Biology Midterm #2 Fall 2026

What is energy? What are the two types?

Energy - The capacity to do work or cause change

1) Potential
2) Kinetic

What is the “ultimate” source of energy for the planet? And what is the most convenient way to measure energy?

The sun is the ultimate energy source. Heat is the best way to measure energy.

What is a calorie?

A unit of measurement for energy, which is the amount of heat it takes to raise the temperature of 1 gram of water by 1 degree celsius.

Compare oxidation vs. reduction

Oxidation - loss of electrons
Reduction - gain of electrons

What is the first law of thermodynamics?

Energy cannot be created or destroyed, only transformed. During conversions, some energy is lost as heat.

What is the second law of thermodynamics?

Entropy (disorder) is continuously increasing → An increase in entropy favours spontaneity, but it doesn't guarantee that a process is spontaneous.

Define Gib’s Free Energy, Enthalpy, and Entropy.

GFE (G) - Energy available to do work = DeltaH - T(DeltaS)

Enthalpy - Energy in a molecules bonds

Entropy - Disorder (or unavailable energy)

Compare positive vs. negative deltaG

(+) - products have more free energy than reactants - Enthalpy is increased and/or Entropy is decreased - Endergonic

(-) - Products have less free energy than reactants - Enthalpy is decreased and/or Entropy is increased - Exergonic

What is activation energy? What is a consequence of a larger required amount of AE?

Extra energy required to destabilize existing bonds and initiate a chemical reaction

Higher activation energy = slower reaction

What are two ways to increase reaction rate?

1) Increase temperature of molecules

2) Lower activation energy

What are catalysts? What are the two things they can’t do?

Substances that influence chemical bonds in a way that lowers activation energy

1) Can’t make endergonic (non-spontaneous) reactions exergonic (spontaneous)

2) Can’t alter the proportion of reactant turned into product

What are ATP/ADP/AMP and what are they made of?

ATP - Primary energy currency of the cell - Made of ribose (5C sugar), adenine, and 3 Phosphates.
ADP - Adenosine diphosphate
AMP - Adenosine monophosphate

Describe the ATP cycle

1) ATP Hydrolysis - ATP loses its terminal phosphate and becomes ADP + P, releasing free energy (spontaneous)

2) ATP Synthesis - Energy is used to add phosphate to ADP, reforming ATP (non-spontaneous)

Why is ATP not a suitable long-term energy storage? What are some better options for long term energy storage?

1) Phosphate bonds too unstable and cells only store a few seconds worth of ATP

2) Carbohydrates and fats are much better long-term energy storages

What are enzymes?

Globular shaped biological catalysts - most are proteins, and some are RNA - Speed up reactions without being changed or consumed in a reaction

Explain the 5 steps in Enzyme-Substrate interactions. What is the short form equation of this process?

1) Substrate approaches the enzyme's active site.

2) Binding occurs between the substrate and active site (induced fit - substrate slightly alters shape of enzyme active site)

3) Enzyme-substrate complex forms.

4) Reaction occurs: Enzyme lowers activation energy, converting substrate into products.

5) Products are released, leaving the enzyme ready to be reused.

Short form: E + S → [ES] → E + P

Where can enzymes be found?

Suspended in the cytoplasm, attached to the cell membrane, or in organelles

What are multi enzyme complexes? What are two reasons as to why they are efficient?

Groups of two or more enzymes that are physically attached to each other and work together to carry out a series of chemical reactions.

They are efficient because:

1) They prevent unwanted side reactions
2) Products can easily be passed to the enzyme (products of one reaction become substrates for the next)

What is the only RNA based enzyme? What are the two processes that it carries out? Give an example of each.

Ribozymes

1) Intramolecular Catalysis - RNA cleaves its own bonds, removing the intron and allowing the exons to join together, producing mRNA

2) Intermolecular catalysis - RNA catalyzes another molecule (peptide bond formation during protein synthesis)

List the 5 factors that enzyme function relies on

1) [Substrate] : [Enzyme] ratio
2) pH
3) Temperature
4) Presence of inhibitors
5) Presence of activators or cofactors

Describe all four types of inhibition

Competitive - a molecule competes with the substrate for an enzymes active site

Non-Competitive - a molecule binds outside active site → changes enzyme shape, preventing substrate binding

Feedback - as [end products] increases, the chance for allosteric inhibition → slows reaction

Environmental - extreme conditions (pH or temp) reduce/stop enzyme function

What are cofactors and their two types?

