Exam 2 Flashcards
FtsZ is the homologue for
tubulin
MreB is the homologue for
actin
CreS is the homologue for
Intermediate filaments
FtsZ is found in
Many bacteria
MreB is found in
Rods
CreS is found in
Curved bacteria, rare
What does FtsZ do?
Forms ring during septum formation
What does MreB do?
Maintains shape by positioning peptidoglycan synthesis machinery
What does CreS do?
Maintains shape in curved bacteria
Phases of binary fission
- young cell at early phase of life
- parent cell prepares for division (enlarges cell wall, cell membrane, and overall volume)
- septum begins to grow inward as the chromosomes move toward opposite ends of the cell, cytoplasmic components are distributed to the two developing cells
- septum is synthesized completely through the cell center, creating two separate cell chambers
- daughter cells are divided
Septum
a partition that forms during cell division to divide two daughter cells
Where will new cell wall form?
at septum
Exponential growth
When a growing bacterial population is doubling at regular intervals
Generation time
Doubling time
Most bacterial chromosomes are
circular
Origin of replication
site where replication begins
Terminus
site where replication is terminated, located opposite of the origin
Replisome
group of proteins needed for DNA synthesis
Replication forks
the Y-shaped structure where DNA is replicated
DNA replication proceeds
bidirectionally
What does it mean for origins to be partitioned?
moved to opposite ends of the cell
What pushes chromosomes to opposite ends?
Replisome
If ______ is mutated, chromosomes do not separate
MreB
T / F : Replisomes stay still, DNA moves
T
Septation
formation of cross walls between daughter cells
Steps of septation
- selection of site for septum formation
- assembly of Z ring (linkage of Z ring to plasma membrane)
- assembly of cell wall synthesizing machinery
- constriction of cell and septum formation
Septation is related to
cytokinesis
Polymerization of ______ forms Z ring
FtsZ
_____ forms Z ring in right place
MinCDE
_____ blocks FtsZ binding
MinC
FtsZ has to bind where
mid-cell
T / F : MinCDE is constantly moving
T
___ and ____ link Z ring to plasma membrane
FtsA and ZipA
Autolysins
enzymes that degrade peptidoglycan
Autolysins cleave between
NAM and NAG
Transpeptidases
peptidoglycan crosslinking enzymes
Inhibit transpeptidases –>
cell death
New peptidoglycan synthesis in cocci
only forms at the central septum
New peptidoglycan synthesis in rods
occurs throughout the cell prior to formation, occurs at the septum during formation
Where you find MreB –>
where you find peptidoglycan synthesis
______ plays a critical role in determining rod shape
MreB
MreB is absent in
cocci
MreB is found where in rods?
distributed in helices along the length of the cell
Vibrio bacteria contain
both FtsZ and MreB
What gives vibrio bacteria their shape?
crescentin (CreS)
Extremophiles
grow under harsh conditions that would kill most other organisms
Hypotonic solution
lower osmotic concentration outside the cell
What happens in a hypotonic solution?
water enters the cell, cell swells and may burst
How cells adapt to hypotonic solution
microbes reduce osmotic concentration of cytoplasm (MS channels in plasma membrane allow solutes to leave)
Hypertonic solution
higher osmotic concentration outside the cell
What happens in a hypertonic environment?
water leaves the cell, membrane shrinks from the cell wall (plasmolysis) may occur
How do cells adapt to hypertonic environments?
microbes increase solute concentration to increase their internal osmotic concentration
Halophiles
grow optimally in the presence of NaCl or other salts at a concentration > 0.2M
Extreme halophiles
require salt concentration of 2M to 6.2M
Halotolerant
can grow under elevated salt conditions but do not require high salt for growth
Acidophiles
growth optimum between pH 0 - 5.5
Neutrophiles
growth optimum between pH 5.5 - 7
Alkaliphiles
growth optimum between pH 8.5 - 11.5
Most bacteria that cause infections in humans are
neutrophiles
Plasma membrane is impermeable to proton
acidophiles
Acidic tolerance response
pump protons out of the cell (costs ATP), synthesize acid and heat shock proteins that protect cytoplasmic proteins
T/ F : microbes cannot regulate their internal temperature
T
Cardinal growth temperatures
minimal, maximal, optimal
Psychrophiles
0oC to 20oC
Psychrotrophs
0oC to 35oC
Mesophiles
30oC to 45oC
Thermophiles
55oC to 85oC
Hyperthermophiles
85oC to 113oC
How do thermophiles adapt to temperatures?
