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microbio km > microbio lecture 6 chapter 7 > Flashcards

microbio lecture 6 chapter 7 Flashcards

1
Q

DNA: Blueprint of Life

A

Incredible diversity of life dictated by information within DNA

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2
Q

what are the composed nucleotides?

A

Adenine (A), Thymine (T), Cytosine (C), Guanine (G)

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3
Q

What does each nucleotide contain?

A

a nucleobase

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4
Q

How many nucleotides encode a specific amino acid?

A

3

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5
Q

What makes up protein?

A

Amino acids

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6
Q

What determines the structure and function of protein?

A

The sequence of amino acids

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7
Q

proteins serve as

A

structural components of cells

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8
Q

enzymes…

A

direct cellular activities (biosynthesis+energy conversion)

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9
Q

genome

A

complete set of genetic information

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10
Q

the genome consists of

A

chromosome plus (technically) plasmids

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11
Q

all cells have…

A

DNA genome

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12
Q

viruses may have…

A

RNA genome

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13
Q

gene

A

functional unit; encodes a gene product

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14
Q

gene

A

usually a protein

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15
Q

genomics

A

study of nucleotide sequence of DNA

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16
Q

cells must accomplish two tasks to multiply

A

DNA replication & Gene expression

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17
Q

Gene expression

A

DNA is decoded so cell can synthesize gene products

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18
Q

transcription

A

information in DNA is copied into RNA

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19
Q

translation

A

RNA used to synthesize encoded protein

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20
Q

(central dogma of molecular biology) information flows from…

A

DNA –> RNA –> protein

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21
Q

DNA forms…

A

double-stranded helix

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22
Q

carbon atoms of pentose sugar are

A

numbered

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23
Q

nucleotides joined between

A

5’PO4 and 3’OH

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24
Q

joining of the nucleotides alternating sugar and phosphate forms

A

sugar-phosphate backbone

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25
Q

single DNA strand will have a

A

5’ end and 3’end

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26
Q

strands are ______, held together by ______
_______ between nucleobases

A

complementary; hydrogen bonds

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27
Q

base pairing

A

Adenine (A) to thymine (T) (two hydrogen bonds)
Cytosine (C) to guanine (G) (three hydrogen bonds)

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28
Q

strands are

A

anti-parallel; oriented in opposite directions

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29
Q

characteristics of RNA (ribonucleic acid)

A

Ribose instead of deoxyribose
Usually shorter single strand

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30
Q

(in RNA) ___________ in place of thymine

A

uracil

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31
Q

RNA is synthesized from…

A

DNA template strand

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32
Q

RNA molecule is ______

A

transcript

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33
Q

for RNA, base-pairing rules apply except

A

uracil pairds with adenine

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34
Q

transcript ___________ separates from DNA

A

quickly

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35
Q

what are the three types of RNA (ribonucleic acid)?

A

Messenger RNA (mRNA)
Ribosomal RNA (rRNA)
Transfer RNA (tRNA)

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36
Q

cells ________ expression of certain genes

A

regulate

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37
Q

within minutes of being produced, mRNA transcripts undergo

A

rapid degradation

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38
Q

DNA replication usually __________ from origin of replication

A

bidirectional

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39
Q

two replication forks….

A

meet at terminating site when process complete

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40
Q

replication is _______________

A

semiconservative

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41
Q

semiconservative

A

DNA contains one original, one newly synthesized strand

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42
Q

initiation of DNA replication ->

A

enzymes need to get started

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43
Q

DNA ________ and ___________ bind to origin of replication

A

gyrase; helicase

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44
Q

functions of DNA gyrase and helicases

A

Break and unwind DNA helix and expose single-stranded region that can act as a template

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45
Q

Primase (an RNA polymerase) function

A

synthesizes short regions of RNA called
primers

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46
Q

DNA replication is complicated and requires….

A

coordinated action of many enzymes and other components

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47
Q

Many of the enzymes form “assembly lines” called…

A

replisomes

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48
Q

___________ is absolutely needed for DNA synthesis

A

Primase RNA polymerase

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49
Q

The DNA Polymerase (replicase) is unable to

A

initiate strand synthesis de novo.

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50
Q

dna polymerase requires a

A

3’-OH Group to attach to.

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51
Q

RNA polymerase CAN initiate

A

stand synthesize de novo, giving the -OH group need by DNA pol-ase

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52
Q

DNA polymerases synthesize in the _______ direction

A

5’ to 3’

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53
Q

DNA polymerase powers reaction with

A

Hydrolysis of high-energy phosphate bond powers

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54
Q

DNA polymerase can only _____ nucleotides, not initiate

A

add

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55
Q

since DNA pol-ase cannot initiate synthesis, they require….

