Deck 4: Translation and Protein Structure

Question 1

How many water molecules would be produced in making a polypeptide that is 14 amino acids long?

Answer 1

13

Question 2

What is wrong with this diagram of secondary structure in a polypeptide chain?

A)It has two amino ends.
B)The directionality of the polypeptide chain reverses orientation between the arrows representing a ? sheet.
C)? sheets cannot form when the arrows are pointed in opposite directions.
D)Nothing is wrong with the diagram.

Answer 2

It has two amino ends.

Question 3

You have two types of cells that both produce a particular protein. You notice that when you heat up the cells, the first type of cell's protein loses function while the second type of cell's protein retains function. How is this possible?

A)The protein of the second type of cell has a completely different primary structure from the protein of the first type of cell.
B)The second type of cell expresses a chaperone protein that the first type does not.
C)The first cell has weaker mRNA.
D)None of the other answer options is correct.

Answer 3

B

Question 4

Which of the following actions would affect the secondary, but not primary, structure of a protein?

A)change the sequence of amino acids
B)break the ionic bonds between amino acids
C)break the hydrogen bonds between amino acids
D)disrupt the interactions between two different polypeptide chains

Question 5

Which one of the following can contribute to a protein's tertiary structure?

A)ionic bonding
B)van der Waal's forces
C)covalent bonding
D)hydrogen bonding
E)All of the other answer options are correct.

Question 6

The function of a protein is dependent upon the shape into which the chain of amino acids folds. Many noncovalent interactions are responsible for maintaining the protein's shape. Assume you have isolated a protein from an organism in its proper shape, and you have treated it with an enzyme that selectively targets and breaks only the peptide bonds in the proteins. Would the protein retain its shape under these conditions?

A)Yes; once noncovalent bonding determines the shape of a protein, the peptide bonds are no longer necessary.
B)Yes; because the noncovalent interactions that determine the shape of a protein are stronger than the peptide bonds.
C)No; while the noncovalent bonds determine the shape of a protein, the peptide bonds are required to hold the amino acids together.
D)Yes; but the shape would be affected to a greater extent by changes in temperature.

Question 7

X-rays are waves of electromagnetic radiation with an extremely short wavelength (0.01 to 10 nanometers). They can be used in X-ray crystallography to infer the arrangement of atoms in a crystal because:

A)all X-rays bounce off the surface of the crystal.
B)they can be used on live cells without isolating the protein in question.
C)their wavelength allows them to determine the amino acid sequence of the protein.
D)some X-rays pass through the crystal and scatter in different directions.
E)all X-rays pass through the crystal without changing direction.

Question 8

Proteins that do not refold properly after being heated generally require the assistance of which one of the following types of molecules in cells?

A)polymerases
B)ribosomes
C)enhancers
D)chaperones
E)transferases

Question 9

Which one of the following amino acids has its R group covalently linked to the amino group?

A)glycine
B)serine
C)cysteine
D)glutamic acid
E)proline

Question 10

How many water molecules would be produced in making a polypeptide that is 14 amino acids long?

A)0
B)13
C)14
D)28

Question 11

The function of a protein is dependent upon the shape into which the chain of amino acids folds. Many noncovalent interactions are responsible for maintaining the protein's shape. Assume you have isolated a protein from an organism in its proper shape, and you have treated it with an enzyme that selectively targets only the peptide bonds in the proteins. Would the protein retain its shape under these conditions?

Question 12

Two major types of protein secondary structures are referred to as:

A)elementary and primary.
B)amino and carboxyl.
C)residual and permanent.
D) helix and  sheet.
E)ionic and covalent.

Question 13

Secondary structure is characterized by which one of the following types of interactions?

A)hydrogen bonding within the peptide backbone
B)a covalent bond between two cysteines
C)ionic bonding between an acidic R group and a basic R group
D)hydrogen bonding between R groups of amino acids
E)the covalent bond between an amino nitrogen and a carboxyl carbon

Question 14

At physiological pH, the ionized state of the amino (NH₂) group in the R group of lysine is:

A)NH₂.
B)NH₃⁺.
C)NH₄⁺⁺.
D)NH^-.

