Midterm #1 Flashcards
What are the 3 domains of life?
Bacteria
Archaea
Eukarya
How did diversity of life arise?
Evolution
What is LUCA?
Last Universal Common Ancestor
How do we know when O2 appeared in our biosphere?
Oxygen interacting with iron which precipitates into sediments
Robert Hooke
1665- first book devoted to microscopic observations
Antoin Van Leeuwenhoek
1676- first to see bacteria
Ferdinand Cohn
~1850’s - first to see bacterial endospores
Louis Pasteur
1864- disproved spontaneous generation theory
Robert Koch
germ theory of infectious disease
Light microscopy
compound light microscope uses light to illuminate cells
- many different kinds
What are the two sets of lenses that form an image?
objective and ocular
Phase-Contrast Microscopy
- invented by Fritz Zernike in 1936
- phase ring amplifies difference in refractive index of cell and surroundings
- improves contrast
- allows visuals of live samples
Dark-Field Microscopy
- light reaches the specimen from the sides
- image appears light on a dark background
Fluorescence Microscopy
-used to visualize specimens that fluoresce (emit light) whether they do so naturally or with a stain
Differential Interference Contrast (DIC) Microscopy
- uses polarizer to make two distinct beams of polarized light
- gives structures a 3-D appearance
Atomic Force Microscopy (AFM)
a stylus helps to generate an image by measuring weak repulsive forces b/w stylus and specimen
Confocal Scanning Laser Microscopy (CSLM)
uses computerized fluorescence microscope coupled with a laser source to generate 3-D image
Transmission electron microscopes
electromagnets function as lenses
Electron microscopes
uses electrons instead of photons to image cells and structures
Scanning electron microscopes
scattered electrons are collected by a detector and an image is producedx
Which two microbials do not live next to each other?
cyanobacteria and clostridium
Why is seeing images of microbial cells important?
to be able to look at structure-function relationship since seeing is believing
What are the major cell morphologies?
coccus (spherical)
rod (cylindrical)
spirillum (spiral)
What cells have unusual shapes?
spiroschetes
appendaged bacteria
filamentous bacteria
What does morphology not predict?
physiology, ecology, phylogeny of prokaryotic cells
Advantages of small cells?
- more surface area
- support greater nutrient exchange
- grow faster
Cytoplasmic membrane
thin structure that surrounds the cell and a barrier that separates the cytoplasm from the environment
What functions do membranes perform for the cell?
- permeability barrier
- anchor for proteins
- sire for energy conservation (ETC)
Integral membrane proteins
membrane proteins that are firmly embedded in the membrane
peripheral membrane proteins
membrane proteins where one portion is anchored in the membrane
archaeal membranes
ether linkages in phospholipids of archaea
What kind of linkages do bacteria and archaea have in phospholipids?
ester
What are the three classes of nutrient transport?
simple transport
group translocation
ABC system
Simple transport
the nutrient is simply transported by a transporter
Group translocation
substance transported is chemically modified during transport across the membrane and requires 5 proteins
ABC system
often involved in uptake of organic compounds, inorganic nutrients and trace metals
Peptidoglycan
a classification of bacteria
Gram-negative
two layers: peptidoglycan and outer membrane
- appear red
Gram-positive
one layer: peptidoglycan
- appear purple
Gram-stain
differential stains separate bacteria into groups (gram positive or negative)
What prokaryotes lack cell walls?
mycoplasmas (bacteria) and thermoplasma (archaea)
Gram-positive cell wall
90% peptidoglycan
have teichoic acids embedded or lipoteichoic acids (have a lipid covalently bonded to it)
Gram-negative cell wall
~10% peptidoglycan
composed of outer membrane (LPS)
Lipopolysaccharide (LPS)
consists of core polysac and o-polysac
replaces most phospholipids in outer half of the membrane
Endotoxin
the toxic component of the LPS
Lipid A
endotoxin that is released when gram-negative cells are lysed
Periplasm
space located b/w cytoplasmic and outer membranes
porins
channels for movement of hydrophilic low-molecular-weight substances
What is different about archaea?
