test 2 for bio (set 2)

Front: What is energy, and what are its two states?

Back: Energy is the capacity to do work and exists in two states:

Kinetic energy: The energy of motion (moving objects)

Potential energy: Stored energy (objects not moving but with the potential to)

Front: What are some forms of energy?

Back:

Mechanical energy

Heat

Sound

Light

Electric current

Radioactivity

Note: Heat is a common way to measure energy, as all forms of energy can be converted to heat.

Front: What does thermodynamics study?

Back: The study of energy transformations.

Front: What is a kilocalorie (kcal)?

Back:

1 kcal = 1000 calories

It is used to measure food energy.

Front: How does the Sun power ecosystems?

Back:

Sunlight provides energy that powers ecosystems.

Estimated energy from sunlight reaching Earth: 1.3 × 10^24 calories per year.

Plants, algae, and certain bacteria convert sunlight into energy through photosynthesis.

Front: What are oxidation and reduction in redox reactions?

Back:

Oxidation: Loss of an electron.

Reduction: Gain of an electron.

These reactions transfer electrons that hold potential energy, changing the energy states of molecules involved.

Front: What is energy and its two states?

Back: Energy is the capacity to do work and exists in two states:

Kinetic energy: Energy of motion (moving objects).

Potential energy: Stored energy (objects not moving but have potential to).

Front: What are other forms of energy?

Back:

Mechanical energy

Heat

Sound

Light

Electric current

Radioactivity

Note: Heat is a common way to measure energy, as all energy forms can convert into heat.

Front: What does thermodynamics study?

Back: Thermodynamics is the study of energy transformations.

Front: What is a kilocalorie (kcal)?

Back: A kilocalorie (kcal) equals 1000 calories and is used to measure food energy.

Front: How does the Sun power ecosystems?

Back:

The Sun provides energy that powers ecosystems.

Estimated sunlight energy reaching Earth: 1.3 × 10^24 calories per year.

Plants, algae, and certain bacteria convert light into energy through photosynthesis.

Front: What occurs during a redox reaction?

Back:

Oxidation: Loss of an electron.

Reduction: Gain of an electron.

These reactions transfer electrons holding potential energy, altering the energy states of molecules.

Front: How do cells store and release energy in ATP?

Back:

ATP provides energy for cells.

Energy is stored in the bonds holding the phosphate groups.

When these bonds break (via hydrolysis), energy is released.

ATP is called the "Energy currency" of the cell, powering many cellular processes.

Front: What is the structure of ATP?

Back: ATP consists of three components:

Ribose: A five-carbon sugar.

Adenine: An organic molecule made of carbon and nitrogen.

Phosphate groups: A chain of three phosphate groups attached to ribose.

These phosphate groups are highly negatively charged and repel each other, storing energy.

Front: Where is energy stored in ATP?

Back:

Energy is stored in the bonds between the phosphate groups.

These bonds are unstable and break easily during hydrolysis, releasing large amounts of energy.

High-energy bonds exist between the last two phosphate groups.

Front: What is ATP hydrolysis, and how does it drive endergonic processes?

Back:

ATP hydrolysis: ATP is broken down via hydrolysis, releasing energy.

The released energy drives endergonic (energy-requiring) reactions.

Front: What is the ATP cycle?

Back:

Cells constantly recycle ATP through the ATP cycle.

ATP is synthesized from ADP (adenosine diphosphate) and an inorganic phosphate (P) using energy from exergonic reactions.

Cells do not store large amounts of ATP; they continuously break it down and rebuild it.

Front: How much energy does ATP release upon hydrolysis?

Back: ATP hydrolysis releases 7.3 kcal/mol of energy, which is used for cellular processes.

Front: What role do enzymes play in chemical reactions?

Back: Enzymes are proteins that act as catalysts, speeding up chemical reactions by lowering the activation energy needed to start the reaction.

Front: What is a substrate in an enzyme-catalyzed reaction?

Back: A substrate is the reactant in an enzyme-catalyzed reaction.

Front: How do enzymes lower activation energy?

