AP Biology Unit 3: Cellular Energetics

Enzymes

Catalyze biological systems and reactions by lowering the activation energy

Substrates

Molecules that bind with enzymes at the active site

Induced fit

When protein or enzyme changes to better fit a substrate

Temperature and pH effect on enzymes

Can cause them to denature, as enzymes are proteins, and decrease function; enzyme structure is dependent on hydrogen bonding

Enzyme properties

Return to OG state at the end of a reaction; they are specific and only bind with one or a couple of substrates

Competitive inhibition

Substrate other than the intended one binds to the active site —> reaction doesn’t take place; competitive inhibitors can be out-competed by lots of substrate —> can still meet max reaction rate

Allosteric competitive inhibition

Competition binds to an allosteric site and not the active site; changes the enzyme so the intended substrate can’t bind anymore

Non-competitive inhibition

Both the intended and “inhibitor” substrates can bind to the enzyme, but if they both do, the reaction won’t proceed; can’t ever reach the maximum reaction rate because the enzyme is “poisoned” by the inhibitor; the amt of substrate can’t fix that

Cooperactivity

A substrate is an allosteric activator and increase the activity of another active site when it binds

Cofactor vs coenzyme

Cofactor: non-protein “helper molecule” that attaches temporarily; coenzymes are a subset of cofactors but are organic molecules

Feedback inhibition

The end product of a metabolic pathway acts on a key enzyme that regulates pathway entry, leading to more of the end product not being produced; stops more product from being made until the supply is used up; usually occurs at the 1st committed step

Enzyme kinetics graph

Shows what happens when equal amt of enzyme is added to different substrate concentrations to help find the initial velocity (V0) for all concentrations; substrate concentration on x, velocity on y; when plateau, enzyme is saturated —> rate is limited by the enzyme concentration

Vmax on enzyme kinetics graph

Maximum velocity, or the maximum rate at a certain concentration; the y-value of the plateau

km on enzyme kinetics graph

Substrate concentration ½ of the way to Vmax; lower km means higher affinity to bind to substrate, higher km means lower affinity

Phosphorylation

Adding a phosphate group to a glucose —> makes the glucose polar, which mens it can’t leave the cell via diffusion; cell can retain more glucose; couples ATP hydrolysis and glucose + PO4 → glucose-6-phosphate to make a favorable reaction overall; also uses enzyme, hexokinase to carryout a nucleophilic attack on the phosphate

Metabolism, Catabolism, Anabolism

Taking energy and making it useful is metabolism; catabolism is breaking down energy into building blocks, while rebuilding is anabolism

Photoautrophs vs heterotrophs

Self-feeders that use light (plants) vs different feeders (humans, etc)

Light-dependent reactions products and reactants

Takes place in thylakoid membrane!!! Light and H2O make ATP from ADP and reduce NADP+ to NADPH, as well as make O2 as a byproduct

Light-independent reaction/Calvin Cycle products and reactants

Uses ATP, NADPH, and CO2 to make glucose (sugar) !!!

PSII (light dependent)

Photons excite electrons, which move to a higher energy state → enter a gradient; p680, a special pair, oxidizes water to get oxygen and H+ (O2 is byproduct); electrons move down electron transport chain, drive pumping of H+ in a concentration gradient from the stroma into thylakoid interior, creates ATP via chemiosmosis

Chemiosmosis

H+ is pumped across thylakoid membrane from energy from the electron transport chain, creating a concentration gradient of H+; H+ passes through ATP synthase (embedded in membrane), synthesizing ATP

PSI

SImilar to PSII, electron joins P700 and goes down the transport chain; NADPH is made from NADP+ via NADP+ reductase → chemiosmosis

Cyclic photophosphorylation

When electrons repeatedly go through PSI but don’t end up in NADPH; can occur when there is already enough NADPH, or when plants need extra ATP

Non-cyclic photophosphorylation (standard)

Electrons are removed from water and passed through PSII and PSI before ending up in NADPH

Calvin Cycle (light-independent), in stroma

Uses ATP and NADPh to fix carbon from CO2

Carbon fixation

CO2 combines with RuBP to make a 6-carbon compound, splits into 2 molecules of 3-PGA, catalyzed by Rubisco

Reduction

ATP and NADPh are used to convert the 2 3-PGA into 3-carbon sugars (G3P); NADPH reduces the intermediate to make G3P

Regeneration

Some G3P molecules go to make glucose while some are recycled to regenerate the RuBP acceptor; regeneration uses ATP and a complex network of reactions

Photosynthesis evolution

Cyanobacteria can do photosynthesis; ancestors changed the atmosphere; Great Oxygenation Even introduced O2 to air in large percentage; endosymbiotic theory 0> we believe chloroplasts are descendants of the ancestors of cyanobacteria

Cellular Respiration

C6H12O6 → 6CO2 + 6H2O; delta G is very negative, very spontaneous?

Electron carriers in cellular respiration

NAD+ and FAD; when they gain electrons, they gain hydrogen too; when they drop off electrons, go back to OG state

Glycolysis

6 carbon sugar becomes 2 molecules of pyruvate, ATp is made, NAD+ → NADH

Pyruvate oxidation

Pyruvates enter mitochondrial matrix and make acetyl coA (bound to coenzyme A); CO2 is released and NADH is generated

Citric acid cycle

Acetyl CoA and 4-carbon molecule regenerate the OG 4-carbon starting molecules; produces ATP, NADH, and FADH2

Oxidative phosphorylation

NADH and FADH release electrons; that energy is used for protons to flow; at the end of the electron transport chain, H2O is formed

Anaerobic cellular respiration

Similar to regular aerobic respiration, but a different molecule is used at the end of the electron transport chain in place of O2

Fermentation

Only energy extraction process is glycolysis; puruvate is made ut doesn’t go through the electron transport chain; NADH drops off electrons as it goes, so glycolysis keeps going

Lactic acid fermentation

NADH transfers electrons to pyruvate and lactate

Alchohol fermentation (yeast cells)

NADH donates electrons to pyruvate derivative(ethanol)