Unit 2: Energy of Life

Energy

Capacity or power to do work

Potential energy

Stationary/stored energy to be released

• Chemical, gravitational, nuclear, elastic

Kinetic energy

Energy in motion

• Mechanical, electrical, thermal, sound

First law of thermodynamics

Energy cannot be created nor destroyed (only transferred)

Second law of thermodynamics

Energy cannot change form without loss of useable energy (heat)

Systems in thermodynamics

Specific portion of universe being studied

Entropy

Amount of disorder in a system (or surrounding environment)

• Nature favors this

• Cells battle against increase of this with energy

  • Ex: sodium-potassium pump

Low entropy

High potential energy

• Less stable

High entropy

Low potential energy

• Already a mess

Metabolism

Sum of all chemical reactions that occur in a cell

Anabolic pathways

Require input of energy to synthesize complex molecules

• Absorb energy (endergonic)

Catabolic pathways

Involve changing complex molecules into simpler ones

• Release energy (exergonic)

Change in Gibbs free energy

𝜟G = G_products - G_reactants

Endergonic

Energy is entering the system

• Non-spontaneous reaction

Exergonic

Energy is exiting the system

• Spontaneous reaction

E_a

Activation energy

• Higher in endergonic reactions

Energy coupling

Allow free energy from exergonic reactions to allow endergonic reactions proceed

Phosphorylation

Addition or removal of a phosphate group to activate or deactivate the function of a protein

ATP synthase

Turns like a windmill when hydrogen ions move across and creates energy (ADP → ATP)

Oxidation

To lose

Reduction

To gain

Activation energy

Required for a reaction to take place

Enzyme

Protein that catalyzes metabolic reactions

Induced fit

When the enzyme folds around the substrate more tightly to form a more precise fit

Enzyme specificity

Ability of enzyme to choose exact substrate from group of similar chemical molecules

High specificity

Amino acid r-groups bind with specific substrates

Low specificity

Amino acid r-groups bind with diverse substrates

Factors that affect rate of enzymic activity

1. Substrate concentration

2. Temperature

3. pH

Cofactors

Inorganic molecules that stabilize substrates

Coenzymes

Organic molecules that stabilize substrates

Competitive inhibition

Substrates compete for a binding site

• Enzyme is “off" when binding sites are full

Allosteric inhibition

Active site becomes unavailable (changes shape) when regulatory molecule binds to a different site on the enzyme

• Enzyme is “off"

Allosteric activation

Active site becomes available (changes shape) when regulatory molecule binds to a different site on the enzyme

• Enzyme is “on"

Feedback inhibition

Regulates metabolic pathways which use many enzymes to produce product

Chloroplast

• Has its own DNA and ribosomes that are different from the rest of the cell

• Outer and inner membranes

Stroma

Liquid matrix inside chloroplast

Thylakoids

Flattened sacks

Granum

Stack of thylakoids

Light reactions

2 H₂O + 2 NADP⁺ + 3 ATP + 3P_i → O₂ + 2 NADPH + 3 ATP

• First step in photosynthesis

• In thylakoids

NADP⁺

Empty electron carrier (positive charge)

Chlorophylls

Pigment that absorbs the most light

• Violet-blue and red

Carotenoids

Pigment that absorbs the least light

• Blue and green

Photosystem II

• First photosystem

• Light absorbed at reaction center

• Electrons are lost and sent down ETC (PQ is used)

• Water supplies replacement electrons

Photolysis

Splitting of H₂O due to the absorption of light energy

PQ

• Amphipathic

• Inflates thylakoids with H⁺ ions

PC

Brings electrons to Photosystem I through cytochrome complex

Photosystem I

• Reaction center loses electrons

• Gets oxidized and NADP⁺ is reduced to NADPH

Noncyclic path

Straight path from H₂O to NADPH

• Photons → PS II reaction center → pheophytin → PQ → cytochrome complex → PC → PSI reaction center → ferredoxin → NADP⁺ reductase

Cyclic path

Uses extra boost of ATP to energize PSI reaction center (only PSI used)

• Photons → PSI reaction center → ferredoxin → PQ → (ATP produced via proton-motive force) cytochrome complex → PC → back to PSI reaction center

Calvin cycle

3 CO₂ + 6 NADPH + 9 ATP → 1 G3P 6 NADP⁺ + 9 ADP + 8 P_i

• Second step of photosynthesis

• In stroma

• Three parts

  • Fixation, reduction, and regeneration

Fixation

3 RuBP + 3 CO₂ → (rubisco) → 6 3PGA

• Adding carbon to create 6 carbon molecule

Reduction

6 3PGA + 6 ATP + 6 NADPH → 6 ADP + 6 NADP⁺ + 6 G3P (5 G3P & 1 G3P)

• 2 G3P → 1 glucose

• Increasing potential energy

Regeneration

5 G3P + 3 ATP → 3 ADP + 3 RuBP

• 3 cycles make 6 G3P

• 5 G3P regenerates 3 RuBP

• 1 G3P exits to cytoplasm

Photorespiration

• When Rubisco fixes oxygen instead of carbon dioxide

• Wasteful loss of energy and fixed carbon

• When CO₂ levels are low and O₂ levels are high, often under hot, dry conditions when stomata are closed

• Reduces the efficiency of photosynthesis

Cellular respiration

Four phases

• Glycolysis

• Pyruvate oxidation

• Citric/Krebs Cycle

• Electron Transport Chain

Glycolysis

• First step of cellular respiration

• In cytoplasm

• Two phases

  • Energy investment and energy harvest

• Glucose (6-carbon) is broken down into two molecules of pyruvate (3-carbon)

• Does not require oxygen

• Produces a net gain of 2 ATP and 2 NADH per glucose molecule

Energy investment

• 2 ATP used to phosphorylate glucose and convert it into fructose-1,6-bisphosphate

• Prepares molecule for splitting into two 3-carbon sugars

• Activates glucose for breakdown

Energy harvest

• Two 3-carbon sugars are converted into 2 pyruvate molecules

• Generates energy (4 ATP produced and 2 NADH produced)

• Net gain: 2 ATP (4 made - 2 used)

Substrate-level phosphorylation

Occurs when enzyme forms ATP by transfering phosphate group from phosphorylated substrate to ADP