bio unit 3 exam

metabolism

teh totality of an organism’s chemical reactions

catabolic pathway

metabolic pathway that breaks down larger molecules into simpler molecules and releases energy

anabolic pathway

metabolic pathway that builds larger molecules out of simpler molecules and require energy

what kind of energy is chemical

potential

what kind of energy is thermal

kinetic

1st law of thermodynamics

energy can be transferred or transformed but it cannot be created nor destroyed

2nd law of thermodynamics

every energy transfer or transformation increases the entropy of the universe

• heat lost to environment → increase

• breaking molecules → increase

• decrease → requires external energy

spontaneous reactions

reactions that increase entropy will occur spontaneously, which is energetically favorable

free energy

G; the energy available to perform work when pressure and temperature and constant; ∆G = ∆H - T∆S where H=enthalpy, and S=entropy; a measure of how far a system is from equilibrium; does NOT give info about speed at which a process occurs

∆G<0

reaction is exergonic and spontaneous

∆G>0

reaction is endergonic and not spontaneous

∆G = 0

equilibrium

endergonic reaction

requires energy

exergonic reaction

realeases energy

exergonic and endergonic reaction coupling

an endergonic reaction can only proceed if it’s coupled with an exergonic reaction with a greater amount of ∆G; ex: ATP hydrolysis (ex) is coupled with (en) reactions

transition state

unstable species that exists half way between the products and reactants of a reaction

activation energy

E_A; the difference in G between the reactants and the transition state; determines reaction rate; the higher th E_A, the slower the reaction

catalyst

accelerates reactions by lowering their E_A; not consumed by reactions they accelerate

enzymes

catalysts of life; accelerate reactions by stabilizing the transition state → lowering the E_A; usually proteins and sometimes RNA

active site

microenvironment created by enzymes to bind their substrates (reactants) and stabilize their transition state; specialized for different substrates; holds substrates and contorts them to resemble the transition state

induced fit

binding of the substrate causes a shape change that forms the active site and activates the enzyme; will not occur if a differently shaped molecule tries to bind; ex: hexokinase changes shape upon binding to glucose, forming active site and preventing water from accessing it and disrupting the reaction

catalytic cycle

1. substrates enter active site

2. enzyme arranges them to resemble the transition state; may interact via non-covalent interactions to stabilize the shape; might exclude potentially interfering molecules

3. the active site lowers E_A

4. interconversion between products and reactants is accelerated

5. the enzyme does not bind as tightly to the products as it does the substrates so it releases the products and not the substrates

6. the enzyme is regenerated so it can catalyze again

competitive inhibitor

resemble the substrate and block access to the active site; can be overcome by increasing substrate concentration; ex: penicilin inhibits the enzyme that is important for bacterial cell wall synthesis

noncompetitive inhibitor

binds elsewhere on the enzyme from the active site and changes its shape; cannot be overcome by increasing substrate concentration; ex: hydrogen cyanide inhibits a mitochondrial enzyme required for ATP synthesis

allostery

the regulation of a process by the binding of a molecule far from where that process occurs

allosteric regulators

molecules that cause the shape change in enzymes causing them to be more or less active (activators or inhibitors); often metabolic products upstream or downstream in the metabolic pathway of the reaction catalyzed by an enzyme

cooperativity

for enzymes with multiple subunits; substrate binding causes a shape change in one subunit and it’s communicated to other subunits

• positive → shape change in one subunit encourages the same change in other subunits

• negative → shape change in one subunit discourages the same change in other subunits

feedback inhibition

downstream metabolite accumulates and it binds to an enzyme and allosterically or competitively inhibits it

feedforward activation

upstream metabolite accumulates and it binds to an enzyme and allosterically activates it

oxidation

loss of electrons; LEO; exergonic product will have lower ∆G

reduction

gaining ellectrons; GER; endergonic product will have higher ∆G

reducing agent

a substance that loses electrosn and becomes oxidized

oxidizing agent

a substance that gains electrons and is reduced

oxidation and reduction coupling

reduction (unfavorable) can be powered by being paired with oxidation (favorable)

electrons in redox reactions

electrons have greater PE in less electronegative atoms → electrons lose or make available energy when they transfer to more electronegative atoms;

carbon oxidation

carbon can partially lose electrons; the more bonds a less electronegative atom shares with more electronegative atoms, the more oxidized it becomes; carbon oxidation releases energy, so much so that cellular respiration has to break it up into ordered steps to harvest it

glycolysis investment phase

• 1 molecule of ATP is used to phosphorylate and isomerize glucose into fructose and another is used to phosphorylate that fructose and break it into 1G3P and 1DHAP, which is isomerized into another G3P

