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Self-Study Flashcards

1
Q

deoxyribonucleic acid (DNA)

A

is the carrier of genetic information in both prokaryotes and eukaryotes

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2
Q

genome

A

Total genetic information of an organism

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3
Q

chromosomes

A

Genetic information (DNA) divided into independent domains

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4
Q

genes

A

Segments of DNA that are transcribed to direct the transcription of RNA

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5
Q

composition of nucleic acids

A

bases, sugars, and phosphate groups

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6
Q

purines

A

Double rings: adenine (A) and guanine (G)

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7
Q

Pyrimidines

A

Single rings: cytosine (C), thymine (T), uracil (U)

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8
Q

pyrimidine found in DNA only

A

Thymine

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9
Q

pyrimidine found in RNA only

A

Uracil

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10
Q

Purines/pyrimidine bases and pentose

A

nucleoSides

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11
Q

The pentose in RNA

A

Ribose

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12
Q

The pentose in DNA

A

deoxyribose

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13
Q

Phosphorylated nucleosides (such as mono, di or tri phosphates)

A

NucleoTides

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14
Q

how many bonds for AT base pairing?

A

2 hydrogen bonds

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15
Q

how many bonds for GC base pairing?

A

3 hydrogen bonds

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16
Q

enzyme

A

a catalyst, increases the rate of a chemical reaction but is not itself changed in the reaction

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17
Q

The molecule(s) acted upon by the enzyme

A

substrate(s)

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18
Q

contains the substrate binding site and the catalytic site of the enzyme

A

active site

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19
Q

Nucleases

A

hydrolyzes phosphodiester bonds

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20
Q

hydrolysis

A

breakdown of compound by chemical reaction with H2O

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21
Q

exonucleases

A

cleave the last nucleotide residue at either of the two terminals

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22
Q

endonucleases

A

cleave phosphodiester bonds in the interior of the polynucleotide

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23
Q

Nucleases that act only with specific base sequences

A

restriction endonucleases

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24
Q

DNA conformation primarily found in cells

A

B-DNA

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25
Q

conformation DNA-RNA hybrid during transcription

A

A-DNA

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26
Q

conformation found within DNA sequences that control gene transcription.

A

Z-DNA

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27
Q

Denaturation …

A

occurs at high temperatures, extreme pH ranges or extreme ionic strengths; under these conditions the double strands of DNA completely separate

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28
Q

Topoisomerases

A

Specific enzymes that regulate superhelices. They catalyze the breaking and rejoining of DNA strands

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29
Q

phosphodiesterases

A

any enzyme that breaks a phosphodiester bond

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30
Q

Type I topoisomerases

A

breaks only one DNA strand, allowing it to rotate about the other to relieve the supercoil, and ligates the break after supercoil is relieved

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31
Q

Type II topoisomerases

A

breaks both DNA strands, relaxes the supercoil, and then reseals the DNA

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32
Q

gyrases

A

topoisomerases that relieve supercoiling generated by the unwinding of DNA

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33
Q

cruciforms

A

Regions of DNA in which interchain hydrogen bonds are disrupted and intrachain bonds form - function in control of replication and transcription.

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34
Q

generally forms in DNA regions with a string of purine bases

A

Triple-stranded DNA with Hoogsteen base pairing (triplex)

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35
Q

In eukaryotic cells, almost all DNA is associated with a complex of basic proteins called …

A

Histones

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36
Q

Prokaryotic DNA does not contain histones; the DNA is associated with

A

HU proteins.

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37
Q

composition of histones

A

2 each of H2A, H2B, H3, and H4, forms histone disk around which DNA if supercoiled

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38
Q

H1 histone

A

An additional histone protein that does not form part of the disk but serves to stabilize the DNA which wraps around the histone octamer

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39
Q

Nucleosome

A

DNA with the histone disk (octamer) but no H1

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40
Q

Chromatosomes

A

DNA with the histone disk and the H1 histone

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41
Q

Nucleofilament

A

contains nucleosomes and chromatosomes

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42
Q

Chromatin

A

DNA with its associated proteins (nucleoproteins including nonhistone and histone proteins)

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43
Q

site of attachment of the chromosome to the mitotic spindle

A

centromere

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44
Q

The ends of chromosomes are called

A

telomeres

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45
Q

In prokaryotic cells, DNA is organized in a single chromosome that is a

A

double-stranded circular supercoil

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46
Q

Bacterial chromosomes are compacted into ….. by interaction with HU proteins, cations, polyamines, RNA and other nonhistone proteins

