Chapter 10 Molecular Biology

List the three key steps of initiation.

1. The mRNA binds to the small ribosomal subunit 2. Initiator tRNA binds to the start codon, 3. The large ribosomal subunit binds to the small subunit.

A sample of DNA contains 20% adenine. What percentage of guanine does it contain?

30%

Suppose you are analyzing a person's DNA. You are able to learn the quantity of nucleotides--that is, you can measure how many A, C, T, and G nucleotides are present in a person's DNA. In the sample you are currently analyzing, you find that 15% of the nucleotides are C. What percentage of the nucleotides are A?

35%

Changing the second base of the codon a. always changes the amino acid that is encoded. b. never changes the amino acid that is encoded. c. sometimes changes the amino acid that is encoded. d. All of the above are correct.e. None of the above is correct.

A

Students are usually surprised to discover that viruses can infect bacteria. What type of virus infects bacteria?

A bacteriophage

What did the structure of DNA's double helix suggest about DNA's properties? A. DNA stores genetic information in the sequence of its bases. B. DNA can be replicated by making complementary copies of each strand. C. DNA can change. Errors in copying can result in changes in the DNA sequence that could be inherited by future generations. D. DNA is found in the nucleus.

A, B, C

Consider the following sentence: "The dog did not eat." Which of the following variations of this sentence is most like a base substitution mutation? A. The did dog not eat. B. The doe did not eat. C. The dog did not et. D. The dog dog did not eat.

B

Diabetes mellitus is a metabolic disease that is characterized by the buildup of glucose in the blood, or hyperglycemia. Diabetes results either from the pancreas not being able to produce the hormone insulin (type 1 diabetes) or if the body's cells become resistant to insulin (type 2 diabetes). Insulin is a protein that binds to receptors on cell surfaces to allow glucose to enter the cell. In order to manage the disease, type 1 diabetics require frequent insulin injections. Until the 1970s, insulin was obtained from processing the pancreases of large mammals such as cows and pigs; it was then purified for medicinal use. This all changed in the 1970s with the advent of recombinant DNA technology, which allows scientists to insert genes from other species into bacterial plasmids and have bacteria produce proteins from these other species' genes. In 1978, the gene that codes for human insulin was added to a bacterial plasmid and bacteria were used to produce human insulin. These bacteria acted as mini-factories that produced human insulin for type 1 diabetes patients. Today, the production of human insulin from bacteria is commonplace and is a multibillion dollar market for pharmaceutical companies. In order to add the gene for human insulin to a bacterial plasmid, the DNA molecules have to be "cut" with enzymes called restriction endonucleases and then pasted back together with enzymes called DNA ligases. Imagine that during this process, the first five nucleotides of the human insulin gene were accidentally cut out before it was pasted into the bacterial plasmid. What is the most likely outcome if this plasmid was added to bacterial cells? A. The human insulin protein would be produced as normal. B. The human insulin protein would not be produced because transcription would not take place since the RNA polymerase would not recognize the promoter. C. The human insulin protein would be shorter than normal because it will be missing one amino acid. D. The human insulin protein would not be produced because the start codon is missing.

B

Dilated cardiomyopathy (DCM) is a common cause of sudden death and heart failure. Many mutations can cause DCM, but several of them are linked to the protein troponin, which is an essential protein that helps regulate muscle contraction in the heart. The A159E mutation causes an A amino acid to be replaced with an E amino acid (their structures are shown here). What effects do you think the A159E mutation will have on the troponin protein? A. The mutation will probably make troponin more stable at low pH and at higher temperatures since the E amino acid is acidic. B. Since the E amino acid is hydrophilic, it will try to be exposed on the surface of the protein and thus will disrupt the tertiary structure and potentially the function of troponin. C. If the A amino acid is replaced by the basic E amino acid, then the secondary and tertiary structures will be affected and troponin will likely not fold correctly. D. The mutation will not affect troponin function since both the A and E amino acids are hydrophobic and thus the troponin structure will not be affected.

