Genetics Exam 3

The following diagram represents DNA that is part of the RNA-coding sequence of a transcription unit. The bottom strand is the template strand. 5'-ATAGGCGATGCCA-3' 3'-TATCCGCTACGGT-5' <-- Template Strand

5'- AUAGGCGAUGCCA-3'

_____ of acetyl groups to the tails of histone proteins by acetyltransferases loosens chromatin structures, _____ transcription.

Addition; stimulating

Which of these statements are points that complicate belief in the "one gene, one protein" hypothesis? Mark the statements that are true. If all are true, mark (d)

All of the above are true

In the torpedo model of eukaryotic transcription termination, an enzyme cleaves the RNA transcript at a cleavage site (the poly-A signal sequence). The Rat protein is than loaded onto the 5' end of the piece of RNA that is still threaded through the RNA polymerase. When this exonuclease catches up to the RNA polymerase:

It causes the RNA polymerase to disassociate from the remaining RNA fragment and the DNA template

In bacteria, what is the purpose of the Shine-Delgarno sequence on the mRNA?

It is where the 16S rRNA component of the small ribosomal subunit binds to the mRNA

In the image above, based on the positions of the genes, the enhancer, and the insulator, which genes are most likely to me stimulated by the enhancer?

Gene A Gene B

A geneticist conducts the experiment outlined in Figure 15.8, but this time she combines guanine nucleotides (instead of uracil) with polynucleotide kinase. In which tube should radioactively labeled protein appear?

Gly

Small nuclear ribonucleoproteins (snRNPs) are ___, and several snRNPs assemble to form a ___.

- Increase stability of the mRNA - Assists in transport of the mRNA to the cytoplasm - Facilitates attachment of the ribosome to the mRNA

Define a negatively controlled, inducible operon. Also, provide an example. Mark as correct answers the correct definition, and the example. Therefore, you should have a total of 2 answers selected.

- The lac operon - A repressor protein, if bound to the operator sequence, represses transcription. But a metabolite coming from the environment can bind to the repressor protein, either preventing its binding to the operator sequence or making it fall off, thereby inducing transcription

In the trp operon attenuation system, if the amino acid tryptophan is abundant, then there is plenty of trp amino acids to be tacked onto its set of isoaccepting tRNAs. This causes or allows (Mark the 2 statements that are correct):

- The ribosome not to pause when it encounters the two trp encoding codons on the trp mRNA. - The ribosome hits the translation stop codon in leader sequence two, which allows leader sequences 3 and 4 in the mRNA to hairpin, causing disassociation of the RNA polymerase from the DNA template at this location. This "attenuates" (stops) transcription of the trp biosynthetic genes before RNA polymerase reaches those genes on the DNA template

In the trp operon attenuation system, if the cell is starved of tryptophan, then there is little trp amino acid available to be tacked onto its set of isoaccepting tRNAs. This causes or allows (Mark the two statements that are correct):

- The ribosome to pause at the two trp encoding codons in leader sequence 1 - Hairpinning of leader sequences 2 and 3, allowing the RNA polymerase to continue transcription through leader sequence 4 and into the trp biosynthesis genes

Define a negatively controlled, repressible operon. Also provide an example. Mark as correct answers the correct definition, and the example. Therefore, you should have a total of 2 answers selected.

- The trp operon - A repressor protein, if bound to the operator sequence, represses transcription. But a metabolite coming from the environment is needed to allow that repressor protein to be able to bind to the operator sequence

Malaria, one of the most pervasive and destructive of all infectious diseases, is caused by protozoan parasites of the genus Plasmodium, which are transmitted from person to person by mosquitoes. Plasmodium parasites are able to evade the host immune system by constantly altering the expression of their var genes, which encode Plasmodium surface antigens. Individual var genes are expressed when chromatin structure is disrupted by chemical changes in histone proteins. Which types of chemical changes in the histone proteins might be responsible for the decrease in expression of the Plasmodium's var genes?

- de-acetylation of histone proteins - demethylation of histone proteins

What are the 3 primary regions of both prokaryotic and eukaryotic mRNAs?

5' UTR, protein coding region, 3' UTR

Although there are some points of discrepency between the steps of different models of spliceosome assembly, certain points are in common in all models. The U1 snRNP binds to the ___, then ____ snRNP binds to the branchpoint. Then U4,U5,U6 as a tri-partite snRNP particle join the spliceosome. After U4 (and very likely U1) snRNPs have been released, this allows for base pairing between the snRNAs of the U2 and ___ snRNPs. This interaction exposes the catalytic site of the U6 snRNP, which is now able to perform both transesterification reactions to splice out the intron (as a lariat) between the 2 exons.

