Micro ch 6

*Recall all cells need to accomplish 2 fundamental tasks to grow: must continually synthesize new parts which allow it to enlarge and divide PLUS they need to harvest energy and convert it to a form that can power the various reactions.

• Metabolism is the sum total of all chemical reactions in a cell
• separated into 2 components:
• Catabolism - "catapulting" and breaking compounds apart for energy
• Anabolism - Synthesizing and "rebuild"

• the set of processes that degrade compounds, releasing their energy
• Cells capture that energy and use it to make ATP in anabolism
• the process also produce precursor metabolites used in biosynthesis (anabolism)

• also called Biosynthesis
• the set of processes that cells use to synthesize and assemble the subunits of macromolecules, using ATP for energy
• Subunits of macromolecules include amino acids, nucleotides, and lipids
• *Uses the APT and precursor metabolites produced in catabolism

• the capacity to do work
• Can exist as: 
• Potential energy = stored energy
• Kinetic energy = energy of motion
• *Energy can never be created or destroyed; it can be changed from one form to another

• refers to organisms that harvest energy from sunlight, using it to power the synthesis of organic compounds from CO2
• By doing so, they convert the kinetic energy of photons (particles that travel at speed of light) to potential energy of chemical bonds

• refers to organisms that obtain energy by degrading organic compounds
• Thus, they depend on metabolic activities of photosynthetic organisms

a chemical reaction that releases energy because the starting compounds have more free energy than the products

chemical reaction that requires a net input of energy because the products have more free energy than the starting compounds

• the series of sequential chemical reactions that converts a starting compound to the end product
• Can be linear, branched, or cyclical
• Critical components include: enzymes, ATP, the chemical energy source and terminal electron acceptor, and electron carriers

• The intermediates and end products are sometimes organic acids, which are weak
• Depending on pH of environment, these occur as either undissociated or dissociated (ionized) form
• Names are often used interchangeably - ex: pyruvic acid and pyruvate (an ion)
• Can be made into glucose or fatty acid

• Proteins that function as biological catalysts, accelerating the conversion of one substance, the substrate, into another, the product
• Works by lowering activation energy
• W/o enzymes, energy-yielding reactions would still occur, but at rates so slow they would be insignificant
• *Enzymes are specific to their step

the energy it takes to start a reaction

• ATP
• the main energy currency of cells, serving as the ready and immediate donor of free energy
• Composed of ribose, adenine, and 3 phosphate groups arranged in tandem
• *Cells constantly produce ATP during exergonic reactions of catabolism and then use it to power endergonic reactions of anabolism

• ADP
• viewed as an acceptor of free energy
• *Cells produce "energy currency" by using energy to add an inorganic phosphate group (P_i)  to ADP, forming ATP

• Substrate-level phosphorylation
• Oxidative phosphorylation

• used by chemoorganotrophs
• Synthesis of ATP using the the energy released in an exergonic reaction (energy-releasing) during the breakdown of the energy source

Synthesis of ATP using the energy of a proton motive force created by harvesting chemical energy

• the form of energy that results from the electrochemical gradient established by the electron transport chain
• Recall H+ are outside cell, OH- are inside cell; they stay attracted to each other. Energy can be harvested when protons are allowed to move back into cell

• used by photosynthetic organisms to generate ATP
• uses the sun's radiant energy and an electron transport chain to create a proton motive force

• *Recall certain atoms are most electroneg than others (meaning they have a greater affinity or attraction for electrons).  Likewise, certain molecules have a greater affinity for electrons than other molecules
• When electrons move from a molecule that has a relatively low electron affinity (tends to give up electrons) to one that has a higher electron affinity (tends to accept electrons), energy is released
• This is how cells obtain energy to make ATP
• *The greater the difference btwn the electron affinities of the energy source and the terminal electron acceptor, the more energy released

refers to the chemical that serves as the electron donor

the chemical that ultimately accepts the electrons

• also called oxidation-reduction reactions
• Method in which cells remove electrons from an energy source
• *The substance that LOSES electrons is oxidized by the reaction
• *The substance that GAINS the electrons is reduced

