AP Bio Unit 4: Cellular Energetics Vocab

Energy is stored in ______ molecules.

Organic (carbs, lipids, proteins)

Endergonic

Energy enters the process

Exergonic

Energy exits the process

Oxidation

Loses electron

• Adds O, removes H

• Releases energy

• Exergonic

Reduction

Gains electron

• Removes O, adds H

• Stores energy

• Endergonic

Electron Carriers

• Moves electrons by shuttling H atoms around, creating a gradient

• When electrons move down the gradient through ATP synthase enzyme, ATP is generated

• A phosphate group is added to ADP, storing energy in ATP

• Each carrier is more electronegative than the previous (think of stairs), and is oixdation/exergonic

In the Calvin Cycle, NADPH oxidize to ______.

NADP⁺

In the Calvin Cycle, ATP reduces to ______.

ADP

In the Krebs Cycle, NAD⁺ reduces to _____.

NADH

In the Krebs Cycle, FAD reduces to _____.

FADH₂

Photosynthesis

Converts light energy to chemical energy of food

Photosynthesis Products

ATP & NADPH (P for photosynthesis)

NADPH (in photosynthesis)

The electron carrier for photosynthesis (stores energy)

Mesophyll

The middle of a leaf, chloroplasts are found here

Stomata

Pores in the leaf and site of gas exchange (CO₂ enters & O₂ exits)

Thylakoids

The flat green “pancakes”. Stores chlorophyll and collect sun energy for the first part of photosynthesis.

Grana

Stacks of thylakoids and helps increase surface area

Stroma

The fluid that surrounds the thylakoids and is the site for the second half of photosynthesis. Also contains ribosomes & chloroplast DNA.

Photosynthesis Equation

6CO₂ + 6H₂O + Light Energy → C₆H₁₂O₆ + 6O₂

Steps of Photosynthesis

LIGHT → Light reactions in thylakoids → ATP, NADPH → Calvin cycle in stroma → ORGANIC COMPOUNDS (carbs)

Light Reactions (Light Dependent)

Light energy converted into ATP & NADPH using electrons from H₂0

Calvin Cycle (Light Independent)

Takes the ATP from the light Reactions to power chemical reactions (with the enzymes) to convert CO₂ and the H from H₂O into glucose. Produces ADP & NADP⁺.

6 cycles = 1 molecule of glucose

Calvin Cycle Products

ADP & NADP⁺

Carbon in the Calvin Cycle

R: 3 CO₂ + 3 RuBP acceptors → P: 6 G3P

ATP in the Calvin Cycle

R: ATP → P: 9 ADP (6 in reduction, 3 in regeneration)

NADPH in the Calvin Cycle

R: 6 NADPH → P: 6 NADP⁺ (during reduction)

Rubisco

An enzyme in the Calvin Cycle that “fixes” the carbon dioxide into a carbohydrate during the Carbon Fixation stage

Photosystems (PS)

Large complexes of proteins and pigments (light-absorbing molecules) that are optimized to harvest light.

→ 2 types: PSI & PSII

PS II

• Provides energy for ATP

• Restored by splitting the water and releasing O₂ & H⁺

• First protein of the ETC

PS I

• The second input of light re-energizes electrons

• Provides energy to create NADPH

• The third protein (after PSII & the cytochrome complex)

NADPH

Another form of stored energy (like ATP)

Electron Transport Chain (ETC in photosynthesis)

• A cycle of oxidation & reduction to pass electrons on

• Uses electrons’ energy to pump protons ( H⁺ ) into the thylakoid through active transport (against the gradient)

ATP Synthase (photosynthesis)

• The enzyme in the ETC

• Uses protein gradient (high H⁺ inside thylakoid & low H⁺ outside thylakoid) to make ATP

• Passive diffusion of H+ provides energy to add phosphate back onto ATP

The three Calvin Cycle steps

Carbon Fixation, Reduction, & Regeneration

Carbon Fixation

Carbon dioxide is “fixed” into a carbohydrate by the enzyme Rubisco. Carbon dioxide is “fixed” from inorganic form into organic molecule

Reduction

• 6 ATP and 6 NADPH are used to make 6 G3P molecules

• ADP and NADP go back to the light reactions to be reused and re-energized

Regeneration

1 G3P leaves the cycle while the other 5 G3P use 3 more ATP to regenerate 3 RuBP to repeat the cycle and the carbon dioxide can be “fixed” into a carbohydrate.

