Biochemistry Exam 1
the protein involved in separating the DNA strands at the initiation of DNA replication is called: a) helices b) DNA polymerase I c) DNA polymerase II d) primase e) DNA gyrase
a
which is the most correct about the alpha helical structure of polypeptide chains in proteins? a) primarily dependent upon hydrogen bonding b) primary dependent upon disulfide linkages c) found in all proteins d) refers to interactions between adjacent chains in fibrous proteins
a
which nucleotide is found only in tRNA? a) pseudouridine b) uridine c) thymine d) ribose e) adenosine
a
amino acid found in large amounts in collagen is: a) proline b) lysine c) arginine d) asparagine e) histidine
a (glycine is also abundant )
The term denaturation, when used in connection with nucleic acids or proteins, refers to a change in the structural characteristics due to: a) disruption of covalent bonds b) disruption of non-covalent bonds c) binding of toxic compounds d) changes in primary structure e) changes in state of aggregation
b
because of phosphate groups, DNA is: a) basic b) acidic c) neutral d) tight bounded e) none of the above
b
what is contained within a nucleoside? a) ribose moiety, a nitrogenous base, and a phosphate covalently attached to the ribose 5' carbon b) a ribose moiety, a purine or pyrimidine, and a phosphate covalently linked to the 3' carbon of the ribose c) a ribose moiety and a nitrogenous base d) a deoxyribose, a purine or pyrimidine, and a phosphate linked to the ribose 5' carbon by a hydrogen bond
c
which amino acid contains a sulfur atom? a) arginine b) aspartate c) methionine d) leucine e) serine
c
which describes side chain of leucine: a) sulfhydryl group b) alcoholic group c) branched chain hydrocarbon d) no side chain e) acidic
c
which is a correct statement about the process of replication? a) only 1 strand of the DNA duplex is copied b) sigma factor is required for recognition of the point at which replication will be initiated c) the DNA of mammalian chromosomes replicate bidirectionally d) the only enzyme required for replication is DNA polymerase e) replication is conservative
c
which of the following is a general feature of both RNA & DNA? a) in vivo, they are double helical structures formed from 3 separate chains b) they are alkaline stable c) they form complementary G-C base pairs d) they contain small amounts of pseudouridine e) they interact with histones for form nucleosomes
c
amino acid containing an amide functional group in its side chain: a) proline b) hysine c) arginine d) asparagine e) histidine
d (other is glutamine)
which amino acid group has a guanidinium group in side chain? a) arginine b) aspartate c) methionine d) leucine e) serine
a
peptide bond has all except: a) planarity b) freedom to rotate c) polarity d) greater stability in trans configuration e) partial double bond character
b
the nucleoside sequence 5'-ATTGCAG-3' should pair with: a) 5'-TAACGTC-3' b) 5'-CTGCAAT-3' c) 3'-ATTGCAG-5' d) 3'-CTGCAAT-5'
b
a helix is an example of: a) quaternary structure b) tertiary structure c) secondary structure d) primary structure e) none
c
some frameshift mutations produced by a single nucleotide insertion may be corrected by a a) transition b) transversion c) single nucleotide deletion d) missense mutation
c
what are complementary base pairs in DNA? a) A:U & G:C b) A:T & G:U c) A:G & U:C d) A:T & G:C e) A:C & G:T
d
each of the following describes tRNA except: a) end terminates in CCA b) synthesized with extra bases on the 3' and 5' ends c) extended structure looks like cloverleaf d) furnishes a codon for protein synthesis e) has many bases which are modified
d - it furnishes an anticodon, not codon
following oxidative deamination with nitrous acid and several rounds of replication, which of the following base pairs would you expect to replace the complementary base pair A-T? a) T-G b) G-C c) C-G d) T-A e) G-T
b
all of the following amino acids are optically active (4 different substituents) except: a) leucine b) alanine c) glycine d) cysteine e) lysine
c
5'-methylcytosine residues in DNA are hot-spots for mutations because they: a) can be deaminated to thymine b) can stimulate Z-DNA formation c) can easily tautomerize d) cannot base pair with guanine
a
DNA synthesis is called: a) replication b) transcription c) translation d) transformation e) polymerization
a
a mutation in which an A-T base pair in DNA is replaced by a G-C base pair is referred to as a(n) _____________ mutation: a) transition b) transversion c) insertion d) inversion e) deletion
a
after deamination of cytidine resides in DNA, the new residue will complement with: a) adenosine b) inosine c) thymidine d) guanosine e) uridine
