Bio 302 Exam 1 Study Guide PDF

Earth History and Evolution Key ingredients for life :essential elements, water, energy Oldest rocks -4.3 bya Significant events in earth history ○ 4.5 bya earth formation (use meteors to find earths age) ○ 4.3 bya oldest rocks in Quebec, evidence for presence of li...

Earth History and Evolution Key ingredients for life :essential elements, water, energy Oldest rocks -4.3 bya Significant events in earth history ○ 4.5 bya earth formation (use meteors to find earths age) ○ 4.3 bya oldest rocks in Quebec, evidence for presence of liquid water ○ 3.5-.8 bya evidence of microbial life Evidence: stromatolites, carbon isotypes, microfossils ○ 2.7 bya oxygenic photosynthesis by cyanobacteria ○ 2.4 bya great oxidation event O2= 1ppm ○ 2 bya oldest known eukaryotic microfossil ○ 1.9-.4 bya multicellular microfossils ○ 0.6 bya O2 at present levels, large multicellular organisms Stromatolites: layered structures formed by trapping, binding, and cementation of sediment by microbial films Carbon isotypes: ○ Carbon occurs in 12C, 13C, 14C ○ Organisms prefer “light” carbon, where organisms present there is more 12C than 13C incorporated into complex organics (like rocks) 12C in rocks from greenland 3.85 bya Microfossils Origin of life series ○ Panspermia: life came from elsewhere ○ Abiotic formation of cellular components (ex amino and nucleic acids) ○ Surface catalyzed: using properties of clay mineral surfaces for catalysis/polymerization ○ RNA world: information and catalysts, could catalyze own synthesis Implications of oxygenated environment ○ Toxic atmosphere ○ Condition for evolution of new metabolic pathways (presence of SO4’2, Fe3+, NO3, oxygen respiration) ○ Energetic advantage of O2 respiration (rapid diversification) ○ Formation of O3 ozone layer Prior to this life couldn’t exist on surface, only in water Banded iron formations: laminated sedimentary rocks formed in deep water deposits of alternating Fe rich minerals (oxidized iron) and iron poor silicates Oldest eukaryotic microfossil: Grypania spiralis (alga) Eukaryote: nuclear membrane, mitochondria, chloroplasts ○ Origin of mitochondria/chloroplast (2bya) Contain ribosomes (70S not 80S) Have 16S rRNA not 18S Antibiotics that affect bacteria also affect M and C Circular DNA, no histones Divide by binary fission  Consistent with fossil record Limited horizontal transfer Molecular phylogenetic markers ○ 16S and 18S (only for eukaryotes) rRNA ○ Present in all cellular organisms ○ Single evolutionary origin and single function ○ Consists of slowly and quickly evolving regions ○ DNA genetic material shared throughout tree LUCA: last universal common ancestor ○ Possessed all characteristics shared by both domains Chapter 2 Outer envelope of bacterial cell: cell membrane→cell wall→outer membrane (gram -) → capsule/slime layer→S layer ○ Protect from toxins and predators ○ Allow nutrients in ○ Allow reproduction Cell membrane/cytoplasmic membrane: lipids (HYDROPHOBIC) ○ Bacteria and eukaryotes Phospholipids Acetogenic fatty acids (builts form acetate 2C) Fatty acids attached to glycerol via ester bond ○ Archaea Unique lipids Isoprenoid instead of acetogenic fatty acids Ether linkage to glycerol May have phospholipid bilayer or monolayer May not even have phosphate so no phospholipid ○ Cell membrane (both) Fluid Primary layer between cytoplasm and external environment ○ Cell membrane uses Creates osmotic barrier (normal cytoplasm has more solutes than environment) Energy generation via H+/Na+ gradient transport/transporters, diffusion of water and gases O2, CO2, N2, H2S Signaling ○ characteristic Bact & Euk Archaea Glycerol linkage Ester bond Ether bond lipid Acetogenic fatty acid isoprenoid ○ Also in membrane  Proteins Compounds changing fluidity Eukaryotes: sterols Bacteria: hopanoids Archaea: terpenoids Common bacterial shapes ○ Coccus (sphere) ○ Rod (oval) ○ Spirillum ( curved rod) Cell wall ○ Cell wall + cytoskeleton determines shape ○ Gives physical strength for osmotic pressure (more ions inside the cell than outside) ○ Made of peptidoglycan polymer of sugars and amino acids aka murein ○ Hydrophillic→ hinders passage of hydrophobic moles ○ Bacteria Bacteria peptidoglycan= murein N-acetylmuramic acid and N-acetylglucosamine Contains both D and L amino acids (D aa for crosslinking) B-1,4 linkages of sugars that are hydrolyzed by lysozyme