micro exam 3 Flashcards
1
Q
mRNA can be “read” in discrete sets of three neucleotides
A
codon
2
Q
the sequence of codons is “read” in only one way
A
reading sequence
3
Q
eukaryotes ability to cut and paste mRNA molecules so they can encode more than one polypeptide
A
alternative splicing
4
Q
the RNA product of a gene that codes for a protein is a
A
mRNA
5
Q
only one strand of the DNA codes for the mRNA directly
A
template strand
6
Q
the complementary strand of the DNA is called the ___ because it is the same neucleotide sequence as the mRNA
A
coding strand
7
Q
this important site is located at the start of the gene
A
promoter
8
Q
enxyme that synthesizes mRNA
A
RNA polymerase
9
Q
the initially transcribed portion of the gene doees not always code for amino acids
A
leader sequence
10
Q
bacteria have a leader sequence with a region called ___ which is important in the initiation of translation
A
Shine-Dalgarno sequence
11
Q
reagion of the gene immediatly downstream of the leader
A
coding region
12
Q
amino acid that initiates protien synthesis
A
N-formylmethionine
13
Q
signals the end of the protien and stops the ribosome during translation
A
stop codon
14
Q
contains sequences that prepare the RNA polymerase for release from the template strand
A
trailer sequence
15
Q
a sequence that signals the RNA polymerase to stop transcription and is involved in dislodging the RNA polymerase from the template DNA
A
terminator
16
Q
the modification of precursor RNA molecules
A
posttranscriptional modification
17
Q
carries amino acids during protien synthesis
A
transfer RNA
18
Q
molecules are components of ribosomes
A
ribosomal RNA
19
Q
bears the message for protien synthesis
A
messenger RNA
20
Q
composed of five polypeptides and catalyzes RNA synthesis
A
RNA polymerase core enzyme
21
Q
has no catalytic activity but helps the core enzyme recognize the promoter
A
sigma factor
22
Q
only this can begin transcription but core enzyme completes RNA synthesis once it has been initiated. when all 6 subunits are together
A
RNA polymerase holoenzyme
23
Q
transcription involves three processes
A
initiation
elongation
termination
24
Q
bacterial promoters havetwo characteristic features
A
a sequence of 6 bases (TTGACA) 35 base pairs befor transcription starts Pribnow box (TATAAT) 10 base pairs before transcription starts
25
the -10 and -35 sequences are similar in all promoters and are called
consensus sequences
26
a region of DNA about 16-20 neucleotides is unwound and becomes the ___which moves with the RNA polymerase as it synthesizes mRNA from the template DNA
transcription bubble
27
this terminator follows a nucleotide dequence that, when transcribed into RNA, forms hydrogen bonds within the single-stranded RNA. creates a hairpined stem-loop structure which causes RNA polymerase to stop transcription
intrinsic or rho-independent termination
28
requires the aid of a protien called a rho factor which binds to mRNA and moves along the molecule until it reaches the RNA polymerase halted at the terminator by a stem-loop structure that form in mRNA causes the RNA polymerase to dissociate with the DNA template
rho-dependent termination
29
how many letters are codons
3
30
what are the letters for the start codon
AUG
31
serves at the start site for translation by coding for the initiator RNA
start codon
32
name the three stop codons
UGA
UAG
UAA
33
another name for stop codons
nonsense codons
34
are diret amino acid incorporation into protiens
sense codons
35
the genetic code exhibits this because there are up to six different codons for a given amino acid
code degeneracy
36
the codons for a particular amino acid most often differ in the third position
wobble
37
involves decoding the mRNA and covanlently linking amino acids together to form a polypeptide
translation
38
where does translation take place
the ribosome
39
translation starts at the ___ and ends at the ___ (direction)
N-terminus
| C-terminus
40
a complex of mRNA with several ribososomes attached
polyribosome or polysome
41
the process in which amino acids are attached to tRNA molecules.