Back: Enzymes bind to substrates (reactant molecules) and stress bonds, making it easier for reactions to happen by lowering the activation energy required.

Front: What are active sites on enzymes?

Back: Active sites are regions where substrates bind to the enzyme, forming an enzyme-substrate complex that lowers activation energy and facilitates the reaction.

Front: What is the induced fit model?

Back: When a substrate binds to the enzyme's active site, the enzyme slightly changes shape to improve the fit between the enzyme and substrate, enhancing the reaction.

Front: What are the different forms of enzymes?

Back:

Multienzyme complexes: Groups of enzymes working together to carry out a series of reactions efficiently.

Ribozymes: Non-protein enzymes made of RNA that catalyze reactions like protein enzymes.

Front: What factors influence enzyme activity?

Back:

Temperature: Enzyme activity increases with temperature up to an optimal point; too high temperatures denature enzymes.

pH: Each enzyme has an optimal pH (most work best between 6-8).

Inhibitors/Activators:

Inhibitors: Substances that block enzyme activity.

Activators: Substances that increase enzyme activity.

Front: What are enzyme cofactors?

Back:

Cofactors are additional molecules, often metal ions, that enzymes need to work properly.

They assist in catalysis.

Front: How do human enzymes perform optimally?

Back: Human enzymes work best at temperatures between 35-40°C and at pH levels between 6-8.

Front: What is competitive inhibition in enzymes?

Back: Competitive inhibition occurs when an inhibitor competes with substrates for the enzyme's active site, blocking the reaction.

Front: What is noncompetitive inhibition?

Back: Noncompetitive inhibition happens when an inhibitor binds elsewhere on the enzyme, changing its shape and preventing substrate binding.

Front: What is metabolism?

Back: Metabolism consists of chemical reactions that occur in pathways, divided into:

Anabolic pathways: Build molecules and require energy.

Catabolic pathways: Break down molecules and release energy.

Front: What is feedback inhibition?

Back: Feedback inhibition occurs when the final product of a pathway binds to an allosteric site on the first enzyme in the pathway, stopping the process.

Front: How are organisms classified based on how they obtain energy?

Back:

Autotrophs (producers): Produce their own organic molecules through photosynthesis.

Heterotrophs (consumers): Live on organic compounds produced by other organisms.

Front: What is cellular respiration?

Back: Cellular respiration is a series of reactions where:

Oxidation: Electrons are lost.

Reduction: Electrons are gained.

Front: What is dehydrogenation?

Back: Dehydrogenation is the loss of electrons accompanied by protons, resulting in the loss of a hydrogen atom (1 electron, 1 proton).

Front: What happens during redox reactions?

Back: During redox reactions, electrons carry energy from one molecule to another.

Front: What is NAD+ and its function?

Back:

NAD+ (Nicotinamide Adenosine Dinucleotide) is an electron carrier and enzymatic cofactor.

It accepts 2 electrons and 1 proton to become NADH.

The reaction is reversible.

Front: What are the final electron acceptors in cellular respiration?

Back:

Aerobic Respiration:

Final acceptor: Oxygen (O₂).

Example: Human cells use this for efficient ATP production.

Anaerobic Respiration:

Final acceptor: Inorganic molecules (e.g., sulfate, nitrate, sulfur).

Example: Some bacteria and archaea in oxygen-deprived environments.

Fermentation:

Final acceptor: Organic molecules (e.g., pyruvate, acetaldehyde).

Example: Human muscles use lactic acid fermentation; yeast uses alcohol fermentation to produce ethanol and CO₂.

Front: What are electron carriers?

Back:

Electron carriers can be soluble, membrane-bound, or move within membranes (e.g., mitochondria).

They can be reversibly oxidized and reduced (e.g., NAD⁺ to NADH).

Some carry only electrons, others carry electrons and protons.

Front: How do cells use ATP?

Back:

Cells use ATP to drive endergonic reactions.

Hydrolyzing the terminal phosphate releases 7.3 kcal/mol of energy (ΔG).

Front: What are the two mechanisms for ATP synthesis?

