Practice Questions - Translation & Amino Acids Proteins PDF

Practice questions: Translation, Amino acids and proteins 1. A researcher is studying diet soft drinks containing aspartame. These drinks have the warning that phenylketonurics should not consume drinks containing this sweetener. Chemical analysis shows that aspartame is an artificial di...

Practice questions: Translation, Amino acids and proteins 1. A researcher is studying diet soft drinks containing aspartame. These drinks have the warning that phenylketonurics should not consume drinks containing this sweetener. Chemical analysis shows that aspartame is an artificial dipeptide sweetener that contains phenylalanine. Which of the following best describes this amino acid? A. Contains a hydroxyl group B. An aromatic amino acid C. Contains a sulfhydryl group D. A dietary nonessential amino acid E. A branched-chain amino acid 2. A researcher is studying the neurotransmitter GABA. He observes that it can be formed by the decarboxylation of the alpha-carboxyl group of a specific amino acid. Which of the following amino acids is most likely a precursor of this neurotransmitter? A. Glycine B. Tryptophan C. Glutamate D. Aspartate E. Glutamine F. Tyrosine 3. A researcher is studying the secondary structure of an enzyme involved in intermediary metabolism. He observes that it contains alpha-helices. Which of the following best describes this structure? A. Stabilized by peptide bonds B. Stabilized by phosphodiester linkages C. Contains amino acids with their side chains towards the outside of the helix D. A structure favored by a high amount of proline residues E. Retained when the protein is heated to high temperatures 4. A research group is studying covalent bonds and noncovalent bonds that are found in the tertiary structure of proteins. One group studies covalent bonds which are formed by the side chains of amino acids. Which of the following bonds is most likely being studied by this research group? A. Ionic bonds between aspartate and lysine B. Hydrogen bonds between serine and glutamate C. van der Waals forces found in the alpha-helix D. Disulfide bonds between two cysteine residues E. Hydrophobic forces between valine and isoleucine 5. A research group is studying E. coli metabolism. It is observed that glucose may be converted to chorismate which is a common intermediate in the pathways for histidine, phenylalanine, tyrosine, and tryptophan synthesis. It is observed that if tryptophan is needed the cell forms an mRNA that allows the production of the five enzymes needed for the trp synthesis pathway to function. Which of the following best describes gene expression in these bacteria? A. Five mRNA’s are produced for the pathway which allow production of the five enzymes B. One polypeptide is post-translationally processed to produce five enzymes  C. Some internal AUG sequences must be recognized as start codons D. Formyl-methionine is incorporated into the polypeptide when the ribosome recognizes the AUG codons on this mRNA E. The AUG start codon on this mRNA is found in an intron 6. A researcher is studying translation and the RNA required for this process. The figure shows the various positions of nucleotides in the t-RNA and mRNA. Which of the following positions best indicates the first nucleotide of the anticodon? A. 1 B. 2 C. 3 D. 4 E. 5 F. 6 7. A research laboratory studies a disease causing gene that leads to loss of function of an enzyme in a metabolic pathway. Karyotyping and DNA microarray shows that the chromosome structure is unchanged. Northern blot analysis shows no change in the mRNA transcript of the gene. Western blot shows a smaller than normal protein is formed. Which of the following mutations is most likely consistent with these findings? A. One base pair insertion in an exon B. Insertion of GCG in an exon C. The codon CCC is mutated to CCG D. Splice site mutation E. 99% reduction in promoter function 8. A researcher is studying insulin which undergoes modification after it has been synthesized. It is observed that the primary insulin translation product undergoes modifications to produce the mature insulin hormone. Which of the following modifications is most likely observed during this process? A. Phosphorylation of serine residues B. Hydrolytic cleavage of specific peptide bonds C. Addition of sugar residues to the protein (glycosylation) D. Chemical modification of some amino acid side chains E. Removal of formyl-methionine groups from the N-terminal end of the protein  9. A researcher has developed a bacterial strain in the laboratory with reduced rates