Exam 2 Flashcards
(357 cards)
1
Q
Heterotroph
A
Use organic molecules as carbon sources
2
Q
Autotrophs
A
Use carbon dioxide as their sole or principal carbon source
3
Q
Phototrophs
A
Use light (energy source)
4
Q
Chemotrophs
A
Energy from oxidation of chemical compounds (energy source)
5
Q
Lithotrophs
A
reduced inorganic substances (electron source)
6
Q
Organotrophs
A
extracts electrons from reduced organic compounds
(electron source)
7
Q
What would it mean for an organism
to be a photolithoautotroph?
A
- Gets energy from light
- Gets electrons from inorganic minerals
- Gets carbon from CO2
8
Q
Photoorganoheterotroph
A
- Gets energy from light
- Gets electrons from organic minerals
- Gets carbon from Organic carbon
9
Q
Chemolithoautotroph
A
- Gets energy from inorganic chemicals
- Gets electrons from inorganic minerals
- Gets carbon from CO2
- Certain bacteria & Archaea
10
Q
Chemoorganoheterotroph
A
- Gets energy from organic chemicals
- Gets electrons from organic minerals
- Gets carbon from organic carbon
11
Q
Respiration
A
- Chemoorgantrophic pathway
- Uses electron transport chain
- Aerobic respiration
- Anaerobic respiration
12
Q
Aerobic respiration
A
Final electron acceptor is oxygen
13
Q
Anaerobic respiration
A
Final electron acceptor is different oxidized molecule such as NO-3 , SO2- , or Fe3+
14
Q
Fermentation
A
- Chemoorganotrophic pathway
- No Electron Transport Chain, substrate-level phosphorylation only
- Electron acceptor is an intermediate of the pathway used to oxidize the organic energy source
15
Q
Amphibolic pathway
A
Embden Meyerhof pathway can “run in reverse” to convert 2 pyruvate molecules back into a glucose molecule
16
Q
Embden-Meyerhof Pathway
A
- Starts with glucose
- Net yield: 2 ATP, 2 NADH, 2 pyruvate
- Amphibolic pathway
17
Q
Entner-Doudoroff Pathway
A
- Used by Gram negative bacteria
- Replaces the 6-carbon phase of the Embden-Meyerhof pathway
- Net yield per glucose molecule: 1 ATP, 1 NADPH, 1NADH
18
Q
Pentose-Phosphate Pathway
A
- Can operate at the same time as glycolytic pathway or Entner-Doudoroff pathway
- Can be aerobic or anaerobic
- Amphibolic pathway, but does not make ATP
- More of an anabolic role (ribose 5-phosphate builds precursors for amino acids, nucleic acids)
19
Q
Bacterial Electron Transport Chain: Flexible
A
- Electron carriers can be replaced or different terminal oxidases may be used
- Located in plasma membrane
20
Q
Bacterial Electron Transport Chain: Branched
A
Electrons may enter the chain at several points and leave through several terminal oxidases
21
Q
Bacterial Electron Transport Chain: Shorter
A
Fewer protons transported across the membrane and therefore less energy
22
Q
Dissimilatory nitrate reduction (card 1)
A
-Use of nitrate as terminal electron acceptor
- making it unavailable to cell for assimilation or uptake
23
Q
Denitrification
A
Reduction of nitrate to nitrogen gas (N2)
24
Q
Anaerobic Respiration (more details)
A
- Same electron transport chain, but oxygen free
- dissimilatory nitrate reduction
- denitrification
- yields less ATP bc molecules are less electronegative than O2
25
Fermentation (more details)
- Simpler, produces less ATP than respiration
1. does NOT involve electron transport chain
2. Pyruvate or other derivatgive is final e- acceptor
3. Oxygen not needed
4. Substrate-level phosphorylation of ATP only
26
Lactic acid fermentation
- Reduction of pyruvate to lactate (lactic acid)
- Used by many species of Lactobacillus
27
Alcoholic fermentation
- Reduction of pyruvate to acetaldehyde
- then alcohol thru enzyme called alchol dehydrogenase
- Used by yeasts
28
Mixed acid fermentation
- Excretion of a mixture of acids (that is, acetic, lactic, succinic and formic acids)
- Ex. E.Coli
29
Butanediol fermentation
- Butanediol is the end product
- Some ethanol, lactic acid and formate are also made
- Ex. Klebsiella, Enterobacter sp.
30
What’s the difference between
photosynthesis and phototrophy?
