VIII - Genetics Flashcards
(170 cards)
1
Q
Central Dogma
A
Replication → Transcription → Translation
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)
3
Q
Deoxynucleotides covalently linked by 3’,5’-phosphodiester bonds
A
DeoxyAdenylate, DeoxyGuanylate, DeoxyCytidylate, Thymidylate
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
5
Q
Enzymatically cleaves phosphodiester bonds at the ends
A
Exonucleases
6
Q
Enzymatically cleaves phosphodiester bonds in the middle
A
Endonucleases
7
Q
Strands that run in opposite directions
A
Antiparallel Strands
8
Q
Held together by hydrogen bonds and hydrophobic interactions, adenine to thymine, guanine to cytosine
A
Complementary Base airing
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
10
Q
Temperature at which one half of the helical structure is lost (denaturation)
A
Melting Temperature
11
Q
DNA: right-handed helix with 10 residues per 360° turn
A
B-DNA
12
Q
DNA: moderately dehydrated B form, right-handed with 11 base pairs per turn
A
A-DNA
13
Q
DNA: left-handed helix that contains about 12 base pairs per turn, alternating purines and pyrimidines
A
Z-DNA
14
Q
Five classes of small, positively charged proteins that form ionic bonds with negatively charged DNA
A
Histones
15
Q
2 each of histones H2A, H2B, H3 and H4 form a structural core around which DNA is wrapped creating a
A
nucleosome
16
Q
The DNA connecting the nucleosomes is called _____ and is bound to histone ___.
A
linker DNA, H1
17
Q
Further packing of DNA due to hydrophobic interactions and in association with other non-histone proteins compacts it into
A
chromatin
18
Q
Chromatin: densely packed and transcriptionally inactive during interphase, observed by electron microscopy
A
Heterochromatin
19
Q
Chromatin: transcriptionally active that stains less densely
A
Euchromatin
20
Q
Nucleofilament, nucleosomes that are packed more tightly, organized into loops that are anchored by a nuclear scaffold containing several proteins
A
Polynucleosome
21
Q
DNA: coding regions are interrupted by
A
intervening sequences
22
Q
DNA: more than half of eukaryotic DNA is
A
unique, non-repetitive
23
Q
DNA: at least 30% of the genome consists of
A
repetitive sequences
24
Q
DNA: 1% of cellular DNA is in the
A
mitochondria
25
Occurs in the S phase of the cell cycle, semi-conservative
DNA Replication
26
DNA synthesis begins at a short sequence composed almost exclusively of AT base pairs
Origin of Replication
27
DNA Synthesis: strands are separated locally forming two
replication forks
28
DNA Synthesis: Sequence of Enzymes
DNA A Protein → Helicase → Single-Stranded DNA-Binding Proteins → DNA Topoisomerases → Primase → DNA Polymerase III → DNA Polymerase I → Ligase
29
DNA Synthesis: group of proteins that recognize the origin of replication
DNA A Protein
30
DNA Synthesis: unwinds the double helix ahead of the advancing replication fork
Helicase
31
DNA Synthesis: maintain the separation of the parental strands
Single-Stranded DNA-Binding Proteins
32
DNA Synthesis: remove supercoils that interfere with the further unwinding of the double helix
DNA Topoisomerases
33
DNA Topoisomerases: cleaves 1 strand
Swivelase (Type I)
34
DNA Topoisomerases: cleaves both strands, target of quinolone antibiotics
Gyrase (Type II)
35
DNA Synthesis: synthesize short stretches of RNA called primers, needed by DNA polymerase to begin DNA chain elongation
Primase
36
DNA Synthesis: catalyzes chain elongation using 5'-deoxyribonucleoside triphosphates as substrates, proofreads the newly synthesized DNA using its 3'→5' exonuclease activity
DNA Polymerase III
37
DNA polymerases are only able to read the template in the _____ direction and synthesize in the _____ direction
reads 3'→5', synthesizes 5'→3'
38
DNA Synthesis: fragments of the lagging strand
Okazaki Fragments
39
DNA Synthesis: removes RNA primers using its 5'→3' exonuclease activity and fills the resulting gaps
