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168 Cards in this Set
- Front
- Back
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What is the specific defective DNA repair mechanism in xeroderma pigmentosa?
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Nucleotide excision repair
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What is the inheritance pattern of xeroderma pigmentosa?
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Autosomal recessive
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What codon is the mRNA initiation codon?
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AUG (or, rarely, GUG) (remember, AUG inAUGurates protein synthesis)
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What type of RNA is the largest?
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mRNA
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What enzyme elongates the leading strand of DNA synthesis by building on an RNA primer?
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DNA polymerase III
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How many hydrogen bonds are there between adenine and thymine?
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Two
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What enzyme charges tRNA by adding an amino acid to it?
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Aminoacyl-tRNA synthetase
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How many nucleotides make up the structure of an average tRNA?
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Approximately 75 to 90
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List the three parts of eukaryotic RNA processing.
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Capping on the 5' end, polyadenylation on the 3' end, and splicing out of the introns
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What is the function of single-stranded binding proteins?
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Single-stranded binding proteins prevent strands from reannealing
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What histone type is found between the nucleosome cores (the histone octamers)?
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H1
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In what direction relative to the mRNA does the ribosome shift after the formation of a peptidyl bond?
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Toward the 3' end
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The enzyme hypoxanthine-guanine phosphoribosyl transferase is responsible for the formation of what two products in the purine salvage pathway?
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Inosinic acid and guanylic acid
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What commonly results from a mutation within a promoter?
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A significant decrease in gene transcription
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Name the enzyme that proofreads the match between a tRNA and its amino acid.
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Aminoacyl-tRNA synthetase
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What is the total energy expenditure required in the addition of a single amino acid to a protein in translation?
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Four high-energy phosphoanhydride bonds per amino acid added; two adenosine triphosphate bonds to load tRNA; one guanosine triphosphate bond to load the ribosome and one to translocate the polypeptide chain
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When referring the "P site" of a ribosome, what does the "P" stand for?
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Peptidyl; the P site accommodates the growing polypeptide chain
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In what type of nucleic acid is thymine found?
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DNA
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What is called when a purine is substituted for a pyrimidine or when a pyrimidine is substituted for a purine?
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Transversion
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In eukaryotes, what enzyme makes tRNA?
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RNA polymerase III
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During DNA and RNA synthesis, what is the target of the incoming nucleotide?
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The 3'-hydroxyl of the nascent chain; the 5'-triphosphate provides the energy for the new bond
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β-thalassemia is due to a mutation causing splicing defects in a process that combines different exons within a single gene. What mechanism allows the same gene to encode for multiple different proteins?
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Alternative splicing; in this case the alternative splicing yields a pathological protein
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What is the function of primase?
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It makes an RNA primer on which DNA polymerase III can then initiate replication
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Does charging a tRNA molecule with an amino acid require energy?
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Yes, adenosine triphosphate is hydrolyzed in the process
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What does DNA polymerase III require to initiate replication?
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RNA primer
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In protein synthesis, what is the role of initiation factors?
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To assemble the 40S ribosomal subunit with the initiation tRNA
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What is the term for the initial (unprocessed) RNA transcript?
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Heterogeneous nuclear RNA
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What poisonous protein, which inhibits RNA polymerase II, is found in death cap mushrooms?
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α-Amanitin; it causes liver failure when consumed
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Which histone is not part of the nucleosome core?
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H1
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What molecule provides the energy for the binding of tRNA to the ribosome/mRNA complex?
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Guanosine triphosphate
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Deoxyuridine monophosphate (dUMP) is converted to deoxythymidine monophosphate (dTMP) by which enzyme?
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Thymidylate synthase
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What molecule provides the energy for the charging of tRNA?
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Adenosine triphosphate
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In eukaryotes, what enzyme makes rRNA?
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RNA polymerase I
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Which protein unwinds the DNA template at the replication fork?
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Helicase
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In base excision repair, what does the apurinic/apyrimidinic endonuclease do?