Photosynthetic organisms use light energy to ultimately make sugar, while phototrophic organisms may only convert light energy to chemical energy (ATP)
31
Chlorophyll
Used by cyanobacteria to do oxygenic phososynthesis
32
Bacteriochlorophyll a,b
Found in purple&green bacteria, anoxygenic photosynthesis
33
Bacteriorhodopsin
Used by halophilic archaea to capture light energy and use it to fuel proton pump (chemical energy)
34
Anabolic reactions in microbes
1. Cell wall (peptidoglycan)
2. Amino acids (enzymes, ribosomes)
3. Nucleic acids (reproduction/repair)
4. Lipids (membranes, LPS)
35
Bactoprenol
transports NAG-NAM-pentapeptide units across the cell membrane
36
Carbohydrate Synthesis
- Complex process
- Bactoprenol; key target for antibiotics
- cross links are formed by transpeptidation
37
Synthesis of Amino acids
- many precursor metabolites are used as starting substrates for synthesis of amino acids
- carbon skeleton is remodeled
- amino group and sometimes sulfur are added
38
Steps of synthesis of amino acids
1. Inorganic nitrogen assimilation
2. sulfur assimilation
3. Amino acid biosynthetic pathways
4. Anaplerotic reactions
39
Transaminases
Nitrogen can be transferred to other carbon skeletons by this
40
Assimilatory Nitrate Reduction
- Used by bacteria to reduce nitrate to ammonia
- then incorporate it into an organic form
41
Nitrogen Fixation
- Reduction of nitrogen (N2) to ammonia (NH3)
- catalyzed by nitrogenase
- found only in a few bacteria and archaea
42
Sulfur assimilation
- Sulfur needed for: synthesis of amino acids and synthesis of several coenzymes
- Sulfur obtained from: either external sources or intracellular amino acid reserves and inorganic sulfate
43
Amino acid biosynthetic pathways
- used in the synthesis of multiple amino acids
- A single precursor metabolite can give rise to several amino acids
44
Anaplerotic reactions
- regeneration of intermediate molecules
- carbon skeletons used for: biomass & extract energy from carbon-carbon bonds
- citric acid cycle intermediates are used
45
Lipid Synthesis
- Necessary for all membranes
- most bacterial and eukaryal lipids contain fatty acids
46
Lipopolysaccharide synthesis
- important component of gram negative bacterial outer membrane structure
- combines lipid and carbohydrate anabolic pathways: Lipid A (core branch) & O-antigen (branch)
47
What cellular structures are unique to bacteria?
Peptidoglycan cell walls, 70s ribosomes
48
Which type of bacterial fermentation is used in the dairy industry?
Lactic acid fermentation
49
Which phototrophic pigment molecule is found in archaea?
Bacteriorhodopsin
50
Name some terminal electron acceptors in anaerobic respiration
Nitrate, sulfate, iron
51
Biocide
Antimicrobial agents that control microorganisms
52
Sterilization
Process in which all living entites are destroyed or removed from an object
- sterilant is the chemical agent
53
Disinfection
Killing, inhibition, or removal of disease causing microorganisms
54
Sanitization
reduction of microbial population to levels deemed safe by public health standards
55
Antisepsis
destruction of microbes on living tissue
56
Antiseptics
Chemical agents applied to tissue to kill or inhibit growth
57
Depth filter
fibrous materials that have been bonded into a think layer filled with narrow channels
58
Membrane filter
Porous membranes with defined pore sizes that remove microorganisms
59
High-efficiency particulate air (HEPA) filters
- used in laminar flow safety cabinets
- exclude 99.97% of particles
- Covid-19 showed this filter to be effective
60
Moist heat
- destroys viruses, fungi, and bacteria by degrading nucleic acids, denaturing proteins and disrupting cell membranes
- boiling will not destroy endospores and does not sterilize
61
autoclave
- device used to steam sterilization
- above 100C (15 psi)
62
pasteurization
- controlled heating at temperatures below boiling
- process does not sterilize, but does kill pathogens and slows spoilage
63
Ultraviolet radiation
- 260nm wavelength most lethal
- causes thymine dimers preventing replication and transcription
64
chemotherapy
application of chemicals to kill microorganisms
65
Cidal agents
- agent that kills
66
Static agents
- agents that inhibit growth
67
Phenolics
- denature proteins, disrupt cell membranes
- used in hospital settings
68
Halogens
- Iodine, oxidizes cell components and proteins
- Used as a skin antiseptic
69
Chlorine
- Oxidizes cellular components, destroys vegetative bacteria and fungi
- bleach
70
Metals
- inactive proteins, only copper and silver used
- copper sulfate treats algal blooms in lakes
71
Quaternary ammonium compounds
- Detergents that have broad spectrum antimicrobial activity
- effective disinfectants, but cannot kill endospores
72
Broad-spectrum antibiotics
kills a wide variety of bacteria
73
Narrow-spectrum antibiotics
specifically kill one or a few kinds of bacteria
74
Penicillins
- inhibit peptidoglycan synthesis
- Ex. penicillin, amoxicllin
75
Cephalosporins
- inhibit peptidoglycan synthesis but broader spectrum than pencillins and cephalosporins
- used to treat severe infections
- Ex. imipenem, meropenem
76
Glycopeptides
- inhibit the synthesis of peptidoglycan by binding to amino acids in the cell wall
- Ex. Vancomycin ("drug of last resort)
77
Aminoglycosides
- Block the A site of the ribosomes so no new amino acids can be added
- Ex. Streptomycin, neomycin kanamycin
