Exam 2 Flashcards
Phases of Bacterial Growth
- Lag phase - prep cell machinery for growth
- Log phase - exponential growth
- Stationary phase - growth stops, growth machinery turned off, stress response turned on
- Death phase - exponential cell death
Quorum Sensing
bacteria communicate with each other and trigger genes for group behavior like antibiotics, virulence factor, biofilm formation
Continuous Culture
- Fresh medium drips into a culture flask and spent media/waste is excreted
- See bacteria response to food/antibiotics, study growth curve, discover exact environment and optimum growth requirements
Chemically defined media
Media where you know exact components and exact quantities
Complex media
media containing unknown quantities of nutrients and components, useful for growing wide range of bacteria
Auto vs Heterotrophs
- Make carbon compounds from CO2 (plants, cyanobacteria)
- Obtain carbon compounds from other organisms (proteobacteria)
Photo vs Chemotrophs
- Use light as energy source
- Use energy stored in compounds as energy source (lithotrophs, organotrophs)
Litho vs Organotrophs
- Inorganic compounds (rock/sand)
- Organic compounds (proteobacteria, most bacteria, humans, dogs)
Nitrogen cycle
Nitrogen gas (N2)
Nitrogen Fixation
Ammonia (NH4+)
Nitrifier
Nitrate (NO3-)
Denitrifier
Nitrogen gas (N2)
Significance of nitrogen cycle
Need to fix nitrogen gas into ammonia to be used for biosynthesis (make DNA/RNA)
Bacteria by temperature
Psychrophile (0-20, 4)
-flexible proteins
Mesophile, human pathogens (20-45, 37)
Thermophile (40-70)
-tight proteins
Hyperthermophile (70-100+)
-tight proteins
Barophiles/piezophiles
Bacteria growing in extremely high pressures such as deep within the ocean
Halophiles
Archaea that require salt concentrations, have high number of sodium pumps to bring in salt and water, present in sea water or salt flats
Bacteria based on pH
Acidophiles
- Stomach, Vagina
- Proton pumps
Neutralophiles
- Blood, everything else
Alkaliphiles
- Intestines
- Proton Pumps
Bacteria based on O2 utilization
Strict Aerobes
- top of tube
Microaerophilic
- specific range in middle of tube
Facultative anaerobes
- throughout tube, concentrated at top
Aerotolerant anaerobes
- throughout tube
Strict Anaerobes
- bottom of tube
Culturing anaerobes
Anaerobe (gas pak) jar - palladium packet replaces O2 with other molecule like CO2
Anaerobic chamber - vacuum O2, pump in CO2 and N2, glove ports
Endospores
Occur in gram positive bacteria, cell is not metabolically active, possesses thick spore coat/cortex layer/dipicolinic acid and calcium ions
Catabolism
Break up larger molecules, energy releasing
Anabolism
Form larger molecules, energy capturing
Oxidation
Lose electron, lose hydrogen, gain oxygen
Reduction
Gain electron, gain hydrogen, lose oxygen
Glycolysis
Glucose split into 2 pyruvate, form 2 ATP and 2 NADH
Fermentation
in absence of oxygen, NADH returns electron to pyruvate to be reused for next glucose molecule as NAD+
Fermentation byproducts
Result of bacteria or yeast
- alcohol
- cheese
- butter
- yogurt
Fermentation Tests
MacConkey Agar (for Gram -)
- ferment lactose pink
- no fermentation beige
Sorbitol Broth Test (broth, sorbitol, phenol red)
- ferment sorbitol yellow and gas
- no fermentation stays red
TCA
- Pyruvate enters as Acetyl CoA
- Becomes amino acids or nucleobases
- Forms 6 NADH, 4 CO2, 2 FADH, 2 ATP
ETC
Electrons from coenzymes are passed between protein to create concentration and chemical gradient, ATP synthase uses protons to create 34 ATP
Uses of PMF
ATP formation, flagellar rotation, drug efflux pump (antibiotic resistance), anti/uni/symport for nutrient uptake
Lithotrophy
Inorganic molecule (Ferrous iron Fe2+, ammonium, H2) serves as electron donor, O2 or other gas is electron acceptor
Nitrogen fixation and ammonia incorporation
Microbes fix N2 into NH4+ to be incorporated into amino acids to avoid acidity
QUIZ Q:
Why are we not surrounded by large mountains of fast-dividing bacterial cells?
