Deck 9: Proteins and Their Synthesis

Question 1

In Neurospora,a linear biochemical pathway synthesizes an amino acid Z.E1,E2,and E3 are enzymes that catalyze the three reactions. Null mutants for the enzyme E2 gene will grow on minimal medium supplemented with compounds:

A)W or X.
B)Y or Z.
C)W or X or Y or Z.
D)Z only.
E)W only.

Answer 1

Y or Z.

Question 2

Two gametes,each carrying a mutant recessive allele for a different gene/enzyme in the adenine biosynthetic pathway,come together to form a diploid embryo.The individual derived from this embryo will display a:

A)lethal phenotype in media lacking adenine supplementation.
B)wild-type phenotype,capable of synthesizing adenine.
C)a weak adenine requirement for survival (intermediate phenotype).
D)a profound defect in adenine synthesis as two enzymes are missing.
E)embryonic lethality.

Answer 2

B

Question 3

DNA probes are often synthesized based on knowledge of the protein produced by a gene.What might be a potential problem of synthesizing DNA probes in this manner?

A)The deduced DNA probe would be missing introns associated with prokaryotic genes.
B)Because codons in DNA are redundant,knowing which codon to assign an amino acid may be difficult.
C)The deduced DNA probe would be missing introns associated with eukaryotic genes.
D)Because codons in DNA are redundant,knowing which codon to assign an amino acid may be difficult,as well as the deduced DNA probe would be missing introns associated with eukaryotic genes.
E)None of the answer options are correct.

Answer 3

D

Question 4

Formation of the peptide bond could be described as:

A)a spontaneous reaction between two peptides,forming a covalent bond.
B)a ribosome-catalyzed process occurring in the nucleus.
C)a tRNA catalyzed process.
D)a ribosome-catalyzed dehydration reaction (H₂0 released).
E)transcription,a key process in gene expression.

Question 5

The amber mutations initially discovered by Sydney Brenner and colleagues was eventually shown to include a(n):

A)unusual amino acid that generated an amber color in the affected bacteria.
B)premature stop codon within the gene's open reading frame.
C)insertion mutation that creates a translational frameshift.
D)previously unknown signal for speeding the translation process.
E)a deletion mutation that creates a translational frameshift.

Question 6

The alpha-helix structure is stabilized by:

A)covalent bonds between adjacent functional groups.
B)hydrogen bonds along the peptide backbone.
C)association with helicase stabilizing enzymes.
D)noncovalent interactions with water.
E)cationic elements found in water solutions.

Question 7

Which of the following constitutes the primary structure of a protein?

A)the folding of a polypeptide chain
B)the linear sequence of amino acids in a polypeptide chain
C)the polypeptide chains stacked on top of each other
D)a pleated sheet
E)several polypeptide subunits

Question 8

We know that DNA and RNA (each with four nucleotide components)both use a three nucleotide genetic code and 64 codons (4³ = 64).Knowing that the minimum number of codons for the genetic code is 21 (20 amino acids,1 stop codon),what codon size would be required if only three nucleotides were present in the genome?

A)2 nucleotides per codon
B)3 nucleotides per codon
C)4 nucleotides per codon
D)5 nucleotides per codon
E)6 nucleotides per codon

Question 9

Fibrous proteins contain a structure that is:

A)rounded and compact.
B)globular.
C)only comprised of secondary structure.
D)linear/extended.
E)random and variable.

Question 10

A biochemical pathway making flower pigments shows the following sequential color conversions (each arrow represents an enzyme-catalyzed step).
A plant is homozygous for mutations in enzyme "B," inactivating the active site for this enzyme.The resulting flowers will be:

A)orange.
B)blue.
C)yellow.
D)red.
E)white.

Question 11

How many nucleotides would be expected for a gene coding for a protein with 300 amino acids?

A)300
B)100
C)600
D)1200
E)900

Question 12

In vitro (in a test tube)translation of a synthetic RNA with the repeating sequence (AGA)₂₀ would produce which of the following?

A)polypeptides containing arginine,polypeptides containing glutamic acid,and polypeptides containing lysine
B)polypeptides containing arginine
C)polypeptides containing a mixture of amino acids (mostly arginine,glutamic acid,and lysine)
D)no translation product because the translation start site was not included on the RNA
E)polypeptides starting with methionine,followed by arginine additions

Question 13

Francis Crick proposed "adapter" molecules to serve as an intermediary between mRNA and the synthesis of protein.Key to any model of how RNA is "read" in the process of protein synthesis would be a consideration of how:

A)amino acids are selected for addition to the new protein.
B)the RNA code was read by the translation enzyme.
C)peptide bonds are formed.
D)one codon could select a specific amino acid.
E)All of the answer options are correct.