Back:

Substrate-level phosphorylation:

Phosphate group is directly transferred to ADP (e.g., during glycolysis).

Oxidative phosphorylation:

ATP synthase uses energy from a proton gradient.

Front: What are the stages of glucose oxidation in cellular respiration?

Back:

Glycolysis: Breaks sugar in half.

Pyruvate oxidation: Prepares halves for energy extraction.

Citric acid cycle: Extracts energy from the halves.

Electron transport chain: Converts stored energy into ATP.

Front: What is the energy yield of glucose oxidation?

Back:

Free energy of glucose oxidation: -686 kcal/mol (exergonic reaction).

This energy is released in small steps, not all at once.

Front: What is glycolysis?

Back:

Converts 1 glucose (C₆H₁₂O₆) into 2 pyruvate molecules (3 carbons each).

A 10-step biochemical pathway occurring in the cytoplasm.

Net production:

2 ATP (via substrate-level phosphorylation, 4 ATP are made but 2 are used).

2 NADH (produced by NAD⁺ reduction).

Front: What happens in the priming phase of glycolysis?

Back:

Glucose (6-carbon sugar) is phosphorylated using 2 ATP, making it unstable.

Result: 6-carbon sugar diphosphate, ready for cleavage.

Front: What is the cleavage phase of glycolysis?

Back:

The 6-carbon molecule is split into two 3-carbon molecules: glyceraldehyde-3-phosphate (G3P).

Each molecule retains a phosphate group.

Front: What is the energy payoff phase of glycolysis?

Back:

Each G3P molecule is oxidized, transferring electrons to NAD⁺, forming NADH.

High-energy phosphate groups are transferred to ADP, producing ATP.

Final products per glucose:

2 Pyruvate molecules.

2 NADH.

Net gain of 2 ATP (4 ATP made, 2 used earlier).

Front: What are the three phases of glycolysis?

Back:

Priming: Glucose is phosphorylated and made reactive.

Cleavage: Splits glucose into two 3-carbon molecules (G3P).

Energy payoff: Produces ATP, NADH, and pyruvate.

Front: What must happen to NADH for glycolysis to continue?

Back: NADH must be recycled back to NAD⁺ by:

Aerobic respiration: Using oxygen as the final electron acceptor, producing significant ATP.

Fermentation: Occurs without oxygen, using organic molecules as the final electron acceptor (e.g., lactic acid or ethanol).

Front: What is the fate of pyruvate in aerobic and anaerobic conditions?

Back:

Aerobic respiration: Pyruvate is oxidized to acetyl-CoA, entering the citric acid cycle.

Anaerobic respiration: Pyruvate is reduced to regenerate NAD⁺ (e.g., lactic acid or ethanol formation).

Front: Where does pyruvate oxidation occur, and what are its products?

Back:

Location:

In eukaryotes: Mitochondrial matrix.

In prokaryotes: Plasma membrane.

Products per pyruvate:

1 CO₂ (from decarboxylation).

1 NADH.

1 Acetyl-CoA (2 carbons attached to coenzyme A).

Front: What happens during pyruvate oxidation?

Back:

CO₂ is released: One carbon from pyruvate is removed as a waste product.

NADH is produced: Electrons from pyruvate are transferred to NAD⁺.

Acetyl-CoA is formed: Remaining 2-carbon molecule binds to coenzyme A.

Front: What is the citric acid cycle, and where does it occur?

Back:

The citric acid cycle (Krebs cycle) oxidizes the acetyl group from acetyl-CoA.

It takes place in the mitochondrial matrix.

A nine-step biochemical pathway.

Front: What are the steps of the citric acid cycle?

Back:

Acetyl-CoA combines with oxaloacetate to form citrate.

Citrate is rearranged and decarboxylated.

Oxaloacetate is regenerated to complete the cycle.

Front: What are the products of the citric acid cycle per acetyl-CoA?

Back:

2 CO₂ molecules.

3 NADH.

1 FADH₂.

1 ATP.

Oxaloacetate is regenerated for the next cycle.

Front: Where does the citric acid cycle occur?

