BIOC 385 EXAM 4
Based on the figure below, cleavage at which two sites followed by DNA strand rejoining would lead to no change in the existing genetic information?
1 and 3
What role does the branch point have in RNA splicing?
It initiates the first transesterification reaction.
What is a Holliday junction in the context of meiotic DNA recombination in gametes?
It is where two strands of DNA from sister chromatids cross over each other prior to branch migration.
When the Trp repressor is bound to the trp operon, it results in the __________ by RNA polymerase.
inhibition of transcriptional initiation
Lysogeny by bacteriophages causes what result to the host DNA?
integration of virus DNA into host DNA
The Ames test is designed to identify mutation rates using a strategy based on ___________.
the frequency of new mutations that compensate for an existing mutation
Long noncoding RNA (lncRNA) is generated from _____________.
the transcription of genomic DNA.
Long noncoding RNA (lncRNA) is generated from________________.
the transcription of genomic DNA.
Choose the correct word for each blank shown below and record your answer. In the presence of glucose, CRP does not bind to the lac operon because cAMP levels are __(1)__. In thepresence of lactose alone, lac repressor does not bind DNAbecause __(2)____binds to the repressor, and under theseconditions, the observed level of lac operon expression is very__(3)__ . When both glucose and lactose are present, a very__(4)__ level of lac operon expression is observed
(1) low, (2) allolactose, (3) high, (4) low
Select the two statements below that describe the similarities in DNA replication by DNA polymerase and RNA transcription by RNA polymerase in E. coli.
- A specific region of the DNA is recognized and bound by the polymerases in both processes. - The direction of enzyme movement on the template strand in both processes is 3' to 5'.
What explains the observation that a single eukaryotic protein coding gene can give rise to multiple different proteins, i.e., why are there only ~25,000 human genes in the genome, but ~150,000 different proteins in the human "proteome?" Choose the TWO best answers.
- Genes can contain more than one polyadenylation site, which alters the 3' of the mRNA transcript and the inclusion/exclusion of exons. - mRNA transcripts from the same gene can be differentially spliced to include/exclude exons.
Nirenberg and colleagues determined a portion of the genetic code using filter binding assays that included ribosomes, trinucleotides and tRNA molecules charged with radioactively-labeled amino acids. Choose the answer below that correctly answers the following three questions in order: 1) If the trinucleotide sequence is CAG, which amino acid will be bound to the filter paper? 2) If the wobble position of the trinucleotide sequence is changed to a U, which amino acid will be bound to the filter paper? 3) True or False: Two distinct tRNA molecules with different anticodon sequences MUST be used to recognize the codons AGA and AGG.
1) Gln, 2) His, 3) False
Which five statements below are correctregarding the process of prokaryotic DNA replication? 1. b-clamp keeps DNA Pol bound to DNA 2. Coding strand serves as the template 3. DNA replication is semiconservative 4. Gyrase unwinds the DNA double helix 5. DNA Pol I synthesizes leading strand 6. Telomerase replicates telomeres 7. DNA replication requires a primer 8. Lagging strand has Okazaki fragments 9. DNA replication is bidirectional 10. DNA replication is unique to bacteria
1, 3, 7, 8, 9
Put the 10 steps shown below in the correct order describing the spliceosome reaction cycle ___The U1-U2 snRNP complex binds to the GU sequence at the 5'end of the intron. ___The U2-U5-U6 snRNP complex is bound to the lariat RNA structure and dissociates from mRNA. ___The U2 snRNP translocates to the adenine residue at the intronic branch site. ___The hydroxyl group at the 5' end of the intron attacks the phosphate at the 3' end of the intron. ___The U2 snRNP is released from the complex and the U5 and U6 snRNPs associate with U4 snRNP. ___The hydroxyl group of the branch point adenine attacks the phosphate at the 5' end of the intron. ___RNA Pol II finishes transcribing across an entire intron and is in the middle of a 3' exon. ___The U4-U5-U6 tri-snRNP complex binds to U2 at the branch point along with the U1 snRNP. ___The U1 and U4 snRNPs dissociate from the precatalytic complex leaving U2-U5-U6 behind. ___The U2, U5, and U6 snRNPs dissociate from the lariat RNA structure and intronic RNA is released.
