Study Guide Bio Test 2

kinetic energy

energy of motion

thermal energy

a type of kinetic energy from moving molecules felt as heat

Potential energy

stored energy

Free energy (G)

energy available to do work

Exergonic

release energy

endergonic

require energy input

Describe the structure of ATP

Adenine (nitrogen base) + ribose (sugar) + 3 phosphate groups.

atp cycle

ATP is broken into ADP + Pi (releasing energy); it’s regenerated in cellular respiration.

how does atp relate to energy in living cells

Powers cellular processes like muscle contraction, active transport, and biosynthesis.

catalyst

is a substance that speeds up a chemical reaction without being consumed. In cells, catalysts are enzymes.

Describe how enzymes catalyze chemical reactions and their optimal conditions

Enzymes lower activation energy needed to start a reaction.

Work best at specific temperatures and pH (optimum conditions).

The active site binds the substrate specifically.

autotrophs

Use inorganic carbon (CO₂) to make food (e.g., plants).

heterotrophs

Rely on organic carbon from other organisms (e.g., animals).

phototrophs

use light for energy

chemotrophs

use chemical compounds for energy

energy

is the capacity to do work or cause change.

Catabolic pathways

Break down molecules to release energy (e.g., cellular respiration).

Anabolic pathways:

Build complex molecules using energy (e.g., protein synthesis)

Kinetic energy:

Motion energy (e.g., flowing electrons, muscle contraction).

Potential energy:

Stored energy (e.g., chemical bonds in glucose or ATP).

Explain the first law of thermodynamics in your own words and how they impact living organisms

Energy cannot be created or destroyed—only transferred or transformed.

Cells convert food energy into ATP.

Explain the second law of thermodynamics in your own words and how they impact living organisms

• Every energy transfer increases entropy (disorder).

  • Organisms must constantly use energy to maintain order.

Define free energy and explain its relevance to entropy (disorder)

Free energy (G): Usable energy available to do work.

As entropy increases, usable free energy decreases (less order = less available energy for work).

Distinguish between exergonic and endergonic reactions in terms of free energy change

Exergonic: Releases free energy (ΔG < 0); spontaneous.

Endergonic: Requires energy input (ΔG > 0); non-spontaneous.

Describe the structure of ATP

ATP: Adenine + ribose + 3 phosphates.

dentify the major class of macromolecules to which ATP belongs

Belongs to the nucleic acid class (it’s a nucleotide derivative).

Explain how ATP performs cellular work

ATP donates a phosphate group (phosphorylation) to a molecule, providing energy.

Atp and its relationship to “energy-coupled” reactions

Couples exergonic ATP breakdown to endergonic cellular reactions.

Describe the function of enzymes in biological systems

• Enzymes speed up reactions by lowering activation energy.

• They are highly specific to their substrate

Explain why an investment of activation energy is necessary to initiate a spontaneous reaction

Even spontaneous (exergonic) reactions need an initial input of energy to break existing bonds.

Activation energy (EA)

is the energy needed to start the reaction

Explain how enzyme structure determines enzyme specificity

Enzymes have an active site whose shape matches a specific substrate.

The lock-and-key or induced fit model explains how only specific substrates bind.

Explain how enzymes serve to increase the rate of chemical reaction

Enzymes lower the activation energy, making it easier and faster for the reaction to occur.

They don’t change the energy released or required, just the speed.

Understand the relationship between Vmax and substrate concentration in the Michaelis-Menten method

Vmax is the maximum rate of reaction when the enzyme is saturated.

As substrate concentration increases, the reaction rate increases until it levels off at Vmax.

how does temp affect enzyme activity

Temperature: Too low = slow; too high = denatures enzyme.

how does pH affect enzyme activity

Each enzyme has an optimal pH (e.g., pepsin in stomach = acidic).

how do cofactors affect enzyme activity

Help enzymes function (e.g., metal ions, vitamins)

how do inhibitors affect enzyme activity

Competitive: Block active site.

