1) active site has affinity for substrate, which will bind specifically

2) once bound in active site, substrate forced to adopt conformation that increases likelihood it will react

3) products released & enzyme is free for 'use' in another cycle

redox rxns
-purpose

-oxidation v reduction

-provide E for all cell growth; E released from these reactions is conserved in synthesis of E-rich compounds like ATP

-oxidation: loss of electron from atom/molecule; compound being oxidized is DONOR

-reduction: gain of electron by atom/molecule; compound being reduced is ACCEPTOR

-electrons go down tower

-electrons are donated from redox couples above & are accepted by redox couples below

-electrons always donated by reduced form

-molecule/compound on LEFT is reduced/receives electron & molecule/compound on RIGHT is oxidized/donates electron

-neg values on top of tower

-farther electron drops from donor to acceptor, greater E released

-oxygen is strongest naturally-occuring e- acceptor

-couples in middle can be acceptors OR donators, depending on w/ whom they're reacting

electron carriers

-purpose

-2 types

-carry 1 or 2 electrons at time, transfer electrons by interacting w/ proteins or enzymes

-2 types: freely diffusible (coenzymes) & covalently attached to enzymes in cytoplasmic membrane (prosthetic group)

NAD+/NADH recycling

-2 types of reactions

-reaction 1: enzyme 1 reacts w/ electron donor & oxidized form of coenzyme NAD+ (NAD+ becomes NADH)

-reaction 2: enzyme 2 reacts w/ electron acceptor & reduced form of coenzyme NADH (NADH becomes NAD+)

high energy bonds & E-rich compounds

-3 characteristics

-2 types of phosphate bonds

-E released from redox rxns is conserved in form of E-rich compounds, often phosphorylated compounds

-these compounds are then used by cells to power E-consuming functions

-phosphate can be bound to organic compound in 2 ways:

1) acid anhydride bond--2 acyl groups bound to same oxygen

2) ester bond

-hydrolysis of thioester bond releases enough energy for ATP synthesis

-coenzyme A derivatives are particularly important for energetics of fermenting organisms

catabolism: chem. rxns that are degradative & regarded as C-consuming & E-generating

fermentation: growth substrate serves as electron donor & cellular organic compound serves as electron acceptor in redox reactions that provide energy for ATP production by substrate-level phosphorylation
*DOESN'T CONSUME OXYGEN*

sugar catabolism, GLYCOLYSIS

-2 stages

-characteristics

stage 1: preparatory rxns, E investment to be recovered later

stage 2: making ATP & pyruvate

-doesn't require oxygen; takes place in anaerobes & aerobes

-found in many organisms

-splits glucose (6 C) into pyruvate (3 C)

-produces 2 ATP

-low energy yield compared to respiration

E-D pathway:
glucose --> 2 pyruvate + 1 NADH + 2 ATP

pentose-phosphate pathway:

glucose --> CO2 + 5/3 pyruvate + 1 NADPH + 5/3 NADH + 5/3 ATP

process of fermentation

3 steps

-characteristics

1) organic compound is e- donor

2) electron flow goes from initial electron donor to NADH & finally to reduced organic compound produced by reduction of intermediary metabolite

3) ATP is produced from catabolism & is consumed for cell synthesis

-anaerobic process but can also take place in aerobic conditions

-involves no membranes

-has low E yield

ethanol fermentation

2 pyruvate + 2 NADH --> 2 ethanol + 2 CO2 + 2 NAD+

TOTAL: glucose --> 2 ethanol + 2 CO2 (hetero fermentation)

lactic acid fermentation

2 pyruvate + 2 NADH --> 2 lactate + 2 NAD+

TOTAL: glucose --> 2 lactate (homo fermentation)

mixed acid fermentation

-Which pathways produce/recycle which product(s)?

pyruvate --> acetate
produces ATP

pyruvate --> ethanol
produces 2 NAD+

pyruvate --> formate

requires NAD+, produces NADH

pyruvate --> lactate

produces NAD+

pyruvate --> succinate

produces 2 NAD+

butanol-acetone fermentations

-uses

-some Clostridium species can produce solvents

-first world war: acetone needed to make cordite for ammunition

-automobile production: solvent needed for car paint, butanol is perfect precursor for butyl acetate production

