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BCHEM 2ND SHIFT > LEC: Nucleic Acids > Flashcards

LEC: Nucleic Acids Flashcards

1
Q

Parts of a nucleotide

A

Base, monosaccharide, phosphate

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2
Q

Which bases are classified as purine?

A

Adenine, Guanine

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3
Q

Which bases are classified as pyrimidine?

A

Cytosine, Thymine, Uracil

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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

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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

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6
Q

serves as a common currency into which energy gained from food is converted and stored.

A

Adenosine 5’-triphosphate (ATP)

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7
Q

Identify the structure: the sequence of nucleotides, beginning with the nucleotide that has the free 5’ terminus.

A

primary

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8
Q

Identify the structure: The ordered arrangement of nucleic acid strands.

A

secondary

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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

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10
Q

DNA is coiled around proteins called ____

A

histones

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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

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12
Q

The negatively-charged DNA molecules and positively-charged histones attract one another and form units called _____.

A

nucleosomes

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13
Q

A core of eight histone molecules around which the DNA helix is wrapped.

A

Nucleosome

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14
Q

Nucleosomes are further condensed into _____

A

chromatin

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15
Q

Chromatin fibers are organized into loops, and the loops into the bands that provide the superstructure of _____

A

chromosomes

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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.

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17
Q

This RNA transports amino acids to site or protein synthesis

A

tRNA (transfer)

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18
Q

This RNA combines with proteins to form ribosomes, the site of protein synthesis

A

rRNA (ribosomal)

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19
Q

This RNA directs amino acid sequence of proteins

A

mRNA (messenger)

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20
Q

This RNA processes initial mRNA to its mature form in eukaryotes

A

snRNA (small nuclear)

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21
Q

This RNA affects gene expression; important in growth and development

A

miRNA (micro)

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22
Q

This RNA affects gene expression; used by scientists to knowck out a gene being studied

A

siRNA (small interfering)

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23
Q

A segment of DNA that carries a base sequence that directs the synthesis of a particular protein, tRNA, or mRNA.

A

Gene

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24
Q

A section of DNA that, when transcribed, codes for a protein or RNA.

A

Exon

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25
Q

A section of DNA that does not code for anything functional

A

Intron

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26
Q

T/F: in bacteria, the gene is continuous

A

T

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27
Q

T/F: in higher organisms, the gene is continuous

A

F. It is discontinuous

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28
Q

T/F: there is only 1 gene in a single DNA molecule

A

F. there are many

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29
Q

_____ may lead to new treatments for cancer, infectious diseases, and chronic illnesses.

A

Manipulating RNA

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30
Q

____ drugs are already on the market with more in stages of clinical trials.

A

RNA-based

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31
Q

Enumerate the 2 functions of DNA in the chromosome

A

(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.

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32
Q

Replication begins at a point in the DNA called the origin of replication or a _____

A

replication fork

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33
Q

This reaction eliminates some of the positive charges on histones and weakens the strength of the DNA-histone interaction

A

acetylation-deacetylation of lysine residues on histones

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34
Q

_____ temporarily introduce either single- or double-strand breaks in DNA

A

Topoisomerases (also called gyrases)

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35
Q

Once the supercoiling is relaxed, the broken strands are joined together and the _____ diffuses from the location of the replication fork.

A

topoisomerase

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36
Q

Replication of DNA molecules starts with the _____ of the double helix which can occur at either end or in the middle.

A

unwinding

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37
Q

Special unwinding proteins called _____, attach themselves to one DNA strand and cause the separation of the double helix.

A

helicases

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38
Q

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.

A

Primers

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39
Q

The enzyme enables complementary base pairing with high specificity.

A

DNA polymerase

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40
Q

Millions of copies of selected DNA fragments can be made within a few hours with high precision by a technique called _____

A

polymerase chain reaction (PCR)

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41
Q

Identify the structure: Order of bases in the polynucleotide sequence

A

primary

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42
Q

Identify the structure: Three-dimensional conformation of the polynucleotide backbone

A

secondary

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43
Q

Identify the structure: Supercoiling of the molecule

A

Tertiary

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44
Q

Identify the structure: Interaction with other classes of macromolecules, such as proteins

A

quaternary

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45
Q

_____ or _____ bases bonded to sugars, which in turn are bonded to phosphate groups

A

Purine, pyrimidine

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46
Q

Nitrogen-containing aromatic compounds that make up the coding portion of nucleic acids

A

Nucleic acid bases

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47
Q

Compounds that contain a six-membered ring

A

Pyrimidine

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48
Q

Compounds that contain a six-membered ring fused to a five-membered ring

A

Purine

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49
Q

Parent compounds of adenine and guanine

A

Purine

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50
Q

Lacks phosphate group (Nucleoside or nucleotide)

