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Questions and Answers
What is primarily released during the light reactions of photosynthesis?
What is primarily released during the light reactions of photosynthesis?
The Calvin cycle requires more NADPH than ATP for the synthesis of G3P.
The Calvin cycle requires more NADPH than ATP for the synthesis of G3P.
False
What is the role of Rubisco in the Calvin cycle?
What is the role of Rubisco in the Calvin cycle?
Rubisco catalyzes the carbon fixation process.
The Calvin cycle must complete _____ turns to produce one G3P molecule.
The Calvin cycle must complete _____ turns to produce one G3P molecule.
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Match the following processes with their corresponding characteristics:
Match the following processes with their corresponding characteristics:
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What is the primary final electron acceptor in aerobic respiration?
What is the primary final electron acceptor in aerobic respiration?
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Fermentation produces more ATP than oxidative phosphorylation.
Fermentation produces more ATP than oxidative phosphorylation.
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What process occurs during anaerobic respiration when oxygen is not available?
What process occurs during anaerobic respiration when oxygen is not available?
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In the citric acid cycle, pyruvate is converted to __________ before entering the cycle.
In the citric acid cycle, pyruvate is converted to __________ before entering the cycle.
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Match the following terms with their definitions:
Match the following terms with their definitions:
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Which of the following statements is true regarding the Second Law of Thermodynamics?
Which of the following statements is true regarding the Second Law of Thermodynamics?
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The energy produced from ATP hydrolysis is used exclusively for cellular respiration.
The energy produced from ATP hydrolysis is used exclusively for cellular respiration.
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What is the role of ATP synthase in cellular respiration?
What is the role of ATP synthase in cellular respiration?
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The conversion of pyruvate to __________ occurs during alcohol fermentation.
The conversion of pyruvate to __________ occurs during alcohol fermentation.
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What drives the phosphorylation of ADP to form ATP?
What drives the phosphorylation of ADP to form ATP?
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Which statement correctly describes a spontaneous process?
Which statement correctly describes a spontaneous process?
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Endergonic reactions release free energy to their surroundings.
Endergonic reactions release free energy to their surroundings.
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What is the equation that relates change in free energy (∆G) to change in enthalpy (∆H) and change in entropy (∆S)?
What is the equation that relates change in free energy (∆G) to change in enthalpy (∆H) and change in entropy (∆S)?
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A process with __________ ∆G is considered spontaneous.
A process with __________ ∆G is considered spontaneous.
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Which of the following statements about ATP hydrolysis is true?
Which of the following statements about ATP hydrolysis is true?
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Match the type of reaction with its definition:
Match the type of reaction with its definition:
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ATP serves as the energy shuttle for cellular work.
ATP serves as the energy shuttle for cellular work.
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What role do enzymes play in chemical reactions?
What role do enzymes play in chemical reactions?
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An __________ inhibitor binds to the active site of an enzyme.
An __________ inhibitor binds to the active site of an enzyme.
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What is feedback inhibition?
What is feedback inhibition?
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All redox reactions involve complete transfer of electrons.
All redox reactions involve complete transfer of electrons.
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What process allows cells to couple exergonic and endergonic reactions?
What process allows cells to couple exergonic and endergonic reactions?
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In cellular respiration, the breakdown of glucose is an __________ process.
In cellular respiration, the breakdown of glucose is an __________ process.
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Which of the following describes a redox reaction?
Which of the following describes a redox reaction?
