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121 Cards in this Set
- Front
- Back
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One tRNA can recognize several degenerative codons. Which hypothesis is associated with that fact?
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Wobble hypothesis
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Name 3 unique structural features of tRNA.
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(Any three)
Nucleosides are highly modified Anticodon 3'-CCA acceptor arm for aminoacylation Many non-Watson Crick base pairs |
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Which of the following introduces a Stop codon?
a. Missense mutation b. Silent mutation c. Nonsense mutation d. None of the above |
c. Nonsense mutation
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Name the two tasks of aminoacyl-tRNA synthetase.
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Catalyzing the (amino acid specific) aminoacyl-AMP formation
tRNA is charged with the amino acid specified by mRNA |
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What is the function of ribosomes and what are the components in prokaryotes and eukaryotes.
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Site of protein synthesis
Composed of rRNA and proteins Prokaryotes: 30S + 50S = 70S 30S subunit contains 16S RNA & 21 proteins; 50S subunit contains 23S & 5S RNA & 32 proteins. Eukaryotes: 40S + 60S = 80S 40S subunit contains 18S RNA & 34 proteins; 60S subunit contains 28S, 5.8S, & 5S RNA & 50 proteins |
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What are the major differences in the initiation of ribosomal protein biosynthesis between prokaryotes and eukaryotes in respect to the N-terminal residue?
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N-terminal residue is formyl-methionine (fMet) in prokaryotes vs. methionine in eukaryotes
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What are the major differences in the initiation of ribosomal protein biosynthesis between prokaryotes and eukaryotes in respect to the selection of translation start site?
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Prokaryotes: Shine-Dalgarno seqeunce upstream of AUG start codon is recognized by 3'-end 16S rRNA.
Eukaryotes: eIF4 binds to 5' cap of mRNA and walks downstream to first AUG start codon. |
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Associate the following term with one of the steps in protein biosynthesis AND with prokaryotes or eukaryotes.
EF-Tu |
Elongation/Binding - Prokaryotes
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Associate the following term with one of the steps in protein biosynthesis AND with prokaryotes or eukaryotes.
eIF-3 |
Initiation - Eukaryotes
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Associate the following term with one of the steps in protein biosynthesis AND with prokaryotes or eukaryotes.
EF-G |
Elongation/translocation - Prokaryotes
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Associate the following term with one of the steps in protein biosynthesis AND with prokaryotes or eukaryotes.
IF-1 |
Initiation - Prokaryotes
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Associate the following term with one of the steps in protein biosynthesis AND with prokaryotes or eukaryotes.
RF-1 |
Termination/Release - Prokaryotes
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Name the 3 steps of elongation phase of ribosomal protein biosynthesis.
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Binding of aminoacyl tRNA
Transpeptidation Translocation |
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Name 3 different types of posttranslational modification.
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Phosphorylation, methylation, glycosylation, proteolysis, acetylation or disulfide formation
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Which region of the DNA does the RNA polymerase bind?
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Promoter
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Which region of the DNA sequence does the repressor bind?
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Operator
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Which of the following DNA sequences do you expect to be palindromic: promoter, operator or repressor and why?
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Operator
Characteristic for DNA that specifically binds proteins |
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Name 3 (of the 4 discussed) modes of regulation of tryptophan biosynthesis.
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Feedback inhibition
Transcriptional repression Attentuation Unregulated second promoter constitutively expresses TrpC and TrpB to prevent interruption of Trp biosynthesis under starvation conditions. |
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Why is "attenuation" as discussed in class (formation of different hairpins depending on condition) a regulatory mechanism that only exists in prokaryotes?
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Cooperative interaction between transcription and translation. Coupled transcription-translation only exists in prokaryotes where there is no compartmentalization.
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Which covalent modifications on the following biomolecules commonly affects gene expression in eukaryotes?
a. Histone b. DNA |
a. Acetylation
b. Methylation |
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What is meant by degeneracy of the genetic code?
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One amino acid is usually encoded by several triplet codons (except Trp and Met)
or Triplet codons allow 4^3 = 64 base permutations, encoding only 20 amino acids (and stop codons). |
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Why can one tRNA recognize several degenerate codons?
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Wobble base pairs possible between mRNA codon and tRNA anticodon.
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Define the term transition
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Purine-to-purine (A-->G) or pyrimidine-to-pyrimidine (C-->U) mutation
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Define the term transversion
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Purine-to-pyrimidine (A-->C) mutation or vice versa
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Define the term missense mutation
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Changes in amino acid code
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Define the term nonsense mutation
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Introduces a stop codon
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Define the term silent mutation
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Amino acid code remains unchanged (due to degeneracy)
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What are supressor mutations?
