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Bacterial Genetics > Bact Gen - Chapter 1 > Flashcards

Bact Gen - Chapter 1 Flashcards

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Biology 101 flashcards
1
Q

Bacteria are ___ organisms.

A

relatively simple

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2
Q

Many types of bacteria are hard/easy to manipulate in the lab.

A

easy

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3
Q

____ have remained largely unchanged throughout evolution.

A

central cellular functuions

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4
Q

____ originally identified in bacteria are highly similar in
all organisms – cancer research

A

DNA repair responses

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5
Q

Bacteria are essential for ecology of the Earth by:

A

Nitrogen -fixation, degradation of recalcitrant natural polymers, detoxification of poisonous compounds, production of
greenhouse gases

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6
Q

Bacteria capable of surviving in extreme environments. Ex. high temperature, pressure, and osmolarity

A

extremophiles

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7
Q

Perform
functions which allow other
organisms to survive

A

symbiotic bacteria

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8
Q

Many bacteria are _____
of humans, plants, and
animals

A

pathogens

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9
Q

Of the 10^14 cells in a human, __% are human!

A

10

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10
Q

___ can be studied to learn about antibiotics, medicines, foods,
chemicals, & molecular biology
tools.

A

bacterial genetics

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11
Q

All organisms on Earth belong to one of three divisions:

A

Eubacteria, Archae, or Eukaryotes

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12
Q
  • Familiar - E. coli, Staphylococcus aureus
  • Most are single celled and rod shaped or spherical
  • Some are multicellular with complicated developmental cycles
  • Distinguished by biochemical criteria: ribosomal RNA sequence
A

Eubacteria

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13
Q
  • Single celled organisms- differ biochemically from Eubacteria
  • Majority are extremophiles- high temperature, pressure, osmolarity
  • May be more closely related to eukaryotes than eubacteria
A

Archae

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14
Q
  • Diverse organisms- plants, animals, and fungi
  • Can be single or multicellular
  • Very similar at the biochemical level (macromolecular synthesis)
A

Eukaryotes

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15
Q

the study/manipulation of DNA to characterize cellular

and organismal functions

A

genetics

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16
Q

mutants that are altered in the function being studied
are isolated. The changes in the DNA (mutations) are localized in the
chromosome by genetic crosses. Functions of the genes affected can
sometimes be deduced by the phenotype displayed.

A

Classical genetics

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17
Q

Individuals that differ from the normal, or wildtype,

members of the species by an observable attribute, or phenotype.

A

mutants

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18
Q

a gene is first cloned from an organism
and altered in a test tube before reintroducing it back
into cells to determine the effect of the alteration.

A

reverse genetics

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19
Q

____ is made possible by the development of modern molecular
genetic techniques

A

reverse genetics

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20
Q

Both ____ and ____ have strengths and
weaknesses and the two approaches often complement
each other

A

classical and reverse genetics

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21
Q

Bacteria are _________, one copy or allele of each gene

A

haploid

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22
Q

Most higher organisms are ____ (two copies of each gene).

A

diploid

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23
Q

With haploid organisms the effects of the mutation are ____.

A

immediate

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24
Q

all progeny are genetically identical to

parents (________)

A

clones

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25
Q

ability to isolate clones

A

colony formation

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26
Q

large numbers of bacteria can be

diluted to manageable numbers by ____.

A

serial dilution

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27
Q

Bacteria have short ____.

A

generation times

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28
Q

A major advantage that allows us to identify rare

individual mutants among billions of normal bacteria

A

selection

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29
Q

Some selective conditions include:

A

nutrients/nutrient limitation
temperature
antibiotics

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30
Q

Bacteria can be stored in a ____ state, which prevents the need to continuously propagate them.

A

dormant

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31
Q

Methods of storing bacteria:

A

dormant spores
frozen in glycerol
dried down

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32
Q

Storing stocks of bacteria can be useful for accumulating a variety of different ____ for genetic experiments.

A

clones

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33
Q

Includes transformation, conjugation, and transduction.

A

genetic exchange

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34
Q

In the early 1950’s who discovered that DNA was a double helical structure by X-ray diffraction?

A

Rosalind Franklin and Maurice Wilkins

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35
Q

in 1953 ___ proposed the now famous model for the structure of DNA.