NO peptidoglycan or outer membrane
pseudomurein
pseudomurein
polysac similar to peptidoglycan that is composed of N-acetylglucosamine and N-acetyloamiuronic acid found in cells walls of certain archaea
S layer
found in both bacteria and archaea
made of protein and is present OUTSIDE other cell wall layers
Capsule and slime layer
layer of polysac made of carb polymers and assists with attaching to surfaces
Pili
filamentous protein structures, longer than fimbriae, assist with surface attachment, and facilitate with genetic exchange bw cells
fimbriae
filamentous protein structure that enables organisms to stick to surfaces or form pellicles
Carbon storage polymers
poly-B-hydroxybutyric acid and glycogen
sulfur globules
composed of elemental sulfur
polyphosphares
accumulations of inorganic material
carbonare minerals
composed of barium, strontium, and magnesium
Gas vesicles
decrease cell density causing buoyancy in planktonic cell composed of GvpA and GvpC
Endospores
contain dipicolinic acid and is rich in Ca2+
why do some species of bacteria make endospores?
bc highly differentiated cells are resistant to heat, harsh chemicals and radiation
flagella
structure that assists in swimming
flagella in bacteria
has several components, filament composed of flagellin, moved by rotation
flagella in archaea
half the diameter of bacterial, composed of several different proteins, moved by rotation
gliding motility
flagella independent, requires surface contact
taxis
directed movement in response to chemical or physical gradients
chemotaxis
response to chemicals
attractants and receptors are sensed by chemoreceptors
phototaxis
response to light
aerotaxis
response to oxygen
asmotaxis
response to ionic strength
hydrotaxis
response to water
metabolism
the breaking down of ‘food’ for energy and building up of cell components
catabolism
the breaking down and release of energy
anabolism
the building up of cell components requiring energy
What do you need to consider when growing a culture of microbes?
nutrient, temp and atmosphere requirements and pH
Microorganisms grouped into energy classes
- chemoorganotrophs
- chemolithotrophs
- phototrophs
- heterotrophs
- autotrophs
Exergonic
reactions with a negative G that RELEASE free energy
Endergonic
reactions with a positive G that REQUIRE energy
Free energy formation
how to calculate free energy yield of a reaction
oxidation
removal of electrons from a substance
reduction
addition of electrons to a substance
always works in pairs - donor or acceptor
electron carriers
common link to diverse enzyme reactions
prosthetic groups
electron carrier that is attached to enzymes
coenzymes
electron carrier that is diffusible
- NAD+ and NADP
Glycolysis
a common pathway for catabolism of glucose (anaerobic with 3 stages)
Fermentation
substrate-level phosphorylation
ATP is directly synthesized from an energy-rich intermediate
Respiration
oxidative phosphorylation
ATP is produced from PMF formed by transport of electrons
Aerobic respiration
oxidation using O2 as the terminal electron acceptor and has higher ATP than fermentations
NADH dehydrogenases
proteins bound to inside surface of cytoplasmic membrane
active site bind NADH and accepts 2 electrons and 2 protons that are passed to flavoproteins
Flavoproteins
contains flavin prosthetic group (FMD, FAD) that accepts 2 electrons and protons but donates the electrons only to the next protein in the chain
Cytochromes
proteins that contain heme prosthetic groups
accept and donate a single electron via the iron atom in heme
Iron-sulfur proteins
contain clusters of iron and sulfur
reduction potentials vary depending on number and position of Fe and S atoms
carry electrons
Quinones
- hydrophobic non-protein containing molecules that participate in electron transport
- accept electrons and protons but pass along electrons only
Proton motive force
electron transport system in cytoplasmic membrane so that electrons are separated from protons
ATP synthase
complex that converts PMF into ATP
F1 of ATPase
multiprotein extramembrane complex that faces cytoplasm
F0 of ATPase
proton-conducting intramembrane channel
CAC and glyoxylate cycle
organic acids can be metabolized as electron donors and carbon sources by many microbes
Anaerobic respiration
the use of electron acceptors other than oxygen (NO3-,Fe3+,SO42-, CO32-)
less energy released compared to aerobic
Chemolithotrophy
uses inorganic chemicals as electron donors (H2S, H2, Fe2+, NH3) and is typically aerobic
Phototrophy
uses light as energy source
photophosphorylation
light-mediated ATP synthesis
photoautotrophs
use ATP for assimilation of CO2 for biosynthesis
Photoheterotrophs
use ATP for assimilation of organic carbon biosynthesis
Adenosine diphosphoglucose (ADPG)
precursor for glycogen biosynthesis
uridine diphosphoglucose (UDPG)
precursor for glucose biosynthesis
Rho-dependent termination
rho protein recognizes specific DNA (RNA) sequences and causes a pause in the RNA polymerase
Unit of Transcription
unit of chromosome bounded by sites where transcription of DNA to RNA is initiated and terminated
Ending translation
translational termination occurs when the ribosome reaches a “stop” codon
Signal sequences
found on proteins requiring transport from cell
The Tat system
proteins to be exported, that fold in the cytoplasm, are exported by a transport system distinct from Sec, called the Tat protein export system (Fe-S proteins and redox proteins)
Batch culture
a closed-system microbial culture of fixed culture of volume
What are the 4 phases of the growth curve for a closed system of cells?