a
bonds principally responsible for secondary structure of proteins: a) hydrogen bonds b) hydrophilic bonds c) hydrophobic bonds d) electrostatic bonds e) covalent bonds
a
collagen is a protein whose conformation is characterized by: a) triple helix b) double alpha helix c) antiparallel beta-sheet region d) mostly random coil regions e) lack of any stable conformation
a
deamination of 5'-methylcytosine in DNA is mutagenic because it a) produces thymine b) produces uracil c) changes a base but doesn't disrupt hydrogen bonding d) cannot be repaired
a
formation of peptide bond between 2 amino acids: a) creates partial double bond character among 4 atoms b) permits unrestricted rotate about each chemical bond c) places alpha carbons in centers of 2 different planes d) retains chemical properties of typical ester bond
a
helicase a) unwinds double stranded DNA by breaking base pairs b) will decrease the writhing number of negatively supercoiled DNA c) will increase the linking number of negatively supercoiled DNA d) nicks one strand of double stranded DNA e) cuts both strands of double stranded DNA
a
hydrophobic effect is generally thought to be the result of: a) minimization of disruption of normal structure of water by hydrophobic molecules b) repulsive forces between polar water and nonpolar hydrophobic molecules c) maximization of order in the mixture of water and hydrophobic molecules d) all of the above e) none of the above
a
major functional groups present in collagen which are directly involved in formation of crosslinks: a) aldehydes derived from lysine b) aldehydes derived from hydroxyproline c) ketone bodies derived from hydroxyalanine d) schiff bases involving proline & acetaldehyde
a
secondary structure of proteins: a) is maintained by hydrogen bonds b) refers to proteins consisting of 2 or more subunits held together by non covalent forces c) encompasses ant hydrogen bonded interaction found in proteins d) refers to proteins consisting of 1 or more polypeptide chains plus a nonprotein moiety e) is only founding fibrous proteins
a
what is the function of the 5' exonuclease activity of bacterial DNA polymerase? a) remove mismatched based pairs during replication b) removes pyrimidine dimers c) removes the RNA primers of okazaki fragments d) initiates mRNA synthesis e) processes precursors or ribosomal RNA
a
which about DNA is incorrect? a) contains equal amounts of A, T, C, & G on a molar basis b) molar content of A in a 2 stranded DNA molecule is equal to molar content of T c) resistance of DNA to denaturation in heat can be related to GC content d) denaturation of DNA is associated with increased UV absorption e) at neutral pH, DNA has large net negative charge
a
which interaction may participate in stabilization of tertiary structure by covalently linking different polypeptide chains? a) disulfide bond b) electrostatic bond c) hydrogen bond d) hydrophobic interaction e) peptide bond
a
with respect to mutations, a) transitons arise the replacement of one purine to another purine for one pyrimidine for another pyrimidine b) transversions arise from the replacement of one pyrimidine for another pyrimidine c) transitions arise though deletions of a nucleotide in the DNA seq d) transversions arise though the insertion of a nucleotide in the DNA seq e) both transitions and transversions
a
xeroderma pigmentosa is a genetically inherited disorder in which the cells of patients are: a) unable to excise thymine dimers b) unable to ligate okazaki fragments c) unable to remove RNA primers d) unable to fill gaps in DNA e) unable to relax supercoiling
a
which mutation would you except to cause dramatic alteration in functional performance of polypeptide chain (assuming replacement not in active site): a) replace glutamate for lysine b) replace valine for alanine c) replace aspartic acid for glutamic acid d) replace lysine for arginine
a (glutamate is negatively charged/acidic, lysine is positively charged/basic)
histones are: a) basic proteins associated with RNA b) basic proteins associated with DNA c) acidic proteins which bind chromosomal nucleoprotein d) proteins exclusively found in the nucleolus e) proteins which are tissue specific
b
primary structure of protein refers to: a) ability to form intrachain hydrogen bonds b) amino acid sequence c) folding induced by disulfide linkages d) ability to form subunit structures e) ability to form interchain hydrogen bonds
b
the purpose of the short RNA chains which are synthesize during DNA replication is to: a) code for genes necessary for replication b) provide a primer for DNA synthesis c) maintain DNA strands in an open (i.e. not base-paired) form so that polymerases can recognize the template strand d) reduce superhelical density e) provide a template for ligation of okazaki fragments