Question 15

At physiological pH, the ionized state of the carboxyl (COOH) group in the R group of aspartic acid is:

A)COOH.
B)COOH⁺.
C)COO^-.
D)CO^-O^-.

Question 16

The covalent bond between adjacent amino acids in a polypeptide chain is referred to as a(n) _____ bond.

Question 17

 helices are stabilized by hydrogen bonds between amino acids that are _____ residues apart.

A)2
B)4
C)10
D)20
E)100

Question 18

Which one of the following amino acids is MOST likely to participate in hydrogen bonding with water?

A)alanine
B)asparagine
C)leucine
D)phenylalanine
E)valine

Question 19

What is wrong with this diagram of secondary structure in a polypeptide chain? (Hint: In the representation of ? sheets as paired arrows, the convention is that the amino end is at the base of the arrow and the carboxyl end is at the tip.)

A)It has an amino end and a carboxyl end.
B)The directionality of the polypeptide chain reverses orientation between the arrows representing a ? sheet.
C)? sheets cannot form when the arrows are pointed in the same direction.
D)Nothing is wrong with the diagram.

Question 20

The individual polypeptide chains in a multi-subunit protein each have their own primary, secondary, and tertiary structure.

Question 21

Which one of the following is NOT a component of an amino acid?

A) carbon
B)amino group
C)triphosphate group
D)R group
E)carboxyl group

Question 22

The unfolding of a protein by heat or chemical treatment is referred to as:

A)disaggregation.
B)uncoupling.
C)denaturation.
D)hydrolysis.
E)depolymerization.

Question 23

All  sheets are comprised of protein strands running antiparallel to each other.

Question 24

Proteins that prevent inappropriate folding of newly synthesized proteins are called:

A)chaperones.
B)enzymes.
C)polymerases.
D)ribosomes.
E)synthetases.

Question 25

Secondary structures are stabilized by which type of interaction?

A)hydrophobic clustering
B)disulfide linkages
C)ionic bonding
D)hydrogen bonding
E)van der Waals forces

Question 26

Amino acids with hydrophobic R groups are most often found buried in the interior of folded proteins.

Question 27

X-ray crystallography was used to determine the structure of:

A)cholesterol.
B)vitamin B12.
C)myoglobin.
D)insulin.
E)All of these choices are correct.

Question 28

The interactions between amino acids are major factors in determining the shape of a protein. These interactions can be effected by the environment surrounding a protein. Explain how the temperature, pH, ion concentration, and hydrophilic or hydrophobic properties of the environment may impact the shape of a protein, and therefore its function.

Question 29

 helices are coils with how many amino acids per complete turn?

A)2)5
B)3)6
C)4)8
D)10
E)20

Question 30

You are studying a protein that you call Protein X. There is an aspartic acid at a key position in Protein X that is important in the folding and stabilization of that protein. If this aspartic acid is changed to a different amino acid, which one of the following amino acid substitutions is MOST likely to allow the protein to fold normally?

A)threonine
B)glycine
C)arginine
D)glutamic acid
E)serine

Question 31

In a ribbon model of a polypeptide, broad arrows indicate:

A) sheets.
B) helices.
C)disulfide linkages.
D) sheets and  helices.
E)All of these choices are correct.

Question 32

The sequence of amino acids in a protein is referred to as its primary structure.

Question 33

The fully folded structure of a functional protein composed of a single polypeptide chain is referred to as the _____ structure.

A)primary
B)secondary
C)tertiary
D)quaternary

Question 34

A cooperative effect can occur in some types of multi-subunit proteins, leading to improved function of the subunits when bound to each other.

Question 35

Which one of the following interactions is NOT a stabilizing force at the tertiary level of protein organization?

