LEC: Nucleic Acids Flashcards
(151 cards)
1
Q
Parts of a nucleotide
A
Base, monosaccharide, phosphate
2
Q
Which bases are classified as purine?
A
Adenine, Guanine
3
Q
Which bases are classified as pyrimidine?
A
Cytosine, Thymine, Uracil
4
Q
A compound that consists of D-ribose or 2-deoxy-D-ribose bonded to a purine or pyrimidine base by a -N-glycosidic bond
A
Nucleoside
5
Q
A nucleoside in which a molecule of phosphoric acid is esterified with an –OH of the monosaccharide, most commonly either at the 3’or the 5’–OH.
Guanidine 3’-triphosphate (3’-GTP)
A
Nucleotide
6
Q
serves as a common currency into which energy gained from food is converted and stored.
A
Adenosine 5’-triphosphate (ATP)
7
Q
Identify the structure: the sequence of nucleotides, beginning with the nucleotide that has the free 5’ terminus.
A
primary
8
Q
Identify the structure: The ordered arrangement of nucleic acid strands.
A
secondary
9
Q
A type of 2° structure of DNA in which two polynucleotide strands are coiled around each other in a screw-like fashion
A
Double helix
10
Q
DNA is coiled around proteins called ____
A
histones
11
Q
T/F: histones are rich in acidic amino acids with negative charge
A
F. They are rich in basic amino acids with positive charge
12
Q
The negatively-charged DNA molecules and positively-charged histones attract one another and form units called _____.
A
nucleosomes
13
Q
A core of eight histone molecules around which the DNA helix is wrapped.
A
Nucleosome
14
Q
Nucleosomes are further condensed into _____
A
chromatin
15
Q
Chromatin fibers are organized into loops, and the loops into the bands that provide the superstructure of _____
A
chromosomes
16
Q
Enumerate the 3 differences in the structure of DNA and RNA
A
(1) DNA bases are A, G, C, and T; the RNA bases are A, G, C, and U.
(2) The sugar in DNA is 2-deoxy-D-ribose; in RNA it is D-ribose.
(3) DNA is almost always double stranded; there are several kinds of RNA, all of which are single-stranded.
17
Q
This RNA transports amino acids to site or protein synthesis
A
tRNA (transfer)
18
Q
This RNA combines with proteins to form ribosomes, the site of protein synthesis
A
rRNA (ribosomal)
19
Q
This RNA directs amino acid sequence of proteins
A
mRNA (messenger)
20
Q
This RNA processes initial mRNA to its mature form in eukaryotes
A
snRNA (small nuclear)
21
Q
This RNA affects gene expression; important in growth and development
A
miRNA (micro)
22
Q
This RNA affects gene expression; used by scientists to knowck out a gene being studied
A
siRNA (small interfering)
23
Q
A segment of DNA that carries a base sequence that directs the synthesis of a particular protein, tRNA, or mRNA.
A
Gene
24
Q
A section of DNA that, when transcribed, codes for a protein or RNA.
A
Exon
25
A section of DNA that does not code for anything functional
Intron
26
T/F: in bacteria, the gene is continuous
T
27
T/F: in higher organisms, the gene is continuous
F. It is discontinuous
28
T/F: there is only 1 gene in a single DNA molecule
F. there are many
29
_____ may lead to new treatments for cancer, infectious diseases, and chronic illnesses.
Manipulating RNA
30
____ drugs are already on the market with more in stages of clinical trials.
RNA-based
31
Enumerate the 2 functions of DNA in the chromosome
(1) It reproduces itself. This process is called replication.
(2) It supplies the information necessary to make all the RNA and proteins in the body, including enzymes.
32
Replication begins at a point in the DNA called the origin of replication or a _____
replication fork
33
This reaction eliminates some of the positive charges on histones and weakens the strength of the DNA-histone interaction
acetylation-deacetylation of lysine residues on histones
34
_____ temporarily introduce either single- or double-strand breaks in DNA
Topoisomerases (also called gyrases)
35
Once the supercoiling is relaxed, the broken strands are joined together and the _____ diffuses from the location of the replication fork.
topoisomerase
36
Replication of DNA molecules starts with the _____ of the double helix which can occur at either end or in the middle.
unwinding
37
Special unwinding proteins called _____, attach themselves to one DNA strand and cause the separation of the double helix.
helicases
38
short—4 to 15 nucleotides long—RNA oligonucleotides synthesized from ribonucleoside triphosphates. They are needed to initiate the primase-catalyzed synthesis of both daughter strands.
Primers
39
The enzyme enables complementary base pairing with high specificity.
