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BIO105 - Genetics > Chapter 5b - The Central Dogma Revisited > Flashcards

Chapter 5b - The Central Dogma Revisited Flashcards

1
Q

DNA -> mRNA

A

transcription

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2
Q

where does mRNA leave through

A

nuclear pores

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3
Q

mRNA -> protein

A

translation

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4
Q

used to synthesize proteins

A

ribosome

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5
Q

model of DNA replication in humans

A

semiconservative

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6
Q

direction of synthesis during DNA replication

A

5’ to 3’ direction

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7
Q

needed for initiation

A

primer

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8
Q
  • enzymes and proteins needed in DNA replication
  • large protein complex that carries out DNA replication, starting at the replication origin
A

replisome

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9
Q

allows each strand of DNA to serve as a template for a new strand

A

base pairing

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10
Q
  • in DNA, adenine (A) forms a base pair with thymine (T) using two hydrogen bonds, and guanine (G) forms a base pair with cytosine (C) using three hydrogen bonds
  • in RNA, thymine is replaced by uracil (U)
A

Watson–Crick base pairing

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11
Q
  • labeled “parent” nucleotides in DNA strands with heavy nitrogen = 15N
  • label new nucleotides with lighter isotope = 14N
A

Meselson & Stahl

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12
Q

Models of DNA replication

A
  1. conservative
  2. semiconservative
  3. dispersive
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13
Q

parental double helix remains intact and all new copy is made

A

conservative

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14
Q

two strands of the parental molecule separate, and each functions as a template for synthesis of a new complementary strand

A

semiconservative

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14
Q

each strand of both daughter molecules contains a mixture of old and newly synthesized parts

A

dispersive

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15
Q

how are base pairs bonded

A

hydrogen bonding

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16
Q

the initiating point that generates a replication bubble

A

origin of replication

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17
Q

unwound and open region of DNA where DNA replication occurs

A

replication bubble

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18
Q

region where a cell’s DNA double helix has been unwound and separated to create an area where DNA polymerases and the other enzymes involved can use each strand as a template to synthesize a new double helix

A

replication fork

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19
Q

formed at all potential origins of replication through the action of the origin recognition complex (ORC), Cdc6, Cdt1, and the Mcm2-7 complex

A

pre-replicative complex (pre-RC)

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20
Q

powers nucleotide addition

A

pyrophosphate hydrolysis

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21
Q

bond between two nucleotides (sugar-phosphate)

A

phosphodiester bond

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22
Q

Different DNA Polymerases

A
  1. DNA polymerase I
  2. DNA polymerase II
  3. DNA polymerase III
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23
Q

DNA polymerase I

A
  • 5’-3’ polymerization
  • 3’-5’ proofreading
  • 5’-3’ exonuclease activity
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24
Q

DNA polymerase II

A
  • DNA repair functions
  • restarts replication after damaged DNA halts synthesis
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25
Q

DNA polymerase III

A

primary replication enzyme

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26
Q

DNA polymerase IV

A
  • 5’-3’ polymerase activity
  • DNA repair
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27
Q

DNA polymerase V

A
  • 5’-3’ polymerase activity
  • DNA repair
  • translesion DNA synthesis
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28
Q

how are incorrect nucleotides removed

A

3’-5’ proofreading

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29
Q

pair of abnormally chemically bonded adjacent thymine Bases in DNA, resulting from damage by ultra-violet irradiation

A

thymine dimer

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30
Q

cuts the damaged DNA strand at two points and the damaged section is removed

A

nuclease

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31
Q

repair synthesis and fills in missing nucleotides

A

DNA polymerase

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32
Q

seals the free end of the new DNA to the old DNA, making the strand complete

A

DNA ligase

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33
Q

unwinds parental double helix at replication forks

A

helicase

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34
Q

binds to and stabilizes single-stranded DNA until it can be used as a template

A

single-strand binding protein

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35
Q

corrects “overwinding” ahead of replication forks by breaking, swiveling, and rejoining DNA strands