Lysozyme breaks down cell wall by breaking B-1,4 linkages Gram + Thick cell wall (murein) Crosslinking of peptides alanine and lysine Contains teichoic acids (chains of sugar alcohols linked by phosphodiester bonds) ○ Aid in adhesion ○ Covalently bond to murein Gram - thin cell wall In periplasm Crosslinking of peptides alanine and DAP ○ What happens to gram + bacterial cell when lysozyme added to cell under condition where cell is in solution with ionic strength> cellular contents (hypertonic solution), Cell will shrink Hypotonic solution then cell explodes Quiz 1 ○ Ether linkage-archaea ○ Mars rover- panspermia ○ LUCA-DNA as genetic material ○ Bact and Archaea- 16S rRNA only ○ Small microbe- diffusion as better diffusive uptake and main intracellular mechanism of transport and only uptake  ○ Bacteria fluidity- hopanoid ○ Cell membrane- lipid, hydrophobic ○ 12C enriched for organisms evidence I Cell wall Bacteria ○ Gram + ○ Gram - ○ mycobacteria/acid fast Gram resistant Thin murein layer Cell wall contains waves= mycolic acids (covalently attached to cell wall) so HYDROPHOBIC II Cell wall Archaea ○ Pseudomurein ○ B-1,3 linkage between sugars (lysozyme doesn't work) ○ L amino acids in peptide crosslinks III No cell wall ○ Bacteria and archaea lack cell wall ○ Ex mycoplasmas, thermoplasmas Outer membrane ○ Only in gram - ○ Forms periplasm ○ Made of LPS composed of Lipid A (endotoxin, fatty acids), core polysaccharide (constant), O-antigen subunits (highly variable, ~40 sugars, virulence factor, elicits strong antibody response) ○ Prevent hydrophobic and hydrophilic molecules ○ Contains porins which allow small “600-700” Da hydrophilic molecules to pass ○ Contains transporters for large hydrophilic and hydrophobic ○ Basically hydrophilic In gram - bacteria ○ Does Small hydrophilic compound pass through: Outer membrane yes because of porins Cell wall yes since its hydrophilic Cell membrane no since its all lipids and keeps out hydrophilic ○ Does Large hydrophilic compound pass through Outer membrane no they need transporters Cell wall yes its hydrophilic Cell membrane no because of lipids ○ Does Hydrophobic compound pass through Outer membrane no because LPS block it Cell wall no because wall is hydrophilic and don't pass hydrophobic Cell membrane yes because membrane hydrophobic S layer ○ Outermost layer ○ cystalline/ordered structure  ○ Can self assemble ○ Made of protein or glycoprotein ○ Additional surface layer for some bacteria and archaea ○ Allows passage of low molecular weight solutes ○ Can be protective barrier layer for cells without cell walls ○ Resistant to environmental assaults- phagocytosis, viral infection, proteo ○ Helps with adherence to surface capsule/slime layer ○ Slime layer not attached to cell ○ Made of high molecular weight polysaccharides ○ Helps with adhesion, phagocytosis, dessication ○ Both prevent phagocytosis→ considered virulence factor→ increases effectiveness of colonization, evade immune system Flagella ○ Most common form of movement (swimming) ○ Can be external or internal in periplasm ○ Aid in adhesion ○ Flagella rotate by molecular motor powered by proton motive force/gradient (pmf) Helical ○ Filament:5-10 uM, helical, hollow, made of flagellin, can self assemble ○ Hook: short curved structure, connects filament to cell, made of single protein ○ Basal body: made of 15 proteins forming rings and rods, molecular motor Pili/fimbrea ○ Protein filaments: thinner and shorter than flagella, made of pilins ○ Can be distributed over entire cell or at ends ○ Adhesion: at tops of pili that aid in adhesion ○ Used for motility (twitching) Transfer of material Adhesion ○ Use ATP for movement, no motor Polymerization (stretch) then depolymerization (pull) characteristic pili flagella monomers pilins flagellins use Twitching motility, Swimming motility, adhesion, material transfer adhesion assembly Chaperones at cell surface Self assembles at tip Movement occurs by Twitching (polymerization Swimming (flagella rotation and depolymerization) by molecular motor) energy ATP Proton motive force/gradient  Quiz 2 ○ Pili- twitching, poly +depoly ○ Crystalline- S layer ○ C6H12O6- small hydrophilic so goes through outer membrane and cell wall (C6*12, H12*2, O6*16 < 600-700 Da) ○ Flagella- assist in adhesion ○ LPS- outer membrane gram negative ○ Cell wall as osmotic barrier → false, only osmotic pressure ○ Lysozyme works on gram + and - ○ All Bacteria cell wall does not allow all hydrophilic compounds to pass through (mycobacteria only one that does not, hydrophobic) Chapter 3 Nucleoid ○ Transcription only takes place at interface of nucleoid and cytoplasm (dynamic) ○ Generally 1 condensed, supercoiled, circular chromosome, but can be linear , can be >1 ○ No membrane ○ Genome size 500,000 bp to 10 mill bp Difference in size because organisms that live in changing environments have larger size for more viability ○ Plasmids : extrachromosomal elements, not required for viability under all conditions Cytoplasm ○ Large concentration of ribosomes ○ Viscous as a result of high concentration of molecules Molecular crowding which helps confine DNA to nucleoid and helps proteins fold and helps protein-protein interactions take place) ○ Molecules transported by diffusion Other internal structures ○ Membranes for photosynthesis and energy generation ○ Carboxysomes Icosahedron Protein shell Holds rubisco and carbonic anhydrase ○ Enterosomes ○ Gas vesicles ○ Magnetosomes ○ Poly beta hydrocy alkanate (PHA) ○ Polyphosphate granules ○ Sulfur granules Photosynthetic membranes: thylakoids Carboxysomes ○ Block O2 which is inhibitor of rubisco  ○ C source for anabolic rxns ○ Autotrophs use inorganic carbon CO2 ○ Calvin benson cycle (rubisco) ATP and NADPH required ○ Used to improve crop yields ○ ○ CA= carbonic anhydrase RUBP= ribulose bisphosphate PGA= phosphoglycerate Enterosomes ○ Protein shell ○ Contain metabolic enzymes for degrading specific compounds (ethanolamine) ○ Sequester toxic metabolic intermediates Gas vesicles ○ Protein shell ○ Can affect buoyancy Magnetosomes ○ Membrane bound magnetite (Fe3O4) bilipid membrane ○ Allows bacteria to orient in Earths magnetic field PHB (poly beta hydroxy butyrate)  ○ Lipid polymer ○ Synthesized when there is excess carbon ○ Poly beta hydroxy alkanate (PHA) PHB most common Could be precursor for biodegradable plastic Polyphosphate granules ○ Produced when growth limited by another compound Sulfur granules ○ Not formed as a result of growth limitation ○ Elemental S in organisms that oxidize sulfide (S2-) ○ H2S→ S ○ Elemental S in then oxidized to sulfate (SO4^2-) when sulfide no longer available ○ S→ SO4^2- ○ Energy rxn H2S–(O2) →S –(O2) →SO4^2- H2S(transient gas, reacts w/ O2 chem) Gram - cell Sporulation from endospores ○ Only in gram + ○ Sporulation triggered by nutrient depletion ○ Develops inside and differentiates from mother cell ○ Survival mech that can resist heat, radiation, desiccation, ROS ○ Most resistant of all known biological structures ○ Can germinate when environmental conditions improve ○ Known only in Firmicute phylum of Gram + ○ Endospore layers (in to out) 1 cell membrane 2 cortex of murein 3 cell membrane 4 spore coat (protein)  5 Exosporium protein Inside is desiccated cytoplasm (DNA, ribosomes, dipicolinic acid DPA ) Higher survival percentage of spore with DPA Chapter 4 What makes up a cell, cell=C5H7O2N growth= increase in # of cells and size of individual cell Microbial Cells divide by binary fission (not eukaryotes) ○ FtsZ makes contristicing ring at septum where cell partition ○ Zring closes as cell divides ○ Recruits ether cell division proteins to Z ring ○ Plays same role in mitochondria and chloroplasts Bacterial growth ○ 1 turbidity ○ 2 colony formation ○ 3 counting cells under microscope ○ 4 flow cytometry Phases of growth ○ lag=cells adjust to new condition Turn on genes, make needed proteins ○ Exponential ○ stationary= nutrients used up, waste products accumulate, no change in cell #/mL ○ death= cell die off exponentially Exponential phase ○ Only phase readily reproducible ○ Constant growth rate ○ All cell constituents increase in same proportion ○ Mean cell size constant ○ Described mathematically N=No2n N= # of cells No= original # of cells n= # of generations n=ln(N/No)/ln2 n=(logN-logNo)/0.301 Generation time=time it takes cell to double g=t/n t=elapsed time n=# of generations Growth dN/dt=kN k=ln(N/No)/t k=specific growth rate k=2303(logN-logNo)/t  Ex you start a growth experiment with 103 bacterial cells. After 3 hours of exponential growth you have 106 cells. How many generations passed? What was the doubling time? What was the growth rate? ○ n=(logN-logNo)/0.301 ○ n=(log106-log103)/0.301=~10 ○ Generation time=t/n ○ g=3 hr/10=~0.3 hours ○ k=2303(logN-logNo)/t ○ k=2303(6-3)/3 hr= 2303 hr-1 Growth rate affects physiological state: cell size and macromolecule composition ○ Faster growing cells need more ribosomes(RNA and protein), must be bigger to hold them Maintaining exponential growth through dilution and chemostat ○ No lag phase when diluted, just exponential phase ○ Chemostat: limiting nutrient controls growth rate Density of culture is constant Growth in nature environment ○ Most growth in stationary phase ○ Most growth at biofilm Cells attached to surface or floating in polysaccharide/protein/DNA matrix EPS= exopolymeris substances Biofilms: characterized by steep chem gradients Protection against chemicals Allows cells to stay in good place Biofilms: cells attached to surfaces in protein, DNA, and polysaccharide matrix ○ Sessile (attached) vs planktonic (suspended in liquid) ○ Steep chemical gradients ○ Protection from chemicals antibiotics, ROS, etc ○ Heterogeneous ○ 1 initial attachment ○ 2 irreversible attachment (all cells in contact with surface) ○ 3 maturation I (several cells thick in EPS matrix) ○ 4 maturation II (cells cluster reach max thickness) ○ 5 dispersion (cells evacuated interior portions of cells clusters forming void spaces) Quiz 3 ○ Divide by binary fission ○ CO2 can’t diffuse in and out of carboxysome ○ Sporulation triggered by nutrient depletion ○ 1g DNA, 8 generations = 1*2^8=256 ○ Carbon mass makes up 50% of bacteria ○ Cant survive outside of host ○ Bilipid membrane → magnetosome ○ Exp growth not maintained  Factors affecting growth ○ 1 nutrients: properties of media/environment ○ 2 temperature: microbes can grow at -12C to 121 C, optimal temp used to describe those microbes ○ 3 hydrostatic pressure Barophiles: grow optimally at high pressure Most microbes can tolerate high hydrostatic pressure because membranes permeable to H2O ○ 4 osmotic pressure: 0.5-2 M salt ○ 5 pH: 1-11.5 Optimal growth at low pH acidiphiles Optimal growth at high pH alkaliphiles Cytoplasm is always neutral (pump H+ in or out) How they thrive at high hydro pressure ○ DNA more negatively supercoiled ○ More unsaturated fatty acids in membranes to increase fluidity ○ Pressure resistant proteins ○ Chaperones How we study non culturable microbes 99% ○ 1 environmental parameters: geochemistry: what chemicals can support life (ex oxygen depletion) ○ 2 microscopy: staining, fluorescence with probes ○ 3 16S rRNA gene sequence: who is there ○ 4) metagenome(all genomes in a sample) and single cell genomes Genetic potential Optimal growth temp ○  Psychrophiles ~15C and lower optimal temp Mesophiles: moderate temps Thermophiles: 45C to 80C Hyperthermophiles: >80C >65C no Euk >72-74C no phototrophs >95C no bacteria What allows high temp growth ○ Stable membranes: monolayer membranes, ether bonds ○ Thermal stable proteins: more salt bridges (interactions between positive and negative amino acids) ○ Chaperones ○ DNA binding proteins ○ DNA positive supercoiling (at normal temp DNA is negatively supercoiled) ○ More salts to stabilize proteins and DNA ex Mg2+ Halophiles: optimal growth at high salt ○ No pressure against cell wall since water moves out of cell and cell shrinks ○ Challenges Need osmotic/turgor pressure to expand cell wall Less water activity← effective concentration (most water ordered around ions) Less water activity leads to slower growth ○ Produce compatible solutes (ex trehalose) to create turgor pressure ○ Uptake K+ to increase turgor pressure ○ Grow in salt crystals Ex biologus strain 302 can grow in temps ranging from 70 to 90C with an optimum growth temp of 86C. Draw a growth curve for the microbe at 70,86, and 90C and note phases of growth. All other growth conditions are constant ○ Stationary phase the same because same nutrients available (growth conditions constant) Chapter 5 metabolism=sum of chemical processes in living system catabolism=metabolism involved in energy generation anabolism= metabolism involved in biosynthesis What do cells need to grow ○ Minor and major elements( ex carbon, nitrogen, sulfur etc) and water ○ Energy: always from redox rxns ○ Reducing equivalents: [H+]= H+ + e- Carriers NAD+/NADH, NADP+/NADPH ○ Approx half of E colis games are required for metabolism Both energy (high energy phosphate bonds) and reducing equivalents are required for biosynthesis Classification system for microbes based on energy and carbon source