Chapter 12: Transcription Flashcards
1
Q
1) Which of the following is true regarding the genetic code?
A) The genetic code is degenerate.
B) The genetic code is overlapping.
C) The genetic code is considered to not be universal.
D) The genetic code has three start codons and one stop codon.
E) The genetic code is ambiguous.
A
A
2
Q
2) If there were 75 naturally occurring amino acids then what is the smallest codon size? A) 1 B) 2 C) 3 D) 4 E) 5
A
D
3
Q
3) When scientists were attempting to determine the structure of the genetic code, Crick and coworkers found that when three base additions or three base deletions occurred in a single gene,
the wild-type phenotype was sometimes restored. These data supported the hypothesis that
________.
A) AUG is the initiating triplet B) the code is triplet
C) the code is overlapping
D) there are three amino acids per base
E) the code contains internal punctuation
A
B
4
Q
4) The experiments that deciphered the genetic code used an enzyme called polynucleotide phosphorylase. If researchers added this enzyme to a large quantity of only guanine (G)
ribonucleoside diphosphates then a RNA molecule would be produced that would code for which amino acid?
A) phenylalanine (phe) B) lysine (lys) C) proline (pro) D) glycine (gly) E) arginine (arg)
A
D
5
Q
5) In 1964, Nirenberg and Leder used the triplet binding assay to determine specific codon assignments. A complex of which of the following components was trapped in the nitrocellulose
filter?
A) charged tRNA, RNA triplet, and ribosome
B) ribosomes and DNA
C) sense and antisense strands of DNA
D) uncharged tRNAs and ribosomes
E) free tRNAs
A
A
6
Q
6) What is the name given to the three bases in a messenger RNA that bind to the anticodon of tRNA to specify an amino acid placement in a protein? A) wobble B) procodon C) cistron D) codon E) rho
A
D
7
Q
7) What is the initiator triplet in both bacteria and eukaryotes? What amino acid is recruited by this triplet?
A) UAA, UGA, or UAG; arginine
B) AUG; arginine
C) UAA, UGA, or UAG; methionine
D) UAA, UGA, or UAG; no amino acid called in
E) AUG; methionine
A
E
8
Q
8) Due to the wobble hypothesis, which position in the codon, if changed to a different nucleotide, would be least likely to cause a change in the amino acid encoded?
A) third nucleotide of the codon B) any nucleotide of the codon. C) first nucleotide of the codon D) second nucleotide of the codon E) Either the first or second nucleotide of the codon.
A
A
9
Q
9) A particular mRNA is 300 nucleotides long. If a mutation in the middle of the sequence changed a codon from a AAA to a UAA then what would be a reasonable prediction?
A) The protein coded by this mRNA would be shorter.
B) The protein coded by this mRNA would kill the cell.
C) The protein coded by this mRNA would not form due to a failure in initiation.
D) The protein coded by this mRNA would be longer.
E) The protein coded by this mRNA would be the same size.
A
A
10
Q
10) The genetic code is fairly consistent among all organisms. The term often used to describe such consistency in the code is \_\_\_\_\_\_\_\_. A) exceptional B) universal C) trans-specific D) overlapping E) None of the above
A
B
11
Q
11) The nuclear genetic code is considered universal with a few exceptions. Some of these exceptions are found when comparing the nuclear genetic code of humans to what?
A) acterial genetic code
B) chimpanzee’s genetic code C) angiosperm’s genetic code
D) phage M2 genetic code
E) human mitochondrial genetic code
A
E
12
Q
12) The finding that some phage genes have multiple initiation sites is evidence against what characteristic of the genetic code?
A) The genetic code is commaless.
B) The genetic code is unambiguous. C) The genetic code is a triplet code.
D) The genetic code is universal.
E) The genetic code is nonoverlapping.
A
E
13
Q
13) The relationship among a gene, a messenger RNA, and a protein is that ________.
A) mRNAs make genes, which then make proteins
B) mRNAs make proteins, which then make genes
C) genes make proteins, which then make mRNA
D) genes make mRNA, which then make proteins
E) proteins make mRNA, which then make genes
A
D
14
Q
14) Which of the following bacterial RNA polymerase subunits is found in the holoenzyme, but not the core enzyme? A) β (beta) B) β′ (beta prime) C) ω (omega) D) α (alpha) E) σ (sigma)
A
E
15
Q
15) An mRNA that is being produced comes off of the ________.
