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

Unit 5: Central Dogma of Molecular Biology Flashcards

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
Q

Identify the class of DNA polymerase:
polymerization of the newly formed DNA strand

A

DNA Pol III

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26
Q

Identify the class of DNA polymerase:
repairing enzymes

A

DNA Pol II, IV, V

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27
Q

Identify the term:
removing incorrect nucleotides during DNA replication

A

proofreading

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28
Q

Identify the term:
removing incorrect nucleotides from DNA and replacing them with correct ones

A

repair

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29
Q

Identify the term:
complex of DNA polymerase, the RNA primer, primase, and helicase at the replication fork

A

replisomes

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30
Q

Identify the complex:
carry out DNA replication

A

replisomes

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31
Q

Identify the enzyme:
class II topoisomerase

A

DNA gyrase

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32
Q

Identify the enzyme:
catalyzes reactions involving relaxed, circular DNA with a nick in one strand to the supercoiled form with the nick sealed

A

DNA gyrase

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33
Q

T/F:
Prokaryotic DNA is positively supercoiled.

A

false; negatively
(opening the helix during replication introduces positive supercoils ahead of the replication fork)

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34
Q

Identify the enzyme:
fights positive supercoils and places negative supercoils ahead of the replication fork

A

DNA gyrase

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35
Q

Identify the enzyme:
ensures that the newly synthesized DNA automatically assumes the supercoiled shape

A

DNA gyrase

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36
Q

Identify the enzyme:
helix-destabilizing protein that promotes unwinding by binding at the replication fork

A

helicase

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37
Q

Identify the protein:
stabilizes single-stranded regions by binding tightly to them

A

single-strand binding protein (SSB)

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38
Q

Identify the NA:
serves as a primer in DNA replication

A

RNA

39
Q

Identify the enzyme:
makes a short section of RNA to act as a primer for DNA synthesis

A

primase

40
Q

Identify the complex:
located at the replication fork; consists of the RNA primer, primase, and helicase

A

primosome

41
Q

Identify the enzyme:
commences synthesis of DNA

A

DNA polymerase III

42
Q

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

A

DNA Pol I

43
Q

Identify the enzyme:
responsible for the final linking of the new strand

A

DNA ligase

44
Q

Identify the protein:
part of the Pol III enzyme that opens the sliding clamp and inserts the DNA chain

A

clamp loader

45
Q

Identify the term:
errors in replication that occur spontaneously only once in every 109-1010 base pairs and can be lethal to organisms

A

mutations

46
Q

Identify the process:
where cut-and-patch process catalyzed by Pol I takes place

A

replication

47
Q

Identify the process:
removal of the RNA primer by the 5’ exonuclease function of the polymerase

A

cutting

48
Q

Identify the process:
the incorporation of the required deoxynucleotides by the polymerase function of the same enzyme

A

patching

49
Q

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

A

Nick translation

50
Q

Identify the agents:
bring about a mutation

A

mutagens

51
Q

Enumerate:
inclusions of mutagens

A
  1. ultraviolet light
  2. ionizing radiation
  3. various chemical agents or free radicals
52
Q

Enumerate:
DNA damage types

A
  1. endogenous
  2. exogenous
53
Q

Enumerate:
endogenous DNA damage types

A
  1. cellular metabolic processes
  2. mismatch of DNA bases
  3. hydrolysis
  4. oxidation
  5. alkylation
54
Q

Enumerate:
exogenous DNA damage types

A
  1. environmental factors
  2. UV radiation
  3. ionizing radiation
  4. chemical agents
55
Q

Enumerate:
4 repair mechanisms

A
  1. mismatch repair
  2. base-excision repair
  3. nucleotide-excision repair
  4. nonhomologous DNA end-joining (NHEJ)
56
Q

Identify the repair mechanism:
enzymes recognize that 2 bases are incorrectly paired

A

mismatch repair

57
Q

Identify the enzyme:
In mismatch repair, area of mismatch is removed, and area is replicated again by?

A

DNA polymerases

58
Q

Identify the repair mechanism:
damaged base is removed by DNA glycosylase leaving an AP site (apurinic or apyridiminic)

A

base-excision repair

59
Q

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 ____________.

