TEST 2 Flashcards
(256 cards)
1
Q
decontamination
A
treatment of object to make safe to handle
2
Q
disinfection
A
targets death of pathogens not all microbes or endospores
3
Q
sterilization
A
kills all microbes and viruses
4
Q
heat sterilization
A
wet heat better than dry heat
5
Q
pastuerization
A
-uses heat to reduce microbial load but not all microbes
-kills pathogens
6
Q
UV sterilization
A
used to sterilize food surgical tools lab equipment
7
Q
D10 value
A
ionizing radiation needed to reduce bacteria 10 fold
8
Q
filter sterilization
A
-used on heat sensitve liquids and gases
-pores are to small for microbes to go through
9
Q
membrane filters
A
common for liquids
10
Q
nucleopore filters
A
thin irradiated film used to visualize microbes for electron microscopy
11
Q
-cidal
A
kills microbes
12
Q
-static
A
stops growth of microbes
13
Q
sanitizers
A
reduce microbial number but doesnt sterilize
14
Q
antiseptic
A
kills/inhibits growth of microbes nontoxic to living tissue
15
Q
purines
A
G A 2 ringed
16
Q
pyrimidines
A
T C 1 ring
17
Q
GC bond
A
3 h bonds
18
Q
TA bond
A
2 h bonds
19
Q
-lytic
A
lyses all cells destroying even dead cells
20
Q
negative supercoiling
A
coils increase becoming tightly wound
21
Q
positive supercoiling
A
coils decrease becoming loosely wound
22
Q
topoisomerase
A
inserts and removes supercoiles
23
Q
DNA gyrase
A
introduces supercoils via double strand breaks
24
Q
3 rnas and functions
A
mRNA- carries info of DNA gene to ribosome
tRNA-brings amino acid to mRNA converting it into amino acid sequence
rRNA-ribosomal rna, ribosome component
25
3 stages of biologic information flow
replication
transcription
translation
26
eukaryotic transcription
1 gene to 1 mRNA
mRNA exported to cytosol
27
prokaryotic transcription
several genes to 1 mRNA
transcription and translation in cytosol
28
plasmids
circular and double stranded
29
transposable elements
-segments of DNA inserted into other DNA molecules
-moves site to site
30
R plasmids
grants antibiotic resistance to bacteria
31
bacteriocins
proteins killing closely related species of same species
can be encoded by plasmids
32
rhizobia
plasmid encoded function is to fix nitrogen
33
semiconservative dna replication
2 of the 4 DNA strands in the new cells are the DNA strands from the original cell
34
DNA pol Family A
-DNA repair and Okazaki fragment maturation
-exonuclease activity
35
DNA pol Family B
-Main polymerase in eukaryotes
-exonuclease activity
36
DNA pol Family C
-Main polymerase in bacteria
-exonuclease activity
37
DNA pol Family X
-monomeric
-fills gaps for DNA repair
38
DNA pol Family Y
-low fidelity, translesion synthesis
-no exonuclease activity
39
DNA pol Family RT
-reverse transcriptase
-uses RNA to make DNA to produce more RNAs
40
Archaeal DNA polymerases
Family B&D
PolB3 present in all archaea
PolB1/2 in some archaea
41
virus DNA polmerases
-DNA viruses utilize host DNA polymerase for proliferation
42
DNA helicase
unwinds DNA for replication
43
Prokaryote vs Eukaryote origin of replication
-prokaryotes-have one origin of replication on circular chromosome
-eukaryotes- have multiple origins of replications on 1 linear chromosome out of all of the linear chromosomes
44
DNA ligase
seals the nicks in the DNA backbone after primers have been removed and filled with DNA
45
leading strand
continuous
5>3 strand synthesis
1 primer
46
lagging strand
discontinuous
5>3 strand synthesis
multiple primers
47
replisome
large replication complex of proteins
48
DNA vs RNA