Cofactors (2 types) - Molecules/atoms that improve enzyme function

1) Metal ions - Assist by adding or removing e- from substrate

2) Coenzymes (not proteins, and come from vitamins) - Attach to the enzyme to form a complete active site

What are Allosteric enzymes and the two types?

Allosteric enyzmes regulate enzyme activity and exist in active/non-active forms

1) Allosteric activator - binds to allosteric site → changes enzyme shape in a way that stabilizes the active form

2) Allosteric inhibitor - binds to allosteric site → change enzyme shape in a way that stabilizes the inactive form

What is metabolism? What are the two types?

The total of all chemical reactions carried out by organisms

1) Anabolic - expenditure of energy to build up molecules
2) Catabolic - the harvest of energy by breaking down molecules

By what two process do cells harvest energy? Which type of organism uses each?

1) Cellular respiration - cells extract energy from organic molecules. Used by heterotrophs
2) Photosynthesis - cells extract energy from sunlight and store it in glucose’s chemical bonds. Used by autotrophs

Where does most of cellular respiration happen?

Mitochondria (also produces some of it’s own proteins needed for cellular respiration)

Describe the cellular respiration chemical reaction. What are the two kinds of cellular respiration?

C6H12O6 + 6O2 → 6CO2 + 6H2O + energy

1) Aerobic - Uses oxygen to help in the production of ATP - makes 686kcal/mol glucose

2) Anaerobic - Usually uses substances like NO3- or SO4- to help in the production of ATP - makes 14.6kcal/mol glucose
→ fermentation - organic molecule is reduced by gaining an e-

What is oxidative phosphorylation?

The oxidation of NADH and FADH₂ and transfer of H+ into the inter membrane space → creates an H⁺ electrochemical gradient that powers chemiosmsosis → provides the energy to drive the phosphorylation of ADP into ATP using ATP synthase

What are the 4 stages of oxidation of glucose? How many stages each?

1) Glycolysis (10 Rxns)

2) Pyruvate Oxidation (1Rxn)

3) Citric acid cycle (9 Rxns)

4) Oxidative Phosphorylation in the ETC

What are the 3 broad steps in glycolysis? Net production?

1) Glucose priming (getting ready to split)

2) Cleavage and rearrangement

3) Oxidation and ATP formation

Net production - 2 ATP, 2 NADH,, and 2 Pyruvate

What happens to Pyruvate in/out of the presence of Oxygen?

In Oxygen - Pyruvate is oxidized to Acetyl CoA which enters the citric acid cycle (Aerobic Respiration)

Out of Oxygen - Pyruvate is reduced in order to oxidize NADH back to NAD+ (fermentation)

What are two important electron carriers in cell respiration and their oxidation/reduction reactions?

NAD+/NADH (nicotinamide adenine dinucleotide)

- gets oxidized by losing 2e- and 1H+ → NAD+
- gets reduced by gaining 2e- and 1H+ → NADH

FAD/FADH2 (flavin adenine dinucleotide)
- gets oxidized by losing 2e- and 2H+ → FAD
- gets reduced by gaining 2e- and 2H+ → FADH2

How does NAD+ act as a cofactor to enzymes? (3 steps)

1) Enzyme binds NAD+ and substrate (energy rich molecule)

2) 2e- and 1H+ (a hydride ion (H-)) is transferred to NAD+ → NADH (a second proton is sometimes donated to the solution)

3) NADH diffuses away and can donate e- to other molecules

What happens to electrons carriers in their reduced form? Oxidized form?

Reduced - They go to the electron transport chain (ETC)

Oxidized - They go into glycolysis

What is the change in free energy from hydrolyzing (breaking the bond of) the terminal phosphate on ATP?

delta G = -73kcal/mol

What is chemiosmosis?

The movement of H⁺ ions down their electrochemical gradient through ATP synthase, providing the energy to produce ATP.

What are the two mechanisms by which ATP is produced?

Substrate-level phosphorylation - direct transfer of a phosphate group from a phosphorylated substrate molecule to ADP, producing ATP. Takes place on an enzyme.