DNA polymerase
40
Millions of copies of selected DNA fragments can be made within a few hours with high precision by a technique called _____
polymerase chain reaction (PCR)
41
Identify the structure: Order of bases in the polynucleotide sequence
primary
42
Identify the structure: Three-dimensional conformation of the polynucleotide backbone
secondary
43
Identify the structure: Supercoiling of the molecule
Tertiary
44
Identify the structure: Interaction with other classes of macromolecules, such as proteins
quaternary
45
_____ or _____ bases bonded to sugars, which in turn are bonded to phosphate groups
Purine, pyrimidine
46
Nitrogen-containing aromatic compounds that make up the coding portion of nucleic acids
Nucleic acid bases
47
Compounds that contain a six-membered ring
Pyrimidine
48
Compounds that contain a six-membered ring fused to a five-membered ring
Purine
49
Parent compounds of adenine and guanine
Purine
50
Lacks phosphate group (Nucleoside or nucleotide)
Nucleoside
51
Considered the normal, physiological DNA form
B-DNA
52
Right-handed helix, with an inner diameter of 11Å
B-DNA
53
10 base pairs per turn of the helix
B-DNA
54
Right-handed helix but thicker than B-DNA
A-DNA
55
11 base pairs per turn of the helix
A-DNA
56
T/F: A-DNA are often found in in vivo techniques
F. A-DNA are not found in in vivo techniques
57
Left-handed double helix
Z-DNA
58
May play a role in the regulation of gene expression
Z-DNA
59
Occurs in nature and usually consists of alternating purine-pyrimidine bases
Z-DNA
60
Produced by flipping one side of the backbone 180˚ without disturbing the backbone covalent bonds or hydrogen bonds
Z-DNA
61
In standard B-DNA, each base is rotated ____ (what angle) with respect to the preceding one
32°
62
Perfect for maximal base pairing but not optimal for maximum overlap of bases
B-DNA
63
T/F: Bases that are exposed to the major groove must come in contact with water
F. minor grooves must come in contact with water
64
Which is more optimal, base-pairing or base stacking?
Base stacking
65
Type of double-stranded DNA in which the 5′ and 3′ ends of each strand are joined by phosphodiester bonds
Circular DNA
66
Cut the phosphodiester backbone of one strand, pass the other end through, and reseal
Class I Topoisomerase
67
Cut both strands, pass some of the remaining DNA helix between the cut ends, and reseal
Class II Topoisomerase
68
Bacterial topoisomerase that introduces negative supercoils into DNA
DNA gyrase
69
Enzymes that relax supercoiling in closed circular DNA
Topoisomer (gyrase)
70
Complex of DNA and protein found in eukaryotic nuclei
Chromatin
71
T/F: the structure and spacing of nucleosome does not affect the chromatin function
F
72
Bases absorb light in the ____-wavelength region
260-nm
73
T/F: As the DNA is heated and the strands separate, the wavelength of absorption changes and the amount of light absorbed increases
F. the wavelength does not change
74
T/F: renaturation is possible in DNA
T (on slow cooling)
75
used to monitor the dissociation and reassociation of ribosomes
Analytical ultracentrifugation
76
Identify the RNA: Initially formed as a larger precursor molecule called heterogeneous nuclear RNA (hnRNA)
mRNA
77
Identify the RNA: Present in cells in relatively small amounts and is short-lived
mRNA
78
Identify the RNA: recently discovered
snRNA
79
Identify the RNA: Protection mechanism in many species, with the siRNAs being used to eliminate expression of an undesirable gene; used in the study of gene expression
RNA interference
80
Identify the RNA: used in the treatment of hepa C
miRNA
81
Identify the RNA: used in the treatment of ebola virus
siRNA
82
Used to develop treatments for cystic fibrosis and sickle-cell anemia
CRISPR (Cas)
83
Clustered regularly interspaced short palindromic repeats
CRISPR (Cas)
84
Promising and controversial model for study for future therapies
Long noncoding RNA (lncRNA)
85
Process of duplication of DNA
Replication
86
Process of formation of RNA on a DNA template
Transcription
87
Process of protein synthesis
Translation
88
_____ are those viruses in which RNA is the genetic material rather than DNA
Retroviruses
89
Enzyme that directs the synthesis of DNA on an RNA template
Reverse transcriptase
90
Retroviruses are catalyzed by ____
Reverse transcriptase
91
Scheme used to describe the manner in which information is transferred in a cell
Central dogma of molecular biology
92
DNA double helix unwinds at a specific point called an _____
origin of replication
93
Points at which new polynucleotide chains are formed
Replication forks
94
Bubble, or eye, of newly synthesized DNA between regions of the original DNA is a manifestation of the advance of the two replication forks in opposite directions
θ structure
95
Synthesized continuously from its 5′ end to its 3′ end at the replication fork on the exposed 3′ to 5′ template strand
Leading strand
96
Synthesized semidiscontinuously in small fragments, or Okazaki fragments
Lagging strand
97
Fragments are linked together by the enzyme _____
DNA ligase
98
This compound has been widely used in the treatment of AIDS (acquired immune deficiency syndrome), as has 2′-3′-dideoxyinosine (DDI)
