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DISP Biology > DNA Replication, Transcription, and Translation > Flashcards

DNA Replication, Transcription, and Translation Flashcards

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1
Q

What is the central dogma of molecular biology?

A

DNA makes RNA, RNA makes protein

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2
Q

What are the two kinds of nucleic acid?

A

DNA and RNA

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3
Q

How do DNA and RNA differ?

A

in chemical composition and structure

  • RNA is single-stranded; DNA double
  • RNA is made of ribose; DNA of deoxyribose (missing an OH group that RNA has)
  • RNA contains uracil; DNA contains thymine
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4
Q

Who first suggested a double-helical model for the structure of DNA?

A

James Watson and Francis Crick

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5
Q

How did they figure out that DNA must have a double-helix structure?

A

best way molecule could fit together from the evidence they had (including x-ray crytallography)

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6
Q

What was the chemical evidence about the structure of DNA?

A

puring and pyrimiding nigrogenous bases; deoxyribose sugar, phosphate

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7
Q

What is the biological evidence about the structure of DNA?

A

ratios between bases (proportion of A = T; C = G)

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8
Q

What is the physical evidence about the structure of DNA?

A

x-ray crystallography; 2 nm diameter, double helical structure

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9
Q

What does the fact that nitrogenous bases are located on the inside of a DNA molecule indicate about their nature?

A

they’re relatively hydrophobic

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10
Q

What deductions did evidence from Rosalind Frankland’s work enable Watsom to make?

A
  • DNA was helical
  • width of the helix
  • spacing of the nitrogenous bases
  • nitrogenous bases on inside
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11
Q

What is Chargaff’s rule?

A

the proportion of A = T; C = G

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12
Q

Does A + C have to equal G + C?

A

no

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13
Q

What are the two types of nitrogenous basees?

A

pyrimidines and purines

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14
Q

What is the difference between a pyrimidine and a puring?

A

purines are made of two carbon-nitrogen ring bases (4 N in total); pyrimidines are made of one nitrogen ring base (2 N in total)

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15
Q

What type of nitrogenous base is adenine?

A

purine

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16
Q

What type of nitrogenous base is thymine?

A

pyrimidine

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17
Q

What type of nitrogenous base is guanine?

A

purine

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18
Q

What type of nitrogenous base is cytosine?

A

pyrimidine

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19
Q

What two components of a DNA molecule interact to form the phosphate-sugar backbone of DNA?

A

the free 3’-OH group of deoxyribose in the 1st nucleotide and the 1st 5’ phosphate in the 2nd nucleotide (5’P - 3’OH)

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20
Q

How many nucleotides may be present in a single DNA molecule?

A

many millions

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21
Q

How many strands is a DNA molecule made of?

A

2

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22
Q

How are the two strands of a DNA molecule oriented with respect to each other?

A

antiparallel (one strand goes from 3’ to 5’; other from 5’ to 3’)

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23
Q

What are the base pairings in a DNA molecule?

A

A:T and C:G

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24
Q

How many hydrogen bonds are present between adenine and thymine?

A

2

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25
Q

How many hydrogen bonds are present between cytosine and guanine?

A

3

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26
Q

In what direction does a DNA molecule grow?

A

from 5’ to 3’ (must add 5’P to free 3’ OH)

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27
Q

What do restriction enzymes do?

A

break DNA phosphodiester bond at a recognized “binding site”

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28
Q

How did evidence indicate that a purine and a pyrimidine had to pair (instead of purine-purine or pyrimiding-pyrimidine)?

A

process of elimination - knew that the pairing had to be 2 nm wide; only pair that fit that was purine-pyrimidine?

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29
Q

How did evidence indicate that A paired with T and C paired with G?

A

only pairings that allowed bases to hydrogen bind

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30
Q

What would the diameter of a DNA molecule be if a pyrimidine bonded to another pyrimidine, and how does that relate to the X-ray data?

A

less than 2.0 nm (too thin compared to X-ray data)

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31
Q

What would be the diameter of a DNA molecule if purines bonded to pyrimidines, and how does that relate to the X-ray data?

A

larger than 2.0 nm (too thick compared to X-ray data)

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32
Q

How do the amount of DNA per cell and the number of sets of chromosomes per cell relate?

A

by a precise correlation

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33
Q

How does the molecular composition of DNA compare between all the different cells of an organism?