Bacteria run out of nutrients
QUIZ Q:
20 cells grows to 10000 cells in 3 hours
exponential growth
QUIZ Q:
barophilic organisms in the ocean floor are also
Pschrophilic
QUIZ Q:
Single species biofilm in lungs of cystic fibrosis patients
P. aeruginosa
QQ:
Organism that is a spore-forming bioweapon
B. anthracis
QQ: NOT during lag - components synthesized, growth genes turned on, cells largest, cells detecting environment
cells largest
QQ:
Conversion of N2 to NH4+
Nitrogen fixation
QQ:
what organism grow in middle of tube
Microaerophile
QQ:
when a microbe is found in environment below minimum growth temperature
growth slows or stops bc enzymatic processes become sluggish
QQ: palladium packet purpose
catalyze reaction between H2 and O2 to remove O2
QQ: Oxygenic photosynthesis strips electrons from
H2O
QQ: products of glycolysis
2 pyruvate, 2 net ATP, 2 NADH
QQ: In phenol broth red test, yellow and bubble indicate
acidic fermentation products, gas production
QQ: which requires energy - ATP hydrolysis/production, NAD+ oxidation/reduction
ATP production, NAD+ reduction
QQ: enzymes increase reaction rates by
decreasing activation energies
QQ: organism gains energy using H2 electron donor, sulfate electron acceptor
Anaerobic lithotroph
QQ: A problem with nitrogen fixation is final product ___ is toxic to cells
ammonia
QQ: Oxidative phosphorylation requires (enzyme)
ATP synthase
QQ: Which is true about metabolic reactions - all release energy, organisms use the same reactions to maintain life, all catalyzed by enzymes, always use or produce ATP
catalyzed by enzymes
Intermediate Step of CR
Pyruvate into Acetyl CoA, 2 NADH, 2 CO2
CQ:
false about plasmids - small number of genes for particular environments, contain virulence genes that confer disease properties, plasmids are essential for survival, plasmids transferred horizontally
essential for survival
CQ: which level of control is most drastic and difficult to reverse
changing DNA sequence
What is PCR
rapidly replicate DNA and compare it to a sample to test for an exact match
Bacterial genome description
single chromosome, circular, makes up the nucleoid
Stages of DNA Replication
Initiation - DNA helicase unwinds, primer tells polymerase where to start, DNA polymerase loaded on
Elongation - extension of DNA by adding nucleotides in 5’ to 3’ direction
Termination - ter site indicates stop of replication
Enzymes in DNA replication
DNA primase, DNA helicase, RNA primer, DNA ligase, DNA Gyrase - supercoils
Holoenzyme
RNA polymerase and a sigma factor - guides RNA polymerase to a promoter
Levels of gene regulation
- Change DNA sequence
- Control Transcription - repressors, activators, sigma factors
- Control Translation - repressor proteins blocks initiation sequences
- Posttranslational control - activate, deactivate, degrade protein
Operon components
Promoter, regulatory protein gene, regulatory protein (repressor or activator), regulatory sequence, target gene
Examples of repressor proteins
CtxR repressor indicates presence of iron and prevents toxin release, Lacl repressor indicates lack of lactose and prevents lactase release
Signal transduction
sense outside of the cell to transmit information that triggers a gene
Point Mutations
Missense - different amino acid
Nonsense - stop codon
Silent - same amino acid
Frameshift mutations
Insertions and Deletions
Inversion Mutation
Segment of DNA is reversed end to end
Pyrimidine dimers
UV radiation causes one strands bases to bind with each other
Repair of Mutations
- Base excision repair - damaged base is excised, abasic site signals DNA polymerase I to bind
- Methyl Mismatch repair - methyl groups added to their own DNA to prevent restriction endonuclease from altering own genome
- SOS repair - cell recognizes it is under stress and induces more mutations to try to fix unresolved issues
Use of plasmids and restriction endonuclease in bitotechnology
Plasmids carry specific genes and restriction endonucleases recognize restriction enzyme cites to cut out specific genes
Gel electrophoresis
Separate DNA by size and charge to analyze sequence
Recombinant DNA
DNA molecule containing sequences from different source of organisms
DNA hybridization
Induce fluorescent labels to label probe DNA
DNA sequencing
read sequence of base pairs in a DNA molecule
Horizontal vs Vertical Gene Transfer
Horizontal - cell to cell
Vertical - mother to daughter
Transformation
importing free DNA info cell, can be induced by Calcium chloride and heat shock, or Electroporation (shock cells)
Fred Griffith Experiment
Live avirulent + dead virulent killed the mice, proves transformation between species and happens due to cell death
Conjugation
Donor sends DNA through conjugation/sex pillus
Generalized Transduction
Bacteriophage infects host cell, as DNA is packaged in capsids, some are filled with host DNA which is then injected into new host
Specialized Transduction
Bacteriophage infects host cell and DNA is integrated into host genome, capsid fills with bacteriophage DNA and some host DNA, which is then injected into new host
DNA Restriction and Modification
Restriction endonuclease cleaves incoming phage DNA while avoiding methylated DNA
Generalized Recombination
Incoming DNA that is homologous to the genome is attached
Site-specific Recombination
Recombination sites on incoming DNA triggers recombinase enzymes to insert it into the genome
Transposition
Transposase binds to transposons/transposable elements and inserts sequence into another area of the genome
Molecular Clock
A process in which the differences between a gene present in multiple species are recorded. Scientists then use the amount of those differences and the known mutation rate to estimate divergence time
- gene should have same function
- generation time should be same
- average mutation rate remains constant among species and across generations
Degenerative/reductive evolution
lack of selection pressure causes a loss of traits/functions
Endosymbiosis
mutualistic relationship between host and symbiont where each is required for normal growth and development
Annotation of DNA sequence
understanding what the sequence of DNA means
Functional genomics
Predicting possible gene functions
Taxonomy
classifying microbes into different groups
QQ: Molecular clock is a gene whose sequence can be used to measure
Divergence time
QQ: which does not lead to divergence - transduction, transposition, fossilization, mutation
fossilization
QQ: why might organism transform homologous DNA
to repair own damaged genome
QQ: without selective pressure, species at risk of experiencing
devolved/reductive evolution
QQ: not a good scenario for a molecular clock - GT same, nonessential gene, same gene function, average MR is constant
Nonessential gene
QQ: repair process leads to abasic site
Base excision repair
QQ: template with 5 TTGCAGCT 3
5’ AGCUGCAA 3’
QQ: RNA that is translated
mRNA
QQ: DNA probes used to identify particular DNA sequence
DNA hybridization
QQ: DNA replication enzymes in order
helicase, primase, DNA polymerase, (ligase), (gyrase)