A) template strand in bacteria and the coding strand in eukaryotes
B) coding strand in bacteria and the template strand in eukaryotes
C) coding or template strand in both bacteria and eukaryotes depending upon the species
D) template strand in both bacteria and eukaryotes
E) coding strand in both bacteria and eukaryotes
A
D
16
Q
16) When considering the initiation of transcription, one often finds consensus sequences located in the region of the DNA where RNA polymerase(s) binds. Which of the following is a common consensus sequence? A) TTTTAAAA B) satellite DNAs C) TATAAT D) any trinucleotide repeats E) GGTTC
A
C
17
Q
17) A mutation in a particular bacterial gene prevents the formation of a hairpin loop. This is most likely to affect which part of transcription?
A) This mutation will not affect any aspect of transcription in bacteria.
B) This mutation will affect initiation, elongation, and termination.
C) This mutation will affect elongation.
D) This mutation will affect termination. E) This mutation will affect initiation.
A
C
18
Q
18) Eukaryotic transcription is different than bacterial transcription because eukaryotic transcription ________.
A) occurs in the cytoplasm
B) requires the uncoiling of the chromatin fiber
C) only requires one RNA polymerase
D) does not require the mRNA to be modified
E) does not require general transcription factors to initiate transcription
A
B
19
Q
19) Which transcription factor binds directly to the TATA-box sequence? A) TFIIA B) TFIIB C) TFIID D) enhancers E) TFIIC
A
C
20
Q
20) A mutation of what type of sequence is predicted to have the greatest effect on the rate of transcription? A) enhancer B) silencer C) termination sequence D) proximal-promoter element E) core promoter
A
E
21
Q
21) Which mRNA modification is likely absent if the mRNA is degrading prematurely from the 5′ end of the mRNA?
A) RNA editing
B) splicing together of exons
C) addition of the 7-methylguanosine cap to the 5′ end
D) removal of introns
E) addition of the 3′ polyadenylated tail
A
C
22
Q
22) It has been recently determined that the gene for Duchenne muscular dystrophy (DMD) is more than 2000 kb (kilobases) in length; however, the mRNA produced by this gene is only about 14 kb
long. What is a likely cause of this discrepancy?
A) The DNA represents a double-stranded structure, whereas the RNA is single-stranded.
B) The exons have been spliced out during mRNA processing.
C) When the mRNA is produced, it is highly folded and therefore less long.
D) There are more amino acids coded for by the DNA than by the mRNA.
E) The introns have been spliced out during mRNA processing.
A
E
23
Q
23) An intron is a section of ________.
A) DNA that is removed during DNA processing
B) the carbohydrate that serves as a signal for RNA transport
C) RNA that is removed during RNA processing
D) protein that is clipped out posttranslationally
E) the transfer RNA (tRNA) that binds to mRNA codon
A
C
24
Q
24) If one compares the base sequences of related genes from different species, one is likely to find that corresponding \_\_\_\_\_\_\_\_ are usually conserved, but the sequences of \_\_\_\_\_\_\_\_ are much less well conserved. A) chaperons; exons B) exons; introns C) introns; exons D) introns; proteins E) introns; chaperons
A
B
25
```
25) In which cellular organelle do the three posttranscriptional modifications often seen in the maturation of mRNA in eukaryotes occur?
A) mitochondrion
B) cytoplasm
C) lysosome
D) nucleus
E) Golgi
```
D
26
26) Which of the following intron groups is matched appropriately with a true statement?
A) Group I introns are removed from rRNAs that are found in mitochondria and chloroplasts.
B) Spliceosomal introns are removed using large protein-based enzyme complexes.
C) Group I introns are removed from rRNAs using large protein-based enzyme complexes.
D) Spliceosomal introns are removed using the catalytic ability of the intron itself.
E) Group II introns are removed from mRNA in mammals.
B
27
27) The type of RNA modification that requires guide RNAs is ________.
A) addition of the 7-methylguanosine cap to the 5′ end
B) splicing together of exons
C) RNA editing
D) removal of introns
E) addition of the 3′ polyadenylated tail
C
28
Describe the direction of information flow in living systems. Use appropriate, scientific 28) terms in your description.
DNA is replicated and passed to offspring through a variety of reproductive processes. Information contained in the
base sequences of DNA is transcribed into a variety of RNAs. Certain RNAs (tRNA) carry amino acids to the site of translation where proteins are assembled. Other RNAs (mRNA and rRNA) provide a mechanism for ordering the sequence of amino acids in proteins.