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Match the following terms to their correct definitions:
Match the following terms to their correct definitions:
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Study Notes
Course Information
- Course Title: AUBIO 111: Functional Biology
- Instructor: Dr. Kevin Yoon, PhD
- Email: [email protected]
- Semester: Fall 2024
- Section: A01
Midterm 2 Review
- Date: Monday, November 25th
- Time: 11:00 AM - 12:00 PM
- Format: In-person
- Materials: Physical copies; bring OneCard or student ID number
- Duration: 60 minutes
- Total marks: 40
- Multiple choice questions: 26 marks (1 min 30 sec per mark)
- Short answer questions: 14 marks
- Recommended materials: Blue or black pens; calculators not necessary
Content Outline
- Metabolism and Enzymes (8 marks)
- Cellular Respiration (9 marks)
- Photosynthesis (10 marks)
- Cell Communication (11 marks)
- Cell Cycle/Mitosis (12 marks)
- Disclaimer: This is a brief review, not a comprehensive coverage of the concepts.
Chapter 8: An Introduction to Metabolism
- An organism's metabolism transforms matter and energy according to the laws of thermodynamics.
- The free-energy change (∆G) of a reaction determines if a reaction will occur spontaneously.
- ATP powers cellular work by coupling exergonic reactions to endergonic reactions.
- Enzymes speed up metabolic reactions by lowering activation energy barriers.
- Regulation of enzyme activity helps control metabolism.
Metabolic Pathways
- Metabolic pathways begin with a substrate/reactant and end with a product.
- Each step is catalyzed by a specific enzyme.
- Regulation of key steps in the pathway is vital.
- Catabolism releases energy, while anabolism consumes it.
- Pathways are often interconnected.
Energy
- Energy is the capacity to cause change.
- Energy exists in various forms, some of which can perform work.
- Forms of energy include kinetic energy, thermal energy/heat, potential energy, and chemical energy.
- Energy can be converted (transformed) from one form to another.
Laws of Thermodynamics
- Thermodynamics is the study of energy transformations.
- An isolated system cannot exchange energy or matter.
- A closed system can exchange energy but not matter.
- An open system can exchange both energy and matter.
- Organism's are open systems.
- Primarily focused on the first and second law of thermodynamics.
The First Law of Thermodynamics
- The total energy of the universe is constant; energy cannot be created or destroyed.
- Energy can be transferred and transformed.
The Second Law of Thermodynamics
- Every energy transfer or transformation increases the entropy (disorder) of the universe.
- Some energy is unusable after each transfer or transformation.
- Spontaneous processes are characterized by a decrease in free energy and increase in entropy.
- ∆Stotal = ∆Ssystem + ∆Ssurroundings
Free-Energy Change (∆G)
- ∆G = ∆H - T∆S (H = enthalpy or total energy; T = absolute temperature, S = entropy, -T∆S is the entropy change.)
- ∆G < 0 (negative value) → Spontaneous (exergonic) reaction
- ∆G > 0 (positive value) → Non-spontaneous (endergonic) reaction
- ∆G = 0 (zero) → System in equilibrium.
Free Energy, Stability, and Work
- Free energy is a measure of a system's instability, its tendency to change to a more stable state.
- Equilibrium is a state of maximum stability.
- A process is spontaneous and can perform work only when it is moving towards equilibrium.
- During a spontaneous change, the free energy decreases and the stability of the system increases.
Exergonic and Endergonic Reactions
- Exergonic reactions: net release of free energy, spontaneous (∆G < 0)
- Endergonic reactions: absorb free energy from their surroundings, nonspontaneous (∆G > 0)
ATP Powers Cellular Work
- Chemical, transport, and mechanical work are the three main kinds of cellular work.
- Cells manage energy resources by energy coupling: use of an exergonic process to drive an endergonic one.
- ATP (adenosine triphosphate) is the cell's energy shuttle.
ATP Hydrolysis
- Bonds between phosphate groups of ATP can be broken by hydrolysis, releasing free energy.
- The released energy comes from the chemical change to a state of lower energy, not from the phosphate bonds themselves.
How ATP Hydrolysis Powers Cellular Work
- In the cell, the energy from the exergonic reaction of ATP (adenosine triphosphate) hydrolysis can be used to drive an endergonic reaction.
- Overall, the coupled reactions are exergonic (∆GNet < 0).