• overall, per glucose, 2 ATP are used and 2 G3P are produced

glycolysis payoff phase

• 1 NAD+ is reduced to 1 NADH to harvest electrons

• 1ATP are generated through substrate phosphorylation after addition of 1 inorganic phosphate

• another high energy intermediate powers more substrate-level phosphorylation → 1 more ATP, losing 1 H2O to become that intermediate

• these are all per single G3P molecule

• overall, per glucose, 4ATP are generated, 2 H2O are created, 2 NAD+ are reduced to NADH and the G3P become 2 pyruvate

substrate-level phosphorylation

metabolic process that produces ATP by directly transferring an inorganic phosphate from a high energy intermediate to ADP

NAD+ and FAD+

modified RNA molecules and electron carriers because electrons lose little energy when transferred fro carbon to them and they can pass electrons to more electronegative atoms to release energy

high-energy intermediate

removal of its phosphate can power ATP synthesis (ADP → ATP); exs:1,3-BPG and PEP

glycolysis overall

• purpose is to oxidize 1 glucose (6C) to produce 2 pyruvate (3C each)

• mechanism to make ATP without O2

• 4 electrons are harvested - 2 ATP and 2 NADH

• occurs in cytoplasm

• inputs: 1 glucose, 2 NAD+, 2 ATP, 2 ADP, 2 P_i

• outputs: 2 pyruvate, 2 NADH, 2ATP, and 2 H2O

pyruvate oxidation

• pyruvate dehydrogenase decarboxylates (removes a carboxyl group as CO2) and oxidizes pyruvate to harvest 2 more electrons (for 2 pyruvate, 1 electorn each) through NAD+ reduction to NADH and H+

• pyruvate is turned into an acetyl group which is attached to coenzyme A (CoA) to form acetyl CoA

pyruvate oxidation inputs and outputs per pyruvate

• inputs: 1 pyruvate, 1 NAD+, 1 CoA

• outputs: 1 acetyl-CoA, 1 CO2, 1 NADH, 1 H+

ex of coupling reaction in glycolysis

reaction 1: ATP hydrolysis (exergonic) drives an unfavorable reaction (endergonic) forward

ex of structural isomerization in glycolysis

reaction 2: 6-membered ring → 5 membered ring making molecule more reactive for next step

ex of redox and hydration in glycolysis

reaction 6:

• redox - NAD+ is reduced to NADH and the carbon on G3P is oxidized

• dehydration - phosphate group is added to carbon via dehydration

ex of substrate-level phosphorylation

reaction 7: phosphate group is removed from intermediate and added to ADP

citric acid cycle process

1. acetyl coA (2C now that 1C lost through CO2) is added to oxaloacetate (4C) to create citrate (6C)

2. 2C from citrate are removed as CO2 and fully oxidized → powers reduction of 3 NAD+ (again per acetyl CoA) (results in NADH and H+) and 1 FAD (results in FADH2) and the synthesis of 1 ATP through substrate-level phosphorylation

3. The original 4C oxaloacetate is regenerated and reused in the cycle

citric acid cycle overall and inputs/outputs per acetyl coa

• turns over twice per molecule of glucose

• inputs: 1 acetyl coa, 3 NAD+, 1 FAD, 1 ADP, 1 P_i, 1 oxaloacetate (regenerated)

• outputs: 2 CO2, 3 NADH, 3 H+, 1 FADH2, 1 ATP, 1 CoA, 1 oxaloacetate

oxidative phosphorylation electron transport chain

transports electrons while pumping protons from mitochondrial matrix into intermembrane space; FADH2 enters through a different complex from NADH and generates less energy (because its electrons have less PE); oxygen is the final electron acceptor → forms H2O

oxidative phosphorylation chemiosmosis

movement of ions across a sempermeable space (inner mitochondrial membrane) down a concentration gradient to generate ATP; as H+ ions move down gradient, they pass through ATP synthase, which adds P_i to ADP to make ATP

oxidative phosphorylation overall

• generates an electrochemical gradient where H+ are concentrated in intermembrane space