- inhibit the small (30s) subunit
78
Tetracyclines
- prevent tRNAs from binding to ribosomes
- Ex. minocycline, doxycycline
- inhibit small (30s) subunit
79
Macrolides
- bind to 50s subunit, preventing ribosomes assembly
- Ex. Z-pak, erythomycin
80
Lincosamides
- Bind 50s subunit
- Ex. Clindamycin, lincomycin
81
Fluoroquinolones
- target protein of the bacterial replication machinery (gyrase and topoisomerase) blocking DNA pol III
- Ex. Ciprofloxacin, levofloxacin
82
Folate synthesis inhibition
- requires folate (Vitamin B9) to complete DNA replication
- sulfonamides compete w other intermediates in pathways that produce folate, inhibiting synthesis
83
Kirby-bauer method
- disks with antibiotic at known concentration placed onto inoculated plate
84
Zone of inhibition
Clearance area in a kirby-bauer method
85
E-test
- strip with a gradient of antibiotics is placed on inoculated plate
- where ellipse intersects the scale shows the dosage at which bacteria is susceptible
86
Methicillin-resistant staphylococcus aureus (MRSA)
responsible for many cases of post surgical sepsis and death
87
Clostridium difficile (C-diff)
- causes extreme diarrhea which can be fatal
- difficult to treat because spores remain resistant and can germinate, causing relapse
88
reverse transcriptase inhibitors
- used to treat HIV and AIDS
89
Amphotericin B
- binds to ergosterol (similar to cholesterol), dissolves cell membrane
- anti-fungal drug
90
Azoles
- block synthesis of ergosterol
- anti-fungal drug
- Ex. ketaconazole
91
Anti-malarial drugs
- chloroquine, lariam, artimisin used in combination to destroy malaria infected red blood cells
- resistance growing across the world
92
Anti-giardia drugs
- Metronidazole
- effective against Trichomonas vaginalis
93
Overcoming drug resistance
1. Tighter controls over use of antibiotics in animal feed
2. Limiting over-prescription of antibiotics to patients
3. Combination therapies (multiple drugs)
4. targeted biological therapy
94
Phages
viruses that prey on bacteria
95
Reproductive strategies
- reproduce by binary fission
- reproduce by forming a bud or multiple fission
- must replicate and segregate the genome prior to division
96
Bacterial cell cycle
1. period of growth after the cell is born
2. chromosome replication and partitioning
3. Cytokinesis, during which a septum and daughter cells are formed
97
FtsZ
Protein that establishes divison site at mid-cell, defines plane of division
98
Peptidoglycan synthesis
- plays a role in determine cell shape
99
Coccus (shape)
- peptidoglycan forms at central septum
- FtsZ localization placement involved
100
Elongasome
rod complex
101
MreB
protein scaffold on cytoplasmic face of cell membrane
102
Crescentin
protein that localizes asymmetrically, giving rise to vibrio shape
103
Bacterial growth
- referred to as population growth rather than growth of individual cells
104
Batch culture
incubated in a closed vessel with a single batch of medium
105
Lag Phase
- bacterial growth curve
- cell synthesizing new components
- replenish spent materials
- Adapt to new medium or conditions
- eventually, cells replicate DNA, increase in mass, divide
106
Exponential phase
- bacterial growth curve
- rate of growth and division is constant and maximal
- population is uniform
107
Stationary Phase
- bacterial growth curve
- closed system, growth ceases
- viable cells remains constant
108
reasoning for stationary phase
1. Nutrient limitation
2. limited oxygen availability
3. toxic waste accumulation
4. carrying capacity reached
109
Death phase
- bacterial growth curve
- number of viable cells declines exponentially
- nutrient deprivation and build up of waste causes harm
110
Long-term stationary phase
- bacterial growth curve
- bacterial population continually evolves
- process marked by successive waves of genetically distinct variants
- natural selection occurs within a single culture
111
extremophiles
Grow under harsh conditions that would kill most other organisms
112
Halophiles
- require NaCl at a concentration > 0.2 M
113
Extreme halphiles
- require salt concentrations 3M-6.2 M
114
Salt in halophiles
- accumulate K and Cl in cytoplasm
- proteins need high salt levels
115
Salt out halophiles
- keep salt ions outside of cell
- synthesizes compatible solutes that do not interfere with growth
116
Acidophiles
- growth best between pH 0-5.5
- pump protons (H+0
117
Alkaliphiles
- growth best between pH 8-11.5
118
Psychrohiles
0 to 20C
119
Psychrotrophs
0 to 35C
120
Mesophiles
20 to 45C
121
Thermophiles
45 to 85C
122
Hyperthermophiles
85 to 100C
123
Adapting to temperature
- protein structure stabilized by a variety of means
1. more H bonds
2. more proline, less flexible peptides
3. Chaperones aid in folding
- membranes stabilized by variety of means
1. more saturated, more branched, higher molecule weight
2. ether linkages, resistant to hydrolysis
124
obligate aerobe
requires O2
125
Obligate anaerobe
usually killed in presence of O2
126
Microaerophile
requires 2-10% O2
127
Facultative anaerobes
doesn't require O2 but grow better in its presence
128
Aerotolerant anaerobes
grow with or without O2
129
Reactive oxygen species (ROS)
- oxygen reduced
- superoxide radical
- hydrogen peroxide (H2O20
- hydroxyl radical
130
Aerobes produce protective enzymes
- Superoxide dismutase (SOD)
- Catalase
- Peroxidase
131
Biofilms
- Slime enclosed communities of microbes
- ubiquitous in nature in water