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The expression of nonsense mutations are suppressed
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Can you generalize which bases (or regions) in the tRNA determine with which amino acid the tRNA should be charged?
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No. Recognition elements vary from tRNA to tRNA.
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Like tRNAs, release factors can recognize certain mRNA codons. Which codons do they recognize and how do release factors structurally differ from tRNAs?
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They recognize Stop codons (UAA, UAG, UGA)
They are PROTEINS instead of RNA (shape and size similar) |
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What is the structural basis for the antibiotic activity of puromycin?
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(Two of the following)
Binding to A-site without need for elongation factors Structurally resembles the 3'-end of tyrosyl-tRNA^Tyr and thus competes with aminoacyl-tRNAs Transpeptidation cannot occur because of an amide bond between sugar and Tyr (instead of ester bond) leading to early termination |
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Give 2 examples of posttranslational modifications and describe their significances for one process each.
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(Any two)
Acetylation- Important for regulation of gene expression Phosphorylation - Regulates signaling to transcription factors Proteolytic processing - Required to generate active proteins Glycosylation (and sulfation) - Important to molecular recognition |
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Define the term repressor
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Protein that binds to the operator sequence to inhibit gene transcription
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Define the term operator
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DNA sequence to which the repressor binds
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Define the term promoter
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DNA sequence to which the RNA polymerase binds
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What is the major difference between the repressor of the lactose operon and the repressor of the tryptophan operon?
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If no inducer present, the Lac repressor binds to the operator, thus repressing gene expression
Trp repressor only binds to operator (and represses gene expression) when co-repressor (two tryptophan molecules) is present |
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What is feedback inhibition (in tryptophan biosynthesis)?
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The end product of biosynthesis (tryptophan) inhibits its own biosynthesis (ideally at an early stage) by enzyme inactivation.
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How does acetylation of histones affect gene expression; positively or negatively and why?
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Positively
Acetylation reduces the attraction of DNA and proteins, allowing a more open structure, facilitating RNA polymerase binding. |
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What are the two functions of the AUG codon?
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1. Encodes for methionine
2. Initiation signal for translation |
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Modification of tRNA is closely associated with the Wobble hypothesis. What is the Wobble hypothesis?
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One tRNA can recognize several degenerative codons because third anticodon position (5' end) is often times modified, with the formation of non-Watson-Crick base pairs possible.
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How could a frameshift be caused?
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Insertion/deletion of bases
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How do organisms (prokaryotes vs. eukaryotes) ensure that the correct reading frame is used?
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Prokaryotes: Sequential, non-overlapping reading frame
Eukaryotes: Collinear, non-overlapping, gap-free Ensures that the translation will occur only in one reading frame |
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Which enzyme aminoacylates tRNA and how is amino acid specificity and tRNA specificity ensured?
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Aminoacyl tRNA Synthetase
Correct amino acid for transfer onto tRNA (by catalyzing the amino acid specific aminoacyl-AMP formation). tRNA charged with the amino acid specified by the mRNA |
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In which direction does protein synthesis occur?
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5' --> 3'
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Name the steps in protein synthesis
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1. Initiation
2. Elongation 3. Termination 4. Posttranslational modification |
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What is the function of the Shine-Dalgarno sequence and how is it being recognized by the ribosome?
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Selection of translation start site in prokaryotes
Recognized by 3'-end of 16S rRNA of the ribosome |
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Which protein factors are required in protein synthesis: initiation for prokaryotes vs. eukaryotes?
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Prokaryotes: IF1, IF2, IF3
Eukaryotes: eIF-n |
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Which protein factors are required in protein synthesis: elongation for prokaryotes vs. eukaryotes?
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Prokaryotes: EF-Tu (binding), EF-G (translocation)
Eukaryotes: EF-1alpha (binding), EF-2 (translocation) |
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Which protein factors are required in protein synthesis: termination for prokaryotes vs. eukaryotes?
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Prokaryotes: RF-1, RF-2, RF-3
Eukaryotes: eRF |
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Name and briefly describe the 3 steps of the elongation phase of ribosomal protein biosynthesis.
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1. Binding - Binding of aminoacyl tRNA
2. Transpeptidation - RNA catalyzed peptidyl transferase reaction 3. Translocation - Moving the nascent polypeptide from the A site to the P site and moving the uncharged tRNA to the E site (exit) |
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What is the major energy source in protein synthesis?
