Bact Gen - Chapter 1 Flashcards
1
Q
Bacteria are ___ organisms.
A
relatively simple
2
Q
Many types of bacteria are hard/easy to manipulate in the lab.
A
easy
3
Q
____ have remained largely unchanged throughout evolution.
A
central cellular functuions
4
Q
____ originally identified in bacteria are highly similar in
all organisms – cancer research
A
DNA repair responses
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
6
Q
Bacteria capable of surviving in extreme environments. Ex. high temperature, pressure, and osmolarity
A
extremophiles
7
Q
Perform
functions which allow other
organisms to survive
A
symbiotic bacteria
8
Q
Many bacteria are _____
of humans, plants, and
animals
A
pathogens
9
Q
Of the 10^14 cells in a human, __% are human!
A
10
10
Q
___ can be studied to learn about antibiotics, medicines, foods,
chemicals, & molecular biology
tools.
A
bacterial genetics
11
Q
All organisms on Earth belong to one of three divisions:
A
Eubacteria, Archae, or Eukaryotes
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
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
14
Q
- Diverse organisms- plants, animals, and fungi
- Can be single or multicellular
- Very similar at the biochemical level (macromolecular synthesis)
A
Eukaryotes
15
Q
the study/manipulation of DNA to characterize cellular
and organismal functions
A
genetics
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
17
Q
Individuals that differ from the normal, or wildtype,
members of the species by an observable attribute, or phenotype.
A
mutants
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
19
Q
____ is made possible by the development of modern molecular
genetic techniques
A
reverse genetics
20
Q
Both ____ and ____ have strengths and
weaknesses and the two approaches often complement
each other
A
classical and reverse genetics
21
Q
Bacteria are _________, one copy or allele of each gene
A
haploid
22
Q
Most higher organisms are ____ (two copies of each gene).
A
diploid
23
Q
With haploid organisms the effects of the mutation are ____.
A
immediate
24
Q
all progeny are genetically identical to
parents (________)
A
clones
25
ability to isolate clones
colony formation
26
large numbers of bacteria can be
| diluted to manageable numbers by ____.
serial dilution
27
Bacteria have short ____.
generation times
28
A major advantage that allows us to identify rare
| individual mutants among billions of normal bacteria
selection
29
Some selective conditions include:
nutrients/nutrient limitation
temperature
antibiotics
30
Bacteria can be stored in a ____ state, which prevents the need to continuously propagate them.
dormant
31
Methods of storing bacteria:
dormant spores
frozen in glycerol
dried down
32
Storing stocks of bacteria can be useful for accumulating a variety of different ____ for genetic experiments.
clones
33
Includes transformation, conjugation, and transduction.
genetic exchange
34
In the early 1950's who discovered that DNA was a double helical structure by X-ray diffraction?
Rosalind Franklin and Maurice Wilkins
35
in 1953 ___ proposed the now famous model for the structure of DNA.
Francis Crick and James Watson
36
DNA is a ____ handed helix.
right
37
DNA has a ____ backbone.
sugar-phosphate
38
Helices are connected by ____ between nucleobases (purines and pyrimidines)
hydrogen bonding
39
Spacing between helices result in ____.
major and minor grooves
40
1 helical turn is how many base pairs?
10 (3.4 nm in length)
41
Two ring bases, adenine and guanine.
purine
42
One ring bases, thymine cytosine and uracil.
pyrimidine
43
In DNA, all 4 bases are attached to the 5-carbon sugar ____.
deoxyribose
44
Deoxyribose lacks an oxygen at the ____ carbon.
2nd
45
base + sugar + one or more phosphates
deoxynucleotides (nucleotides)
46
base + sugar but no phosphate
deoxynucleosides
47
Collectively the four deoxynucleoside triphosphates are ____.
dNTPs
48
Deoxynucleotides are linked together by ____.
phosphodiester bonds
49
The phosphate attached to the ____ of one nucleotide is attached to the ____ of the next nucleotide.