2, 8, 3, 7, 10, 6, 1, 4, 5, 9
If the following mRNA was added to a cell-free translation system, how many unique protein sequences would be generated based on codon usage? 5'-ACCACCACCACCACCACCACCACCACCACCACC-3'
3
Put the following steps in the correct order to synthesize DNA. 1. Addition of an RNA primer 2. Extension of the RNA primer 3. Conversion of double-stranded DNA to single-stranded DNA 4. Synthesize new DNA
3; 1; 2; 4
Match the name of the DNA repair mechanism with the correct description. ____ Repairs nucleotide bases without requiring DNA ligase. ____ Is needed to repair chemical damage in DNA effecting more than one nucleotide, such as cyclobutane pyrimidine dimers. ____ Functions with DNA replication to remove incorrect nucleotides from the nascent strand. ____ Requires an endonuclease to remove an abasic nucleotide before DNA Pol I can replace a portion of the strand. 1. Mismatch repair 2. Base-excision repair 3. Nucleotide-excision repair 4. Direct repair
4,3,1,2
Radioactively-labeled aminoacyl-tRNA with the anticodon of 5'-CUG-3' was used in the Nirenberg-Leder experiment. They found that radioactivity was retained on the filter, which meant that _______________ was the sequence of the mRNA used in the experiment.
5'-CAG-3'
Based on the sequence of the double stranded DNA shown above, which sequence below corresponds to the mRNA transcript?
5'-CGCUAUAGCGUUU-3'
If one parent has Lynch syndrome, but the other does not, what is the likelihood that the child will also have Lynch syndrome?
50%
The ribosomal peptidyl transferase enzyme is required for peptide bond formation during proteinsynthesis. What subunit of the prokaryotic ribosome contains this enzyme and what is its composition?
50S subunit; RNA
Put the 10 steps shown below in the correct order describing mismatch DNA repair in E. coli. ___MutS-MutL-MutH dissociates, and daughter DNA is removed by an exonuclease. ___ MutH proteins bind to hemimethylated GATC sites in DNA near the mismatch mutation. ___The daughter strand DNA is methylated at the adenine residue within GATC sequences. ___MutL protein forms a complex with MutS through an ATP-dependent association. ___A MutS-MutL-MutH complex loops out the mutated DNA using ATP hydrolysis. ___DNA Pol III resynthesizes the daughter strand, and the DNA nick is sealed by ligase. ___The DNA is threaded through the MutS-MutL complex in the direction of MutH. ___The endonuclease activity of MutH makes a single-strand cut in the daughter DNA. ___Homodimer of MutS protein binds to the mismatch mutation in double-stranded DNA. ___Single strand DNA binding protein binds to the parental DNA strand to protect it.
7, 1, 10, 3, 5, 9, 4, 6, 2, 8
Where would an amino acid be attached to the tRNA below?
A
Which chromatin modification in eukaryotes is associated with activation of gene transcription?
Acetylation of lysine residues on histone proteins by the enzyme histone acetyltransferase.
What accounts for the high fidelity of DNA polymerization?
Active site geometry ensures that only correct sized nucleotide base pairs are formed, and 3' to 5' proofreading removes incorrect nucleotides.
Which of these RNAs listed below are classified as noncoding RNA (ncRNA)?
All of these
Match the description of eachmode of regulation with the illustrationdiagrammed at the right and record youranswer in the order of 1->4 1. _ Ligand-regulated de-repression 2. _ Ligand-regulated repression 3. _ Ligand-regulated activation 4. _ Ligand-regulated de-activation
B, A, D, C
Place the following steps in the correct order describing the steps required for synthesis of a membrane-bound protein. A. GTP binds to SRP. B. Protein synthesis occurs on free ribosome. C. Protein synthesis halts. D. SRP binds to the signal peptide sequence.
BDCA
Why are the BRCA1/BRCA2 genes considered tumor suppressor genes?
Because BRCA1/BRCA2 encode DNA repair enzymes that normally prevent cancer mutations.
Why does adding a higher concentration of a mutagenic compound to the filter paper on the bacterial plate yield MORE bacterial colonies than a filter paper containing a lower concentration of the same mutagenic compound?
Because a higher concentration of mutagen causes more reversion mutations of the His- phenotype.
An Ames test of a compound suspected to be a mutagen was examined before and after incubation with rat liver extract. Based on the results shown, what do you conclude?
Compound is mutagenic without liver enzymes and this activity is further enhanced by liver enzymes.
Which bacterial DNA polymerase is responsible for genome duplication and in which direction?
DNA polymerase III in the 5' to 3' direction
Which enzyme synthesizes the RNA primer for DNA replication?
DNA primase
The enzyme responsible for generating siRNA from double strand RNA is ____________.
Dicer
The name of the enzyme responsible for generating siRNA is ______________.
Dicer
The correct order for codons 1, 2, and 3 written 5' to 3' on the mRNA strand is:
GGC, AUG, GAG
What is the amino acid sequence (start at N-term) encoded by these three mRNA codons?
Gly-Met-Glu
Which of the following statements is correct regarding self-splicing introns?
