AP Bio - Unit 3. Cellular Energetics

First Law of Thermodynamics

energy cannot be created or destroyed, only transformed

Free Energy

the energy available to do work (can be transformed); also depends on the disorderness (entropy) of the system

Second Law of Thermodynamics

systems trend from order to disorder

Entropy

disorderedness of the system

Exergonic

release energy & reduce the usable free energy in the system

Endergonic

require energy, and increase the usable free energy in the system

Metabolic Pathways

allow for a more efficient transfer of energy; the product of one reaction is the substrate for the next reaction

Catabolic

break down

Anabolic

build up

Activation Energy

the amount of energy required for a reaction to proceed

Enzymes

biological catalysts that decrease the activation energy of a reaction; increase the reaction rate; allows metabolism to keep up with the demands of life; recyclable (can be reused); do not change free energy of reactions; required for majority of reactions in biological systems

Active Site

has a shape that only allows the substrate to fit

Lock and Key Model

illustrates specificity of active site (active site does not change shape)

Induced Fit Model

describes a small conformational change that occurs when substrate binds active site; more accurate model

Cofactor

inorganic molecules (like metal or ions)

Coenzyme

carbon-based molecules

Conditions that affect Enzyme Activity: pH, temperature & salinity

all enzymes have optimal conditions for function; enzyme activity increases as the optimal condition is approached; optimal temp = molecular collisions bond with enzyme & substrate (before denaturation)

-temp: does not denature unless past optimal temp

-pH: decreases both before and after optimal temp

Denaturation

outside of optimal conditions, pH, high temp, and salinity can cause enzymes/proteins to denature, or unfold; loss of biological function results; denaturation disrupts 2 and 3 structure (breaks H bonds, interrupts R group interactions)

Renaturation

refolding; regain biological activity

Low Temperatures

slow reactions down; no denaturation, just slow (less kinetic energy)

Substrate Concentration

enzymes are saturated when all active sites are occupied

Saturation

maximum rate of reaction

Enzyme Concentration

more enzymes = more activity (to a point, eventually there is more enzyme than substrate)

Inhibitors

molecules that block enzyme function

Reversible

inhibitor can be removed from the enzyme

Irreversible

inhibitor cannot be removed from the enzyme (covalently bound)

Competitive Inhibition

molecule “competes” directly with substrate; fits in active site; if reversible, overcome by increasing [substrate]

Non-Competitive (Allosteric) Inhibition

molecule binds to the enzyme NOT in the active site

Allosteric Inhibitor

bind to the allosteric site (not in the active site) on the enzyme and cause a shape change

Allosteric Activators

bind to enzymes and make them functional

Photosynthesis

a process through which solar energy is converted to chemical energy (sugars)

Evolution of Photosynthesis

changed Earth’s atmosphere

-Lots of CO₂ and other molecules not supportive of life (H_2, CO, NH₃)

—

-Lots of O₂ (less not great stuff)

Cyanobacteria

increased O₂ in early atmosphere

Light Reaction Location

thylakoid membrane

Light Reaction Inputs & Outputs

inputs: photons, water

outputs: NADPH, ATP, O₂

Step 1 of LR

photosystem II absorbs light energy, a photon excites 2 e- from chlorophyll in PSII

Photosystem (PS)

a complex of protein & chlorophyll

Light Energy

different pigments absorb different wavelengths of energy; different organisms produce different pigments

Step 2 of LR

a molecule of H₂O is split:

photolysis: H₂O → ½O₂ + 2 H⁺ + 2 e^-

[H+] increases in thylakoids space/lumen (more acidic)

Step 3 of LR

electrons are transported through the ETC

energy from the e- is used to pump more H+ into the thylakoid (more acidic)

PSI absorbs photon re-energizes e-

Electrochemical Gradient

difference in [H+]

Step 4 of LR

NADP+ is reduced to NADPH

e- from PSI are used to reduce NADP+ to NADPH; H+ also used

NADP+ is the final e- acceptor

NADPH - Calvin Cycle

Oxidation

loss of electrons

Reduction

gain of electroons

Cyclic (Nonlinear) Electron Flow

no NADP+ around to accept e-

PSI e- are recycled

NADP+ is not reduced to NADPH

Calvin Cycle Location

stroma

Calvin Cycle Inputs & Outputs

inputs: ATP, NADPH, CO₂

outputs: NADP+, ADP + Pi, carbohydrates

Phase 1: Carbon Fixation (CC)