at high temperatures, protein structure can be stabilized via more H bonds, more proline, chaperones
What stabilizes membrane in thermophiles?
increase in saturated, branched chain and higher molecular weight lipids (diglycerol tetraethers), and ether linkages (in archaeal membranes)
More prolines –>
decreased flexibility
Aerobe
grows in presence of atm oxygen, 20% O2
Obligate aerobe
requires O2
Anaerobe
grows in absence of O2
Obligate anaerobe
requires the absence of O2, usually killed in presence of O2
Microaerophiles
require 2-10% O2
Facultative anaerobes
if necessary, can grow without O2 (grow better in its presence)
Aerotolerant anaerobes
grow equally well with or without O2
Oxic
environment in which oxygen is dissolved
Anoxic
environment depleted of dissolved oxygen
ROS examples
superoxide radical, hydrogen peroxide, hydroxyl radical
Protective enzymes aerobes produce
superoxide dismutase (SOD), catalase, peroxidase
Why would something not grow when oxygen is present?
some microbe have no way to get rid of ROS
Barotolerant
adversely affected by increased pressure
Barophilic (peizophilic)
require or grow more rapidly in the presence of increased pressure
Barophilic microbes do what to adapt to increased pressure?
change membrane fatty acids
Examples of ionizing radiation
X and gamma rays
Ionizing radiation causes what
- disruption of chemical structure of many molecules, like DNA
- mutations –> death
Polyextremophiles can withstand ____ Gy units
5,000
____ Gy units will kill a human
5
____ Gy units will kill E. colo
200-800
Radiation damage example
UV
Wavelength most effectively absorbed by DNA is ___
260 nm
To protect themselves from UV radiation, many bacteria produce
carotenoid pigments
During a dormant, metabolically inactive state, microbes are
breaking down ribosomes, synthesizing starvation response proteins
Persister cells are
completely dormant
What do antibiotics not kill and most likely contribute to recurring infections like kidney stones?
Persister cells
______ is representative of how bacteria grow naturally
biofilms
_____ growth is when microbes grow free-floating in liquid
planktonic
Growth of microbes attached to surfaces in colonies
biofilm growth
Biofilm formation cycle
–> –> Planktonic bacteria –> attachment –> cell-cell adhesion –> proliferation –> maturation –> dispersion –> planktonic bacteria –>
Biofilm matrix is composed of
- polysaccharides
- proteins
- DNA
Bacteria imbedded deep in biofilm may become
persisters
Quorum sensing is _____ dependent
density
Low cell density
autoinducer diffuses out
High cell density
autoinducer diffuses in
Two major autoinducer molecules of quorum sensing
- N-acyl-homoserine lactones (AHLs)
- Autoinducer peptides (AIPs)
N-acyl-homoserine lactones (AHLs) are found in
Gram (-) bacteria
Autoinducer peptides (AIPs) are found in
Gram (+) bacteria
Peptones
protein hydrolysates (fragments) prepared by partial digestion of various protein sources
TSA media
support the growth of many microorganisms
Enriched media
general purpose media supplemented by blood or other special nutrients
Selective media
favor the growth of some microorganisms and inhibit the growth of others
Differential media
distinguish between different groups of microorganisms based on their biological characteristics
4 phases of growth curve
lag phase, exponential phase, stationary phase, death phase
Lag phase
- cells adapting to environment, synthesizing new components
- no growth
- need a lot of ribosomes for fast growth
Exponential phase
- also called log phase
- rate of growth is consistent and maximal
- high degree of nutrient availability
- high metabolic rate
- most uniform stage
Stationary phase
- in a closed system / batch culture, nutrients are depleted, metabolic byproducts build up
- population growth stops
- cells enter stationary phase
- total number of viable cells remains constant
Death phase
- entry into stationary phase due to starvation and other stressful conditions activates survival strategy
^ morphological changes
^ decrease in size, protoplast shrinkage, nucleoid condensation
^ dismantling of ribosomes
Continuous culture
maintain a culture in exponential phase indefinitely
Direct cell counts
- spread and pour plates
- counting chambers
- optical density
Viable counting methods
- only counts alive cells
- CFUs
- spread and pour plate techniques
Catabolism
- breakdown of organic molecules for energy
- typically a large, complex molecule broken down into smaller simpler ones
- generate precursors for biosynthesis
Anabolism
- requires energy