- can be formed on any conditioned surface
132
Extracellular polymeric substance (EPS)
- microbes reversibly attach to conditioned surface and release polysaccharides, proteins and DNA
133
Emergent properties
the whole system is greater than the sum of its individual parts
134
Quorum sensing
- bacterial cells communicate via small molecules that diffuse the environment
- number of microbes must be present and participating
135
Culture medium
Solid or liquid mixture of nutrients and other compounds
136
defined/synthetic medium
each ingredient can be defined with a chemical formula
137
Complex media
Contain some ingredients of nonspecific chemical composition
138
Supportive media
- sustain growth of many microorganisms
- trypic soy brother and agar
139
Enriched media
- supportive media supplemented with special nutrients
- blood agar
140
selective media
- allow the growth of particular microorganisms, while inhibiting the growth of others
- gram negative bacteria grows on bile salts, gram positive bacteria cannot
141
Differential media
- distinguish among different groups of microbes and permit identification of microbes
142
replication fork
where DNA is unwound
143
Replicon
portion of the genome that contains an origin and is replicated as a unit
144
Bidirectional replication
comes from a single origin
145
Replisome
- 12 proteins involved in replication
- two replisomes move in either direction away from the origin
146
Helicase
ring encircles DNA, disrupts H-bonds and provides force to move the replisome
147
template
directs synthesis of complementary strand
148
Primer
DNA or RNA strand
149
dNTPS
deoxynucleotide triphospahtes
150
Single-stranded DNA binding proteins
Coat single stranded DNA to protect it from damage
151
Topoisomerases
Relieve twist generated by rapid unwinding of double helix, prevents supercoiling
152
Primase
synthesizes short complementary strands of RNA primers
153
Okazaki fragements
- Lagging strand is synthesized in short fragments
- joined by DNA ligase
154
Catenanes
form when topoisomerase break and rejoin DNA strands to ease supercoiling
155
recombinase
catalyze an intramolecular crossover that separates 2 chromosomes
156
Promoter
located at the start of the gene
157
Leader
transcribed into mRNA but is not translated into amino acids
158
Shine-Dalgarno sequence
important for translation initiation
159
Coding region
- begins with DNA sequence 3' - TAC - 5'
- produced codon AUG
- ends w stop codon, followed by trailer sequence
160
Trailer sequence
prepares RNA polymerase for terminator sequence
161
Point mutation
protein-coding genes can affect protein structure
types:
1. silent (codes for same amino acid)
2. Missense (codes for different amino acid)
3. Nonsense (insert STOP codon)
4. Frameshift 9changes reading framed)
162
Tautomerization mutation
- nitrogenous base of nucleotide shifts to tautomeric form allowing for unique base pairing
- "C" - A
- "T" - G
163
Transition mutations
lead to stable alteration of nucleotide sequence
164
Transversion mutations
when a purine is substituted for a pyrimidine, causing steric problems
165
Proofreading
- correction of errors in base pairing made during DNA replication
- errors corrected by DNA polymerase
166
Mismatch repair
- mismatch correction enzyme scans newly synthesized DNA for mismatched pairs
- mismatched pairs removed and replaced by DNA polymerase
167
Excision repair
- corrects damage that distorts the DNA double helix
- Nucleotide excision pair
- base excision repair
168
recombinational repair
- corrects DNA that has both bases of a pair missing or damaged
169
RecA
- aligns damaged DNA to the second copy of the genome
- acts a protease, destroying LexA, to increase production of excision repair enzymes
170
Vertical Gene transfer
- in eukaryotes, sexual reproduction is accompanied by genetic recombination
- by binary fission
171
Horizontal gene transfer (HGT)
- bacteria and archaea doesn't reproduce sexually
- gene from one independent, mature organism to another
- antibiotic resistance gene
172
Conjuagtion
- DNA transferred from a donor cell
- similar to sexual reproduction, but lacks crossing over and fertilization
173
Transformation
- DNA acquired directly from environment
- "naked" plasmids
174
Transduction
DNA transported in a bacteriophage
175
Fate of DNA in recipient cell
1. integration
2. separate existence of DNA
3. Remain in cytoplasm
4. degradation
176
integration
donor DNA pairs with recipient DNA and recombine
177
Separate existence of DNA
DNA persists separate from recipient chromosome if donor DNA is able to replicate
178
Degradation
Led by CRISPR/Cas, preventing the formation of a recombinant cell
179
transposition
genetic elements move within and between genomes via this
180
transposable elements
jumping genes
181
Insertion sequences
- simplest transposable elements
- short sequence of DNA
182
Conjugation Plasmids
- Small, double stranded DNA molecules
- can exist independently from host chromosome
- have own replication origins, replicate autonomously, and are stably inherited
- direct formation of sex pilus
183
transduction
- occurs during lytic cycle
- during virion assembly, genomes mix
- once DNA is in recipient cell, it's incorporated into chromosome
184
Immunity genes
Resistance genes that exist in nature to protect antibiotic producing microbes from their own antibiotics
185
resistance genes can be found on...