-present interest: butanol as biofuel--has close properties to gasoline, can be direct replacement for gasoline in conventional vehicles

calculating efficiency of yeast ethanol fermentation

-steps

1) calculate total E released by rxn (free energy in kJ/mol)

delta G = delta G0 of products - delta G0 of reactants

2) calculate overall efficiency

efficiency = 100 x energy in ATP generated (2 ATP, so 2 x -32)

energy available

Stickland reaction (redox reaction)

-characteristics

-produces?

coupled amino acid fermentation

-1 amino acid (alanine) is e- donor

-other amino acid (glycine) is e- acceptor

-other amino acids can be catabolized in these types of fermentations

-produces 3 ATP & acetate

-2 substrates required (A & B)

-substrate A is oxidized to P

-substrate B is reduced to Q

-electron transfer reactions drive ATP synthesis by oxidative phosphorylation

1) oxidation of initial electron donor & NADH production

2) membrane-associated electron transport chain reoxidizes NADH & pumps protons outside cell

3) proton transport back into cell by ATP synthase drives ATP production

-glucose is completely oxidized to CO2 through glycolysis & citric acid cycle

-as carbons are oxidized, NAD+ is reduced to NADH

-during this process some energy is generated by substrate-level phosphorylation but most E is generated by oxidative phosphorylation

-CAC only active in respiratory conditions

citric acid cycle

-reactants & products

-electron carriers in ETC are all associated w/ membrane

-electrons entering ETC travel from most negative potential to most positive

-e- carriers that transfer both e- & H+ alternate w/ carriers that transfer e- only

-this alternance b/w carriers forces protons out of cell

-protons come from NADH & from H2O disassociate into H+ & OH-

-PMF has 2 components: pH gradient & electrochemical gradient

2 types of electron carriers involved in respiration

1) flavines

2) quinones

1) flavines--covalently attached to protein called flavoprotein

(3 adjacent hexagons)

2) diffuse freely in membrane

(one hexagon w/ many attachments)

-covalently attached to proteins

-iron-sulflur clusters in iron-sulfur proteins

-hemes in heme-containing proteins (cytochromes)

-contains flavoproteins & other iron-sulfur proteins

-FMN binds 2 electrons & 2 H+ coming in from NADH

-FMN transfers e- to successive Fe/S proteins in complex

-E gained from 2 electrons transferred from FMN to successive Fe/S proteins is used to extrude 4 H+ outside membrane

quinones carry 2 e- & 2 H+

-2 e- carried by Fe/S proteins are transferred to quinone

-b/c Fe/S protein doesn't transfer H+,  2 H+ loaded onto quinone w/ 2 e- come from dissociation of water

-reduced quinone moves to complex III where it gives 2 e- & extrudes 2 H+ outside membrane

contains cytochromes & Fe/S protein

-2 e- from QH2 are transferred to Fe/S protein

-Fe/S protein transfers  2 e- one @ time to cytochrome c, soluble protein on surface of membrane

-cytochrome c finally transfers e- to complex IV

-E from 2 e- transfer is used to extrude 2 H+ outside membrane

-complex IV uses e- to reduce oxygen to water (2 H+ are consumed in this last step)

1) movement of protons through subunit makes subunits rotate

2) torsion of subunits make beta subunits change conformation

3) release of conformational strain provides enough E for ATP synthesis

4) 3-4 protons translocate to produce 1 ATP

glycolysis: 8 ATP

CAC: 15 ATP (x 2)

total: 38 ATP/glucose

1) chemoorganotrophic respiration: org. compound is oxidized & electrons are transferred to oxygen or other acceptor

2) chemolithotrophic respiration: inorg. compound is oxidized & electrons transferred to oxygen or other acceptor

-in absence of oxygen, other e- acceptors can be used

-b/c these e- acceptors have redox potentials less positive than O2/H2O, less E is released when they're used

-anerobic respiration also uses electron transport systems

-e- acceptors can be org. molecules

*ones at bottom of arrow/chart are e- acceptors!*

assimilative

-when org. compounds are reduced by microorganisms as sources of cellular nitrogen, sulfur, or carbon