A

Nucleoside

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51
Q

Considered the normal, physiological DNA form

A

B-DNA

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52
Q

Right-handed helix, with an inner diameter of 11Å

A

B-DNA

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53
Q

10 base pairs per turn of the helix

A

B-DNA

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54
Q

Right-handed helix but thicker than B-DNA

A

A-DNA

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55
Q

11 base pairs per turn of the helix

A

A-DNA

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56
Q

T/F: A-DNA are often found in in vivo techniques

A

F. A-DNA are not found in in vivo techniques

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57
Q

Left-handed double helix

A

Z-DNA

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58
Q

May play a role in the regulation of gene expression

A

Z-DNA

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59
Q

Occurs in nature and usually consists of alternating purine-pyrimidine bases

A

Z-DNA

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60
Q

Produced by flipping one side of the backbone 180˚ without disturbing the backbone covalent bonds or hydrogen bonds

A

Z-DNA

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61
Q

In standard B-DNA, each base is rotated ____ (what angle) with respect to the preceding one

A

32°

62
Q

Perfect for maximal base pairing but not optimal for maximum overlap of bases

A

B-DNA

63
Q

T/F: Bases that are exposed to the major groove must come in contact with water

A

F. minor grooves must come in contact with water

64
Q

Which is more optimal, base-pairing or base stacking?

A

Base stacking

65
Q

Type of double-stranded DNA in which the 5′ and 3′ ends of each strand are joined by phosphodiester bonds

A

Circular DNA

66
Q

Cut the phosphodiester backbone of one strand, pass the other end through, and reseal

A

Class I Topoisomerase

67
Q

Cut both strands, pass some of the remaining DNA helix between the cut ends, and reseal

A

Class II Topoisomerase

68
Q

Bacterial topoisomerase that introduces negative supercoils into DNA

A

DNA gyrase

69
Q

Enzymes that relax supercoiling in closed circular DNA

A

Topoisomer (gyrase)

70
Q

Complex of DNA and protein found in eukaryotic nuclei

A

Chromatin

71
Q

T/F: the structure and spacing of nucleosome does not affect the chromatin function

A

F

72
Q

Bases absorb light in the ____-wavelength region

A

260-nm

73
Q

T/F: As the DNA is heated and the strands separate, the wavelength of absorption changes and the amount of light absorbed increases

A

F. the wavelength does not change

74
Q

T/F: renaturation is possible in DNA

A

T (on slow cooling)

75
Q

used to monitor the dissociation and reassociation of ribosomes

A

Analytical ultracentrifugation

76
Q

Identify the RNA: Initially formed as a larger precursor molecule called heterogeneous nuclear RNA (hnRNA)

A

mRNA

77
Q

Identify the RNA: Present in cells in relatively small amounts and is short-lived

A

mRNA

78
Q

Identify the RNA: recently discovered

A

snRNA

79
Q

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

A

RNA interference

80
Q

Identify the RNA: used in the treatment of hepa C

A

miRNA

81
Q

Identify the RNA: used in the treatment of ebola virus

A

siRNA

82
Q

Used to develop treatments for cystic fibrosis and sickle-cell anemia

A

CRISPR (Cas)

83
Q

Clustered regularly interspaced short palindromic repeats

A

CRISPR (Cas)

84
Q

Promising and controversial model for study for future therapies

A

Long noncoding RNA (lncRNA)

85
Q

Process of duplication of DNA

A

Replication

86
Q

Process of formation of RNA on a DNA template

A

Transcription

87
Q

Process of protein synthesis

A

Translation

88
Q

_____ are those viruses in which RNA is the genetic material rather than DNA

A

Retroviruses

89
Q

Enzyme that directs the synthesis of DNA on an RNA template

A

Reverse transcriptase

90
Q

Retroviruses are catalyzed by ____

A

Reverse transcriptase

91
Q

Scheme used to describe the manner in which information is transferred in a cell

A

Central dogma of molecular biology

92
Q

DNA double helix unwinds at a specific point called an _____

A

origin of replication

93
Q

Points at which new polynucleotide chains are formed

A

Replication forks

94
Q

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

A

θ structure

95
Q

Synthesized continuously from its 5′ end to its 3′ end at the replication fork on the exposed 3′ to 5′ template strand

A

Leading strand

96
Q

Synthesized semidiscontinuously in small fragments, or Okazaki fragments

A

Lagging strand

97
Q

Fragments are linked together by the enzyme _____

A

DNA ligase

98
Q

This compound has been widely used in the treatment of AIDS (acquired immune deficiency syndrome), as has 2′-3′-dideoxyinosine (DDI)

A

3′-azido-3′-deoxythymidine (AZT)

99
Q

Number of nucleotides incorporated before the dissociation of enzyme from the template