of translation. It has a mutation which confers decreased activity in peptide bond formation during ribosomal protein synthesis. A Mutation in which of the following is most consistent with these findings? A. The EF-Tu protein B. One of the ribosomal proteins C. One of the ribosomal RNAs D. The Shine-Dalgarno sequence of the mRNA E. The ribosomal protein release factors 10. A research group is investigating the structure and function of a membrane transport protein. One group discovers a single base substitution in the gene for the protein. They observe that this causes the loss of an important alpha-helical segment of the protein. Which of the following codon changes best explains these findings? (Refer to the standard genetic code table) (Please note that a standard table showing the genetic code would be included if this question were on an exam). A. CUC to CCC B. GUU to GCU C. UUG to CUG D. AUC to GUC E. GUG to CUG 11. A researcher working for NASA examines a rock sample returned by a space probe sent to the planet Mars. She isolates viable microorganisms from the sample. It is observed that the organism utilizes a genetic code that initially appeared to be the same as that found in living bacterial cells on earth. Five properties of the Martian code are listed below. Which of the properties of the code in the novel organism is most likely different from the terrestrial (earth) genetic code? A. Each codon consisted of three bases B. An amino acid could have more than one codon C. The genetic code was overlapping D. UAA acted as a termination codon E. All proteins started with formyl-methionine 12. A 56-year-old man is admitted to hospital because of a 6-day history of fever and productive cough. Physical examination shows bilateral consolidation over both lungs and a diagnosis of bacterial pneumonia is made. He is prescribed the antibiotic erythromycin. Which of the following processes is most likely inhibited by this antibiotic? A. Peptide bond formation during translation in bacteria B. Initiation of translation in bacteria C. Initiation of transcription in bacteria D. Bacterial DNA replication E. The translocation step of translation in bacteria Additional Practice questions in the Lippincott’s Biochemistry textbook: DNA structure and replication: Pg 416 Questions: 29.2 – 29.5 Concept map on page 414 RNA structure, synthesis and processing: Pg 430 Questions: 30.1 - 30.5 Concept map on page 429 Protein synthesis: Pg 447 Questions: 31.1-31.3, 31.5-31.9 Concept map on page 446 Amino acids: Pg 12 Questions: 1.1-1.3 Concept map on page 11 Structure of proteins: Pg 24 Questions: 2.1-2.3 Concept map on page 23 Practice questions with explanations: 1. A researcher is studying diet soft drinks containing aspartame. These drinks have the warning that phenylketonurics should not consume drinks containing this sweetener. Chemical analysis shows that aspartame is an artificial dipeptide sweetener that contains phenylalanine. Which of the following best describes this amino acid? A. Contains a hydroxyl group Incorrect: a hydroxyl group is found in serine, threonine or tyrosine B. An aromatic amino acid correct, Phenylalanine is an aromatic amino acid. Phenylalanine is used to form tyrosine in humans (by hydroxylation); Tryptophan is also an aromatic amino acid C. Contains a sulfhydryl group Incorrect: a sulfhydryl (thiol) group is found in cysteine D. A dietary nonessential amino acid Incorrect: phenylalanine is a dietary essential amino acid E. A branched-chain amino acid Incorrect: branched-chain amino acids are valine, leucine and isoleucine 2. A researcher is studying the neurotransmitter GABA. He observes that it can be formed by the decarboxylation of the alpha-carboxyl group of a specific amino acid. Which of the following amino acids is most likely a precursor of this neurotransmitter? A. Glycine : Incorrect: glycine is not decarboxylated B. Tryptophan: Incorrect: tryptophan is the precursor of serotonin C. Glutamate correct: Glutamic acid or glutamate is decarboxylated to form GABA (gamma- aminobutyric acid). GABA is an inhibitory neurotransmitter D. Aspartate: Incorrect: aspartate is not used to form GABA, does not have a gamma-carboxyl group E. Glutamine: Incorrect: glutamine needs first to be deaminated to form glutamate F. Tyrosine: Incorrect: : Tyrosine is a precursor of catecholamines (dopamine, norepinephrine and epinephrine) 3. A researcher is studying the secondary structure of an enzyme involved in intermediary metabolism. He observes that it contains alpha-helices. Which of the following best describes this structure? A. Stabilized