29
Sidney Brenner argued that the code was nonoverlapping because he considered that coding restrictions would occur if it were overlapping. A second major argument against an overlapping code involved the effect of a single nucleotide change. In an overlapping code, how many adjacent amino acids would be affected by a single nucleotide change? In a nonoverlapping code, how many amino acid(s) would be affected?
two; one
30
From the late 1950s to the mid-1960s, numerous experiments using in vitro cell-free systems provided information on the nature of the genetic code. Briefly explain how the use of polynucleotide phosphorylase and the triplet binding assay were used to decipher the genetic code and why the triplet binding assay was more precise.
Use of polynucleotide phosphorylase for the random assembly of nucleotides provided for the assembly of RNA homopolymers and random heteropolymers, which when placed in the cell-free protein-synthesizing system, provided products (polypeptide chains) for analysis. The triplet binding assay along with the use of repeating copolymers were used to verify information provided earlier and to establish the ordered codon assignments.
31
Suppose that in the use of polynucleotide phosphorylase, nucleotides A and C are added in a ratio of 1A:5C. What is the probability that an AAA sequence will occur?
1/6 × 1/6 × 1/6 = 1/216
32
"Breaking the genetic code" has been referred to as one of the most significant scientific achievements in modern times. Describe (in outline or brief statement form) the
procedures used to break the code.
(a) use of polynucleotide phosphorylase for the production of synthetic "mRNAs"
(b) introduction of synthetic mRNAs into the cell-free protein-synthesizing system
(c) frameshift mutations in the rII region of T4 phage to show code is triplet and degenerate (d)triplet binding assay to produce mRNA–tRNA-ribosome complex
(e) development of regular copolymers for use in the cell-free protein-synthesizing system
33
Reading the RNA sequences in a 5′ to 3′ direction, a base at the first position of an anticodon on the tRNA would pair with a base at the ________ position of the mRNA.
third
34
Explain the "wobble hypothesis" and why it allows a single tRNA to recognize more than one codon.
The relaxed pairing at the third position of the codon and the first position of the anticodon are less constrained and do
not need to follow the traditional base pair rules. This allows for a single tRNA to recognize multiple codons.
35
A particular mRNA makes a protein that has a unformylated methionine as its first amino acid. Did this mRNA come from a bacterial or a eukaryotic cell? Explain.
Eukaryotic cell. Eukaryotic mRNA code for proteins starts with an unformylated methionine whereas bacterial mRNA
code for proteins starts with a formylated methionine.
36
Write a sequence of mRNA that codes for five amino acids and the mRNA should contain proper punctuation and polarity
5′ AUG (any four amino acid coding codons) and (UAA, UGA, or UAG) 3′
37
There is some indication that the code is in some way ordered; a certain pattern exists. Describe an observation that supports this view.
Certain amino acids may be grouped according to the middle base; for example, U or C in the second position often specifies hydrophobic amino acids. Also, codons with the same two starting letters frequently encode the same amino acid.
38
The finding that virtually all organisms use the same genetic code provides the basis for declaring that the code is universal. Name at least two exceptions to such universality.
mitchondrial DNA; Mycoplasma capricolum; some protozoans
39
In the context of molecular genetics, how does one reconcile the terms overlapping genes and 39) nonoverlapping code?
The genetic code contains codons that are nonoverlapping; however, overlapping genes are observed in some viruses
in which, due to differential use of AUG to initiate translation, the same mRNA can yield different protein products.
40
What are three observations that suggested eukaryotic RNA was an intermediate between DNA and protein
(1) DNA is found in the nucleus and protein synthesis occurs in the cytoplasm, (2) RNA is synthesized in the nucleus
and has a chemical similarity to DNA, and (3) RNA is transported out of the nucleus and into the cytoplasm where
protein translation occurs.
41
Describe the effects of mutating a sigma factor gene in bacteria.
The core RNA polymerase enzyme will form. Since there are more than one sigma factor genes, by mutating a single
sigma factor gene there will be some holoenzymes that will not form which will affect specific gene transcription.
42
In a particular bacterial mutant, a specific gene is not producing a mRNA or the corresponding protein. Researchers sequence the gene and determine that there are no mutations in the coding portion of the gene. What could explain these observations?
One of the two consensus sequences are likely mutated. Either the Pribnow box (TATA AT) or the −35 sequence (TTGACA).
43
Describe how rho-dependent termination occurs in bacteria.
A bacterial protein called rho factor binds to an mRNA at the rut site. It moves along the mRNA in a 5′-to-3′ direction
chasing after the RNA polymerase. When it reaches the hairpin loop it removes it and then proceeds to break through
the hydrogen bonds holding the RNA-DNA together, which successfully removes the RNA polymerase.