A

nucleoids

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47
Q

What is this sequence? 5’GGAATCGATCTTAAGATCGATTCC3’ 3’CCTTAGCTAGAATTCTAGCTAAGG5’

A

inverted repeat or palindrome

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48
Q

What is this sequence? 5’GGAATCGATCTTTTCTAGCTAAGG3’ 3’CCTTAGCTAGAAAAGATCGATTCC5’

A

Mirror repeat

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49
Q

What is this sequence? 5’GGAATCGATCTTGGAATCGATCTT3’ 3’CCTTAGCTAGAACCTTAGCTAGAA5’

A

direct repeat

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50
Q

noncoding sections of RNA

A

introns

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51
Q

coding sections of nucleotides (DNA or RNA)

A

exons

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52
Q

the removal of introns during transcription

A

splicing

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53
Q

short segments of RNA used to start DNA replication

A

primer

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54
Q

What is a DNA polymerase?

A

enzyme that carries out replication of DNA. It cannot start DNA synthesis, needs a primer

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55
Q

primers are synthesize by….

A

primase

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56
Q

In prokaryotes, removal of a mispairing during replication is done by …

A

Pol I, II, and III (acting as 3’–>5’ exonucleases)

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57
Q

enzyme that removes primers in prokaryotes

A

Pol I - acting as a 5’–>3’ exonuclease

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58
Q

What is released when a phosphodiester bond is formed?

A

pyrophosphate

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59
Q

What is semi-conservative replication?

A

the two parental strands separate, each strand is a template for synthesis of a complementary daughter strand

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60
Q

DNA helicases

A

unwinds the strands of DNA, allowing strands to separate

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61
Q

series of short pieces of DNA on the lagging strand

A

okazaki fragments

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62
Q

What are the functions of DNA polymerase I?

A

* primarily synthesizes that the lagging strand * can proofread the newly synthesized DNA and remove errors (3’—>5’ exonuclease activity) * only Pol I can remove primers (5’–>3’ exonuclease activity) * intermediate processivity

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63
Q

What are the functions of DNA polymerase II?

A

* involved primarily in DNA repair * can proofread DNA and remove errors (3’—>5’ exonuclease activity) * low processivity

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64
Q

What are the functions of DNA polymerase III?

A

* primarily synthesizes the leading strand * can proofread DNA and remove errors (3’—>5’ exonuclease activity) * high processivity

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65
Q

processivity

A

ability of an enzyme to remain on its substrate during synthesis

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66
Q

sliding clamp

A

prevents pol III from dissociating from the template until replication is complete

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67
Q

Origin of Replication (Ori)

A

sequence on the DNA strand where DNA polymerase and the primase initially bind

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68
Q

How many point (s) of origin of replication for prokaryotic cells?

A

One

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69
Q

How many point (s) of origin of replication for eukaryotic cells?

A

multiple points

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70
Q

In eukarytic cells, what are DNA segments between origins of replication called?

A

replicons

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71
Q

What phase of the cell cycle does replication in eukaryotic cells occur?

A

S (Synthesis) phase

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72
Q

What is the cell cycle controlled by in eukaryotic cell replication?

A

Cyclin-dependent kinases (CDKs)

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73
Q

What are the characterictics of DNA pol delta (eukaryotic)?

A

* high processitivity * catalyzes replication of the leading strand * proofreading function (3’—>5’ exonuclease activity)

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74
Q

The high processitivity of pol delta is due to what?

A

proliferating cell nuclear antigen (PCNA) - serves as a clamp

75
Q

What are the characteristics of DNA pol alpha (eukaryotic)?

A

* low processivity * synthesizes the lagging strand * functions as a primase * disassembles the nucleosome prior to DNA replication

76
Q

enzyme used in the replication of eukaryotic telomeres

A

telomerase (a reverse transcriptase)

77
Q

reverse transcriptases

A

enzymes that use RNA as a template for DNA synthesis

78
Q

rearranging DNA sequences by breaking and rejoining existing DNA molecules

A

DNA recombination

79
Q

What is homologous genetic recombination?

A

DNA versions (alleles) of the same gene can be switched from one chromatid to another allowing for recombination of genes

80
Q

At what stage does homologous genetic recombination occur?

A

prophase of meiosis

81
Q

What is conservative site-specific recombination?

A

insertion of bacteriophage DNA into bacterial genome

82
Q

Transposition

A

jumping genes or movement of DNA from one site to another within a chromosome

83
Q

What type of RNA is a direct carrier of genetic information from DNA to protein?