A

it’s the same

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34
Q

How does the composition of both RNA and proteins compare between different cell types?

A

highly variable

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35
Q

How does the stability of DNA and RNA/proteins compare?

A

DNA is more stable, while RNA and proteins are synthesized and degraded quite rapidly in living organisms

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36
Q

Why is DNA more stable than RNA?

A

it’s double-stranded and lacks an OH group that could be acted upon

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37
Q

What were the three possible models for DNA replication?

A

conservative, semiconservative, and dispersive

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38
Q

What does the conservative model of DNA replication predict the products of the first and second replication will be?

A

first replication: one DNA molecule of both template strands; one of both copied strands
second replication: 3 molecules of all copied strands; 1 molecule of original template strands

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39
Q

What does the semiconservative molel predict the products of the 1st and 2nd replication will be?

A

1st: 2 molecules each of 1 template and 1 copied strand
2nd: 2 molecules with 1 parent and 1 copied strand; 2 with just copied strands

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40
Q

What does the dispersive model predict the products of the 1st and 2nd replication to be?

A

1st: 2 molecules with bits of template in each strand
2nd: 4 of the same

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41
Q

What experimental procedure was used to show that the semiconservative model was correct?

A

bacteria were cultured in a medium with a heavy N isotope, then transferred to a medium with a lighter isotope; the DNA sample was then centrifuged after the 1st and 2nd replications

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42
Q

How did centrifuging the products from the 1st and 2nd replications from the bacteria DNA replication experiment support the semiconservative model?

A

more dense DNA settled to the bottom while less dense settled on top; the results only matched the semiconservative model

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43
Q

What is the origin of repliaction?

A

where DNA replication starts on a chromosome

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44
Q

How many origins of replication are found on a circular choromosome?

A

1

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45
Q

How many origins of replication are found in a eukaryotic chromosome

A

many

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46
Q

Why can 1 strand of DNA serve as a remplate for a new one?

A

the 2 strands are complimentary

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47
Q

Why do circular chromosomes not have the same problems with replication as eukaryotes?

A

eukaryotic chromosomes are linear, so it’s not possible to replicate all strands in 5’ to 3’ direction (whereas in circular, can just continue around molecule in correct direction until it’s all done)

also, linear chromosomes end up losing some of their end each time (primers added)

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48
Q

How is the leading strand synthesized?

A

continuously, moving toward the replication fork

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49
Q

How is the lagging strand synthesized?

A

as a series of segments (okazaki fragments)

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50
Q

Why is a primer required for repliacion?

A

DNA polymerases can’t initiate synthesis (on a single strand) - need something to build on

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51
Q

What is a primer?

A

short stretch of RNA, synthesized by primase, using parental DNA strand as template

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52
Q

In what direction can a new strand elongate in replication and why?

A

5’ to 3’ since polymerase can only add nucleotides to free 3’ end of growing strand

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53
Q

What does helicase do?

A

enzyme that untwists double helix at replication fork

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54
Q

What do single-strand binding proteins do?

A

bind/stabilize by replication fork during replication - prevent retwisting

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55
Q

What is another name for topoisomerase?

A

gyrase

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56
Q

What does topoisomerase do in replication?

A

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

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57
Q

What does primase do in replacation?

A

makes the primer

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58
Q

How many RNA primers are needed to synthesize the leading tsrand?

A

1

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59
Q

What happens after the lagging strand is synthesized in fragements?

A

DNA polymerase I replaces RNA primer with DNA; DNA ligase joins sugar phosphate backbones of fragments into continuous strand

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60
Q

How long is each okazaki fragment?

A

1000-2000 nucleotides long

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61
Q

How many RNA primers does the lagging strand need?

A

one for every Okazaki fragment

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62
Q

What model does DNA polymerase follow to synthesize DNA/

A

replication machine - “reels” in parental DNA and “extrudes” newly-made daughter DNA molecules (assisted by other proteins)

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63
Q

What occurs immediately after DNA synthesis?

A

proofreading

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64
Q

WHat enzyme proofreads DNA?

A

DNA polymerase

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65
Q

What can happen in DNA polymerase misses mistakes?

A
  • mismatch repair (other enzymes correct)
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66
Q

What kind of mistakes can be corrected in DNA proofreading?

A

DNA damage by expoure to harmful chemical or physical agents or other spontaenous changes

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67
Q

What is nucleotide excision repair?

