BMSC 210 - Part 1

tasnimjaisee's version from 2017-10-06 06:16

Lecture 2

Question Answer
A single colony can contain how many individual cells?10^7 cells
What are some properties of ALL cells?Growth – Metabolism – Evolution
What are some properties of SOME cells?Differentiation – Communication – Genetic exchange – Motility
Steps in how we decide phylogenetic tree draw?Isolate DNA - rRNA copies gene by PCR - Sequence - Analyze - Generate tree
S unit in bacteria and archaea?16
S unit in eukarya?18
Robert Hooke1665 – first book devoted to microscopic observations
Van Leeuwenhoek1676 – first to see bacteria
Ferdinand Cohn~1850’s – first to see bacterial endospores
Louis Pasteur1864 – disproved “spontaneous generation theory” / 1885 – vaccine to a boy bitten bit a rabid dog
Koch's postulates - Microscopy staining (2)All disease cases have pathogen - Absent from healthy animals
Koch's postulates - Laboratory culturesPathogen must be grown in pure culture
Koch's postulates - Experimental animalsPure culture pathogen caused healthy animals disease
Koch's postulates - Laboratory reisolation and culture (2)Pathogen are isolated - Shown to be same as original

Lecture 3

Question Answer
Types of light microscopyBright‐field – Phase‐contrast – Dark‐field – Fluorescence
How do compound light microscope work?Uses visible light to illuminate cells
Bright-field microscopyDifferences in contrast (density) of specimen & surroundings
What does Bright-field microscopy use for lenses?Objective and ocular
Equation for Bright‐field scope (3)Total magnification = objective magnification = ocular magnification; max magnification use ~2000x
Phase‐Contrast Microscopy (3)No stain - live samples - Dark cells on light background
Dark‐Field Microscopy (3)Light in specimen from the sides - Lighted cells on dark background - Observe mobility
Types of 3D MicroscopyDIC, AFM, CSLM
Differential Interference Contrast (DIC) MicroscopyCreates 2 polarized light beams
DIC microscope is used if which microscope does not view the specimen correctly?Bright‐field microscopy
Atomic Force (AFM) MicroscopyStylus measures weak repulsive forces between it & specimen
Confocal Scanning Laser (CSLM) Microscopy (2)Uses laser - Each layer is focused on
Types of electron microscopesTransmission electron (TEM) microscopes and Scanning electron (SEM) microscopes
Transmission Electron (TEM) MicroscopyHigh vacuum - Electromagnets lenses - Thin & stained organisms
Scanning Electron (SEM) MicroscopySpecimen coated - Electron beam scans - large specimens observed
Major cell morphologiesCoccus/cocci - Rod - Spirillum
Coccus (pl. cocci)spherical or ovoid
Spirillumbent rod shape
SpirochetesLong wavy
Appendaged bacteriaPump
What does morphology typically does not predict of prokaryotic cell?Physiology - Ecology - Phylogeny
Morphology is important for?Nutrition uptake - Viscus motility - Gliding motility
What is the best for viscus motilityHelical/spiral cells
What is the best for gliding motilityfilamentous
↑ Numerical apertureBetter resolution - higher magnification
↓ Short wavelengths = ?Better resolution