A

messenger RNA (mRNA)

84
Q

What is the half-life for mRNA?

A

minutes to several hours (shortest half life of all RNAs)

85
Q

what is a poly A tail?

A

* many mRNA’s contain a poly A tail (20-200 adenine nucleotides) * length of tail determines stability of the mRNA

86
Q

describe the general structure of a eukaryotic mRNA

A

* 5’-methylated cap (inverted methylated base) * leader sequence (5’-nontranslated sequence) * start codon * stop codon * 3’-nontranslated sequence * poly A tail

87
Q

what is the purpose of the 5’cap on eukaryotic mRNA?

A

guards against attack

88
Q

what % of RNA is made up of tRNA?

A

15%

89
Q

What is the acceptor stem of tRNA?

A

amino acids attach to this active site - which is 3’OH terminal CCA

90
Q

What are the two functions of tRNA?

A

* functions to activate amino acids for protein synthesis * recognizes codons in mRNA to ensure that the correct AA is incorporated into the peptide chain *

91
Q

What is ribosomal RNA (rRNA)?

A

components of ribosomes where protein synthesis takes place

92
Q

What % of cellular RNA is rRNA?

A

80%

93
Q

ribosomes are complexes composed of RNA and protein molecules that form …

A

particles

94
Q

What are Svedberg units (S)?

A

particles are named according to their sedimentation coefficient during centrifuge calculated in S units.

95
Q

What is the size of the small particle in prokaryotic ribosomes?

A

30S subunit (16S rRNA and 21 proteins)

96
Q

What is the size of the large particle in prokaryotic ribosomes?

A

50S (23S and 5S rRNAs and 34 proteins)

97
Q

In prokaryotic ribosomes, the large and small subunits form …

A

the 70S particle

98
Q

What is the size of the small particle in eukaryotic ribosomes?

A

40 S (18S rRNA and 30 proteins)

99
Q

What is the size of the large particle in eukaryotic ribosomes?

A

60S (28S, 5.8S, 5S rRNAs and 50 proteins)

100
Q

In eukaryotic ribosomes, the large and small subunits form …

A

80S particle

101
Q

small nuclear RNA (snRNA)

A

recognizes introns on mRNA participating in splicing

102
Q

Where are rRNAs synthesized?

A

nucleolus

103
Q

small cytoplasmic RNA (scRNA)

A

RNA involved in the selection of proteins for export where it serves as a signal recognition particle

104
Q

What are mitochondrial RNAs (mtRNAs)

A

* includes tRNA, rRNA, and mRNA that are transcribed from mitochondrial DNA * accounts for ~4% of cellular RNA

105
Q

ribonucleoprotein particles (RNP)

A

these small RNA/protein molecules function in RNA processing, splicing, transport, control of translation and protein recognition that target proteins for export

106
Q

RNAs that are enzymes are called…

A

ribozymes

107
Q

Where does transcription take place?

A

nucleus or mitochondria

108
Q

the point at which DNA is initially opended during transcription

A

transcription bubble

109
Q

What is the promoter?

A

nucleotide sequence recognized by RNA polymerase for the initiation of transcription

110
Q

What is the Pribnow box?

A

essential part of the promoter site for DNA transcription, with the sequence TATAAT

111
Q

transcription can be increased by the presence of sequences called

A

enhancers (serve as binding sites for protein)

112
Q

transcription can be decreased by the presence of sequences called

A

repressors

113
Q

Errors in RNA biosynthesis are much more common than in DNA b/c

A

RNA polymerases have no editing or proofreading activity

114
Q

What are the subunits for prokaryotic RNA polymerase?

A

two alphas, beta, beta prime, omega and sigma - forming the holoenzyme

115
Q

what is the core enzyme (prokaryotic RNA pol)?

A

the holoenzyme without sigma subunit

116
Q

What does the sigma subunit of prokaryotic RNA polymerase do?

A

it recognizes the promoter

117
Q

name the product of Eukaryotic RNA polymerase I

A

rRNA

118
Q

name the product of Eukaryotic RNA polymerase II

A

mRNA

119
Q

name the product(s) of Eukaryotic RNA polymerase III

A

tRNA, 5S rRNA

120
Q

name the product (s) of Eukaryotic mitochondrial RNA polymerase

A

all types (rRNA, tRNA, mRNA)

121
Q

name the product (s) of Eukaryotic RNA polymerase in E.coli

A

all types (rRNA, tRNA, mRNA)

122
Q

a mushroom poison

A

amanitin

123
Q

What inhibitor is eukaryotic RNA pol II sensitive to?