A)an ionic bond between a positively charged R group and a negatively charged R group
B)hydrophobic clustering of nonpolar R groups in the interior of a protein
C)hydrogen bonding between the carbonyl oxygen of one peptide bond and an amide hydrogen of a nearby peptide bond
D)disulfide linkages between cysteine residues
E)van der Waals interactions between R groups in close proximity

Question 36

The bond between two amino acids is referred to as a(n) _____ bond.

Question 37

Most proteins retain metabolic activity when denatured.

Question 38

Which of the following statements about amino acids is INCORRECT?

A)A turn or kink in a protein is more likely to be induced by a proline than by a glycine.
B)The bridge between cysteines, which connects parts of a protein, is a stable but noncovalent interaction.
C)At typical cellular pH, the R groups of basic amino acids are positively charged.
D)Not every amino acid is asymmetric.
E)The more glycines that are found in a polypeptide's primary sequence, the more flexible the backbone of that polypeptide.

Question 39

The interactions between amino acids are major factors in determining the shape of a protein. These interactions can be affected by the environment surrounding a protein. Which of the following would have an effect on the shape of a protein?

A)the temperature of the environment
B)the pH of the environment
C)whether the other molecules in the environment are predominantly hydrophilic or hydrophobic
D)the concentrations of ions present in the environment
E)All of the other answer options are correct.

Question 40

Which one of the following amino acids is capable of forming a disulfide linkage with itself?

A)tyrosine
B)cysteine
C)arginine
D)methionine
E)isoleucine

Question 41

Assuming A-U and G-C pairing between the anticodon and the codon, what anticodon in tRNA^Met would pair with the codon 5'-AUG-3'?

A)5'-CAU-3'
B)5'-GUA-3'
C)5'-UAC-3'
D)5'-ATG-3'
E)5'-AUG-3'

Question 42

Imagine that you and your colleagues are working in a lab to develop a protein synthesis system for a new type of synthetic cell. During your brainstorming sessions, you propose that polycistronic mRNA would be much more useful than mRNA that is only translated into one protein. This would allow for multiple proteins necessary for a particular function to be translated together. One of your colleagues says that is a good idea, but if you decide to go with polycistronic mRNA, you'd better make sure to use a prokaryotic translation system. Why might it be problematic to use a eukaryotic translation system with polycistronic mRNA?

A)Introns would always prevent translation of the mRNA.
B)Eukaryotic ribosomes initiate translation by binding to the 5-cap, which is only at the end of the mRNA.
C)Prokaryotic ribosomes do not detach from mRNA when they reach a stop codon.
D)Eukaryotic start and stop codons are different from prokaryotic start and stop codons.

Question 43

An mRNA molecule has a sequence 5'- CAGAUCUAAUGCUUAUCGGAU-3'. When translated in a laboratory setting in which translation can be initiated anywhere along the molecule, how many reading frames are possible?

A)1
B)2
C)3
D)4
E)6

Question 44

You are investigating an abnormal eukaryotic cell line that makes all of its mRNAs much longer than the mRNAs from normal cells. Intrigued, you examine the proteins in these abnormal cells and note that many of them are either much longer or much shorter than the normal proteins from nonmutant cells. Assuming there is just one mutant defect in these cells, which of the below possibilities is MOST likely?

A)A stop codon is mutated.
B)RNA polymerase does not recognize the terminator sequence.
C)The release factor is defective.
D)The spliceosome is nonfunctional.
E)The enzyme that adds the poly-A tail is defective.

Question 45

When a peptide bond is created between two amino acids:

A)the amino group of the first amino acid is joined to the carboxyl group of the second.
B)the carboxyl group of the first amino acid is joined to the amino group of the second.
C)the carboxyl group of the first amino acid is joined to the carboxyl group of the second.
D)the amino group of the first amino acid is joined to the amino group of the second.

Question 46

The genetic code is:

A)different for bacteria than for eukaryotes.
B)ambiguous.
C)redundant.
D)a quadruplet code.
E)comprised of codons which usually differ at the first position.