44
Describe a difference between the RNA polymerases of eukaryotes and prokaryotes.
In eukaryotes, three polymerases (I, II, and III) have been identified; only one has been described in prokaryotes.
45
In eukaryotes, which three factors appear to encourage the specific association of RNA polymerase(s) to a specific region of DNA?
promoters, enhancers, and transcription factors
46
What are four ways that mRNA can be modified?
(1) Adding a modified guanine to the 5′ end, (2) adding a polyadenylation tail to the 3′ end, (3) splicing of introns, and
(4) RNA editing.
47
List four possible reasons that explain the importance of introns.
1) introns allow for alternative splicing,
(2) exon shuffling, which can aid in evolution of new genes,
(3) the intron can be a microRNA itself that can regulated gene expression
4) introns can contain enhancer and silencer sequences
that aid in gene regulation.
48
What is meant by the term heterogeneous nuclear RNA (hnRNA)?
pre-mRNA, primary transcripts before processing in eukaryotes
49
A researcher is looking at a cellular sample using an electron microscope. They observe that while mRNA is being transcribed from the DNA that ribosomes are binding to the mRNA to make proteins. Is this sample from a bacterial or a eukaryotic cell?
Bacteria. Since bacteria lack a nucleus, the ribosomes can bind to the mRNA as it's being synthesized and initiate translation
50
Problems and Discussion Questions
Calculate how many triplet codons would be possible had evolution seized on six bases (three complementary base pairs) rather than four bases with which to construct DNA. Would six bases accommodate a two-letter code, assuming 20 amino acids and start and stop codons?
Six bases taken three at a time would produce 3
(6)^3 , or 216, triplet codes. If the code was a doublet, there would be (6)^2 , or 36, two-letter codes, more than enough to accommodate 20 amino acids and start and stop signals.
51
2. In a heteropolymer experiment using 1/2C : 1/4A : 1/4G, how many different triplets will occur in the synthetic RNA molecule? How often will the most frequent triplet occur?
There will be (3) , or 27, triplets produced. The
| most frequent will be CCC, present (1/2)3 or 1/8 of the time.
52
3. In a copolymer experiment in which the tetranucleotide sequence UUAC is repeated over and over, how many differ- ent triplets will occur in the synthetic RNA, and how many amino acids will occur in the polypeptide when this RNA is translated?
The synthetic RNA will repeat four triplets— UUA, CUU, ACU, and UAC—over and over. Because both UUA and CUU encode leucine, while ACU and UAC encode threonine and tyrosine, respectively, the poly- peptides synthesized under the directions of such an RNA contain three amino acids in the repeating sequence Leu-Leu-Thr-Tyr.
53
4. Actinomycin D inhibits DNA-dependent RNA synthesis. This antibiotic is added to a bacterial culture in which a specific protein is being monitored. Compared to a control culture, into which no antibiotic is added, translation of the protein declines over a period of 20 minutes, until no fur- ther protein is made. Explain these results.
The mRNA, which is the basis for the translation of the protein, has a lifetime of about 20 minutes. When actinomycin D is added, transcription is inhibited and no new mRNAs are made. Those already present support the translation of the protein for up to 20 minutes
54
Why did geneticists believe, even before direct experimental evidence was obtained, that the genetic code would turn out to be composed of triplet sequences and be nonoverlapping? Experimentally, how were these suppositions shown to be correct?
G
55
What experimental evidence provided the initial insights into the compositions of codons encoding specific amino acids?
G
56
How were the specific sequences of triplet codes determined experimentally?
G
57
How were the experimentally derived triplet codon assignments verified in studies using bacteriophage MS2?
D
58
2.Write a short essay that summarizes the key properties of the genetic code and the process by which RNA is transcribed on a DNA template.
The genetic code:
1. Universal: the codon is the same for all the organisms
2. Unambiguous : each codon corresponds to only one AA
3. Degenerate: multiple codons for an AA
4. non-overlapping: the codon does not overlap each other
Transcript in 3 steps:
Initiation: the DNA unwinds and separates to form an open complex. The RNA polymerase bind to the promoter region of DNA
Elongation: RNA polymerase moves along the template strand and adds complementary RNA bases to the growing 3’ end.
Termination: When polymerase transcribed a sequence of DNA
59
Assuming the genetic code is a triplet, what effect would the addition or loss of two nucleotides have on the reading frame? The addition or loss of three, six, or nine nucleotides?
a) the reading frame will be altered if 1-2 nuc is added
| b) the reading frame will not be altered if 3, 6, 9 nucleotides are added
60
4.The mRNA formed from the repeating tetranucleotide UUAC incorporates only three amino acids, but the use of UAUC incorporates four amino acids. Why?