5' intron splice site; U2; U6

How would deletion of the AAUAAA consensus sequence most likely affect a eukaryotic mRNA? Mark all of the correct answers.

?

Put the steps of mRNA 5' capping in chronological order.

?

What makes the bonding of the 5' methylated guanine cap to the RNA being processed to an mRNA unusual?

?

Listed in parts a through g are some mutations that were found in the 5' UTR of the trp operon in E. coli. What will be the most likely effect of each of these mutations on the transcription of the trp structural genes? An answer may be used more than once.

A mutation that prevents the binding of the ribosome to the 5' end of the mRNA 5' UTR -- No gene expression, specifically translation A mutation that changes the Trp codons in region 1 of the mRNA 5' UTR into codons for alanine -- Transcription of the structural genes only when alanine levels are low A mutation that creates a stop codon early in region 1 of the mRNA 5' UTR -- No transcription Deletions in region 2 of the mRNA 5' UTR -- No transcription Deletions in region 3 of the mRNA 5' UTR -- Transcription will proceed Deletions in region 4 of the mRNA 5' UTR -- Transcription will proceed Deletion of the string of adenine nucleotides that follows region 4 in the 5' UTR -- Transcription will proceed

An RNA molecule has the following percentages of bases: A = 23%, U = 42%, C = 21%, G = 14%. What would the percentages of bases in the template strand of the DNA within the region that contains the gene for this RNA?

A=42%, T=23%, C=14%, G=21% A= 42%, T=23%, G=14%, C=21% A=23%, U=42%, C=21%, G=14%

What is the function of allolactose in regulation of the lac operon?

As the inducer, it binds to the lac repressor protein, changing its shape so that it either disassociates from the operator sequence or prevents the lac repressor from being able to bind to the operator sequence in the first place.

Separate from general transcription factors that stimulate basal levels of transcription, what do transcriptional activator proteins do in eukaryotic systems?

Bind to upstream enhancers or regulatory promoter sequences, interacting with co-activator proteins and the Mediator protein complex to help recruit RNA polymerase to the core promoter.

How do transcriptional repressors work in eukaryotes? Mark the two answers that are correct.

Complete with transcriptional activators for binding sites on the DNA Bind to silencer regulatory elements on the DNA

If an altered phenotype is only observed resulting from a DNA mutation under certain environmental conditions; such a mutation is called a:

Conditional mutation

The genetic code is said to be ___ because there are several instances where multiple codons encode the same amino acid. Different codons that specify the same amino acid are said to be ___.

Degenerate; synonymous

What would be the effect of moving the insulator shown in Figure 17.8 to a position between enhancer II and the promoter for Gene B?

Enhancer II cannot stimulate transcription of Gene B Enhancer II can stimulate transcription of Gene A Enhancer I can stimulate transcription of Gene A, but its effect on Gene B is blocked by the insulator

The cAMP + CAP protein activation system of the lac operon allow:

Even higher rates of transcription of the lac operon when glucose concentrations are low because that forces high concentrations of cAMP, which is needed by the CAP activator protein.

Suppose a geneticist introduced a small interfering RNA (siRNA) that was complementary to the FLC mRNA in Figure 17.3. What would be the effect on flowering of Arabidopsis?

FLC regulator protein will not be produced, so genes that repress flowering will not be activated. Flowering will not occur.

RNA synthesis requires an RNA primer for initial synthesis to begin, just like DNA synthesis.

False

What would be the most likely effect of deleting flowering locus D (FLD) from the genome of Arabidopsis thaliana?

Flowering will not occur because deacetylation of histones surrounding FLC will not occur, leading FLC's chromatin to stay acetylated, causing expression of the FLC transcription factor that activates other genes that repress flowering.

What are two reasons for multiple codons being able to encode the same amino acid? Mark the two answers that are correct.

For some amino acids, there are multiple tRNAs (each with different anticodons) that can be charged with the same amino acid

Guide RNA mediated RNA editing is a mechanism by which:

Guide RNAs direct the insertion, deletion, or substitution of nucleotides in an mRNA

What is the difference between a base substitution transition versus transversion? Mark two statements that are correct.

In a transversion, a purine is replaced with a pyrimidine, or a pyrimidine is replaced with a purine. In a transition, a purine is replaced with a purine, or a pyrimidine is replaced with a pyrimidine.

Choose the INCORRECT statement about the 5' cap added to eukaryotic mRNAs.

