Exam 6

Explain what the result would be of a mutation in the repressor that prevented it from binding to tryptophan.

In a mutated cell, tryptophan will be synthesized even when it is present in the cell because the repressor will not bind to the operator. The transcription will not be blocked.

Which of the following statements describes prokaryotic transcription of the lac operon?

Lactose acts as an inducer of the lac operon when glucose is absent.

A mutation in the promoter region of the gene for the clotting factor IX is the cause of hemophilia B, which results in insufficient clotting. What is the likely reason for hemophilia?

Less of the polypeptide is produced because less mRNA is transcribed.

A mutation within the promoter region can alter gene transcription. Describe how this can happen.

Mutated promoters alter the binding site for transcription factors to increase or decrease the rate of transcription.

Discuss the significance of mutations in tRNA and rRNA.

Mutations in tRNA and rRNA would lead to the production of defective proteins or no protein production.

A scientist splices a eukaryotic promoter in front of a bacterial gene and inserts the gene in a bacterial chromosome. Would you expect the bacterium to transcribe the gene?

No, prokaryotes use different promoters than eukaryotes.

What are Okazaki fragments and how they are formed?

Okazaki fragments are short stretches of DNA on the lagging strand, which is synthesized in the direction away from the replication fork.

Explain how we know base pairing takes place between a purine and pyrimidine.

Only the pairing between a purine and pyrimidine can explain the uniform diameter of the DNA double helix. Adenine and thymine form two hydrogen bonds, whereas cytosine and guanine form three hydrogen bonds.

Explain why errors in DNA replication are rare events in cells.

Polymerase I and II are responsible for proofreading and fixing mistakes in the copying process which explains why errors in DNA replication are rare.

Cycloheximide is a compound that binds to eukaryotic ribosomes and inhibits their function. Which of the following events would be observed if cycloheximide is added to cells in culture?

Polypeptides are not synthesized

Compare and contrast the similarities and differences between eukaryotic and prokaryotic DNA.

Prokaryotes have a single, circular chromosome, while eukaryotes have multiple, linear chromosomes. Prokaryotes pack their chromosomes by super coiling, managed by DNA gyrase. Eukaryote chromosomes are wrapped around histone proteins that could form heterochromatin, which is not present in prokaryotes.

Mutations can occur in any part of the DNA. What can happen if there is a mutation in the promoter sequence?

RNA polymerase will not be able to attach.

What process transfers heritable material to the next generation?

Replication

Discuss the contributions of Francis Crick, James Watson, and Rosalind Franklin to the discovery of the structure of DNA.

Rosalind Franklin used X-ray diffraction methods to demonstrate the helical nature of DNA, while Watson and Crick formulated the double stranded structural model of DNA.

You are given three mRNA sequences: 5'-UCG-GCA- AAU-UUA -GUU-3' 5'-UCU-GCA- AAU-UUA -GUU-3' 5'-UCU-GCA- AAU-UAA -GUU-3' Using the table, write the peptide encoded by each of the mRNA sequences.

Serine-alanine-asparagine-leucine-valine Serine-alanine-asparagine-leucine-valine Serine-alanine-asparagine(-stop)

Explain the roles of single stranded proteins, primase and DNA polymerase III at the replication fork.

Single-strand binding proteins bind to single-stranded DNA. Primase synthesizes the RNA primer. DNA polymerase III synthesizes the daughter strand.

An unidentified species has been identified as having 27%27% adenine and 23%23% guanine in its DNA. Identify which of the following species matches this profile and discuss how your answer is consistent with Chargaff's Rules. Species A has 29%29% thymine and 21%21% cytocine, species B has 20%20% adenine and 30%30% thymine, species C has 27%27% thymine and 23%23% cytosine.

Species C is consistent with the experimental results. According to Chargaff's rule, adenine and thymine are equal, and cytosine and guanine are equal.

Discuss how mutations can increase variation within a population.

Substitution mutations may cause a different amino acid to be placed at a specific location, causing small changes in the protein. Frameshift mutations usually cause multiple amino acid changes, increasing chances that a new protein will form, leading to radically different characteristics in the offspring.