A

primers at origin of replication

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56
Q

helicases _____ DNA strands

A

unzip

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57
Q

helicases reveal

A

template sequences

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58
Q

leading strand

A

synthesized continuously

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59
Q

lagging strand

A

synthesized discontinuously

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60
Q

DNA polymerases can only add nucleotides to

A

3’ end

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61
Q

discontinuous synthesis produces

A

Okazaki fragments

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62
Q

different DNA polymerase

A

replaces primers

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63
Q

DNA ligase forms

A

covalent bond between adjacent nucleotides

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64
Q

DNA gyrase

A

Enzyme that temporarily breaks the strands of DNA, relieving the tension caused by unwinding the two strands of the DNA helix.

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65
Q

DNA ligase

A

Enzyme that joins two DNA fragments together by forming a covalent bond between the sugar and phosphate residues of
adjacent nucleotides.

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66
Q

DNA polymerases

A

Enzymes that synthesize DNA; they use one strand of DNA as a template to make the complementary strand. Nucleotides can be
added only to the 3′ end of an existing fragment—therefore, synthesis always occurs in the 5′ to 3′ direction.

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67
Q

Helicases

A

Enzymes that unwind the DNA helix at the replication fork.

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68
Q

Okazaki fragment

A

Nucleic acid fragment produced during discontinuous synthesis of the lagging strand of DNA.

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69
Q

Origin of replication

A

Distinct region of a DNA molecule at which replication is initiated.

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70
Q

Primase

A

Enzyme that synthesizes small fragments of RNA to serve as primers for DNA synthesis.

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71
Q

Primer

A

Fragment of nucleic acid to which DNA polymerase can add nucleotides (the enzyme can add nucleotides only to an existing
fragment).

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72
Q

Replisome

A

The complex of enzymes and other proteins that synthesize DNA.

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73
Q

Replication produces _____ complete copies of DNA

A

2

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74
Q

how many copies of DNA does each daughter cell receive?

A

one

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75
Q

replication of E.coli chromosome takes approx.

A

40 minutes

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76
Q

optimal generation time of E. coli

A

20 minutes

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77
Q

before previous round of replication is complete, cell can

A

initiate another round of replication

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78
Q

each daughter cell inherits

A

one complete chromosome already undergoing replication

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79
Q

transcription

A

RNA polymerase synthesizes single-stranded RNA (mRNA/messenger RNA) from DNA template

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80
Q

RNA polymerase binds to sequence called a

A

promoter

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81
Q

RNA polymerase synthesize in _______ direction

A

5’ to 3’ direction (orientation of newly synthesized strand)

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82
Q

RNA polymerase can ____________ without a primer

A

initiate mRNA synthesis

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83
Q

transcription stops at sequence called a

A

terminator

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84
Q

RNA sequence is _______ AND ________ to DNA template strand

A

complementary; antiparallel

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85
Q

DNA template is ______ strand

A

minus (-)

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86
Q

Complement is ______ strand

A

plus (+)

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87
Q

RNA has same sequence as __________ strand except Uracil instead of Thymine

A

(+) DNA strand

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88
Q

prokaryotic mRNA transcripts

A

Monocistronic
Polycistronic

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89
Q

monocistronic

A

one gene

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90
Q

polycistronic

A

multiple genes

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91
Q

proteins encoded on polycistronic message…

A

generally have related functions

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92
Q

promoter orients

A

direction of transcription

93
Q

promoter is found

A

upstream of gene it controls

94
Q

Once RNA polymerase has moved beyond promoter ___________, allowing rapid and repeated transcription of single gene

A

another RNA polymerase can bind

95
Q

initiation of RNA synthesis (Role of Sigma factors)

A

Sigma factor recognizes promoter

96
Q

various types of sigma factors…

A

recognize different promoters

97
Q

synthesis of sigma factors controls

A

transcription of sets of genes

98
Q

eukaryotic cells and archaea

A

use transcription factors to recognize promoters

99
Q

(−) strand of DNA

A

Strand of DNA that serves as the template for RNA synthesis;
the resulting RNA molecule is complementary to this strand.

100
Q

(+) strand of DNA

A

Strand of DNA complementary to the one that serves as the template for RNA synthesis; the nucleotide sequence of the RNA molecule is the same as this strand, except it has uracil
rather than thymine.

101
Q

Promoter

A

Nucleotide sequence to which RNA polymerase binds to initiate transcription.