-only enough nitrate, sulfate, or CO2 is reduced for biosynthetic needs & product is all assimilated

-many organisms prefer assimilative metabolism

dissimilative

-use of inorg. compounds as e- acceptors in anaerobic respiration

-large amt. of electron acceptor is reduced & product is released in environment

-fewer organisms can carry out dissimilative respiration

-sulfate is most oxidized form of sulfur

-dissimilative: H2S secreted from cell

-APS reduced to sulfite w/ release of AMP

-assimilative: H2S used to build sulfur org. compounds

-second ATP is added to APS to form PAPS, PAPS then reduced to sulfite

-CO2 is electron acceptor, H2 often donor

-uses acetyl-CoA pathway w/ cofactor tetrahydrofolate

-one CO2 is reduced to CH3, other reduced to CO, then combined

-last step, catalyzed by acetyl-CoA synthase complex, is associated w/ NA+  or H+ extrusion outside cell --> creation of Na+/H+ motive force for ATP synthesis

-actogens might grow on glucose as C source & produce 3 acetate molecules: 2 from pyruvate & 1 from 2 CO2 molecules generated by pyruvate-ferredoxin oxidoreductase (that formed 2 acetyl-CoA from pyruvate)

-carried out in 2 domains of life (archaea & eukaryotes)

-requires light-sensitive pigments (chlorophylls)

-involves 2 sets of rxns: ATP production & CO2 reduction to cell material

-some archaea use light to produce E & are autotrophs, but no chlorophyll or bacteriochlorphyll involved

-protein bacteriorhodopsin is conjugated w/ retinal

2 phylogenetically-distinct groups (sulfur & non-sulfur); gram-negative, carry out anoxygenic photosynthesis, & most possess chlorosomes w/ non-unit membranes, they have most efficient photosynthetic antenna complexes

-green sulfur bacteria often have sulfur granules in or attaches to cell

oxygenic: yields O2 (cyanobacteria & algae)

anoxygenic: yields oxidized sulfur, but some also oxidize H2 or organic compounds

-diff. organisms contain diff. chlorophylls or bacteriochlorophylls & various accesory pigments

-chlorophylls are associated w/ photosynthetic membranes

-diff. chlorophylls & diff. accessory pigments absorb diff. types of light

-diff. organisms can co-exist w/ less competition for light energy

-porphyrin ring containing Mg

It absorbs red & blue lights & transmits green light.

-chlorophyll associated w/ oxygenic photosynthesis

-bacteriochlorophyll associated w/ anoxygenic photosynthesis

-carotenoids are present in all photosynthetic organisms

-function primarily in photoprotection, can increase efficiency of light harvesting

-alternating double bonds of long, hydrocarbon chains

-membrane-bound

-large variety of carotenoids in bacteria

-present only in cyanobacteria & red algae

-function in light harvesting

-open-chain tetrapyrroles (phycobilins) attached to proteins

-most abundant phycobilins: phycoerythrin (PE, red), phycocyanin (PE, blue), & allophycocyanin (PA)

-commercial importance: purified from algae & used as non-toxic, non-carcinogenic dyes

-light E converts weak e- donor into strong e- donor

-e- released by P870, travels down e- tower

-protons are extruded through membrane & create PMF

-electrons go back to P870 // cyclic e- flow

-PMF used to drive ATP synthesis --> cyclic photophosphorylation

-in purple bacteria, some NADH is made using e- from donors like H2S

photosystem II

-chlorophyll P680, potential more positive than O2/H2O, allows splitting of water

-light converts reduced P680 into e- donor, P680*

-e- transported through non-cyclic ETC to photosystem I, creating PMF

photosystem I

-clorophyll P700, potential is less positive than O2/H2O, doesn't accept e- from water

-light converts reduced P700 into strong e- donor

-electrons are transported through carriers to drive ATP synthesis (PMF) or to produce NAD(P)H

-e- used to make NAD(P)H are replaced by PS II

-CO2 fixation in photosynthetic organisms

-Calvin Cycle in cyanobacteria, algae, plants, some purple bacteria, some archaea