UUAC -> UUACUUACUUAC
UUA=Leu ,CUU=Leu ,ACU=Thr ,UAC=Tyr
Two codons encode for leu due to the degenerate code, which different codon can code for same amino acid.
UAUC-> UAUCUAUCUAUC
UAU=Tyr ,AUC= Ile, UCU= Ser=, CUA= Leu
Degeneracy is not in this case,
61
5.In studies using repeating copolymers, AC . . . incorporates threonine and histidine, and CAACAA . . . incorporates glutamine, asparagine, and threonine. What triplet code can definitely be assigned to threonine?
ACA
62
In a coding experiment using repeating copolymers (as demon- strated in Table 13.3), the following data were obtained:
AGG is known to code for arginine. Taking into account the wobble hypothesis, assign each of the four codons produced in the experiment to its correct amino acid.
Base on the wobble hypothesis, AG =Arg: AGG,AGA
GA=glytamic:GAG,GAA
AA=lysine: AAG
63
7.In the triplet binding technique, radioactivity remains on the filter when the amino acid corresponding to the codon is labeled. Explain the rationale for this technique.
7
64
8.When the amino acid sequences of insulin isolated from different organisms were determined, differences were noted. For example, alanine was substituted for threonine, serine for glycine, and valine for isoleucine at corresponding positions in the protein. List the single-base changes that could occur in codons of the genetic code to produce these amino acid changes.
Table:
Threonine: ACC, ACU,ACG,ACA
If the first base replace for G
-> Alanine :GCC,GCU,GCG,GCA
Gly:GGU,GGC
If the first base change to A
-> Serine: AGU, AGC.
Isoleucine:AUU,AUC,AUA
If the first base change from A to G
-> Valine: GUU,GUC,GUA.
The difference between 3 components is,A and G
65
9. In studies of the amino acid sequence of wild-type and mutant forms of tryptophan synthetase in E. coli, the following changes have been observed:
Gly- Arg-> Thr (->Ser -> Ile)
Gly- Glu - Val(-> Ala)
Determine a set of triplet codes in which only a single-nucleotide change produces each amino acid change.
First,look at the table codon
```
Arg:AGA, AGG
Ser: ACG
Threonine: ACG
Isoleucine: AUA or AUG
Glutamicm GAA, GAG
Valine: GUG
Ala:GCA, GCG
```
If AGG In arginine change to AGC will code for serine.
If GAG in glu change fo GUG will code for valine
If GAA,GAG change to GCA or GCG will produce alanine.
66
10. Why doesn’t polynucleotide phosphorylase (Ochoa’s enzyme) synthesize RNA in vivo?
PNPase is enzyme with 3’-terminal oligonucleotide polymerase activity and phosphorolytic 3’ to 5’ exoribonucleas activity.
The main function of polynucleotide phosphorylase (PNPase) is the RNA degradation. With a high concentration of the ribonucleotide diphosphates in an in vitro, the direction of the reaction can be forced towards polymerization.
In an in vivo, only degradative process is favored because the concentration of ribonucleoside dephosphate is low.
67
11. Can you hypothesize why a synthetic RNA composed of a mixture of poly U + poly A would not stimulate incorporation of 14C-phenylalanine into protein?
UUC and UUU encode phenylalanine. Mixture of UUA, AUA, UAA sequence are not the codons for phenylalanine. So it will have a lower level of activity
68
12. Predict the amino acid sequence produced during translation by the following short hypothetical mRNA sequences (note that the second sequence was formed from the first by a deletion of only one nucleotide):
Sequence 1: 5′-AUGCCGGAUUAUAGUUGA-3′
Sequence 2: 5′-AUGCCGGAUUAAGUUGA-3′
What type of mutation gave rise to sequence 2?
The amino acid sequence 1: Met-Pro-Asp-Tyr-Ser-termination
The sequence 2: Met-Pro-Asp-termination
The 2 sequence was formed from the deletion of one nucleotide from the first sequence. This causes frameshift mutation.
69
13. A short RNA molecule was isolated that demonstrated a hyperchromic shift, indicating secondary structure. Its sequence was determined to be
5′-AGGCGCCGACUCUACU-3′
(a) Propose a two-dimensional model for this molecule.
(b) What DNA sequence would give rise to this RNA molecule through transcription?
(c) If the molecule were a tRNA fragment containing a CGA anti- codon, what would the corresponding codon be?