B

Life on Mars is finally discovered and a new organism that has six different nucleotides that encode 30 different amino acids is found on this planet. Which of the following nucleotide combinations would encode the minimum number of amino acids needed in this organism? (Note: in the answers, the ^ indicates an exponent. For example, 4^3 means "four raised to the third power," AKA "four cubed," AKA 4 * 4 * 4 = 64) A. four-nucleotide sequence (6^4 combinations) B. two-nucleotide sequence (6^2 combinations) C. one-nucleotide sequence (6^1 combinations) D. three-nucleotide sequence (6^3 combinations)

B

Mutation (change) in a gene that altered the original codon to a stop codon would _______________________________________ a. result in a polypeptide that is one amino acid shorter than the one produced before the mutation. b. result in a shorter polypeptide chain. c. result in an amino acid substitution. d. alter the location at which transcription of the next gene begins. e. alter the reading frame.

B

Translation converts the information stored in ___________ into _________________ a. DNA; RNA b. RNA; a polypeptide c. protein; DNA d. protein; a polypeptide

B

We would expect that a 15-nucleotide sequence that includes a stop codon at the end (as part of the 15-nucleotide sequence) will direct the production of a polypeptide that consists of A. two amino acids. B. four amino acids. C. three amino acids. D. five amino acids.

B

Which of the following statements best describes the end result of bacterial conjugation? A. One cell has lost a chromosome, while the other has gained one. B. One cell has given a copy of a plasmid to another cell and kept one copy for itself. C. The two cells have had an equal exchange of plasmids. D. One cell has lost a plasmid, while the other cell has gained one.

B

What are the chemical components of a DNA molecule? A. amino acids B. phosphate groups C. proteins D. sugars E. nitrogenous bases

B, D, E

Hershey and Chase decided to use radioactively labeled sulfur and phosphorous in their classic experiment. Briefly explain why radioactively labeled carbon would not have worked.

Because radioactively labeled carbon would have showed up in everything (carbon is the element that the molecules of life are based on)

DNA ligase function

Bonds the DNA fragments of the lagging strand together

Every polypeptide chain synthesized from mRNA starts with which amino acid? a. Arginine b. Phenylalanine c. Methionine d. Leucine

C

Frederick Griffith was one of the leading scientists looking at the genetic role of DNA. He was working on two strains of Streptococcus pneumoniae: The rough strain (R) did not cause pneumonia, but the smooth strain (S) did. When Griffith heat-killed the S strain and gave both the heat-killed S strain and the R strain to mice, the mice developed pneumonia and died. What happened in this experiment that caused the mice to develop pneumonia? A. The immune systems of the mice were unable to cope with both the S and R strains simultaneously. B. The R strain mutated spontaneously and thus was able to cause pneumonia. C. Even though the S strain had been heat-killed, it genetically changed the R strain. D. There was more of the R strain added than previously.

C

If a strand of DNA has the sequence AAGCTC, transcription will result in a. a single RNA strand with the sequence TTCGAG. b. a DNA strand with the sequence TTCGAG. c. a single RNA strand with the sequence UUCGAG. d. a DNA strand with the sequence AAGCTC. e. none of the above.

C

It is possible to synthesize proteins in vitro (in a test tube) without the use of living cells. If starting from a mature mRNA transcript, which of the following components would not be needed to do this? A. tRNAs B. amino acids C. adenine molecules D. ribosomes

C

Integrated F factor

Can result in the recombination of genes, but the recipient cell usually remains a recipient cell because the F factor rarely completely transfers.

List the three steps of elongation in order.

Codon recognition, peptide bond formation, and translocation

What property of DNA allowed Watson and Crick great insight into the nature of DNA replication?

Complementary base pairing

Where bacteria transfer DNA to each other through conjugation tubes

Conjugation

DNA polymerase function

Creates DNA by reading a template strand and adding nucleotides with complementary bases

How do retroviruses such as HIV differ from other viruses? A. They have much simpler reproductive cycles than other RNA viruses. B. They can reproduce only inside living cells. C. They contain DNA that is used as a template to make RNA. D. They contain the enzyme reverse transcriptase.

