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Biochemistry > VIII - Genetics > Flashcards

VIII - Genetics Flashcards

1
Q

Central Dogma

A

Replication → Transcription → Translation

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2
Q

Polymer composed of nucleotide builduing blocks, chemical basis of heredity, grouped into genes which are the fundamental units of genetic information, double helix structure with major and minor grooves, contained in the cytoplasm of prokaryotes and the nucleus of eukaryotes

A

Deoxyribonucleid Acid (DNA)

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3
Q

Deoxynucleotides covalently linked by 3’,5’-phosphodiester bonds

A

DeoxyAdenylate, DeoxyGuanylate, DeoxyCytidylate, Thymidylate

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4
Q

5’-OH group attached to 3’-OH group, gives strands directionality, bonds are cleaved hydrolytically by chemicals or hydrolyzed enzymatically by exonucleases or endonucleases

A

3’-5’ Phosphodiester Bonds

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5
Q

Enzymatically cleaves phosphodiester bonds at the ends

A

Exonucleases

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6
Q

Enzymatically cleaves phosphodiester bonds in the middle

A

Endonucleases

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7
Q

Strands that run in opposite directions

A

Antiparallel Strands

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8
Q

Held together by hydrogen bonds and hydrophobic interactions, adenine to thymine, guanine to cytosine

A

Complementary Base airing

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9
Q

In any sample of dsDNA the amount of adenine equals the amount of thymine and the amount of guanine equals the amount of cytosine, total amount of purines equals total amount of pyrimidines

A

Chargaff’s Rule

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10
Q

Temperature at which one half of the helical structure is lost (denaturation)

A

Melting Temperature

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11
Q

DNA: right-handed helix with 10 residues per 360° turn

A

B-DNA

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12
Q

DNA: moderately dehydrated B form, right-handed with 11 base pairs per turn

A

A-DNA

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13
Q

DNA: left-handed helix that contains about 12 base pairs per turn, alternating purines and pyrimidines

A

Z-DNA

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14
Q

Five classes of small, positively charged proteins that form ionic bonds with negatively charged DNA

A

Histones

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15
Q

2 each of histones H2A, H2B, H3 and H4 form a structural core around which DNA is wrapped creating a

A

nucleosome

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16
Q

The DNA connecting the nucleosomes is called _____ and is bound to histone ___.

A

linker DNA, H1

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17
Q

Further packing of DNA due to hydrophobic interactions and in association with other non-histone proteins compacts it into

A

chromatin

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18
Q

Chromatin: densely packed and transcriptionally inactive during interphase, observed by electron microscopy

A

Heterochromatin

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19
Q

Chromatin: transcriptionally active that stains less densely

A

Euchromatin

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20
Q

Nucleofilament, nucleosomes that are packed more tightly, organized into loops that are anchored by a nuclear scaffold containing several proteins

A

Polynucleosome

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21
Q

DNA: coding regions are interrupted by

A

intervening sequences

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22
Q

DNA: more than half of eukaryotic DNA is

A

unique, non-repetitive

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23
Q

DNA: at least 30% of the genome consists of

A

repetitive sequences

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24
Q

DNA: 1% of cellular DNA is in the

A

mitochondria

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25
Q

Occurs in the S phase of the cell cycle, semi-conservative

A

DNA Replication

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26
Q

DNA synthesis begins at a short sequence composed almost exclusively of AT base pairs

A

Origin of Replication

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27
Q

DNA Synthesis: strands are separated locally forming two

A

replication forks

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28
Q

DNA Synthesis: Sequence of Enzymes

A

DNA A Protein → Helicase → Single-Stranded DNA-Binding Proteins → DNA Topoisomerases → Primase → DNA Polymerase III → DNA Polymerase I → Ligase

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29
Q

DNA Synthesis: group of proteins that recognize the origin of replication

A

DNA A Protein

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30
Q

DNA Synthesis: unwinds the double helix ahead of the advancing replication fork

A

Helicase

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31
Q

DNA Synthesis: maintain the separation of the parental strands

A

Single-Stranded DNA-Binding Proteins

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32
Q

DNA Synthesis: remove supercoils that interfere with the further unwinding of the double helix

A

DNA Topoisomerases

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33
Q

DNA Topoisomerases: cleaves 1 strand

A

Swivelase (Type I)

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34
Q

DNA Topoisomerases: cleaves both strands, target of quinolone antibiotics

A

Gyrase (Type II)

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35
Q

DNA Synthesis: synthesize short stretches of RNA called primers, needed by DNA polymerase to begin DNA chain elongation