-DNA-
deoxyribose-2' H bond
thymine
-RNA-
ribose-2' OH bond
uracil
49
primosome
helicase and primase subcomplex within the replisome
50
holoenzyme
RNA polymerase complex of 5 proteins
51
sigma factor
recognizes promoter sequences on DNA
52
pribnow box
TATA
promoter sequence
53
number of Eukaryotic RNA polymerases
3
54
number of archaeal RNA polymerases
1
55
B recognition element
-BRE for short
-upstream of TATA box
-the binding of the transcription factor to the BRE allows for initation of RNA transcription
56
termination method
inverted repeats of TA, creates loops of RNA that fall off of DNA strand
57
exons
gene coding element of RNA
58
introns
nongene coding element of RNA
59
splicing
removal of introns
in eukaryotes this happens in nucleus
60
capping
-addition of methylated guanosine to end of mRNA, other end will start translation
-needed for translation
61
3 protein functions
-catalysts-enzymes
-structure-integral membrane proteins
-regulatory-DNA binding
62
peptide bond
carboxylic acid bonded to nitrogen
63
degenerate code
64 codons to 20 amino acids
64
shine-delgaro sequence
ensures proper reading frame in bacteria and archaea
65
open reading frame
start codon- AUG
followed by a number of codons then the stop codon
66
Subunits of ribosomes in prokaryotes
-has 30s and 50s subunits to from 70s subunits
-needs GTP
67
chaperones
catalyze molecular folding of proteins
found in all domains
68
heat shock proteins
attempts to refold partially denatured proteins for reuse before proteases destroy them
69
cold shock proteins
prevent secondary structure formation in RNA or refold cold-sensitive proteins
70
Translocases
transport proteins into or through bacterial & archaeal membranes
71
translocation systems
sec and tat system
72
sec system
unfolded proteins to be exported are recognized by
-SecA (periplasmic)
-signal recognition particle (SRP;
for membrane-inserted proteins
73
tat system
TatBC recognizes signal sequence, carries folded protein to TatA
membrane transporter
74
common DNA binding protein characteristic
binds to major groove
homodimeric
75
structure of DNA binding protein
helix turn helix
76
zinc finger
DNA-protein binding technique utilizing a zinc ion
77
leucine zipper
DNA-protein binding technique
-Contains regularly spaced leucine residues
-Hold two recognition helices in the correct orientation to bind DNA
78
transcription factor
Proteins that control the rate of transcription by binding to specific DNA
79
activator protein
turns on transcription
80
repressor protein
turns off transcription
81
Allosteric proteins
Conformation altered when effector
molecule binds
82
Effectors
Small molecules that control binding of activators and repressors
83
Inducers
turn on transcription
84
corepressors
turns of transcription
85
Enzyme repression
-preventing the synthesis of an
enzyme unless the product is absent from culture medium
-excess of product decreases enzyme
synthesis
86
Dual functionality
used as positive and negative control
87
two component regulatory system components
Sensor kinase
Response regulator
88
how does the 2 component regulatory system terminate the responce?
A phosphatase removes phosphate from the response regulator
89
sensor kinase
-detects environmental signals and autophosphorylates at
specific histidine residue
-integral to cell membrane
90
response regulator
-DNA-binding protein that regulates transcription
-receives phosphate from sensor kinase
-in cytoplasm
91
what is this picture depicting?