Increase the life span of RNA

The following nucleotide sequence is found on the template strand of DNA. After determining the amino acids of the protein encoded by this sequence using the genetic code, match the altered amino acid sequence of the protein that will be found when each of the following mutation occurs in the template strand of DNA. Sequence of DNA template: 3' - TAC TGG CCG TTA GTT GAT ATA ACT - 5'. From left to right, nucleotide 1 through nucleotide 24. Determine the amino acids of the protein encoded by this sequence by using the genetic code provided.

Mutant 1: A transition mutation at nucleotide 11: N - Met Thr Gly Ser Gln Leu Tyr - C A transition mutation at nucleotide 13: N - Met Thr Ala Asn - C A one-nucleotide deletion at nucleotide 7: N - Met Thr Ala Ile Asn Ile - C A mutation of a T to A transversion at nucleotide 15: N - Met Thr Gly Asn His Leu Tyr - C An addition of TGG after nucleotide 6: N- Met Thr Thr Gly Asn Gln Leu Tyr - C A transition at nucleotide 9: N- Met Thr Gly Ans Gln Leu Tyr - C

The following nucleotide sequence is found on the template strand of DNA. Sequence of DNA template: 3' - TAC TGG CCG TTA GTT GAT ATA ACT - 5'. From left to right, nucleotide 1 through nucleotide 24. Determine the amino acids of the protein encoded by this sequence by using the genetic code provided.

N - Met Thr Gly Asn Gln Leu Tyr - C

For the experiment outlined in Figure 15.8, could Niremberg and Matthaei have substituted RNA polymerase instead of polynucleotide phosphorylase without otherwise modifying the experiment? Why or why not?

No because RNA polymerase needs a template molecule to bind to in order to perform RNA synthesis by complementary base pairing

Match the names of eukaryotic RNA polymerases with the type of RNA they transcribe.

RNA polymerase I -- Transcribes rRNA RNA polymerase II -- Transcribes pre-mRNA, snoRNAs, and some miRNAs and snRNAs RNA polymerase III -- Transcribes small RNA molecules like the 5S rRNA, tRNAs, and some snRNAs and miRNAs RNA polymerase IV -- Transcribes siRNAs in plants

What enzyme is responsible for unwinding the DNA to allow prokaryotic transcription to begin?

RNA polymerase holoenzyme

The fox operon, which has sequences A, B, C, and D (which may represent either structural genes or regulatory sequences), encodes enzymes 1 and 2. These enzymes are normally produced in the presence of compund Fox. Mutations in sequences A, B, C, and D have the following effects, where a plus sign (+) indicates that the enzyme is synthesized and a minus sign (-) indicates that the enzyme is not synthesized. Indicate which sequence (A, B, C, D) is part of the following components of the operon. Each sequence should be used only once.

Regulator gene -- Sequence D Promoter -- Sequence B Structural gene for enzyme 1 -- Sequence A Structural gene for enzyme 2 -- Sequence C

What consensus sequences in the bacterial promoter are the sequences that the sigma factor of the RNA polymerase holoenzyme binds to, to improve binding specificity- i.e. to correctly place the RNA polymerase holoenzyme to the correct spot on the promoter so that transcription will occur just downstream of that at the transcription start site, instead of at random spots along the DNA?

The -10 and -35 consensus sequences

An RNA molecule has the following percentages of bases: A=23%, U=42%, C=21%, G=14% Is this RNA single stranded or double stranded?

The RNA is likely single-stranded

What is the co-repressor of the trp operon?

The amino acid tryptophan

The fox operon, which has sequences A, B, C, and D (which may represent either structural genes or regulatory sequences), encodes enzymes 1 and 2. These enzymes are normally produced in the presence of compund Fox. Mutations in sequences A, B, C, and D have the following effects, where a plus sign (+) indicates that the enzyme is synthesized and a minus sign (-) indicates that the enzyme is not synthesized. Is the fox operon inducible or repressible?

The fox operon is inducible

When using the ChIP method to detect DNA:protein interactions, what piece of information do you already know before beginning the experiment, and what information do you want to gain? Due to the type of information you already know, what are you using as a tool to isolate only the DNA:protein interaction that you are interested in? Mark the correct answers to each question.

The identity of the protein is what you know; and the information you want to gain is the sequence of the DNA that binds to that protein Because you already know the identity of the protein, (and want to find out the sequence of the DNA that binds to it), you want to use a protein specific antibody to isolate the DNA:protein complex of interest.

What enzyme, other protein, RNA, etc., PERFORMS the catalytic activity for peptide bond formation during translation?

The large ribosomal subunit acting as a ribozyme

Which component of the transcription unit indicates which of the 2 DNA strands is to be read as the template and the direction of transcription?

The promoter

A suppressor mutant in which the second mutation causes a return to the wildtype phenotype (away from the mutant phenotype conferred from the first mutation). Which of the following is an example of an intergenic suppressor mutation?