b
which amino acid has more than one carboxyl group? a) serine b) glutamic acid c) lysine d) alanine e) methionine
b
which amino acid residues may participate in strong hydrophobic bonding: a) glycine b) isoleucine c) lysine d) serine e) aspartate
b
which characterizes L-lysine? a) monoamino monocarboxylic amino acid b) diamino monocarboxylic amino acid c) monoamino dicarboxylic amino acid d) aromatic amino acid e) cyclic imino acid
b
which is correct about replication? a) revers transcripterase replicates DNA in the 3' to 5' direction b) eukaryotic DNA replication proceeds bidirectionally with multiple initiation sites c) replication of the leading strand within a replication requires multiple initiation d) since there is more DNA in eukaryotes than prokaryotes, the rate of polymerization per growing fork of nucleotides during DNA synthesis in eukaryotes is much greater than in prokaryotes e) initiation of DNA replication if prokaryotes occurs randomly throughout the genomes
b
which of the following doesnt play a role in prokaryotic replication? a) DNA ligase b) reverse transcriptase c) DNA helicase d) primase e) DNA polymerase I
b
which is responsible for maintenance of protein secondary structure? a) salt bridges b) Hydrogen bonds c) van der Waals forces d) hydrophobic interaction e) disulfide crosslinks
b (dominate in alpha helices and beta sheets)
DNA polymerase I catalyzes the reaction of a: a) deoxynucleoside diphosphate with the 3'-OH end of a DNA chain b) deoxynucleoside diphosphate with the 5'-OH end of a DNA chain c) deoxynucleoside triphosphate with the 3'-OH end of a DNA chain d) deoxynucleoside triphosphate with the 5'-OH end of a DNA chain e) none of these
c
a major force that contributes to the conformation of proteins and in globular proteins that occurs primary in their in their interior is: a) hydrogen bonds b) charged dipoles c) hydrophobic interactions d) disulfide bridges e) hydration by water
c
a template in molecular biology means: a) the sequence of DNA to which the DNA polymerase initially binds b) a protein that has specific binding sites for RNA c) any macromolecule that provides the pattern for the synthesis of another d) a polymer that provides the starting point for further growth of the molecule e) a temperature sensitive mutant
c
all are true except: a) DNA and RNA are both polynucleotides held together by 5' phosphodiester bonds b) 3 of the bases are the same in DNA and RNA c) both DNA and RNA usually exists as watson-crick double helix d) RNA is found in both nucleolus & cytoplasm e) RNA but not DNA is hydrolyzed by base
c
an enzyme which can seal a nick in a DNA duplex is called a: a) sigma factor b) lipase c) ligase d) reverse transcriptase e) nuclease
c
histones are: a) ribosomal proteins which regulate the function of ribosomes b) proteins which bind to tRNA and activate them c) small basic proteins associated with DNA molecule in chromatin of eukaryotic cells d) small acidic proteins involved in gene regulation e) proteins required for binding mRNA to ribosomes
c
if glycine has positive charge in buffer at pH 1, then gly-gly-gly in same buffer should have the charge: a) +3 b) +2 c) +1 d) -1 e) -2
c
major structural protein component(s) of chromatin are: a) tubulin b) actin c) histones d) acidic chromosomal proteins e) myosin
c
semiconservative replication of DNA means that after 2 rounds of replication, a) only 1 of the 2 parental strands is preserved intact in the progeny molecules of DNA b) both parental strands remain intact in 1 of the progeny molecules of DNA c) the 2 parental strands remain intact in different progeny molecules d) 1 of the parental strands is broken down and dispersed in 1 of the progeny molecules of DNA, the other strand remains intact in 1 of the progeny molecules e) neither of the parental strands appears in the progeny molecules of DNA
c
stability of DNA double helix is due to: a) hydrogen bonds between sugar moieties b) hydrogen bonds between complementary bases c) hydrogen bonds between complementary bases, hydrophobic interactions, and favorable van der Waals radii d) covalent bonds between 2 antiparallel DNA strands
c
the Tm (melting temp) of DNA is: a) unrelated to base composition b) constant for all DNA samples c) linearly related to G-C content d) proportional to U content e) none of the above
c
the watson-crick model of DNA double helix led to the prediction that DNA replication is semiconservative b/c: a) phosphate backbone could easily be broken & rejoined b) double helix can assume either B-form or Z-form higher order structure before replication c) each strand could serve as a template for daughter strand synthesis producing pairs of identical molecules d) hydrogen bonds would stabilize important intermediates that arise during synthesis