Lecture 4

Question Answer
Advantages to being small (3)Surface area to volume - nutrient exchange> - Grows fast
Cytoplasmic membrane features (3)Embeds proteins - HBond stabilization & hydrophobic interactions - Mg2+ and Ca2+ ionic bonds stabilization & -ve charged phospholipids
Archaeal lipids lack ___ ___; have ___ instead.Fatty Acids - Isoprenes
What are archaea's major lipids?Glycerol diethers & tetraethers
How do permeability barriers work?Transport proteins accumulate solutes against concentration gradient
Function of cytoplasmic membrane (3)Permeability - Protein Anchor - Energy conservation
3 classes of prokaryote transport systemsSimple transport - Group translocation - ABC system
Prokaryote transport systems: Simple transportMoves in & out
Prokaryote transport systems: Group translocationChemical modification of transported substance by phosphoenolpyruvate
Prokaryote transport systems: ABC transporter (2)Solute is taken in after protein shape alters - ADP+Pi attach to make opening
What does Lac permease of Escherichia coli do?This symporter causes Lactose transport into E. coli - energy‐driven (proton motive force)
Phosphotransferase system in E. coli (4)Substance chemically modified during transport - Moves gluc, frac, man - 5 proteins needed - Energy from phosphoenolpyruvate
How does the phosphotransferase system workPhosphate cascade from phosphoenolpyruvate to Enz llc which transports and phosphorylates sugars
In the phosphotransferase system, which are the non-specific components and why?Enz l and HPr because they transport any sugars
In the phosphotransferase system, which are the specific components and why?Enz lla and Enz llb because they transport specific sugars
In transport, uptake rate shows saturation at which concentrations?low external concentrations
What does the ABC system do for gram negative interaction (2)Periplasmic binding proteins & ATP transport
ABC system gram positive interactionSubstrate‐binding proteins & membrane transport proteins

Lecture 5

Question Answer
Gram‐negative cell wall (Layer#, color, substance(s))2 layers -Red- LPS & peptidoglycan
Gram‐positive cell wall (Layer#, color, substance(s))1 layer -Purple- peptidoglycan
Gram-Staining stepsHeat fix smear flodded with cystal violet (1m) - iodine solution added (1m) - Alcohol decolorization (20s) - Safranin counterstain (1-2m)
What protection does the cell wall play in the life of a cell?Osmotic protection
Gram‐positive cell walls contain which percent of peptidoglycan?90% peptidoglycan
Which acid is common for gram‐positive cell wallsTeichoic acids
Lipoteichoic acidsteichoic acids covalently bound to membrane lipids
MycoplasmasGroup of pathogenic bacteria - Lacks cell wall
ThermoplasmaSpecies of Archaea - Lacks cell wall
What is gram negative bacteria walls made of?10% peptidoglycan and 90% lipopolysaccharide
What do lipopolysacchrides LPS replace in Gram Negative cell wall?most of phospholipids in outer 1/2 of outer membrane
EndotoxinLPS toxic component
Where are lipopolysacchrides found?Outer surface of outer membrane of gram negative bacteria
LPS structureLipid A - Core Polysaccharides - O-Specific Polysaccharides
LPS structure: Lipid A featuresTail, P, GLCN
LPS structure: Core PolysaccharidesKDO, GLU, P
LPS Structure: Lipid A - Endotoxin released if?gram negative cell is lysed
PeriplasmGap between cyroplasm and outer membranes - Houses proteins - Jelly like
PorinsHydrophilic substance, transport channels
What is different about Archaea in general than othersArchaea has no peptidoglycan and no outer membrane
What are the acids, pseudomureins is made of?N‐acetylglucosamine and N‐ acetylalosaminuronic acid
Where are pseudomureins found?cell walls of methanogenic Archaea
Out of (some not all) Arechea, Bacteria and Eukaryotes, which species lack psuedomurein?Arechea
In some archaea the only cell wall is which?S layer
Capsules and Slime Layer Similarities? (4)Carbohydrate made, polysaccharide layer - Attachment - Phagocytosis protection - Resist desiccation
Slime layersLoose
FimbriaeFilaments: Organisms stick to surface/form clumps
Pili (5)Filaments - >fimbriae - Attachment - Facilitate genetic exchange - twitching motility type 4
Carbon storage polymersPHB and Glycogen
Cell InclusionsCarbon storage polymers - Polyphosphates - Sulfur globules
Gas Vesicles (4)Plankton cells - Spindle‐shaped - Proteins made - Water Impermeable
Molecular structure of gas vesiclesGvpA and GvpC: Function by decreasing cell density
Why do some species of bacteria make endospores?Resistant to heat, harsh chemicals and radiation - “Dormant” stage - Ideal for dispersal in wind/water/animal gut - only in gram‐positive bacteria
Stages of sporesVegetative - Developing - Mature
What are the chemical compounds relating to endospore cell structures?Dipicolinic acid - ↑ Ca2+ - SASP in core
Flagella: PeritrichousRandomly distibuted - Slowly in straight line
Flagella: PolarOne from one end - Rapid and spin
Flagella: lophotrichousMultiple ones in one side only
Flagella increase/decrease rotational speed in relation to?Proton motive force strength
Gliding molilityFlagela independent - Slower/smother than swimming
ChemotaxisChemical concentration difference (inorg/org)