DNA Polymerase I
40
DNA Synthesis: seals the nicks between Okazaki fragments and catalyzes the final phospholipid ester linkage
Ligase
41
Prokaryotic Polymerases: gap filling and synthesis of lagging strand
Polymerase I
42
Prokaryotic Polymerases: DNA proofreading and repair
Polymerase II
43
Prokaryotic Polymerases: processive, leading strand synthesis
Polymerase III
44
Eukaryotic Polymerases: gap filling and synthesis of lagging strand
Polymerase α
45
Eukaryotic Polymerases: DNA proofreading and repair
Polymerase ε
46
Eukaryotic Polymerases: DNA repair
Polymerase β
47
Eukaryotic Polymerases: mitochondrial DNA synthesis
Polymerase γ
48
Eukaryotic Polymerases: processive, leading strand synthesis
Polymerase δ
49
Sequence of DNA Replication in Eukaryotes
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
50
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
Telomeres
51
Replace the telomeres in cells that do not age
Telomerase
52
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
Reverse Transcriptase
53
DNA Repair: mismatched strand, escaped proofreading
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
54
DNA Damage: Hereditary Non-Polyposis Colon Cancer
mismatched strand, escaped proofreading
55
DNA Repair: thymine dimers due to exposure of a cell to UV light, prevents DNA from replicating beyond the dimer
removed by UV specific endonucleases (uvrABC excinuclease) and the resulting gap is filled by DNA Polymerase I
56
DNA Damage: Xeroderma Pigmentosum
thymine dimers due to exposure of a cell to UV light, prevents DNA from replicating beyond the dimer
57
DNA Repair: abnormal bases, either spontaneous or due to the action of deaminating or alkylating compounds
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
58
DNA Repair: recognize the abnormal bases and cleave them hydrolytically from the deoxyribose-phosphate backbone, leaving an apyrimidinic or apurinic (AP) site
Glycosylases
59
DNA Repair: make a nick at the 5'-side of the AP site
AP-Endonucleases
60
DNA Repair: removes the single empty sugar-phosphate residue
Deoxyribose-Phosphate Lyase
61
DNA Repair: copying errors (single base or 2-5 base unpaired loops), methyl-directed strand cutting, exonuclease digestion and replacement
Mismatch Repair
62
DNA Repair: methyl-directed strand cutting, exonuclease digestion and replacement
Mismatch Repair
63
DNA Repair: spontaneous, chemical or radiation damage to a single base
Base Excision Repair
64
DNA Repair: base removal by N-glycosylase, abasic sugar removal and replacement
Base Excision Repair
65
DNA Repair: spontaneous, chemical or radiation damage to a DNA segment
Nucleotide Excision Repair
66
DNA Repair: removal of an approximately 30-nucleotide oligomer and replacement
Nucleotide Excision Repair
67
DNA Repair: ionizing radiation, chemotherapy, oxidative free radicals
Double-Strand Break Repair
68
DNA Repair: synapsis, unwinding, alignment, ligation
Double-Strand Break Repair
69
Polymers of nucleotides with ribose instead of deoxyribose and uracil instead of thymine
Ribonucleic Acid (RNA)
70
Nucleic Acids: deoxyribose
DNA
71
Nucleic Acids: thymine
DNA
72
Nucleic Acids: double-stranded helix
DNA
73
Nucleic Acids: Chargaff's Rule
DNA
74
Nucleic Acids: ribose
RNA
75
Nucleic Acids: uracil
RNA
76
Nucleic Acids: single stranded
RNA
77
Genetic Molecules: can be hydrolyzed by alkali to 2',3' cyclic diesters of the mononucleotides
RNA
78
RNA: most common type, associated with several proteins as a component of the ribosoms
Ribosomal RNA (rRNA)
79
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
Transfer RNA (tRNA)
80
RNA: carries genetic information from the nuclear DNA to the cytosol where it is used as the template for protein synthesis
Messenger RNA (mRNA)
81
mRNA Modifications
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
RNA: subset of RNAs significantly involved in mRNA processing and gene regulation