Question 14

While one gene usually specifies one enzyme,which of the following is/are NOT true?

A)One gene can specify a single enzyme if that enzyme contains a single type of polypeptide chain.
B)One gene can specify parts of two enzymes if the enzymes have one type of polypeptide chain in common.
C)One enzyme may be determined by two genes if the enzyme has two different types of polypeptide chains.
D)One mutation may cause multiple nutritional requirements if it interferes with the synthesis of an intermediate common to several pathways.
E)Two mutations in the same gene can never have different effects,even when studied in great biochemical detail.

Question 15

The use of proflavin-induced mutations (like FCO)in the rII genome was found to experimentally support a three-nucleotide explanation for the genetic code because:

A)an insertion mutation could be suppressed by a deletion mutation.
B)the rII genes are easier to mutate than other genes.
C)proflavin was an inexpensive mutagenic compound.
D)a gene with three insertions or three deletions could sometimes provide a functional protein.
E)the rII gene encoded a protein with exactly the correct number of amino acids,as would be explained by a three nucleotide genetic code.

Question 16

The three-dimensional structure of an active hemoglobin (heterotetramer)structure would be referred to as its:

A)primary structure.
B)secondary structure.
C)tertiary structure.
D)quaternary structure.
E)quinternary structure.

Question 17

Which could be an anticodon for the amino acid isoleucine?

A)UAA
B)UAG
C)UAU
D)UAA and UAG
E)UAA,UAG,and UAU

Question 18

In the 1940s,George Beadle and Edward Tatum developed the one-gene-one-polypeptide hypothesis by mutating the genes of Neurospora crassa (bread mold).They identified mutants that were unable to synthesize amino acids,such as arginine.When multiple mutant strains were identified for a single trait (adenine synthesis deficient),they showed that:

A)all the mutants encoded the same single enzyme.
B)genes were transcribed before being translated.
C)each step in the biochemical pathway was mediated by an enzyme encoded by a single gene.
D)the biosynthesis of arginine could occur,even with mutated enzymes.
E)separate genes/enzymes performed identical steps in the pathway.

Question 19

Five nutritional mutants in Neurospora were independently isolated.They all require compound F to grow.Intermediate compounds in the biosynthesis of compound F are known and tested for their ability to support the growth of each mutant.The results are given in the table below,where "+" indicates growth and "0" indicates no growth. $\quad$ $\quad$ $\quad$ $\quad$ $\quad$$\text { Compounds }$
$\begin{array}{lllllll}\text { Mutants }&\text { A } &\text {B} &\text { C }&\text { D }&\text { E }&\text {F}\\\hline1 & 0 & 0 & 0 & + & 0 & + \\2 & 0 & + & 0 & + & 0 & + \\3 & 0 & 0 & 0 & 0 & 0 & + \\4 & 0 & + & + & + & 0 & + \\5 & + & + & + & + & 0 & +\end{array}$
Assuming a linear pathway,what is the order of the compounds A through F?

A)EABCDF
B)ECBDAF
C)ECDBAF
D)EACBDF
E)EBACDF

Question 20

Degeneracy in the genetic code is best illustrated by:

A)stop codons.
B)threonine codons.
C)tryptophan codons.
D)methionine codons.
E)operator sequences.

Question 21

All of the following are associated with ribosomes except:

A)decoding center.
B)peptidyltransferase center.
C)exit site.
D)groove for RNA binding.
E)groove for DNA binding.

Question 22

How does a nonsense suppressor mutation prevent amber mutants from terminating their polypeptides prematurely?

A)The mutation turns the amber codon back into a wild-type codon.
B)The mutation alters a tRNA so that it reads the amber codon and inserts an amino acid.
C)The mutation alters the release factors that would halt synthesis.
D)The mutation results in a wobble that allows synthesis to continue.
E)The mutation replaces the amber codon with an ochre codon.

Question 23

Draw the general formula for an amino acid.What is it that distinguishes the 20 amino acids known to exist in proteins?

Question 24

Distinguish between tRNAs and rRNAs.What does it mean for an RNA to be
functional?

Question 25

A tRNA with the anticodon 3′-ACC-5′ would carry the amino acid:

A)phenylalanine.
B)tyrosine.
C)serine.
D)threonine.
E)tryptophan.