- Lag phase
- Exponential phase
- Stationary phase
- Death phase
Continuous culture
an open-system microbial culture of fixed volume
Chemostat
most common type of continuous culture
- if dilution rate too HIGH = organism WASHED out
- if dilution too LOW = organism DIE
Dilution rate
rate at which fresh medium is pumped in and spent medium is pumped out (controls growth rate)
Flow cytometer
a second method for enumerating cells in liquid reproducing population using laser beams, fluorescent dyes and electronics
Viable counts
measurement of living, reproducing population
Spectrophotometry
turbidity measurements are indirect, rapid, and useful methods of measuring microbial growth
Optical density (OD)
measurement used for turbidity
What conditions affect growth?
- temp
- pH
- osmolarity
- oxygen availability
Cardinal temperatures
the minimum, optimum, and maximum temperatures at which an organism grows
Extremophiles
organisms that grow under very hot and very cold conditions
Psychrophiles
organisms with cold temperatures optima and inhabit permanently cold environment
Psychrotolerant
organisms that can grow at O C but have optima of 20-40 C and more widely distributed in nature than psychrophiles
Thermophiles
organisms with growth temperature optima b/w 45-80D
Hyperthermophiles
organisms with optima greater than 80C
Neutrophiles
organism that grow optimally at pH 5.5-7.9
Acidophiles
organisms that grow best at low pH (<5.5)
Alkaliphiles
organisms that grow best at high pH (>or = 8)
Osmosis
water diffuses from high to low concentrations
Aerobes
requires oxygen (respiration) and grow at full oxygen tension (~21%)
Microaerophiles
can use oxygen only when it is present at levels reduced from that in air due to limited respiration or oxygen sensitivity
Facultative organisms
can live with or without oxygen
Anaerobes
cannot respire oxygen
Aerotolerant anaerobes
tolerate oxygen and grow in its presence even though they cannot respire
Obligate anaerobes
inhibited or killed by oxygen (ex: some bacteria and archaea, fungi, protozoa)
Metabolic Regulation
metabolic activity of a cell = expressed proteins
what are the different types of metabolic regulation?
- degradation
- modification
- allosteric regulation
Negative control
gene that are negatively controlled have a default of ON
Positive control
genes that are positively controlled have a default of OFF
induction
= loss of repression
Repressor gene
a protein that binds the transcription start site of a negatively controlled gene
Global control systems
regulate expression of many different genes simultaneously
Catabolite repression
ex of global control and is the synthesis of unrelated catabolic enzymes is repressed if glucose is present in growth medium
Diauxic growth
two exponential growth phases
Cyclic AMP and CRP
in catabolite repression, transcription is controlled by an activator protein and is a form of positive control
CRP
activator protein
Cyclic AMP
is a key molecule in many metabolic control systems and is derived from a nucleic acid precursor
Sensor kinase
detects environmental signal and autophosphoylates (in cytoplasmic membrane)
Response regulator
DNA-binding protein that regulates transcription (in cytoplasm)
Phototaxis
movement toward light, light sensor replaces MCP’s
aerotaxis
movement toward oxygen, redox protein monitors oxygen level
Quorum sensing
mechanism by which bacteria assess their population density and ensures that a sufficient number of cells are present before initiating a response that to be effective, requires a certain cell density
Acyl homoserine lactone
the first autoinducer to be identified
Heat shock response
largely controlled by alternative sigma factors
Heat shock proteins
counteract damage of denatured proteins and help cell recover from temp stress