A

alpha-amanitin (very sensitive)

124
Q

What inhibitor is eukaryotic RNA pol III sensitive to?

A

alpha-amanitin

125
Q

What inhibitor is eukaryotic mitochondrial RNA pol sensitive to?

A

rifampicin

126
Q

What inhibitor is eukaryotic RNA pol in E.coli sensitive to?

A

rifampicin

127
Q

Which eukaryotic RNA pol is responsible for 50% of cellular RNA biosynthesis?

A

RNA pol I

128
Q

Which eukaryotic RNA pol is responsible for 20-40% of cellular RNA biosynthesis?

A

RNA pol II

129
Q

Which eukaryotic RNA pol is responsible for 10% of cellular RNA biosynthesis?

A

RNA pol III

130
Q

what are the 3 stop codons?

A

UAA, UAG, UGA

131
Q

What is the start codon?

A

AUG (methionine)

132
Q

Which two amino acids only have one code each?

A

Methionine (AUG); Tryptophan (UGG)

133
Q

wobble effect

A

the ability for an anticodon to pair with more than one codon

134
Q

What is inosine (I)?

A

a nucleotide, makes the anticodon less specific

135
Q

Activation of aminoacyl-tRNA synthetases catalyze two reactions?

A

* activation of the AA with ATP forms the aminoacyl group * transfers the aminoacyl group to tRNA

136
Q

what are the 2 methionyl-tRNAs in prokaryotes?

A
  • initiator tRNA (initiates protein synthesis): fmet-tRNA - Met-tRNA - carries Met for other positions in the protein
137
Q

What is the Shine-Dalgarno sequence?

A

the 5’ nontranslated leader sequence of mRNA that allows the mRNA to be correctly aligned on the rRNA small subunit

138
Q

What is the function of antibiotics?

A

to interfere with the ability of cell to synthesize proteins

139
Q
  • Prevents binding of fmet-tRNA to the small subunit of prokaryotic ribosomes - Interferes with initiation of protein synthesis and causes misreading of codons
A

streptomycin

140
Q

What is streptomycin?

A
  • Prevents binding of fmet-tRNA to the small subunit of prokaryotic ribosomes - Interferes with initiation of protein synthesis and causes misreading of codons
141
Q

Inhibits binding of aminoacyl-tRNAs to the mRNA-ribosome complex

A

tetracyclines

142
Q

tetracyclines

A

Inhibits binding of aminoacyl-tRNAs to the mRNA-ribosome complex

143
Q
  • An analog of aminoacyl-tRNA; binds to A-site and stops chain elongation - Works well in both prokaryotes and eukaryotes
A

puromycin

144
Q

puromycin

A
  • An analog of aminoacyl-tRNA; binds to A-site and stops chain elongation - Works well in both prokaryotes and eukaryotes
145
Q

Inhibits peptidyl transferase in prokaryotes

A

erythromycin

146
Q

erythromycin

A

Inhibits peptidyl transferase in prokaryotes

147
Q

inhibits peptidyl transferase in eukaryotes

A

cycloheximide

148
Q

cycloheximide

A

inhibits peptidyl transferase in eukaryotes

149
Q

a toxin from castor beans, inactivates the rRNA by attacking the rRNA and removing adenine

A

ricin

150
Q

ricin

A

a toxin from castor beans, inactivates the rRNA by attacking the rRNA and removing adenine

151
Q

What are the steps involved in protein synthesis?

A
  1. Formation of the protein initiation complex - Shine-Dalgarno sequence pairs with complementary bases of the rRNA on the small ribosome subunit - fMet-tRNAfmet is added at the peptidyl site (P site) 2. Large ribosome subunit joins the initiation complex 3. 2nd AA is placed at the aminoacyl site (A site) 4. Elongation - formation of the peptide chain 5. Protein synthesis is complete with the stop codon moving to the A site 6. Protein is released from the ribosome
152
Q

What is the general structure of amino acids?

A

central alpha carbon with these attachments: * carboxylic group (COOH) amino group (NH2) * hydrogen atom * side chain (R group)

153
Q

which form (isomer) of AA is found in human proteins?

A

L isomer - the AA has its amino group to the left

154
Q

what is the chemical bond formed between amino acids?

A

peptide bond

155
Q

what is glutathione?