Noncompetitive: Bind elsewhere, changing the enzyme’s shape.

Explain how metabolic pathways are regulated by allosteric feedback inhibition

In feedback inhibition, the final product of a pathway binds to an enzyme early in the pathway.

It changes the enzyme’s shape, stopping the reaction—this prevents overproduction.

oxidation

loss of electrons (or H)

reduction

gain of electrons (or H)

oxidation and reduction reactions and explain how these chemical reactions are significant in cellular energy exchanges

These reactions transfer energy by moving electrons — essential in cellular respiration to release energy from glucose.

Describe the role of electron carriers in cellular respiration and photosynthesis

Electron carriers (NAD⁺, FAD, NADP⁺) temporarily hold electrons from food or light.

They carry these electrons to the electron transport chain, where energy is harvested to make ATP.

Substrate-level:

Direct transfer of a phosphate to ADP (in glycolysis & citric acid cycle).

Oxidative phosphorylation

ATP is made using energy from electrons passed through the ETC and a proton gradient.

Cellular respiration equation:

C6H12O6 + 6O2 → 6CO2 + 6H2O + ATP

photosynthesis equation

6CO2 + 6H2O + light → C6H12O6 + 6O2

Relate the three stages of cellular respiration to the specific processes and structures associated with them

Glycolysis (cytoplasm): Glucose → pyruvate + 2 ATP + NADH

Citric Acid Cycle (mitochondrial matrix): Acetyl-CoA → CO₂ + NADH + FADH₂ + 2 ATP

Oxidative Phosphorylation (inner mitochondrial membrane): NADH/FADH₂ → ETC → proton gradient → chemiosmosis

chemiosmosis

powers ATP synthase to make ~26–28 ATP

Carbs:

Main source; glucose goes through full respiration.

Lipids

Fatty acids enter as acetyl-CoA (very high ATP yield).

Proteins

Amino acids deaminated and enter as pyruvate, acetyl-CoA, or cycle intermediates

Write the summary equation for cellular respiration

C6H12O6 + 6O2 → 6CO2 + 6H2O + ATP

Explain in general terms how redox reactions are involved in energy exchanges using electron carriers (NADH and FADH2) as examples

• Food molecules are oxidized; electrons are transferred to NAD⁺ and FAD → NADH/FADH2.

• These carry electrons to the ETC, where energy is used to make ATP.

Describe the role of NAD⁺ in cellular respiration

NAD⁺ is an electron acceptor; it becomes NADH, which stores energy and donates electrons to the ETC

In general terms, explain the role of the electron transport chain in cellular respiration

Accepts electrons from NADH/FADH₂.

Passes them through protein complexes.

Pumps H⁺ across membrane → creates proton gradient → drives ATP synthase.

Name the four stages of cellular respiration and the location of the eukaryotic cell component where each stage occurs

Glycolysis — cytoplasm

Pyruvate oxidation — mitochondrial matrix

Citric acid cycle — mitochondrial matrix

Oxidative phosphorylation — inner mitochondrial membrane

Explain the importance of energy investment/preparatory phase of glycolysis

Uses 2 ATP to destabilize glucose and split it into 2 molecules → allows for net gain of 2 ATP and production of NADH.

Describe where pyruvate is oxidized to acetyl CoA and how this process links glycolysis to the citric acid cycle

In the mitochondrial matrix:

Pyruvate loses CO₂ → becomes acetyl-CoA.

Links glycolysis (sugar breakdown) to citric acid cycle (energy harvest).

List the products of the citric acid cycle. Explain why it is called a cycle

• Products (per glucose): 4 CO₂, 2 ATP, 6 NADH, 2 FADH₂.

• It's a cycle because oxaloacetate is regenerated to accept more acetyl-CoA.

Explain how the electrons flow down the electron transport chain and are coupled to ATP production via chemiosmosis

Electrons move from high energy to low energy proteins in the ETC.

Their energy pumps H⁺ ions across membrane → builds a gradient.

H⁺ flows back through ATP synthase, generating ATP.