Activation Energy Barrier
- Initial energy needed to start a chemical reaction (activation energy or free energy of activation).
- Often supplied in the form of thermal energy that reactant molecules absorb.
Enzymes
- Catalysts that speed up a reaction without being consumed.
- They help the reaction overcome its activation energy barrier.
How Enzymes Speed Up Reactions
- Enzymes catalyze reactions by lowering EA.
- They do not affect the change in free energy (∆G) of a reaction but speed it up; reactions would eventually occur without them.
Catalytic Cycle of an Enzyme
- Substrates enter the active site; enzyme changes shape (induced fit).
- Substrates are held in the active site by weak interactions.
- The active site lowers EA and speeds up the reaction.
- Substrates are converted to products.
- Products are released.
Enzyme Inhibitors
- Competitive inhibitors bind to the active site of an enzyme.
- Compete with the substrate.
- Noncompetitive inhibitors bind to an enzyme at a separate site.
- Cause a conformational change.
Allosteric Regulation
- Most allosterically regulated enzymes contain multiple polypeptide subunits.
- Each enzyme has active and inactive forms.
- Binding of an activator stabilizes the active form of an enzyme.
- Binding of an inhibitor stabilizes the inactive form.
- Cooperativity is a form of allosteric regulation, amplifying enzyme activity.
Feedback Loops
- End product of a reaction affects the reaction.
- Negative feedback inhibition: creation of the end product halts the reaction.
- Positive feedback can have an important role as well.
Chapter 9: Cellular Respiration and Fermentation
- Catabolic pathways yield energy by oxidizing organic fuel.
- Glycolysis harvests chemical energy by oxidizing glucose to pyruvate.
- Pyruvate is oxidized, the citric acid cycle completely oxidizes organic molecules.
- Oxidative phosphorylation, chemiosmosis couples electron transport to ATP synthesis.
- Fermentation and anaerobic respiration enable cells to produce ATP without the use of oxygen; less efficient.
- Glycolysis and the citric acid cycle connect to many other metabolic pathways.
Catabolic Pathways and ATP Production
- Breakdown of organic molecules is exergonic (free energy is released).
- Aerobic respiration consumes organic molecules and O2, yielding ATP (much more efficient than anaerobic respiration or fermentation).
- Anaerobic Respiration uses compounds other than O2.
- Fermenation is partial degradation of sugars without O2.
Cellular Respiration
- Refers to both aerobic and more generally anaerobic respiration, but is often used specifically to refer to aerobic respiration.
- Demonstrated often with glucose: C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O + Energy (ATP and heat)
Redox Reactions
- Reducing agent = electron donor (becomes oxidized)
- Oxidizing agent = electron acceptor (becomes reduced)
- Redox reactions often involve partial electron shifts in covalent bonds rather than complete transfer.
Principles of Redox Reactions
- Oxygen and other electronegative atoms are potent oxidizing agents.
- As organic molecules are oxidized, the electron energy state decreases and is used to synthesize ATP. Glucose becomes oxidized and forms CO2; Oxygen becomes reduced forming water.
Substrate-Level Phosphorylation
- A small amount of ATP is formed during glycolysis and the citric acid cycle via substrate-level phosphorylation.
Overview of Cellular Respiration
- Shows the generalized steps from glucose to ATP production.
- Glycolysis, pyruvate oxidation, citric acid cycle, and oxidative phosphorylation (electron transport and chemiosmosis).
- Each step and its location are noted.
Glycolysis
- Breaks down glucose to pyruvate.
Pyruvate Oxidation & The Citric Acid Cycle
- Breakdown of glucose from pyruvate to acetyl CoA.
- The citric acid cycle completes glucose breakdown.
Oxidative Phosphorylation
- Accounts for most of ATP synthesis.
- Electron transport chain and chemiosmosis.
- H+ gradient created across the inner mitochondrial membrane drives ATP synthesis.