A

plays a role in repairing oxidative damage to cell membrane

156
Q

what is the composition of glutathione?

A

glutamate-cysteine-glycine

157
Q

What is the primary structure of protein?

A

order of the AA residues

158
Q

What is the secondary structure of proteins?

A

folding of the chain

159
Q

What is the tertiary structure of proteins?

A

the 3D structure

160
Q

What is the quaternary structure of proteins?

A

multi-subunit protein composed of discrete polypeptide subunits with non-covalent bonds

161
Q

What are the 4 types of secondary structures in proteins?

A

* alpha helix * beta pleated sheet * beta turn * random coil

162
Q

What are globular proteins?

A
  • have a tertiary structure that resembles globes (e.g. globin) - generally are soluble in aqueous solutions
163
Q

What are fibrillar proteins?

A

* have tertiary structure resembling rods (e.g. collagen) * generally insoluble in aqueous solutions

164
Q

what is the final conformation of protein folding called?

A

native structure

165
Q

chaperones

A

family of proteins that assist in the protein folding process

166
Q

what are the 4 types of interactions/forces that exist during protein folding

A
  • disulfide bonds - hydrophobic interactions - hydrogen bonds - ionic (electrostatic ) interactions
167
Q

what are disulfide bonds?

A

covalent linkages are formed between -SH groups in cysteines to produce cystine (S-S bond)

168
Q

which strutural level (s) does denaturation effect?

A

secondary, tertiary and quaternary structures

169
Q

What are the prokaryotic DNA polymerases

A

Pol I, II, III

170
Q

What are the eukaryotic DNA polymerases?

A

Pol alpha and delta

171
Q

Histone mRNAs lack the …. and have a ….

A

poly A tail; very short half-life

172
Q

Novobiocin

A

an antibiotic that blocks the binding of ATP (blocks type II topoisomerases)

173
Q

Which topoisomerase requires ATP? Type I or Type II?

A

Type II

174
Q

Nalidixic acid

A

-interferes with breakage and rejoining of DNA (inhibits gyrases) - an antibiotic used in urinary tract infections which are often resistant to more commonly used antibiotics

175
Q

Abnormalities in formation of …-stranded DNA may lead to Hereditary Persistence of Fetal Hemoglobin. Transcription of the fetal hemoglobin chain is repressed by ….. If a mutation occurs, base change in the …, the … will not be able to form and fetal hemoglobin chain gene transcription continues.

A

Abnormalities in formation of triple stranded DNA may lead to Hereditary Persistence of Fetal Hemoglobin. Transcription of the fetal hemoglobin chain is repressed by triple-stranded DNA. If a mutation occurs (base change in the polypurines), the triple-helix will not be able to form and fetal hemoglobin chain gene transcription continues.

176
Q

…-stranded DNA forms in the immunoglobulin genes that undergo recombination. This recombination of genes is responsible for antibody diversity. … is also present in the ends ….

A

Quadruplex DNA (four-stranded) forms in the immunoglobulin genes that undergo recombination. This recombination of genes is responsible for antibody diversity. Quadruplex DNA is also present in the ends of chromosomes - the telomeres.

177
Q

3’- azido-2’, 3’-dideoxythymidine (AZT)

A

an inhibitor of reverse transcriptases, used in the treatment of AIDS

178
Q

Rifampicin

A

an antibiotic that inhibits RNA Polymerase by binding to the β subunit

179
Q

Creutzfeldt–Jakob disease (CJD)

A
  • nervous system dysfunction including ataxia, dementia, and paralysis and is almost always fatal. - Fibrous amyloid-like plaques develop in the brain and cause degeneration
180
Q

Creutzfeldt–Jakob disease (CJD) is believed to be caused by a misfolding in the

A

prion protein that changes the protein from its normal soluble cellular conformation to insoluble amyloid fibers.

181
Q

True or False: The primers needed for DNA replication are short segments of RNA

A

True

182
Q

All introns begin with a … sequence, which is the … site and end with …, the … site.

A

All introns begin with a GU sequence, which is the donor site and end with AG, the acceptor site.

183
Q

During its processing the mRNA primary transcript becomes bound to…. … remove introns through splicing. Splice sites are determined by the … : … and ….

A

During its processing the mRNA primary transcript becomes bound to small nuclear ribonucleoproteins, called snRNPs or snurps. Snurps remove introns through splicing. Splice sites are determined by the snurps, U1RNA and U2RNA.

CMB (5 decks)

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