-This picture shows the 2 component regulatory system
-the sensor kinase gives its phosphate to the response regulator which then blocks transcription of certain genes
92
Methyl-accepting chemotaxis proteins (MCPs)
proteins that sense attractants and repellents and interact with cytoplasmic sensor kinases
93
chemoreceptors
clusters of thousands of MCPs
94
2 component regulatory system and flagella
counterclockwise-run
clockwise-tumble
-When MCPs bind repellent or release
attractant, a kinase is phosphorylated
interacts with flagellar motor to induce clockwise rotation and tumbling
-When MCPs bind attractant or release repellent, a kinase is unphosphorylated and not bound to the flagellar motor, resulting in
counterclockwise rotation and running
95
Quorum sensing
regulatory mechanism by which
Bacteria and Archaea
assess their population density near themselves
96
autoinducer
-molecule that indicates to a cell that other cells are nearby
-moves freely about membranes of cells
-reaches high concentrations in a cell when around other cells
-binds to sensor kinases which activates specific genes
97
Acyl homoserine lactone (AHL)
autoinducer
gram negative only
98
archaea uses what as an autoinducer
short peptides
99
Global control systems
regulates transcription of many
different genes in more than one regulon
100
lac operon
when in absense of glucose, this operon activates its genes to be able to use lactose as main energy source
101
diauxic growth
-two separate growth phases of bacteria
-once better energy source is expended a different energy source is utilized
102
lac operon regulation sequences
-lactose must be present to stop lac repressor from being present (negative control)
-cAMP must be present to bind to lac operon to activate (positive control)
103
heat shock responce
global control mechanism to
protect cells from protein denaturation resulting from heat, high solvent levels, osmotic stress, UV light
104
heat shock proteins
proteins that counteract damage of denatured
proteins and help cell recover from stress
105
ncRNA
RNA that does not code for a gene
rRNAs, sRNA, tRNA
106
small RNA
regulates gene expression
107
mechanisms of sRNA
1) decrease expression of mRNA
2)decrease mRNA degradation
4)increase mRNA stability through not letting it express
4)open up a ribosome binding site
108
ribozymes
RNA that acts as a catalyst
109
riboswitches
RNA that regulates gene expression
110
mechanisms of riboswitches
-binds to RNA
-controls at transcription or translation
-changes secondary structure of RNA which can control if its translated or not
- remove stem-loop that terminates
transcription, increasing mRNA and protein levels
111
Aptamer region
-riboswitch control region
-recognition domain that
binds small molecules
112
Feedback Inihibition
mechanism for temporarily turning off the reactions in a biosynthetic pathway
End product of the pathway binds to an early enzyme in the pathway, thus shutting down the pathway because no intermediates are generated
113
Reversible reaction
once levels of end product are limiting, pathway functions
114
the feedback inhibition enzyme has two sites, what are they?
active sites, allosteric protein site for feedback inhibition
115
isoenzymes
different proteins that catalyze
feedback inhibition but are subject to different
regulators
116
post translational regulation for proteins
phosphoylation, methylation, covalent modification (AMP,ADP)
117
PII Signal Transduction Proteins
-found in Bacteria & Archaea
-epigenetic attachments affect activity
-regulates nitrogen metabolism TFs, enzymes, and transport proteins
118
Anti-sigma
factors can inactivate sigma factors
119
Super-resolution microscopy
-Super-resolution microscopy
-Observes dynamic behaviors in real-time
120
Fluorescent Tagging
-Reporter genes encode proteins that are easy to detect or
assay and fused to genes of interest
-Green fluorescent protein used
121
Photoactivated localization microscopy
maps the movement of individual molecules
122
hemimethylation after DNA replication
-only parental strand of DNA is methylated
-methylation allows for a protein to bind to the origin of replication to block DNA synthesis through binding of DNA initiating proteins
123
par system
partitions the correct amount of DNA strands into two separate daughter cells
124
Par S
centromere like sequence near oriC
125
Par A
ATPase
126
Par B
binds the Par complex to the DNA
127
Pop Z
localized to old pole of DNA
anchors the DNA to one spot
128
Decatenation
separation of
replicated sister chromosomes
129
peptidoglycan synthesis
begins with preexsisting peptidoglycan
-rod shaped-
synthesis begins at several points along cell wall
-coccus-
cell walls grow in opposite directions outward
from the FtsZ ring
130
Bactoprenol
has a major role in precursor
insertion of peptidoglycan synthesis
131
biofilm formation steps
Attachment, colonization, development,
and dispersal
132
attachment stage of biofilm
-Random collision accounts for the initial attachment
-Facilitated by flagella and pili or by cell surface proteins
-Attachment is a signal for expression of biofilm-specific genes
-Once committed to biofilm formation, the cell loses flagella and becomes nonmotile
133
how does the metabolism change when switching to a biofilm?
Signals guide bacteria in transitioning from planktonic growth to life in a semisolid matrix
-Switch to biofilm growth triggered by accumulation c-di-GMP
134
c-di-GMP
-Widely distributed only in Bacteria
-c-di-GMP removes cell surface proteins like flagella and pili
-initiates synthesis of peptidoglycan
135
what do antibiotics target?