The second mutation changes the anticodon sequence encoded by a tRNA gene, so that the tRNA happens to still recognize the mutated codon of a different gene, allowing the mRNA transcript (upon transcription) to still be translated as the same polypeptide sequence.

In eukaryotes, after the 43S pre-initation complex forms, what happens as the immediate next step of translation initiation?

The tRNA-iMet that is part of this complex is used by the small ribosomal subunit to scan down the length of the mRNA beginning just 3' of the 5'-methylated guanine cap, until the initiation (start) codon is found in a process called scanning. This is followed by the release of initiation factors that allow the large ribosomal subunit to join

What is the role of the eukaryotic protein TBP, a protein subunit of transcription factor IID (TFIID)? Mark the 2 answers that are correct.

To make TFIID bind to the TATA box consensus sequence in the eukaryotic core promoter region, allowing subsequent addition of the pre-assembled general transcription factors at this location, along with RNA pol. II and other proteins to form the pre-initiation complex. Through its binding to the minor groove of the DNA, the TBP subunit of TFIID bends and partially unwinds the DNA

Alternative splicing can cause the same pre-mRNA to be able to be spliced in more than one way, creating different mRNAs that when translated will cause the creation of different proteins

True

Assume that the number of different types of bases of RNA is four. What would be the minumum codon size (number of nucleotides) required if the number of different types of amino acids in proteins were:

Two different types of amino acids in a protein - The minimum number of nucleotides required in a codon would be 1 8 different types of amino acids in a protein - The minimum number of nucleotides required in a codon would be 2 17 different types of amino acids in a protein - The minimum number of nucleotides required in a codon would be 3 45 different amino acids in a protein - The minimum number of nucleotides required in a codon would be 3 75 different amino acids in a protein - The minimum number of nucleotides required in a codon would be 4

Hemoglobin is a complex protein that contains 4 polypeptide chains. The normal hemoglobin found in adults - called adult hemoglobin - consists of 2 alpha and 2 beta polypeptide chains, which are encoded by different loci. Sickle-cell hemoglobin, which causes sickle-cell anemia, arises from a mutation in the beta chain of adult hemoglobin. Adult hemoglobin and sickle-cell hemoglobin differ in a single amino acid: GTG/CAC/CTG/ACT/CCT/GAG is the normal sequence in which the 6th amino acid from 1 end in adult hemoglobin is glumatic acid (Glu), whereas sickle-cell hemoglobin has valine (Val) as this position. After consulting the genetic code provided, indicate the type and location of the mutation that gave rise to sickle-cell anemia.

Type of mutation - Missense Glumatic acid is encoded by what codon in this sequence? - GAG This codon is mutated to what in order to encode valine? - GUG

In E. coli, what is the first step of translation termination?

When release factor RF-1 or RF-2 proteins bind to the stop codon lying within the A site of the ribosome

Match the following features of miRNAs.

Where do they initiate from? -- From transcription products of distinct genes How does DICER cleave the initial pri-miRNA (the not yet processed miRNA)? -- Dicer cleaves single-stranded RNAs to form short hairpins What does this small RNA silence? -- Silences different genes from the ones they were transcribed from How do they act in animal systems? -- Inhibit translation by staying bound to the targeted mRNA

What factors influence whether methylation of histone tails causes activation or repression of transcription? Mark the 3 answers that are true.

Which amino acids on the histone tail gets methylated How many methyl groups get added The position of the amino acid on the tail

In eukaryotes, where does the small ribosomal subunit bind, and assemble into an initiation complex with initiation factor proteins and the initiator tRNA charged with Met(tRNAiMet)?

c. At the 5' methylated guanine cap on the mRNA

A _____ mutation changes the wildtype phenotype, while a _____ mutation returns the mutant phenotype back to the wildtype phenotype.

forward; reverse

The following amino acid sequence is found in a tripeptide: Met-Trp-His. Give all possible nucleotide sequences on the mRNA, the DNA template strand, and the DNA non-template (coding) strand.

mRNA: 5' AUGUGGCAU 3' DNA template strand: 3' TACACCGTA 5' DNA nontemplate (coding) strand: 5' ATGTGGCAT 3' mRNA: 5' AUGUGGCAC 3' DNA template strand: 5' TACACCGTG 3' DNA non-template (coding strand): 5' ATGTGGCAC 3'

In bacterial Rho-dependent transcription termination, the rho ___ binds to the rut site on the ___. When RNA polymerase encounters a terminator sequence, it pauses, allowing rho to catch up. Using ___ activity, rho unwinds the DNA-RNA hybrid, leading to an end of transcription.

protein; RNA; helicase