Biol 215 Exam 2 Study

What is energy?

The capacity to do work (to cause change).

Compare potential and kinetic energy. Classify different energy forms.

• Potential Energy: Stored energy.

  • Examples: Chemical energy (bonds & atoms), Concentration gradient (across membranes).

• Kinetic Energy: Energy of motion.

  • Examples: Electrical, Radiant, Thermal, Motion energy.

Why do cells need energy? What are types of cellular work?

Cells need energy to perform various functions essential for life. Types of cellular work include

• Synthetic Work: Biosynthesis of macromolecules.

• Mechanical Work: Movement (e.g., muscle contraction, flagella motion).

• Concentration Work: Active transport across membranes.

• Electrical Work: Ion gradients (e.g., nerve signaling).

• Heat Generation: Regulating temperature.

• Light Generation: Bioluminescence.

Define an organism based on its energy-converting abilities (e.g. autotroph, heterotroph, chemotroph, phototroph, photoautotroph, chemoheterotroph).

1. Autotroph - organism that produce organic compounds form inorganic molecules

2. Heterotrophs - organisms that produces organic compounds starting from other organic molecules

3. Phototroph - able to capture light E and transform into chemical E

4. Chemotroph - obtains energy by oxidizing bonds in molecules

Explain how energy and matter are used in the biosphere. Specifically explain this statement: "Energy flows through the biosphere while matter is recycled". Explain why energy must be replenished (i.e. heat loss). 

Energy from the sun enters the biosphere through photosynthesis, powering ecosystems, while matter cycles through various forms and organisms. Energy is lost as heat during these processes, necessitating a constant supply from external sources.

Define 'thermodynamics

The study of Energy transformations. Energy can be converted from one form to another. Cells/organisms extract E and use it to perform work

First Law of Thermodynamics

Energy cannot be created or destroyed, only transformed; for example, in a closed system, the total energy remains constant.

Second Law of thermodynamics

Any energy transfer or transformation, the total entropy of a closed system will always increase, meaning that energy conversions are not 100% efficient and some energy is lost as heat.

Define free energy.

Energy available for work in a system; indicates spontaneity.

Define a spontaneous process

A process that occurs naturally without external intervention, typically accompanied by an increase in entropy.

What does ∆G tell us? What happens when ∆G = 0?

∆G tells us if a reaction is spontaneous.

When ∆G = 0, the system is at equilibrium, meaning no net work can be done.

How do free energy diagrams determine spontaneity?

If final energy is lower than initial energy (∆G < 0), the reaction is spontaneous.

Define and compare exergonic & endergonic reactions.

• Exergonic: Releases energy (∆G < 0).

• Endergonic: Requires energy (∆G > 0).

Provide examples of spontaneous processes. How does initial state compare to final state?

• Examples: Jumping off a diving board, diffusion, chemical reactions.

• Initial state has more energy than the final state.

What is entropy, and how does it relate to thermodynamics?

• Measure of disorder.

• The Second Law of Thermodynamics states that entropy increases with energy transformations.

What is the equilibrium constant (Keq) of a chemical reaction?

Keq is the ratio of products to reactants at equilibrium.

What information about a system can be derived from Keq?

If Keq < 1, more reactants are present. If Keq > 1, more products are present. If Keq = 1, the system is at equilibrium, and no work is done (∆G = 0).

What is activation energy (Ea) barrier, and how does it influence reaction rate?

Reactants must reach a higher energy state before the reaction proceeds. Ea is the amount of energy required for reactants to form products. Higher Ea = slower reaction; Lower Ea = faster reaction.

Does activation energy (Ea) influence ∆G?

No, Ea does not change ∆G.

Define metabolism.

Total collection of chemical reactions occurring in a cell.

Differentiate between catabolic and anabolic processes.

Anabolic: Synthesis pathways, endergonic. Catabolic: Breakdown pathways, exergonic.

What is energy coupling, and how do cells use it?

Links an exergonic reaction (energy-releasing) with an endergonic reaction (energy-consuming). Example: Glutamine formation is coupled to ATP hydrolysis.

What is the molecular structure of ATP?

ATP consists of adenine (nitrogenous base), ribose (sugar), and three phosphate groups.

What type of molecule is ATP?

A nucleotide that provides usable energy for cellular work.

What is 'inorganic phosphate' (Pi)?

A phosphate ion that carries a negative charge.

Types of enzymes involved in phosphate transfer?