1. Bacterial chromosomes
2. Plasmids
3. Transposons
4. other mobile genetic elements
186
R (resistance) plasmid
- can be transferred to other cells by horizontal gene transfer
- genes code for enzymes that destroy or modify drugs
187
Transcription
-DNA-> mRNA
-3 types of RNA are produced: tRNA, rRNA and mRNA
188
Operons
- cluster of genes that are transcribed together to give a single messenger RNA (mRNA) molecule, which encodes multiple proteins
- not common in eukaryotes (monocistronic)
189
polycistronic mRNAs
transcription yields mRNA consisting of a leader, one coding region, a spacer and a second coding region
190
sigma factor
Has no catalytic activity but helps the core enzyme recognize the start of genes
191
RNA polymerase holoenzyme
core enzyme + sigma factor
- only the holoenzyme can begin transcription
192
Transcription cycle in bacteria
1. Sigma factor directs the RNA polymerase core enzyme to the -35 sequence
2. RNA polymerase denatures a short stretch of DNA at the -10 region, forming an open complex that is stabilized by sigma
3. RNA polymerase core synthesis RNA, and sigma dissociates from the core after about 12 ribonucleotides have been linked. Trancription enters the elongation phase
4. Elongation continues until a terminator is encountered. RNA polymerase ceases trancription and the RNA is released
193
Transcription Elongation
- creating the mRNA
- after binding, RNA polymerase unwinds DNA
- ATP, GTP, CTP and UTP incorporated into RNA complementary to DNA template
- RNA synthesis proceeds in a 5' - 3' direction
194
Transcription bubble
- Moves with the polymerase as it synthesizes mRNA
- within the bubble a temporary RNA:DNA. A hybrid is formed
195
Transcription termination mechanisms
1. Intrinsic termination
2. Rho factor-dependent
196
Translation in bacteria
- RNA--> Protein
- decoding mRNA and covalently linking amino acids together to form a polypeptide
- direction of synthesis N terminal --> C terminal
- ribosome = site of translation
197
A (acceptor) site
receives tRNA carrying amino acid
198
P (peptidyl) site
holds tRNA attached to growing polypeptide
199
E (exit) site
empty tRNA leaves ribosome
200
16s rRNA
- needed for initiation of translation
- binds to shine-dalgarno sequence (ribosome binding site)
- binds to 3' CCA end of aminoacyl-tRNA
201
23s rRNA
ribozyme that catalyzes peptide bond formation
202
Initiation of protein synthesis
1. N-formylmethionine tRNA bacterial initiator tRNA ... archaea and eukaryotes use methionine- tRNA
2. 30s initiation complex... initiator tRNA, mRNA and the 30s ribosomal subunit
3. Two initiation factors are involved.. require for formation of the initiation complex, GTP catalyzes energy use for these
203
Elongation of polypeptide
1. Aminoacyl-tRNA binding
2. Transpeptidation reaction
3. Translocation
204
Nonsense (stop) codons
- aid in recognition of stop codons
- No tRNA for a stop codon, so the ribosome halts
205
Polyribosome
complex of mRNA with several ribosomes
206
Chaperones
- proteins that help other proteins fold
- present in all domains of life
207
Trigger factor
- helps fold many cytoplasmic proteins
- masks hydrophobic regions so they don't interact with each other prematurely, or with other proteins
- Also helps proline cis/trans isomerization
208
Sec system
general secretion pathway
209
Tat system
-secretes only folded proteins
- moves across plasma membrane
- proteins must completely fold in the cytoplasm
210
YidC
folding and translocation plasma membrane proteins
211
Translocation
Movement of proteins from cytoplasm to or across the plasma membrane
212
Secretion
movement of proteins from the cytoplasm to external environment
213
Sec Dependent pathway
translocates unfolded proteins across plasma membrane
214
Signal peptide
N-terminal sequence that directs peptide to specific route
215
Signal recognition particle
Protein RNA complex translating ribosomes to identify hydrophobic peptides
216
Inducer
small effector molecule that stimulates gene expression
217
Inducible genes
- genes that encode inducible enzymes
- required only when their substrate is available
218
Corepressor
small effector molecule
219
Repressible genes
Genes for enzymes involved in biosynthetic pathways
220
Regulation of transcription (negative control)
- repressor protein
- binding operator inhibts transcription initiation by blocking RNA polymerase from binding
221
Regulation of transcription (positive control)
- activator protein
- binding to activator binding sites upstream of promoter encourages RNA polymerase to bind
222
Inducible Operon
- normally off
- when lactose is present, repressor is removed
223
tryp operon
- functions in the absence of tryptophan
- when trp present, it acts as corepressor
224
Riboswitches
contain effector binding element in the long reader RNA
225
Small (sRNAs)
- noncoding (ncRNAs)
- doesn't function as mRNA, TRNA or rRNA
226
Antisense RNAs