• *When electrons are removed from a biological molecule, protons (H+) often follow. The result is that an electron-proton pair, or hydrogen atom, is removed.
• Thus, dehydrogenation (removal of a hydrogen atom) is an oxidation. The substance that loses electrons is oxidized by the reaction
• Hydrogenation (the addition of a hydrogen atom) is a reduction. The substance that gains the electrons is reduced
• *remember, electrons are neg. So more electrons will "reduce" charge more

• *When electrons are removed, not removed all at once nor directly moved to terminal electron acceptor.
• Instead it involves step-wise process with electrons initially transferred by carriers
• Also carry protons, can be considered hydrogen carriers
• Cells have different types of electron carriers, each with distinct roles
• Usually referred to by abb that represent their oxidized and reduced forms:
• Includes:
• NAD+/NADH
• NADP+/NADPH
• FAD/FADH₂ 

• Electron carrier
• Nicotinamide Adenine Dinucleotide
• Carries 2 electrons and 1 proton
• Used to generate a proton motive force that can drive ATP synthesis

• Electron carrier
• Flavin Adenine dinucleotide
• Carries 2 electrons and 2 protons (2 hydrogen atoms)
• Used to generate a proton motive force that can drive ATP synthesis

• Electron Carrier
• Nicotinamide adenine dinucleotide phosphate
• Carries 2 electrons and 1 proton
• Used for biosynthesis

• represented by reduced electron carriers because they can easily transfer their electrons to another chemical that has a higher affinity for electrons
• by doing so, they raise energy level of recipient molecule

cellular processes that synthesize and assemble the subunits of macromolecules, using ATP for energy

• intermediates of catabolic pathways which can be used in anabolic pathways
• serve as carbon skeletons from which subunits of macromolecules can be made

• important molecules like glucose and other cells can have different fates
• The molecules that remain on "the highway" are oxidized completely to CO2, releasing max energy
• Some breakdown intermediates, however, can "exit at an off ramp" to be used in biosynthesis
• "Off ramps" are located at steps immediately after a precursor metabolite is made
• So once a precursor metabolite is made in catabolism, can be further oxidized to release energy or used in biosynthesis

• The preferred energy source of many cells 
• Encompasses two key processes:
• 1) oxidizing glucose molecules to generate ATP, reducing power and precursor metabolites
• 2) transferring the electrons carried by NADH and FADH2 (reducing power) to the terminal electron acceptor
• Central metabolic pathways do former, respiration and fermentation do latter

• 3 Key metabolic pathways - the central metabolic pathways - gradually oxidize glucose to CO2 
• Pathways are catabolic, but precursor metabolites and reducing power generated can also be diverted for use in biosynthesis

• amphi meaning both kinds
• Reflects dual role of central metabolic pathways

• Together, these pathways produce ATP, reducing power, and intermediates that function as precursor metabolites
• Includes:
• Glycolysis
• Pentose phosphate pathway
• Tricarboxylic acid cycle (TCA cycle)

In prokaryotic cells, occurs in cytoplasm

In eukaryotic cells, the enzymes of glycolysis and pentose phosphate pathways are located in cytoplasm, whereas those of transition step & TCA are within mitochondrial matrix.Therefore, eukaryotic cells must transport pyruvate molecules into mitochondria for transition step to occur

• Splits glucose and gradually oxidizes it to form two molecules of pyruvate
• Provides the cell with:
• 2 ATP(net) by substrate-level phosphorylation
• 2 NADH + 2+ (reducing pwr)
• 6 precursor metabolites
• *Some microbial cells use an alternative series of reactions called the Entner-Doudoroff pathway

• Also breaks down glucose, but primary role in metabolism is the production of compounds used in biosynthesis, including: 
• NADPH + H+
• 2 precursor metabolites
• Product of the pathway feeds into glycolysis