Explain where and how the electron transport chain creates a proton gradient

Where: Inner mitochondrial membrane.

How: Electrons moving through the ETC pump H⁺ ions into the intermembrane space → creates high H⁺ concentration (proton gradient).

Describe the structure and function of the two subunits of ATP synthase

F₀ subunit: Forms a channel for H⁺ to pass through membrane.

F₁ subunit: Rotates and uses that energy to convert ADP + Pi → ATP.

Summarize the net ATP yield from the oxidation of a glucose molecule

Glycolysis: 2 ATP

Citric Acid Cycle: 2 ATP

Oxidative phosphorylation: ~26–28 ATP

Total: ~30–32 ATP

. Compare the fate of pyruvate in alcohol fermentation and lactic acid fermentation

Alcohol fermentation: Pyruvate → ethanol + CO₂ (yeast).

Lactic acid fermentation: Pyruvate → lactate (muscles, some bacteria).

Compare the processes of fermentation and aerobic cellular respiration

Fermentation: Anaerobic, only 2 ATP, no ETC.

Aerobic respiration: Uses O₂, full oxidation of glucose, up to 32 ATP.

Fermentation is less efficient.

Describe how food molecules other than glucose can be oxidized to make ATP

Fats: Fatty acids → acetyl-CoA → enter citric acid cycle.

Proteins: Amino acids → enter glycolysis or citric acid cycle after deamination.

Carbs: Other sugars converted to glucose or glycolysis intermediates.

Describe how photosynthetic pigments absorb light of specific wavelengths.

Pigment molecules contain conjugated double bonds whose electrons can be excited by photons. The exact spacing of their energy levels means they absorb only photons whose wavelength matches that energy gap (e.g., chlorophyll a peaks at ~430 nm & ~662 nm). Unabsorbed wavelengths are transmitted or reflected, giving leaves their color.

Relate photosynthetic cellular structures to their function, including Photosystems I & II.

Thylakoid membrane houses two large protein–pigment complexes: PS II (starts electron flow, splits H₂O, releases O₂) and PS I (re-energizes electrons to reduce NADP⁺ → NADPH). Embedded cytochrome b₆f and ATP-synthase complete the electron-transport chain (ETC) and chemiosmosis.

Relate the two main stages of photosynthesis to the specific processes and structures associated with them.

Light reactions (thylakoid membrane): PS II → ETC → PS I, producing ATP & NADPH. Calvin cycle (stroma): enzyme RuBisCO fixes CO₂, then reduction & regeneration steps build carbohydrates.

Describe the interaction between the two stages of photosynthesis.

ATP and NADPH made in the light reactions diffuse into the stroma and power the Calvin cycle. The cycle returns ADP, Pi, and NADP⁺ to the thylakoids, sustaining the light reactions—an energy “hand-off” loop.

Describe the structure of a chloroplast.

Double envelope (outer + inner membranes) ➜ stroma (fluid) containing circular DNA & ribosomes ➜ thylakoid membranes folded into stacks (grana) connected by stromal lamellae. Thylakoid lumen is the internal space where H⁺ accumulates.

Write a summary equation for photosynthesis.

6 CO₂ + 6 H₂O + light → C₆H₁₂O₆ + 6 O₂

Describe the two main stages of photosynthesis.

Light reactions capture light to make ATP & NADPH; Calvin cycle uses those to fix carbon into sugars

Explain the role of accessory pigments.

Carotenoids & chlorophyll b broaden the spectrum of light that plants can utilize for energy production

List the wavelengths most effective for photosynthesis.

Blue-violet (~420–470 nm) and red (~650–680 nm) light drive the highest O₂ evolution and carbon fixation.

Explain what happens when chlorophyll in an intact chloroplast absorbs photons.

exciting its electrons, which initiates photosynthesis electrons are transferred through the electron transport chain to produce ATP and NADPH.