Oxidative phosphorylation - ATP synthase uses energy from proton gradient to form ATP

What is the ETC, where does it happen, and what are the 5 steps? Whats weird about Complex 2?

Transfers electrons and uses the released energy to pump H⁺ into the intermembrane space of the mitochondria, creating a gradient used to produce ATP.

• NADH donates electrons to Complex I

• Energy released pumps H⁺ into the intermembrane space.

• Electrons pass to CoQ → QH2 → goes to Complex III, pumping another H⁺.

• Electrons passed to Cytochrome C → goes to Complex IV, pumping another H⁺.

• Oxygen accepts electrons and combines with H⁺ to form H₂O.
  
  FADH₂ enters at Complex 2, bypassing complex 1 → doesn’t pump as much H+

What is the ATP yield in aerobic respiration?

32 ATP total → actual yield = ~30 ATP

State the gross and net productions of ATP/NADH/FADH₂ for all the Rxns in aerobic respiration

1. Glycolysis

• 2 ATP invested

• 4 ATP generated through substrate-level phosphorylation

• Net: 2 ATP

• Also produces 2 NADH
  
  

2. Pyruvate oxidation

• No ATP directly produced or consumed

• Produces 2 NADH per glucose
  
  

3. Krebs cycle

• Two turns per glucose (because glucose produces 2 acetyl-CoA)

• Produces 1 ATP per turn

• Total: 2 ATP

• Also produces 6 NADH and 2 FADH₂
  
  

4. Oxidative phosphorylation (ETC and Chemiosmosis)

• Uses the 10 NADH and 2 FADH₂ generated earlier to make ~28 ATP

Give an example of feedback inhibition for both glycolysis and the citric acid cycle

1) In glycolysis - Phosphofructokinase is allosterically inhibited by ATP and/or citrate.

2) In pyruvate oxidation/citric acid cycle - Pyruvate dehydrogenase inhibited by high levels of NADH

What are methanogens and sulfur prokaryotes?

Methanogens - Archaea that produce methane as a byproduct of obtaining energy in anaerobic environments

Sulfur Prokaryotes - Prokaryotes that use sulfur compounds in their metabolism to obtain energy

What is fermentation and the two kinds?

The reduction of organic molecules in order to regenerate NAD+

1) Ethanol fermentation - occurs in yeast:

Pyruvate + NADH → CO2, ethanol, and NAD+

2. Lactic acid fermentation - occurs in animal cells (especially muscles): Pyruvate + NADH + H+ → Lactate + NAD+

How are proteins catabolized?

Peptidases deaminate the protein (amino group is removed), and the remainder of the amino acid is converted to a molecule that enters glycolysis or CAC.

How are fats catabolized?

Through lipolysis - Triglycerides are broken down into glycerol and fatty acids (glycerol → enters glycolysis)

What are the 5 steps to the hypothetical timeline of metabolism evolution?

1. Ability to store chemical energy in ATP

2. Evolution of glycolysis

3. Anoxygenic photosynthesis (using H2S)

4. Use of H2O in photosynthesis (not H2S) - Began permanent change in Earth’s atmosphere.

5. Evolution of nitrogen fixation

6. Aerobic respiration (most recent)

What is Photosynthesis? Give the full chemical Rxn?

The process by which plants and certain bacteria convert light energy into chemical energy stored glucose using carbon dioxide and water

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

What are the two connected pathways of photosynthesis, what does each do, and where do they occur?

Light dependant (photophosphorylation) (In Thylakoids)

→ Captures light energy and produce ATP/NADPH to supply Calvin cycle with energy

Light Independant (Calvin Cycle) (In Stroma)

→ Uses energy from light dependant Rxns to fix CO2 into organic molecules → sends NADP+ and ADP back to photophosphorylation

What are chloroplasts? What are their main structures?

Chloroplasts are photosynthesis machinery used to provide cells with energy

1) Thylakoid membrane - Membrane surrounding thylakoids that contain chlorophyll and other photosynthetic pigments.
→ contains chlorophyll → clustered into photosystems

2) Grana - Stacks of flattened sacs of thylakoid membranes

3) Stroma - Semiliquid surrounding the thylakoid membranes

4) Stroma Lamela - Connect the grana together

Which organisms use oxygenic vs. anoxygenic photosynthesis?