- complementary to mRNA and function by base pairing
- may inhibit or enhance translation
- some require a chaperone to promote interaction with complementary sequences
227
Global regulatory systems
- affect many genes, operons, and pathways simultaneously
- important for bacteria... responds rapid to wide variety of changing conditions
228
sensor kinase
spans the plasma membrane so a part is exposed to extracellular environment, while other part is in cytoplasm
229
Two component signal transduction
- sensor kinase
- phosphorylates itself, then transfer phosphate to response regulator
230
Phosphorelay systems
- when phosphoryl groups are transferred to many proteins through a complex system
231
Alternate sigma factors
immediately change expression of many genes as they direct RNA polymerase to specific subsets of bacterial promoters
232
Sanger sequencing
- DNA synthesis continues until a ddNTP, rather than a dNTP, is added to the growing chain
- without a 3' - OH group, synthesis stops
- results in a collection of DNA fragments of varying lengths, each ending in the same ddNTP
233
Massively parallel sequencing techniques
thousands of identical DNA fragments are sequenced simultaneously
234
Whole genome sequencing
1. library construction - generates clones of portions of genome
2. random sequencing - determines sequences of genome fragments in vector
3. Fragment alignment and gap closure: computer analysis joins to form contig
4. editing: proofreading ensures all reads of the same sequence are identical
235
Metagenomics
- study of microbial genomes based on DNA extracted directly from the environment
- used to learn more about diversity and metabolic potential of microbial communities
236
Genome annotation
bioinformatics combines biology, mathematics, computer science and statistics to convert raw nucleotide data into the location and potential functions of genes
237
-Omics
other
238
Metatranscriptomics
- extraction of RNA directly from the environment, followed by sequencing and comparison to known sequences
- can identify active microbes
239
Proteomics
- collection of proteins that an organism produces
- provides information about genome function not available from genomics or mRNA studies
240
Core genome
set of genes found in all membranes of a species
241
Pan-genome
every gene in a strain of a species
242
Genetic engineering
modification of the genetic code of a living organism
243
Recombinant DNA
DNA molecules with segments origination from different organisms
244
DNA cloning
Use of enzymes and bacterial cells to modify and amplify DNA
245
Biotechnology
Use of organisms to produce useful products
246
Restriction endonucleases
recognize and cleave specific DNA sequences
247
Restriction enzymes
- cuts both strands at complementary sequence
- produce sticky ends (overhangs) or blunt ends in DNA target
248
Origin of replication
allows independent replication
249
Selectable marker
gene on the plasmid helps survive under certain conditions
250
Multicloning site
cluster of restriction sites
251
PCR
- enables gene amplification
- rapid synthesis of billions of copies of a specific DNA fragment
- oligonucleotide primers
252
oligonucleotides primers
single-stranded DNA molecules, between 15 and 30 nucleotides long
253
Reverse transcriptase PCR
- synthesizes double-stranded DNA from RNA template
- constructs complementary DNA (cDNA)
254
CRISPR-Cas 9
- used for altering genomes in living organisms
- direct modification of genomic DNA in any crll into which DNA can be introduced and expressed
- Cas 9 is endonuclease that cuts both strands of target DNA
255
Pathogens
- disease causing microbes
- must overcome surface barriers and antimicrobial activity
256
Immune system
- composed of widely distributed proteins, cells, tissues, and organs
- neutralize or destroy foreign substances
257
Immunity
- ability of host to resist infection or disease
258
Immunology
study of immune responses and how they protect the host
259
Innate immunity
- first line of defense
- offers resistance to any microbe or foreign material
- includes general mechanisms such as skin, mucus, and antimicrobial chemicals
260
Adaptive immune response
- activated by cells and chemicals of innate immunity
- tailored to a particular foreign agent
- has "memory" - effectiveness increases on repeated exposure to foreign agent
261
Skin (mechanical defense)
- mechanical barrier to microbial invasion
- skin microbiota prevent colonization of pathogens
262
Keratinocytes
cells in outer layer
263
Mucous membranes
- form a protective covering that resists penetration and traps microbial invaders
264
Cell types
1. Epithelial cells
2. Goblet cells- produce mucus
3. paneth cells- secrete antimicrobial peptides
265
Respiratory system
- microbes >10 um usually are trapped by hairs and cilia lining the nasal cavity
- Microbes <10 um pass through the nasal cavity and are trapped in mucociliary escalator
266
lysozyme
