DNA structure, replication, and repair Flashcards
Intervening segments of DNA that do not code for amino acid sequence of the polypeptide product
Intervening sequence or introns
Coding segments of DNA
Exons
In higher eukaryotes, the typical gene has more of which sequences: intron or exons?
Introns
The sequence of DNA that fuctions during cell division as an attachment point for proteins that link the chromosome to the mitotic spindle
Centromere
Sequences of DNA at the ends of eucharyotic chromosomes that help stabilize the chromosome
Telomeres
DNA supercoiling is generally a manifestation of strutural strain. T/F
T
What is supercoiling?
The coiling of a coil, as in a telephone cord
Supercoiling is an intrinsic property of DNA tertiary structure. T/F
T
Many circular DNA molecules remain highly supercoiled even after they are extracted and purified, freed from protein and other cellular components.
What is a nucleosome?
The structural unit composed of a DNA molecule coiled around histone proteins
Histones are very rich in which amino acids?
Arg, Lys
The bead of each nucleosome contains how many molecules?
Eight
The part of the DNA that makes contact with the histone proteins are locally rich in which base pairs?
A-T
Histones are able to undergo which of the following modifications?
A. Acetylation B. Ubiquitination C. Methylation D. All of the Above E. A and B only
D
Which of the ff. statement does not refer to a gene?
A. Locatable region of a genomic sequence
B. Corresponds to the unit of inheritance
C. Associated with regulatory genes transcribed and other functional sequence regions.
D. Region of the genome that is resistant to spontaneous mutation
E. None of the above
E
Which of the following is correct?
A. Humans are the most intelligent organisms because they have the most number of genes
B. Nuclear genes of organelle expression insures survival of prokaryotic-like structures in the cell
C. The fetal gene must undergo massive “rearrangement” to support phenotypic changes with development
D. The more genes an organism has, the better it is for organism protection
E. Junk DNAs are plenty because the junk proteins they encode promote genomic stability
B
Which of the following statements regarding the human mitochondrial genome is “INCORRECT”?
A. It is maternally-derived B. It does not undergo recombination C. It assumes a plasmid structure D. There is an overlapping use of DNA sequences for coding genes E. Introns occur in a few genes
E
What are epigenetic information?
Information that is passed from one generation to the next but is not encoded in DNA sequences
Chromatin regions where active gene transcription if occurring, making it partially decondensed
Euchromatin
The four deoxyribonucleotides of DNA
Deoxyadenylate, deoxyguanylate, deoxycytidylate, thymidylate
The greater the number of supercoils, the less the stress or tortion. T/F
F
The more supercoild, the more stress or tortion
What is negative supercoil?
It is when the molecules is twisted in the opposite direction from the clockwise tuens of the right handed double helix of B-DNA.
What are topoisomerases?
They are enzymes that catalyze the topologic changes of DNA.
Which enzymes can relax or insert supercoils to DNA, using ATP as an energy source?
Topoisomerases
Chromatin consists of which molecules?
DNA molecule and histone and non-histone proteins
What is the most abundant chromatin protein?
Histones
Densely packed transcriptionally inactive chromatin
Heterochromatin
The centromere is rich in which base pair?
A-T
Which enzyme is responsible for telomere synthesis?
Telomerase
The repeat of sequence 5’-TTAGGG-3’ is found on which part of the chromosome?
Telomeres
What does semi-conservative replication mean?
It refers to the DNA replication in which the parent DNA strand is separated, and the daughter DNA molecules synthesized are made of half the parent strand and half a new strand
The phases of DNA replication
Initiation, elongation, termination
Which DNA replication phase is known to be regulated?
Initiation
How often does DNA replication occur?
Once every cell cycle
Which enzyme unzips the double helix?
DNA helicase
The origin of replication is rich in which bases?
A-T
Which direction does DNA helicase unzip DNA?
5’ to 3’
To begin elongation of DNA replication, which primer is synthesized at the beginning of the leading strand?
RNA primer
Which enzyme synthesizes RNA primer in eukaryotes?
DNA polymerase
DNA helicase moves along which strand?
Lagging strand
DNA helicase and the leading strand synthesis move towards the same direction. T/F
T
Which enzyme synthesizes deoxyneucleotides?
DNA polymerase
Which of the following statements is/are FALSE?
A. Polymerases synthesize nucleic acids in the 3’ to 5’
direction.
B. 3’ to 5’ exonuclease activity is utilized for proofreading.
C. Error rates tend to be lower in primed synthesis than in
unprimed synthesis.