A

Francis Crick and James Watson

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36
Q

DNA is a ____ handed helix.

A

right

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37
Q

DNA has a ____ backbone.

A

sugar-phosphate

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38
Q

Helices are connected by ____ between nucleobases (purines and pyrimidines)

A

hydrogen bonding

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39
Q

Spacing between helices result in ____.

A

major and minor grooves

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40
Q

1 helical turn is how many base pairs?

A

10 (3.4 nm in length)

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41
Q

Two ring bases, adenine and guanine.

A

purine

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42
Q

One ring bases, thymine cytosine and uracil.

A

pyrimidine

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43
Q

In DNA, all 4 bases are attached to the 5-carbon sugar ____.

A

deoxyribose

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44
Q

Deoxyribose lacks an oxygen at the ____ carbon.

A

2nd

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45
Q

base + sugar + one or more phosphates

A

deoxynucleotides (nucleotides)

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46
Q

base + sugar but no phosphate

A

deoxynucleosides

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47
Q

Collectively the four deoxynucleoside triphosphates are ____.

A

dNTPs

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48
Q

Deoxynucleotides are linked together by ____.

A

phosphodiester bonds

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49
Q

The phosphate attached to the ____ of one nucleotide is attached to the ____ of the next nucleotide.

A

5’ carbon of the deoxyribose sugar

3’ carbon of the deoxyribose sugar

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50
Q

DNA has ____ construction.

A

antiparallel

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51
Q

5’ end holds a free ____.

A

phosphate

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52
Q

3’ end holds a free ____.

A

hydroxyl group

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53
Q

____ says: no matter the source of DNA, the concentration of A = T and C = G.

A

Chargaff’s Rule

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54
Q

____ and ____ pair with 2 hydrogen bonds.

A

adenine and thymine

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55
Q

____ and ____ pair with 3 hydrogen bonds.

A

cytosine and guanine

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56
Q

DNA replication involves ____ using sequence of the opposite strand as a template.

A

polymerizing deoxynucleotides

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57
Q

Deoxynucleotides are ____ and must be synthesized by a series of enzymatic steps prior to being incorporated into DNA

A

precursors or DNA synthesis

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58
Q

removes oxygen

A

reductase

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59
Q

adds phosphates

A

kinase

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60
Q

removes phosphates

A

phosphatase

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61
Q

links together two molecules

A

synthetase

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62
Q

____ reduces ribose sugar to deoxyribose by changing the OH at the 2’ position to H.

A

ribonucleotide reductase

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63
Q

A kinase adds a phosphate to the deoxynucleotide diphosphate the make the ____.

A

dNTP precursor

64
Q

____ removes 2 phosphates from dUTP to make dUMP.

A

phosphatase

65
Q

dUMP is converted to dTMP by thymidylate synetase using ____ to donate a ____.

A

tetrahydrofolate

methyl group

66
Q

DNA polymerization requires enzymes known as ____, that join deoxynucleotides together to make long chains.

A

DNA polymerases

67
Q

____ attaches the 1st phosphate (alpha) of one dNTP to the 3’ carbon of the sugar of the dNTP previously added to the growing chain.

A

DNA polymerase

68
Q

DNA polymerase releases the last 2 phosphates (beta and gamma) to produce _____.

A

the energy for the reaction

69
Q

Two types of DNA polymerase

A

DNA polymerase III

DNA polymerase I

70
Q

degrade DNA strands by breaking phosphodiester bonds

A

nucleases

71
Q

initiate breaks in the middle of the DNA strand

A

endonucleases

72
Q

Can remove nucleotides only from the ends of DNA

A

exonucleases

73
Q

degrade DNA only from the 3’ end in the 3’-to-5’ direction

A

3’ endonucleases

74
Q

degrade DNA only from the 5’ end in the 5’-to-3’ direction

A

5’ endonucleases

75
Q

form phosphodiester bonds between the ends of two chains of DNA

A

ligases

76
Q

make RNA primers to initiate synthesis of new strands of DNA

A

primases

77
Q

DNA polymerases cannot initiate the synthesis of new strands of DNA, they can only attach ____ to ____.

A

dNTP’s

a free OH group

78
Q

travel with DNA polymerase as part of the DNA replication complex (with the polymerase, they make up the ____.)