1. Phosphorylase: Adds a phosphate group using inorganic phosphate.

2. Kinase: Transfers phosphate from ATP to a molecule.

3. Phosphatase: Removes a phosphate group through hydrolysis.

What are some roles of ATP in the cell?

1. Synthetic work (e.g., photosynthesis).

2. Mechanical work (e.g., weight lifting).

3. Heat production (e.g., when cold).

4. Bioluminescence (e.g., fireflies).

How do motor proteins use ATP?

Motor proteins bind ATP. ATP hydrolysis releases ADP + Pi, causing a conformational change that moves the motor protein along cytoskeletal elements.

Why did ATP evolve as the 'energy currency of the cell'?

1. Opposing negative charges of phosphate groups.

2. Decreased resonance stabilization.

3. Free energy release upon hydrolysis.

How do enzymes function?

Enzymes speed up chemical reactions by lowering activation energy.

What is the enzyme active site?

A cavity on the enzyme’s surface where substrate binding occurs, formed by the protein’s 3D conformation.

How does the active site relate to enzyme specificity?

The active site contains a specific set of amino acids that bind only particular substrates.

Why do living systems require enzymes?

Without enzymes, many biochemical reactions would take thousands of years. For example, sucrose breakdown without an enzyme would take 500 years but is sped up 200 trillion times with sucrase.

Compare uncatalyzed and catalyzed reaction rates.

Enzyme-catalyzed reactions occur much faster than uncatalyzed reactions.

What are the six major enzyme classes?

1. Oxidoreductases – Catalyze oxidation-reduction reactions.

2. Transferases – Transfer functional groups.

3. Hydrolases – Break bonds using water.

4. Lyases – Break bonds without water.

5. Isomerases – Rearrange molecules.

6. Ligases – Join molecules together.

What are some common enzyme types within the six classes?

1. Nuclease: Breaks nucleic acids by hydrolyzing nucleotide bonds.

2. Protease: Breaks proteins by hydrolyzing amino acid bonds.

3. Synthase: Synthesizes molecules by condensing smaller molecules.

4. Phosphorylase: Adds phosphate from inorganic sources.

5. Kinase: Transfers phosphate groups using ATP.

6. Phosphatase: Removes phosphate groups via hydrolysis.

7. ATPase: Hydrolyzes ATP to release energy.

8. ATP Synthase: Produces ATP.

How are enzymes regulated in the cell?

Enzymes are influenced by temperature (too high can denature proteins) and pH (optimal pH varies per enzyme).

What are competitive inhibitors?

Molecules that bind to the active site of an enzyme, preventing the substrate from binding.

What are noncompetitive inhibitors?

Molecules that bind to an allosteric site, causing a conformational change that slows down enzyme activity.

What is negative allosteric regulation?

When an inhibitor binds to an allosteric site, decreasing enzyme activity.

What is positive allosteric activation?

When an activator binds to an allosteric site, allowing the substrate to bind and increasing enzyme activity.

What is genetic regulation of enzymes?

The control of enzyme production through gene expression.

How does enzyme localization regulate enzyme activity?

By restricting enzymes to specific locations in the cell where their activity is needed.

Why is studying enzyme kinetics important?

It helps us understand how fast an enzyme converts reactants into products and how inhibitors or activators affect reaction rates.

What is an application of enzyme kinetics?

The antibiotic penicillin inhibits enzymes involved in bacterial replication.

How is spectrophotometry used to analyze enzyme kinetics?

It measures the amount of light absorbed by a sample, allowing researchers to track the rate at which substrate disappears or product forms.

Why do you need a light-absorbing species for spectrophotometry to work?

The sample must absorb light at a specific wavelength to measure concentration changes over time.

What is the relationship between reaction velocity and substrate concentration in Michaelis-Menten kinetics?

A hyperbolic relationship—velocity increases with substrate concentration until it reaches Vmax.

What is the Michaelis-Menten equation?

V = Vmax[S] / (Km + [S]).

What is Vmax?

The maximum reaction velocity an enzyme can achieve.

Why is there a limiting reaction velocity for an enzyme-catalyzed reaction?

Because all enzyme active sites become saturated with substrate at high concentrations.

What is Km?

The Michaelis constant, which represents the substrate concentration at which the reaction velocity is half of Vmax.

What does Km tell us?

It indicates an enzyme’s substrate affinity—lower Km means higher affinity, and higher Km means lower affinity.