Question 26

The ribosome in eukaryotes can be described as being composed of:

A)rRNAs and over 50 different proteins.
B)a 50S subunit and a 30S subunit,forming a 70S ribosome.
C)proteins in quaternary structure,binding tRNAs within the nucleus.
D)a large enzyme complex that is found only on the endoplasmic reticulum membrane.
E)rRNAs,protein subunits,ATP,and aminoacyl-tRNA synthetase.

Question 27

The A site,P site,and E site each control ______________ (in order)during translation.

A)binding incoming tRNAs (A),retention of the peptide chain during elongation (P),exit of deacylated tRNAs (E)
B)activation of tRNAs (A),protease-based release of the protein product (P),exit of empty rRNAs (E)
C)activation of ribosome activity (A),processing of amino acids (P),elongation of the peptide chain (E)
D)amino acid bond transfer (A),protein processing (P),and elongation of the peptide chain (E)
E)binding incoming tRNAs (A),retention of the peptide chain during elongation (P),exit of deacylated tRNAs (E)as well as activation of ribosome activity (A),processing of amino acids (P),elongation of the peptide chain €

Question 28

Which of the following are types of posttranslational processing that will not occur in a prokaryote?

A)addition of a phosphate group
B)removal of a phosphate group
C)addition of a co-factor
D)cleavage of a mitochondrial targeting sequence
E)None of the answer options are correct.

Question 29

Macrolides are antibiotics that kill bacteria by:

A)inhibiting tRNA charging.
B)releasing the protein before translation is complete.
C)blocking the exit tunnel for "empty tRNAs."
D)competing for tRNA binding in the "A site."
E)causing tRNAs to be destroyed.

Question 30

In bacteria,the Shine-Dalgarno sequence is found on the mRNA and is recognized by the ________________________ to reveal __________________________.

A)the 16S rRNA;the translation STOP codon
B)the 30S subunit;the translation START codon
C)initiator tRNA;the translation START codon
D)ribosome A site;the translation START codon
E)amber tRNA;the translation STOP codon

Question 31

During the initiation of prokaryotic translation,a defect in IF3 function would generate:

A)inefficient association of the 30S and 50S subunits.
B)proteolysis of the 50S subunit.
C)an inability of tRNA and mRNA binding to the 30S subunit.
D)premature association of the 30S and 50S subunits.
E)normal progression of translation (no defect).

Question 32

The aminoacyl-tRNA synthetase enzymes are responsible for:

A)synthesizing tRNA molecules in the nucleus from rRNA genes.
B)adding amino acids to appropriate tRNAs (charging the tRNA).
C)regulating the process of amino acid synthesis.
D)catalyzing the enzymatic step of peptide bond formation during translation.
E)matching each tRNA with the appropriate mRNA codon.

Question 33

Signal peptidase activity is responsible for:

A)directing defective proteins to the ubiquitin-proteasome pathway.
B)adding a signal phosphate group to some proteins,regulating their activity.
C)removing a hydrophobic secretion signal from the N-terminus of a protein.
D)adding a signal glycosylation modification to a new protein.
E)destroying peptide bonds in defective proteins.

Question 34

The "wobble" base is a tRNA site where:

A)inosine nucleotide can sometimes be found.
B)mutations often create severe mutations in the encoded protein.
C)the amino acid is closely located to facilitate its addition to the new protein.
D)aminoacyl-tRNAs read the tRNA specificity.
E)tRNAs display structural instability.

Question 35

The DNA sense strand for a particular amino acid is 5′-ATG-3′.What RNA sequence would be transcribed for this codon,what tRNA anticodon would recognize it,and what amino acid would be added in response to this codon?

A)5′-CAU-3′ (RNA sense);3′-GUA-5′ (tRNA anticodon);histidine
B)3′-AUG-5′ (RNA sense);3′-UAC-5′ (tRNA anticodon);valine
C)5′-CAU-3′ (RNA sense);3′-AUG-5' (tRNA anticodon);histidine
D)5′-UUU-3′ (RNA sense);3′-AAA-5′ (tRNA anticodon);phenylalanine
E)5′-AUG-3′ (RNA sense);3′-UAC-5′ (tRNA anticodon);methionine

Question 36

The "wobble" base is less important than the other two nucleotides in a codon and is found:

A)at the 5′ end of the RNA codon's sense strand.
B)at the 3′ end of the mRNA codon's antisense strand.
C)at the 3′ end of the tRNA anticodon.
D)at the 5′ end of the tRNA anticodon.
E)within a tRNA hairpin loop structure.