c
which of the following is not true of eukaryotic DNA replication? a) it is semiconservative b) it is discontinuous c) it proceeds 3' to 5' on the lagging strand d) it proceeds 5' to 3' on the leading strand e) it requires DNA polymerase activity
c
why is DNA synthesis started with ribonucleotides rather than deoxyribonucleotides? a) to mark the newly synthesized strand b) RNA polymerase makes fewer errors when priming than DNA polymerase would c) DNA polymerase can't prime d) to mark the lagging strand for DNA ligase
c
DNA polymerase I: a) nicks DNA to initiate DNA replication b) has a DNA ligase activity for completing DNA application c) synthesizes DNA in a >5' direction d) requires a primer with a free 3'-OH e) is used only to repair DNA
d
DNA replication a) is bidirectional proceeding from a single initiation point on each chromosome in eukaryotic cells b) is unidirectional in prokaryotic cells c) doesn't require ATP d) is initiated on RNA primers e) involves the formation, and not the cleavage of phosphodiester bonds
d
DNA synthesis requires a primer. A primer is: a) an available serine hydroxyl (-OH) group on DNA polymerase III for imitation of DNA synthesis b) the complementary strand of DNA c) an available 5'-triphosphate on the nitrogenous bases used in synthesis d) a short oligonucleotide with an available hydroxyl group on the ribose or deoxyribose e) a short oligonucleotide with an available 2'-hydroxyl group on the ribose or deoxyribose
d
a break of phosphodiester bond in one strand of a double-stranded DNA molecule can be repaired by: a) polynucleotide phosphorylase b) polynucleotide phosphorylase c) exonuclease III d) DNA ligase e) DNA polymerase
d
a peptide bond: a) contributes atoms to hydrophobic interactions b) exhibits unrestricted rotation around the C-N bond c) forms between the side chains of glutamate and lysine residues d) is planar and partially ionic
d
amino acid side chains which may be involved in hydrogen bonding in proteins includes: a) leucine b) isoleucine c) alanine d) tyrosine e) phenylalanine
d
cysteine can be converted to cystine by: a) acylation b) peptide bond formation c) reduction d) oxidation e) esterification
d
double stranded DNA molecule can be denature or melted by: a) treatment with protease b) x-ray diffraction c) high concentration of NaCl d) high pH e) C and D
d
each of the statements about DNA replication is true except: a) DNA replication can be bidirectional b) DNA replication can be semiconservative c) DNA replication in humans involves RNA d) DNA replication requires only 1 protein, namely, DNA polymerase
d
enzymes that catalyze stepwise hydrolysis of mononucleotides from one end of a polynucleotide chain are: a) polymerases b) endonucleases c) ligases d) exonuclease e) nickases
d
in the watson-crick structure of DNA: a) DNA strands run parallel b) ratio of G:A = 1 c) ratio of A:U = 1 d) # purines = # pyrimidines e) 2 of the above are correct
d
ionizing radiation is capable of producing genetic mutations by: a) base-changes in the DNA b) base-deletions in the DNA c) breaking chromosomes d) all of the above e) A and B
d
regarding tRNA structure, which is correct? a) nucleotide sequence CCA is always present at terminus of functional tRNA b) there is appreciable secondary structure in native tRNA c) unusual nucleoside called pseudouridine (C-C linkage between ribose and uracil) is almost always present d) all of the above e) none of the above
d
the structure (CH3)2-CH-CHNH2-COOH is which amino acid? a) isoleucine b) threonine c) arginine d) valine e) lysine
d
type of nucleic acid that may contain small quantities of a variety of modified ribonucleotides: a) mRNA b) rRNA c) nucleolar RNA d) tRNA e) mitochondrial RNA
d
which amino acid has uncharged side chain at pH 7? a) lysine b) aspartate c) arginine d) serine e) glutamate
d
which amino acid would be considered the most polar? a) alanine b) proline c) isoleucine d) threonine e) phenylalanine
d
which of the following is a ribonucleoside which contains an amino group? a) thymine b) uridine c) thymidine d) cytidine e) deoxyadenosine
d
which of the following is a target for base excision repair? a) deaminated adenine in RNA b) methylated cytosine in DNA c) methylated adenine in RNA d) deaminated cytosine in DNA
d (RNA doesn't get repaired... d is right b/c there is enzyme that removes uracil DNA, which results from deamination of cytosine)