Group I introns use an exogenous guanosine as a cofactor.
What are the functions of the HAT and HDAC enzymes with regard to regulating gene expression in eukaryotic cells?
HAT activates the gene and HDAC represses the gene.
Why do helicase and gyrase need to work together to keep the replication fork moving forward?
Helicase unwinds DNA and gyrase relieves the torsional strain created by the unwinding.
What are the functions of enzymes helicase and gyrase in DNA replication?
Helicase unwinds DNA and gyrase relieves the torsional strain.
Assume that you have identified all the cis-acting sites in a prokaryotic genome for a particular trans-acting transcription factor. What is the function of this transcription factor when binding to these sites?
It is not possible to predict the function from the sites since could activate or repress at different sites.
Assume that you have identified all the cis-acting sites in a prokaryotic genome for a particulartrans-acting transcription factor. What is the function of this transcription factor when binding to these sites?
It is not possible to predict the function from the sites since could activate or repress at different sites.
Which statement below best explains the advantage of alternative splicing in RNA processing?
It provides multiple protein product from a single precursor mRNA transcript in different cells.
What is the function of the enzyme telomerase in eukaryotic DNA synthesis?
It synthesizes DNA on the lagging strand at the ends of chromosomes.
How does the antibiotic puromycin block protein synthesis?
It terminates protein synthesis by accepting the polypeptide chain.
Under what conditions do the highest rates of transcriptional initiation of the lac operon occur ?
Low glucose and high lactose
Lynch syndrome is a human genetic disease characterized by ~100-fold higher incidence ofcolon cancer in men and women - and uterine cancer in women - by the age 50, as compared to thegeneral population. Which statement below best describes the genetic cause of Lynch syndrome.
Lynch syndrome is caused by defects in the human mismatch repair enzymes hMLH1 and hMSH2.
Five different TATA Binding Protein (TBP) mutations are shown below. If these mutations were located in the region of the protein that is required for direct binding to the TATAA DNA sequence, which mutation would most likely be a conservative missense mutation that does not alter TBP function?
Lys -> Arg
How are RNA tertiary structures different from protein tertiary structures?
RNA adopts multiple structures, whereas protein structures are restricted.
Identify one way in which RNA splicing can give rise to multiple mRNA transcripts from a gene containing 3 exons and 2 introns.
Splicing between the 3' end of exon 1 and 5' end of exon 3.
Why does RNA contain uracil and DNA contain thymine?
Spontaneous cytosine deamination generates uracil, which base pairs with adenine during replication, and thereby converts a C-G base pair to a T-A base pair.
Why does RNA contain uracil and DNA contain thymine? Choose the ONE best answer to this question.
Spontaneous cytosine deamination generates uracil, which base pairs with adenine during replication, and thereby converts a C-G base pair to a T-A base pair.
Record T (true) or F (false) for statements below regarding protein synthesis. Record as a->e T F a. Prokaryotic and eukaryotic ribosomes both contain RNA that functions as a catalytic enzyme. T F b. The wobble position in tRNA is 5' nucleotide in the anti-codon and 3' nucleotide in mRNA codon. T F c. Ribosomal E, P, and A sites align tRNA anti-codons with the corresponding mRNA codons. T F d. Accurate protein synthesis requires tRNA synthetases to link GTP to 3' end of tRNA molecules. T F e. Cells contain only ~30 tRNA molecules, of which 3 correspond to termination tRNA molecules.
T, T, T, F, F
If the following mutations were to occur in codon 22 of an important tumor suppressor gene that contains a total of 351 codons, which would have the greatest likelihood of increasing the cancer risk in that person? The DNA sequence on the left of the arrow is the codon for the initial, non-mutated gene, while the DNA sequence on the right of the arrow is the same codon after mutation.
TAC -> TAG
Which one of the descriptions below would have the fewest allowable base pairing combinations in the wobble position?
The 5' position in the tRNA is cytosine
Prokaryotic and eukaryotic DNA polymerases rarely make mismatched base pairs because ____________.
The active site does not fit mismatches well
In which direction is mRNA synthesized by prokaryotic and eukaryotic RNA polymerases?
The mRNA is synthesized with 5' to 3' phosphodiester linkages.
RNA is more susceptible to backbone hydrolysis than DNA because of which chemical property?
The presence of a 2' OH group
Which of the following statements is correct regarding spliceosome-mediated trans splicing?
The spliceosome mechanism involves two transesterification reactions.
Which of the following statements about pluripotent stem cells is true?
They can develop into many different cell types under the right conditions.
How do bacterial sigma factor proteins promote RNA synthesis?