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GTP
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What are chaperones?
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Other proteins required to assist with the correct protein folding
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How is targeting to specific organelles ensured?
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Localization signal sequences - Nuclear localization signal (NLS)
(interaction with carrier proteins) Glycosylation - Hydrophobic anchoring sequence (membrane-bound proteins) |
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What characteristics would suggest a nonribosomal (rather than ribosomal) biosynthesis?
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D-amino acids
Unusual amino acids Modified units (N-methylated) |
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Name features of an operon
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Regulatory gene (with own promoter)
Control elements (promoter and operator) Structural genes |
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Why is coordinate expression of a biosynthetic pathway important?
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Ensures a 1:1:1 ratio of all proteins
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With respect to gene expression regulation, what do the terms trans and cis refer to?
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Trans refers to the ability to diffuse to site of action, whereas Cis have only effect on genes immediately downstream.
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Aberrant of lack of certain transcription factor activity is associated with diseases such as cancer or inflammation. How are these transcription factors commonly regulated?
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Nuclear translocation
Posttranslational modification (Phosphorylation) |
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In eukaryotes, which two factors determine whether regions are transcriptionally active and what is the physical basis for each?
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1.) Acetylation of ε-lysine residue.
Reduction of net charge and electrostatic interaction between DNA and histones for activation of gene expression 2.) DNA methylation Proteins recognize and bind methylated DNA that prevents binding of transcription factors (gene silencing) ? |
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Some natural products are modified peptides which are made by nonribosomal peptide synthetases. Which of the following features would suggest that a peptide is made nonribosomally? More than one answer may be correct.
a. Amide nitrogen is methylated. b. Contains D-amino acids in its sequences. c. Contains only L-amino acids in its sequence. |
a. Amide nitrogen is methylated.
b. Contains D-amino acids in its sequences. |
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Which of the following is the terminal part of the acceptor stem structure of tRNA read 5'-->3'
a. ACC b. ARC c. CCA d. UGA e. GUA |
c. CCA
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Which of the following is/art not a termination codon in E. coli:
a. AAA b. AGA c. AAG d. UGU e. All of the above |
e. All of the above
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Which of the following serves as the poly adenylation site in eukaryotic transcription:
a. AUAAAA b. AAUAAA c. AAAUAA d. All of the above e. None of the above |
b. AAUAAA
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Which of the following is a component of the large subunit of ribosome in E. coli?
a. 16S rRNA b. 18S rRNA c. 23S rRNA d. All of the above e. None of the above |
c. 23S rRNA
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Which of the following is used as a direct energy source for translation
a. ATP b. CTP c. GTP d. UTP e. All of the above |
c. GTP
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Which of the following is not a GTP binding protein in protein biosynthesis?
a. EF-G b. EF-Ts c. EF-Tu d. IF3 e. IF2 |
d. IF3
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RF3:
a. Binds to GTP b. Hydrolyses GTP c. Promotes release of nascent polypeptides d. All of the above e. None of the above |
d. All of the above
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During translation, incoming aminoacyl-tRNA binds to ribosomes at which of the following sites to continue biosynthesis of polypeptide:
a. A site b. E site c. P site d. All of the above e. None of the above |
a. A site
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Initiator tRNA (formyl-Met) binds to the ribosome at which of the following sites to start translation:
a. A site b. E site c. P site d. All of the above e. None of the above |
c. P site
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Which of the following are part of post-translational processing of a pre-mRNA
a. Addition of 7-methylguanine to 5' end b. Addition of 3' poly A tail c. Splicing d. All of the above e. None of the above |
d. All of the above
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Match the following
Binds to the 23S rRNA and interferes with translocation step a. Chloramphenicol b. Erythromycin c. Tetracycline d. TATA box e. Helix-Turn-Helix |
b. Erythromycin
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Match the following