Back: The citric acid cycle takes place in the mitochondria.

Front: What is the condensation reaction in the citric acid cycle?

Back:

Reaction: Acetyl-CoA (2C) combines with oxaloacetate (4C) to form citrate (6C).

Enzyme: Catalyzed by Citrate Synthase.

Byproduct: CoA is released as CoA-SH (sulfhydryl group).

Once acetyl-CoA enters the cycle, the process is irreversible.

Front: How does isomerization occur in the citric acid cycle?

Back:

Reaction: Citrate (6C) is rearranged into isocitrate (6C).

Enzyme: Aconitase.

Purpose: Prepares molecules for oxidation by putting them into the correct shape for energy extraction.

Front: What happens during the first oxidation in the citric acid cycle?

Back:

Reaction: Isocitrate (6C) is oxidized to alpha-ketoglutarate (5C).

Enzyme: Isocitrate dehydrogenase.

Products:

NAD⁺ gains electrons, forming NADH.

1 CO₂ is released.

This is the first energy-yielding step of the cycle.

Front: What occurs during the second oxidation in the citric acid cycle?

Back:

Reaction: Alpha-ketoglutarate (5C) is oxidized to succinyl-CoA (4C).

Enzyme: Various.

Products:

1 CO₂ is released.

NAD⁺ picks up electrons, forming NADH.

Coenzyme A (CoA) attaches to form succinyl-CoA.

Front: What happens during substrate-level phosphorylation in the citric acid cycle?

Back:

Reaction: Succinyl-CoA (4C) releases CoA, forming succinate (4C).

Energy:

Drives GDP → GTP.

GTP transfers a phosphate to ADP, forming ATP.

Prepares succinate for further oxidation.

Front: What happens during the third oxidation in the citric acid cycle?

Back:

Reaction: Succinate (4C) is oxidized to fumarate (4C).

Enzyme: Succinate dehydrogenase.

Products:

FAD picks up electrons, forming FADH₂ (which carries electrons to the ETC).

Links the cycle to the electron transport chain.

Front: How is oxaloacetate regenerated in the citric acid cycle?

Back:

A water molecule is added to fumarate, converting it to malate (4C).

Malate is oxidized to oxaloacetate (4C).

NAD⁺ gains electrons, forming NADH.

Oxaloacetate is regenerated to restart the cycle.

Front: What are the products of the citric acid cycle per acetyl-CoA?

Back:

4 CO₂ (carbon dioxide released).

6 NADH (electron carrier for the ETC).

2 FADH₂ (another electron carrier for the ETC).

2 ATP (via substrate-level phosphorylation).

Front: What role do NADH and FADH₂ play in the Electron Transport Chain (ETC)?

Back:

NADH and FADH₂ donate electrons to the ETC.

These electrons pass through protein complexes in the inner mitochondrial membrane, driving proton (H⁺) pumping into the intermembrane space and creating a proton gradient.

Front: What is the final electron acceptor in the Electron Transport Chain?

Back: Oxygen (O₂) is the final electron acceptor, combining with electrons and protons to form water (H₂O).

Front: What is chemiosmosis?

Back:

Protons (H⁺) flow back into the mitochondrial matrix through ATP synthase.

This proton movement spins ATP synthase, powering the conversion of ADP + Pi (inorganic phosphate) into ATP via oxidative phosphorylation.

Front: How does ATP synthase function?

Back:

ATP synthase is a rotary motor driven by the proton gradient.

It has two subunits:

F₀: Membrane-bound complex where protons flow, causing rotation.

F₁: Stalk and knob complex with enzymatic activity; rotation changes its conformation to synthesize ATP.

Front: How much ATP is produced in the Electron Transport Chain?

Back:

30 ATP per glucose for eukaryotes.

32 ATP per glucose for bacteria.

P/O ratio: Amount of ATP synthesized per O₂ molecule. This calculation has been debated over time.

Front: What are two key control points for feedback inhibition in respiration?

Back:

In glycolysis:

Phosphofructokinase is allosterically inhibited by ATP and/or citrate.