D

In which of the following ways does a prion differ from both cellular life and viruses? A. Prions lack protein. B. Prions lack a cell membrane. C. Prions cause brain diseases. D. Prions lack nucleic acid.

D

What organelle is directly responsible for protein synthesis? a. Nucleus b. Chloroplast c. Mitochondria d. Ribosome

D

Which of the following is not a component of a nucleotide? a. A phosphate group b. A pentose (five-carbon sugar) c. A nitrogenous base d. All of the above are components of a nucleotide

D

Which of the following processes occurs in the nucleus of a cell? a. RNA splicing b. Addition of a 5′ cap c. Addition of a 3′ tail d. All of the above occur in the nucleus of a cell.

D

Contains the nitrogenous base thymine: _________

DNA

_____ is a long linear polymer found in the nucleus of a cell, shaped like a double helix, and associated with the transmission of genetic information.

DNA

A sequence of DNA reads ACTGAGTCA. The next base would have to be a. C. b. T. c. A. d. G. e. any of those four bases.

E

You are a molecular biologist working at Johns Hopkins. You are able to create a DNA molecule that was made with radioactively labeled carbon atoms. The radioactively labeled DNA is then allowed to undergo DNA replication using a pool of normal ("unlabeled") nucleotides. Briefly describe the makeup of the two resulting molecules of DNA.

Each of the new DNA molecules would consist of one radioactively labeled strand and one unlabeled strand.

List the basic steps in the replication cycle of a typical enveloped RNA virus.

Entry of the viral genome, uncoating of the protein coat, RNA synthesis by virus, protein and RNA synthesis, and assembly of the new viral components.

True or false: DNA replication is fully conservative in that you have the original molecule of DNA intact at the end and a brand-new synthesized piece of DNA. If false, make it a correct statement.

False, DNA replication is semiconservative.

True or false: A retrovirus needs reverse transcriptase to make viral DNA from the host-cell RNA. If false, make it a correct statement.

False, a retrovirus needs reverse transcriptase to make viral DNA from the viral RNA.

True or false: The flow of genetic information goes from RNA → DNA → protein. If false, make it a correct statement.

False, it goes from DNA → RNA → protein.

True or false: A codon reads AUA. The anticodon that recognizes it is TAT. If false, make it a correct statement.

False, it would be UAU because an anticodon is found on tRNA.

________ found that harmless bacteria became pathogenic when mixed with pathogenic bacteria that had been killed.

Frederick Griffith

How does the flow of genetic information differ in a retrovirus when compared with any cell?

In a retrovirus the flow is reversed: Instead of DNA → RNA, it's RNA → DNA.

The genetic code is often described as being redundant but not ambiguous. Briefly explain what this means.

It means that most amino acids have multiple codons that specify them, but no codon specifies more than one amino acid.

You are a biochemist working for a pharmaceutical company. You have been tasked with identifying a sample of nucleic acid. It is determined that the sample contains the bases cytosine, guanine, adenine, and phosphate groups. Will you be able to determine conclusively whether the sample is RNA or DNA? Briefly explain your answer.

No, because all of the listed components could be found in a sample of DNA or RNA.

DNA sequence in front of the gene that determines the start of transcription:

Promotor

The principal role of _____ is to act as a messenger carrying instructions from DNA out of the nucleus for the synthesis of proteins.

RNA

Why do RNA viruses tend to mutate at a fast rate?

RNA does not have the same proofreading capabilities as DNA

Creates an RNA copy of a gene:

RNA polymerase

Plasmid F Factor

Results in the second cell becoming a donor cell due to the complete transfer of the F factor as a plasmid.

Reverses the flow of genetic information

Retrovirus

A molecule that makes DNA from RNA

Reverse transcriptase

A _____ serves as the site of protein synthesis in the cytoplasm.

Ribosome

A sequence of bases that determines the end of the gene:

Terminator

A mutation has occurred in the promoter sequence of a gene. Briefly explain what effect that mutation will likely have on transcription of the gene.

The efficiency of RNA polymerase binding may be affected, and thus the rate of transcription for that gene may decrease or transcription may not occur at all.