3′-azido-3′-deoxythymidine (AZT)
99
Number of nucleotides incorporated before the dissociation of enzyme from the template
Processivity
100
T/F: DNA polymerase catalyzes de novo synthesis
F. DNA cannot catalyze de novo synthesis
101
Identify the DNA polymerase: Repairing and patching DNA
DNA pol I
102
Identify the DNA polymerase: Polymerization of the newly formed DNA strand
DNA pol III
103
Identify the DNA polymerase: Repairing enzymes
DNA pol II, IV, V
104
Removing incorrect nucleotides during DNA replication
Proofreading
105
Removing incorrect nucleotides from DNA and replacing them with correct ones
Repair
106
2 exonuclease activities
Proofreading and repair
107
Complex of DNA polymerase, the RNA primer, primase, and helicase at the replication fork
Replisomes
108
Catalyzes reactions involving relaxed, circular DNA with a nick in one strand to the supercoiled form with the nick sealed
DNA gyrase: Class II topoisomerase
109
Prokaryotic DNA is _____ (positively/negatively) supercoiled
negatively
110
Opening the helix during replication introduces _____ (positive/negative) supercoils ahead of the replication fork
positive
111
DNA gyrase fights _____ (positive/negative) supercoils
positive
112
Stabilizes single-stranded regions by binding tightly to them
Single-strand binding protein (SSB)
113
Promotes unwinding by binding at the replication fork
Helicase
114
Helix-destabilizing protein
Helicase
115
T/F: Primer activity was first observed in vivo
T
116
____ serves as a primer in DNA replication
RNA
117
Enzyme that makes a short section of RNA to act as a primer for DNA synthesis
Primase
118
Complex at the replication fork that consists of the RNA primer, primase, and helicase
Primosome
119
Errors in replication that occur spontaneously only once in every 109–1010 base pairs and can be lethal to organisms
mutations
120
Cut-and-patch process catalyzed by _____ (what polymerase) takes place during replication
Pol I
121
Removal of RNA primer or DNA mistakes by Pol I using its 5′ → 3′ exonuclease activity as it moves along the DNA and then filling in behind it with its polymerase activity
Nick translation
122
Agents that bring about a mutation
mutagens
123
Leads to a break in phosphodiester backbone of the DNA strand
Free radicals
124
Creates pyrimidine dimers
UV light
125
___ electrons from two carbons on each of the two pyrimidines form a cyclobutyl ring that distorts the normal shape of the DNA
π
126
In BER, the damaged base is removed by _____
DNA glycosylase
127
Identify the damage: Pose a big threat to the stability of the genome
Double-stranded breaks (DSB)
128
Natural process in which genetic information is rearranged to form new associations
Genetic recombination
129
DNA recombination occurs in specific zones of the chromosome, which are called _____
hot spots
130
Describes how recombination occurs by the breakage and reunion of DNA strands so that physical exchange of DNA parts takes place
Holliday model
131
Which is more complicated, eukaryotic or prokaryotic DNA replication?
Eukaryotic
132
Enumerate the reasons why eukaryotic DNA replication is more complicated
Multiple origins of replication
Need to control the timing to that of cell divisions
Involvement of more proteins and enzymes
133
Identify the eukaryotic replication complex: Bound to the DNA throughout the cell cycle but serves as an attachment site for several proteins that help control replication
Origin recognition complex (ORC)
134
Identify the eukaryotic replication protein: Protein whose binding prepares for the start of DNA replication
Replicator activator protein (RAP)
135
Identify the eukaryotic replication factor: Proteins that are essential for DNA replication; Some are cytosolic
Replication licensing factors (RLFs)
136
Combination of the DNA, ORC, RAP, and RLFs that makes DNA competent for replication
Pre-replication complex (pre-RC)
137
Proteins that are produced in one part of the cell cycle and degraded in another
Cyclins
138
Cyclins combine with _____
cyclin-dependent protein kinases (CDKs)
139
Eukaryotic replication: In the ___ phase, DNA has been replicated
G2
140
Identify the polymerase: Makes primers
Polymerase α
141
Identify the polymerase: Principal DNA polymerase in eukaryotes
Polymerase δ
142
Identify the polymerase: Involved in leading strand replication
Polymerase ε
143
Identify the polymerase: a repair enzyme
Polymerase β
144
Identify the polymerase: carries out DNA replication in mitochondria
Polymerase γ
145
This polymerase interacts with PCNA (proliferating cell nuclear antigen)
Polymerase δ
146
This polymerase may replace polymerase δ in lagging strand synthesis
Polymerase ε
147
Eukaryotic equivalent of the part of Pol III that functions as a sliding clamp (β)
PCNA
148
Trimer of three identical proteins that surround the DNA
PCNA
149
Special structures found in the ends of eukaryotic chromosomes
Telomeres
150
Ribonuclear protein that contains a section of RNA that is the complement of the telomere
Telomerase
151
Function of telomerase
Provides a mechanism for synthesis of telomeres; reactivated in cancer cells