Chemiosmosis
- Use of energy in a H+ gradient (proton-motive force) to drive cellular work.
- H+ is pumped from the mitochondrial matrix to the intermembrane space, creating a gradient that drives ATP synthesis.
- ATP synthase uses the exergonic flow of H+ to drive the phosphorylation of ADP.
Energy Production Summary/Overview
- The total ATP yield from maximum oxidation of glucose is about 30–32 ATP molecules.
Producing Energy Without O2 (Anaerobic Respiration & Fermentation)
- Anaerobic respiration utilizes an electron transport chain but with a final electron acceptor other than O2.
- Fermentation enables glycolysis to continue to make ATP by substrate-level phosphorylation in the absence of oxidative phosphorylation driven by the ETC.
Alcohol Fermentation
- Pyruvate is converted to ethanol (yeast).
- Releases CO2 and regenerates NAD+.
- Used in brewing, winemaking, and baking
Lactic Acid Fermentation
- Pyruvate is reduced to lactate.
- Used by some fungi and bacteria in food production (cheese and yogurt)
- Regenerates NAD+ so glycolysis can continue producing a small amount of ATP when oxygen is scarce.
Chapter 10: Photosynthesis
- Photosynthesis converts light energy into chemical energy (food).
- Light reactions convert solar energy into chemical energy of ATP and NADPH.
- Calvin cycle uses chemical energy of ATP and NADPH to reduce CO2 to sugar.
Location of Photosynthesis (in Plants)
- Leaves are the major locations of photosynthesis.
- Large, flat area for sunlight exposure.
- Found in mesophyll cells between epidermal layers.
- Chlorophyll found in internal thylakoid membranes (stacked into grana).
- Thylakoid lumen is the internal soluble compartment.
Photosystem
- System of chlorophyll and protein subunits.
- Reaction centre complex surrounded by light-harvesting complexes.
- Light-harvesting complexes transfer photons to the reaction center.
Linear Electron Flow
- Photosystem II (PSII) is where water is split.
- Electrons are passed through the electron transport chain to Photosystem I(PSI) converting NADP+ to NADPH.
- ATP is produced from ADP utilizing the energy released from the electrons passed down the electron transport chain
Cyclic Electron Flow
- PSII is not involved
- Only PSI is used and produces only ATP but no NADPH.
The Calvin Cycle
- Carbon enters as CO2 and leaves as glyceraldehyde 3-phosphate (G3P).
- Cycle must turn three times to produce one G3P. This fixes three CO2 molecules.
Photorespiration
- Rubisco uses O2 instead of CO2 which is a wasteful energy consumption pathway in C3 plants.
- Results in the release of CO2 without making sugars or ATP
Chapter 11: Cell Communication
- External signals are converted into cellular responses.
- Reception, Transduction, and Response (stages) are noted.
- Apoptosis is programmed cell death and integrated multiple cell signaling pathways.
Ability to Respond
- Ability of a cell to respond depends on the presence of specific receptors to the signal.
- A signal must be recognized as a signal to be effective.
Cell Signaling Types (Local Signaling)
- Juxtacrine: two cells are touching or right beside each other.
- Paracrine: nearby cells communicate through ligands.
- Endocrine (hormones-long distance signaling): two cells communicate via bloodstream.
Cell Signaling Types
- Reception, Transduction, and Response
Reception (signal input)
- Binding between signal molecule (ligand) and receptor is highly specific.
- A conformational change in the receptor is often the initial transduction of the signal.
- Most signal receptors are plasma membrane proteins (cell-surface receptors).
Intracellular Receptors
- Intracellular receptor proteins are found in the cytosol or nucleus of target cells.
- Small or hydrophobic chemical messengers can readily cross the membrane and activate these receptors.
Transduction (relay of signals)
- Usually involves multiple steps, allowing signal amplification.
- Provides more opportunities for coordination and regulation of the cellular response.
