BIO61 EXAM II

aerobic respiration

a catabolic pathway for organic molecules using O as the final e- acceptor in an e- transport chain and ultimately producing ATP; this is the most efficient catabolic pathway and is carried in most eukaryotic cells & many prokaryotic organisms

fermentation

a catabolic process that makes a limited amount of ATP from glucose or other organic molecules without an ETC & that produces a characteristic end product such as ethyl alcohol or lactic acid

anaerobic respiration

a catabolic pathway in which inorganic molecules other than O accept e- at the downhill end of e- transport chains

redox reactions

a chemical reaction involving the complete or partial transfer of one or more e- from on reactant to another; short for reduction-oxidation reaction

oxidation

the complete or partial loss of e- from a substance involved in a redox reaction

reduction

the complete or partial addition of e- from a substance involved in a redox reaction

oxidizing agent

the e- acceptor in a redox reaction

reducing agent

the e- donor in a redox reaction

coenzymes

an organic molecule serving as a cofactor, most vitamins function as coenzymes in metabolic reactions

cofactor

any non-protein molecules or ion that is required for the proper functioning of an enzyme; cofactors can be permanently bound to the active site or may bind loosely & reversibly along with the substrate during catalysis

NAD+

the oxidized form of nicotinamide adenine dinucleotide, a coenzyme that can accept e- becoming NADH; NADH temporarily stores e- during cellular respiration (empty form & oxidizing agent during respiration)

dehydrogenases

• remove a pair of H (two protons & one e-) from the breaking down of glucose

• dehydrogenase always has NAD+ and will transfer one proton & both e- and reduce to NADH

• transfer of e- neutralizes charge on NAD+

• extra proton goes into solution

NADH

the reduced form of nicotinamide adenine dinucleotide that temporarily stores e- during CR; NADH acts as an e- donor to the ETC (full form)

electron transport chain (cellular respiration)

• in the mitochondria, the e- carried by NADH & FADH will be delivered to ETC which is embedded in inner membrane

• as e- flows through ETC, they release energy which is used to pump protons, which creates electrochemical gradient

• gradient is source of energy that creates ATP

terminal electron acceptor (cellular respiration)

• at the end of chain, e- will be depleted in energy, leave, and combine with O2 to form H2O

glycolysis

DEF: a series of reactions that ultimately splits glucose into pyruvate; glycolysis occurs in almost all living cells, serving as the starting point for fermentation or cellular respiration

• takes place in cytosol & anaerobic pathway

• produces ATP & NADH from NAD+

• per glucose in glycolysis, two NADH are produced, two ATP are used and four produced (net of two ATP)

energy investment phase

OVERALL: ATP destabilizes glucose (isomerizing into fructose & breaking molecule in half to three C sugars)

EI PHASE: added & used two ATP, turned energized glucose into fructose, energized again & split into two pieces

steps of energy investment phase

1. Glucose enters cell through transporter & hexokinase phosphorylates glucose and replaces H of OH- with phosphate group to form "glucose 6-phosphate"

2. "Glucose 6-phosphate" converted to fructose 6-phosphate by phosphoglucoseisomerase

3. Phosphofructokinase adds P group & replaces H to create "fructose-1 6-biphosphate"

4. Aldolase cleaves sugar molecule into two trioses (DHAP ketone & G3P aldehyde)

5. Isomerase isomerizes DHAP (eventually become G3P) and G3P (will go into energy payoff) back and forth, rearranges bonds, and moves carbonyl group

steps of energy payoff phase

1. 2 G3Ps (two for every glucose) and Hs will be stripped from G3P (oxidized) and NAD+ will be reduced to NADH and create 2NADH by triosephosphate dehydrogenase

2. 2ATP is created from 2G3Ps & result is "3 phospho-glycerate" by phosphoglycerokinase

3. Enzyme relocates remaining phosphate group by phosphoglyceromutase

4. Enolase removes water from "2-phosphoglycerate" to form "PEP" (double bond)

5. Kinase creates 2 ATP from PEP molecules & bonds have been arranged to create pyruvate (carboxyl & acetyl group)

pyruvate oxidation

the conversion of pyruvate into acetyl-CoA by the enzyme complex called the pyruvate dehydrogenase complex

• produces two NADH per glucose

acetyl-CoA

acetyl coenzyme A; the entry compound for the CAC in CR formed from a 2-carbon fragment of pyruvate attached to coenzyme

• coenzyme A is a vitamin derived group & makes whatever is attached to more reactive & less stable