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It cuts the DNA at a apyrimidinic site and removes the empty sugar
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What enzyme converts ribonucleotides to deoxyribonucleotides?
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Ribonucleotide reductase
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What quality of trimethoprim makes it a good antibiotic?
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Its target is bacterial dihydrofolate reductase, inhibiting DNA synthesis
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Name four drugs that interfere with pyrimidine synthesis.
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Hydroxyurea, 5-fluorouracil, methotrexate, trimethoprim
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What nucleotide has a methyl group?
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Thymine
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What is the significance of the genetic code being unambiguous and yet redundant?
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Whereas each codon specifies a single amino acid, an amino acid can be coded for by multiple codons
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True or False? Poly-A polymerase requires a template.
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False; poly-A polymerase does not require a template
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Patients with xeroderma pigmentosum show excessive sensitivity to what? What organ is most affected?
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Ultraviolet light; the skin
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In eukaryotes, what enzyme makes mRNA?
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RNA polymerase II
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Rank the following types of mutations in order of severity: missense, silent, nonsense.
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Nonsense (a stop codon) > missense > silent
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What is transcriptionally active DNA called?
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Euchromatin; it is uncondensed and accessible to replication enzymes
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If a tRNA had a methionine bound to it, what would the sequence of the codon it binds read? (Give this in order from the 5' end to the 3' end.) What would its anticodon sequence read? (Give this in the same order.)
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Codon = AUG; anticodon = CAU
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What is the treatment for orotic aciduria?
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Oral uridine administration
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What enzyme does hydroxyurea inhibit?
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Ribonucleotide reductase
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Where does eukaryotic DNA replication begin?
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At a consensus sequence of base pairs; this is AT-rich
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In what direction does protein synthesis proceed?
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From N to C
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Predominance of which two amino acids gives histones a positive charge?
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Lysine and arginine
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What part of a tRNA lies opposite from its 3' aminoacyl end?
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The anticodon end
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Covalent alterations involve what kinds of posttranslational protein modifications?
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Phosphorylation, glycosylation, and hydroxylation
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5-fluorouracil inhibits ______, while methotrexate and trimethoprim both inhibit ______.
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Thymidylate synthase; dihydrofolate reductase
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Onto which end of the newly synthesized DNA molecule does DNA polymerase III add the next subunit?
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3'. This is 5' to 3' synthesis
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True or False? An enhancer that regulates expression can be located close to the gene it regulates, far from the gene it regulates, and within the gene that it regulates.
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TRUE
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Which molecules are responsible for assembling the 40S subunit with the initiator tRNA?
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Eukaryotic initiation factors
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DNA polymerase I and III are _____ (prokaryotic/eukaryotic) enzymes.
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Prokaryotic
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Accuracy in which two nucleotide positions of an mRNA codon is required for proper protein synthesis.
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First and second (tRNA wobble hypothesis)
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How many rings do purine molecules have?
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Two
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Approximately how many adenosine monophosphates get added to the 3' end of mRNA during polyadenylation?
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200
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Xeroderma pigmentosum is associated with what cancer?
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Melanoma
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Converting phosphoribosyl pyrophosphate into inosinic acid requires ______,______,______, and ______.
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Glycine, aspartate, glutamine, tetrahydrofolate
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What enzyme degrades the RNA primer and replaces it with DNA during prokaryotic DNA replication?
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DNA polymerase I
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Why are antibiotics such as chloramphenicol, clindamycin, and macrolides selective for bacteria and not toxic to human cells?
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They affect the 50S subunit of the ribosome, which is found in prokaryotic cells
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What is the end product of guanosine and adenosine degradation?
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Uric acid; uric acid is eventually renally excreted
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What mechanism allows the same gene to encode for multiple different proteins?
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Alternative splicing of exons
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Xeroderma pigmentosa results in an inability to repair what specific DNA error?
