosome recognize where to start translation?) The small ribosomal subunit binds to the ___ sequence, which is about 6 nucleotides upstream from the start codon.
The ribosome-binding site of prokaryotes is also known as the _____.
What does a bacterial RNA polymerase produce when it transcribes a protein-coding gene?
Initiation will be inhibited because sigma cannot bind to the promoter.
How is a mutation in a bacterial cell that deletes three base pairs 10 base pairs upstream from the +1 site likely to affect transcription and why?
There are three principles to keep in mind when predicting the sequence of the mRNA produced by transcription of a particular DNA sequence.
The RNA polymerase reads the sequence of DNA bases from only one of the two strands of DNA: the template strand.
The RNA polymerase reads the code from the template strand in the 3' to 5' direction and thus produces the mRNA strand in the 5' to 3' direction.
In RNA, the base uracil (U) replaces the DNA base thymine (T). Thus the base-pairing rules in transcription are A→U, T→A, C→G, and G→C, where the first base is the coding base in the template strand of the DNA and the second base is the base that is added to the growing mRNA strand.
Suppose that a portion of double-stranded DNA in the middle of a large gene is being transcribed by an RNA polymerase. As the polymerase moves through the sequence of six bases shown in the diagram below, what is the corresponding sequence of bases in the RNA that is produced?
Coding strand: 3'CCGAGT5'
Template strand: 5'GGCTCA3'
RNA polymerase II
During transcription in eukaryotes, a type of RNA polymerase called ___ moves along the template strand of the DNA in the 3'→5' direction. However, for any given gene, either strand of the double-stranded DNA may function as the template strand.
the base sequence of the gene's promoter
For any given gene, what ultimately determines which DNA strand serves as the template strand?
In eukaryotes, binding of RNA polymerase II to DNA involves several other proteins known as transcription factors. Many of these transcription factors bind to the DNA in the promoter region (shown below in green), located at the ___ end of the sequence on the template strand. Although some transcription factors bind to both strands of the DNA, others bind specifically to only one of the strands.
Transcription factors do not bind randomly to the DNA. Information about where each transcription factor binds originates in the base sequence to which each transcription factor binds. The positioning of the transcription factors in the ___ region determines how the RNA polymerase II binds to the DNA and in which direction transcription will occur.
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