A

accessory proteins

DNA polymerase III holoenzyme

79
Q

keep the DNA polymerase from falling off of the DNA

A

Beta clamp

80
Q

Other proteins form a ____ to allow the polymerase to release when required (example, during lagging strand synthesis)

A

clamp loader

81
Q

Additional proteins traveling with the DNA polymerase are ____ and serve editing functions to correct any mistakes made by the polymerase

A

exonucleases

82
Q

The ___ experiment helps show semiconservative replication in DNA.

A

Meselson-Stahl Experiment

83
Q

Replication begins at __ and moves in ___.

A

one point

both directions

84
Q

Before replication can occur, the template strands must be ___.

A

separated

85
Q

The structure where the strands are separated and new DNA is being synthesized.

A

replication fork

86
Q

DNA stands are separted by proteins called ___.

A

DNA helicases

87
Q

a doughnut shaped protein complex which surrounds the DNA ahead of the replication fork.

A

DnaB helicase

88
Q

To keep the stands from coming back together _____ bind and prevent the premature formation of double stranded DNA.

A

single stranded binding proteins (SSB)

89
Q

Antiparallel strands require different strategies since DNA polymerase III can only move in the _____ direction.

A

3’-to-5’

90
Q

On one strand DNA Pol III initiated DNA
synthesis from an ___ and proceeds
in the 3′-to-5′ direction

A

RNA primer

91
Q

This newly synthesized continuous strand is referred to as the ____.

A

leading strand

92
Q

DNA Pol III polymerizes short pieces called

___ in the opposite direction to that in which the fork is moving

A

Okasaki fragments

93
Q

___ is required for starting each Okasaki fragment

A

an RNA primer

94
Q

___ produces the required primers at 3′-GTC-5′ sequences

A

DnaG primase

95
Q

Pol III continues on the ___ until it encounters the previously synthesized piece

A

lagging strand

96
Q

RNA primers are removed by ___ and ___.

A

Rnase H and DNA polymerase I

97
Q

DNA polymerase I removes the RNA primer using ____ and replaces it with DNA using upstream Okazaki fragments as a primer

A

5’ exonuclease activity

98
Q

Okazaki fragments are joined by ___

A

DNA ligase

99
Q

A break or nick in the DNA exists between Okazaki fragment and RNA primer

A

“nick translation”

100
Q

The trombone model of replication helps explain the replication of the ___ strand.

A

lagging

101
Q

The lagging strand loops out as the ___ is synthesized

A

Okazaki fragment

102
Q

The loop is relaxed as the ___ releases the lagging-strand polymerase which hops ahead to the next primer

A

sliding clamp

103
Q

When replicating the lagging strand, DNA polymerase is released when it reaches a ____. By this time the next primer has been added and the polymerase hops ahead again.

A

nick

104
Q

DNA must be faithfully replicated to prevent ___ (mutations).

A

changes in the DNA sequence

105
Q

Sometimes the wrong base is inserted into the growing chain of DNA. Such mutations are called ____ (created distortion in the helix)

A

mismatch mutations

106
Q

2 methods for correcting replication errors:

A

Editing functions and Methyl directed mismatch repair

107
Q

___ check the newly replicated DNA for mistakes and removes the incorrectly paired bases.

A

Editing proteins

108
Q

If an incorrect base is inserted the editing function ____ until the incorrect nucleotide is removed.

A

stops replication

109
Q

Since the new DNA strand grows in the 5’-to-3’ direction, ____ is required to remove incorrectly inserted bases.

A

3’ exonuclease activity

110
Q

DNA pol I possess 3’ exonuclease activity but DNA pol III requires accessory proteins (encoded by the ___ gene; also called ___)

A

dnaQ

mutD

111
Q

mutD mutants, which have a mutation in the mutD gene have much ___ rates of ____ than do wild type cells.

A

higher

spontaneous mutations

112
Q

____ have 3’ and 5’ exonuclease activity

A

DNA pol I

113
Q

A way for the organism to tell which strand is correct and which is incorrect

A

methyl directed mismatch repair

114
Q

E. coli uses the ___ of the DNA strands to distinguish between the new and old DNA.

A

methylation state

115
Q

The enzyme ___ adds a methyl group to the A’s of the GATC/CTAG only after incorporation into the new DNA strand

A

deoxyadenosine methylase (Dam methylase)

116
Q

DNA in the new strand is ___ and DNA at this site is said to be ___ (only methylated on one strand)

A

temporarily unmethylated

hemimethylated

117
Q

The new strand is identified by the lack of ___.