102
Q

RNA polymerase

A

Enzyme that synthesizes RNA using one strand of DNA as a template; synthesis always occurs in the 5′ to 3′ direction

103
Q

Sigma factor

A

Component of RNA polymerase that recognizes the promoter regions. A cell can have different types of σ factors that recognize different promoters, allowing the cell to transcribe
specialized sets of genes as needed.

104
Q

Terminator

A

Nucleotide sequence at which RNA synthesis stops; the RNA polymerase falls off the DNA template and releases the newly
synthesized RNA.

105
Q

translation

A

process of decoding information in mRNA

106
Q

translation is…

A

The process of protein synthesis

107
Q

major components of translation are

A

mRNA, ribosomes (contain rRNA), tRNAs, and accessory proteins

108
Q

mRNA is

A

temporary copy of genetic information

109
Q

Cell must decode the information imbedded in ….; translating them into the amino acid sequence contained in a protein

A

linear array of the mRNA nucleotide sequence

110
Q

Genetic code =

A

three nucleotides

111
Q

three nucleotides =

A

a codon = one amino acid

112
Q

more than one codon can specify

A

a specific amino acid; code is degenerate

113
Q

the genetic code is practically

A

universal; w/ minor exceptions, it is used by all living things

114
Q

stop codes

A

UAA, UAG, UGA

115
Q

start code

A

AUG

116
Q

nucleotide sequence defines

A

coding region

117
Q

sequences

A

designates beginning, end of region to be translated

118
Q

ribosomes serve as

A

translation “machines”

119
Q

the ribosome aligns

A

and forms peptide bonds between amino acids

120
Q

ribosomes locate punctuation sequences

A

on mRNA molecules

121
Q

the ribosome begins at

A

start site, moving along in 5’ to 3’ direction

122
Q

any given sequence has 3 different reading frames, which ribosomes

A

maintain in correct frame

123
Q

Prokaryotic ribosomes are comprised of______, each made of protein and ribosomal RNA (rRNA)

A

30s and 50s subunits

124
Q

three reading frames possible, or ways in which

A

triplets of nucleotides can be grouped

125
Q

if translation begins at wrong spot, or in “wrong reading frame”, a very…

A

different, and likely nonfunctional protein or a premature termination will result

126
Q

transfer RNAS (tRNAS) deliver

A

correct amino acids

127
Q

each tRNA has

A

specific anticodon sequence; base-pairs with codon

128
Q

each TRNA carries appropriate

A

amino acids specified by codon

129
Q

after delivering amino acid,

A

tRNA can be recycled

130
Q

initiation of translation: part of ribosome binds to mRNA sequence called

A

the ribosome binding site

131
Q

the ribosome binding site is _________ of the start codon

A

upstream

132
Q

first AUG after that site serves as _________, where complete ribosome assemble

A

start codon

133
Q

initiating tRNA brings _______ ________ of methionine

A

tRNA –> occupies P-site

134
Q

elongation of polypeptide chain

A

ribosome has two sites to which tRNAs can bind

135
Q

tRNA recognizes that next codon occupies __________, brings correct amino acid

A

empty A-site

136
Q

A-site and P-site now occupied

A

by correct tRNAs

137
Q

rRNA creates _______ between their amino acids

A

peptide bond

138
Q

Amino acid from tRNA in P-site added to

A

amino acid carried by tRNA in A-site

139
Q

Ribosome advances along mRNA in _________ direction

A

5’ to 3’

140
Q

process of elongation of polypeptide chain 1

A
  • Initiating tRNA exits through E-site
  • Remaining tRNA carrying both amino acids occupies P-site
  • A-site temporarily empty
  • A tRNA that recognizes codon in A-site quickly attaches
141
Q
A
  • Peptide bond formed between amino acids
  • Ribosome advances one codon on mRNA
  • tRNA exits E-site
  • tRNA with growing protein occupies P site
  • new tRNA occupies A-site
  • The process repeats
142
Q

Termination

A

Elongation continues until ribosomes reaches a stop codon

143
Q

in termination, enzymes break covalent bond

A

joining polypeptide to tRNA

144
Q

in termination, ribosome falls off

A

mRNA

145
Q

after falling off, mRNA disassociates into

A

component subunits (30s and 50s)

146
Q

subunits can be reused to

A

initiate translation at other sites

147
Q

translation in prokaryotes begins before

A

transcription is complete

148
Q

transcription and translation are

A

linked in prokaryotes

149
Q

once a ribosome clears initiating sequences, another ribosome can bind, forming…

A

polyribosome or polysome

150
Q

Anticodon

A

Sequence of three nucleotides in a tRNA molecule that is complementary to a particular
codon in mRNA. The anticodon allows the tRNA to recognize and bind to the appropriate
codon.