-Calvin Cycle requires ATP, NADPH, & 2 specific enzymes

-reverse CAC in purple bacteria & green sulfur bacteria

-hydroxypropionate pathway in green non-sulfur bacteria

6 CO2 + 12 NADPH + 18 ATP --> fructose-6P + 12 NADP+ + 18 ADP + 18 Pi

fermentation: low E yield, enough available for growth, can exist in anaerobic environment, only mechanisms available to some organisms like lactic acid fermenters

anaerobic respiration: more E than fermentation, requires specialized pathways

aerobic respiration: most E comes from respiration using oxygen

photosynthesis: high E yield, not many microbes have this ability

2 major phyla of archaea:
crenarchaeota

euryarchaeota

crenarchaeota--contain both hyperthermophiles & cold-dwelling organisms

euryarchaeota--contain hyperthermophiles, extreme halophiles, & methanogens

-Alessandro Volta showed that bubbles emanating from agitated lake bottoms are flammable

-Carl Woese accumulated evidence from 16S rRNA sequences that life is divided into 3 domains

-originally not accepted by population, now widely accepted

-chemolithotrophs, chemoorganotrophs--aerobic & anaerobic respiration, fermentation

-phototrophs use light to make ATP

-some produce methane

-proteins have to be stable & active @ high temperatures

-their 3-D structures & amino acid contents are similar to those of mesophilic proteins

HOW IS IT DONE?

-highly hydrophobic core

-more salt bridges on protein surface

-shorter surface loops

-high salt & compatible solute cxns

-reverse DNA gyrase

-DNA-binding proteins wind DNA into compact structures

-DNA from hyperthermophiles don't have higher CG contents than DNA from other organisms

-16s rRNAs have up to 15% more GC pairs compared to other organisms

life at high salt concentrations

salt-in strategy

salt-in strategy
-intracellular ionic cxns are similar to those of surrounding medium

-intracellular ionic composition are diff. than those of surrounding medium

enzymes & structural cell components are adapted to presence of high salt

-ion pumps Na+ out of cell & K+ in

-stabilization of cell components: extracellular Na+ stabilizes glycoproteins of cell wall, intracellular K+ stabilizes proteins & ribosomes

-DNA contains > 60% GC

-extreme halophilic archaea called haloarchaea

-most are photoheterotrophs = gain E from light, but get C from organic molecules

-most haloarchaea are obligate anaerobes

-retinal: carotenoid conjugated to bacteriorhodopsin

-upon excitation by light, retinal changes from trans to cis configuration

-this change is coupled to proton translocation through membrane

-PMF used by ATP synthase

-PMF also used to pump out Na+

-oxygenic phototroph

-anoxygenic phototrophic purple bacteria

-only carried out by strictly anaerobic archaea called methanogens

-methane production from CO2, acetate, or methanol

-CO2 + 4 H2 --> CH4 + 2 H2O

-acetate --> CH4 + CO2

-methanogenesis creates PMF that fuels ATP production

-strictly anaerobic processes

-use unusual coenzymes

-methanogens are mostly autotrophs, using acetyl-CoA pathway for biosynthesis

cold-dwelling

-represent up to 40% of prokaryotes in deep ocean waters

-fix CO2 // likely to play major role in global C cycle

-oxidize ammonia to nitrite (nitrification), provide major source of nitrite for marine photoplankton (imp. role in ocean's N cycle)

-some form symbioses w/ marine mammals

-dual membrane-enclosed nucleus is defining organelle of eukaryotes

-other membrane-enclosed organelles (mitochondrian, golgi apparatus, e.r., chloroplasts...)

-both contain small genomes of circular DNA

-can only be replicated from pre-existing mitochondria & chloroplasts

-some eukaryotic chromosomes contain bacterial genes

-encode their own bacterial-type ribosomes

-sensitive to several antibiotics specific to bacteria

-16S rRNA analysis shows phylogenetic relationship to bacteria

protists: unicellular & colonial microbial eukaryotes other than fungi

protozoa: unicellular heterotrophic protists

reductive evolution: group initially defined by possession of trait, often includes members that have lost trait

convergent evolution: superficially-similar forms of organisms have evolved independently in distantly-related groups