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Thymidine dimers
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True or False? RNA is synthesized in the 3'-to-5' direction.
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False; RNA is synthesized in the 5' to 3' direction
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At the start of protein synthesis, methionine sits in which site on the ribosome?
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In the P site
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What enzyme catalyzes the formation of adenosine monophosphate from adenine?
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Adenine phosphoribosyl transferase
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What is the name of the portions of a gene that contain the actual genetic information coding for the protein?
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Exons (remember: EXons EXit and are EXposed)
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Is a promoter upstream or downstream of its gene locus?
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Upstream
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What is a "nonsense mutation"?
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A DNA change that results in an early-stop codon
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In prokaryotes, what enzyme makes rRNA, mRNA, and tRNA?
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RNA polymerase
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In de novo nucleotide synthesis, _____ (purines/pyrimidines) are made from IMP precursors, while _____ (purines/pyrimidines) are made from orotate precursors.
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Purines; pyrimidines
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What is the shape of the intermediate that is formed during mRNA splicing?
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Lariat
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What type of inheritance does Lesch-Nyhan syndrome demonstrate?
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X-linked recessive
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What type of bond links nucleotides?
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3'-5' phosphodiester bond
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What is the charge on histone octamer?
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Positive; giving the histones affinity for negatively charged DNA
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What is the order of the positions of the ribosome that the tRNA occupies during translation?
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A, P, E (think of "going APE")
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During protein synthesis, the incoming amino acid binds to which site on the ribosome?
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The A site
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When the ribosome shifts after the formation of a peptidyl bond, in what position does the tRNA with the growing peptide chain end up?
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The P site
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What are the substrates of the reaction that is catalyzed by aminoacyl-tRNA synthetase?
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The uncharged tRNA, the appropriate amino acid, and ATP
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What is the purpose of DNA topoisomerases creating a nick in the DNA helix?
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To relieve supercoils
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What are the three pyrimidines?
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Cytosine (C), thymine (T), and uracil (U) (remember: CUT the PY [pie]: PYrimidines)
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In eukaryotes, AUG codes for what amino acid?
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Methionine
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In what type of nucleic acid is uracil found?
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RNA
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When the ribosome shifts after the formation of a peptidyl bond, where is the uncharged tRNA found?
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In the E position
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What are the sizes of the two subunits of the eukaryotic ribosome called?
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The 60S subunit and the 40S subunit
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Where on a tRNA does the amino acid that will be incorporated into the protein bind?
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The 3' end
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What three-nucleotide sequence do all eukaryotic and prokaryotic tRNAs have at their 3' ends?
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CCA
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What is the mechanism of the antineoplastic drug 6-mercaptopurine?
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Blocks de novo purine synthesis
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What type of RNA is the most abundant?
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rRNA
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List three stop codons.
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UGA, UAA, UAG (remember, UGA = U Go Away; UAA = U Are Away; UAG = U Are Gone)
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What enzyme in the purine salvage pathway catalyzes the formation of guanosine monophosphate from guanine?
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Hypoxanthine-guanine phosphoribosyl transferase
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In single-stranded DNA repair, how are nucleotide excision and base excision repair different?
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During nucleotide repair, the entire nucleotide structure is removed and replaced; during base excision repair, the base is clipped off of the sugar and repaired without the whole backbone of the DNA being taken apart
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What enzyme has exonuclease activity in prokaryotic DNA replication?
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DNA polymerase III has 3' to 5' exonuclease activity for proofreading
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What is the cofactor in the thymidylate synthase reaction?
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The reaction requires N5N10 methylene tetrahydrofolate, which is generated by dihydrofolate reductase
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How many rings do pyrimidine molecules have?
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One
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What are the elements that make up the promoter region?
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The promoter region is an AT-rich sequence with TATA and CAAT boxes
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What is it called when a mutation in DNA results in no change to the amino acid that is being coded for?
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Silent mutation
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Which drug category inhibits DNA gyrase (a specific prokaryotic topoisomerase)?