amino acid activation
42
holds the activated amino acid
the acceptor stem of tRNA
43
amino acid is attached where in the tRNA molecule
to the terminal adenylic acid
44
complementary to the mRNA codon
anticodon
45
two other arms on tRNA molecule that have unique neucleotides
D arm and T arm
46
amino acids are activated for protien synthesis through a reaction catalysed by enzymes called
aminoacyl-tRNA synthetases
47
the region of the ribosome directly responsible for translation
translational domain
48
this is the rRNA which is part of the 30S subunit needed to start initiation of translation
16S rRNA
49
16S rRNA binds to this which helps position the mRNA on the ribosome
Ribosome binding site or Shine-Dalgarno sequence
50
ribozyme that catalyzes peptide bond formation
23S rRNA
51
protien synthesis is broken down into three parts
initiation
elongatin
termination
52
bacteria begin protien synthesis with a modified molecule, which is coded for by the start codon
N-formylmethionyl-tRNA (fMet)
53
how many initiation factors are necessary to make the initiation complex
3
54
this is hydrolyzed during the association of 50S and 30S subunites
GTP
55
elongation cycle is composed of three phases
aminoacyl-tRNA binding
transpeptidatino reaction
translocation
56
elogation cycle is aided by
elongation factors
57
an amino acid corresponding to the proper mRNA codon is added to the C-terminal end of the polypeptide chain as the ribosome moves down the mRNA in the 5 prime 3 prime direction
elongation
58
ribosome has three sites for binding tRNAs
peptidyl site
aminoacyl site
exit site
59
transpeptidation is catalyzed by this whic is part of the 50S ribosomal subunit
peptidyl transferase
60
three things happen simultaneously during translocation
the peptidyl tRNA moves from A site to P site
the ribosome moves one codon along the mRNA so a new codon is in site A
the empty tRNA moves from P site to E site and leaves the ribosome
61
enzymes that are needed at all times are called
housekeeping enzymes and are produced by housekeeping genes
62
housekeeping genes that are expressed continuously
constitutive genes
63
genes that encode for inducible enzymes
inducible genes
64
when an enzymes levels rise because of the presense of this
inducer
65
the genes for enzymes involved in biosynthesic pathways and are necessary for the synthesis and are persent unless the end product of their patheay is available
repressible genes/enzymes
66
occurs when the binding of the protien to DNA inhibits initiation of transcription
negativee transcriptional control
67
regulatory protiens that bind and inhibit transcription are
repressor protiens
68
occurs when the binding of the protein to the DNA promotes transcription initiation
positive transcriptional control
69
regulatory protiens that promote transcription
activator protiens
70
in bacteria repressor protiens bind a region called this which usually overlaps or is downstream of the promotor
the operator
71
activator protiens bind to
activator-bindng sites
72
the repressor protien is active and prevents transcription when the substrate of the pathway is not available. it is inactivated by binding of the inducer
negatively controlled inducible genes
73
the repressor protien is initially synthesized in an inactive form called the aporepressor. it is activated by vinding of the corepressor
negatively controlled repressible genes
74
protien synthesized in an inactive form
aporepressor
75
activator is activated by the inducer
positively regulated inducible gene
76
activator is inactivated by an inhibitor
positivly regulated repressible gene
77
the genes coding for nonregulatory polypeptides are simply lined up together on the DNA, and a single polycistronic mRNA carries all the messages
structural genes
78
sequence of bases coding for one or more polypeptides together with the promotor and operator or activator-bindng sites
operon
79
what are the three enzymes the lac operon codes for
beta-galactosidease
beta-galactosidease permease
beta-galactosidesase transacetylase
80
tryptophan operon is regulated by
trp repressor
81
a regulatory system that uses the transfer of phosphoryl groups to control gene trasncription and protien activity.
two component signal transduction system
82
spans the cytoplasmic membrane so that part of it is exposed to the extracellular environment, while another part is exposed to the cytoplasm and cant sense specific changes in the environment and communicate information to the cells interior
sensor kinase proteint
83
a DNA binding protien that when activated by teh sensor kinase, can act as either an activator or repressor. it promotes transcription of genes or operons whoes expression is needed for acclimation to the detected environmental stimulus. it inhibits transcription of genes or operons whoe products are no longer needed
response-regulator protien
84
when transcription is terminated in the leader region
attenuation
85
when transcribed these sequences form stem-loop secondary structures in the newly formed mRNA molecule
attanuator sequences
86
when these attenuator regions are paired together they form a secondary structure called a pause loop that causes RNA polymerase to stall
1 and 2
87
when these regions pair it form the termination loop
3 and 4
88
if the leader sequence of an mRNA is folded one way, transcription continues, if folded another transcription is terminated, the leader region is called a
riboswitch
89
the production of riboflavin biosynthetic enzymes is repressed by this which is derived from riboflavin
flavin mononucleotide
90
these sequences give rise to competing terminator and antiterminator sequences
T box
91
a large number of RNA molecules have been discovered that are noncoding RNA molecules called
small RNAs
92
sRNAs that regulate transcription by base pairing to the target mRNA and thus are complementary
antisense RNAs
93
most antisense RNA molecules work with this protein to regulate their target RNAs
Hfq protein
94
chaperone protein that interacts with RNA to promote changes in its structure
Hfq protein
95
control of metabolic pathways brought about by odulating the activity of certain regulatory enzymes that function in the pathway
posttranslational regulation
96
posttranslational regulation can occur by
allosteric control or covalent modification
97
regulatory systems that affect many genes and pathways simultaneously
global regulatory systems
98
a collection of genes or operons that is controlled by a common regulatory protein
regulon
99
operon network under the control of a common global regulatory protein but whose constitutent operons also are controlled separately by their own regulators
modulon
100
can immediately change expression of many genes as they direct RNA polymerase to specific subsets of bacterium's genome
alternate sigma factors
101
sigma factors recognize promoters that differ in sequence..