• Tricarboxylic acid cycle
• As prelude, a single reaction called the transition step converts the pyruvate from glycolysis into acetyl-CoA
• The TCA cycle then accepts the 2-carbon acetyl group, oxidizing it to release 2 molecules of CO2
• Together, these two steps generate most reducing power of all central metabolic pathways

• repeated twice to oxidize two molecules of pyruvate to acetyl-CoA, generates:
• 2 NADH + 2 H+ (reducing power)
• 1 precursor metabolite

• repeated twice to incorporate two acetyl groups, generates:
• 2 ATP by substrate-level phophorylation
• 6 NADH + 6H+ (reducing power)
• 2 FADH2
• Two different precursor metabolites

• A relatively small amount of ATP is made by substrate-level phosphorylation
• The reducing power accumulated during the oxidation steps, however, can be used to generate ATP by oxidative phosphorylation

• transfers the electrons extracted from glucose to the electron transport chain, which then uses electrons to generate a proton motive force
• Includes aerobic respiration and anaerobic respiration

• O2 serves as the terminal electron acceptor
• Uses the electron transport chain
• ATP generated:
• 1) 2 in glycolysis (net), 2 in TCA cycle = 4 total
• 2) 34
• 3) 38

• Molecule OTHER THAN O2 used as terminal electron acceptor (such as nitrate or sulfate)
• Uses electron transport chain
• ATP Generated: Numbers varies; however, the ATP yield is less than that of aerobic respiration but more than fermentation

• *cells that don't respire are limited by inability to recycle reduced electron carriers. If not reduced, none will be able to accept electrons = no more glucose can be broken down. Fermentation provides a solution
• Cells break down glucose through glycolysis only and then use pyruvate or a derivative as a terminal electron acceptor
• By transferring the electrons carried by NADH to pyruvate or a derivative, NAS is regenerated
• Does NOT use electron transport chain
• Does NOT use TCA cycle
• ATP generated: via substrate-level phosphorylation 2 in glycolysis (net), via oxidative phosph 0, totaling 2 ATP

Those that cannot respire, either because a suitable inorganic terminal electron acceptor is not available or because they lack an electron transport chain

• place on enzymes surface, typically a relatively small crevice
• Critical site to which substrate binds by weak forces
• causes shape of flexible enzyme to change slightly
• After reaction, products (substrate) is released, leaving enzyme unchanged and free to combine with new substrate molecules

• A non-protein component that assists some enzymes
• Magnesium, zinc, copper and other trace elements often function as cofactors

• Organic cofactors that function as loosely bound carriers of molecules or electrons
• Include the electron carriers FAD, NAD, and NADP
• Transfer substances from one compound to another, but in different ways.
• Most are derived from vitamins
• *Most prokaryotes can synthesize these vitamins; humans and animals must ingest

• Nicotinamide adenine dinucleotide
• Is a coenzyme derived from Niacin
• Transfers hydride ions (2 elect and 1 prot)
• Carrier of reducing pwer

• Flavin adenine dinucleotide
• Is a coenzyme derived from Riboflavin
• Transfers hydrogen atoms (2 e & 2 p)
• Carrier of reducing power

• Coenzyme A
• Derived from Pantothenic acid
• Transferred from Acyl groups
• Carries the acetyl group that enters the TCA cycle

• Is a coenzyme
• Derived from Thiamine
• Transfers Aldehydes
• Helps remove CO2 from pyruvate in the transition step

• Coenzyme derived from Pyridoxine
• Transfers Amino groups in amino acid synthesis

• Coenzyme derived from folic acid
• Transfers 1-carbon molecules
• Ex: 1 carbon donor in nucleotide synthesis

• Each enzyme has narrow range of conconditions - including temp, pH, and salt concentration
• Most enzymes operate best at low sat and pH values slightly above 7

• allo mean other, stereos means shape
• Refers to enzymes that can be controlled to regulate activity in metabolic activity
• They have an allosteric site as well as a active site
• When a regulatory molecule binds to allosteric site, changes enzyme shape.
• Alters relative affinity of enzyme for it's substrate... it can increase or decrease affinity
• Either way, the substrate cannot fit in it's usual spot due to change in shape of enzyme