-chlorophyll-containing organelle found in phototrophic eukaryotes

-flattened membrane discs called thylakoids

-lumen of chloroplast called stroma

-stroma contains large amts of rubisco

-rubisco is key enzyme in Calvin Cycle

-cell walls contain chitin

-achlorophyllous chemoorganotrophs, mostly aerobes

-eukaryotes most closely-related to animals

-commonly filamentous, some unicellular, some differentiate into mushrooms

-roles in nature: players in decomposition & mineralization of organic carbon, many parasites of plants & animals, major source of food spoilage

-mostly terrestrial, dominate microbial biomass in soil

-absorptive nutrition: secrete digestive enzymes & absorb broken-down molecules from environment

glomeromycetes: small group w/ major ecological importance, form symbiosis w/ most terrestrial plant roots, enhance nutrient uptake

ascomycetes: form spores in sac

basidiomycetes: form spores in basidium ('little pedestal'), most form large fruiting bodies

mushrooms: macroscopic sexual spore-bearing structures of Basidiomycetes, some edible, others poisonous

Penicillium species: cheese-making, antibiotic production

unicellular yeasts: grow by budding division, mother cell covered w/ bud scars

-evolutionarily distinct from cyanobacteria & brown algae

-photoautotrophs: E from light, oxygenic photosynthesis, CO2 fixation through Calvin Cycle

-2 membranes surround chloroplast

-contain chlorophyll a in chloroplasts

-unicellular, filamentous, & colonial forms

-green algae have chlorophylls, but not phycobilins; red algae have chlorophylls & phycobilin phycoerythrin (allows red algae to absorb blue & green lights), can grow in deeper waters

-several red algae species are edible (used for sushi)

-red algae contain valuable polymers called sulfated polygalactans

diatoms & kelps (secondary endosymbiotic algae)

-2 distinguishing traits: 2+ membranes surround chloroplasts & secondary endosymbiotic algae have both phototrophic & heterotrophic metabolisms (mixotrophic metabolism)

diatoms:

-unicellular, marine, & freshwater phototrophic organisms

-crush-resistant cell wall of silica

-conduct 1/5 of all photosynthesis on Earth & produce as much biomass as rain forests

-frustules of dead diatoms form thick sedimental rocks called diatomaceous earth--many uses in everyday life

kelps:

-contain vacuoles of leucocin, oily lipid used as E storage (gives colour to brown algae)

-kelp forests float thanks to gas vacuoles

euglenids:

-non-pathogenic, combine phototrophy  & heterotrophy

-live exclusively in aquatic habitat

kinetoplastids:

-have kinetoplast (mass of DNA in their single mitochondria)

-free-living or animal parasites

dinoflagellates
-2 flagella around cells make them spin

-marine & freshwater phototrophic organisms

-secondary or tertiary endosymbiants

-free-living or in symbiosis w/ animals in coral reefs

-can cause poisonous red tides which release toxins that kill fish & shellfish (human poisoning by neurotoxins)

apicomplexa
-all have 'apical complex' of microtubules @ one end of cell

-obligate parasites of animals

cercozoans:

-move & feed through pseudopods

-foraminifers--produce shells made of calcium carbonate

-radiolaria--produce shells made of silica

-foraminifers & radiolara form large part of reef formations, sedimentary rocks, & beach sand

amoebozoa:

-terrestrial & aquatic protists, use pseudopods to move & feed

-can be free-living in aquatic & soil environments or parasites of animals

cellular slime molds

-vegetative state: individual haploid cells w/ amoebid motility

-when starved, haploid cells aggregate & produce slug

-slug differentiates into stalk-&-head fruiting body

-cells in head differentiate into spores

-mature spores are dispersed by wind & germinate into vegetative amoeba

diploid sexual process:

-Dictyostelium can also produce sexual spores

-2 amoeba conjugate

-resulting diploid cell surrounds itself w/ cellulose & can remain dormant (macrocyst)

-macrocyst then undergoes meiosis to form new haploid amoebas

1) often found growing on rocks, trees, or other surfaces

2) lichens are examples of mutualism (coexistence of 2 organisms  that benefit each other)

3) lichens consist of fungus & phototrophic partner (alga or cyanobacterium) w/ chlorophyll & carotenoid pigments

4) phototroph is primary producer & fungus provides anchor & protection from element