Comparison of Molecular Switches
- Similarities and differences of signaling by protein phosphorylation and using GTP-binding proteins.
Signal Cascade
- One active kinase can phosphorylate multiple target molecules.
- Results in signal amplification.
Second Messengers
- Small, non-protein, water-soluble molecules or ions, that spread throughout a cell by diffusion.
- Examples include cyclic AMP (cAMP) and calcium ions (Ca2+).
- Second messengers participate in pathways initiated by GPCRs and RTKs.
cAMP
- Many adenyl cyclases are activated downstream of GPCRs.
- cAMP activates protein kinase A, which phosphorylates various other proteins.
- Regulation is provided by G-protein systems.
Calcium Ions and Inositol Triphosphate (IP3)
- Activated G proteins activate phospholipase C.
- Triggers production of two signaling molecules (DAG and IP3).
- Leads to calcium ion release into the cytosol and activation of protein kinase C.
Response (signal output)
- Ultimately, a signal transduction pathway leads to regulation of one or more cellular activities.
- Underlying molecular response may occur in the nucleus or cytoplasm.
Responses to regulate the signal
- Amplification of the signal
- Specificity of the response
- Overall efficiency of response, enhanced by scaffolding proteins
- Signal termination.
Apoptosis
- Programmed (controlled) cell death.
- Cellular components systematically broken down and digested by scavenger cells.
Molecular Basis of Apoptosis
- Caspases are the main proteases.
- Carry out apoptosis via a cascade.
Chapter 12: Cell Cycle/Mitosis
- Cell division results in genetically identical daughter cells.
- Mitotic phase alternates with interphase.
- Regulated by a molecular control system.
- Cancer is characterized by uncontrolled cell cycle.
How Do Cells Divide?
- Eukaryotic cell division consists of mitosis (division of the genetic material) and cytokinesis (division of the cytoplasm).
- Specialized cell division (meiosis) produces non-identical haploid cells.
- The process is discussed in the context of chromosomes and their movements.
Chromosomes
- DNA is packaged into chromosomes, which consists of chromatin (DNA and protein).
- Chromosomes condense during cell division.
(Replicated) Chromosomes vs. Chromatids
- A replicated chromosome consists of two sister chromatids held together by cohesins.
- The centromere is the constricted region that links sister chromatids and is where microtubules attach.
Phases of the Cell Cycle
- Interphase: cell growth and DNA replication.
- Mitotic phase: mitosis (division of genetic material), and cytokinesis (division of cytoplasm).
- G1 phase ("first gap"), S phase ("synthesis"), and G2 phase ("second gap"), subphases of interphase.
How Do Cells Divide (Mechanisms)?
- Overview of mechanisms of cell division in eukaryotes (mitosis) and prokaryotes (binary fission)
Mitotic Spindle
- Protein complexes that help in moving chromosomes to opposite poles during mitosis; involved in chromosome separation.
Cytokinesis
- Cytokinesis involves the formation of a cleavage furrow in animal cells and a cell plate in plant cells.
- Contractile ring of microfilaments and myosin in animal cells, while vesicles fuse to form the cell plate in plants to separate the daughter cells.
Cell Cycle Control System
- Sequential events of the cell cycle are directed by a cell cycle control system.
- Cell cycle pauses at specific checkpoints to ensure accurate progression.
Cyclins and Cyclin-Dependent Kinases (CDKs)
- Two types of regulatory proteins involved in cell cycle control: Cyclins and CDKs.
- Cyclins control CDK activity; binding of cyclin activates CDK.
- Cyclic dependent kinases (CDKs) activity is proportional to the concentration of cyclin present.
Questions?
- Open-ended question for potential questions from the class on the material.
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Description
Test your knowledge on the light reactions of photosynthesis and key processes in cellular respiration. This quiz covers important concepts such as the Calvin cycle, ATP synthase, and fermentation. Challenge your understanding of how energy is produced and utilized in living organisms.