A

Primase

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36
Q

DNA Synthesis: catalyzes chain elongation using 5’-deoxyribonucleoside triphosphates as substrates, proofreads the newly synthesized DNA using its 3’→5’ exonuclease activity

A

DNA Polymerase III

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37
Q

DNA polymerases are only able to read the template in the _____ direction and synthesize in the _____ direction

A

reads 3’→5’, synthesizes 5’→3’

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38
Q

DNA Synthesis: fragments of the lagging strand

A

Okazaki Fragments

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39
Q

DNA Synthesis: removes RNA primers using its 5’→3’ exonuclease activity and fills the resulting gaps

A

DNA Polymerase I

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40
Q

DNA Synthesis: seals the nicks between Okazaki fragments and catalyzes the final phospholipid ester linkage

A

Ligase

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41
Q

Prokaryotic Polymerases: gap filling and synthesis of lagging strand

A

Polymerase I

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42
Q

Prokaryotic Polymerases: DNA proofreading and repair

A

Polymerase II

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43
Q

Prokaryotic Polymerases: processive, leading strand synthesis

A

Polymerase III

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44
Q

Eukaryotic Polymerases: gap filling and synthesis of lagging strand

A

Polymerase α

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45
Q

Eukaryotic Polymerases: DNA proofreading and repair

A

Polymerase ε

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46
Q

Eukaryotic Polymerases: DNA repair

A

Polymerase β

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47
Q

Eukaryotic Polymerases: mitochondrial DNA synthesis

A

Polymerase γ

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48
Q

Eukaryotic Polymerases: processive, leading strand synthesis

A

Polymerase δ

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49
Q

Sequence of DNA Replication in Eukaryotes

A

identification of the origins of replication → unwinding (denaturation) of dsDNA to provide an ssDNA template → formation of the replication fork → initiation of DNA synthesis and elongation → formation of replication bubble with ligation of the newly synthesized DNA segments → reconstitution of chromatin structure

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50
Q

Stretches of highly repetitive DNA found at the ends of linear chromosomes, as cells divide and age, these sequences are shortened contributing to cell death

A

Telomeres

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51
Q

Replace the telomeres in cells that do not age

A

Telomerase

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52
Q

Retroviruses such as HIV carry their genomes in the form of ssRNA molecules, used to make a DNA copy of RNA, integrates the copy into the host cell DNA, lacks proofreading, contributes to high mutation rate

A

Reverse Transcriptase

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53
Q

DNA Repair: mismatched strand, escaped proofreading

A

identification of the mismatched strand, endonuclease nicks the mismatched strandd and the mismatched base is removed, DNA polymerase I and DNA ligase complete the repair

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54
Q

DNA Damage: Hereditary Non-Polyposis Colon Cancer

A

mismatched strand, escaped proofreading

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55
Q

DNA Repair: thymine dimers due to exposure of a cell to UV light, prevents DNA from replicating beyond the dimer

A

removed by UV specific endonucleases (uvrABC excinuclease) and the resulting gap is filled by DNA Polymerase I

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56
Q

DNA Damage: Xeroderma Pigmentosum

A

thymine dimers due to exposure of a cell to UV light, prevents DNA from replicating beyond the dimer

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57
Q

DNA Repair: abnormal bases, either spontaneous or due to the action of deaminating or alkylating compounds

A

Specific glycosylases recognize the abnormal bases and cleave them hydrolytically from the deoxyribose-phosphate backbone, leaving an apyrimidinic or apurinic (AP) site, AP-endonucleases make a nick at the 5’-side of the AP site, deoxyribose-phosphate lyase removes the single empty sugar-phosphate residue, DNA polymerase and DNA ligase complete the repair

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58
Q

DNA Repair: recognize the abnormal bases and cleave them hydrolytically from the deoxyribose-phosphate backbone, leaving an apyrimidinic or apurinic (AP) site

A

Glycosylases

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59
Q

DNA Repair: make a nick at the 5’-side of the AP site

A

AP-Endonucleases

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60
Q

DNA Repair: removes the single empty sugar-phosphate residue

A

Deoxyribose-Phosphate Lyase

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61
Q

DNA Repair: copying errors (single base or 2-5 base unpaired loops), methyl-directed strand cutting, exonuclease digestion and replacement

A

Mismatch Repair

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62
Q

DNA Repair: methyl-directed strand cutting, exonuclease digestion and replacement