• makes the most ATP in cellular respiration

cellular respiration overall atp yield

• glycolysis - 2

• pyruvate oxidation - 0

• CAC - 2

• oxidative phosphorylation - 26-28

how much energy is harvested from glucose

most of the energy stored in glucose is lost as heat

fermentation

anaerobic metabolic process that microorganisms use to break down glucose into pyruvate into ethanol, lactate, etc.; doesn’t make any additional ATP from glycolysis but does regenerate NAD+

photoautotrophs

organisms that use light as source of energy to synthesize organic substances

open stomata

CO2 is allowed in and water and oxygen is allowed out

closed stomata

no CO2 exchange but no water loss

photosynthesis overall reaction

energy + 6O2 + 6H2O → C6H12O6 + 6O2; carbon in CO2 is reduced; H2O is oxidized; anabolic and endergonic; overall increase in free energy (→ ∆G>0 → endergonic)

photosystem ii purpose

take electrons from water and excite them to a higher energy level

etc 1 purpose

h+ pumps; to generate a H+ gradient to power ATP synthase and move electrons PSI

photosystem i purpose

to excite the electrons further

etc 2 purpose

NADP+ reductase; move high energy electrons to reduce NADP+

photosystem ii output

high energy electrons that are passed to the etc1

etc1 output

h+ gradient established across the thylakoid membrane and electrons passed to psi

photosystem i output

higher energy electrons that are passed etc2

etc 2 output

NADPH which goes to the light-independent reactions

light reactions purpose

transform light energy into chemical energy (ATP) and reducing power (NADPH) to be used by the light independent reactions

pigments

located in the thylakoid membrane of the chloroplast; absorb specific wavelengths of light; major ones are chlorophyll a and chlorophyll b

ps ii process

1. a photon excites electrons in pigments, which results in energy from the electrons being passed from pigment to pigment until they are passed to the p680 molecules in the reaction center

2. the energy passed to p680 makes it lose a high-energy electron (oxidizes it) and gives it to the primary electron acceptor

3. the lost electron is replaced by an electron derived from the splitting of water into 2e-, 2H+ (thylakoid space), and 1O (finds another and makes O2)

P680+

the form P680 takes when it hasn’t regained electrons yet; strongest biological oxidizing agent known

etc 1 process

1. Pq and Pc carry out redox reactions as electrons flow (are passed from molecule to molecule) down the etc

2. electron transport releases free energy that is used to pump protons into thylakoid space

3. proton gradient is generated across thylakoid membrane

4. chemiosmosis - as H+ ions go back into stroma down concentration gradient, they pass through ATP synthase

ps i process

1. electron from etc chain arrives at ps i and joins the p700 pair of chlorophylls in the reaction center

2. light energy is absorbed by pigments and passed inward to the reaction center, causing an electron in P700 to be transferred to an aceptor molecule

3. the P700 pair’s missing electron is replaced by a new electron from PSII

etc 2 process

• the high energy electron is passed down the same kind of chain that ends with NADP+ reductase

• NADP+ gets the electron and becomes NADPH

photosynthesis

• location

• where are H+ concentrated

• how is H+ gradient used

• source of e-

• final electron acceptor

• location - chloroplast

• H+ concentration location - thylakoid space

• H+ gradient used - to make ATP with atp synthase

• e- source - water

• final electron acceptor - NADP+

cellular respiration

• location

• where are H+ concentrated

• how is H+ gradient used

• source of e-

• final electron acceptor

• location - mitochondrion

• H+ located - intermembrane space

• H+ gradient used - to make atp with atp synthase

• source of e- - NADH, FADH2

• final electron acceptor - O2 → H2O

calvin cycle stages

1. fixation - moving C from an inorganic to organic form

2. reduction - add e- to C from NADPH

3. regeneration - remake the molecule needed to accept the CO2

calvin cycle output

g3p

rubisco

enzyme that fixes carbon in the calvin cycle

rubisco * come back with notes