Many antibiotics inhibit bacterial protein synthesis. For example, tetracycline blocks the A site on the bacterial ribosome, and chloramphenicol blocks peptidyl transfer. What specific effect would you expect each of these antibiotics to have on protein synthesis? Tetracycline would directly affect: tRNA binding to the ribosome Ribosome assembly Growth of the protein chain Chloramphenicol would directly affect: tRNA binding to the ribosome Ribosome assembly Growth of the protein chain

Tetracycline would directly affect tRNA binding to the ribosome. Chloramphenicol would affect the growth of the protein chain.

What would happen if bacteria did not have trp R?

The cell would make tryptophan when it was not needed.

The E. coli bacteria can have several mutations that affect the lac operon system. One mutation inhibits the ability of RNA polymerase to bind to the lac operon. How would this affect the cell?

The cell would not be able to process lactose.

How do the linear chromosomes in eukaryotes ensure that their ends are replicated completely?

The ends of the linear chromosomes are maintained by the activity of the telomerase enzyme.

You are looking at two fragments of DNA. Both have the sequence CATTCTG on one strand and GTAAGAC on the other. One of the fragments is exposed to UV light, the other is not. What will happen to the fragments and how might these mutations be repaired?

The fragment exposed to UV light contains thymine dimers. Thymines lying adjacent to each other can form thymine dimers when exposed to UV light. They can be repaired by nucleotide excision.

What characteristic of the genetic code points to a common ancestry for all organisms?

The genetic code is almost universal.

Transcribe and translate the following DNA sequence (nontemplate strand): 5'-ATGGCCGGTTATTAAGCA-3'

The mRNA would be 5'-AUGGCCGGUUAUUAAGCA-3' and the protein will be MAGY.

You sequence a gene of interest and isolate the matching mRNA. You find that the mRNA is considerably shorter than the DNA sequence. Why is that?

The processed mRNA is shorter because introns were removed.

What happens when tryptophan is present?

The repressor binds to the operator, and RNA synthesis is blocked

What would be the result of a mutation in the repressor protein that prevented it from binding lactose?

The repressor will bind the operator in the presence of lactose.

Why is the stop codon necessary for translation

The stop codon ends translation which allows the polypeptide strand to be released.

What could happen if a cell had too much of an activating transcription factor present?

The transcription rate would increase, altering cell function.

You are given three mRNA sequences: 5'-UCG-GCA- AAU-UUA -GUU-3' 5'-UCU-GCA- AAU-UUA -GUU-3' 5'-UCU-GCA- AAU-UAA -GUU-3' Using the peptide encoded by each of the above, compare the three peptides obtained. How are peptides 2 and 3 different from 1? What would be the consequence for the cell in each case?

There is a silent mutation in peptide 2 and peptide 3 has a stop codon due to mutation.

What do figures X and Y in the graphic illustrate? a

Transcription and translation in a prokaryotic cell (figure X) and a eukaryotic cell (figure Y).

The lac operon consists of regulatory regions such as the promoter as well as the structural genes lacZ, lacY, and lacA, which code for proteins involved in lactose metabolism. What would be the outcome of a mutation in one of the structural genes of the lac operon?

Transcription will continue but lactose will not be metabolized properly.

Some hereditary and age-related diseases are caused by translation errors. Explain why an error in translation may cause disease.

Translation is the process used by ribosomes to synthesize proteins from amino acids. If there is an error in this process, the correct proteins will not be made to build important body tissue or perform vital functions thus leading to hereditary and age-related diseases.

In E. coli, the trp operon is on by default, while the lac operon is off. Why do you think that this is the case?

b The trp operon synthesizes tryptophan which is essential for the cell and therefore remains ON, whereas the lac operon synthesizes enzymes for the breakdown of a sugar that is not always available and remains OFF by default.

What property of DNA fragments accounts for their movement through the gel towards the cathode during gel electrophoresis?

charge

Which of the following cell structures does not contain heritable information?

cytoplasmic membrane

Which deletion is in a repressor involved in regulating the gene?

deletion 1

The level of transcription of a gene is tested by creating deletions in the gene as shown in the illustration. These modified genes are tested for their level of transcription: (++) normal transcription levels; (+) low transcription levels; (+++) high transcription levels. Which deletion is in an enhancer involved in regulating the gene?

deletion 3

What is the major challenge in the production of RNA in eukaryotes compared to prokaryotes?

exporting the mRNA across the nuclear membrane

What is illustrated by the image below?