D. Both A and C.
A
Which of the following statements is/are FALSE?
A. Replication of double-stranded DNA is a semiconservative process
B. DNA synthesis is continuous on the lagging strand
C. DNA synthesis is a continuous on the leading strand
D. Both B and C
B
The entire complex responsible for coordinated DNA synthesis at a replication fork
Replisome
Okazaki fragments are found of which DNA strand?
Lagging strand
Which enzymes seal the fragments of newly synthesized DNA?
DNA ligase
Which of the following DNA molecules will form the most stable hairpin loop structure?
A. 5’ATGCCCGATGCCGGAT3’
B. 5’AAAAAAAATTTTTTTTTT3’
C. 5’CGGUUUCCGGGAAACC3’
D. 5’GGGGGGGCCCCCCCCC3’
D
Which of the following is true about ligases?
A. Catalyze highly exergonic reactions to join nucleic acid strands
B. Covalently join ends of nucleic acids
C. Hydrolyze phosphodiester bonds of sugar phosphate backbone
D. Initiate DNA synthesis by extending RNA primers
B
A hydrolase that catalyzes the hydrolysis of phosphodiester bonds of a nucleic acid backbone.
Nuclease
A nuclease that catalyzes the stepwise removal of single nucleotide residues from one end of a nucleic acid chain
Exonuclease
A nuclease that catalyzes the hydrolysis of Endo-
phosphodiester bonds between nucleotide residues that may occur anywhere along the length of a nucleic acid strand or duplex.
Endonucleases
An enzyme that catalyzes the formation of a phosphodiester bond between terminal nucleotide residues (usually a 3’ terminal nucleotide residue and a 5’ terminal nucleotideresidue), producing a continuous sugar-phosphate backbone structure
Nucleic acid ligase
An enzyme that catalyzes the polymerization of a nucleic acid from nucleoside triphosphates.
Nucleotide polymerase
Which of the following statements is/are TRUE regarding nucleases?
(a) A recognition sequence of a restriction enzyme is said to be a palindrome if it is complementary to itself.
(b) A 3’ to 5’ endonuclease catalyzes the hydrolytic removal of individual nucleotide residues from the 3’ end of a nucleic acid strand.
(c) Cohesive ends are produced when the positions of hydrolytic cleavage due to the action of a restriction enzyme on the two strands of a DNA double helix are staggered with respect to one another.
(d) All of the above
(e) (a) and (b) only
A
Which of the following statements is/are TRUE regarding nucleic acid ligases?
(a) They catalyze the recombination of nucleic acid molecules.
(b) They covalently join the ends of nucleic acid strands.
(c) They hydrolyze high-energy bonds such as the phosphoanhydride bonds of ATP.
(d) All of the above
(e) (a) and (b) only
D
Which of the following statements is/are TRUE regarding nucleic acid polymerases?
(a) Nucleic acid polymerization occurs in the 5’ to 3’ direction.
(b) 3’ to 5’ exonuclease activity is utilized for proofreading.
(c) Error rates are typically higher in unprimed synthesis than in primed synthesis.
(d) All of the above
(e) (a) and (b) only
D
DNA can direct the synthesis of new DNA, while RNA can direct the synthesis of new RNA. T/F
T
DNA can direct the synthesis of RNA and vice versa. T/F
T
The totality of genetic information in a biologic system
Genome
The junction at which point the separated complementary strands join form a double helix
Replication fork
In replication, which enzyme destroys the RNA primer so that it can be replaced by a deoxynucleotide?
Exonucleases
Exposed template DNA is maintained in a single-stranded form by molecules which minimize the formation of hairpin loop structures along the
template that would otherwise interfere with DNA polymerization. What is this molecule?
Single strand binding protein (SSBP) or helix-destabilizing protein
For the following DNA sequence, determine the sequence and direction of the complementary strand.
5 – ATCGATCGATCGATCG – 3
(A) 5 – ATCTATCGATCGATCG – 3 (B) 3 – ATCGATCGATCGATCG – 5 (C) 5 – CGAUCGAUCAUCGAU – 3 (D) 5 – CGATCGATCGATCGAT – 3 (E) 3 – CGATCGATCGATCGAT – 5
D
In DNA, the bond between the deoxyribose sugar and the phosphate is which of the following?
(A) A polar bond (B) An ionic bond (C) A hydrogen bond (D) A covalent bond (E) A van der Waals bond
D
The backbone of a DNA strand is composed of which of the following?
(A) Sugars and bases (B) Phosphates and sugars (C) Bases and phosphates (D) Nucleotides and sugars (E) Phosphates and nucleosides
B
Which of the following statements is INCORRECT?