A

Mismatch Repair

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63
Q

DNA Repair: spontaneous, chemical or radiation damage to a single base

A

Base Excision Repair

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64
Q

DNA Repair: base removal by N-glycosylase, abasic sugar removal and replacement

A

Base Excision Repair

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65
Q

DNA Repair: spontaneous, chemical or radiation damage to a DNA segment

A

Nucleotide Excision Repair

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66
Q

DNA Repair: removal of an approximately 30-nucleotide oligomer and replacement

A

Nucleotide Excision Repair

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67
Q

DNA Repair: ionizing radiation, chemotherapy, oxidative free radicals

A

Double-Strand Break Repair

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68
Q

DNA Repair: synapsis, unwinding, alignment, ligation

A

Double-Strand Break Repair

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69
Q

Polymers of nucleotides with ribose instead of deoxyribose and uracil instead of thymine

A

Ribonucleic Acid (RNA)

70
Q

Nucleic Acids: deoxyribose

71
Q

Nucleic Acids: thymine

72
Q

Nucleic Acids: double-stranded helix

73
Q

Nucleic Acids: Chargaff’s Rule

74
Q

Nucleic Acids: ribose

75
Q

Nucleic Acids: uracil

76
Q

Nucleic Acids: single stranded

77
Q

Genetic Molecules: can be hydrolyzed by alkali to 2’,3’ cyclic diesters of the mononucleotides

78
Q

RNA: most common type, associated with several proteins as a component of the ribosoms

A

Ribosomal RNA (rRNA)

79
Q

RNA: smallest, adaptor molecule that carries a specific AA to the site of protein synthesis, contains many unusual bases and extensive intra-chain base pairing

A

Transfer RNA (tRNA)

80
Q

RNA: carries genetic information from the nuclear DNA to the cytosol where it is used as the template for protein synthesis

A

Messenger RNA (mRNA)

81
Q

mRNA Modifications

A

adenine nucleotides on the 3’-end (poly-A tail), cap on the 5’-end consisting of 7-methylguanosine attached backward (5’-5’) through a triphosphate linkage

82
Q

RNA: subset of RNAs significantly involved in mRNA processing and gene regulation

A

Small Nuclear RNA (snRNA)

83
Q

4-subunit enzyme that synthesizes RNA, possesses 5’→3’ polymerase activity

A

RNA Polymerase

84
Q

Transcription: recognizes the nucleotide sequence (promoter region) at the beginning of the length of the DNA to be transcribed

A

Sigma Factor

85
Q

Transcription: required for termination of transcription of some genes

A

Rho Factor

86
Q

DNA Polymerase: nucleic acid synthesized

87
Q

DNA Polymerase: template

88
Q

DNA Polymerase: substrates

A

dATP, dGTP, sCTP, dTTP

89
Q

DNA Polymerase: primer

A

RNA (or DNA)

90
Q

DNA Polymerase: proofreading

91
Q

RNA Polymerase: nucleic acid synthesized

92
Q

RNA Polymerase: template

93
Q

RNA Polymerase: substrates

A

ATP, GTP, CTP, UTP

94
Q

RNA Polymerase: proofreading

95
Q

Sequence of DNA Transcription in Prokaryotes

A

Initiation → Elongation → Tremination

96
Q

DNA Transcription: RNA polymerase holoenzyme binds to the promoter region

A

Initiation

97
Q

DNA Transcription: stretch of six nucleotides (5’-TATAAT-3’) centered about 8-10 nucleotides to the left of the transcription start site

A

Prinbow Box

98
Q

DNA Transcription: second consensus nucleotide sequence (5’-TTGACA-3’) about 35 bases to the left of the transcription site

A

-35 Sequence

99
Q

DNA Transcription: RNA polymerase copies one strand of the DNA double helix, pairing Cs wiht Gs and As with Us, substrates are ribonucleotide triphosphates

A

Elongation

100
Q

DNA Transcription: may be accomplished by RNA polymerase alone or with ρ factor

A

Termination

101
Q

DNA Transcription Termination: binds to a C-rich region near the 3’-end of the newly synthesized RNA and migrates along the 5’→3’ direction until the termination site is reached

102
Q

DNA Transcription Termination: requires a stable hairpin loop turn and a palindrome sequence

A

ρ Independent Termination

103
Q

RNA Polymerase: rRNAs in the nucleolus

A

RNA Polymerase I

104
Q

RNA Polymerase: mRNAs

A

RNA Polymerase II

105
Q

RNA Polymerase: tRNAs and snRNAs in the nucleoplasm

A

RNA Polymerase III

106
Q

DNA Transcription: binding sites for proteins called general transcription factors hich in turn interact with each other with RNA polymerase II