(d) If the molecule were an internal part of a message, what amino acid sequence would result from it following translation?
The two-dimensional structure for this molecule:
3’-UCCGUGGCUGAGAUGA-5’
b) 5’-TCCGCCGGCTGAGATGA-3’
c) Codon: GCU
d) arg-arg-arg-leu-tyr-incomplete
70
14.A glycine residue is in position 210 of the tryptophan synthetase enzyme of wild-type E. coli. If the codon specifying glycine is GGA, how many single-base substitutions will result in an amino acid substitution at position 210? What are they? How many will result if the wild-type codon is GGU?
Unclear
71
15. (a) Shown here is a hypothetical viral mRNA sequence:
5′-AUGCAUACCUAUGAGACCCUUGGA-3′
Assuming that it could arise from overlapping genes, how many different polypeptide sequences can be produced? What are the sequences?
(b) A base-substitution mutation that altered the sequence shown in part (a) eliminated the synthesis of all but one polypeptide. The altered sequence is shown here:
5′-AUGCAUACCUAUGUGACCCUUGGA-3′ Determine why.
The original sequence is 5′-AUGCAUACCUAUGAGACCCUUGGA-3′
The change is 5′-AUGCAUACCUAUGUGACCCUUGGA-3′
There is a change in the base present at the 14th position from A to U. So they change from AGA to UGA, which is stop codon. Due to this, the second overlapping sequence becomes 5’-AUGUGACCUUGGA-3’
This mRNA sequence cannot be synthesized into a protein because of the presence of stop codon.
72
16. Most proteins have more leucine than histidine residues, but more histidine than tryptophan residues. Correlate the number of codons for these three amino acids with this information.
Six codons codes for leucine, one for tryptophan and two are responsible for coding of amino acid histidine
73
17. Define the process of transcription. Where does this process fit into the central dogma of molecular biology (DNA makes RNA makes protein)?
The flow of genetic information from the DNA to RNA and finally conversion to protein is referred to as the central dogma of molecular biology.
The transcript and translate involves in the central dogma, where a copy of the segment of RNA is synthesized is referred as trans and the synthesizes of RNA is done by the RNA polymerase enzyme.
74
18. What observations suggested the existence of mRNA?
Bacteriophage DNA.
First, in eu cells, the genetic materials are present in the nucleus while synthesis of protein in the cytoplasm. So, DNA doesn’t participate in the synthesis of protein.
Second, ribonucleic acid RNA is chemically the same when compared to the deoxyribonucleic acid DNA.
75
19. Describe the structure of RNA polymerase in bacteria. What is the core enzyme? What is the role of the sigma subunit?
In prokaryotes, RNA polymerase is composed of 5 subunits: 2 alpha, 1 beta, 1 beta prime, and 1 omega subunit.
The core enzyme is responsible for the catalytic activity
The sigma subunit provides the specificity of RNA polymerase to promoter allows the DNA strand to transcribe.
76
20, Write a paragraph describing the abbreviated chemical reactions that summarize RNA polymerase-directed transcription.
The chemical equation:
n(NTP) -> (NMP)n +n(PPi)
NTP: Nucleoside Triphosphates
NMP: Nucleoside Monophosphate
Ribonucleoside triphosphates and a DNA template in the presence of RNA polymerase and Mg+ ion produce a ribonucleosie monophosphate polymer and pyrophosphate. The polymer grows by sequential addition of ribonucleoside monophosphate that is derived from ribonucleoside triphosphates with the release of pyrophosphates.
77
21.Messenger RNA molecules are very difficult to isolate in bacteria because they are rather quickly degraded in the cell. Can you suggest a reason why this occurs? Eukaryotic mRNAs are more stable and exist longer in the cell than do bacterial mRNAs. Is this an advantage or a disadvantage for a pancreatic cell making large quantities of insulin?
The mRNA of bacteria is difficult to isolate because it degrades rapidly.
If it not degrade immediately, it produces a huge amount of proteins by utilizing all of its nutrients
Thus, mRNA degrade quickly because it produces a number of proteins.
The stable mRNA produce insulin without undergoing the whole process of transcription -> pancreatic cells produce and secrete insulin faster
78
22. Present an overview of various forms of posttranscriptional RNA processing in eukaryotes. For each, provide an example.