- the synthesis of large complex organic molecules from simpler ones
ΔG (-)
- spontaneous
- gives off energy
- exergonic
- catabolism
ΔG (+)
- not spontaneous
- requires energy
- endergonic
- anabolism
Hydrolysis of ATP to ADP is
endergonic
ATP is said to have ___ phosphate transfer potential
high
RNA nucleotides / other energy sources
GTP, CTP, UTP
E0 (standard reduction potential)
equilibrium constant for a redox reaction
More negative E0 =>
better electron donor
More positive E0 =>
better electron acceptor
If electrons passed from a donor pair to an electron pair with more (+) E0
energy is released (ΔG is negative)
T / F : first electron carrier has the most negative E0
T
Electron carriers are located in ________ of bacteria and archaeal cells
plasma membranes
Common electron carries
NAD, NADP
Important consequence of ETC is the formation of a _____
proton gradient
Protons re-enter the cell through _____ and generate _____
ATP synthase, ATP
Protons are transported out of the cell during oxidation of _____
NADH
T / F : biochemical pathways exist in isolation
F
_____ are molecules that speed up reactions
enzymes
Enzymes can either be
protein or RNA (ribozymes)
Protein catalysts
substance that increases the rate of a reaction without being permanently altered, high specificity
Substrates
reacting molecules
Enzymes can be composed of
one or more polypeptide and/or non-protein components
Apoenzyme
protein component of an enzyme
Cofactor
nonprotein component of an enzyme
Prosthetic group
cofactor firmly attached
Coenzyme
cofactor loosely attached, can act as carriers/shuttles
Holoenzyme =
apoenzyme + cofactor
Common nonprotein cofactor
metals
How many major classes of enzymes?
6
Enzyme speeds up reaction by
lowering energy of activation
Enzyme activity of significantly impacted by
- substrate concentration
- pH
- temperature
Denaturation
loss of enzyme’s structure and activity when temperature and pH rise too much above optima
3 major mechanisms for conservation of energy
- metabolic channeling
- regulation of synthesis of a particular enzyme (transcriptional and translational)
- direct stimulation or inhibition of the activity of a critical enzyme (post-translational)
Compartmentation
- periplasmic space of Gram (-) bacteria
- differential distribution of enzymes and metabolites among separate cell structures or organelles
Two important reversible control measures for post-translational regulation of enzyme activity
- allosteric regulation
- covalent modification
Allosteric effector
- binds noncovalently at regulatory site
- changes shape of enzyme and alters activity of catalytic site
- positive effector increases enzyme activity
-negative effector inhibits the enzyme
Covalent modification enzymes
- reversible on and off switch
- addition or removal of a chemical group (ex: phosphorylation)
Feedback inhibition
when product of pathway builds up it inhibits the pathway
3 major main metabolic requirements
- energy (ATP)
- electrons (NADH)
- carbon
Heterotrophs carbon sources
reduced, preformed, organic molecules from other organisms
Chemotrophs energy sources
oxidation of organic or inorganic compounds
Autotrophs carbon sources
CO2, sole or principal biosynthetic carbon source
Phototrophs energy source
light
Lithotrophs electron source
reduced inorganic molecules
Organotrophs electron source
organic molecules
Majority of pathogens are
chemoorganoheterotrophs
3 processed by which chemoheterotrophs utilize organic molecules for energy
- aerobic respiration
- anaerobic respiration
- fermentation
Respiration involves used of an ______, while fermentation does not
electron transport chain
In respiration, ATP is primarily made by
oxidative phosphorylation
Fermentation uses an ______ electron acceptor
endogenous
Endogenous means something
exists already in the cell
In fermentation, ATP is synthesized only by
substrate-level phosphorylation
Most pathways generate ____ or intermediates of the pathways used in _____ metabolism
glucose, glucose
Amphibolic pathways
have both catabolic and anabolic activity
Examples of amphibolic pathways
TCA cycle, Embden-Meyerhof pathways, pentose phosphate pathway
__________ is the process that can completely catabolize an organic energy source to CO2 using ___, ____, and ____
aerobic respiration, glycolysis, TCA cycle, ETC
Glycolysis
glucose –> pyruvate
Aerobic respiration produces
ATP and high energy electron carriers
3 common glycolysis pathways
Embden-Meyerhof pathway, Entner-Duodoroff pathway, pentose phosphate pathway
What is the most common glycolytic pathway?