A

methylation

118
Q

Mutants that lack either functions or mismatch repair have unacceptably _________.

A

high mistake rates

119
Q

Editing and mismatch repair are essential for ___.

A

maintaining replication fidelity and stability of the genome.

120
Q

time in which a cell is born, grows larger, and divides into two progeny cells

A

cell division cycle

121
Q

the process by which the larger cell splits into two new cells

A

cell division

122
Q

time from the point when a cell is born until it divides

A

division time or generation time

123
Q

the original cell before division

A

mother cell

124
Q

the two progeny cells after division

A

daughter cells

125
Q

the DNA molecule that carries most of the bacterium’s normal genes

A

chromosome

126
Q

generally circular in contrast to eukaryotic chromosomes which are linear with free ends

A

bacterial chromosomes

127
Q

bacterial chromosomes are much less structured than eukaryotic DNA which is wrapped around proteins called ___

A

histones

128
Q

Replication begins at a unique site called the ___.

A

oriC (origin of chromosomal replication)

129
Q

Replication is ___ with two replication forks proceeding in opposite directions away from the oriC

A

bi-directional

130
Q

Sometimes the wrong base is inserted into the growing chain of DNA. Such mutations are called ____ (created distortion in the helix)

A

mismatch mutations

131
Q

2 methods for correcting replication errors:

A

Editing functions and Methyl directed mismatch repair

132
Q

___ check the newly replicated DNA for mistakes and removes the incorrectly paired bases.

A

Editing proteins

133
Q

If an incorrect base is inserted the editing function ____ until the incorrect nucleotide is removed.

A

stops replication

134
Q

Since the new DNA strand grows in the 5’-to-3’ direction, ____ is required to remove incorrectly inserted bases.

A

3’ exonuclease activity

135
Q

DNA pol I possess 3’ exonuclease activity but DNA pol III requires accessory proteins (encoded by the ___ gene; also called ___)

A

dnaQ

mutD

136
Q

mutD mutants, which have a mutation in the mutD gene have much ___ rates of ____ than do wild type cells.

A

higher

spontaneous mutations

137
Q

____ have 3’ and 5’ exonuclease activity

A

DNA pol I

138
Q

A way for the organism to tell which strand is correct and which is incorrect

A

methyl directed mismatch repair

139
Q

E. coli uses the ___ of the DNA strands to distinguish between the new and old DNA.

A

methylation state

140
Q

The enzyme ___ adds a methyl group to the A’s of the GATC/CTAG only after incorporation into the new DNA strand

A

deoxyadenosine methylase (Dam methylase)

141
Q

DNA in the new strand is ___ and DNA at this site is said to be ___ (only methylated on one strand)

A

temporarily unmethylated

hemimethylated

142
Q

The new strand is identified by the lack of ___.

A

methylation

143
Q

Mutants that lack either functions or mismatch repair have unacceptably _________.

A

high mistake rates

144
Q

Editing and mismatch repair are essential for ___.

A

maintaining replication fidelity and stability of the genome.

145
Q

time in which a cell is born, grows larger, and divides into two progeny cells

A

cell division cycle

146
Q

the process by which the larger cell splits into two new cells

A

cell division

147
Q

time from the point when a cell is born until it divides

A

division time or generation time

148
Q

the original cell before division

A

mother cell

149
Q

the two progeny cells after division

A

daughter cells

150
Q

the DNA molecule that carries most of the bacterium’s normal genes

A

chromosome

151
Q

generally circular in contrast to eukaryotic chromosomes which are linear with free ends

A

bacterial chromosomes

152
Q

bacterial chromosomes are much less structured than eukaryotic DNA which is wrapped around proteins called ___

A

histones

153
Q

Replication begins at a unique site called the ___.

A

oriC (origin of chromosomal replication)

154
Q

Replication is ___ with two replication forks proceeding in opposite directions away from the oriC

A

bi-directional

155
Q

Sequences of DNA where proteins act to initiate replication are called ___ as opposed to the actual proteins that act on these sites which are called ____.

A

trans-acting proteins

Bacterial Genetics (3 decks)

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