phenotypic changes as a result of pH changes b

Prokaryotes regulate gene expression at the level of transcription whereas eukaryotes regulate at multiple levels including epigenetic, transcriptional and translational.

promoters

Which property of proteins refers to the assembly of multiple polypeptide chains?

quaternary structure

What happens in the absence of tryptophan?

the repressor dissociates from the operator

Which of the following would be a good application of plasmid transformation?

to make copies of DNA

How would you reorder the following statements so that they are in the proper sequence for protein synthesis.1) The P-site amino acid detaches from its tRNA.2) tRNA translocates to the P site.3) A small ribosomal subunit binds with mRNA.4) A peptide bond is catalyzed by peptidyl transferase and forms between the new amino acid and a polypeptide chain.5) An aminoacyl-tRNA binds to the A site.

3, 5, 4, 2, 1

What do RNA and DNA have in common?

Both contain four different nucleotides.

A mutation has occurred in the DNA and in the mRNA for a gene. Discuss which would have a more significant effect on gene expression. Why?

Both will result in the production of defective proteins. The DNA mutation, if not corrected, is permanent, while the mRNA mutation will only affect proteins made from that mRNA strand. Production of defective protein ceases when the mRNA strand deteriorates.

Explain how forensic scientists are able to use DNA analysis to identify individuals.

Comparison of DNA from a known source or individual with analysis of the sequence of an unknown sample of DNA allows scientists to find out if both of them are similar or not.

Lactose digestion in E. coli begins with its hydrolysis by the enzyme ββ-galactosidase. The gene encoding ββ-galactosidase, lacZ, is part of a coordinately regulated operon containing other genes required for lactose utilization. Which of the following figures correctly depicts the interactions at the lac operon when lactose is not being utilized?

D

You isolate a cell strain in which the joining together of Okazaki fragments is impaired and suspect that a mutation has occurred in an enzyme found at the replication fork. Which enzyme is most likely to be mutated?

DNA ligase

Compare and contrast the roles of DNA polymerase I and DNA ligase in DNA replication.

DNA polymerase I removes the RNA primers from the developing copy of DNA. DNA ligase seals the ends of the new segment, especially the Okazaki fragments.

DNA replication is bidirectional and discontinuous; explain your understanding of those concepts.

DNA polymerase reads the template strand in the 3' to 5' direction and adds nucleotides only in the 5' to 3' direction. The leading strand is synthesized in the direction of the replication fork. Replication on the lagging strand occurs in the direction away from the replication fork in short stretches of DNA called Okazaki fragments.

Which of the following is not a true statement comparing prokaryotic and eukaryotic DNA replication?

DNA replication always occurs in the nucleus.

Information about four different DNA samples is provided below. The percentage of each base is shown. What can be concluded from the data below?

DNA samples 1 and 4 are likely the same species.

What would happen if RNA polymerase II did not have proofreading capabilities?

Defective or no proteins would be made.

Explain what an enhancer is and how an enhancer that is located thousands of nucleotides away from the gene it controls can still affect that gene.

Enhancers are the specific sites that bind transcription factors and allow for the interaction of activators.

Explain how fast DNA sequencing can change the way doctors treat disease.

Faster genetic sequencing will help in quick analysis of the genetic makeup of bacteria that can cause diseases in humans for better and more efficient treatments. Also, sequencing of a cancerous cell's DNA can provide better ways to treat or prevent cancer.

Explain the events taking place at the replication fork. If the gene for helicase is mutated, what part of replication will be affected?

Helicase separates the DNA strands at the origin of replication. Topoisomerase breaks and reforms DNA's phosphate backbone ahead of the replication fork, thereby relieving the pressure. Single-stranded binding proteins prevent reforming of DNA. Primase synthesizes RNA primer which is used by DNA polymerase to form a daughter strand. If helicase is mutated, the DNA strands will not be separated at the beginning of replication.

A frameshift mutation that results in the insertion of three nucleotides is often less deleterious than a mutation that results in the insertion of one nucleotide. Why?

Addition of three nucleotides does not shift the reading fram

Can you predict how alternative splicing may lead to an economy of genes? Do you need a different gene for every protein that the cell can produce?

Alternative splicing can lead to the synthesis of several polypeptides from a single gene.