Small Nuclear RNA (snRNA)
83
4-subunit enzyme that synthesizes RNA, possesses 5'→3' polymerase activity
RNA Polymerase
84
Transcription: recognizes the nucleotide sequence (promoter region) at the beginning of the length of the DNA to be transcribed
Sigma Factor
85
Transcription: required for termination of transcription of some genes
Rho Factor
86
DNA Polymerase: nucleic acid synthesized
DNA
87
DNA Polymerase: template
DNA
88
DNA Polymerase: substrates
dATP, dGTP, sCTP, dTTP
89
DNA Polymerase: primer
RNA (or DNA)
90
DNA Polymerase: proofreading
present
91
RNA Polymerase: nucleic acid synthesized
RNA
92
RNA Polymerase: template
DNA
93
RNA Polymerase: substrates
ATP, GTP, CTP, UTP
94
RNA Polymerase: proofreading
absent
95
Sequence of DNA Transcription in Prokaryotes
Initiation → Elongation → Tremination
96
DNA Transcription: RNA polymerase holoenzyme binds to the promoter region
Initiation
97
DNA Transcription: stretch of six nucleotides (5'-TATAAT-3') centered about 8-10 nucleotides to the left of the transcription start site
Prinbow Box
98
DNA Transcription: second consensus nucleotide sequence (5'-TTGACA-3') about 35 bases to the left of the transcription site
-35 Sequence
99
DNA Transcription: RNA polymerase copies one strand of the DNA double helix, pairing Cs wiht Gs and As with Us, substrates are ribonucleotide triphosphates
Elongation
100
DNA Transcription: may be accomplished by RNA polymerase alone or with ρ factor
Termination
101
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
ρ Factor
102
DNA Transcription Termination: requires a stable hairpin loop turn and a palindrome sequence
ρ Independent Termination
103
RNA Polymerase: rRNAs in the nucleolus
RNA Polymerase I
104
RNA Polymerase: mRNAs
RNA Polymerase II
105
RNA Polymerase: tRNAs and snRNAs in the nucleoplasm
RNA Polymerase III
106
DNA Transcription: binding sites for proteins called general transcription factors hich in turn interact with each other with RNA polymerase II
Promoter Sequences
107
Promoter Sequences
TATA (Hogness) box, CAAT box, GC box
108
DNA Transcription: DNA sequences that increase the rate of the initiation of transcription by binding to specific transcription factors called activators
Enhancers
109
RNA Post-Transcription Modifications: Linear copy of the transcriptional unit, the segment of DNA between specific initiation and termination sequences
Primary Transcript
110
RNA Post-Transcription Modifications: synthesized from long precursor preribosomal RNAs which are cleaved and trimmed by ribonucleases
rRNA
111
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
tRNA
112
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
mRNAs
113
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
Operons
114
Proteins translated by RER ribosomes
secreted proteins, proteins inserted into the cell membrane, lysosomal enzymes
115
Proteins translated on free cytoplasmic ribosomes
cytoplasmic and mitochondrial proteins
116
Consists of three bases (triplet) written in 5'→3' direction
codon
117
Nonsense Codon
UAA, UAG, UGA
118
Initiation Codon
AUG (Methionine)
119
Genetic Code: a specific codon always codes for the same AA
Specific
120
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
Universal
121
Genetic Code: a given AA may have more than 1 codon coding for it
Redundant/Degenerate
122
Genetic Code: read from a fixed strating point as a continuous sequence of bases taken three at a time
Non-Overlaping
123
Requirements for Translation
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
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
tRNA
125
Accurate base-pairing is required only in the first 2 nucleotide positions of an mRNA codon
tRNA Wobble
126
Large complexes of protein and RNA, 2 subunits
Ribosomes
127
Prokaryotic Ribosomes
30s + 50s = 70s
128
Eukaryotic Ribosomes
40s + 60 = 80s
129