• refers to allosteric enzymes 
• A mechanism in a biosynthetic pathway in which the end product generally acts as the allosteric inhibitor
• Allows the cell to shut down a pathway when product begins accumulating

• Enzymes can be inhibited by a variety of compounds other than regulatory
• Includes competitive inhibition and noncompetitive inhibition

• Inhibitor binds to the active site of the enzyme, blocking access of the substrate to the site
• Ex: Sulfa drugs are competitive inhibitors that are used as antibacterial meds

• Recall inhibitor changes shape of enzyme so substrate can no longer bind
• Is a reversible action

• Inhibitor permanently changes the shape of the enzyme, making the enzyme nonfunctional
• Inhibitor binds to a site other than active site, changing shape permanently 
• Enzyme poisons such as mercury are used in certain antimicrobial compounds

• Investment or preparatory phase consumes energy as 2 different steps each transfer high-energy phosph group to 6-carbon sugar. The 6 carbon sugar is then split to yield two 3-carbon molecules, each w phosphate molecule
• *Eukaryotic cells, both phos come from ATP
• *Bacteria, first one added as glucose is transported into cell via group translocation; next from ATP
• Pay-off phase oxidizes and rearranges 3-carbon molecules, generating 1 NADH & 2 ATP in process & ultimately pyruvate.
• *The steps occur twice for each molecule of glucose that enters glycolysis, as 6-carbon molecule split into 3-carbon in previous phase

• Is particularly important due to contribution to biosynthesis
• Generates:
• NADPH = reducing power in varied amt
• 2 intermediate precursor
• G3P (Glyceraldehyde 3-phosphate) is a product, which can enter a step in glycolysis for further breakdown

Links the previous pathways (Glycolysis & Pentose Phosphate pathway) to TCA cycle

• *The is the mechanism used by respiration to synthesize ATP
• Involves 2 sequential processes:
• 1- the electron transport chain generates a proton motive force
• 2- The enzyme ATP synthase uses the energy of the proton motive force to drive the synthesis of ATP

• A hypothesis developed by Peter Mitchell in 1961 that proposed the remarkable process which links the electron transport chain to ATP synthesis
• Later received Nobel Prize

A group of membrane-embedded electron carriers that pass sequentially from one to another, ejecting protons in the process

• In prokaryotes, the electron transport chain is located in the cytoplasmic membrane
• In eukaryotic cells it is in the inner membrane of the mitochondria

• Because of order of different carriers in ETC and relative affinities for electrons, energy is gradually released as electrons are passed from one carrier to another (much like a ball falling down flight of stairs)
• The energy release is coupled to the ejection of protons, moving them from the inside of the cell to the outside or, in the case of mitochondria, from the matrix to region btwn inner & outer membrane
• This ejection of protons creates a proton gradient - an electrochemical gradient - across membrane.
• Energy of the gradient, proton motive force, is then harvested by the cell to synthesize ATP

• Important characteristic of electron carriers is some accept only hydrogen atoms (proton-electron pairs), whereas others accept only electrons
• When a hydrogen carrier passes electrons to a carrier that accepts electrons, but not protons, the protons are released to the outside of cell (or intermembrane space of mitochondria)
• Net effect is components of ETC pump protons from one side of membrane to other, establishing concentration gradient across membrane

• quinones
• cytochromes
• flavoproteins

• Has 4 different protein complexes, 3 of which are proton pumps.
• In addition, 2 electron carriers shuttle electrons btwn complexes:
• Complex I
• Complex II
• Complex III
• Complex IV

• In ETC of Mitochondria
• also called NADH dehydrogenase complex
• Accepts electrons from NADH, ultimately transferring them to Ubiquinone (Coenzyme Q)
• In process, 4 protons are moved across membrane