A. Nucleases catalyze hydrolysis of phosphodiester bonds.
B. An exonuclease catalyzes stepwise removal of single nucleotide residues.
C. A restriction enzyme is a type of endonuclease.
D. The DNA sequence “GCAACG” is a palindromic DNA sequence.
D
Which of the following statements is INCORRECT?
A. Ligases catalyze recombination of nucleic acid molecules.
B. Ligases covalently join the ends of nucleic acid strands.
C. Ligases hydrolyze high-energy phosphoanhydride bonds.
D. Ligases initiate DNA synthesis by extending RNA primers.
D
Which of the following statements is CORRECT?
A. Nucleic acid polymerization occurs in the 3’ to 5’ direction.
B. 5’ to 3’ exonuclease activity is utilized for proofreading.
C. Error rates tend to be higher in primed synthesis than in unprimed synthesis.
D. DNA primase catalyzes unprimed synthesis of RNA primers using a DNA template.
D
Which of the following properties of DNA is false?
A. forms Watson-Crick base pairing
B. nucleotides are joined by phosphodiester bond
C. has a 5’ to 3’ directionality
D. made up of nucleotides UMP, GMP, CMP, and AMP
E. used as template for RNA synthesis
D
Which of the following is/are FALSE?
A. Every DNA contains deoxyribose and every RNA contains ribose
B. Every DNA contains thymine and every RNA contains uracil
C. In DNA, each nitrogenous base is covalently linked to a phosphate
C
Which is/are FALSE?
A. A-DNA is predominant
B. A-DNA is left-handed
C. B-DNA is right-handed
D. A and B
D
Which of the following statements is CORRECT?
A. There is repulsion of groups in DNA at neutral pH
B. The sugar residues are negatively charge at neutral pH
C. The sugar residues are positively charge at neutral pH
D. The phosphate groups are neutral at neutral pH
A
In which of the following cellular compartments is DNA found?
a. Nucleus
b. Nucleus and mitochondria only
c. Nucleus and cytoplasm
d. Nucleus, mitochondria and cytoplasm
e. Nucleus, mitochondria and chloroplast
e
The following exhibit circular forms of DNA except:
a. mitochondrial DNA
b. x chromosome
c. puc16
d. bacterial genome
e. plasmid
b
Responsible for excising mispaired DNA sequences
a. Helicase
b. Topoisomerase
c. RNA polymerase
d. DNA polymerase
d
About the DNA, which of the following is false?
a. Watson-Crick base pairing
b. Nucleotide connected by phosphodiester bonds
c. The components are ATP, GTP, CTP, TTP
d. Used as template for protein synthesis
d
Which of the following interactions LEAST contributes to the stability of the double-helical structure of DNA?
A. Hydrogen bonding between thymine and adenine
B. Hydrogen bonding between cytosine and guanine
C. Hydrophobic stacking interactions between stacked base pairs
D. Electrostatic interactions between sugar-phosphate backbones
D
Nuclease for proof reading during DNA replication
3’ to 5’ exonuclease
Nuclease that removes RNA primer so that it can be replaced by DNA
5’ to 3’ exonuclease
DNA polymerase in prokaryotes with 3’ to 5’ exonuclease activity
DNA polymerase I, III
DNA polymerase in prokaryotes with 5’ to 3’ exonuclease activity
DNA polymerase I
DNA polymerase in prokaryotes that synthesizes DNA in gaps between Okazaki fragments
DNA polymerase I
Which of the following processes does not require energy from the phosphoanhydride bonds of ATP?
a. Helicase-catalyzed unwinding of DNA
b. Polymerase-catalyzed synthesis of nucleic acids (DNA or RNA)
c. Endonuclease-catalyzed cutting of DNA
d. Ligase-catalyzed joining of DNA
c
When a mismatch occurs in DNA replication, how is the mistake identified?
The parent DNA strand is methylated. The mistake would be on the unmethylated, therefore, newly synthesized strand
Which of the following statements is/are TRUE regarding nucleic acid synthesis?
(a) Replication of double-stranded DNA is regarded as a semiconservative process since each daughter molecule consists of a template DNA strand derived from the parent
molecule and a newly synthesized complementary DNA strand.
(b) DNA synthesis is continuous on the leading strand and discontinuous on the lagging strand.
(c) The strand of a double-stranded DNA molecule that serves as the actual template for the transcription of RNA is referred to as the antisense strand.
(d) All of the above
(e) (a) and (b) only
d
