Unit 3 AP Exam Review

Enzymes, Cellular Energy, Cellular Respiration, Photosynthesis

Enzymes

Function and Mechanism

The monomer of an enzyme is an amino acid.

Enzymes are shape-specific. Their specific substrates bind at the active site like a lock-and-key mechanism, forming an enzyme-substrate complex. The substrates are then converted into products through chemical reactions.

The function of enzymes is to catalyze biological processes—increase reaction rate—by lowering activation energy. However, they do not affect the Gibbs Free Energy of a reaction.

Environmental Impacts on Enzyme Function: Denaturation

Enzyme structure is affected by temperature and pH. Every enzyme has a set of optimal conditions for function. Outside of these conditions, enzymes can denature, changing shape and losing function because they cannot bind substrates to its active site.

• High temperatures denature enzymes while low temperatures typically slow activity.

• Molecules moves faster in higher temperatures and slower in lower temperatures.

Denaturation is reversible if it is mild: the protein can refold itself, undergoing renaturation.

• For example, hemoglobin is reversible after denaturation but alpha-synuclein is non-reversible.

Environmental Impacts on Enzyme Function: pH

pH increases when concentration of hydrogen ions decreases and vice versa (inverse relationship).

When pH increases or decreases outside the optimal range, the enzyme will denature and function will eventually stop.

Environmental Impacts on Enzyme Function: Concentrations

Increased reactant concentration increases reaction rate up to a certain point (unless you continue to add more enzymes).

Decreased concentration of products also increases forward reaction rate because the formation of products are favored.

Inhibitors

A competitive inhibitor competes with the substrate to bind to the active site.

• To overcome competitive inhibitors, researchers can increase substrate concentration until the competitive inhibitor is basically outcompeted.

A noncompetitive inhibitor binds to something other than the active site and changes the shape of the enzyme.

• Allosteric inhibitors are one type that changes the shape of the active site to prevent subs

Inhibitors slow reaction rates.

First and Second Laws of Thermodynamics

First Law: All energy is conserved in a reaction. Energy cannot be created nor destroyed.

• Cellular processes are powered by an external source of energy such as ATP, sunlight, and batteries. If an organism loses energy or energy flow, it will be unable to perform necessary life functions and will die.

Second Law: Everything in the universe goes towards disorder. Spontaneous processes lead to an increase in entropy.

• Entropy(order) is maintained in a system by forward and reverse reactions which keep proceeding in order to maintain equilibrium.

Coupling: Endergonic and Exergonic Reactions

Endergonic reactions absorb energy.

Exergonic reactions release energy.

In energy coupling, endergonic and exergonic reactions are paired so that the energy released by an exergonic reaction can power an endergonic reaction.

Reaction Pathways

In a metabolic pathway, the products of one reaction are the reactants of the subsequent reaction.

Cells undergo the stepwise function to control energy released through cellular respiration in order to efficiently harvest energy from glucose and other fuel molecules while preventing the potential for the overwhelming release of energy that could damage the cell, such as heat damage.

Photosynthesis

Fueled by energy from sunlight

Photosynthesis was first evolved in cyanobacteria. The greatest evidence for this is the Great Oxidation Event, the oxygenation of Earth's atmosphere, which coincides with the rise of cyanobacteria and their oxygen-producing photosynthesis.

Light-Dependent Reactions

4 Steps

Part of photosynthesis, occurs within the thylakoid membranes of chloroplasts, where chlorophyll molecules capture light energy

1. Photolysis: Light energy absorbed by photosystems I and II, excites electrons in chlorophyll and splits water molecules to produce oxygen, hydrogen ions(protons), and electrons.

2. Electron Transport Chain: Excited electrons from photosystem II are passed along the ETC, releasing energy that is used to pump protons from the stroma into the thylakoid space. A proton gradient is created because there is a higher concentration of protons in the thylakoid space than the stroma.

3. Photophosphorylation: Uses chemiosmosis (ATP synthesis); Protons flow along the gradient, from high to low concentration, through the ATP synthase enzyme, providing energy to convert ADP and inorganic phosphate into ATP.