Because the two strands of DNA run in opposite directions, only one strand is synthesized continuously. The other strand is sometimes referred to as the lagging strand. Briefly explain why this is an appropriate name for this strand of DNA.

The lagging strand has to wait for the double helix to unwind enough for the DNA polymerase to attach and add new nucleotides. Overall, this is due to the fact that DNA polymerase can add nucleotides only to the 3 ́ end of the strand.

Which viral life cycle can be triggered to enter into the other one? What triggers that process?

The lysogenic cycle can be converted into the lytic cycle. Usually, some kind of external stressor can initiate that process.

Origin of replication

The site of the start of DNA replication

Replication bubble

The site where DNA replication is occurring

A human cell has a mutation in a gene, the effect of which is a lack of certain receptor proteins on the surface of the cell. Would a typical enveloped virus be able to infect that cell? Briefly explain your answer.

The virus would be impeded in entering that particular cell because the virus would have trouble adhering to the cell.

How were Watson and Crick able to rule out that the bases paired with themselves?

They were able to rule this out because the X-ray data indicated that a molecule of DNA had a uniform diameter. This would not be possible if the bases paired with themselves.

Briefly explain how one gene could produce multiple polypeptides. RNA splicing can put the exons back together in different combinations.

This can produce many alternate polypeptides.

"Genotype determines phenotype" is a common saying. Briefly explain what this means.

This means that an organism's genes (genotype) largely determines the physical outcome of the character.

A ribosome is formed such that it has a P-site but no A-site. Briefly describe how this would affect translation.

This would essentially stop translation because tRNA could not come and sit in the empty A site.

The process by which the message in a gene is copied into RNA.

Transcription

_____ is the first step of gene expression, during which a particular segment of DNA is used to make a strand of RNA.

Transcription

__________ converts the DNA message into an RNA message.

Transcription

A biochemist identifies a new toxin that closes the nuclear pores of a cell's nucleus. What cellular process would be disrupted by this toxin? Which one would not be?

Transcription would not be altered because it occurs in the nucleus, whereas translation would be affected because it occurs on a ribosome in the cytosol of the cytoplasm.

When a bacteria has genes transferred to it from a virus

Transduction

Where a bacterium takes up DNA from its environment

Transformation

A colony of bacteria is being grown in a liquid medium. A microbiologist adds a chemical that will cause most, but not all, of the bacteria to lyse (split open). Which method of gene transfer is likely to occur at this point? Briefly explain your answer.

Transformation because there will be a large amount of bacterial DNA in the surrounding environment.

The process by which mRNA is used by a ribosome to synthesize polypeptides.

Translation

_____ is the process in which mRNA codons are used to make an amino acid sequence.

Translation

True or false: The F factor can exist as an integrated piece of DNA in the bacterial chromo-some or as a plasmid. If false, make it a correct statement.

True

True or false: The cap and tail are not part of the message used to construct a polypeptide. If false, make it a correct statement.

True

A(n) ________________ is the protein coat of a virus.

capsid

The RNA strand grows one amino acid at a time.

elongation

A mutation that involves the addition or deletion of a nucleotide that results in a shift in the reading frame

frameshift mutation

RNA splicing removes _________ from the mRNA while keeping the ____________

introns exons

Serves as a messenger for taking genetic information from the nucleus to the cytoplasm:

mRNA

The RNA copy of the DNA message

mRNA

A mutation that changes an amino acid

missense mutation

A mutation that changes a codon to a stop codon

nonsense mutation

The monomers of nucleic acids: _______

nucleotides

Polymer of nucleotides

polynucleotide

A misfolded protein

prion

The RNA that is a component of the ribosomal subunits

rRNA

A mutation that does not change the amino acid

silent mutation

Formed by covalent bonds between nucleotides

sugar-phosphate backbone

Has an anticodon and carries an amino acid

tRNA

The RNA that binds to the amino acid and binds to the mRNA; brings each new amino acid to the growing polypeptide

tRNA

What process links DNA to RNA?

transcription