A

Promoter Sequences

107
Q

Promoter Sequences

A

TATA (Hogness) box, CAAT box, GC box

108
Q

DNA Transcription: DNA sequences that increase the rate of the initiation of transcription by binding to specific transcription factors called activators

109
Q

RNA Post-Transcription Modifications: Linear copy of the transcriptional unit, the segment of DNA between specific initiation and termination sequences

A

Primary Transcript

110
Q

RNA Post-Transcription Modifications: synthesized from long precursor preribosomal RNAs which are cleaved and trimmed by ribonucleases

111
Q

RNA Post-Transcription Modifications: made from longer precursor molecules, must have intervening sequences (introns) removed, 5’ and 3’-ends are trimmed by ribonuclease, a 3’-CCA sequence is added and bases at specific positions are modified producing unusual bases

112
Q

RNA Post-Transcription Modifications: a 7-methylguanosine cap is attached to the 5’-terminal end and a long poly-A tail is attached to the 3’-end, introns are removed and exons are spliced together with the help of snRNAs

113
Q

Set of structural genes coding for a group of proteins required for a particular metabolic function along with the regulatory region that controls the expression of the structural genes

114
Q

Proteins translated by RER ribosomes

A

secreted proteins, proteins inserted into the cell membrane, lysosomal enzymes

115
Q

Proteins translated on free cytoplasmic ribosomes

A

cytoplasmic and mitochondrial proteins

116
Q

Consists of three bases (triplet) written in 5’→3’ direction

117
Q

Nonsense Codon

A

UAA, UAG, UGA

118
Q

Initiation Codon

A

AUG (Methionine)

119
Q

Genetic Code: a specific codon always codes for the same AA

120
Q

Genetic Code: it has been conserved from very early stages of evolution with only slight differences in the manner in which the code is translated

121
Q

Genetic Code: a given AA may have more than 1 codon coding for it

A

Redundant/Degenerate

122
Q

Genetic Code: read from a fixed strating point as a continuous sequence of bases taken three at a time

A

Non-Overlaping

123
Q

Requirements for Translation

A

AAs, specific RNA for each AA, one aminoacyl-tRNA synthetase for each AA, mRNA coding for the protein, ribosomes, protein factors, energy (ATP, GTP)

124
Q

Has an attachment site for a specific amino acid at its 3’-end, has an anticodon region that can recognize the codon specifying the AA it is carrying

125
Q

Accurate base-pairing is required only in the first 2 nucleotide positions of an mRNA codon

A

tRNA Wobble

126
Q

Large complexes of protein and RNA, 2 subunits

127
Q

Prokaryotic Ribosomes

A

30s + 50s = 70s

128
Q

Eukaryotic Ribosomes

A

40s + 60 = 80s

129
Q

Ribosomes: binds an incoming amonoacyl-tRNA

130
Q

Ribosomes: occupied by peptidyl-tRNA

131
Q

Ribosomes: occupied by an empty tRNA as it is about to exit the ribosome

132
Q

Amino-acetyl-tRNA sythetase uses an ATP to scrutinize an AA before it binds to tRNA, incorrect bond is hydrolyzed by synthetase, the AA-tRNA bond has the energy for formation of peptide ond, a mischarged tRNA reads the usual codon by inserts the wrong AA

133
Q

Sequence in Translation

A

Initiation → Elongation → Termination

134
Q

Sequence in Translation: activated by GTP hydrolysis, initiation factors (eIFs) help assemble the 40s ribosomal subunit with the initiator tRNA and are released with the complex

A

Initiation

135
Q

Translation: purine-rich region of the mRNA base pairs with a complementary sequence

A

Shine-Dalgarno Sequence

136
Q

Translation: used to position eukaryotic mRNA on the ribosome

137
Q

Translation: aminoacyl-tRNA binds to the A site (except Methionine), enzyme peptidyltransferases catalyze peptide bond formation by transfering the growing polypeptide to the amino acid on the A site, the ribosome then advances 3 nucleotides toward the 3’ end, moving the peptidyl tRNA to the P site (translocation)

A

Elongation

138
Q

Translation: releasing factors are proteins that hydrolyze the peptidyl-tRNA bond when a sto codon ccupies th A site, completed protein is released from the ribosome through hydrolysis

A

Termination

139
Q

Energy Requirements for Translocation

A

tRNA aminoacylation (ATP→AMP), loading tRNA onto ribosome (GTP→GDP), translocation (GTP→GDP)

140
Q

Post-Translational Modification

A

trimming of excess AAs, Phosphorylation, Glycosylation, Hydroxylation, defective proteins or those destined for rapid turnover are marked for destruction by Ubiquitin and are degraded by Proteasomes