Embden-Meyerhoff
Embden-Meyerhof (EM) pathway occurs in the ____ of most microorganisms, plants, and animals
cytoplasmic matrix
Two phases of EM pathway
- six carbon phase
- three carbon phase
The 6 carbon phase of the EM pathway costs the cell ___ ATP
2
The 3 carbon phase of the EM pathway generates ____ ATP and ____ NADH
4, 2
EM pathway net gain
2 AT, 2 NADH
Etner-Duodoroff (ED) pathway net yield per glucose molecule
1 ATP, 1 NADH, 1 NADPH
The ED pathway is used by
soil bacteria and a few Gram (+) bacteria
T / F : the pentose phosphate pathway (PP) can operate aerobically or anaerobically
T
The PP pathway produces
NADPH and precursor molecules needed for biosynthesis
T / F : TCA cycle is the source of many important carbon precursor molecules
T
In TCA cycle, each glucose produces
6 molecules of CO2, 8 NADH, 2 FADH2, 2 GTP (or ATP)
Each acetyl-CoA molecule oxidized in TCA cycle generates
2 CO2, 4 NADH, 1 FADH2, 1 GTP (or ATP)
How many ATP directly synthesized from oxidation of glucose to CO2?
4
T / F : most ATP made when NADH and FADH2 are oxidized in ETC
T
Shorter chain / more branched ETC
less efficient
Paracoccus denitrificans are
facultative anaerobic soil bacterium
ETC of E. coli is a ____ pathway
branched
Upper branch of E. coli ETC
- stationary phase and low aeration
- less efficient
Lower branch of E. coli ETC
- log phase and high aeration
- more efficient
Proton motive force (PMF)
the chemical and electrical potential difference between proton levels inside vs outside membrane
Flow of protons reentering the cell is an exergonic or endergonic process?
exergonic
Energy can be harnessed to synthesize ATP via
oxidative phosphorylation
Proton motive force can also be used for
flagella rotation, secondary active transport
Diffusion of ____ back across membrane drives formation of ____
protons, ATP
ATP synthase F0 portion is in the _____
plasma membrane
ATP synthase F1 portion is in the ____
cytoplasm
F1 component
3 beta subunits and gamma subunit
How PMF drives ATP synthesis
- flow of electrons causes gamma subunit to rotate
- rotation of gamma subunit induces conformation changes in beta subunits
- conformation changes result in formation of ATP from ADP + Pi
Maximum total ATP yield during aerobic respiration is
32
T/ F : anaerobic respiration generally yields more energy because E0 of electron acceptor is more negative than E0 of O2
F
Denitrification in soil causes
loss of fertility
Fermentation: NADH is oxidized to
NAD+
T / F : oxygen is needed for fermentation
F
T / F : electron acceptor is often pyruvate or derivative in fermentation
T
T / F : no ETC in fermentation
T
T/ F : oxidative phosphorylation occurs in fermentation
F
T / F : ATP is formed by substrate level phosphorylation in fermentation
T
Disaccharides and polysaccharides are cleaved by
hydrolases and phosphorylases
What is converted into other sugars that enter the glycolytic pathway?