Inhibits binding of aminoacyl-tRNA to the ribosome a. Chloramphenicol b. Erythromycin c. Tetracycline d. TATA box e. Helix-Turn-Helix |
c. Tetracycline
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Match the following
Inhibits the peptidyltransferase activity by acting as a competitive inhibitor a. Chloramphenicol b. Erythromycin c. Tetracycline d. TATA box e. Helix-Turn-Helix |
a. Chloramphenicol
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Match the following
Present in many DNA binding proteins as a DNA binding motif a. Chloramphenicol b. Erythromycin c. Tetracycline d. TATA box e. Helix-Turn-Helix |
e. Helix-Turn-Helix
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Match the following
Found in many eukaryotic promoter region a. Chloramphenicol b. Erythromycin c. Tetracycline d. TATA box e. Helix-Turn-Helix |
d. TATA box
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Shine-Delgarno (SD) sequence can form base pairs with which of the following:
a. 5S rRNA b. 16S rRNA c. 18S rRNA d. 23S rRNA e. 28S rRNA |
b. 16S rRNA
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Which of the following loop is a part of the cloverleaf structure of tRNA:
a. CCA b. ERE c. GRE d. HSE e. TRU |
a. CCA
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Which of the following is a component of ribosome in E. coli
a. 18S rRNA b. 23S rRNA c. 28S rRNA d. All of the above e. None of the above |
b. 23S rRNA
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In E. coli, the start aminoacyl-tRNA (formyl-Met) is escorted by IF2 to:
a. The A site of the ribosome b. The B site of the ribosome c. All of the above d. None of the above |
d. None of the above
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Which of the following is a termination codon in E. coli:
a. AAA b. AGA c. AAG d. All of the above e. None of the above |
e. None of the above
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A Shine-Dalgarno (SD) sequence is usually:
a. Present at the 5' of the initiation codon AUG in bacterial mRNAs b. Present at the 3' of the initiation codon AUG in bacterial mRNAs c. Complementary to the 5' end of 16S rRNA d. All of the above e. None of the above |
a. Present at the 5' of the initiation codon AUG in bacterial mRNAs
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Which of the following is not part of the cloverleaf structure of tRNA?
a. The ACC loop b. The anticodon loop c. The D loop d. The T C loop e. The variable loop |
a. The ACC loop
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Which of the following is a component of ribosome in E. coli
a. 5S rRNA b. 16S rRNA c. 23S rRNA d. All of the above e. None of the above |
d. All of the above
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In E. coli, the start aminoacyl-tRNA (formyl-Met) is escorted by IF2 to:
a. The A site of the ribosome b. The E site of the ribosome c. The P site of the ribosome d. All of the above e. None of the above |
c. The P site of the ribosome
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Which of the following does not bind to GTP in prokaryotic translation process:
a. EF-G b. EF-Tu c. RF1 d. IF2 e. RF3 |
c. RF1
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Which of the following participates directly in powering the translocation step
a. ATP b. CTP c. GTP d. UTP e. All of the above |
c. GTP
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Which of the following antibiotics acts as a competitive inhibitor of peptidyl-transferase
a. Tetracycline b. Cloramphenicol c. Erythromycin d. Puromycin e. Streptomycin |
b. Cloramphenicol
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Which of the following antibiotics causes premature chain termination
a. Tetracycline b. Cloramphenicol c. Erythromycin d. Puromycin e. Streptomycin |
d. Puromycin
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Which of the following RNA polymerases is most sensitive to alpha-amanitin:
a. RNA polymerase I b. RNA polymerase II c. RNA polymerase III d. All of the above e. None of the above |
b. RNA polymerase II
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Which of the following is characteristic of an intron
a. GA.../...UG b. GC.../..GG c. GG.../...CG d. GU.../...AG e. None of the above |
d. GU.../...AG
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Match the following
DNA binding site for Glucocorticoid Receptor a. CAAT box b. Poly A c. GRE d. M^7G e. Zinc Finger |
c. GRE
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Match the following
Found at the 5' end of most eukaryotic mRNAs a. CAAT box b. Poly A c. GRE d. M^7G e. Zinc Finger |
d. M^7G
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Match the following
Found at the 3' end of most eukaryotic mRNAs a. CAAT box b. Poly A c. GRE d. M^7G e. Zinc Finger |
b. Poly A
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Match the following
Present in many eukaryotic DNA binding proteins as a DNA binding motif a. CAAT box b. Poly A c. GRE d. M^7G e. Zinc Finger |
e. Zinc Finger
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Match the following
Found in many eukaryotic promoter regions a. CAAT box b. Poly A c. GRE d. M^7G e. Zinc Finger |
a. CAAT box
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Which of the following helps to escort the initiation aminoacyl-tRNA to ribosome:
a. IF1 b. IF2 c. IF3 d. RF1 e. RF2 |
b. IF2
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Which of the following serves as the initiation codon for protein biosynthesis:
a. AGU b. AUG c. GAU d. GUA e. UAG |
b. AUG
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Which of the following is not a termination codon in E. coli
a. UAA b. UAG c. UGA d. UGG e. None of the above |
d. UGG
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EF-G
a. Binds to GTP b. Hydrolyses GTP c. Is responsible for translocation d. All of the above e. None of the above |
d. All of the above
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Which of the following is an example of ribozyme
a. 5S rRNA b. 5.8S rRNA c. 16S rRNA d. 18S rRNA e. 23S rRNA |
e. 23S rRNA
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Match the following
Binds to the 23S rRNA and interferes with translocation step a. Chloramphenicol b. Erythromycin c. Puromycin d. Streptomycin e. Tetracycline |
b. Erythromycin
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Match the following
Interferes with normal base pairing between anticodons and codons a. Chloramphenicol b. Erythromycin c. Puromycin d. Streptomycin e. Tetracycline |
d. Streptomycin
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Match the following
Is partially responsible for proofreading function in protein biosynthesis a. Aminoacyl-tRNA synthetase b. Shine-Dalgarno (SD) sequence c. The S7 factor d. The CCA arm e. Ubiquitin |
a. Aminoacyl-tRNA synthetase
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Match the following
Is responsible with proper alignment for starting translation in prokaryotes a. Aminoacyl-tRNA synthetase b. Shine-Dalgarno (SD) sequence c. The S7 factor d. The CCA arm e. Ubiquitin |
b. Shine-Dalgarno (SD) sequence
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Match the following
Is involved in the intracellular protein degradation in eukaryotes a. Aminoacyl-tRNA synthetase b. Shine-Dalgarno (SD) sequence c. The S7 factor d. The CCA arm e. Ubiquitin |
e. Ubiquitin
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Match the following
Is responsible for regulating the level of itself by binding to its mRNA a. Aminoacyl-tRNA synthetase b. Shine-Dalgarno (SD) sequence c. The S7 factor d. The CCA arm e. Ubiquitin |
c. The S7 factor
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Match the following
Where amino acids will be attached in the aminoacylation reaction a. Aminoacyl-tRNA synthetase b. Shine-Dalgarno (SD) sequence c. The S7 factor d. The CCA arm e. Ubiquitin |
d. The CCA arm
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Which of the following serves as stop codons for translation:
a. UAA b. UAG c. UGA d. All of the above e. None of the above |
d. All of the above
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Which of the following can base-pair with the 3' sequence of 16S rRNA
a. 5' cap b. Shine-Dalgarno sequence c. 3' poly A tail d. All of the above e. None of the above |
b. Shine-Dalgarno sequence
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A typical tRNA has the following structures
a. An anticodon loop b. An ACC arm at the 5' end c. An ACC loop d. All of the above e. None of the above |
a. An anticodon loop
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Which of the following inhibits the binding of aminoacyl tRNA to the ribosome?
a. Chloramphenicol b. Erythromycin c. Puromycin d. Streptomycin e. Tetracycline |
e. Tetracycline
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Which of the following blocks the translocation step during translation
a. Chloramphenicol b. Erythromycin c. Puromycin d. Streptomycin e. Tetracycline |
b. Erythromycin
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Which of the following RNA polymerases is least sensitive to alpha-amanitin
a. RNA polymerase I b. RNA polymerase II c. RNA polymerase III d. All of the above e. None of the above |
a. RNA polymerase I
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Which of the following is an example of Special Promoter and Enhancer Elements
a. CAAT box b. TATA box c. GRE d. All of the above e. None of the above |
c. GRE
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Which of the following serves as a DNA binding motif
a. snRNA b. The Zinc Finger c. 7-methylguanosine triphosphate d. All of the above e. None of the above |
b. The Zinc Finger
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Alternative splicing can generate
a. Same mRNA from same gene in different tissues b. Same mRNA from different genes in different tissues c. Different mRNAs from the same gene in different tissues d. All of the above e. None of the above |
c. Different mRNAs from the same gene in different tissues
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Match the following
Helps attach initiator tRNA to P site of ribosome a. IF1 b. IF2 c. EF-G d. EF-Tu e. RF3 |
b. IF2
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Match the following
Carries tRNA into A site of ribosome a. IF1 b. IF2 c. EF-G d. EF-Tu e. RF3 |
d. EF-Tu
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Match the following
Promotes dissociation of 70S ribosome to its 30S and 50S subunits a. IF1 b. IF2 c. EF-G d. EF-Tu e. RF3 |
a. IF1
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Match the following
Is a GTPase that promotes release of nascent polypeptide chain a. IF1 b. IF2 c. EF-G d. EF-Tu e. RF3 |
e. RF3
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Match the following
Is a GTPase that facilitates translocation a. IF1 b. IF2 c. EF-G d. EF-Tu e. RF3 |
c. EF-G
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