Question 47

You are investigating an abnormal eukaryotic cell line that makes all of its mRNAs much longer than the mRNAs from normal cells (that is, they have more nucleotides than usual). Intrigued, you examine the proteins in these abnormal cells and note that many of them are either much longer or much shorter than the normal proteins from nonmutant cells. Assuming there is just one mutant defect in these cells, what is that defect?

Question 48

How many different mRNA sequences could encode the amino acid sequence Ser-Leu-Ser-Arg?

Question 49

Which of the following statements is TRUE regarding glycine?

A)Glycine is an asymmetric amino acid.
B)Glycine is a large, polar amino acid.
C)Glycine increases the flexibility of the peptide backbone.
D)Glycine is similar to tyrosine in terms of structure and chemical properties.
E)Glycine is special because it contains a -SH group important in protein folding.

Question 50

Assuming that transcription and translation both proceed from left to right, which is the correct orientation of the DNA template, the RNA transcript, and the protein product?

A)
$\begin{array}{ll}\text { DNA template }&5^{\prime}-\ldots \ldots \ldots-3^{\prime}\\\text { RNA transcript }&5^{\prime}-\ldots \ldots \ldots-3^{\prime}\\\text { Protein product }&\mathrm{H}_{2} \mathrm{~N}-\ldots \ldots \ldots-\mathrm{COOH}\\\end{array}$


B)
$\begin{array}{ll}\text { DNA template }&3^{\prime}-\ldots \ldots \ldots,-5^{\prime}\\\text { RNA transcript }&5^{\prime}-\ldots \ldots \ldots,-3^{\prime}\\\text { Protein product }&\mathrm{HOOC}-\ldots \ldots \ldots . .-\mathrm{NH}_{2}\end{array}$


C)
$\begin{array}{ll}\text { DNA template }&5^{\prime}-\ldots \ldots \ldots-3^{\prime}\\\text { RNA transcript }&5^{\prime}-\ldots \ldots \ldots-3^{\prime}\\\text { Protein product }&\mathrm{HOOC}-\ldots \ldots \ldots . .-\mathrm{NH}\\\end{array}$


D)
$\begin{array}{ll}\text { DNA template }&3^{\prime}-\ldots \ldots \ldots,-5^{\prime}\\\text { RNA transcript }&5^{\prime}-\ldots \ldots \ldots,-3^{\prime}\\\text { Protein product }&\mathrm{H}_{2} \mathrm{~N}-\ldots \ldots \ldots-\mathrm{COOH}\end{array}$

Question 51

An mRNA molecule is synthesized that has a random sequence consisting of 25% A, 25% U, and 50% C. Among the amino acids in the polypeptide chains resulting from translation in a laboratory setting in which translation can be initiated anywhere along the mRNA molecule, what is the expected frequency of phenylalanine codons?

A)1/64
B)1/32
C)3/64
D)3/32
E)1/16

Question 52

Imagine a scenario in which codons consisted of two bases instead of three, but in which there were still 20 amino acids that could be incorporated into proteins during translation. How many codons would be possible with a two-base codon system? Would be possible to code for 20 amino acids with only 16 different codons?

Question 53

Which of the following statements is TRUE regarding a basic amino acid?

A)The hydrophilic R group of a basic amino acid will be located in the interior of a protein.
B)The positively charged R group of a basic amino acid could bind DNA.
C)The R group of a basic amino acid would only be able to form covalent bonds with other molecules.
D)A basic amino acid would be considered both polar and hydrophobic.
E)All of these choices are correct.

Question 54

Translation in a test tube does not require an AUG codon to start translation, but can start anywhere. Once translation begins, however, it translates successive triplets just like translation in a cell. Consult the standard genetic code and specify what polypeptide sequence (or sequences) you would expect to be translated from an mRNA molecule with the sequence 5'-CAGCAGCAGCAG … -3' if translation occurred in a test tube.