-Inhibition of protein synthesis
-Many antibiotics target DNA replication, RNA synthesis, and translation
-peptidoglycan synthesis
(targets DNA gyrase and topoisomerase to prevent DNA unwinding)
(targets RNA synthesis by blocking RNA polymerase active site or RNA elongation)
(can bind to ribosomal binding site to prevent translation)
(can bind to ribosomal subunit leading to error filled proteins)
136
Endospore formation
-triggered by damaging external events
-monitors external environment through 5 sensory kinases (resembles 2 component regulatory system)
-initates when Spo0A gets phosphorylated a lot
137
proteins emmited during endospore formation
-toxic protein that lyses other cells for nutrients
-protein that delays sporulation in other cells
-antitoxin protein to protect themselves from other sporulating cells
138
3 stages of endospores
activation, germination,
outgrowth
139
Germination Receptors
-within the inner membrane surrounding the endospore core exsists these receptors
-senses and binds nutrients
140
Activation of endospore steps
-release of DPA
-rehydration of core
-transcription and translation increase
141
Germination of endospore steps
-removal of the cortex is a
major event
-full rehydration of core
-metabolically active
142
Outgrowth of endospore steps
-elongates allowing escape of spore from mother cell
-fully metabolically active
143
heterocyst
-dedicated cells to nitrogen fixation
-anoxic
144
heterocyst formation
-inactivation of photosystem
-grows thickened cell wall to prevent 02 diffusion
-expresses nitrogenase
-triggered by limited amount of fixed nitrogen
145
Pseudomonas aeruginosa biofilm technique
-quorum sensing through acyl homoserine lactones in large amounts needed to begin colony growth
146
Vibrio cholerae
-quorum sensing opposite of pseudomonas aeruginosa
-must be in low population density area to establish colony
147
aquiring antibiotic resistance
-horizontal gene transfer through plasmids
-chromosomal mutations
148
efflux pump
-transport molecules, including antibiotics, out of the cell
-lowers intracellular concentration allowing cell to survive at higher external cellular concentrations
149
Selectable mutations
gives advantage
(ex antibiotic resistance)
requires screening to find the genes
150
Auxotroph
has an additional nutritional
requirement for growth compared to prototroph
151
prototroph
wild type bacteria, no additional requirement for life
152
Complementation
isolation of several strains
followed by comparative genetic analyses
153
Replica plating
-screens for nutritionally defective mutants
-transfers colonies from main plate
-if colony is unable to grow on medium
lacking a nutrient indicates mutation
154
Spontaneous mutations
-Occur without external intervention
-most result from occasional errors by DNA
polymerase during replication
155
Induced mutations
-Caused environmentally or deliberately
-Can result from exposure to natural radiation or chemicals that chemically modify DNA
156
point mutations
-Change only one base pair
-Occurs via single base-pair substitution
-Phenotypic change depends on the exact location of the mutation
157
Silent mutations
do not affect the sequence of encoded polypeptide or phenotype
158
Missense mutation
changes the sequence of amino acids in
polypeptide
159
Nonsense mutation
mutates a stop codon into the amino acid chain
160
Transitions
-base pair substitution switches it with another base pair of its own kind
-purine to purine
-pyrimidine to pyrimidine
161
Transversions
-base pair substiution switches it with a base pair of a different kind
-purine to pyrimidine & vice versa
162
Frameshift mutations definition
single base pair deletions
or insertions that result in a shift in the reading
frame
163
frameshift mutation effects
-changes entire polypeptide sequence downstream
-can gain/lose thousands of codons
-can be lethal
164
Mutagens
chemical, physical, or biological agents that
increase mutation rates, induce mutations
165
Nucleotide base analogs
-resemble nucleotide bases
but have faulty base pairing
166
chemical mutagens
intercacalating agents
alkylating agents
167
Nonionizing radiation
-base pairs absorb UV
-forms pyrimidine dimers
-UV kills cells due to its effects on DNA
168
Ionizing radiation
-more powerful than nonionizing (UV)
-creates free radicals which are damaging
-creates double/single stranded breaks in DNA backbone
169
SOS repair system
-Initiates many DNA repair processes
-Also allows DNA repair to occur without a template (translesion synthesis; high error rate)
-E Coli's SOS system controls ~40 genes
170