A

nuclease cuts out and replaces damaged stretch of DNA

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68
Q

What does DNA ligase do?

A

rebuilds the sugar-phosphate backbone of DNA whenever DNA is cut and nucleotides are replaced

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69
Q

What is the error rate after prroofreading?

A

Low but not zero

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70
Q

What happens when DNA sequence changes become permanent?

A

can be passed onto next generation (mutations)

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71
Q

What are the source of genetic variation upon which natural selection operates?

A

mutations (changes in DNA sequence)

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72
Q

Why do DNA molecules become progressively shorter after each replication?

A

can’t complete the 5’ ends, so repeated rounds of replication produce shorter DNA with uneven ends

73
Q

Why isn’t progressive shortening a problem for prokaryotes?

A

have circular chromosomes

74
Q

What is a codon?

A

3 nucleotide “word” that codes for an amino aid

75
Q

What is transcribed into complementary, non-verlapping codons of mRNA?

A

codons of a gene

76
Q

What happens to mRNA codons?

A

translated into a chain of amino acids, forming polypeptide

77
Q

What happens if codons are not read in the correct reading frame?

A

frameshift mutation

78
Q

What is the correct reading frame?

A

correct groupings of nucleotides necessary for the specified polypeptide to be proudced

79
Q

What are telomeres?

A

special nucleotide sequences at ends of eukaryotic chromsomes (TTAGGG repeated 100-10000 times in humans)

80
Q

What is the function of telomeres?

A

postpone the erosion of genes near the ends; may protect cells from cancerous growth by limiting number of cell divisions

81
Q

What is connected to aging?

A

shortening of telomeres?

82
Q

What catalyzes the lengthening of telomeres in germ cellls?

A

telomerase

83
Q

What is there evidence of activity of in cancer cells?

A

telomerases

84
Q

What is the central dogma of molecular biology?

A

concept that cells are governed by sequential, one-way chain of command (DNA –> RNA –> protein)

85
Q

What is encoded into DNA by triplet code?

A

instructions for assembling amino acids into proteins

86
Q

How many total codons are there?

A

64

87
Q

How many codons code for amino acids?

A

61

88
Q

How many “stop” signal codons are there, and what do they do?

A

3; signal to end translation

89
Q

Why is the code redundant?

A

more than one codon may specify a particular amino acid

90
Q

Wh is the code not ambiguous?

A

no codon specifies more than one amino acid

91
Q

What is transcription?

A

the syntehsis of an RNA strand using info in DNA

92
Q

What is produced by transcription?

A

mRNA (messenger RNA) - the transcript

93
Q

What is translation?

A

the synthesis of a polypeptide, using info in the mRNA

94
Q

Where does translation occur?

A

on ribosomes

95
Q

What two things does translation requrie?

A

rRNA (ribosomal RNA) on ribosomes; tRNA (transfer RNA)

96
Q

Is the template strand the same strend for a given gene?

A

yes, always

97
Q

What is transcription unit?

A

the stretch of DNA that is transcribed?

98
Q

What is the promoter?

A

DNA sequence where RNA polymerase attaches to start transcription

99
Q

What is the terminator?

A

the sequnce that signals the end of transcription (ONLY in bacteria)

100
Q

What are the 3 stages of transcription?

A

initiation, elongation, termination

101
Q

What happens in the initian stage of transcription?

A

promoters signal transcriptional start point on DNA, transcription factors mediate binding of RNA polymerase and initiation of transcription

102
Q

What is a transcription initiation complex?

A

the completed assembly of transcription factors and RNA polymerase II bound to a promoter

103
Q

What is the TATA box and what is it crucial for?

A

part of promoter; crucial in forming intation complex in eukaryotes

104
Q

Why is the TATA box a good target site for inhibiting transcription?

A

it’s necessary ton initiate transcription - stick chemicals there to stop binding

105
Q

What is the role of transcription factors?

A

mediate the binding of RNA polymeraase and the initiation of transcription - ensure bonding, increase promoter binding

106
Q

What would happen if transcription factors were note present (or were removed on purpose)?

A

reduction in efficiency of trasncription

107
Q

What happens in the elongation phase of transcription?

A

RNA polymerase moves along DNA, untwisting double helix and transcriping genes

108
Q

At what point of the growing RNA molecule are nucleotides added?