Question 55

An RNA molecule has a sequence 5'- GCGAUCUAAUGCUUUUCGGAA-3'.
How many reading frames are possible if this molecule is translated in a laboratory setting in which translation can be initiated anywhere along the molecule? How many reading frames are possible when this molecule is translated in a cellular environment?

Question 56

The bond that forms between amino acids:

A)connects amino groups and carboxyl groups of adjacent amino acids.
B)connects hydrogen atoms of adjacent amino acids.
C)connects amino groups and R groups of adjacent amino acids.
D)connects water molecules and carboxyl groups of adjacent amino acids.
E)A peptide bond can form between any chemical groups of adjacent amino acids.

Question 57

Consider the following two statements about protein structure: 1 - All polypeptides have tertiary structure.
2 - All proteins have quaternary structure.
Which of the two statements above is CORRECT?

A)Statements 1 and 2 are both true.
B)Statements 1 and 2 are both false.
C)Statement 1 is true; statement 2 is false.
D)Statement 1 is false; statement 2 is true.

Question 58

How many different mRNA sequences could encode the amino acid sequence Met-Leu-Val-His?

Question 59

Imagine that you and your colleagues are working in a lab to develop a protein synthesis system for a new type of synthetic cell. During your brainstorming sessions, you propose that polycistronic mRNA (an mRNA with multiple start and stop codons) would be much more useful than mRNA that is only translated into one protein (with just one start and stop codon). This would allow for multiple proteins necessary for a particular function to be translated together. One of your colleagues says that is a good idea, but if you decide to go with polycistronic mRNA, you'd better make sure to use a prokaryotic translation system. Why might it be problematic to use a eukaryotic translation system with polycistronic mRNA?

Question 60

Explain how all 64 possible combinations of A, C, G, and U encode just 20 amino acids and three stop codons.

Question 61

Which of the mRNA sequences would be translated in a test tube as the three different polypeptide chains polyserine, polyglutamine, and polyvaline, assuming that laboratory conditions were such that translation could start anywhere along the mRNA molecule?

A)5'-AUCGAUCGAUCG….-3'
B)5'-GCUAGCUAGCUA….-3'
C)5'-GUCAGUCAGUCA….-3'
D)5'-ACUGACUGACUG….-3'
E)None of the other answer options is correct.

Question 62

When a charged tRNA is about to bind to the vacant A site of a ribosome, where is the growing polypeptide?

A)in the A site
B)in the P site
C)in the E site
D)The polypeptide is equally likely to be in any of the three sites.

Question 63

Examine the figure below, which depicts one stage in the process of translation in a eukaryote. What will happen when the ribosome shifts one codon further on the mRNA, assuming the next codon is NOT a stop codon?

A)The tRNA carrying the polypeptide will be in the P site.
B)The tRNA that was carrying the polypeptide will be ejected from the ribosome.
C)The sites of the ribosomes will be relabeled (from left to right)P, A, E.
D)A new tRNA will bind to the ribosome.
E)The tRNA that is shown in the A site in the figure above will be ejected from the ribosome.

Question 64

Design an mRNA sequence that would be translated in a test tube as a polypeptide consisting of alternating His and Thr.

Question 65

Which of the amino acid(s) are encoded by just one codon? Which amino acids are encoded by the greatest number of codons?

Question 66

Which of the diagrams below shows what one would see in the electron microscope during the transcription of a polycistronic bacterial operon that codes for two proteins?

A)A
B)B
C)C
D)D

Question 67

A messenger RNA consisting of a single triplet repeated over and over again is expected to be translated in a test tube into three distinct polypeptides depending on exactly where translation begins under conditions where translation does not need to start at an AUG. A researcher translated the mRNA sequence 5'-GUAGUAGUA… -3' in a test tube and discovered only two polypeptides, namely polyvaline and polyserine. Explain where these polypeptides come from and why there are only two.

