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Chapter 8-9 (Life is Work Living cells require transfusions of energy…

- - - - Step 2: Remaining 2-carbon fragments is oxidized and the electron transfer to NAD+, storing energy; NADH.
      - Step 3: Coenzymes (CoA) - sulfur compound derived from B vitamin, attached via sulfur atom to 2-carbon intermediate - making Acetyl CoA.
        
        High potential energy, highly exergonic.
      - Step 1: Pyruvate's Carboxyl somewhat oxidized and carry little chemical energy - 1st step when CO2 is released.
    - - Step 5: directly produces ATP because the substrate’s link to Coenzyme A is sufficiently energetic to power the reaction. In mitochondria, the enzyme links to the Succinyl–CoA and uses the energy from releasing the coenzyme, to add a phosphate (P) to GDP to produce GTP. In the cytoplasm, a variation on this enzyme can produce ATP directly. This also begins the manipulation of the substrate to re-produce its original form.
      - Step 4: a highly-developed complex of 24 enzymes. Labeled here α–Ketoglutarate dehydrogenase, this complex transfers also electrons to NAD+producing NADH, removes another carbon atom as carbon dioxide (transforming the substrate from a 5-carbon to a 4-carbon molecule), and relinks the Coenzyme A to the substrate.
      - Step 3: With the citrate rearranged, the process begins in earnest; the Isocitrate dehydrogenase links to the D–Isocitrate, which transfers an electron to the NAD+, Nicotinamide adenine dinucleotide, producing its energized form NADH. With the electron removed, the enzyme then detaches a carbon atom to form a molecule of carbon dioxide. This transforms the substrate from a 6-carbon molecule to a 5-carbon molecule.
      - Step 6: With the carbons removed, the rearrangement process begins manipulating the hydrogen. When the Succinate dehydrogenase links to the substrate, it releases two hydrogen atoms attaching them to a carrier, ubiquinone (Q), or FAD Flavin adenine dinucleotide. With the additional 2 electrons ubiquinone forms ubiquinol (QH2 or FADH2) which is then transferred to power the electron transport chain.
      - Step 1: put energy into the system. The Citrate synthase links to the Oxaloacetate substrate which can then bind to the Acetyl–CoA’s acetyl group, which then releases the Co-enzyme A.
      - Step 8: Finally, the Malate dehydrogenase recreates the Oxaloacetate substrate and moves electrons from the NAD+ to form NADH, the last energy produced by the Krebs cycle. While anaerobic reactions produce NADH, it cannot move from the cytoplasm to the mitochondria to be processed in the electron transport chain, but the Malate can be transported across the mitochondria’s membrane, so the anaerobic NADH transforms Oxaloacetate into Malate, which is then converted back into Oxaloacetate to produce NADH for the production of ATP.
  - - - ~ Uphill: Reduced when accepts electrons from it's top neighbor.
        ~ Downhill: Oxidized as it passes electrons to it's more electronegative neighbor.
      - ~ Cytochromes: an electron-transferring protein with a chemical group called heme (iron group. hemoglobin).
        
        Cytochromes A, B and C participate in the electron transfer during respiration and photosynthesis.
      - ~ Electron transport chain makes NO ATP DIRECTLY.
    - - How to hydrogen ions get pumped through the transport chain?
        ~ only certain electron transports in the chain accept and release protons (H+) along with electrons.
        ~ Proton-Motive Force: energy that is generated by the transfer of protons or electrons across an energy-transducing membrane and that can be used for chemical, osmotic, or mechanical work.
    - - Second: ATP yields slightly depending on the type of shuttle used to transport electrons from the cytosol into the mitochondria.
      - Third: Reducing the yield of ATP with Proton-Motive Force generated by the redox reactions of respiration to drive work.
      - First: Phosphorylation and Redox Reactions are not directly coupled to each other there is never a whole number.
  - - - ~ Obligate Anaerobes: are organism which can only live in environments which lack oxygen.
        
        Unlike the majority of organisms in the world, these organisms are poisoned by oxygen.
        
        ~ Facultative Anaerobes: an organism that makes ATP by aerobic respiration if oxygen is present, but is capable of switching to fermentation or anaerobic respiration if oxygen is absent.
    - - Alcohol Fermentation: a process in which some sugars (as glucose) are converted into alcohol and carbon dioxide by the action of various yeasts, molds, or bacteria on carbohydrate materials.
        
        some of which do not themselves undergo fermentation but can be hydrolyzed into fermentable substances.
      - Lactic Acid Fermentation: a biological process by which glucose, fructose, and sucrose are converted into cellular energy and the metabolite lactate.
  - - - ~ Fermentation: a partial degradation of sugars or other organic fuel that occurs without the use of oxygen.
        ~ Aerobic Respiration: oxygen consumed as a reactant along with the organic fuel.
        ~ Cellular Respiration: a set of metabolic reactions and processes that take place in the cells of organisms to convert biochemical energy from nutrients into adenosine triphosphate (ATP), and then release waste products.
        
        includes both anaerobic and aerobic.
    - - Oxidation of Organic Fuel Molecules During Cellular Respiration
        ~ Organic molecules that have an abundance of hydrogen are excellent fuels because their bonds are a source of "hilltop" electrons, energy may be released.
      - Stepwise Energy Harvest via NAD+ and the Electron Transport Chain
        ~ NAD+: nicotinamide adenine dinucleotide, is a coenzyme found in all living cells, and it's required for the fundamental biological processes that make life possible.
        ~ NADH: the reduced form, or NADH. The molecule acts as a shuttle for electrons during cellular respiration.
        
        At various chemical reactions, the NAD+ picks up an electron from glucose, at which point it becomes NADH.
        