Question 37

Evidence that amino acids were "illiterate," or passively added to the newly synthesized protein at the direction of the tRNA to which they are attached,was derived from experiments with:

A)nickel hydride,altering the amino acids attached to charged tRNAs to determine if they were still utilized by the ribosome.
B)proflavin-based mutations on subsets of anticodons to determine if the mutations affect the charging of tRNAs.
C)abnormal forms of the aminoacyl-tRNA transferase enzymes.
D)chemically synthesized,novel amino acid structures.
E)eukaryotic ribosomes combined with prokaryotic tRNAs.

Question 38

The anticodon on the tRNA molecule:

A)binds to the mRNA in a complementary fashion.
B)is oriented and written in the 5′ $\to$ 3′ direction.
C)is a catalytic part of protein synthesis.
D)is the same for all tRNA molecules.
E)contains amino-acyl-tRNA synthetase.

Question 39

The ribosome is the primary site of:

A)oxidative phosphorylation.
B)protein packaging.
C)protein synthesis.
D)cellular respiration.
E)amino acid storage.

Question 40

The proteome for humans is about 70,000 proteins whereas only 21,000 protein-coding genes have been discovered.Which statement could explain this?

A)Splicing of eukaryotic mRNA can result in the production of more than one protein from a single gene.
B)Many of our proteins are actually produced by symbiotic organisms in our bodies.
C)Splicing of eukaryotic mRNA can result in the production of more than one protein from a single gene and many of our proteins are actually produced by symbiotic organisms in our bodies.
D)We do not know enough about the human genome to explain this fact.

Question 41

Describe the types of RNAs participating in translation.

Question 42

NASA scientists brought back from Mars a molecule they think is similar to DNA.Just like DNA,it is transcribed into an mRNA-like molecule.Unlike mRNA,though,it appears to use only three bases (A,C,and T).Assuming that proteins were still made from this mRNA molecule and it was thought that 30 amino acids existed for this organism,what is the minimum number of bases likely to be in a codon? Explain your answer.

Question 43

You believe you created a protein translation machine that operates outside of the cell.If you combine the "translation machine" with an mRNA and charged tRNAs,a protein product is generated.However,as you do additional experiments,you find that though the correct amino acids are joined together,the protein is nonfunctional.What might be missing in your system,causing these synthesized proteins to lack activity?

Question 44

Diagram the process of translation,showing the sequential steps of tRNA entry,amino acid transfer,and eventual tRNA release.This is a multi-step process,so you will need to diagram at least three consecutive steps as a new tRNA moves through this process.

Question 45

Crick,Brenner,and colleagues conducted experiments in 1961 using mutants in the rII locus of the T4 phage.They were able to show that certain mutations could be reversed if they first consisted of an insertion and then a deletion (or first a deletion and then an addition).Explain why-in Crick and colleagues' experiments-that the "revertant" phenotypes did not look exactly like the wild types.

Question 46

A gene makes a polypeptide 30 amino acids long containing an alternating sequence of phenylalanine and tyrosine.Assuming Phe = UUU and Tyr = UAU in mRNA,what are the sequences of nucleotides corresponding to this sequence in the following?
a)the mRNA strand (sense)
b)the non-template DNA strand (antisense or noncoding strand)
c)the template DNA strand (sense or coding stand)
d)the tRNA anticodon
e)Do you think that the sequence is the only possible one for these amino acids? Assume that the wobble position for each of these codons can be changed to the base cytosine.Answer questions (a)through (d)again with this new information.

Question 47

Many antibiotics operate by interfering with translation-associated process or other essential cellular functions.How does tetracycline inhibit cellular translation? If tetracycline inhibits such an important process,why is it not lethal to humans when ingested to treat infection?

Question 48

You found a mouse gene sequence containing an open reading frame that should produce a 43 kDa protein.You express this protein in cultured mouse cells by transforming the cells with a plasmid bearing your gene of interest.When you isolate proteins from these cells and probe for your protein of interest,you find that the detected protein is 49 kDa.Why might your protein be larger than expected when analyzed by immunoblot?

Question 49

Many antibiotics target prokaryotic ribosomal function,blocking translation and causing rapid death in susceptible microbial populations.You have been assigned to a structure-based drug design project for a biotechnology company.In order for an antibiotic to be effective,it must be able to block an essential ribosomal function,and the drug must have access to the portion of the enzyme or enzyme complex being targeted.What processes/enzymes might you target in your drug design?

Question 50

Why is the attachment of an amino acid to the correct tRNA considered to be such an important step in protein synthesis?

Question 51

Which codons are susceptible to being converted to a "UAG" STOP codon with only a single nucleotide mutation?

Question 52

What is post-translational processing? Why is it important for protein function?

Question 53

Describe how it was determined that the genetic code was not overlapping.What evidence was used to support this?