by peptide bonds Incorrect: The primary structure is stabilized by peptide bonds. The α- helices are stabilized by hydrogen bonds B. Stabilized by phosphodiester linkages Incorrect: Phosphodiester linkages are found in nucleic acids (DNA and RNA) C. Contains amino acids with their side chains towards the outside of the helix – Correct: The side chains of amino acids in the alpha helix are oriented towards the outside of the helix  D. A structure favored by a high amount of proline residues Incorrect: Proline disrupts the formation of alpha-helices E. Retained when the protein is heated to high temperatures Incorrect: On heating, proteins lose their secondary, tertiary and quaternary structures and become denatured – only the primary structure is intact 4. A research group is studying covalent bonds and noncovalent bonds that are found in the tertiary structure of proteins. One group studies covalent bonds which are formed by the side chains of amino acids. Which of the following bonds is most likely being studied by this research group? A. Ionic bonds between aspartate and lysine Incorrect: the bonds between aspartate and lysine are noncovalent ionic bonds B. Hydrogen bonds between serine and glutamate Incorrect: hydrogen bonds between serine and glutamate are noncovalent bonds C. van der Waals forces found in the alpha-helix Incorrect: van der Waals forces found in the alpha- helix are very weak noncovalent bonds D. Disulfide bonds between two cysteine residues correct. Disulfide bonds are generally not broken during conformational change or denaturation. Special reagents like sodium dodecyl sulfate (SDS) to cleave the disulfide linkages. Disulfide links are covalent bonds between cysteine residues. E. Hydrophobic forces between valine and isoleucine Incorrect, hydrophobic forces between valine and isoleucine side chains are noncovalent 5. A research group is studying E. coli metabolism. It is observed that glucose may be converted to chorismate which is a common intermediate in the pathways for histidine, phenylalanine, tyrosine, and tryptophan synthesis. It is observed that if tryptophan is needed the cell forms an mRNA that allows the production of the five enzymes needed for the trp synthesis pathway to function. Which of the following best describes gene expression in these bacteria? A. Five mRNA’s are produced for the pathway which allow production of the five enzymes : No, this is bacteria, the typical mRNA for a biosynthetic reaction is polycistronic, meaning that one mRNA will be used for the synthesis of all the enzymes needed for that pathway. This provides a strategy of regulation – it simplifies things for the bacterial cell B. One polypeptide is post-translationally processed to produce five enzymes No, This will not happen in bacteria – this is like invoking a complex solution to a simple problem: instead the bacteria forms a polycistronic mRNA that contains all the messages that would fall under the same regulation In eukaryotes, there are examples of this post-translational processing: for instance, some peptide neurotransmitters (encephalins, endorphins, others) are derived from a larger precursor polypeptide that is broken up to yield many other smaller neurotransmitters (neuropeptides). C. Some internal AUG sequences must be recognized as start codons This is the correct answer – Since there are multiple open reading frames for the ribosome to recognize on a polycistronic mRNA, some of those AUG codons that come after the first AUG must be recognized as ‘start’ for protein synthesis. Remember, the first AUG of the protein starts with the formyl-Met, then the internal AUG (for that protein) get the normal Met The next protein that is produced though, also must start with the formyl-Met D. Formyl-methionine is incorporated into the polypeptide when the ribosome recognizes the AUG codons on this mRNA – This is not correct. This is true only for the ‘first’ codon of each open reading frame found on the mRNA.  