Explain how the photosynthetic ETC connects the two photosystems.

he electron transport chain (ETC) acts as a bridge between photosystem II (PSII) and photosystem I (PSI)

Describe linear electron flow and indicate where ATP & NADPH are formed

a pathway in photosynthesis where electrons move from water to NADP+ through Photosystem II (PSII) and Photosystem I (PSI), ultimately producing NADPH and ATP ATP is primarily formed during the electron transport chain between PSII and PSI, utilizing the energy released as electrons move down the chain. NADPH is formed when electrons from PSI reduce NADP+.

Compare the ETC in respiration vs. photosynthesis (location & H⁺ storage).

Respiration: inner mitochondrial membrane; pumps H⁺ into the intermembrane space, Photosynthesis: thylakoid membrane; pumps H⁺ into the thylakoid lumen

State the function of each Calvin-cycle phase.

1. Carbon fixation: RuBisCO attaches CO₂ to RuBP → 3-PGA. 2. Reduction: ATP + NADPH convert 3-PGA → G3P (some exits as sugar). 3. Regeneration: ATP rearranges remaining G3P to regenerate RuBP acceptor.

describe the role of atp in the calvin cycle

ATP supplies energy for phosphorylation steps

Describe the role of NADPH in the Calvin cycle.

NADPH donates high-energy electrons to reduce 3-PGA → G3P, turning inorganic carbon into a carbohydrate.

List the possible fates of photosynthetic products.

G3P can: ① form sucrose for transport; ② be polymerized into starch for storage; ③ enter glycolysis/cellular respiration for ATP; ④ provide carbon skeletons for amino acids, lipids, nucleotides; ⑤ be converted to cellulose for cell-wall synthesis.

Catabolism

Metabolic break-down pathways that oxidize large molecules into smaller ones, releasing energy that is captured as ATP or reducing equivalents (NADH, FADH₂).

3 Where is the greatest energy input in a diagram?

Look for the tallest “hump” on an energy-profile graph or the table row with the highest ΔG‡ (activation-energy) value— that is where the system absorbs the most energy.

Free-energy equation & ΔG

ΔG = ΔH − TΔS
• ΔG < 0 ⇒ exergonic (spontaneous).
• ΔG > 0 ⇒ endergonic (requires energy).

Enzyme inhibitors (competitive)

Competitive inhibitors resemble the substrate, bind the active site, and raise apparent Km while Vmax stays the same

Energy coupling

The cell pairs an exergonic reaction (e.g., ATP → ADP + Pi, ΔG ≈ −30 kJ mol⁻¹) to an endergonic one, effectively driving unfavourable processes forward.

Table clue (catalyzed vs. uncatalyzed):

catalyzed reaction shows a far lower Ea value or a steeper rate constant (k).

Glycolysis location & purpose

Cytoplasm; splits glucose into 2 pyruvate, nets 2 ATP + 2 NADH as rapid “priming” stage regardless of O₂.

Where NAD⁺ comes from anaerobically

Fermentation (lactic acid or ethanol) re-oxidizes NADH → NAD⁺ so glycolysis can keep running without an ETC.

Respiration vs. Photosynthesis similarities

Both use electron-carrier chains, proton gradients, and ATP synthase; differ in energy source (food vs. light) and direction of electron flow.

Electron flow

Glucose → NADH/FADH₂ → ETC complexes I–IV → O₂ (final e⁻ acceptor) forming H₂O.

Role of NAD⁺ in glycolysis

acts as an essential electron carrier

Where carbohydrate synthesis occurs

calvin cycle chloroplast stroma

Electron movement in light reactions

electrons are energized by light and move through a series of molecules, ultimately powering the production of ATP and NADPH, which are then used in the Calvin cycle. This process involves two photosystems (PSII and PSI) and an electron transport chain.

Product of carbon fixation phase

3-phosphoglycerate (3-PGA).

Products of light-dependent reactions

ATP (adenosine triphosphate) and NADPH (nicotinamide adenine dinucleotide phosphate)

Rubisco’s role

converting atmospheric carbon dioxide into organic compounds