A

topoisomerase

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36
Q

synthesizes a single RNA primer at the 5’ end

A

primase

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37
Q

elongates strand, adding on to the primer

A

DNA polymerase III

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38
Q

removes primer from 5’ end of strand and replaces it with DNA, adding on to the adjacent 3’ end

A

DNA polymerase I

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39
Q

joins the nicks in DNA strand

A

DNA ligase

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40
Q

both daughter strands are laid down in the ___ direction

A

5’ to 3’

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41
Q

transcribed DNA strand

A

template strand

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42
Q

untranscribed DNA strand

A

coding strand

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43
Q

untranscribed DNA strand = __ RNA

A

same sequence as RNA

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44
Q
  • region containing the RNA polymerase, DNA, and the RNA product
  • molecular structure formed during DNA transcription when a limited portion of the DNA double helix is unwound
  • size ranges from 12 to 14 base pairs.
A

transcription bubble

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45
Q

enzyme used in making mRNA

A

RNA polymerase

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46
Q

Steps in Transcription

A
  1. Initiation
  2. Elongation
  3. Termination
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47
Q

RNA polymerase binds to promoter sequence on DNA

A

Initiation

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48
Q

Role of promoter

A
  1. starting point
  2. template strand
  3. direction on DNA
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49
Q

direction on DNA when transcribing

A
  • always read DNA 3’-5’
  • build RNA 5’-3’
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50
Q

Components of RNA polymerase holoenzyme

A
  1. 2 αββ’ - core enzyme
  2. (2 αββ’) δ - RNA polymerase holoenzyme
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51
Q
  • these proteins bind to genes at sites known as enhancers
  • help to determine which genes will be switched on, and they speed the rate of transcription
A

activators

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52
Q

site where activators bind to

A

enhancers

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53
Q
  • these proteins bind to selected sets of genes at sites known as silencers
  • interfere with the functioning of activators and thus slow transcription
A

repressors

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54
Q

sites where repressors bind to

A

silencers

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55
Q

these “adapter” molecules integrate signals from activators and perhaps repressors and relay the results to the basal factors

A

coactivators

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56
Q

in response to injunctions from activators, these factors position RNA polymerase at the start of the protein-coding region of a gene and send the enzyme on its way

A

basal factors

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57
Q
  • define the direction of transcription and indicate which DNA strand will be transcribed;
  • this strand is known as the sense strand
A

Promoter sequences

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58
Q

Promoter sequences are also known as __ __

A

sense strand

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59
Q

stop site of transcription

A

terminator

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60
Q

RNA polymerase copies DNA as it unwinds

A

elongation

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61
Q

how many base pairs are transcribed at a time

A

~20 base pairs

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62
Q

simple proofreading during elongation stage in transcription

A
  • 1 error/10^5 bases
  • make many mRNAs
  • mRNA has short life
  • not worth editing
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63
Q

direction of transcription

A
  • “downstream”
  • reads DNA 3’-5’
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64
Q

where does RNA polymerase stop

A

termination sequence

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65
Q

refers to two areas of a DNA strand whose base-pair sequences are inverted repeats of each other

A

Dyad symmetry

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66
Q

what is made when there is dyad symmetry in the DNA

A

hairpin turn

67
Q

Different types of termination in transcription

A
  1. Rho-independent termination
  2. Rho-dependent termination
68
Q

palindromic GC-rich region (hairpin loop) followed by a stretch of AAAAAAA in the DNA being transcribed

A

Rho-independent termination

69
Q
  • a hexamer which acts as a RNA-DNA helicase
  • GC region slows down RNA pol and Rho factor catches up and dissociated RNA from transcription bubble
A

Rho-dependent termination

70
Q

DNA __ leave nucleus

71
Q

where is DNA wound on

A

histone proteins

72
Q

noncoding sequence of eukaryotic DNA

73
Q

coding sequence of eukaryotic DNA

74
Q

Transcription in Eukaryotes

A
  1. RNA polymerase 1
  2. RNA polymerase 2
  3. RNA polymerase 3
75
Q
  • only transcribes rRNA genes
  • makes ribosomes
A