Hydrolyzes bond of bacterial cell wall (tears)
267
Lactoferrin
Sequesters iron, reducing its availability for microbes, limiting their ability to multiply (breastmilk)
268
Bacteriocins
Toxic peptides produced by normal microbiota, kill closely related species
269
Chemical defense: major activities
1. stimulate an inflammatory response by helping to recruit white blood cells
2. lysing microbial cell membranes
3. Promoting phagocytosis of microbial invaders
270
Cytokines
1. regulators of innate immunity
2. regulators of adaptive immunity
3. Stimulators of hematopoiesis
271
Chemokines
stimulate cell migration
272
Interleukins
Produced by one white blood cell, act on another
273
Interferons
regulatory cytokines produced in response to infection
274
Colony stimulating factors
Stimulate growth and differentiation of immature white blood cells in bone marrow
275
Tumor necrosis factor
stimulate an inflammatory response
276
leukocytes
- White blood cells in the immune system
- originate from hematopoietic precursor stem cells
277
Cells on the immune system
1. Mast cells
2. granulocytes
3. monocytes, macrophages, and dendritic cells
4. innate lymphoid cells
278
Mast cells
- inflammatory
- not phagocytic
- role in allergic responses
- similar to basophils
279
Granulocytes
- irregularly shaped nuclei with 2 to 5 lobes
- cytoplasm has granules with reactive substances that kill microbes
- 3 types: basophils, eosinophils, neutrophils
280
Eosinophils (granulocyte)
- worm and fungal infections
- allergy
- inflammatory reactions
281
Basophils (granulocytes)
- inflammatory events
- allergies
282
neutrophils (granulocytes)
- blood phagocytes
- active engulfers and killers of bacteria
283
Monocytes
- produced in bone marrow and enter the blood
- after 8 hrs, they migrate into tissues and mature into macrophages
- elevated in acute illness stage
284
Macrophages
- larger than monocytes
- highly phagocytic
- serve as sentinel cells
285
Dendritic cells
- antigen presenting
- long cellular projections
- present in skin and mucous membranes
- programmed to detect and phagocytose pathogens
286
Antigen presenting
display foreign antigens on their surfaces to share vital information with lymphocytes to stimulate an adaptive immune response
287
Antibody dependent cell mediated cytotoxicity
when non-self proteins are generated and detected
288
B cells
Bone Marrow
289
T cells
Thymus
290
Primary organs and tissues
hematopoietic stem cells differentiate into immune cells
291
Secondary organ and tissues
where lymphocytes are activated by antigen interaction
292
thymus
- primary lymphoid organ
- precursor cells move, enter from bone marrow
- negative selection
- remaining cells become mature T cells and enter the bloodstream where they await activation by innate immune cells
293
negative selection
removal of T cells not able to distinguish between self and non self antigens
294
Bone Marrow
- primary lymphoid organ
- site of B cell maturation
- maturation involves removal of self-reactive cells
- enter bloodstream and migrate to lymph nodes and spleen to await introduction to the antigen
295
Spleen
- secondary lymphoid organ
- filters blood and traps blood borne particles by phagocytes and B cells
- present antigens to T cells, activating specifc immune response
296
Lymph Nodes
- secondary lymphoid organ
- capture pahgocytosed antigens and present them to T cells
- outer region is rich in B cells that can bind antigen directly from blood
297
Follicles
inner region where T cells await interaction B cells
298
Microbe-associated molecular patterns
- alert host about the presence of microbe
299
Toll-like receptors
- pattern recognition receptor
- transmembrane proteins that detect microbe associated molecular patterns
- stimulate immune response
300
Antigen presenting cells
macrophages and dendritic cells
301
Exocytosis
- process used by neutrophils to expel microbial fragments after they have been digested
- leads directly to antigen presentation
302
Inflammation
- innate response
- release of chemical signals that trigger vasodilation
- defense reaction to issue injury
303
Selectins
- cell adhesion molecules on activated endothelial cells that line blood vessels nearby
- cause neutrophils to roll along endothelium where they encounter pro-inflammatory signals
304
integrins
adhesion receptors on neytophils activated by selectins
305
Chemotaxis
chemotactic factors at infection site
306
Cardinal signs
1. redness
2. warmth
3. pain
4. swelling
5. altered function
307
kallikrein
tissue injury leads to activation of this
308
bradykinin
cleavage of kallikrein releases this
- swelling
309
fibrin clot
restrict infectious agents to bloodstream
310
Chronic inflammation
- causes permanent tissue damage
- granuloma
311
granuloma
mass of cells that form when phagocytic cells can't destroy pathogen and instead attempt to wall off the site
312
name two physical barriers to infections. How are they different?