RuBisCo combines RuBP (5-carbon molecule) & CO₂ to make 2× 3-carbon molecules: 3-PGA

RuBisCo

enzyme that makes CO₂ usable

Photorespiration

occurs when RuBisCo fixes O₂ instead of CO₂ 

results in lost energy & carbon

Phase 2: Reduction (CC)

energy from ATP & NADPH is used to convert 3-PGA to G3P

Phase 3: Regeneration (CC)

most of the G3P made is used to regenerate RuBP

RuBP rengernation requires ATP

RuBP regeneration makes this a cycle

C3 Plants

subject to photorespiration

C4 Plants

reduce photorespiration by fixing CO₂ with a different enzyme (also reduce H₂O loss)

Cam Plants

avoid photorespiration by fixing CO₂ with another enzyme & separating reactions by time of day

Cellular Respiration Goal

obtain universal chemical energy stored in organic molecules (like glucose)

Glycolysis

nearly all organisms perform glycolysis

evolved before photosynthesis - doesn’t require oxygen

evolved before endosymbiosis - doesn’t require mitochondira

takes place in cytosol / cytoplasm

Glycolysis: Energy Investment Phase

goal: convert glucose to 2x G3P

energy consumption: 2 ATP / glucos

Glycolysis: Energy Payoff Phase

glycolysis: make pyruvate, ATP & NADH

energy production: 4 ATP / 2 NADH

NADH

NADH is an e- carrier

Substrate-Level Phosphorylation

the formation of ATP from ADP & a phosphorylated metabolic intermediate

Krebs Cycle Goal

make energy-carrying molecules (ATP, NADH & FADH₂)

Krebs Cycle Location

mitochondrial matrix

The Fate of Pyruvate

transported into mitochondrial matrix, pyruvate is oxidized to acetyl CoA

FADH₂

carries electrons₂

Krebs Cycle: Transition

inputs: 2 pyruvate; 2 NAD+

outputs: 2 acetyl CoA, 2 CO₂, 2 NADH

Krebs Cycle: Krebs

inputs: 2 acetyl CoA; 6 NADH+, 2 FAD, 2 ADP + Pi

outputs: 4 CO₂, 6 NADH, 2 FADH₂, 2 ATP

ETC

goal: make lots of ATP

location: mitochondrial inner membrane / cristae (folds)

NADH & FADH₂ are oxidized (lose e-)

O₂ is the final electron acceptor - it gets reduced & forms H₂O

H+ pumped from matrix to intermembrane space

powered by movement of e- through ETC proteins

intermembrane space: high [H+] = acidic

Oxidative Phosphorylation

e- transferred from ETC to O₂

H+ flow with gradient through ATP synthase (chemiosmosis)

ETC Summary

inputs: 6 O₂, 10 NADH, 2 FADH₂

outputs: 6 H₂O, 10 NAD+, 2 FAD, 34 ATP (theoretical max)

Uncoupling the ETC from Oxd. Phos.

H+ gradient not used for chemiosmosis (ATP Synthase)

instead, powers uncoupling proteins in mito IM

H+ move through UCP

Movement of H+ through UCP

generates heat; health’s endotherms regulate body temperature

Anaerobic Respiration

something else (NOT O₂) acts as the final e- acceptor in the ETC

nitrate, sulfate

some types of bacteria are obligated anaerobes

Fermentation Location

cytoplasm/cytosol

Fermentation Benefit

replenish NAD+ by reducing pyruvate

the only ATP produced comes from glycolysis (not fermentation)

Alcoholic Fermentation

reduces pyruvate to ethanol

yeast & bacteria
when [ethanol] gets high (10-15%), cells can die

NOT reversible

Alcoholic Fermentation Not Reversible

pyruvate = 3 carbons

CO₂ diffuses out of cell

ethanol = 2 carbons

Lactic Acid Fermentation

redcues pyruvate to lactate

animal & bacterial cells

reversible in presence of O₂

Reversible in Presence of O₂

lactate & pyruvate = 3-carbon molecules

Reversing Lactic Acid Fermentation in Mammals

lactate is made in muscles when under low O₂ conditions, like working out, and travels through blood

converted to pyruvate in liver

pyruvate is used in aerobic respiration (O₂ is present - like during a cool down)