amino acids are classified according to nature of side chain. all are correctly classified except: a) serine: polar, uncharged b) glutamic: polar, acidic c) arginine: polar, basic d) histidine: nonpolar, uncharged e) phenylalanine: nonpolar, uncharged
d (its polar)
all are correct about RNA polymerase and DNA polymerase except: a) both require a template b) both require nucleotide triphosphates as substrates c) both elongate in the 5' direction d) both require a primer e) both are required for replication in certain systems
d (only DNA poly does)
Which of the following statements best supports the Watson-Crick structure of DNA? a) Of the DNA examined from a wide variety of sources, the adenine and cytosine contents are always equal b) a non-virulent pneumococcus can be transformed to a virulent strain by the addition of DNA c) mRNA will hybridize with DNA d) of the DNA exam from a wide variety of sources, the adenine and guanine contents are always equal e) the sum of the prunes present in a wide variety of DNA exam is always equal to the sum of the pyrimidines present
e
chemicals that bind to DNA by interacting between the bases a) can cause frameshift mutations b) can cause deletion mutations c) can cause insertion mutations d) are generally planar hydrophobic molecules e) all of the above
e
frameshift mutations are possible because of: a) redundant (degenerate) code b) intra-allelic supervisor c) nonsense code d) universality of the code e) non-overlapping code
e
helicases a) cut 1 strand of the double helix b) cut both strands of the double helix c) requires ATP d) unwind the double helix e) C and D
e
okazaki fragments are associated with: a) resolution of recombination intermediates b) splicing of transcripts c) resolution of DNA replication at telomeres d) replication of the leading strand e) replication of lagging strand
e
okazaki fragments are: a) the RNA primer in DNA synthesis b) pieces of DNA produced by restriction enzyme digestion c) unique to eukaryotes d) RNA fragments produced by splicing of primary transcripts e) stretches of DNA synthesized on the lagging strand
e
short chains of nucleic acid can be isolated from cells in which DNA is undergoing replication. these segments, known as okazaki fragments, have which of the following properties? a) they are double stranded b) they are removed by nuclease activity c) they are DNA_RNA hybrids d) they arise form the nicking of the sugar phosphate backbone of the parental DNA chain e) they contain covalently linked DNA and RNA
e
side chain of phenylalanine: a) sylfhydryl group b) alcoholic group c) branched chain hydrocarbon d) no side chain e) aromatic ring
e
the structural stability of the double helix of DNA is ascribed in part to: a) hydrogen bonding between adjacent purine bases b) ionic bonding between stacked purine and pyrimidine bases c) hydrogen bonding between adjacent pyrimidine bases d) the helical structure of the molecule e) hydrogen bonding between the purine and the pyrimidine bases
e
the three-dimensional structure of protein is maintained by: a) disulfide linkages b) hydrophobic bonds c) hydrogen bonds d) ionic bonds e) all of the above
e
what covalent bonds are commonly found in proteins? a) hydrogen bonds b) hydrophobic bonds c) pleated sheet d) electrostatic bond e) disulfide bond
e
which of the following groups of amino acid residues would be expected to have all their side chains in a charged state at physiological pH? a) Glu Tyr Asn b) Met Cys Lys c) His Ser Arg d) Asp His Tyr e) Arg Asp Lys
e
which of the following statements concerning native DNA is correct? a) 2 strands are same in base sequence b) sugar-phosphate backbones contain the 5 carbon sugar ribulose c) analysis A=G and C=T is expected d) structure can be disrupted by high salt e) none of the above
e
which type of nucleic acid forms a high energy bond with an amino acid during protein synthesis? a) mRNA b) mitochondrial RNA c) nuclear DNA d) rRNA e) tRNA
e
which of the following enzymes is most sensitive to inhibition by alpha-amanatin? a) prokaryotic DNA polymerase I b) prokaryotic DNA polymerase II c) eukaryotic DNA polymerase alpha d) eukaryotic RNA polymerase I e) eukaryotic RNA polymerase II
e (doesn't affect DNA polymerases)
which describes side chain of glutamine: a) branched chain hydrocarbon b) sulfhydryl group c) aromatic ring d) methyl group e) amide
e (other is asparagine)
all of the following concerning properties of nucleic acids are correct except: a) RNA is hydrolyzed to 2'-3' nucleotides by alkali b) DNA is denatured by alkali c) DNA is denatured by high temp d) denaturation of DNA is accompanied by hyperchromism (increased UV absorption) e) RNA can't form a watson-crick type double helix
e (tRNA can, partially)