A

Processivity

100
Q

T/F: DNA polymerase catalyzes de novo synthesis

A

F. DNA cannot catalyze de novo synthesis

101
Q

Identify the DNA polymerase: Repairing and patching DNA

A

DNA pol I

102
Q

Identify the DNA polymerase: Polymerization of the newly formed DNA strand

A

DNA pol III

103
Q

Identify the DNA polymerase: Repairing enzymes

A

DNA pol II, IV, V

104
Q

Removing incorrect nucleotides during DNA replication

A

Proofreading

105
Q

Removing incorrect nucleotides from DNA and replacing them with correct ones

A

Repair

106
Q

2 exonuclease activities

A

Proofreading and repair

107
Q

Complex of DNA polymerase, the RNA primer, primase, and helicase at the replication fork

A

Replisomes

108
Q

Catalyzes reactions involving relaxed, circular DNA with a nick in one strand to the supercoiled form with the nick sealed

A

DNA gyrase: Class II topoisomerase

109
Q

Prokaryotic DNA is _____ (positively/negatively) supercoiled

A

negatively

110
Q

Opening the helix during replication introduces _____ (positive/negative) supercoils ahead of the replication fork

A

positive

111
Q

DNA gyrase fights _____ (positive/negative) supercoils

A

positive

112
Q

Stabilizes single-stranded regions by binding tightly to them

A

Single-strand binding protein (SSB)

113
Q

Promotes unwinding by binding at the replication fork

A

Helicase

114
Q

Helix-destabilizing protein

A

Helicase

115
Q

T/F: Primer activity was first observed in vivo

A

T

116
Q

____ serves as a primer in DNA replication

A

RNA

117
Q

Enzyme that makes a short section of RNA to act as a primer for DNA synthesis

A

Primase

118
Q

Complex at the replication fork that consists of the RNA primer, primase, and helicase

A

Primosome

119
Q

Errors in replication that occur spontaneously only once in every 109–1010 base pairs and can be lethal to organisms

A

mutations

120
Q

Cut-and-patch process catalyzed by _____ (what polymerase) takes place during replication

A

Pol I

121
Q

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

A

Nick translation

122
Q

Agents that bring about a mutation

A

mutagens

123
Q

Leads to a break in phosphodiester backbone of the DNA strand

A

Free radicals

124
Q

Creates pyrimidine dimers

A

UV light

125
Q

___ electrons from two carbons on each of the two pyrimidines form a cyclobutyl ring that distorts the normal shape of the DNA

A

π

126
Q

In BER, the damaged base is removed by _____

A

DNA glycosylase

127
Q

Identify the damage: Pose a big threat to the stability of the genome

A

Double-stranded breaks (DSB)

128
Q

Natural process in which genetic information is rearranged to form new associations

A

Genetic recombination

129
Q

DNA recombination occurs in specific zones of the chromosome, which are called _____

A

hot spots

130
Q

Describes how recombination occurs by the breakage and reunion of DNA strands so that physical exchange of DNA parts takes place

A

Holliday model

131
Q

Which is more complicated, eukaryotic or prokaryotic DNA replication?

A

Eukaryotic

132
Q

Enumerate the reasons why eukaryotic DNA replication is more complicated

A

Multiple origins of replication
Need to control the timing to that of cell divisions
Involvement of more proteins and enzymes

133
Q

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

A

Origin recognition complex (ORC)

134
Q

Identify the eukaryotic replication protein: Protein whose binding prepares for the start of DNA replication

A

Replicator activator protein (RAP)

135
Q

Identify the eukaryotic replication factor: Proteins that are essential for DNA replication; Some are cytosolic

A

Replication licensing factors (RLFs)

136
Q

Combination of the DNA, ORC, RAP, and RLFs that makes DNA competent for replication

A

Pre-replication complex (pre-RC)

137
Q

Proteins that are produced in one part of the cell cycle and degraded in another

A

Cyclins

138
Q

Cyclins combine with _____

A

cyclin-dependent protein kinases (CDKs)

139
Q

Eukaryotic replication: In the ___ phase, DNA has been replicated

A

G2

140
Q

Identify the polymerase: Makes primers

A

Polymerase α

141
Q

Identify the polymerase: Principal DNA polymerase in eukaryotes

A

Polymerase δ

142
Q

Identify the polymerase: Involved in leading strand replication

A

Polymerase ε

143
Q

Identify the polymerase: a repair enzyme

A

Polymerase β

144
Q

Identify the polymerase: carries out DNA replication in mitochondria

A

Polymerase γ

145
Q

This polymerase interacts with PCNA (proliferating cell nuclear antigen)

A

Polymerase δ

146
Q

This polymerase may replace polymerase δ in lagging strand synthesis

A

Polymerase ε

147
Q

Eukaryotic equivalent of the part of Pol III that functions as a sliding clamp (β)

A

PCNA

148
Q

Trimer of three identical proteins that surround the DNA

A

PCNA

149
Q

Special structures found in the ends of eukaryotic chromosomes

A

Telomeres

150
Q

Ribonuclear protein that contains a section of RNA that is the complement of the telomere

A

Telomerase

151
Q

Function of telomerase

A

Provides a mechanism for synthesis of telomeres; reactivated in cancer cells

BCHEM 2ND SHIFT (7 decks)

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