RNA polymerase 1

76
Q

transcribes genes into mRNA

A

RNA polymerase 2

77
Q

only transcribes tRNA genes

A

RNA polymerase 3

78
Q

each RNA polymerase has a __ __ __ it recognizes

A

specific promoter sequence

79
Q

transcription factors bind to promoter region upstream of gene

A

initiation complex

80
Q

turn on or off transcription

A

suite of proteins which bind to DNA

81
Q

recognition site for transcription factors

A

TATA box binding site

82
Q

what do the transcription factors trigger

A

binding of RNA polymerase to DNA

83
Q

Eukaryotic Termination of Transcription

A
  1. Poly-adenylation signal
  2. Downstream Terminator Sequence
84
Q

eukaryotic mRNA needs work after transcription

A

primary transcript (pre-mRNA)

85
Q

edit out introns

A

mRNA spicing

86
Q

what is made after mRNA processing

A

mature mRNA

87
Q

what is added to protect mRNA from enzymes in cytoplasm

A
  • 5’ cap
  • polyA tail
88
Q

addition of methylated G nucleotide to the 5’ end of the transcript

89
Q

when does capping occur

A

right after about 30 nucleotides RNA have been synthesized

90
Q

purpose of capping

A
  • protects growing RNA transcript from degradation
  • ribosome recognition during translation
91
Q

addition of 100-200 residues of poly A’s to the 3’ end even before termination of transcription has completed

92
Q

where is the tail located

A

10-30 nucleotides upstream from site of cleavage

93
Q

tailing signals __ _ __ to cleave a portion of the transcript before the poly A tail is synthesized

A

poly A polymerase

94
Q

purpose of tailing

A
  1. aids in export of mature mRNA from nucleus
  2. prevents degradation from 3’ end
  3. serves as recognition signal for ribosome
95
Q

intrns are cut out of immature RNA transcripts

96
Q

splicing signals tell __ where to ‘cut and paste’ exons

A

spliceosomes

97
Q

what do introns have that are recognized by spliceosomes

A

consensus sequence on 5’ and 3’ ends

98
Q

key components of the spliceosome and are absolutely required for pre-mRNA splicing

A

Spliceosomal snRNPs

99
Q

snRNPs

A

small nuclear RNA

100
Q

discarded byproducts of RNA splicing, the process by which genetic instructions for making proteins are assembled

101
Q

ribonucleic acid (RNA) enzyme that catalyzes a chemical reaction

102
Q

some mRNA can __ itself

103
Q

discovered that RNA actively aids chemical reactions in cells

A
  • Sidney Altman
  • Thomas R. Cech
104
Q

cellular process in which exons from the same gene are joined in different combinations, leading to different, but related, mRNA transcripts

A

Alternative splicing

105
Q

splicing must be __

106
Q

a single base added or lost throws off the __ __

A

reading frame

107
Q

Components of the Translation Machinery

A
  1. ribosome
  2. messenger RNA (mRNA)
  3. transfer RNA (tRNA)
  4. amino acyl synthetase
  5. protein factors
  6. peptidyl transferase
108
Q

protein factory composed of aggregates of RNA and protein 70S in prokaryotes and 80S in eukaryotes

109
Q

protein __ in prokaryotes

110
Q

protein __ in eukaryotes

111
Q

what does ribosome facilitate

A

coupling of tRNA anticodon to mRNA codon

112
Q

structure of ribosome

A
  • large subunit
  • small subunit
113
Q

sites in ribosome

A
  1. A site
  2. P site
  3. E site
114
Q

holds tRNA carrying next amino acid to be added to chain

115
Q

A site

A

aminoacyl-tRNA site

116
Q

holds tRNA carrying growing polypeptide chain

117
Q

P site

A

peptidyl-tRNA site

118
Q

empty tRNA leaves ribosome

119
Q

E site

120
Q

70S ribosome of prokaryotes

A
  • 50S large subunit
  • 30S small subunit
121
Q

80S ribosome of eukaryotes

A
  • 60S large subunit
  • 40S small subunit
122
Q

bears amino acid sequence

A

messenger RNA (mRNA)