A

3’ end

109
Q

What is the rate of transcription in eukaryotes?

A

40 nucleotides per second

110
Q

How is transcription terminated in bacteria?

A

polymerase stops transcription at end of terminator site and mRNA is translated into protein without further modification

111
Q

How is transcription terminated in eukaryotes?

A

RNA polymerase II transcribes the polyadenylation signal sequence (string of As) before being released

112
Q

What postranscriptional modifications are done to mRNA?

A
  • 5’ end gets modified nucleotide 5’ cap

- 3’ end gets poly-A-tail

113
Q

What is the funciton of postranscriptional modifications?

A

faciliate export of mRNA to cytoplasm, protect it from hydrolytic enzyemes, help ribosomes attach to 5’ end

114
Q

What are introns?

A

long noncoding stretches of nucelotides that lie between coding regions

115
Q

What are exons?

A

sequences that are eventually expressed (usually translated into amino acid sequences)

116
Q

What does RNA splicing do?

A

removes introns and joins exons, creating mRNA molecule with continuous coding sequence

117
Q

What are spliceosomes?

A

complexes of proteins plus several small nuclear ribonucleoproteins (snRNPs) that recognize thesplice sites

118
Q

What is a protein domain?

A

a discrete region of the modular architecture of a protein

119
Q

What may code for different domains in a protein?

A

different exons

120
Q

What may be the result of exon shuffling?

A

the evolution of new proteins

121
Q

What is the functional and evolutionary importance of introns?

A
  • some contain sequences that may regulate gene expression (rather than coding for protein)
  • alternative RNA splicing
122
Q

What is alternative RNA splicint?

A

some genes can encode more tahn one kind of polypeptide, depending on which segments are treated as exons during splicing

123
Q

What adavantage does alternative RNA splicing give?

A

can produce more different proteins than there are genes

124
Q

Where does protein synthesis occur?

A

on ribosomes

125
Q

What 2 steps are required for accurate translation?

A
  • correct match between transfer RNA and amino acid

- correct match between tRNA anticodon and mRNA codon

126
Q

What is the anticodon?

A

region of tRNA of 3 bases gthat are complementary to a codon in mRNA

127
Q

How long is a single tRNA strand?

A

80 nucleotides long (small)

128
Q

What does the 2D structure of a tRNA molecule look like?

A

cloverleaf

129
Q

What is the 3D structure of a tRNA molecule?

A

L-shaped molecule (due to hydrogen bonds twisting and folding it)

130
Q

Why are the ends of tRNA molecules not identical?

A

one end binds to specific amino acid; other has anticodon that corresponds to that amino acid

131
Q

What does a tRNA anticodon base pair with?

A

complementary codon on mRNA

132
Q

What is wobble?

A

flexible pairing at the 3rd base of a codon to allow some tRNAs to bind to more than one codon

133
Q

Why is a mutation within a wobble base not necessarily have an affect?

A

codons can have interchangeable nucleotides - if some are switched, may still code for same amino acid

134
Q

What does the enzyme aminoacyl-tRNA synthetase do?

A

ensures a corect match by joining a specific amino acid to a specific tRNA (requires energy from ATP)

135
Q

What are the 2 ribosomal subunits (large ans small) made of?

A

proteins and ribosomal RNA (rRNA)

136
Q

WHat do ribosomes do?

A

faciliate specific coupling of tRNA anticodons with mRNA codons in protein synthesis

137
Q

How many sides where tRNAs can attach to ribosomes contain, and what are they called?

A

3; E, P, A

138
Q

What ribosomal site do polypeptides grow out of?

A

P site

139
Q

What is the A site in a ribosome?

A

initial attachment site - holds tRNA that carries next amino acid to be added to the chain

140
Q

What is the P site in a ribosome?

A

the central site - holds the tRNA that carries the growing polypeptide chain

141
Q

What is the E site in ribosome?

A

exit site - where discharged tRNAs leave the ribosome

142
Q

What are the two ends of a protein?

A

carboxyl and N-terminus

143
Q

What do free ribosomes do and where are they located?

A

in cytosol; mostly synteheize proteins that function in hte cytosol

144
Q

What do bound ribosomes do and where are thy found?

A

attached to the ER; a=make proteins of the endomembrane system and proteins secreted from the cell

145
Q

Where does polypeptide syntehsis always beigin?