They recruit RNA polymerase to specific sequences at the 5' end of genes.
Why is Ser-tRNAThr hydrolyzed by the threonyl-tRNA synthetase editing site, but Thr-tRNAThr is released by the enzyme without hydrolysis?
Threonine does not fit in the editing site, but serine does, so it is hydrolyzed and the tRNA is recycled.
Which of the following statements best describes how the terms trans-acting and cis-acting apply to gene regulation?
Trans-acting factors are proteins that bind to specific DNA sequences, which are themselves cis-acting sites in DNA.
Which statement below most accurately describes the function of trans- and cis-acting factors in mediating gene regulation?
Trans-acting factors can bind to specific DNA sequences whereas cis-acting sites are DNA sequences.
When tryptophan levels inside a bacterial cell are elevated then _________________.
Trp repressor is bound to DNA.
What is the correct order of RNA processing events in eukaryotes beginning with phosphorylation of the RNA Pol II CTD?
What is the correct order of RNA processing events in eukaryotes beginning with phosphorylation of the RNA Pol II CTD?
Choose the best answer that correctly identifies the labeled DNA and RNA sequences. Your choices for A, B, C, D, E are shown in the box. 5'.....GGCAUGUGCCAAUGCC.....3' (X) 3'.....CCGTACACGGTTACGG......5' (Y) 5'.....GGCATGTGCCAATGCC......3' (Z)
X is RNA Z is DNA coding Y is DNA template.
The 3'-hydroxyl group used to initiate DNA synthesis comes from______________.
a RNA primer.
A Holliday junction can best be defined as a region of ________________.
a quadruplex DNA structure
When a cytosine is deaminated to form uracil and removed by glycosylase enzymes, a(n) __________ site is generated.
abasic
In the Nirenberg-Leder experiment, the _________ was radioactively-labeled.
aminoacyl-tRNA
The Nirenberg-Leder experiment used radioactive _______to decipher the Genetic Code.
aminoacyl-tRNA
The roles of U1, U2, U4, U5, and U6 in the spliceosome complex are to________________.
bind mRNA and facilitate the splicing reaction.
The Tus-Ter complex terminates DNA synthesis by _______
blocking helicase function
The Tus-Ter complex terminates DNA synthesis in E. coli by________________.
blocking the opening of helicase.
The Tus-Ter complex terminates E. coli DNA synthesis by ____________.
blocking the opening of the DNA helix at the fork by helicase
Inosine is formed by _______________.
deamination of adenosine
Individuals with mutations of BRCA have increased incidence of cancer because of their___________.
decreased ability to repair double-strand DNA breaks.
Homologous recombination repairs ___________.
double strand breaks in DNA
A reporter gene can be defined as a gene that_________________.
encodes a product that is easy to detect.
If 15N DNA (heavy) replicated using conservative replication in 14N (light) media, the outcome would be different than semi-conservative replication, and in this case, the two daughter DNA double strands would be ______________after one generation.
heavy only for one daughter DNA and light only for the other daughter DNA
One of the most common binding interactions between proteins and DNA are __________ bonds.
hydrogen
The function of the beta-clamp in DNA replication is to_____________.
keep the Pol III complex associated with the DNA.
The DNA sequence of prokaryotic gene promoters are____________.
largely conserved.
Which amino acid residues on histones are acetylated?
lysine
A common chemical modification found in RNA is __________________.
methylation of nucleotide bases in tRNA
The MutS-MutL-MutH protein complex is required for _________________.
mismatch DNA repair
The figure below shows __________ autoregulation and that __________.
negative; reaches a steady state of expression.
What are two mechanisms used by DNA polymerase to limit the number of misincorporated nucleotides?
nucleotide size, 3' to 5' endonuclease
A lipid-modified protein is most likely localized to the _______________.
plasma membrane
When there is no lactose in a cell, transcription of the lac operon_______________.
production of lac operon does not depend on lactose concentration.
Which two noncoding RNA molecules are recycled intact after each round of protein synthesis?
rRNA and tRNA
The primary function of transcriptional activator proteins is to _________________.
recruit other transcription factors to the gene promoter.
The initiation of transcription in eukaryotes_________________.
requires many more transcription factors than prokaryotic transcription.
The spliceosome ___________.
resembles group II introns in its mechanism and product.
The spliceosome________________________.
resembles group II introns in its mechanism and product.
What are the two main types of stem cells?
somatic and embryonic
The control point for prokaryotic gene regulation primarily occurs at the point of ____________.
transcriptional initiation.
The ______________ requires hydrolysis of GTP as a key step in the insertion of a newly synthesized protein into the ER lumen.
transfer of the signal peptide sequence into the translocon