141
Q

Antibiotics: binds to the 30s subunit and distorts its structure, interfering with the initiation of protein synthesis

A

Streptomycin

142
Q

Antibiotics: prevents binding of aminoacyl tRNAs to the A site

A

Tetracycline

143
Q

Antibiotics: inhibits prokaryotic peptidyltransferase

A

Chloramphenicol

144
Q

Antibiotics: bind irreversibly to the 503 subunit of the bacterial ribosome, thus inhibiting translocation

A

Clindamycin, Erythromycin

145
Q

Antibiotics: binds to the β-subunit of bacterial DNA-dependent RNA polymerase and thereby inhibits RNA synthesis

A

Rifampicin

146
Q

An exotoxin of Corynebacterium diphtheriae inactivates eEF-2 and thereby specifically inhibits mammalian protein synthesis

A

Diphtheria Toxin

147
Q

Any permanent heritable change in the DNA base sequence of an organism, has the potential to change the base sequence of mRNA and the amino acid sequence of proteins

148
Q

Point Mutations: purine-pyrimidine to purine-pyrimidine

A

Transition

149
Q

Point Mutations: purine-pyrimidine to pyrimidine-purine

A

Transversion

150
Q

Mutations: new codon specifies the same AA, often on the 3rd base, no effect of protein

151
Q

Mutations: new codon specifies a different AA

152
Q

Mutations: new codon specifies a stop codon

153
Q

Mutations: deletion or addition of a base

A

Frame Shift

154
Q

Mutations: unusual crossover in meiosis, loss of function

A

Large Segment Deletion

155
Q

Mutations: a splice site is lost, Tay-Sachs, Gaucher, β-thalassemia

A

Splice Donor/Acceptor

156
Q

Mutations: expansors in coding regions cause the protein product to be longer thatn normal and unstable, shows anticipation in pedigree, Huntington, Fragile X, myotonic dystrophy

A

Triple Repeat Expansion

157
Q

Used to deduce original sequence of DNA, dideoxynucleotides halt DNA polymmerization at each base, generating sequences of various lengths that encompass the entire sequence

A

Sanger DNA Sequencing

158
Q

Molecular biology lab procedure that is used to synthesize many copies of a desired fragment of DNA

A

Polymerase Chain Reaction

159
Q

DNA is denatures to generate 2 separate strands, during cooling, excess premade DNA primers anneal to a specific sequence on each strand to be amplified, heat-stable DNA polymerase replicates the DNA sequence following each primer

A

Polymerase Chain Reaction

160
Q

A DNA sample is electrophoresed on a gel and then transferred to a filter which is soaked in denaturant then to a labeled DNA probe that recognizes and anneals to the complementary strand, labeled DNA is them visualized on film, determines which restriction fragments of DNA are associated with a particular gene

A

Southern Blot

161
Q

Involves radioactive DNA probes whoch bind to sample RNA, measures sizes and amounts of specific mRNA molecules

A

Northern Blot

162
Q

Sample protein is separated via gel electrophoresis and transferred to afilter, labelled antibody is used to bind to relevant protein, measures amount of antigen or antibody

A

Western Blot

163
Q

Thousands of nucleic acid sequences are arranged in grids on glass or silicon, DNA or RNA probes are hybridized to the chip, a scanner detects the relative amounts of complementary binding

A

Microarrays

164
Q

Rapid immunologic technique used to test for antigen-antibody reactivity, intense color reaction

A

Enzyme-Linked Immunoabsorbent Assay (ELISA)

165
Q

Fluorescent probe binds to specific gene site of interest, specific localization of genes and direct visualization of anomalies at the molecular level

A

Fluorescence In Situ Hybridization (FISH)

166
Q

Inherited difference in the pattern of restriction, important in understanding various single-gene and multigenic diseases, diagnostic tool for diseases involving single-base changes or deletions/insertions of DNA into a restrictions fragment

A

Restriction Fragment Length Polymorphism

167
Q

Production of a recombinant DNA molecule that is self-perpetuating

168
Q

DNA fragments are inserted into bacterial plasmids that contain antibiotic resistance genes, the plasmids can be selected for using media containing antibiotic and amplified, restriction enzymes cleave DNA at 4-6 base pairs palindromic sequences, allowing for insertion of a fragment into a plasmid

169
Q

Tissue mRNA is isolated and exposed to reverse transcriptase forming a cDNA (lacks introns) library

170
Q

Treatment option for diseases caused by deficiency of a gene product, a gene is cloned into a vector that will readily be taken up and incorporated into the genome of a host cell

A

Gene Therapy

Biochemistry (14 decks)

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