- skin: dead cells packed together
- Mucosal membranes: live cells that produce mucous moved by cilia
313
Name one antimicrobial product produced by these cells
- lysozyme, lactoferrin
314
what are the 5 types of leukpcytes
- neutrophils
- macrophages
- basophils
- lymphocytes
- eosinophils
315
Name 3 types of phagocytic cells, which are APCs
- neutrophils
- macrophages (APC)
- dendritic cells (APC)
316
what is the importance of antigen presentation
link to the adaptive immune response while killing pathogens
317
Name one mechanism that "amps-up" the immune repsonse
- pro-inflammatory cytokines, interferons, pattern recognition receptors, antigen presentation, fever
318
innate activation can lead to:
- inflammation
- survival
- apoptosis
- immune regulation
- proliferation of immune cells
319
Cytokines comes in multiple forms:
- pro-inflammatory drive cell mediated immunity
- anti-inflammatory drives humoral immunity
320
Specificity
- any particular response acts against one specific target
321
inducibility
cells activate only in response to their specific pathogen
322
clonality
One induced, they replicate exact clones of themselves
323
Discrimination
as a rule, does not act against healthy host cells
324
Memory
long living cells remain to respond more quickly when that pathogen is seen again
325
Adaptive immune response rely on
lymphocytes
326
Humoral response
B cells
327
Cell-mediated response
T cells
328
Adaptive immunity anatomy
- lymphocytes grow in bone marrow
- lymph is intracellular fluid and waste along with APCs
- drains to lymph nodes where APCs and lymphocytes interact
329
lymphocytes act via
receptors on their surfaces
330
NK cells
- innate immunity
- non-specific receptors
- all cells have Nk cell ligands
- all cells have MHC class I
331
Normal Nk cell
tells the NK cell "stop"
332
Abnormal or missin NK cell
tells the cell "kill"
333
Antigens founded
surface of extracellular pathogens, or expressed on the surface of infected cells for intracellular pathogens
334
adaptive immune responses are against
antigens not the pathogen as a whole
335
Adaptive immunity: antigens
- "non-self" molecular shapes
- immune cells can recognize and attack
336
B cell receptor (BCR)
- an immunoglobulin protein (IgD)
337
B cells and antibodies
- multiple of the same BCRs on the surface of each B cell
- Different B cells have different variable regions, recognize different antigens
- if bound to a B cell it is a BCR, if it is free floating it is an antibody
338
B cell response
1. BCR finds its match during an infection
2. Activated by T cell help
3. Clonally replicate
4. some will live for 50+ years, able to produce B cells at the next sign of the SAME pathogen
339
B cells and antibodies order
1. binding to antigen
2. chemical signal
3. becomes plasma cell
4. releases antibodies
340
IgD
- found in: B cells surface
- role: B cell receptor
341
IgM
- found: blood
- role: fixing complement, first antibody response
342
IgG
- found: blood
- Role: fix complement, neutralization, opsonization
343
IgA
- found: mucous, tears, saliva, and breast milk
- role: protect mucous membranes
344
IgE
- found: blood
- role: allergies
345
T cell receptor (TCR)
- NOT an immunoglobulin
- multiple copies of the same receptor per cell
- one antigen is recognized by each cell using the variable region
346
Major Histocompatibility complex (MHC)
- TCR recognize antigens ONLY when presented by this
- antibodies can float through the blood on their own
347
MHC class I
- expressed on all cell types
- presenting antigens
- viral proteins
- mutated proteins
- interacts with: CD8 + T cell (cytotoxic T cells)
348
MHC class II
- found ONLY on antigen presenting cells
- presents antigens from phagocytosis
- interacts with CD4 + T cell (Helper T cells)
349
CD8+: Cytotoxic T cells
- driver of the cell-mediated adaptive immune response
- interacts w/ MHC class I to identify sick cells and kill them
- inducing apoptosis (cell death) using perforin and granzyme
- effective against cancer and viruses
350
CD4+: T helper cells
- drive towards a humoral approach or cellular response
- activate B cells and T cells
- cannot activate without T cell help
351
Protection against re-exposure
- long live plasma cells in bone marrow
- effector T cells
352
3 major lymphocytes
Innate: NK cells
Adaptive: T cells and b cells
353
what receptors are on their surface
- innate: inhibitory and stimulatory receptors
- adaptive: T cells: CD4, CD8 and TCR. B cells: B cell recptor
354
What do these receptors interact with? Cell type? Receptor Type?
- Innate: NK - inhibitory and stimulatory receptors - MHC class I
- Adaptive: T cells - CD4-TCR - MHC class II on APCs. CD8- TCR- MHC class I. B cells - B cell receptor - antigen/pathogen directly
355
How does this kill pathogens
- T cells: recognize abnormal autoantigens perforins/ granzymes trigger apoptosis
- B cells: antibodies bind to promote phagocytosis and compliment, or neutralize directly
356
How do we name the response/
- T cells: cell mediated
- B cells: Humoral
357
The isotypes that naturally protect a breastfed baby in the first 6 months of life are
IgA and IgG