151
Q

mRNA Polyribosome (polysome) Reading frame

A

Type of RNA molecule that contains the genetic information decoded during translation.
Multiple ribosomes attached to a single mRNA molecule.
Grouping of a stretch of nucleotides into sequential triplets that code for amino acids; an mRNA molecule has three potential reading frames, but only one is typically used in
translation.

152
Q

Ribosome

A

Structure that facilitates the joining of amino acids during the process of translation;
composed of protein and ribosomal RNA. The prokaryotic ribosome (70S) consists of a
30S and a 50S subunit.

153
Q

Ribosome-binding site

A

Sequence of nucleotides in mRNA to which a ribosome binds; the first time the codon for
methionine (AUG) appears after that site, translation generally begins.

154
Q

rRNA
start codon

A

Type of RNA molecule present in ribosomes.
Codon at which translation is initiated; it is typically the first AUG after a ribosome-
binding site.

155
Q

Stop codon

A

Codon that terminates translation, signaling the end of the protein; there are three stop
codons.

156
Q

tRNA

A

Type of RNA molecule involved in interpreting the genetic code; each tRNA molecule
carries a specific amino acid dictated by its anticodon.

157
Q

Eukaryotic mRNA synthesized in precursor form:

A

pre-mRNA

158
Q

pre-mRNA

A

must be processed during and after transcription

159
Q

Capping adds methylated

A

guanine derivative to 5’ end

160
Q

Capping binds

A

specific proteins: stabilize, enhance translation

161
Q

3’ end modified via

A

polyadenylation

162
Q

polyadenylatoin

A

adds approx 200 adenine derivatives to new 3’ end

163
Q

polyadenylations creates a poly A tail that

A

stabilizes transcript, enhances translation

164
Q

splicing

A

removes segments of eukaryotic transcript

165
Q

introns

A

non-codings intervening sequences that are removed

166
Q

exons

A

expressed regions that remain

167
Q

eukaryotic mRNA produced within membrane-bound nucleus and must be transported to cytoplasm:

A
  • Translation cannot begin during transcription
  • mRNA typically monocistronic
168
Q

in eukaryotic mRNA,

A

translation begins at first AUG and ribosomes are composed of 40s and 60s subunits

169
Q

differences from prokaryotic ribosomes important in

A

targeting antibiotics

170
Q

Prokaryotes

A
  • mRNA does not have a cap or a poly A
    tail.
  • Transcript (mRNA) does not contain
    introns.
  • Translation of mRNA begins as it is
    being transcribed.
  • mRNA is often polycistronic;
    translation usually begins at the first
    AUG codon that follows a ribosome-
    binding site.
171
Q

Eukaryotes

A
  • Processing of the transcript (pre-mRNA) results in mRNA with a cap at the 5′ end and a poly A tail at the 3′ end.
  • Transcript (pre-mRNA) contains introns, which are removed by splicing.
  • mRNA is transported out of the nucleus so that it can be translated in the cytoplasm.
  • mRNA is monocistronic; translation begins at the first AUG.
172
Q

genes can be routinely

A

expressed or regulated

173
Q

operon

A

A set of regulated genes transcribed as single mRNA along with its
control sequences

174
Q

lac operon

A

lactose metabolism

175
Q

regulon

A

Separate operons controlled by single regulatory mechanism

176
Q

global control

A

is simultaneous regulation of numerous genes

177
Q

enzymes can be grouped by

A

type of regulation

178
Q

constitutive enzymes synthesized constantly

A
  • Typically indispensable roles in central metabolism (for example, enzymes of glycolysis)
179
Q

Inducible enzymes synthesized only when needed

A

Avoids waste of resources

180
Q

example of inducible enzymes

A

for example, B-galactosidase turned on only when lactose present)

181
Q

Repressible enzymes are

A

produced routinely, but are turned off when not needed

182
Q

mechanisms to control transcription

A

Must be readily reversible, allow cells to control relative number of transcripts produced

183
Q

two most common regulatory mechanisms are

A

alternative sigma factors and DNA-binding proteins

184
Q

Standard sigma factor is loose component of RNA polymerase

A

recognizes promoters for genes expressed during routine growth conditions

185
Q

Alternative sigma factors recognize

A

different sets of promoters to control expression of specific groups of genes

186
Q

example of alternative sigma factors

A

sporulation in Bacillus subtilis controlled by multiple different alternative sigma factors

187
Q

DNA-binding proteins can act

A

as repressors

188
Q

Repressor

A

blocks transcription (negative regulation)

189
Q

Represser binds to operator, stops

A

RNA polymerase

190
Q

Repressors are _______, having binding site that alters ability to bind to DNA

A

allosteric

191
Q

Two general mechanisms of repressors

A

induction and repression

192
Q

induction

A

repressor binds to operator, blocks transcription

193
Q

inducer

A

binds to repressor, repressor unable to bind

194
Q

Repression

A

repressor cannot bind to operator

195
Q

Corepressor attaches to the repressor, complex now..