Capping at 5’end
Tail at 3’end
Splicing
RNA editing
79
23. One form of posttranscriptional modification of most eukaryotic pre-mRNAs is the addition of a poly-A sequence at the 3′ end. The absence of a poly-A sequence leads to rapid degradation of the transcript. Poly-A sequences of various lengths are also added to many bacterial RNA transcripts where, instead of promoting stability, they enhance degradation. In both cases, RNA secondary structures, stabilizing proteins, or degrading enzymes interact with poly-A sequences. Considering the activities of RNAs, what might be general functions of 3′-polyadenylation?
The 3′-polyadenylation is to
1) stops the degradation of transcribed mRNA
2) the proteins formed from mRNA with the tail are more stable
Functions:
1) increase the length of the poly-A-tails -> increase the stability of mRNA.
2) help the movement of mRNA from nucleus to cytoplasm
3) the tail binds with poly-A-binding protein, which takes mRNA from the nucleus to the cytoplasm
80
24. Describe the role of two forms of RNA editing that lead to changes in the size and sequence of pre-mRNAs. Briefly describe several examples of each form of editing, including their impact on respective protein products.
The transcript pre-mRNA undergoes a process called RNA editing,. The removal of introns increase the efficiency of translation.
There are two forms of RNA editing
1) substitution editing in chloroplast and mitochondrial DNA, which nucleotides present in mRNA are edited by chemical modifications. For example, changes the codon CAA to UAA “stop codon” -> reduces the size of the protein.
2) deletion/insertion editing in mitochondrial RNA, which nucleotides are either inserted or removed from the mRNA bases. For example, adds uridine in the pre-mRNA that forms the initiation align rest of the sequence -> produce proteins with wrong sequence
The two forms of RNA editing are important as they change the sequence and size of the pre-mRNA. The correct mRNAs code for correct proteins. There are many diseases that are caused by the production of wrong proteins
81
25. Substitution RNA editing is known to involve either C-to-U or A-to-I conversions. What common chemical event accounts for each?
D
82
26) Which of the following intron groups is matched appropriately with a true statement? 26) A) Group I introns are removed from rRNAs that are found in mitochondria and chloroplasts.
B) Spliceosomal introns are removed using large protein-based enzyme complexes.
C) Group I introns are removed from rRNAs using large protein-based enzyme complexes. D) Spliceosomal introns are removed using the catalytic ability of the intron itself.
E) Group II introns are removed from mRNA in mammals.
B
83
27) The type of RNA modification that requires guide RNAs is ________. 27) A) addition of the 7-methylguanosine cap to the 5′ end
B) splicing together of exons
C) RNA editing
D) removal of introns
E) addition of the 3′ polyadenylated tail
C
84
28) Describe the direction of information flow in living systems. Use appropriate, scientific 28) terms in your description.
DNA is replicated and passed to offspring through a variety of reproductive processes. Information contained in the
base sequences of DNA is transcribed into a variety of RNAs. Certain RNAs (tRNA) carry amino acids to the site of translation where proteins are assembled. Other RNAs (mRNA and rRNA) provide a mechanism for ordering the sequence of amino acids in proteins.
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29) Sidney Brenner argued that the code was nonoverlapping because he considered that 29) coding restrictions would occur if it were overlapping. A second major argument against
an overlapping code involved the effect of a single nucleotide change. In an overlapping
code, how many adjacent amino acids would be affected by a single nucleotide change? In
a nonoverlapping code, how many amino acid(s) would be affected?
two; one
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30) From the late 1950s to the mid-1960s, numerous experiments using in vitro cell-free 30) systems provided information on the nature of the genetic code. Briefly explain how the
use of polynucleotide phosphorylase and the triplet binding assay were used to decipher
the genetic code and why the triplet binding assay was more precise.
Use of polynucleotide phosphorylase for the random assembly of nucleotides provided for the assembly of RNA
homopolymers and random heteropolymers, which when placed in the cell-free protein-synthesizing system, provided products (polypeptide chains) for analysis. The triplet binding assay along with the use of repeating copolymers were used to verify information provided earlier and to establish the ordered codon assignments.
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31) Suppose that in the use of polynucleotide phosphorylase, nucleotides A and C are added in 31) a ratio of 1A:5C. What is the probability that an AAA sequence will occur?
K 1/6 × 1/6 × 1/6 = 1/216
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32) "Breaking the genetic code" has been referred to as one of the most significant scientific 32) achievements in modern times. Describe (in outline or brief statement form) the
procedures used to break the code.
(a) use of polynucleotide phosphorylase for the production of synthetic "mRNAs"
(b) introduction of synthetic mRNAs into the cell-free protein-synthesizing system
(c) frameshift mutations in the rII region of T4 phage to show code is triplet and degenerate (d)triplet binding assay to produce mRNA–tRNA-ribosome complex
(e) development of regular copolymers for use in the cell-free protein-synthesizing system
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33) Reading the RNA sequences in a 5′ to 3′ direction, a base at the first position of an anticodon on the tRNA would pair with a base at the ________ position of the mRNA.