• Also called succinate dehydrogenase complex
• Accepts electrons from TCA cycle, when FADH2 is formed during oxidation of succinate
• *note electrons carried by FADH2 enter ETC "downstream" of those carried by NADH. Because of this, a pair of electrons carried by NADH result in more protons being expelled than does a pair carried by FADH2
• Electrons are then transferred from complex II to ubiquinone

• also called cytochrome complex 
• accepts electrons from ubiquinone, which has carried them from either complex I or II
• Pumps 4 protons across membrane before transferring the electrons to cytochrome c

• also called cytochrome c oxidase complex
• accepts electrons from cytochrome c and pumps two protons across membrane
• Terminal oxidoreductase, meaning it transfers the electrons to the terminal electron acceptor ( O2)

• There are many types and arrangements so it varies among different species
• Some processes can use molecules other than O2 (anaerobic), but harvests less energy than aerobic

• When growing aerobically in glucose-containing medium, E coli uses 2 different NADH dehydrogenases:
• A proton pump functionally equivalent to complex I
• A succinate dehydrogenase functionally equivalent to complex II

Ecoli can also produce other alternatives. Although doesn't have equivalent of complex III or cytochrome c, quinones shuttle electrons directly to 1 or 2 variations of ubiquinol oxidase, which is equivalent to complex IV

• Works optimally in high o2 and expels 4 protons
• The other ejects only 2 (?)

Enzyme ATP synthase uses energy of proton motive force to synthesize ATP by allowing protons to flow back into cell (or matrix of mitochondria) in controlled manner, simultaneously using the energy released to add a phosphate group to ADP

*One molecule of ATP is formed from the entry of approx 3 protons

• Lactic acid
• Ethanol
• Butyric acid
• Propionic acid
• Mixed acid
• 2, 3-Butanediol

*Lynette probably manipulated everyone 2, bitch.

• Produced when pyruvate itself acts as terminal electron acceptor
• Creates texture and flavor of cheese, pickles, cured sausages and other foods
• Also causes food spoilage and tooth decay

Ex: Streptococcus, Lactobacillus

• Produced when CO2 removed from pyruvate, generating acetaldehyde when becomes the electron acceptor
• Makes beer, wine, bread
• Also important biofuel

Ex: Saccharomyces

• produced by Clostridium species, which are obligate anaerobes
• Produces organic solvents butanol and actone

• generated by adding CO2 to pyruvate, making a compound to act as terminal electron acceptor
• After NADH reduces it, further reduced to propionate
• Makes swiss cheese

• Polysaccharides
• Proteins
• Lipids

Amylases: enzymes made by a wide variety of organism to digest starch

Cellulases: Produced by relatively few organisms, enzyme which breaks down cellulose

Lipases: enzymes that hydrolyze fats

Proteases: enzymes that hydrolyze proteins

organisms that obtain energy by oxidizing reduced inorganic chemicals such as hydrogen gas (H2)

• Hydrogen bacteria: oxidize hydrogen gas
• Sulfur bacteria: oxidize hydrogen sulfide
• Iron bacteria: oxidize reduced forms of iron
• Nitrifying bacteria: includes 2 groups= one oxidizes ammonia (forming nitrite); the other oxidizes nitrite (producing nitrate)

• They extract electrons from inorganic energy sources, passing them to an electron transport chain that generates a proton motive force
• The energy of this gradient is then harvested to make ATP

• the capture and subsequent conversion of radiant energy into chemical energy
• Generally considered in two distinct stages:
• Light-dependent reactions
• Light-INdependent reactions

• Light reactions: also called light-dependent reactions
• capture radiant energy and convert it to chemical energy in the form of ATP

• Light-Independent reactions: also called light-independent reactions
• uses the ATP to synthesize organic compounds
• Involves carbon fixation, which converts CO2 into organic compounds

• Protein complexes within photosynthetic membranes
• Specialize in capturing and using the energy of light
• Includes Chlorophylls, Bacteriochlorophylls, and accessory pigments

• found in plants, algae, and cyanobacteria
• various types are designated with a letter following the term
• Ex: chlorophyll a.