Lecture 6= Lecture 6

Question Answer
CatabolismBreaking down of "food" for energy and building blocks
AnabolismBuilding of cell components building blocks and energy
What do you need to consider if you want to grow a culture of microbes?Nutrients - Atmosphere - Temperature - pH - Pressure
Catabolic reactionsEnergy‐releasing metabolic reactions
Complex mediumMade from digests of microbe products
Defined mediumPrepared by adding pure organic/inorganic precise amounts to distilled water
Microorganisms are grouped into 5 energy classesChemorganotrophs – Chemolithotrophs – Phototrophs - Heterotrophs - Autotrophs
Exergonic-ΔG; release free energy
Endergonic+ΔG; require energy
How does catalytic breakdown of enzyme work?Substrate binds - Bond is strained - Products are released unbounded
Oxidationremoval of electrons from a substance
Reductionaddition of electrons to a substance
Cells conserve (capture) energy by?Coupling energy from catabolic reactions
Classes of electron carriersProsthetic groups - Coenzymes (diffusible)
NAD+ and NADH facilitate which type of reaction?redox; recycled
Two reaction series are linked to energy conservation in chemoorganotrophsfermentation and respiration
Substrate level phosphorylationFermentation - Produces ATP
Oxidative phosphorylationRespiration - Produces ATP
What is the end product of glycolysisPyruvate --> Fermentation products are made from it
Reducing power generated during creation of 1,3‐ Bisphosphoglcerate is consumed to create?End product lactate from pyruvate
If pyruvate was not reduced to lactate, what would happened?Built up reduced NADH; cycle stop
Net yield of how many ATP generated for each glucose fermented to lactate?2
How is Respiration different from fermentation?Reducing power isn't degradation - Transferred to “terminal electron acceptor”
Aerobes terminal electron acceptor is?O2
In aerobic respiration, oxidation using O2 as ___ ___ ___terminal electron acceptor
Aerobic respiration, has higher ATP than ___Fermentation
Electron transport systems: Conserve ___ released during transfer and use it to ___ ___Energy - Synthesize ATP
NADH dehydrogenases steps (3)Active site binds NADH - Accepts 2 electrons & 2 protons→passed to flavoproteins
FlavoproteinsFlavin prosthetic group accepts 2 electrons & 2 protons - donates only electrons to next protein in chain
CytochromesHeme prosthetic groups proteins: Accept and donate a single electron via iron atom
Iron–sulfur proteins (2)Reduction potentials depends on Fe and S atoms' number & position - Carry electrons
Quinones (3)Hydrophobic non‐protein molecules - Accept electrons & protons - Donates electrons
Enzyme spontaneous reaction is met ___ than having no enzyme (earlier/later)Earlier
In redox tower, being good acceptors which rate of free energy is released?Higher
Electrons can be caught by acceptors at any intermediate level as long as?Donor couple is more negative than the acceptor couple
FMN, FAD are examples of which group?Flavin prosthetic group
Prosthetic group functionAttach to enzymes
Coenzyme examplesNAD+ and NADP
ATP is produced at the expense of the ___ ___ ___, which is generated by ___ ___Proton motive force; Electron transport
Respiration: Electron Carriers TypesAerobic respiration - Electron transport systems - NADH dehydrogenases - Flavoprteins - Cytochromes - Iron-Sulfer prteins - Quinones