        ~ Electron Transport Chain: A group of compounds that pass electron from one to another via redox reactions coupled with the transfer of proton across a membrane to create a proton gradient that drives ATP synthesis.
      - The Principle of Redox
        ~ Redox Reactions: a type of chemical reaction that involves a transfer of electrons between two species.
        
        any chemical reaction in which the oxidation number of a molecule, atom, or ion changes by gaining or losing an electron.
        
        ~ Oxidation: A chemical reaction in which there is the loss of electrons or gain (or increase in the proportion) of oxygen, hence, resulting in an increase in oxidation state by a molecule, atom or ion.
        ~ Reduction: Involves a half-reaction in which a chemical species decreases its oxidation number, usually by gaining electrons. The other half of the reaction involves oxidation, in which electrons are lost.
        
        ~ Reducing Agent: Involves a half-reaction in which a chemical species decreases its oxidation number, usually by gaining electrons.
        
        The other half of the reaction involves oxidation, in which electrons are lost.
        
        ~ Oxidizing Agent: a substance that accepts or receives electron from another substance, hence, is consequently reduced.
        
        Most of the oxidizing agents have high oxidation numbers or highly electronegative so that they can gain one or two extra electrons by oxidizing a substance.
    - - ~ Substrate-Level Phosphorylation: a metabolic reaction that results in the formation of ATP or GTP by the direct transfer of a phosphoryl (PO3) group to ADP or GDP from another phosphorylated compound.
  - - - ~ Beta Oxidation: the catabolic process by which fatty acid molecules are broken down in the cytosol in prokaryotes and in the mitochondria in eukaryotes to generate acetyl-CoA, which enters the citric acid cycle, and NADH and FADH2, which are co-enzymes used in the electron transport.
- - - - Conversion reaction coupled with ATP hydrolysis
      - Free-Energy change for coupled reaction
      - Glutamic Acid conversion to glutamine.
      - ATP through transport and mechanical work
        
        The Regeneration of ATP
  - - - ~ Enzyme: a substance produced by a living organism which acts as a catalyst to bring about a specific biochemical reaction.
        ~ Catalyst: a substance that increases the rate of a chemical reaction without itself undergoing any permanent chemical change.
    - - ~ Active Site: the specific region of an enzyme where a substrate binds and catalysis takes place or where chemical reaction occurs.
        
        It is a structural element of protein that determines whether the protein is functional when undergoing a reaction from an enzyme.
      - ~ Induced Fit: proposed mechanism of interaction between an enzyme and a substrate.
        
        It postulates that exposure of an enzyme to a substrate causes the active site of the enzyme to change shape in order to allow the enzyme and substrate to bind.
    - - Variety of mechanisms that lower activation energy and speed up reactions:
        
        As active site and enzyme clutch, enzymes may stretch towards transition state form.
        
        Active site may also provide a microenvironment more conductive to a particular type of reaction than a solution, without an enzyme.
        
        2 or more reactants, active site provides a template for substrates to have proper connection.
        
        Amino acids in a active site can directly participate, sometimes evolve the covalent bonding.
    - - Cofactors
        Definition: mostly metal ions or coenzymes, are inorganic and organic chemicals that assist enzymes during the catalysis of reactions.
        ~ Coenzymes: are non-protein organic molecules that are mostly derivatives of vitamins soluble in water by phosphorylation; they bind apoenzyme to proteins to produce an active holoenzyme.
      - Enzyme Inhibitors
        ~ Competitive: a fake substrate binds to the active site of an enzyme, it can't be processed in the same way and it won't turn into a product.
        
        bind the active site of an enzyme, preventing a real substrate from binding and a product from being formed.
        
        ~ Non-Competitive: a type of enzyme inhibition where the inhibitor reduces the activity of the enzyme and binds equally well to the enzyme whether or not it has already bound the substrate.
      - Temperature and pH
        ~ Enzymes work best under some conditions under other conditions; optimal conditions favor the most active shape for the enzyme.
        
        thermal agitation - disruptions of hydrogen bonds, ionic bonds, and other weak bonds.
        
        optimal pH most enzymes are at their best is around 6-8.
  - - - Free Energy, Stability, and Equilibrium
        ~ Equation of the difference of free energy of final and initial:
        ΔG = G(initial) - G(final)
    - - Equalibrium and Metabolism
        ~ Isolated System: Reactions in this type of system eventually reach equalibrium.
      - Equilibrium and Metabolism
        ~ Open System: A metabolic pathway that will never reach equilibrium and it continues to work throughout its life.
      - Equilibrium and Metabolism
        ~ Multi-Open System: constantly pulled, kept out of equalibrium.
  - - - Allosteric Activation and Inhibition
        ~ A. Activation: occurs when the binding of one ligand enhances the attraction between substrate molecules and other binding sites.
        
        An example is the binding of oxygen molecules to hemoglobin, where oxygen is effectively both the substrate and the effector.
        
        ~ A. Inhibition: the negative control of enzyme activity, by binding an inhibitory substance (effector molecule) to the enzyme.
        
        This binding doesn't happen at the active site but leads to a conformational change which - in the negative control - reduces their affinity for their substrates.
        
        ~ Cooperativity: a phenomenon in which the shape of one subunit of an enzyme consisting of several subunits is altered by the substrate (the substance upon which an enzyme acts to form a product) or some other molecule so as to change the shape of a neighbouring subunit.
      - Feedback Inhibition
        Definition: a cellular control mechanism in which an enzyme's activity is inhibited by the enzyme's end product.
        
        This mechanism allows cells to regulate how much of an enzyme's end product is produced.
  - - - ~ Catabolic Pathways: release energy by breaking down complex molecules to simpler compounds.
        ~ Anabolic Pathways: consume energy to build complicated molecules from simpler ones.
      - ~ Bioenergetics: the study of how energy flows through living organisms.