monosaccharides
Triglycerides are hydrolyzed to ___ and ____ by ___
glycerol, fatty acids, lipases
Protease
hydrolyzes protein to amino acids
T / F : proteins cannot be used as a carbon source
F
Deamination
removal of amino group from amino acid
Over half the photosynthesis on earth is carried out by ___
microbes
2 part of photosynthesis
light and dark reactions
Light reactions (description and what it is related to)
- light energy is trapped and converted to chemical energy, catabolism
Dark reactions (description and what it is related to)
- energy produced in the light reactions is used to reduce CO2 and synthesize cell constituents (anabolism)
Major light-absorbing pigments are
chlorophylls
____ transfer light energy to chlorophylls
accessory pigments
T / F : accessory pigments absorb the same wavelengths of light than chlorophylls
F
Examples of accessory pigments
carotenoids and phycobiliproteins
Antennas
highly organized arrays of chlorophylls and accessory pigments
Photosystems
Antenna and its associated reaction-center chlorophyll
Photosystem I
cyclic (no reducing power generated, ATP) or non-cyclic (reducing power generated, works with photosystem II, NADPH
Photosystem II
non-cyclic (ATP + NADPH made)
Five bacterial phyla that carry out anoxygenic photosynthesis
- proteobacteria
- chlorobi
- chloroflexi
- firmicutes
- acidobacteria
T / F : most anoxygenic phototrophs are strict anaerobes
T
Anoxygenic phototrophs use ____ instead of chlorophylls
bacteriochlorophyll
In anoxygenic photosynthesis, 1. ETC is cyclic or noncyclic, and 2. one or two photosystems involved?
cyclic, one
What is generated and synthesized in anoxygenic photosynthesis?
PMF generated, ATP synthesized
Chlorophyll-independent phototrophic bacteria and archaea use ____
bacteriorhodopsin
Aspects of chlorophyll-independent phototrophy
use bacteriorhodopsin, PMF is generated, ETC is not involved
How many precursor metabolites are there?
12
How are precursor metabolites generated?
glycolysis, pentose phosphate pathway, TCA cycle
What can be generated from the 12 precursor metabolites?
amino acids, lipids, DNA (purine, pyrimidines)
Where does the Calvin Cycle occur in cyanobacteria, some nitrifying bacteria, and thiobacilli?
carboxysomes
Carboxysomes
inclusion bodies that may be the site of CO2 fixation
3 phases of the calvin cycle
- the carboxylation phase
- the reduction phase
- the regeneration phase
How many ATP and NADPHs are used in the incorporation of 1 CO2 in the calvin cycle
3 ATP, 2 NADPH
_____ catalyzes the addition of CO2 to ribulose-1,5-biphosphate (RuBP), forming two molecules of ____
rubisco, 3-phosphoglycerate
3-phosphoglycerate is reduced to
glyceraldehyde 3-phosphate
In the reduction phase of the Calvin cycle, ___ ATP is/are used and ___ NADPH is/are used
1,1
How many ATP are used in the regeneration phase?
1
What is produced in the regeneration phase?
carbohydrates
How many times must the Calvin cycle be completed to generate one 6-carbon molecule?
6 times
To make one molecule of glucose, how many molecules of CO2, ATP and NADPH are required?
6 CO2, 18 ATP, 12 NADPH
Gluconeogenesis
synthesis of glucose and related sugars from non-glucose precursors
Gluconeogenesis synthesizes ____ and ____ which then results in the synthesis of
glucose and fructose, monosaccharides
UDP is involved in the synthesis of
polysaccharides
Peptidoglycan synthesis utilizes what two carrier molecules
UDP derivatives and bactroprenol
First step of peptidoglycan synthesis
biosynthesis of UDP-NAG
UDP-NAG is processed into
UDP-NAM
Bactroprenol
55 carbon lipid used to transport NAG-NAM-pentapeptide (PDG monomer) units across the cell membrane
Brief overview of how precursor metabolites are synthesized into amino acids
- carbon skeleton is remodeled
- amino group added (group containing N)
- sometimes sulfur group added
T /F : ammonia is easily incorporated into organic material because it is more reduced than other forms of inorganic nitrogen
T
Nitrate reduction to nitrite is catalyzed by
nitrate reductase
Reduction of nitrite to ammonia is catalyzed by
nitrite reductase
Reduction of atmospheric nitrogen to ammonia is catalyzed by
nitrogenase
Nitrogenase is found only in
bacteria and archaea
Nitrogen fixation cost
16 ATP, 8 electrons
T / F : nitrogen fixation can consume up to 10% of cellular ATP
F, up to 20%
Sulfur is needed for the synthesis of what amino acids?
cysteine and methionine
How many ATP are used in assimilatory sulfate reduction?
2
First step in assimilatory sulfate reduction involves
sulfate activation
In assimilatory sulfate reduction, sulfate is activated and then converted into _____
phosphoadenosine 5’-phosphosulfate (PAPS)
The sulfate in PAPS is reduced to
sulfite and hydrogen sulfite
How many NADPH used in assimilatory sulfate reduction?