G3P (Glyceraldehyde-3-phosphate)

• End product of the Calvin Cycle

• Energy-rich, 3-carbon sugar

• Exits chloroplast into cell’s cytoplasm and is an important intermediate to other molecules

• 2 G3Ps = 6-carbon glucose molecule, 6x cycle = 1 glucose molecule

Mitochondria

Double membrane energy harvesting organelle

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Structure:

• Smooth outer membrane

• Folded inner membrane (folds are the cristae, increasing surface area)

• Intermembrane space: fluid-filled space between membranes

• Matrix: inner fluid-filled space

• DNA, Ribosomes

• Enzymes: free & membrane-bound

Cellular Respiration Stages

1. Glycolysis

2. Pyruvate Oxidation (link reaction)

3. Krebs/Citric Acid Cycle

4. Electron Transport Chain (oxidative phosphorlaytion)

Aerobic

With oxygen

• Pyruvate oxidation

• Krebs cycle

• ETC

• Glycolysis

Anaerobic

Without oxygen

• Fermentation

• Glycolysis (can occur w/ or w/o)

NADH

The electron carrier used in cellular respiration (stores energy)

Glycolysis

• Occurs outside of mitochondria in the cytoplasm

• Can occur with or without O₂

  • With: respiration

  • Without: fermentation

• Partially oxidizes glucose (6C) to 2 pyruvates (3C)

• Net gain: 2 ATP + 2NADH

• Also makes 2H₂O

Glycolysis Steps: Energy Investment

• Endergonic

• Invest some ATP

• Glucose is phosphorylated, rearranged, and split into 2 G3P molecules

Glycolysis Steps: Energy Payoff

• Exergonic

• Harvest a little ATP and a little NADH

• G3P gives H (is oxidized) to NAD⁺ (is reduced) to make NADH

• G3P is broken down into pyruvate

• An intermediate molecule (PEP) donates a P to ADP to make ATP

  • Substrate level phosphorylation - an enzyme catalyzes the transfer of a P from a substrate (PEP) to ADP to make ATP

Pyruvate Oxidation

• If oxygen is present, pyruvate enters the mitochondrial matrix

• Pyruvate → Acetyl CoA 

• Acetyl CoA =  Coenzyme; a molecule that attaches to an enzyme’s active site to help catalyze a reaction

• CO₂, NADH, a 2 carbon sugar are produced (x2 since we start with 2 pyruvates)

Krebs/Citric Acid Cycle

• Occurs in mitochondrial matrix

• Acetyl CoA (combines with oxaloacetate) —> Citrate —> many rxns —> CO₂ + NADH + FADH₂ released

• Citrate is later broken down to make oxaloacetate so that it can combine with Acetyl CoA again (two Acetyl CoAs)

• Glucose has been fully oxidized

Net gain: 

• 2 ATP (produced by substrate-level phosphorylation)

• 6 NADH, 2 FADH₂ (electron carriers)

• CO₂ released

Glucose is oxidized when

C₆H₁₂O₆ → CO₂

Single Cycle of the Krebs Cycle

2 x CO₂

1 x ATP

1 x FADH₂

3 x NADH + H⁺

Two Cycles of the Krebs Cycle

4 x CO₂

2 x ATP

2 x FADH₂

6 x NADH + H⁺

ETC (cellular resp)

• Occurs along the cristae in the inner membrane of mitochondria

• Produces 26-28 ATP

• 2 FADH₂ and 10 NADH molecules produced in glycolysis and the Krebs Cycle, donate high-energy electrons to energy carrier molecules

• H⁺ ions pumped across inner mitochondrial membrane to the intermembrane space as the electrons pass from one carrier to another to create an H⁺ gradient

• At the end, H⁺ diffuses down the gradient and through the ATP synthase (ADP → ATP) to the matrix, where they transfer their energy to ATP (chemiosmosis)

• Oxygen is the final electron acceptor in the form of water

Chemiosmosis

The movement/diffusion of ions (H⁺) across a selectively permeable membrane, down their electrochemical gradient

Chemiosmotic Theory

Explains the function of ETCs and how the transfer of electrons down an electron transport system through a series of oxidation-reduction reactions releases energy. The energy allows certain carriers in the chain to transport H⁺/protons across a membrane.

Oxidative Phosphorylation

A metabolic pathway that uses energy released by the oxidation of nutrients to produce adenosine triphosphate (ATP)

H⁺

H → e^- + H⁺

ATP synthase (cellular resp)

As the H+ ions pass through the enzyme, part of the enzyme rotates. This causes the other part of the enzyme to shift into its active form so that ADP and P can fit at the active site and be joined to make ATP.

