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Biochem-Lec > Unit 5: Central Dogma of Molecular Biology > Flashcards

Unit 5: Central Dogma of Molecular Biology Flashcards

(94 cards)

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1
Q

Enumerate the sequence:
encoding of genetic information

A
  1. replication
  2. transcription
  3. translation
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2
Q

Identify the process:
process of duplication of DNA (requires RNA)

A

replication

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3
Q

Identify the process:
process of formation of RNA on a DNA template

A

transcription

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4
Q

Identify the process:
process of protein synthesis

A

translation

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5
Q

T/F:
During transcription, base sequence of DNA is reflected in the base sequence of RNA

A

true

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6
Q

T/F:
During translation, amino acid sequence of the protein reflects the sequence of bases in the gene that codes for that protein

A

true

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7
Q

Identify the term:
viruses in which RNA is the genetic material rather than DNA

A

retroviruses

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8
Q

Identify the enzyme:
catalyzes retroviruses and directs the synthesis of DNA on an RNA template

A

reverse transcriptase

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9
Q

Identify the type of organisms:
where most of the details of the replication process were first investigated

A

prokaryotes (E. coli)

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10
Q

Identify the process:
involves separation of the 2 original strands and production of 2 new daughter strands using the original strands as templates

A

DNA replication

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11
Q

T/F:
each daughter strand contains 1 template strand and 1 newly synthesized strand

A

true

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12
Q

Identify the point:
where DNA double helix unwinds

A

origin of replication

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13
Q

T/F:
polynucleotide chains are synthesized in one direction only from the origin of replication

A

false;
in either both or in one direction
(DNA replication is bidirectional in most organisms.)

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14
Q

T/F:
at each origin of replication there are 4 replication forks

A

false;
2 replication forks

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15
Q

Identify the points:
at which new polynucleotide chains are formes

A

replication forks

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16
Q

Differentiate prokaryotes and eukaryotes:
based on numbers of origin of replication and bubble

A

prokaryotes: 1 origin of replication, 1 bubble
eukaryotes: several origins of replication, several bubbles

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17
Q

Identify the enzyme:
acts as a nucleophile by attacking the phosphorus adjacent to the sugar in the incoming nucleotide, which has a 5’-triphosphate on its sugar

A

DNA polymerase

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18
Q

Enumerate:
2 types of strands

A
  1. leading strand
  2. lagging strand
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19
Q

Identify strand based on polymerization mode:
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

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20
Q

Identify strand based on polymerization mode:
synthesized semidiscontinuously in small fragments or Okazaki fragments

A

lagging strand

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21
Q

T/F:
in the lagging strand, 3’ end of each fragment is closer to the replication fork than the 5’ end

A

false;
5’ end is closer

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22
Q

T/F:
DNA polymerase catalyze de novo synthesis

A

false;
cannot catalyze

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23
Q

Enumerate:
requirements of DNA polymerase reactions

A
  1. presence of primer
  2. all 4 deoxyribonucleoside triphosphates
  3. Mg2+
  4. DNA template
  5. all 4 ribonucleoside triphosphates
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24
Q