• found in anoxygenic photosynthetic bacteria
• Absorb wavelengths not absorbed by chlorophylls, allowing bacteria to grow in habitats where other photosynthetic organisms cant

• increase the efficiency of light capture by absorbing wavelengths not absorbed by the other pigments
• include caroteniods and phycobilins

• electron donors in the photosynthetic process
• When exited by radiant energy, these emit high-energy electrons, which are then passed to electron transport chain similar to respiration

make up a complex that acts as a funnel, capturing the energy of light and then transferring it to the reaction-center pigment

• to accomplish 2 tasks:
• Use radiant energy to fuel ATP synthesis (photophosphorylation)
• Need to generate reducing power to fix CO2

*Depending on method used to fix CO2, type of reducing power required may be either NADPH or NADH

Radiant energy captured by photosynthetic pigments excited the reaction-center chlorophyll, causing it to emit a high energy electron, which is then passed to electron transport chain

• *Two distinct photosystems used by cyanobacteria and chloroplasts
• the sequential absorption of energy by the two allows process to raise the energy of electrons stripped from water to a high enough level to be used to generate a proton motive force as well as produce reducing power
• Process is organic, which generates O2

• Used when cells need to synthesize ATP but not reducing power (NADPH)
• radiant energy is absorbed, the reaction-center chlorophylls emit high-energy electrons which are passed to electron carrier, which then transports them to proton pump (similar to complex III in mitochondria)
• After being used to move protons across membrane, electrons returned to photosystem I (cyclic photophosphorylation)

• Refers to electrons that have followed a cyclical path
• the molecule that serves at the electron donor is also the terminal electron acceptor

• Used when photosynthetic cells must produce both ATP and reducing power
• *The electrons emitted by photosystem I ARE NOT passed to the proton pump but instead reduce NADP+ to NADPH

• *Although this provides reducing power, cell must now use another source to replenish electrons emitted by reaction-center chlorophyll. Cell also still needs to generate proton motive force 
• This is where photosystem II comes in

• When it absorbs radiant energy, the reaction-center chlorophylls emit high energy electrons that can be donated to photosystem I
• Emitted electrons are replenished from extracting electrons from water & donating them to reaction-center chlorophyll
• Removal of electrons from 2 molecules of water generates O2

• Only have single photosystem, can't use water as electron donor for reducing power
• These bacteria use electron donors such as hydrogen gas (H2), hydrogen sulfide (H2S) and organic compounds
• Ex: Purple & green bacteria

synthesize ATP using photosystem similar to photosystem II; however, they use reversed electron transport , expending ATP to run the electron transport chain in the reverse direction

• have photosystem similar to photosystem I
• Electrons emitted can generate a proton motive force or reduce NAD+

Used by chemolithoautotrophs and photoautotrophs to use carbon dioxide (CO2) to synthesize organic compounds

Calvin Cycle

• also called Calvin cycle
• Process has 6 "turns" in the cycle
• has 3 essential stages:
• Incorporation of CO2 into an organic compound
• reduction of the resulting molecule
• regeneration of the starting compound

• One molecule of the 6 carbon sugar fructose can be generated for every 6 turns of the cycle
• Consumes 18 ATP and 12 NADPH+ & H+

• The fatty acid components of fat are synthesized by progressively adding 2-carbon units to an acetyl group
• The glycerol component is synthesized from dihydroxyacetone phosphate

• Proteins are composed of various combos of usually 20 different amino acids
• Important ones are glutamate and aromatic

• Synthesis of glutamate is essential as it provides a mechanism for cells to incorporate nitrogen into organic molecules
• Synthesized in single step reaction that adds ammonia to precursor metabolite α-ketoglutarate, produced in the TCA cycle

• Requires multistep branching pathway
• Allosteric enzymes regulate key steps of the pathway

Purines (double-ring) and pyrimidine (single ring) nucleotides are made in distinctly different manners

But who really cares