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Fluoroquinolones; they impair bacterial DNA synthesis
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Hereditary nonpolyposis colon cancer results from loss of what DNA repair mechanism?
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The mismatch repair system
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What is the charge on DNA?
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Negative
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What is the name for a stretch of DNA that alters gene expression by binding transcription factors?
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Enhancer
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What binds to a primary mRNA transcript and forms a spliceosome?
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Small nuclear ribonucleoprotein particles and other proteins
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What is the name for a DNA site where negative regulators (repressors) bind?
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Silencer
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When does DNA polymerase III stop adding deoxynucleotides to the 3' end?
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When it reaches the primer of the preceding fragment
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At the start of protein synthesis, what process occurs at the same time as the hydrolysis of methionine's bond with its tRNA?
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The formation of a peptidyl bond between methionine and the second amino acid in the polypeptide
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What enzyme in the purine salvage pathway catalyzes both the conversion of hypoxanthine into xanthine and the conversion of xanthine into uric acid?
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Xanthine oxidase
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What is the result of clindamycin binding to the 50S subunit?
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Translocation of the tRNA is blocked
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How do aminoglycosides interfere with protein synthesis?
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They inhibit formation of the initiation complex, causing misreading of mRNA
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What series of bases encodes the polyadenylation signal?
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AAUAAA
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True or False? In eukaryotes, RNA polymerases have a proofreading function.
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False; RNA polymerases have no proofreading function in eukaryotes
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What enzyme is affected by chloramphenicol?
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50S peptidyltransferase
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Pyrimidines are made from orotate precursor, with _____ added later.
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Phosphoribosyl pyrophosphate
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A frameshift mutation tends to yield what?
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A truncated or nonfunctional protein
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Converting carbamoyl phosphate into orotic acid requires _____.
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Aspartate
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True or False? Eukaryotic DNA has more than one origin of replication.
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TRUE
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What enzyme in the purine salvage pathway catalyzes the formation of inosinic acid from hypoxanthine?
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Hypoxanthine-guanine phosphoribosyl transferase
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How many times does the DNA loop around each octamer (nucleosome core)?
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Two
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Patients with which disease make antibodies to spliceosomal small nuclear ribonucleoproteins?
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Lupus
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Which synthetic pathway utilizes the conversion of orotic acid to uridine monophosphate?
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The de novo pyrimidine synthesis pathway
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In DNA mismatch repair, how does the repair mechanism recognize the new strand (and thereby avoid replacing bases on the original template strand of DNA)?
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The mismatch repair mechanism recognizes the template (and, therefore, the older strand) by its degree of methylation and excises the mismatched base from the new strand
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What is it called when a DNA mutation yields a single changed amino acid?
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Missense mutation; the severity of the mutation depends on the location of the change and the chemical similarity of the new amino acid to the old
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What gets placed on the 5′ end during the process of capping?
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7-Methyl-guanosine
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What are the two precursors to creating the pyrimidine ring?
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Carbamoyl phosphate and aspartate
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What enzyme has 5' → 3' exonuclease activity?
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DNA polymerase I (removes RNA primer)
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Where do macrolides and clindamycin bind?
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The 50S subunit
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What is the inheritance pattern of orotic aciduria?
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Autosomal recessive
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What kind of mutation is a DNA change that results in the misreading of all nucleotides downstream of it?
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Frameshift
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Lesch-Nyhan syndrome is the result of an absence of what enzyme?
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Hypoxanthine-guanine phosphoribosyl transferase; remember the mnemonic, He's Got Purine Recovery Trouble
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Severe combined immunodeficiency disease may be caused by a deficiency of what enzyme of the purine salvage pathway?
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Adenosine deaminase
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What is it called when one purine is substituted for the other purine or when one pyrimidine is substituted for the other pyrimidine?
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Transition
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How many codons code for methionine?