• carboxyl group has been removed & sulfur in CoA makes it reactive

• once acetyl CoA is created, it can enter the CAC

citric acid cycle

a chemical cycle involving eight steps that completes the metabolic breakdown of glucose molecules begun in glycolysis by oxidizing acetyl-CoA derived from pyruvate to CO2; occurs within mitochondria in eukaryotic cells and in the cytosol of prokaryotes; together with pyruvate oxidation, the second major stage in CR

• for every turn of the cycle, each a-CoA is broken down into CO2 molecules

• acetyl-CoA combines with four C compounds to form a six C compound

• as bonds are being rearranged, energy is being released and captured in the form of coenzymes & will produce 3 NADH, one FADH2, & 1 ATP per turn of cycle

oxidative phosphorylation process

• complexes I-IV serve as e- acceptors & donors and are reduced & oxidized through the passing of e-

1. NADH in matrix diffuse to inner membrane, unloads e- to comp. I, will be reduced and NADH oxidized to NAD+

2. FADH2 diffuse to membrane but will transfer e- to comp. III (FADH2 oxidized to FAD & comp. II reduced)

3. once e- transferred to comp. I & II, e- will flow through chain & end up on water if O is present (if O is not present, e- will back up and NADH & FADH2 cannot unload e- and prevents oxidation)

4. E- transferred to Q → comp. III → cytochrome C → comp. IV → O to form H2O

5. while they are flowing, e- lose energy & used to pump protons from matrix across inner membrane into intermembrane space which will create electrochemical gradient

proton motive force

the potential energy stored in the form of protons ECG generated by pumping of H ions across biological membrane during chemiosmosis

• only I, III, IV pump protons with NADH & NADH makes more of an ECG than FADH2

chemiosmosis

an energy coupling mechanism that uses energy stored in the form of a H gradient across a membrane to drive cellular work such as the synthesis of ATP; under aerobic conditions, most ATP synthesis in cells occur by chemiosmosis

• uses energy source from proton motive force to create ATP

ATP synthase

a complex of several membrane proteins that functions in chemiosmos with adjacent ETCs, using the energy of H+ ions proton concentration gradient to make ATP; ATP syntheases are found in inner mitochondrial membrane of eukaryotic cells & in plasma membranes of prokaryotes

• the opening through which p+ can diffuse back into matrix & flow of protons is transformed into a rotation which phosphorylates ADP into ATP

• when diffusing down ETC, protons enter channel in stator of ATP synthase, enter rotor which turns and enters matrix through another channel in stator

• turning of catalytic knob changes shapes of subunits and forces ADP and inorganic phosphate together (energy coupling mechanism)

ATP production from cellular respiration

• through oxidative phosphorylation: 2.5 ATP/NADH, 1.5 ATP/FADH2, creates about 26-28 ATP

• if shuttle system brings NADH into mitochondria, 4 ATP from glycolysis & CAC, 25 ATP from NADH & 3 ATP from FADH2 (32 ATP)

• if shuttle system brings FADH2: 4 ATP from glycolysis & CAC, 20 ATP from 8 NADH, 6 ATP from 4FADH2 (30 ATP)

• aerobic CR creates 30-32 ATP per glucose molecule

• fermentation with only glycolysis produces 2 ATP/glucose

substrate level phosphorylation

the enzyme catalyzed formation of ATP by direct transfer of a phosphate group to ADP from an intermediate substrate in catabolism (takes place in glycolysis & CAC, simple)

oxidative phosphorylation

the production of ATP using energy derived from the redox reactions of an ETC; third major stage of CR

citric acid cycle process

citrate (6C) → isocitrate → alpha ketogluterate (5C) → succinyl-CoA (4C) → 4C succinate → fumarate (4C) → malate (4C) → oxaloacetate (4C)

photosynthesis

the conversion of light energy to chemical energy that is stored in sugars or other organic compounds; occurs in plants, algae, and certain prokaryotes

mesophyll

leaf cells specialized for photosynthesis; in most plant mesophyll cells are located between the upper & lower epidermis

stoma

a microscopic pore surrounded by guard cells in the epidermis of leaves and stems that allow gas exchange between the environment and the interior of the plant

light reactions

DEF: the first of two major stages in photosynthesis preceding the Calvin cycle; these reactions which occur on the thylakoid membrane of the chloroplast or on membrane of certain prokaryotes convert solar energy to chemical energy of ATP & NADPH releasing oxygen in the process

• reactants: water, NADP+, ADP, inorganic phosphate, light

• products: oxygen, NADPH & ATP (made for Calvin cycle)