E. The AUG start codon on this mRNA is found in an intron – Incorrect: Remember - introns are only found in the eukaryote 6. A researcher is studying translation and the RNA required for this process. The figure shows the various positions of nucleotides in the t-RNA and mRNA. Which of the following positions best indicates the first nucleotide of the anticodon? A. 1 – is the first base of the codon B. 2 – is the third base of the anticodon C. 3 – this is the 3’ end of the t-RNA and the site where the amino acid binds to the t-RNA D. 4 – This is the 5’ end of the t-RNA E. 5 – Correct answer – This is the site of the wobble in codon anticodon interactions (non- traditional base pairing between codon and anticodon) F. 6 – this is the 3rd base of the codon and in the site of wobble in codon –anticodon interactions Note the naming convention of nucleic acids We always name nucleic acids (NA) from the 5’ to the 3’ direction. Notice that when the anticodon of the tRNA is base paired with the codon of mRNA, the directionality must be reversed. We call this antiparallel, and the sequences will hybridize when they are complimentary 7. A research laboratory studies a disease causing gene that leads to loss of function of an enzyme in a metabolic pathway. Karyotyping and DNA microarray shows that the chromosome structure is unchanged. Northern blot analysis shows no change in the mRNA transcript of the gene. Western blot shows a smaller than normal protein is formed. Which of the following mutations is most likely consistent with these findings? A. One base pair insertion in an exon – Correct answer Will not alter genomic structure Will not alter mRNA (usually) Will lead to frameshift, and likely to form an early stop codon – leads to truncated protein B. Insertion of GCG in an exon Will lead to the incorporation of one more amino acid into the polypeptide This will not change the apparent size of the protein on a typical western blot, since the size increase is very minimal  Use the table of the genetic code in your handout to determine which amino acid is introduced into the protein as a result of the mutation. GCG codes for Alanine C. The codon CCC is mutated to CCG This may change one amino acid into another or may be silent Which amino acid has been changed, what is it changed into, use the genetic code chart to decipher this – From the genetic code table, CCC is Proline is mutated to CCG which is also Proline – This is a silent mutation. Note that since the mutation is at the 3rd base of the codon, there is no change in the amino acid at this position as a result of this mutation (degeneracy of the codon) D. Splice site mutation This leads to a splicing defect. As a result of the splicing defect, the mRNA is shorter or longer than normal, which is NOT observed in the Northern blot in this patient E. 99% reduction in promoter function This will lead to a reduced level of mRNA expression, and the signal on the Northern blot will be less intense than in the normal control. There would be reduced transcription and reduced translation. The protein would not be smaller than normal, it would be reduced amounts of the protein 8. A researcher is studying insulin which undergoes modification after it has been synthesized. It is observed that the primary insulin translation product undergoes modifications to produce the mature insulin hormone. Which of the following modifications is most likely observed during this process? A. Phosphorylation of serine residues : Incorrect – This modification occurs in regulatory enzymes by protein kinase A in the presence of glucagon B. Hydrolytic cleavage of specific peptide bonds – Correct - removal of signal peptide and C peptide to convert pre-proinsulin to mature insulin. Inter and intra-chain disulfide bonds are created between the A and B chains of insulin C. Addition of sugar residues to the protein (glycosylation) – Occurs in glycoproteins. Insulin is NOT a glycoprotein D. Chemical modification of some amino acid side chains – like hydroxylation occurs post- translationally in proline and lysine residues in collagen E. Removal of formyl-methionine groups from the N-terminal end of the protein – this post- translational modification occurs only in prokaryotes and not in eukaryotes 9. A researcher has developed a bacterial strain in the laboratory with reduced rates of translation. It has a mutation which confers decreased activity in peptide bond formation during ribosomal protein synthesis. A Mutation in which of the following is most consistent with these findings? A. The EF-Tu protein – Incorrect: is a protein factor required for the elongation step in prokaryotic translation B. One of the ribosomal proteins – Incorrect: The RNA component of the larger subunit of the ribosome has peptidyl transferase activity C. One of the ribosomal RNAs – Correct answer - catalytic ribosomal RNA on the larger subunit participates in the activity of peptidyl transferase and facilitates peptide bond formation during translation (protein synthesis) D. The Shine-Dalgarno sequence of the mRNA Incorrect – Shine Dalgarno sequence participates in the initiation of prokaryotic translation and helps in alignment of the mRNA on the ribosome E. The