123
Q

prokaryotic mRNA

A

multiple translation start site

124
Q

eukaryotic mRNA

A

single translation start site

125
Q

start codon

126
Q

carries the amino acids to the ribosomes

127
Q

three-nucleotide or triplet sequence found on mRNA that codes for a certain amino acid during translation

128
Q

three-nucleotide sequence found on tRNA that binds to the corresponding mRNA sequence

129
Q

structure of tRNA

A

“clover leaf” structure

130
Q

where is the anticodon found

A

“clover leaf” end

131
Q

where is amino acid found

A

3’ end of tRNA

132
Q

enzyme which bonds amino acid to tRNA

A

aminoacyl tRNA synthetase

133
Q

bond requires energy (aminoacyl tRNA synthetase )

A

ATP -> AMP

134
Q

energy stored in tRNA-amino acid bond

A
  • unstable
  • amino acid is released easily
135
Q

Step 1 of binding amino acid with tRNA

A

AA + ATP –> AA-AMP + PPi

136
Q

Step 2 of binding amino acid with tRNA

A

AA-AMP + tRNA –> AA-tRNA + AMP

137
Q

for initiation, elongation and termination of translation

A

protein factors

138
Q

catalyzes peptide bond formation

A

peptidyl transferase

139
Q

determined 3-letter (triplet) codon system

140
Q
  • determined mRNA-amino acid match
  • added fabricated mRNA to test tube of ribosomes, tRNA and amino acids
A
  • Nirenberg
  • Khorana
141
Q

UUU

A

phenylalanine (phe)

142
Q

point mutations

A
  • silent mutations
  • substitutions
143
Q

frameshifts mutations

A
  • insertions
  • deletions
144
Q

features of the genetic code

A
  1. universal
  2. triplet
  3. non-overlapping
145
Q

almost all organisms follow the same codon assignments

146
Q

three base code for one amino acid

147
Q

start codon

A
  • AUG
  • methionine
148
Q

stop codons

A
  • UAA
  • UAG
  • UGA
149
Q

the base at 5’ end of the anticodon is not spatially confined as the other two bases allowing it to form hydrogen bonds with any of several bases located at the 3’ end of a codon

A

wobble hypothesis

150
Q

several codons code for one amino acid

A

redundant or degenerate

151
Q

are represented by related codons

A

structurally similar amino acids

152
Q

movement of ribosome

A

5’ to 3’

153
Q

translation in prokaryotes

A

simultaneous with transcription

154
Q

time it takes from DNA to protein in eukaryote

155
Q

Building of polypeptide

A
  1. initiation
  2. elongation
  3. termination
156
Q

brings together mRNA, ribosome subunits, initiator tRNA

A

initiation

157
Q

adding amino acids based on codon sequence

A

elongation

158
Q

end codon

A

termination

159
Q

in prokaryotes, initiation requires the binding of rRNA to where?

A

Shine Dalgarno sequence (AGGA)

160
Q

first amino acid in prokaryotes

161
Q

eukaryotic inititaion of translation

A

starts with AUG nearest to 5’ terminus of mRNA

162
Q
  • steps needed to release the completed polypeptide chain involves the dissociation of the ribosome
  • very slow step
A

termination of translation

163
Q

N-terminal sorting signal that targets the linked protein to the secretory pathway in eukaryotes and prokaryotes

A

signal peptides

164
Q

possible destinations of proteins after synthesis

A
  1. secretion
  2. nucleus
  3. mitochondria
  4. chloroplasts
  5. cell membrane
  6. cytoplasm

BIO105 - Genetics (19 decks)

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