Oxygenic
1) Cyanobacteria
2) Seven groups of algae
3) All land plants

Anoxygenic
1) 4 different groups of bacteria

Compare wavelengths from UV to infrared in the electromagnetic spectrum (in nanometers)

UV < 400 < visible light < 700 < infrared

Whats the relationship between wavelength and energy of a photon?

As wavelength decreases, energy increases (this is why UV is harmful)

What are the two types of chlorophyll?

1) Chlorophyll a (green pigment)
→ Main type of chlorophyll

2) Chlorophyll b (yellowish-green pigment)
→ supports chlorophyll “a” by expanding the range of wavelength that can be absorbed

What are carotenoids?

Red, orange, and yellow accessory pigments that absorb additional wavelengths of light and provide photoprotection.

What are the 2 components of photosystems and their functions?

Antenna complex

→ captures photons

→ many chlorophyll molecules

→ energy passed between molecules continues until passed to reaction centre

Reaction Centre

→ a type of chlorophyll that receives energy from antenna pigment molecules → excited electrons donated to a primary electron acceptor → e- gets replaced by electron donor

What are the 4 steps in a light dependant rxn?

1) Primary photo event

→ Photon of light is captured by a pigment molecule

2) Charge separation

→ Energy is transferred to the reaction center → an excited electron is

transferred to an acceptor molecule

3) Electron transport

→ Electrons move through carriers to reduce NADP+

4) Chemiosmosis

→ Produces ATP

What is cyclic photophosphorylation?

The process by which electrons loop through PSI, creating an electrochemical gradient that powers ATP synthase to phosphorylize ADP into ATP

What is non-cyclic photophosphorylation?

Electrons passed from PSII to PSI → creating an electrochemical gradient → powers ATP synthase to phosphorylize ADP into ATP.

Provides ATP and NADPH for Calvin cycle

Describe whats made and used in one turn of the Calvin cycle. Whats made on the third turn? How many cycles to form 1 molecule of glucose?

1 turn makes:
2 NADP⁺

3 ADP
1 free carbon

1 turn uses:
3 ATP
2 NADPH
1 CO₂

The third turn produces the 3rd carbon which makes a G3P molecule
6 cycles are needed to make 2 G3P → 1 glucose

What are the 3 phases of the Calvin cycle?

1) Carbon fixation

RuBP + CO2 → 3-phosphoglycerate (3-PG) (through rubisco)

2) Reduction

3-PG + ATP + NADPH → G3P + ADP + NADP+ (through PGK)

3) Regeneration of RuBP
G3P + ATP → RuBP + ADP (through G3P Dehydrogenase)

What are Rubisco’s two enzymatic activities?

1) Carboxylation - addition of CO2 to RuBP

2) Photo respiration - oxidation of RuBP by addition of O₂

→ CO2 and O2 compete for the active site on Rubisco

What are the 3 processes of CO2 fixation plants use during photosynthesis? Which plants use which?

1) Calvin cycle (C₃) photosynthesis
→ Fixation of carbon using only RuBisCo directly

2) C4
→ Uses PEP to fixate CO₂
Separates CO2 fixation by cell location

3) CAM
→ Uses PEP to fixate CO₂
Separates CO₂ fixation by time (at night)

Give an example of a C4 plant and a CAM plant

C4 - Corn or sugarcane

CAM - Cacti or pineapple

How many high energy bonds does ATP have?

It has 2 high energy bonds. 3rd one is lower energy

What is Zed scheme?

PSII → PSI creating ATP and reducing NADP+ to NADPH (non-cyclic photophosphorylation)

Under what conditions is photo respiration most likely to occur? Why?

High temperatures and dry conditions (water conservation mode reduces CO2 availability)

What reaction centre is light energy passed in photosynthetic bacteria?

p840

Which molecules in the citric acid cycle have 4 carbons? How many carbons in the acetyl-group in A-CoA?

Oxaloacetate
Fumarate
Malate
Succinate

Acetyl group has 2 carbons

In what molecule and location do C4 plants store CO2?

Stored in malate in bundle sheath cells

What is the rotary motor and its function?

A structure on ATP synthase that rotates as H+ flows down the electrochemical gradient, changing the structure of the enzyme, allowing ADP + Pi to bind and form ATP