Ribosomes: binds an incoming amonoacyl-tRNA
A site
130
Ribosomes: occupied by peptidyl-tRNA
P site
131
Ribosomes: occupied by an empty tRNA as it is about to exit the ribosome
E site
132
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
Charging
133
Sequence in Translation
Initiation → Elongation → Termination
134
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
Initiation
135
Translation: purine-rich region of the mRNA base pairs with a complementary sequence
Shine-Dalgarno Sequence
136
Translation: used to position eukaryotic mRNA on the ribosome
5'-cap
137
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)
Elongation
138
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
Termination
139
Energy Requirements for Translocation
tRNA aminoacylation (ATP→AMP), loading tRNA onto ribosome (GTP→GDP), translocation (GTP→GDP)
140
Post-Translational Modification
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
Antibiotics: binds to the 30s subunit and distorts its structure, interfering with the initiation of protein synthesis
Streptomycin
142
Antibiotics: prevents binding of aminoacyl tRNAs to the A site
Tetracycline
143
Antibiotics: inhibits prokaryotic peptidyltransferase
Chloramphenicol
144
Antibiotics: bind irreversibly to the 503 subunit of the bacterial ribosome, thus inhibiting translocation
Clindamycin, Erythromycin
145
Antibiotics: binds to the β-subunit of bacterial DNA-dependent RNA polymerase and thereby inhibits RNA synthesis
Rifampicin
146
An exotoxin of Corynebacterium diphtheriae inactivates eEF-2 and thereby specifically inhibits mammalian protein synthesis
Diphtheria Toxin
147
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
Mutation
148
Point Mutations: purine-pyrimidine to purine-pyrimidine
Transition
149
Point Mutations: purine-pyrimidine to pyrimidine-purine
Transversion
150
Mutations: new codon specifies the same AA, often on the 3rd base, no effect of protein
Silent
151
Mutations: new codon specifies a different AA
Missense
152
Mutations: new codon specifies a stop codon
Nonsense
153
Mutations: deletion or addition of a base
Frame Shift
154
Mutations: unusual crossover in meiosis, loss of function
Large Segment Deletion
155
Mutations: a splice site is lost, Tay-Sachs, Gaucher, β-thalassemia
Splice Donor/Acceptor
156
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
Triple Repeat Expansion
157
Used to deduce original sequence of DNA, dideoxynucleotides halt DNA polymmerization at each base, generating sequences of various lengths that encompass the entire sequence
Sanger DNA Sequencing
158
Molecular biology lab procedure that is used to synthesize many copies of a desired fragment of DNA
Polymerase Chain Reaction
159
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
Polymerase Chain Reaction
160
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
Southern Blot
161
Involves radioactive DNA probes whoch bind to sample RNA, measures sizes and amounts of specific mRNA molecules
Northern Blot
162
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
Western Blot
163
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
Microarrays
164
Rapid immunologic technique used to test for antigen-antibody reactivity, intense color reaction
Enzyme-Linked Immunoabsorbent Assay (ELISA)
165
Fluorescent probe binds to specific gene site of interest, specific localization of genes and direct visualization of anomalies at the molecular level
Fluorescence In Situ Hybridization (FISH)
166
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
Restriction Fragment Length Polymorphism
167
Production of a recombinant DNA molecule that is self-perpetuating
Cloning
168
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
Cloning
169
Tissue mRNA is isolated and exposed to reverse transcriptase forming a cDNA (lacks introns) library
Cloning
170
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
Gene Therapy