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One (AUG)
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What diagnosis would you suspect in a child with megaloblastic anemia not responsive to B12 or folate administration, failure to thrive, and a normal ammonia level?
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Orotic aciduria
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How does tetracycline interfere with protein translation?
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Tetracycline binds to the 30S subunit of the ribosome, blocking attachment of the aminoacyl tRNA
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What is an example of proteins that are trimmed after translation?
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The removal of N- or C-terminal propeptides from zymogens to generate mature proteins
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What type of RNA is the smallest?
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tRNA
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What enzyme seals pieces together during prokaryotic DNA replication?
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DNA ligase
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What physical property do nucleic acids with increasing proportions of guanine-cytosine bonds display?
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Increasing melting temperatures due to the tighter binding of the strands
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What is the name for the intervening noncoding segments of DNA within a gene?
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Introns (remember: INtrons are INtervening sequences and stay IN the nucleus)
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Where might you see a genetic code that has overlapping genes?
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Some viruses do not adhere to the "commaless, nonoverlapping" genetic code rule
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Which is stronger: a guanine-cytosine bond or an adenine-thymine bond?
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A guanine-cytosine bond, because it has three hydrogen bonds; an adenine-thymine bond only has two
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What is the name of the DNA site at which RNA polymerase and multiple other transcription factors bind?
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Promoter
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Silent mutations are often the result of changes in what position of a codon?
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The third position (due to tRNA wobble)
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Nucleotide = _____ + phosphate
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Nucleoside
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During nucleotide excision DNA repair, what enzyme removes the damaged DNA?
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Endonuclease
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Where does eukaryotic RNA processing occur?
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In the nucleus
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A patient has hyperuricemia, gout, and choreoathetosis. He has mental retardation and signs of self-mutilation. What is the underlying metabolic disorder?
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Lesch-Nyhan syndrome
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What molecule does deamination of cytosine yield?
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Uracil
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How do cells handle defective proteins that are translated?
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Attach ubiquitin to defective proteins to tag them for breakdown
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What are the names of the four subunits of a nucleosome core?
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Histones H2A, H2B, H3, and H4
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Inhibition of which enzyme occurs due to adenosine triphosphate and deoxyadenosine triphosphate accumulation in severe combined immunodeficiency?
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Ribonucleotide reductase
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What is the first step in the base excision repair of damaged DNA?
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Specific glycosylases recognize and remove a single damaged base
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In protein synthesis, what are the three steps of protein elongation?
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(1) Aminoacyl-tRNA binds to the A site; (2) peptidyltransferase adds a peptide to the amino acid chain at site A; and (3) the ribosome advances three nucleotides in the 3′ direction, thereby moving the peptidyl tRNA to the P site
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What is DNA called when it is condensed and transcriptionally inactive?
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Heterochromatin
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In prokaryotes, the initial AUG codes for what amino acid?
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Formyl-methionine
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Nucleoside = _____ + ribose
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Base
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What are the two purines?
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Adenine (A) and guanine (G) (remember: PURe As Gold: PURines)
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When referring the "A site" of a ribosome, what does the "A" stand for?
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Aminoacyl; the incoming aminoacyl tRNA is accommodated in the A site
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Serum studies show increased orotic acid and hyperammonemia; this is consistent with _____ (orotic aciduria/ornithine transcarbamylase deficiency).
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Ornithine transcarbamylase deficiency; orotic aciduria does not have hyperammonemia
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How many subunits make up a nucleosome core?
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Eight; two of each of the four histone types
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How many origins of replication do prokaryotes use in DNA replication?
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One (single)
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Deficiencies in what two enzymes will result in failure to convert orotic acid to uridine monophosphate?
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Orotic acid phosphoribosyltransferase or orotidine 5′-phosphate decarboxylase
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What are the pieces that are formed in discontinuously synthesized DNA called?
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Okazaki fragments on the lagging strand
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What molecule provides the energy for the translocation of the ribosome along the mRNA?
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Guanosine triphosphate
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