Third
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34) Explain the "wobble hypothesis" and why it allows a single tRNA to recognize more than one codon.
The relaxed pairing at the third position of the codon and the first position of the anticodon are less constrained and do
not need to follow the traditional base pair rules. This allows for a single tRNA to recognize multiple codons.
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35) A particular mRNA makes a protein that has a unformylated methionine as its first amino 35) acid. Did this mRNA come from a bacterial or a eukaryotic cell? Explain.
Eukaryotic cell. Eukaryotic mRNA code for proteins starts with an unformylated methionine whereas bacterial mRNA
code for proteins starts with a formylated methionine.
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36) Write a sequence of mRNA that codes for five amino acids and the mRNA should contain 36) proper punctuation and polarity.
5′ AUG (any four amino acid coding codons) and (UAA, UGA, or UAG) 3′
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37) There is some indication that the code is in some way ordered; a certain pattern exists. 37) Describe an observation that supports this view.
Certain amino acids may be grouped according to the middle base; for example, U or C in the second position often specifies hydrophobic amino acids. Also, codons with the same two starting letters frequently encode the same amino acid.
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38) The finding that virtually all organisms use the same genetic code provides the basis for 38) declaring that the code is universal. Name at least two exceptions to such universality.
mitchondrial DNA; Mycoplasma capricolum; some protozoans
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39) In the context of molecular genetics, how does one reconcile the terms overlapping genes and 39) nonoverlapping code?
The genetic code contains codons that are nonoverlapping; however, overlapping genes are observed in some viruses
in which, due to differential use of AUG to initiate translation, the same mRNA can yield different protein products.
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40) What are three observations that suggested eukaryotic RNA was an intermediate between 40) DNA and protein.
(1) DNA is found in the nucleus and protein synthesis occurs in the cytoplasm, (2) RNA is synthesized in the nucleus
and has a chemical similarity to DNA, and (3) RNA is transported out of the nucleus and into the cytoplasm where
protein translation occurs.
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41) Describe the effects of mutating a sigma factor gene in bacteria.
The core RNA polymerase enzyme will form. Since there are more than one sigma factor genes, by mutating a single
sigma factor gene there will be some holoenzymes that will not form which will affect specific gene transcription.
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42) In a particular bacterial mutant, a specific gene is not producing a mRNA or the 42) corresponding protein. Researchers sequence the gene and determine that there are no
mutations in the coding portion of the gene. What could explain these observations?
One of the two consensus sequences are likely mutated. Either the Pribnow box (TATA AT) or the −35 sequence (TTGACA
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43) Describe how rho-dependent termination occurs in bacteria.
A bacterial protein called rho factor binds to an mRNA at the rut site. It moves along the mRNA in a 5′-to-3′ direction
chasing after the RNA polymerase. When it reaches the hairpin loop it removes it and then proceeds to break through
the hydrogen bonds holding the RNA-DNA together, which successfully removes the RNA polymerase.
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44) Describe a difference between the RNA polymerases of eukaryotes and prokaryotes.
In eukaryotes, three polymerases (I, II, and III) have been identified; only one has been described in prokaryotes.
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45) In eukaryotes, which three factors appear to encourage the specific association of RNA 45) polymerase(s) to a specific region of DNA?
promoters, enhancers, and transcription factors
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46) What are four ways that mRNA can be modified?
1) Adding a modified guanine to the 5′ end, (2) adding a polyadenylation tail to the 3′ end, (3) splicing of introns, and
(4) RNA editing.
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List four possible reasons that explain the importance of introns
(1) introns allow for alternative splicing, (2) exon shuffling, which can aid in evolution of new genes, (3) the intron can
be a microRNA itself that can regulated gene expression, and (4) introns can contain enhancer and silencer sequences
that aid in gene regulation.
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What is meant by the term heterogeneous nuclear RNA (hnRNA)?
pre-mRNA, primary transcripts before processing in eukaryotes
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A researcher is looking at a cellular sample using an electron microscope. They observe 49) that while mRNA is being transcribed from the DNA that ribosomes are binding to the
mRNA to make proteins. Is this sample from a bacterial or a eukaryotic cell?
Bacteria. Since bacteria lack a nucleus, the ribosomes can bind to the mRNA as it's being synthesized and initiate
translation.