2
What reduced form of sulfate can be used to make cysteine?
hydrogen sulfide
Fungi combine ___ with serine to make cysteine
hydrogen sulfide
Bacteria combine ___ with O-acetylserine to make cysteine
hydrogen sulfide
Oxaloacetate can generate what amino acids
methionine, threonine, lysine, isoleucine
Nucleoside
nitrogenous base-5 carbon sugar
Nucleotide
nucleoside-phosphate
5’ end of DNA has ____
phosphate group
3’ end of DNA has
-OH group
T / F : most microbes cannot synthesize their own purines and pyrimidines
F
Examples of purines
adenine and guanine
Examples of pyrimidines
uracil, cytosine, and thymine
Purines
cyclic nitrogenous bases consisting of 2 joined rings
Pyrimidines
cyclic nitrogenous bases consisting of a single ring
You cannot synthesize purine unless you have an abundance of __________
ribose-5-phosphate
First purine formed in biosynthesis is
ionsinic acid
Initial products of purine biosynthesis are
ribonucleotides
Pyrimidine biosynthesis begins with _________ and high energy _______
aspartic acid, carbamoyl phosphate
Initial products of pyrimidine biosynthesis are
ribonucleotides
Important difference between purine and pyrimidine biosynthesis
purine ring synthesized attached to ribose, ribose added after synthesis of pyrimidine ring
Compared to soil, waters are ____ oxygen diffusion rate environments
low
Higher levels of CO2 does what to the pH of seawater
decreases it –> more acidic
Estuary
semi-enclosed coastal region where a river meets the sea
Microbes in an estuary must be
halotolerant
Estuarine waters are _____ and ______
calm, nutrient rich
Eutrophication
enrichment of an ecosystem with chemical nutrients, typically compounds containing nitrogen and phosphorus
Eutrophication can lead to
algal blooms
A harmful algal bloom (HAB) occurs when
a single species grows at expense of other members of community
Factors that contribute to Lake Erie’s algal bloom
- warm water
- sunshine
- abundant supply of nutrients
- phosphorus from commercial agricultural runoff
Cyanobacteria release toxins known as ____ into the environments
microcystins
Photosynthetic microbes that fix ~half the world’s carbon inhabit the _____ part of the ocean
upper 200-300 meters
Euphotic zone (photic zone)
0-200m, depth at which light penetrates with sufficient intensity so that the rate of photosynthesis by microscopic autotrophs exceeds the collective rate of respiration
How do we know undiscovered microbes exist?
16S ribosomal subunit
Majority of viruses in the ocean are
bacteriophages
By biomass, _____ and _____ make up ~90% of the microbes in the ocean
bacteria and archaea
By abundance, ____ makes up 94% of all microbes in the ocean
viruses
_____ are now recognized as the most abundant “life form” on earth
Phage particles
Average virus density in seawater is
~1E6 - 1E7 per mL
Soil contains a large variety of
microdomains
T / F : level of microbial diversity in soil exceeds that of any other habitat on earth
T
1 g of soil = ______ cells
1E9 - 1E10
Intrinsic factors
composition, physical and biological state
Extrinsic factors
temperature, relative humidity, gases, contaminating microorganisms
_____ predominates in carbohydrate spoilage
mold
Mold degrades food by
hydrolysis
_______ predominates protein spoilage
bacterial growth
Putrefaction
proteolysis and anaerobic breakdown of proteins; foul smelling amine compounds
Foul smelling amine compounds involved in protein spoilage
cadaverine and putrescine
low pH favors
yeast and mold
_____ temperatures slow microbial growth
lower
______ levels of humidity promote microbial growth
higher
____ promotes microbial growth
oxygen
Methods of food preservation
filtration, temperature control, hydration control, chemicals, radiation
GRAS chemical preservatives include
organic acids, sulfite, ethylene oxide gas, ethyl formate
Major fermentations used in food are
lactic, propionic and alcoholic
12 precursor metabolites
- Acetyl-CoA
- Erythrose 4-phosphate
- Fructose 6-phosphate
- Glucose 6-phosphate
- Glyceraldehyde 3-phosphate
- alpha-Ketogluterate
- Oxaloacetate
- Phosphoenolpyruvate
- Succinyl-CoA
- 3-phospho-glycerate
- Pyruvate
- Ribose 5-phosphate