5' carbon of the deoxyribose sugar
| 3' carbon of the deoxyribose sugar
50
DNA has ____ construction.
antiparallel
51
5' end holds a free ____.
phosphate
52
3' end holds a free ____.
hydroxyl group
53
____ says: no matter the source of DNA, the concentration of A = T and C = G.
Chargaff's Rule
54
____ and ____ pair with 2 hydrogen bonds.
adenine and thymine
55
____ and ____ pair with 3 hydrogen bonds.
cytosine and guanine
56
DNA replication involves ____ using sequence of the opposite strand as a template.
polymerizing deoxynucleotides
57
Deoxynucleotides are ____ and must be synthesized by a series of enzymatic steps prior to being incorporated into DNA
precursors or DNA synthesis
58
removes oxygen
reductase
59
adds phosphates
kinase
60
removes phosphates
phosphatase
61
links together two molecules
synthetase
62
____ reduces ribose sugar to deoxyribose by changing the OH at the 2' position to H.
ribonucleotide reductase
63
A kinase adds a phosphate to the deoxynucleotide diphosphate the make the ____.
dNTP precursor
64
____ removes 2 phosphates from dUTP to make dUMP.
phosphatase
65
dUMP is converted to dTMP by thymidylate synetase using ____ to donate a ____.
tetrahydrofolate
| methyl group
66
DNA polymerization requires enzymes known as ____, that join deoxynucleotides together to make long chains.
DNA polymerases
67
____ attaches the 1st phosphate (alpha) of one dNTP to the 3' carbon of the sugar of the dNTP previously added to the growing chain.
DNA polymerase
68
DNA polymerase releases the last 2 phosphates (beta and gamma) to produce _____.
the energy for the reaction
69
Two types of DNA polymerase
DNA polymerase III
| DNA polymerase I
70
degrade DNA strands by breaking phosphodiester bonds
nucleases
71
initiate breaks in the middle of the DNA strand
endonucleases
72
Can remove nucleotides only from the ends of DNA
exonucleases
73
degrade DNA only from the 3' end in the 3'-to-5' direction
3' endonucleases
74
degrade DNA only from the 5' end in the 5'-to-3' direction
5' endonucleases
75
form phosphodiester bonds between the ends of two chains of DNA
ligases
76
make RNA primers to initiate synthesis of new strands of DNA
primases
77
DNA polymerases cannot initiate the synthesis of new strands of DNA, they can only attach ____ to ____.
dNTP's
| a free OH group
78
travel with DNA polymerase as part of the DNA replication complex (with the polymerase, they make up the ____.)
accessory proteins
| DNA polymerase III holoenzyme
79
keep the DNA polymerase from falling off of the DNA
Beta clamp
80
Other proteins form a ____ to allow the polymerase to release when required (example, during lagging strand synthesis)
clamp loader
81
Additional proteins traveling with the DNA polymerase are ____ and serve editing functions to correct any mistakes made by the polymerase
exonucleases
82
The ___ experiment helps show semiconservative replication in DNA.
Meselson-Stahl Experiment
83
Replication begins at __ and moves in ___.
one point
| both directions
84
Before replication can occur, the template strands must be ___.
separated
85
The structure where the strands are separated and new DNA is being synthesized.
replication fork
86
DNA stands are separted by proteins called ___.
DNA helicases
87
a doughnut shaped protein complex which surrounds the DNA ahead of the replication fork.
DnaB helicase
88
To keep the stands from coming back together _____ bind and prevent the premature formation of double stranded DNA.
single stranded binding proteins (SSB)
89
Antiparallel strands require different strategies since DNA polymerase III can only move in the _____ direction.
3'-to-5'
90
On one strand DNA Pol III initiated DNA
synthesis from an ___ and proceeds
in the 3′-to-5′ direction
RNA primer
91
This newly synthesized continuous strand is referred to as the ____.
leading strand
92
DNA Pol III polymerizes short pieces called
| ___ in the opposite direction to that in which the fork is moving
Okasaki fragments
93
___ is required for starting each Okasaki fragment
an RNA primer
94
___ produces the required primers at 3′-GTC-5′ sequences
DnaG primase
95
Pol III continues on the ___ until it encounters the previously synthesized piece
lagging strand
96
RNA primers are removed by ___ and ___.
Rnase H and DNA polymerase I
97
DNA polymerase I removes the RNA primer using ____ and replaces it with DNA using upstream Okazaki fragments as a primer
5' exonuclease activity
98
Okazaki fragments are joined by ___
DNA ligase
99
A break or nick in the DNA exists between Okazaki fragment and RNA primer
"nick translation"
100
The trombone model of replication helps explain the replication of the ___ strand.
lagging
101
The lagging strand loops out as the ___ is synthesized
Okazaki fragment
102
The loop is relaxed as the ___ releases the lagging-strand polymerase which hops ahead to the next primer
sliding clamp
103
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.
nick
104
DNA must be faithfully replicated to prevent ___ (mutations).
changes in the DNA sequence
105
Sometimes the wrong base is inserted into the growing chain of DNA. Such mutations are called ____ (created distortion in the helix)
mismatch mutations
106
2 methods for correcting replication errors:
Editing functions and Methyl directed mismatch repair
107
___ check the newly replicated DNA for mistakes and removes the incorrectly paired bases.
Editing proteins
108
If an incorrect base is inserted the editing function ____ until the incorrect nucleotide is removed.
stops replication
109
Since the new DNA strand grows in the 5'-to-3' direction, ____ is required to remove incorrectly inserted bases.