3 mechanisms of bacterial genetic exchange
Transformation, transduction,
conjugation
171
Homologous recombination
-A process that results in genetic exchange between homologous DNA from two different sources
172
3 fates of bacterial genetic exchange
-uptake of the genetic info as separate from host genome
-degredation of genetic info
-integrated into host genome
173
Endonuclease
-nicks one strand of the donor molecule for crossing over of genetic info
174
Strand invasion
-single-stranded DNA molecule pairs with and displaces a similar or complementary strand in a double-stranded DNA molecule
-occurs in genetic recombination
175
heteroduplex
-double-stranded DNA molecule formed by the base pairing of two complementary single-stranded DNAs from different chromosomal sources
-can differ slightly in sequence, leading to mismatches within the heteroduplex
-observed during genetic recombination
176
Merodiploid
-strain carries two copies of a chromosomal segment
-(usually one copy on the chromosome, other on plasmid or phage)
177
Complementation
-occurs if a functional wild-type copy is
supplied on a plasmid or bacteriophage, restoring wild-type phenotype
178
Transformation
-Genetic transfer process where
DNA is incorporated into a recipient cell and brings about genetic change
179
Competent
-a cell that can take up DNA and be
transformed; genetically determined
-this is regulated
180
Gram negative sex pilus
-proteins within pilus recognize
and bind extracellular DNA, pilus retraction pulls DNA in
181
Gram positive sex pilus
-pili or secretion system binds DNA and bring it in
182
virus
genetic element that can multiply
only in a living (host) cell
183
Obligate intracellular parasite
Needs host cell for energy, metabolic
intermediates, protein synthesis
184
virion
singluar virus outside of a cell
185
virus structure
head & tail pilus
186
attachment of virus
-requires complementary receptor
(proteins, carbs, other cell structures)
187
Virulence
-relative ability of a pathogen to cause
disease
188
virulence factor
-toxic/destructive substances produced by the pathogen
-enhances invasiveness
189
Transduction
transfer of DNA from one cell to another by a
bacteriophage
190
Generalized transduction
-DNA from any portion of the
host genome is packaged inside the virion
-Donor genes cannot replicate independently
-Will be lost without recombination
191
Specialized transduction
-DNA from host genome is integrated directly into the virus genome
-typically replacing some viral genes
192
what genes can be tranduced
all of them
193
transducing particle
-host DNA packaged into a phage produces this
-makes the DNA defective, wont be able to lead to viral lytic infection
-can be transduced into host cells genoome
194
Gene Transfer Agents (GTAs)
-Defective bacteriophages that transfer DNA between prokaryotic cells
195
Conjugation
-Horizontal gene transfer that
requires cell-to-cell contact
196
Donor cell
contains conjugative plasmid
197
Recipient cell
does not contain plasmid
198
F plasmid
-Contains genes that regulate DNA replication
-contains transposable elements that allows plasmid to integrate into the host chromosome
-contains tra gene that encode transfering functions
199
mechanism of conjugation
-starts w/cell to cell contact
-tra gene nicks plasmid
-plasmid is transferred and replicated in both cells
-takes place in favorable conditions
200
Mobile DNA
-segments of DNA that move from one location to another in other DNA molecules
(TRANSPOSABLE ELEMENTS)
-utilizes inverse repeats for easy movement
201
transposase
enzyme required for transposition
202
insertion sequences
-simplest transposable element
-1000bp
-10-50 inverted repeats
-only gene codes for transposase
203
transposons
-genes vary widely on transposons
-transposase recognizes inverted repeats and moves the transposon
-can create mutant
204
transposase functions
-recognizes cuts and ligates DNA
205
Conservative transposition
-Transposon is excised from one
location and reinserted at a second location
-no duplicates of transposon made
206
Replicative transposition
-A new copy of the transposon is
produced and inserted at a second location
-2 transposons are present, one at old and new spot
207
Sequencing
determining the precise order of
nucleotides in a DNA / RNA molecule
208
Genome annotation
converts sequencing data into a list of genes & functional sequences present in the genome
209
Bioinformatics
storing and analyzing sequences
and structures of nucleic acids and proteins
210
first generation of DNA sequencing
sanger sequencing
able to sequence ~800 bp
211