ribosomal protein release factors Incorrect: participate in termination of translation 10. A research group is investigating the structure and function of a membrane transport protein. One group discovers a single base substitution in the gene for the protein. They observe that this causes the loss of an important alpha-helical segment of the protein. Which of the following codon changes best explains these findings? (Refer to the standard genetic code table) (Please note that a standard table showing the genetic code would be included if this question were on an exam). A. CUC to CCC – Correct answer - Leucine to Proline - the mutation produces a proline that cannot fit into an alpha-helix – Proline is an alpha helix breaker B. GUU to GCU Incorrect: Valine to Alanine (Branched chain amino acid to alanine – both are hydrophobic amino acids) C. UUG to CUG Incorrect: Leucine to leucine – this is a silent mutation – no change in structure D. AUC to GUC Incorrect: Isoleucine to Valine – May have minimal effect on the function as both are branched chain amino acids E. GUG to CUG Incorrect: Valine to Histidine – Branched chain amino acid is replaced by a positively charged amino acid – this would change the charge on the protein and may affect function 11. A researcher working for NASA examines a rock sample returned by a space probe sent to the planet Mars. She isolates viable microorganisms from the sample. It is observed that the organism utilizes a genetic code that initially appeared to be the same as that found in living bacterial cells on earth. Five properties of the Martian code are listed below. Which of the properties of the code in the novel organism is most likely different from the terrestrial (earth) genetic code? A. Each codon consisted of three bases – The codon has 3 bases (triplet). Each triplet codon codes for an amino acid B. An amino acid could have more than one codon – This is degeneracy of the codon C. The genetic code was overlapping – Correct answer - the genetic code found in all known terrestrial organisms is a non-overlapping code D. UAA acted as a termination codon – According to the codon table, UAA, UGA and UAG are termination or STOP codons. They do NOT code for any amino acid E. All proteins started with formyl-methionine – Proteins in bacteria are synthesized using formyl- methionine as the initiator amino acid. However, the f-Met amino acid is generally removed as a result of post-translational processing. Eukaryotic protein synthesis uses AUG as the start codon which codes for Methionine. 12. A 56-year-old man is admitted to hospital because of a 6-day history of fever and productive cough. Physical examination shows bilateral consolidation over both lungs and a diagnosis of bacterial pneumonia is made. He is prescribed the antibiotic erythromycin. Which of the following processes is most likely inhibited by this antibiotic? A. Peptide bond formation during translation in bacteria – Incorrect: This is the mechanism of action of chloramphenicol. Chloramphenicol inhibits bacterial peptidyl transferase activity. Cycloheximide inhibits eukaryotic peptidyl transferase activity on the ribosome. Tetracycline inhibits the aminoacyl tRNA entry into the A site of the ribosome. B. Initiation of translation in bacteria – Incorrect: Streptomycin inhibits initiation of translation C. Initiation of transcription in bacteria – Incorrect: Rifamycin inhibits prokaryotic RNA polymerase and hence inhibits transcription  D. Bacterial DNA replication – Incorrect: DNA gyrase inhibitors like fluoroquinolones and ciprofloxacin inhibit bacterial DNA replication. Actinomycin D inhibits DNA replication and transcription. Cytarabin, Azidothymidine inhibit replication and cell division E. The translocation step of translation in bacteria – Correct answer – Erythromycin inhibits translocation step in the elongation step of bacterial protein synthesis Also note that bacterial translation inhibitors are chloramphenicol, streptomycin, tetracycline and erythromycin. Bacterial transcription inhibitor is rifamycin (Inhibits prokaryotic RNA polymerase). Bacterial DNA gyrase and inhibitors of replication are Fluoroquinolones and ciprofloxacin. Eukaryotic inhibitors of translation are cycloheximide (inhibits peptidyl transferase activity) and diphtheria toxin. Eukaryotic transcription inhibitors are alpha-amanitin (inhibits eukaryotic RNA polymerase-II) and actinomycin D (also inhibits replication) Inhibitors of DNA replication are the nucleoside analogs (cytarabine, azidothymidine), actinomycin-D (intercalating agent and disrupts the template).