A

AP endonuclease
exonuclease

60
Q

Identify the repair mechanism:
common for DNA lesions caused by UV or chemical means

A

nucleotide-excision repair

61
Q

Identify the enzyme:
In nucleotide-excision repair, section containing the lesion is removed by?

A

ABC exinuclease

62
Q

Identify the repair mechanism:
breakage of both strands of a DNA molecule; pose a big threat to the stability of the genome

A

double-stranded breaks (DSB)

63
Q

Enumerate:
double-stranded breaks (DSB) repair mechanisms

A
  1. nonhomologous DNA end-joining (NHEJ)
  2. recombination
64
Q

Identify the repair mechanism:
for mismatch of DNA bases

A

mismatched repair system (MMR)

65
Q

Identify the repair mechanism:
for hydrolysis, oxidation, and alkylation

A

base excision repair (BER)

66
Q

Identify the repair mechanism:
for UV radiation

A

nucleotide excision repair (NER)

67
Q

Identify the repair mechanism:
for ionizing radiation and chemical agents

A

double-strand breaks

68
Q

Identify the process:
natural process in which genetic information is rearranged to form new associations

A

genetic recombination

69
Q

Identify the type of recombination:
involves a reaction between homologous sequences

A

homologous recombination

70
Q

Identify the type of recombination:
involves combination of different nucleotide sequences

A

nonhomologous recombination

71
Q

Identify the zone:
DNA recombination occurs in specific zones of chromosome called?

A

hot spots

72
Q

Identify the model:
describes how recombination occurs by the breakage and reunion of DNA strands so that physical exchange of DNA parts takes place

A

holiday model

73
Q

T/F:
Prokaryotic DNA replication is more complicated than eukaryotic DNA replication.

A

false;
eukaryotic - more complicated

74
Q

Enumerate reasons:
why eukaryotic DNA replication is more complicated

A
  1. multiple origins of replication
  2. need to control the timing to that pf cell divisions
  3. involvement of more proteins and enzymes
75
Q

Enumerate:
In eukaryotic DNA replication, cell growth and division are divided into what phases

A

M
G1
S
G2

76
Q

T/F:
eukaryotic replication can be initiated only by chromosomes from cells that have reached the G1 phase

A

true

77
Q

Identify the protein:
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)

78
Q

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

A

replication activator protein (RAP)

79
Q

Identify the protein:
proteins that are essential for DNA replication; some are cytosolic

A

replication licensing factors (RLFs)

80
Q

Identify the term:
combination of the DNA, ORC, RAP, and RLFs that makes DNA competent for replication

A

pre-replication complex (pre-RC)

81
Q

Identify the protein:
produced in one part of the cell cycle and degraded in another

A

cyclins

82
Q

Identify the enzyme:
cyclins combine with?

A

cyclin-dependent protein kinases (CDKs)

83
Q

Identify the phase in eukaryotic replication:
where DNA has been replicated

A

G2 phase

84
Q

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

A

mitosis

85
Q

Enumerate 5 eukaryotic DNA polymerases

A
  1. polymerase α
  2. polymerase δ
  3. polymerase ε
  4. polymerase β
  5. polymerase γ
86
Q

Identify the type of eukaryotic DNA polymerase:
makes primers

A

polymerase α

87
Q

Identify the type of eukaryotic DNA polymerase:
principal DNA polymerase in eukaryotes

A

polymerase δ

88
Q

Identify the type of eukaryotic DNA polymerase:
involved in leading strand replication

A

polymerase ε

89
Q

Identify the type of eukaryotic DNA polymerase:
a repair enzyme

A

polymerase β

90
Q

Identify the type of eukaryotic DNA polymerase:
carries out DNA replication in mitochondria

A

polymerase γ

91
Q

Identify the term:
eukaryotic equivalent of the part of Pol III that functions as a sliding clamp (β)

A

PCNA

92
Q

Identify the term:
trimer of 3 identical proteins that surround the DNA

A

PCNA

93
Q

Identify the term:
special structures found in the ends of eukaryotic chromosomes

A

telomeres

94
Q

Identify the enzyme:
ribonuclear protein that contains a section of RNA that is the complement of the telomere

A

telomerase

Biochem-Lec (5 decks)

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