In pyruvate oxidation/citric acid cycle:

Pyruvate dehydrogenase is inhibited by high levels of NADH.

Citrate synthase is inhibited by high levels of ATP.

Front: What are the two types of oxidation without oxygen (O₂)?

Back:

Anaerobic respiration:

Uses inorganic molecules (e.g., sulfur, nitrate, carbon dioxide, inorganic metals) as the final electron acceptor.

Fermentation:

Uses organic molecules as the final electron acceptor.

Front: What are methanogens, and how do they perform anaerobic respiration?

Back:

Methanogens reduce CO₂ to CH₄ (methane).

Found in various organisms, including cows.

Front: How do sulfur prokaryotes perform anaerobic respiration?

Back:

Sulfur prokaryotes reduce inorganic sulfate (SO₄) to hydrogen sulfide (H₂S).

Early sulfate reducers contributed to the evolution of photosynthesis.

Front: What is the purpose of fermentation?

Back: Fermentation reduces organic molecules to regenerate NAD⁺, allowing glycolysis to continue.

Front: What are the types of fermentation and their products?

Back:

Ethanol fermentation (in yeast):

Produces CO₂, ethanol, and NAD⁺.

Lactic acid fermentation (in animal cells, especially muscles):

Electrons are transferred from NADH to pyruvate, producing lactic acid.

Front: What is photosynthesis, and what does it produce?

Back:

Photosynthesis is a process where plants use sunlight to make food (glucose).

Plants take in carbon dioxide (CO₂) and water (H₂O), use sunlight, and produce glucose (C₆H₁₂O₆) and oxygen (O₂).

Front: What types of organisms carry out oxygenic photosynthesis?

Back:

Cyanobacteria: Ancient bacteria that perform photosynthesis.

Seven groups of algae: Aquatic organisms that photosynthesize.

Green plants: Photosynthesis occurs in chloroplasts.

Front: What are the two main stages of photosynthesis?

Back:

Light-dependent reactions:

Occur in the thylakoid membranes of chloroplasts.

Use light energy to produce ATP and reduce NADP⁺ to NADPH.

Light-independent reactions (Calvin cycle):

Occur in the stroma of chloroplasts.

Use ATP and NADPH to convert CO₂ into glucose.

Front: What are the main components of a chloroplast?

Back:

Thylakoid membrane: Contains chlorophyll and photosynthetic pigments; organized into photosystems.

Grana: Stacks of thylakoid membranes.

Stroma lamella: Bridges connecting grana, distributing energy.

Stroma: Semi-liquid surrounding thylakoids; site of the Calvin cycle.

Front: What are pigments, and why are they important?

Back:

Pigments: Molecules that absorb light energy in the visible range, capturing sunlight for photosynthesis.

Photon: A particle of light carrying energy; its energy is inversely proportional to wavelength.

Example:

Blue/violet light: Higher energy (shorter wavelengths).

Red light: Lower energy (longer wavelengths).

Plants absorb blue and red light most efficiently.

Front: What is the photoelectric effect, and why is it important in photosynthesis?

Back: The photoelectric effect is the removal of an electron from a molecule by light, exciting electrons in chlorophyll to initiate photosynthesis.

Front: What is the absorption spectrum?

Back:

The absorption spectrum shows the range and efficiency of photons a molecule can absorb.

Different pigments absorb different wavelengths of light.

Example: Chlorophyll absorbs red and blue light but reflects green light (why plants appear green).

Front: What are the main pigments in photosynthesis, and what do they do?

Back:

Chlorophyll a:

Main pigment in plants and cyanobacteria.

Converts light energy into chemical energy.

Absorbs violet-blue and red light.

Chlorophyll b:

Accessory pigment that absorbs wavelengths chlorophyll a cannot.

Enhances light capture and photosynthesis.

Carotenoids:

Absorb blue and violet light, reflecting yellow, orange, and red.

Antioxidants that protect plants from harmful molecules.

Front: What are carotenoids, and why are they important?

Back:

Structure: Carbon rings linked to chains with alternating single and double bonds.