Fermentation

When glycolysis takes place without oxygen (anaerobic)

Fermentation is shown in two parts

Lactic Acid & Alcohol Fermentation

Lactic Acid Fermentation

• (Glucose during glycolysis) → Pyruvate → Lactate

• Ex. fungi, bacteria, human muscle cells

• Used to make cheese, yogurt, acetone, methanol

• Note: Lactate build-up does NOT causes muscle fatigue and pain (old idea)

• Once oxygen is available, lactate is converted back to pyruvate by the liver

Alcohol Fermentation

• (Glucose during glycolysis) → Pyruvate → Ethanol + CO₂

• Ex. bacteria, yeast

• Used in brewing, winemaking, baking

• Over time, the ethanol that is produced by this process kills the yeast and bacteria that do it

Metabolism

The set of chemical reactions that occur in the body’s cells to convert food into energy. Includes anabolic and catabolic reactions.

Anabolic Reactions

Forming bonds between molecules

• Uses dehydration synthesis

• Used to make macromolecules

Catabolic Reactions

Breaking bonds between molecules

• Uses hydrolysis reactions

• Used in digestion

Metabolic Pathways

Chemical reactions of life that are organized in complex pathways.

• Divide chemical reactions into small steps

• Increase efficiency, control, & options for intermediate branching points

ΔG

Change in free energy/ability to do work

Activation Energy

An initial input of energy required to break down large molecules

• Large biomolecules are stable, so they must absorb energy for the bonds to be broken

Catalysts

Help reduce the amount of energy needed to start a reaction (activation energy)

Enzymes

Biiological catalysts

• Generally made of proteins or RNA

• Increases rate of reaction & reduces activation energy

• Required for most biological reactions

• Highly specific

Substrate

Reactant that binds to an enzyme

Enzyme-Substrate Complex

Temporary association when a substrate is bound to an enzyme

Active Site

Enzyme’s catalytic site; substrate fits into active site

Product

The end result of a reaction

Properties of Enzymes: Reaction Specific

Each enzyme works with a specific substrate

Properties of Enzymes: Not consumed in reaction

Enzymes are unaffected by the reaction & can be used thousands of time per second

Properties of Enzymes: Affected by cellular conditions

Any condition that affects protein structure affects enzymes (pH, temp, etc)

Enzymes end in the suffix “_____”

-ase

Induced-Fit

Active site conforms to its substrate’s shape, bringing chemical groups in position to catalyze reactions.

Enzymes in Synthesis Reactions

• Active site orients substrates in correct position for reaction

• Enzyme brings substrate closer together

Enzymes in Digestion Reactions

• Active site binds substrate & puts stress on bonds that must be broken, making it easier to separate molecules

Enzyme concentration ______ (increases/decreases) reaction rate until all substrates are reacted.

Increases

Substrate concentration ______ (increases/decreases) reaction rate until all enzymes are saturated.

Increases

Above optimal temperature impact on enzyme activity

Activity decreases until the enzyme is denatured

Optimal temperature impact on enzyme activity

Maximum rate

Below optimal temperature impact on enzyme activity

Molecules move slower (fewer collisions between substrate and enzyme) until enzyme becomes inactive or denatured

Above optimal pH impact on enzyme activity

Rate decreases; lower [H+] interferes with enzyme shape

Optimal pH impact on enzyme activity

Maximum rate

Below optimal pH impact on enzyme activity

Rate decreases; higher [H+] interferes with enzyme shape (denatures)

Activators

Increases enzyme’s activity - coenzymes & cofactors

• changes enzyme’s shape so it works faster

• helps enzyme bind to substrate

Coenzymes

Non-protein, organic molecules that bind to the enzyme near the active site

Cofactors

Non-protein, small inorganic compounds & ions

Inhibitors

Decrease or block the activity of enzymes, slowing down reaction rates - competitive, noncompetitive/allosteric, & feedback inhibition

Competitve Inhibitor

• Inhibitor & substrate “compete” for active site

• Can overcome inhibition by increasing substrate concentration so it out-competes the inhibitor for the active site on the enzyme

Non-Competitive Inhibitor

• Binds to site other than active site (allosteric site)

  • This causes conformational change that disrupts enzyme function even though substrate still binds

Irreversible Inhibition

Inhibitor permanently binds to enzyme

Allosteric Regulation

• Conformational changes by regulatory molecules 

  • Inhibitors - keeps enzyme in inactive form

  • Activators - keeps enzyme in active form

Feedback Inhibition

• Each product becomes the reactant for the next step.

• When enough final product has been made, the cell needs a way to slow or stop production to avoid wasting energy.

• The final product acts as an allosteric inhibitor of an enzyme early in the pathway.

Photosynthesis ETC

Cellular Respiration ETC