3' exonuclease activity
110
DNA pol I possess 3' exonuclease activity but DNA pol III requires accessory proteins (encoded by the ___ gene; also called ___)
dnaQ
| mutD
111
mutD mutants, which have a mutation in the mutD gene have much ___ rates of ____ than do wild type cells.
higher
| spontaneous mutations
112
____ have 3' and 5' exonuclease activity
DNA pol I
113
A way for the organism to tell which strand is correct and which is incorrect
methyl directed mismatch repair
114
E. coli uses the ___ of the DNA strands to distinguish between the new and old DNA.
methylation state
115
The enzyme ___ adds a methyl group to the A's of the GATC/CTAG only after incorporation into the new DNA strand
deoxyadenosine methylase (Dam methylase)
116
DNA in the new strand is ___ and DNA at this site is said to be ___ (only methylated on one strand)
temporarily unmethylated
| hemimethylated
117
The new strand is identified by the lack of ___.
methylation
118
Mutants that lack either functions or mismatch repair have unacceptably _________.
high mistake rates
119
Editing and mismatch repair are essential for ___.
maintaining replication fidelity and stability of the genome.
120
time in which a cell is born, grows larger, and divides into two progeny cells
cell division cycle
121
the process by which the larger cell splits into two new cells
cell division
122
time from the point when a cell is born until it divides
division time or generation time
123
the original cell before division
mother cell
124
the two progeny cells after division
daughter cells
125
the DNA molecule that carries most of the bacterium's normal genes
chromosome
126
generally circular in contrast to eukaryotic chromosomes which are linear with free ends
bacterial chromosomes
127
bacterial chromosomes are much less structured than eukaryotic DNA which is wrapped around proteins called ___
histones
128
Replication begins at a unique site called the ___.
oriC (origin of chromosomal replication)
129
Replication is ___ with two replication forks proceeding in opposite directions away from the oriC
bi-directional
130
Sometimes the wrong base is inserted into the growing chain of DNA. Such mutations are called ____ (created distortion in the helix)
mismatch mutations
131
2 methods for correcting replication errors:
Editing functions and Methyl directed mismatch repair
132
___ check the newly replicated DNA for mistakes and removes the incorrectly paired bases.
Editing proteins
133
If an incorrect base is inserted the editing function ____ until the incorrect nucleotide is removed.
stops replication
134
Since the new DNA strand grows in the 5'-to-3' direction, ____ is required to remove incorrectly inserted bases.
3' exonuclease activity
135
DNA pol I possess 3' exonuclease activity but DNA pol III requires accessory proteins (encoded by the ___ gene; also called ___)
dnaQ
| mutD
136
mutD mutants, which have a mutation in the mutD gene have much ___ rates of ____ than do wild type cells.
higher
| spontaneous mutations
137
____ have 3' and 5' exonuclease activity
DNA pol I
138
A way for the organism to tell which strand is correct and which is incorrect
methyl directed mismatch repair
139
E. coli uses the ___ of the DNA strands to distinguish between the new and old DNA.
methylation state
140
The enzyme ___ adds a methyl group to the A's of the GATC/CTAG only after incorporation into the new DNA strand
deoxyadenosine methylase (Dam methylase)
141
DNA in the new strand is ___ and DNA at this site is said to be ___ (only methylated on one strand)
temporarily unmethylated
| hemimethylated
142
The new strand is identified by the lack of ___.
methylation
143
Mutants that lack either functions or mismatch repair have unacceptably _________.
high mistake rates
144
Editing and mismatch repair are essential for ___.
maintaining replication fidelity and stability of the genome.
145
time in which a cell is born, grows larger, and divides into two progeny cells
cell division cycle
146
the process by which the larger cell splits into two new cells
cell division
147
time from the point when a cell is born until it divides
division time or generation time
148
the original cell before division
mother cell
149
the two progeny cells after division
daughter cells
150
the DNA molecule that carries most of the bacterium's normal genes
chromosome
151
generally circular in contrast to eukaryotic chromosomes which are linear with free ends
bacterial chromosomes
152
bacterial chromosomes are much less structured than eukaryotic DNA which is wrapped around proteins called ___
histones
153
Replication begins at a unique site called the ___.
oriC (origin of chromosomal replication)
154
Replication is ___ with two replication forks proceeding in opposite directions away from the oriC
bi-directional
155
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 ____.
trans-acting proteins