A

binds to operator and blocks transcription

196
Q

transcriptional regulation by

A

induction and repression

197
Q

DNA-binding proteins

A

can act as activators

198
Q

activator facilitates

A

transcription(positive regulation)

199
Q

Ineffective promoter preceded by

A

activator-binding site

200
Q

The binding of the activator enhances the ability of

A

RNA polymerase to initiate transcription at promoter

201
Q

Inducer binding to the activator allows

A

binding to DNA, and may also interfere with repressor

202
Q

the lac operon

A

Encodes proteins involved with transport and degradation of lactose

203
Q

lac operon turned on when

A

glucose is not available, but lactose is

204
Q

lac operon turned off when

A

glucose is available (cell uses most efficiently metabolized carbon source)

205
Q

when lactose is not available

A

Repressor prevents transcription; binds operator

206
Q

When lactose is present

A
  • Some converted to inducer
    allolactose; binds repressor
  • Repressor releases
    operator
  • RNA polymerase transcribes
    operon
  • Only occurs when glucose is
    not available
207
Q

When both glucose and lactose are present

A

Carbon catabolite repression (CCR)

208
Q

Carbon catabolite repression (CCR)

A

prevents expression of genes that metabolize lactose in presence of glucose

209
Q

CCR prioritize

A

carbon/energy sources; yields diauxic growth

210
Q

glucose transport system senses

A

glucose

211
Q

catabolite activator protein (CAP)

A

required for transcription of lac operon

212
Q

CAP functional only when

A

bound by inducer called cAMP

213
Q

cAMP made only when

A

glucose level is low

214
Q

enzymes that make cAMP

A

activated by idle form of glucose transporter

215
Q

inducer exclusion

A

lactose transporter blocked during glucose transport by active glucose transporter

216
Q

In the initiation stage of transcription,

A

RNA polymerase binds to the promoter and melts a short stretch of DNA. In the elongation stage, sigma factor often dissociates from DNA polymerase, leaving the core enzyme to complete transcription. RNA is synthesized in the 5′ to 3′ direction as the enzyme adds
nucleotides to the 3′ end of the growing chain. In the termination stage, RNA polymerase encounters a terminator, falls off the template, and releases the newly synthesized RNA.

217
Q

When few cells are present,

A

the concentration of the signaling molecule is low.

218
Q

When many cells are present,

A

the signaling molecule reaches a concentration high enough to induce the expression of certain genes.

219
Q

The sensor protein spans the

A

cytoplasmic membrane

220
Q

The response regulator is

A

a protein inside the cell

221
Q

In response to a specific change in the environment,

A

the sensor phosphorylates a region on its internal portion. The phosphate group is transferred to the response regulator, which can then turn genes on or off.

222
Q

In induction, transcription is usually blocked by a repressor bound to the operator.

A

Inducer turns on transcription by binding to the repressor, altering its shape so that it can no longer bind to the operator.

223
Q

In repression,

A

transcription is normally on because the repressor alone cannot bind to the operator

224
Q

A corepressor allows repressor to

A

bind to the operator and block transcription.

225
Q

Transcription is normally off because

A

RNA polymerase cannot bind to the promoter unless the activator is bound to the activator-binding site.

226
Q

inducer binds to the activator,

A

changing its shape and allowing it to
bind to the site. RNA polymerase can then bind to the promoter and initiate transcription.

227
Q

When glucose level is high

A

the unphosphorylated form of the glucose transporter component indicates
that glucose is available in the medium. This is because the phosphorylated transporter donates its phosphate group to glucose during transport into the cell.

228
Q

When lactose is also present, the
unphosphorylated form of the glucose transporter component prevents the lactose transporter (permease) from functioning. Because lactose cannot be moved into the cell, the inducer (allolactose) cannot accumulate, so transcription of the lac operon will be blocked.

A

When glucose level is low, the
phosphorylated form of the transporter component indicates that not much glucose is available in the medium. This is because the phosphorylated transporter cannot donate its phosphate during glucose transport. When glucose is low, but lactose is present, the phosphorylated form of the glucose transporter component activates the enzyme that produces cAMP, which binds to the activator (CAP). The complex of
CAP and cAMP can then bind to the activator-binding site of the lac operon, allowing transcription.

microbio km (6 decks)

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