Identify the class of DNA polymerase:
reparing and patching DNA

A

DNA Pol I

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25
Identify the class of DNA polymerase: polymerization of the newly formed DNA strand
DNA Pol III
26
Identify the class of DNA polymerase: repairing enzymes
DNA Pol II, IV, V
27
Identify the term: removing incorrect nucleotides during DNA replication
proofreading
28
Identify the term: removing incorrect nucleotides from DNA and replacing them with correct ones
repair
29
Identify the term: complex of DNA polymerase, the RNA primer, primase, and helicase at the replication fork
replisomes
30
Identify the complex: carry out DNA replication
replisomes
31
Identify the enzyme: class II topoisomerase
DNA gyrase
32
Identify the enzyme: catalyzes reactions involving relaxed, circular DNA with a nick in one strand to the supercoiled form with the nick sealed
DNA gyrase
33
T/F: Prokaryotic DNA is positively supercoiled.
false; negatively (opening the helix during replication introduces positive supercoils ahead of the replication fork)
34
Identify the enzyme: fights positive supercoils and places negative supercoils ahead of the replication fork
DNA gyrase
35
Identify the enzyme: ensures that the newly synthesized DNA automatically assumes the supercoiled shape
DNA gyrase
36
Identify the enzyme: helix-destabilizing protein that promotes unwinding by binding at the replication fork
helicase
37
Identify the protein: stabilizes single-stranded regions by binding tightly to them
single-strand binding protein (SSB)
38
Identify the NA: serves as a primer in DNA replication
RNA
39
Identify the enzyme: makes a short section of RNA to act as a primer for DNA synthesis
primase
40
Identify the complex: located at the replication fork; consists of the RNA primer, primase, and helicase
primosome
41
Identify the enzyme: commences synthesis of DNA
DNA polymerase III
42
Identify the enzyme: As the replication fork moves away, the RNA primer is removed by this enzyme and then replaced by deoxynucleotides and this enzyme
DNA Pol I
43
Identify the enzyme: responsible for the final linking of the new strand
DNA ligase
44
Identify the protein: part of the Pol III enzyme that opens the sliding clamp and inserts the DNA chain
clamp loader
45
Identify the term: errors in replication that occur spontaneously only once in every 109-1010 base pairs and can be lethal to organisms
mutations
46
Identify the process: where cut-and-patch process catalyzed by Pol I takes place
replication
47
Identify the process: removal of the RNA primer by the 5' exonuclease function of the polymerase
cutting
48
Identify the process: the incorporation of the required deoxynucleotides by the polymerase function of the same enzyme
patching
49
Identify the process: removal of RNA primer or DNA mistakes by Pol I using its 5' to 3' exonuclease activity as it moves along the DNA and then filling in behind it with its polymerase activity
Nick translation
50
Identify the agents: bring about a mutation
mutagens
51
Enumerate: inclusions of mutagens
1. ultraviolet light 2. ionizing radiation 3. various chemical agents or free radicals
52
Enumerate: DNA damage types
1. endogenous 2. exogenous
53
Enumerate: endogenous DNA damage types
1. cellular metabolic processes 2. mismatch of DNA bases 3. hydrolysis 4. oxidation 5. alkylation
54
Enumerate: exogenous DNA damage types
1. environmental factors 2. UV radiation 3. ionizing radiation 4. chemical agents
55
Enumerate: 4 repair mechanisms
1. mismatch repair 2. base-excision repair 3. nucleotide-excision repair 4. nonhomologous DNA end-joining (NHEJ)
56
Identify the repair mechanism: enzymes recognize that 2 bases are incorrectly paired
mismatch repair
57
Identify the enzyme: In mismatch repair, area of mismatch is removed, and area is replicated again by?
DNA polymerases
58
Identify the repair mechanism: damaged base is removed by DNA glycosylase leaving an AP site (apurinic or apyridiminic)
base-excision repair
59
Identify the enzymes: In base-excision repair, sugar and phosphate are removed from the nucleotide by an ____ _____________, and several more bases are removed by an excision ____________.
AP endonuclease exonuclease
60
Identify the repair mechanism: common for DNA lesions caused by UV or chemical means
nucleotide-excision repair
61
Identify the enzyme: In nucleotide-excision repair, section containing the lesion is removed by?
ABC exinuclease
62
Identify the repair mechanism: breakage of both strands of a DNA molecule; pose a big threat to the stability of the genome
double-stranded breaks (DSB)
63
Enumerate: double-stranded breaks (DSB) repair mechanisms
1. nonhomologous DNA end-joining (NHEJ) 2. recombination
64
Identify the repair mechanism: for mismatch of DNA bases
mismatched repair system (MMR)
65
Identify the repair mechanism: for hydrolysis, oxidation, and alkylation
base excision repair (BER)
66
Identify the repair mechanism: for UV radiation
nucleotide excision repair (NER)
67
Identify the repair mechanism: for ionizing radiation and chemical agents
double-strand breaks
68
Identify the process: natural process in which genetic information is rearranged to form new associations
genetic recombination
69
Identify the type of recombination: involves a reaction between homologous sequences
homologous recombination
70
Identify the type of recombination: involves combination of different nucleotide sequences
nonhomologous recombination
71
Identify the zone: DNA recombination occurs in specific zones of chromosome called?
hot spots
72
Identify the model: describes how recombination occurs by the breakage and reunion of DNA strands so that physical exchange of DNA parts takes place
holiday model
73
T/F: Prokaryotic DNA replication is more complicated than eukaryotic DNA replication.
false; eukaryotic - more complicated
74
Enumerate reasons: why eukaryotic DNA replication is more complicated
1. multiple origins of replication 2. need to control the timing to that pf cell divisions 3. involvement of more proteins and enzymes
75
Enumerate: In eukaryotic DNA replication, cell growth and division are divided into what phases
M G1 S G2
76
T/F: eukaryotic replication can be initiated only by chromosomes from cells that have reached the G1 phase
true
77
Identify the protein: 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)
78
Identify the protein: protein whose binding prepares for the start of DNA replication
replication activator protein (RAP)
79
Identify the protein: proteins that are essential for DNA replication; some are cytosolic
replication licensing factors (RLFs)
80
Identify the term: combination of the DNA, ORC, RAP, and RLFs that makes DNA competent for replication
pre-replication complex (pre-RC)
81
Identify the protein: produced in one part of the cell cycle and degraded in another
cyclins
82
Identify the enzyme: cyclins combine with?
cyclin-dependent protein kinases (CDKs)
83
Identify the phase in eukaryotic replication: where DNA has been replicated
G2 phase
84
Identify the process: 1. where DNA is separated into daughter cells 2. dissolved nuclear membrane permits entrance of RLFs that are produced in the cytosol
mitosis
85
Enumerate 5 eukaryotic DNA polymerases
1. polymerase α 2. polymerase δ 3. polymerase ε 4. polymerase β 5. polymerase γ
86
Identify the type of eukaryotic DNA polymerase: makes primers
polymerase α
87
Identify the type of eukaryotic DNA polymerase: principal DNA polymerase in eukaryotes
polymerase δ
88
Identify the type of eukaryotic DNA polymerase: involved in leading strand replication
polymerase ε
89
Identify the type of eukaryotic DNA polymerase: a repair enzyme
polymerase β
90
Identify the type of eukaryotic DNA polymerase: carries out DNA replication in mitochondria
polymerase γ
91
Identify the term: eukaryotic equivalent of the part of Pol III that functions as a sliding clamp (β)
PCNA
92
Identify the term: trimer of 3 identical proteins that surround the DNA
PCNA
93
Identify the term: special structures found in the ends of eukaryotic chromosomes
telomeres
94
Identify the enzyme: ribonuclear protein that contains a section of RNA that is the complement of the telomere
telomerase

Biochem-Lec (5 decks)

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