-10 and -35 position
102
specific sequences recognized by a given sigma factor are called its
consensus sequences
103
under normal conditions a sigma factor called __ directs RNA polymerase activity
sigma70
104
binds to consensus sequences in promoters of genes whose products are needed for flagella biosynthesis and chemotaxis
sigmaF or sigma28
105
if temperatures rise too high ___ produces and stimulates the formation of about 17 heat-shock proteins that protect the cell from thermal destruction
sigmaH or sigma32
106
When bacteria use one energy source have a lag phase and then use a second energy source the biphasic growth pattern is called
diauxic growth
107
inhibition of the synthesis of several catabolic enzymes by a preferred carbon and energy source
catabolite repression
108
coordinated regulation of catabolite operons is brought about by ___ which is also called ___
catabolite activator protein (CAP)
| cyclic AMP receptor protein (CRP)
109
CAP active state when small cyclic neucleotide ___is bound and inactive when free of ___
3 prime 5 prime cyclic adenosine monophosphate (cAMP)
110
a permanent, heritable change in the genetic material
mutation
111
small changes in DNA are sometimes called
microlesions
112
mutations affect only one base pair in a given location
point mutation
113
larger mutations are called
mactolesions
114
arise in all cells and in the absence of any added agent
spontaneous mutations
115
mutations from exposure to a mutagen
induced mutations
116
a physical or chemical agent
mutagen
117
relationship between two structural isomers that are in chemical equilibrium and readily change into another
tautomerism
118
shifts in hydrogen bonding characteristics of bases, allowing purine for purine or pyrimidine for pyrimidine substitutions that can eventually lead to a stable alteration
transition mutations
119
mutations where a purine is substituted for a pyrimidine or a pyrimidine for a purine, rarer due to steric problems
transversion mutations
120
three common types of chemical mutagens
base analogs
DNA-modifying agents
intercalating agents
121
structurally similar to normal nitrogenous bases and can be incorporated into the growing polypeptide chain during repication
base analogs
122
mutagens that change a base's structure and therefore alter its base pairing specificity
DNA-modifying agent
123
distort DNA to induce single nucleotide pair insertions and deletions
intercalating agents
124
the more prevalent form of a gene and its associated phenotype is called
wild type
125
a mutation from a wild type to a mutant form
forward mutation
126
when a second mutation occurs that restores the wild type at the same site as the original mutation
reversion mutation
127
if the second mutation is at a different site than the original mutation
suppressor mutation
128
most common types of point mutations
silent
missense
nonsense
frameshift
129
change the nucleotide sequence of a codon but do not change the amino acid encoded by that codon
silent mutation
130
involve a single base substitution that changes a codon fro one amino acid into a codon for another
missense mutation
131
convert a sense codon to a nonsense codon (stop codon)
nonsense mutations
132
arise from the insertion or deletion of one or two base pairs within the coding region of a gene
frameshift mutation
133
a nearby frameshift that restores the proper reading frame is an example of
intragenic suppressor mutation
134
those that are expressed only under certain environmental conditions
conditional mutations
135
it is unable to grow on medium lacking that molecule but grows when the molecule is provided
conditional phenotype (auxotroph)
136
if the wild type strain from which the mutant arose is a chemoorganotroph able to grow on a minimal medium containing only salts and a carbon source
prototroph
137
using a suitable detection system for finding the mutant phenotype
screening
138
technique used to screen for auxotrophic mutants
replica plating
139
test that determines if a substance increases that rate of mutation, that is if its a mutagen
Ames test
140
the removal of an incorrect nucleotide immediately after its addition to the growing end of the chain
proofreading
141
corrects damage that causes distortions in the double helix
excision repair
142
a repair enzyme called UvrABC endonuclease removes damaged nucleotides an a few nucleotides on either side of the lesion
nucleotide excision repair
143
employs DNA glycosylases to remove damaged or unnatural bases yielding apurinic or apyrimidinic sites
base excision repair
144
a type of DNA repair mechanism in which a damaged nitrogenous base is returned to its normal form
direct repair
145
repairs thymine dimers by splitting them apart with the help of visible light
photoreactivation
146
correction enzyme MutS scans the newly replicated DNA for mismatched pairs
mismatch repair
147
catalyzed by DNA methyltransferases and results in three different products: N6-methyladenine, 5-methyl cytosine and N4-methylcytosine
DNA methylation
148