A

in cytosol

146
Q

What is the exception to polypeptide syntehsis always finishing in the cytosol?

A

pollyypeptide signals the ribosome to attach to the ER

147
Q

What is a polyribosome (Polysome)?

A

a single mRNA translated continuously by many ribosomes

148
Q

What do polyribosomes allow cells to do?

A

make many copies of a polypeptide very queickly

149
Q

In what types of cells are polyribosomes found?

A

both bacteria and eukaryotic cells

150
Q

What are the 3 stages of translation?

A

initiation, elongation, termination

151
Q

What aid in all the translation stages?

A

protein factors

152
Q

Inw hat direction are mRNA base tirplets (codons) read?

A

5’ to 3’ direction

153
Q

In what direction does translation proceed, and why?

A

5’ to 3’, since that’s the direction in which mRNA codons are read

154
Q

What does each codon specify?

A

the amino acid to be placed at the corersponing position along a polypeptide

155
Q

How many amino acids are there?

A

20

156
Q

What occurs in translation initiation?

A
  1. small ribosomal subunit binds with mRNA and initiator tRNA
  2. small subunit moves along mRNA until reaches start codon (AUG)
  3. initiation factors (proteins) bring in large ribosomal subunit aht copmletes the translation initiation complex
157
Q

What is the start codon?

A

AUG

158
Q

What occurs during translation elongation?

A

amino acids are added one by one to preceding amino acid at the C-terminaus of the growing polypeptide chain

159
Q

What are the 3 steps of elongation in translation?

A
  1. codon recognition
  2. peptide bond formation at C-terminus
  3. transloacation
160
Q

What does elongation in translation require?

A

energy and proteins (elongation factors)

161
Q

What are the steps of trnalstion termination?

A
  1. stop codon in mRNA reaches A site
  2. A site accepts protein called release factor
  3. release factor causes addition of watermmoleceule instead of amino acid
  4. reaction releases polypeptide, and translation assembly comes apart
162
Q

Why is a functional protein not immediately released from translation?

A

translation makes a polypeptide, which often requires more work to become functional protein

163
Q

What helps a polypeptide chain fold correcltyl?

A

chaperone protein (chaperonin)

164
Q

What might polypeptides require before being functional proteins?

A

post-translational modifications

165
Q

What are some post-translational modications?

A
  • sugars, lipids, or phosphate groups added to amino acids
  • one or more amino acids removed from amino end
  • some polypeptides activated by enzymes that cleave them
  • other polypeptides combine to form subunits of protein
  • some polypeptides targetted for ER
166
Q

How are protins targetted to the ER?

A

polypeptide gets marked by attaching signal peptide; signal-recognition particle (SRP) binds to signal peptide; SRP brings the signal peptide and its ribosome to the ER

167
Q

What is the role of a signal-recognition particle (SRP)?

A

binds to singla peptide and brings it and its ribosome to the ER

168
Q

Why are transcription and translation simpler in bacteria?

A

no nucleus - both processes can occur in same part of cell; protein syntehsis can begin as soon as transcript syntehsis begins

169
Q

What are some causes of mutaitons?

A

spontaneous mutations from DNA replcation, recombination, or repair; physical/chemcial agents (mutagens)

170
Q

What can mutations affect?

A

proteins sturcutre and function

171
Q

What are point mutaitons?

A

small-scale chemical changes, in ust one base pair of gene

172
Q

What are 2 point muation examples?

A

nucleotide-pair substitutions, nucleotide-pair insertions/deletions

173
Q

What is an example of a disease caused by a poin mutaiton?

A

sickle cell disease (1 change of amino acid)

174
Q

What does a nucleotide-pair substitution do?

A

replaces one nucleotide (and its partner) with another pair of nucleotides

175
Q

What are silent mutations?

A

have no effect on amio acid produced by codon (due to redundancy in genetic code)

176
Q

What are missense mutations?

A

still code for amino acid, but no the correct one (changes the protein)

177
Q

What are nonsense mutaitons?

A

change an aminoa cid codon into a stop codong, nearly always leading to nonfunctional prtoein

178
Q

What are insertions and deletions?

A

additions or losses of nucleotide pairs in a gene

179
Q

Why do insertions and deletions often ahve a more disasterous efect on the resulting protein than substitutions?

A

may alter reading frame, causing farmeshift mutaiton - can mess up every subsequent amino acid

DISP Biology (12 decks)

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