4. NADPH Formation: The electrons flow through the ETC and reach photosystem I where they are re-energized by light and used to reduce NADP+ to NADPH. NADP+ is the final electron acceptor for this ETC.

This NADPH and ATP is used in the Calvin Cycle (light-independent).

Calvin Cycle (Light-Independent Reactions)

A metabolic pathway in photosynthesis that occurs in the stroma of chloroplasts, and uses ATP and NADPH from the light-dependent reactions to convert carbon dioxide into glucose

1. Carbon Fixation: Catalyzed by RuBisCO enzyme, combines CO₂ with 5-carbon RuBP to form 6-carbon compound that quickly separates into 3-carbon 3-PGA

2. Reduction: Uses the energy stored in ATP and NADPH, Converts the compound 3-PGA into G3P, the 3-carbon sugar

3. Regeneration: Converts some G3P into organic molecules like glucose and converts the rest back into RuBP to continue the cycle

General formula of photosynthesis: 6CO₂ + 6H₂O →(light) C₆H₁₂O₆ + 6O₂

Chlorophyll

Location and Function

Pigment molecules in the thylakoid membrane that absorb light energy from photons to excite the electrons in the chlorophyll into a higher energy state, initiating photosynthesis

• The thylakoid membrane is organized into stacks called grana which are interconnected by stromal lamellae, to maximize light absorption.

The high energy electrons move from photosystem II to photosystem I and are transferred through a series of proteins called the electron transport chain.

Fermentation

An anaerobic process that breaks carbohydrate like sugars into products like alcohol, acids or gases, without using oxygen

It does not involve the Krebs cycle or the electron transport chain, which require oxygen. It still regenerates NAD+ from NADH but it generates less ATP than aerobic respiration.

Humans undergo Lactic Acid Fermentation which converts pyruvate to lactic acid during strenuous activity.

Cellular Respiration

3 Steps

The process through which energy is extracted from glucose to produce energy in the form of ATP

1. Glycolysis: Occurs in the cytoplasm and breaks glucose into pyruvate, producing a small amount of ATP and NADH

   • The fact that glycolysis occurs in the cytoplasm shows that it is an ancient pathway that developed before organelles, since the cytosol is a primordial environment.

1. Krebs Cycle(Citric Acid Cycle): Occurs in the matrix and further oxidizes pyruvate(first became acetyl CoA through pyruvate oxidation) to generate ATP, NADH and FADH₂

2. Electron Transport Chain: Occurs in the inner mitochondrial membrane or the cristae and uses electrons from NADH and FADH₂ to generate a large amount of ATP through oxidative phosphorylation(includes chemiosmosis), pumping protons from the matrix to the intermembrane space

   • Oxygen is the final electron acceptor and also combines with protons to form H₂O.

General Equation: C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O + ATP

Electron Transport Chains

Process and Location and Differences

A series of membranes and molecules which moves electrons through a series of redox reactions and release energy to create a proton gradient

• In chemiosmosis, this proton gradient powers ATP synthase.

This process occurs in both cellular respiration and photosynthesis. In cells, it occurs in the thylakoid membrane of chloroplasts, the inner mitochondrial membrane (cristae) for eukaryotes, and the cytoplasmic membrane of prokaryotes.

Another difference between eukaryotes and prokaryotes is the presence of the mitochondria: it’s only in eukaryotes.

Decoupling Oxidative Phosphorylation

The process where the energy generated from electron transport in the mitochondria is released as heat—instead of being used to produce ATP—due to the leakage of protons across the inner mitochondrial membrane independently of ATP synthase.

ATP Hydrolysis

Releases the energy stored in phosphate bonds of ATP

Fitness

High variation at a molecular level increases an organism’s ability to respond to environmental stimulus.

Variation in the number of molecules allows organisms to better survive and reproduce. For example, plant cells with more chlorophyll molecules produce more energy.

Variation in the types of molecules allows organisms to better respond to changes in the environment.