Function:

Absorb photons with a wide range of energies.

Act as antioxidants, scavenging free radicals and protecting plants.

Examples: Phycobiliproteins (important in low-light ocean areas) and anthocyanins (red pigments).

Front: What is the reaction center in photosynthesis?

Back:

A transmembrane protein-pigment complex that captures sunlight in chloroplasts.

When chlorophyll absorbs light, an electron is excited to a higher energy level, which starts the process of photosynthesis.

Oxidized chlorophyll replaces its lost electron by taking one from water, breaking the water molecule and releasing oxygen.

Front: What are the steps in light-dependent reactions of photosynthesis?

Back:

Primary photo event: Photon is captured by a pigment molecule (photosystem).

Charge separation: Energy is transferred to the reaction center, exciting an electron that is passed to an acceptor molecule.

Electron transport: Electrons move through carriers to reduce NADP⁺ to NADPH.

Chemiosmosis: Produces ATP as protons flow through ATP synthase.

Front: What is cyclic photophosphorylation?

Back:

Used by sulfur bacteria with one photosystem.

Generates ATP without producing oxygen (anoxygenic photosynthesis).

Excited electrons pass through the Electron Transport Chain (ETC), creating a proton gradient that drives ATP production.

Front: What are the two types of photosystems in chloroplasts?

Back:

Photosystem I (P₇₀₀): Transfers electrons to NADP⁺, producing NADPH.

Photosystem II (P₆₈₀):

Oxidizes water molecules, releasing oxygen.

Replaces electrons lost by Photosystem I.

Two photosystems are connected by the cytochrome b₆-f complex.

Front: What is unique about Photosystem II?

Back:

Oxidizes water to release oxygen.

Core consists of 10 transmembrane protein subunits with two P680 chlorophyll molecules.

Contains Mg atoms essential for splitting water.

Passes electrons to cytochrome b₆-f complex.

Front: What is unique about Photosystem I?

Back:

Reaction center has 12-14 protein subunits with two P700 chlorophyll molecules.

Accepts electrons from plastocyanin to fill its electron "hole".

Passes electrons to NADP⁺ to form NADPH, used in sugar production during the Calvin cycle.

Front: How does noncyclic photophosphorylation differ from cyclic photophosphorylation?

Back:

Noncyclic photophosphorylation: Produces NADPH and ATP using both Photosystem I and II.

Cyclic photophosphorylation: Produces additional ATP by short-circuiting Photosystem I, creating a larger proton gradient for ATP synthesis.

Front: What is required to build carbohydrates during photosynthesis?

Back:

Energy (ATP): From light-dependent reactions (cyclic and noncyclic photophosphorylation) to drive endergonic reactions.

Reduction potential (NADPH): From Photosystem I, providing protons and energetic electrons to convert CO₂ into glucose.

Front: What is the Calvin cycle, and why is it also called C₃ photosynthesis?

Back:

The Calvin cycle, named after Melvin Calvin, is the process that synthesizes glucose from CO₂ using ATP and NADPH.

It is called C₃ photosynthesis because the first intermediate molecule formed (PGA) has three carbons.

Front: What is the key step of the Calvin cycle?

Back: The attachment of CO₂ to the 5-carbon sugar ribulose 1,5-bisphosphate (RuBP), forming 3-phosphoglycerate (PGA).

Enzyme involved: Ribulose biphosphate carboxylase/oxygenase (RuBisCO).

Front: What are the three phases of the Calvin cycle?

Back:

Carbon fixation:

RuBP (5C) + CO₂ → PGA (3C).

CO₂ attaches to RuBP, forming the first stable intermediate (PGA).

Reduction:

PGA is reduced to glyceraldehyde-3-phosphate (G3P) using ATP and NADPH.

G3P is a high-energy molecule and the building block for glucose and other carbohydrates.

Regeneration of RuBP:

Some G3P molecules are used to regenerate RuBP, enabling the cycle to continue.

Front: Why is the regeneration of RuBP important in the Calvin cycle?

Back: Without RuBP, the plant cannot capture more CO₂, halting photosynthesis.