second generation of DNA sequencing
pyrosequencing- ~700 bp
Ilumina method- ~100bp
SOLiD method- ~100bp
Ion torrent- 300bp
212
third generation of DNA sequencing
Pacific Biosciences SMRT- 2500-3000bp
Oxford nanopore- ~9000bp
213
Functional Open reading Frames
-encodes a protein, can be
identified by computer
214
Codon Bias
Some codons are used more than others
215
Hypothetical proteins
uncharacterized open reading frames
-protein likely exsists, function unknown
216
minimum number of genes for a viable cell
250-300
217
Archaeal Genome composition
-higher # of genes devoted to energy and coenzyme production compare to bacteria
-fewer genes for carbohydrate metabolism and membrane functions
218
Metagenomics
-analyzes DNA or RNA
from environmental sample containing organisms which have not been isolated/identified
219
Metagenome
total gene content of microbial
community
220
Heterologous expression
Expressing a gene in
a different host
221
Genetic engineering
-using in vitro techniques to alter genes in the laboratory
222
Thermocycler
automated PCR machine
223
Quantitative PCR (qPCR)
-variation of pcr technique that quantifies initial amount of DNA
224
Process of PCR
1) Denature
2)DNA polymerase extends primers using the original DNA template
3)Heat again with the target in twice the original amount, cool, and repeat 20–40 times, yielding a 106-108- fold increase
225
gel electrophoresis
-uses agarose gel to separate nucleic acids by size and charge
-smaller nucleic acid chains move further up the gel
226
Molecular cloning
-Movement of a gene from the original source to a small and manipulable genetic element
227
palindrome
inverted repeats
228
cloning vector
-Plasmids designed specifically for cloning DNA
products made by Taq in PCR
229
YACs
yeast artificial chromosome
cloning vector
for cloning into yeast
230
T7 expression vector
-cloned genes are place under this promoter to be able to control transcription/translation highly
-T7 under same controls as lac operon
231
cloning genes via mRNA
-modify the gene expressed in mRNA
(easy to find due to polyA tail)
-use RT-PCR to create desired gene
232
Fusion proteins
-joining target and carrier proteins can
simplify purification
233
Reporter gene fusion
-Coding sequence from reporter is fused with regulatory region from another source to form hybrid gene
234
Reporter gene
-Encodes protein easy to detect and
assay
235
Gene Fusion
- DNA segments from 2 different genes are fused
-promoter can be changed
236
Northern Blot Test
-Detects RNA in a sample
237
Southern Blot Test
-Detects DNA in a sample
238
vaccine creation
-virulence factor removed
-retains immune responce
239
Polyvalent vaccine
-single vaccine that immunizes
against two different diseases
240
Subunit vaccines
-contain only a specific protein from a pathogenic organism
241
vaccinia virus
-used to prepare vaccines
-takes genes as a vector to insert DNA from pathogen that its immunizing against
-tdk (thymidine kinase) gene is used
242
Commensal Bacteria
bacteria innate to the host organism
non pathogenic
243
antibody as anticancer therapy
-antibody complex binds to receptor
and is taken up by cancer cell which triggers immune responce to destroy cell
-uses antibodies to target cancer cells to trigger apoptosis
-antigen has been engineered to carry anticancer antibody
244
Gene mining
-process of identifying and isolating
potentially useful genes from the environment without culturing the organisms that contain them
245
BACs
-bacterial artificial chromosomes
-used for large DNA inserts
246
nonspecific immunity
innate immunity to pathogen
247
specific immunity
adaptive immunity
248
Phage exclusion
-variant of restriction enzyme systems
that recognize and modify incoming foreign DNA, preventing replication
249
Abortive infection
-triggers host suicide, leads to
programmed cell death by toxin–antitoxin systems
(prevents viruses from infecting wider community)
250
CRISPR domain
-domain of DNA where foreign infectious DNA is kept with spacers inbetween each infectious DNA portion
251
CRISPR domain is used for waht
memory bank of DNA to prevent re-infection
adaptive immunity
252
Cas proteins
-endonuclease activity
-Mediate defense and incorporate new spacers into CRISPR region
253
PAM
-protospacers adjacent motif
-the DNA inbetween the spacers in the CRISPR domain but on the invading pathogen
254
cas function
-cleaves the PAMs on the invading pathogen breaking up its DNA
255
Pre-CRISPR RNA
-binds to cas protein
-acts as a complementary DNA strand to the pathogenic DNA, when it binds the protein destroys the DNA
256