corrects damaged DNA in which both bases of a pair are missing or damaged, or where there is a gap opposite a lesion
recombinational repair
149
cuts a piece of template DNA from a sister molecule and puts int into the gap or uses it to replace a damaged strand
RecA protein
150
numerous genes are activated when a repressor called LexA is destroyed
SOS response
151
DNA polymerase IV and DNA polymerase V synthesize DNA across gaps and other lesions that had stopped DNA polymerase III
translesion DNA synthesis
152
an alternate form of a gene
allele
153
the process in which one or more nucleic acid molecules are rearranged or combined to produce a new nucleotide sequence
recombination
154
organisms produced by a recombination
recombinants
155
mechanisms collectively involved in creating recombinants
horizontal gene transfer
156
piece of donor DNA
exogenote
157
another name for a partially diploid cell
merozygote
158
the most common recombination event usually involves a reciprocal exchange between a pair of DNA molecules with the same nucleotide sequence
homologous recombination
159
proposes that duplex DNA with a double-stranded break is processed to create DNA with single stranded ends
double stranded break model
160
contains strands derived from both parent molecules
heteroduplex DNA
161
important in the integration of viral genomes into chromosomes
site-specific recombination
162
the chromosomes of viruses and cells contain pieces of DNA that can move and integrate into different sites in the chromosomes
transposition
163
DNA segments that carry the genes required for transposition are
transposable elements
164
who first discovered transposable elements
Barbara McClintock
165
a short sequence of DNA that contains only the gene for the enzyme transposase and it is bounded at both ends by inverted repeats
insertion sequences
166
required for transposition and accurately recognizes the ends of the IS
transposase
167
mobile genetic elements that contain genes in addition to those required for transposition
transposons
168
involves trasnosase-catalyzed excision of the transposable element, followed by cleavage of a new target site and ligation of the element into this site
simple transposition or cut and paste transposition
169
the original transposition remains at the parental site on the chromosome and a copy is inserted at the target DNA site
replicative transposition
170
small double stranded DNA molecules that can exist independently of host chromosomes
plasmids
171
plasmids that can exist either with or without being integrated into the host chromosomce
episome
172
transfer copies of themselves to other bacteria during a process of conjugation
conjugative plasmids
173
about 100,000 base pairs long and bears genes responsible for cell attachment and transfer between specific e.coli
F factor
174
the transfer of DNA by direct cell to cell contact
conjugation
175
mixed two auxotrophic strains incubated the culture for several hours in nutrient medium, then plated in on minimal medium
Joshua Lederberg and Edward tatum
176
constructed a U tube consisting of two pieces of curved glass tubeing fused at the base to form a U shape with a glass filter between halves, showed that contact between cells was necessary
Bernard davis
177
demonstrated that the gene transfer observed by Lederberg and tatum was unidirectional
William Hayes
178
used to establish contact between F+ and F- cells
sex pillus
179
one strand of the circular DNA is nicked and the free 3 prime hydroxyl end is lengthened while the growing point rolls around the circular template and the 5 prime end of the strand is displaced to form an ever lengthening tail
rolling circle replication
180
the donor transfers chromosomal genes with great efficiency but does not change the recipient bacteria into F+ cells
Hfr conjugation
181
donor in Hfr conjugation
Hfr strain
182
sometimes during excision the plasmid makes an error and picks up a portion of the chromosome
F prime plasmid
183
who discovered transformation
fred griffith
184
the uptake by a cell of DNA, either a plasmid or a fragment of alinear DNA from the medium and the maintenance of the DNA in the recipient in a heritable form
transformation
185
a cell that is able to take up DNA and be transformed
competent cell
186
frequent mode of horizontal gene transfer in nature and is mediated by viruses
transduction
187
viruses that attack bacteria
bacteria phage
188
multiply in their bacterial host immediately after entry
virulent bacteriophages
189
after the number of progeny phages reaches a certain number, they cause the host to lyse
lytic cycle
190
enter the host bacterium and do not immediately kill their hosts
temperate bacteriophages
191
inserted viral genome
prophage
192
the relationship between these viruses and their host
lysogeny
193
bacteria that have been lysogenized
lysogens
194
occurs during the lytic cycle of virulent and some temperate phages. any part of the bacterial genome can be transferred
generalized transduction
195
only specific portions of the bacterial genome are carried by transducing particles
specialized transduction