Question 68

An mRNA with the sequence 5'-UGUGUGUG….-3' codes in a test tube for a polypeptide with the alternating amino acid sequence Cys-Val-Cys-Val-…. You purify charged tRNAs carrying cysteine, whose anticodons bind with the 5'-UGU-3' codon, and you chemically change the cysteine into alanine. If the charged tRNA with the altered amino acid is used in the mixture for a test tube translation (under conditions in which translation does not need to start at an AUG), what polypeptide results from translating 5'-UGUGUGUG….-3'?

Question 69

Which one of the following would LEAST likely be used during the initiation phase of translation?

A)elongation factors
B)tRNA
C)small ribosomal subunits
D)initiation factors
E)mRNA

Question 70

Which of the following is a critical region of a tRNA molecule?

A)amino acid attachment site and start codon
B)anticodon loop and ribosome binding site
C)stop codon and Shine-Dalgarno sequence
D)amino acid attachment site and anticodon loop
E)ribosome binding site and 5 cap

Question 71

Examine the figure below, which depicts on stage in the process of translation in a eukaryote.



What happens next?

A)A polypeptide bond is formed between the arginine and the methionine, transferring the arginine to the P site.
B)A polypeptide bond is formed between the arginine and the valine, transferring the arginine to the P site.
C)A polypeptide bond is formed between the arginine and the valine, transferring the polypeptide to the A site.
D)A polypeptide bond is formed between the arginine and the methionine, transferring the polypeptide to the A site.

Question 72

Examine the figure below, which depicts one stage in the process of translation in a eukaryote. Where will the tRNA be when the large subunit of the ribosome joins the complex?

A)in the A site of the ribosome
B)in the P site of the ribosome
C)Ithe E site of the ribosome

Question 73

Which one of the following is NOT used during translation?

A)initiation factors
B)release factors
C)sigma factors
D)elongation factors
E)All of these choices are correct.

Question 74

Based on the standard genetic code, what polypeptide sequence (or sequences) would you expect to be translated from a messenger RNA with the sequence 5'-AUAUAUAUAU… -3' if translation were occurring in a laboratory setting in which translation can start anywhere along the mRNA molecule.

Question 75

In eukaryotes, the AUG codon that starts translation is:

A)at the 5' end of the mRNA.
B)adjacent to the 5' cap on the mRNA.
C)adjacent to a Shine-Dalgarno sequence.
D)the AUG nearest the 5' cap on the mRNA.
E)None of the other answer options is correct.

Question 76

An mRNA sequence consisting of an alternating sequence of two nucleotides (e.g., 5'-AUAUAU …-3') codes in a test tube for a polypeptide consisting of two alternating amino acids. This means that, in the table organizing the codons in the standard genetic code, the positions of the amino acids must be in:

A)different rows and different columns.
B)different rows but the same column.
C)the same row but different columns
D)None of the other answer options is correct.

Question 77

Which of the following codons is capable of terminating translation?

A)UAG
B)UAA
C)UGA
D)UAG and UAA
E)All of these choices are correct.

Question 78

In Kohrana's experiments, a messenger RNA with the sequence 5'-UUUUUU… -3' coded for a polypeptide with the sequence Phe-Phe-Phe-Phe-…. (polyphenylalanine). Imagine that he added a single nucleotide bearing the base G to one end of the mRNA. The resulting polypeptide was polyphenylalanine with a single Leu at the carboxyl (-COOH) end. Did Kohrana add the G to the 5' or the 3' end of the mRNA?

Question 79

Ribosomes in prokaryotes and eukaryotes are:

A)identical in structure and translate using the same genetic code.
B)identical in structure but translate using different genetic codes.
C)similar in structure and translate using the same genetic code.
D)similar in structure and translate using different genetic codes.

Question 80

In which of the following ribosomal sites does the anticodon of a tRNA pair completely with the mRNA codon?

A)the A site only
B)the P site only
C)the A site and the P site
D)the P site and the E site
E)the A site, the P site, and the E site