How would an enzyme with a low Km function inside a cell?

It has a high affinity for the substrate and requires only a small amount of substrate to become saturated.

How would an enzyme with a high Km function inside a cell?

It has a low affinity for the substrate and requires a high concentration of substrate to reach Vmax.

What is a Michaelis-Menten plot (direct plot)?

A hyperbolic graph showing reaction velocity versus substrate concentration.

What is a Lineweaver-Burk plot (double-reciprocal plot)?

A linear transformation of the Michaelis-Menten equation obtained by plotting 1/V vs. 1/[S].

How does a competitive inhibitor affect kinetic parameters?

Increases Km (decreases enzyme-substrate affinity) but does not affect Vmax.

How does a non-competitive inhibitor affect kinetic parameters?

Lowers Vmax but does not change Km.

What is the ‘fluid mosaic’ model of cell membranes?

A model that describes the membrane as a flexible, dynamic structure with various components (lipids, proteins, and carbohydrates) distributed throughout.

What are the functional roles of cell membranes?

Barrier: Separates the inside of the cell from the external environment. Organization & Localization: Keeps cellular functions compartmentalized. Transport: Controls movement of substances in and out of the cell. Signal Detection & Communication: Allows cells to respond to signals.

What are fatty acids?

Lipids with a carboxyl head and hydrocarbon tail, serving as building blocks for more complex lipids.

What are triglycerides?

Lipids made of glycerol and three fatty acids, used for long-term energy storage.

What are phospholipids?

Lipids with hydrophilic heads and hydrophobic tails, forming the main structure of cell membranes.

What are glycolipids?

Lipids with carbohydrate chains, important for cell recognition and signaling.

What are steroids?

Lipids with four fused rings, including cholesterol, which helps maintain membrane fluidity.

How does substrate concentration (S) affect reaction velocity (v) in Michaelis-Menten kinetics?

Low [S]: v increases linearly with [S]. High [S]: v reaches Vmax and becomes independent of [S]. [S] = Km: v = 1/2 Vmax, meaning the enzyme is at half-max velocity.

What do we mean by membrane "faces" or "leaves"?

Each half of a bilayer is called a face:

• Extracellular face (outside the cell)

• Cytosolic face (inside the cell)

How do glycolipids determine ABO blood groups?

Glycolipids act as antigens on red blood cells (RBCs).

• Antibodies form against antigens not present on an individual’s RBCs.

• Group A: Has A antigens, forms anti-B antibodies.

• Group B: Has B antigens, forms anti-A antibodies.

• Group AB: Has both A and B antigens, no antibodies.

• Group O: Has no antigens, forms both anti-A and anti-B antibodies.

What is the optimal level for total blood cholesterol?

<200 mg/dL

What are lipoproteins, and why are they important?

Lipoproteins transport lipids in the blood.

• Structure:

  • Surface: Phospholipids, cholesterol, proteins

  • Core: Triglycerides and/or cholesterol

• Function: Help in digestion and transport of lipids.

How do HDL and LDL differ in structure and function?

• HDL (High-Density Lipoprotein): “Good” cholesterol, transports cholesterol from body cells → liver.

• LDL (Low-Density Lipoprotein): “Bad” cholesterol, transports cholesterol from liver → body cells.

Why is it incorrect to say "good" and "bad" cholesterol?

Cholesterol itself is the same; the lipoproteins that carry it determine health effects.

What is atherosclerosis?

A vascular disease where artery walls thicken and develop plaque, leading to high blood pressure and potential blockages.

What experimental evidence supports membrane protein mobility?

FRAP (Fluorescence Recovery After Photobleaching):

• Tracks movement of membrane proteins after part of the membrane is bleached.

• Shows lateral movement of proteins through diffusion.

• Proteins can rotate and, less frequently, flip-flop between bilayer layers.

What are the different classes of membrane proteins?

1. Integral proteins: Embedded within the membrane.

2. Peripheral proteins: Attached to membrane surfaces.

3. Lipid-anchored proteins: Covalently bound to lipids.

How does hydropathy analysis predict membrane protein structure?

• Uses known nucleic acid/protein sequences to predict transmembrane segments.

• Identifies clusters of hydrophobic residues.

• Generates a hydropathy index:

  • + values = hydrophobic (likely membrane-spanning)

  • - values = hydrophilic (likely exposed to water)

• Data is plotted on a hydropathy plot.

How can a hydropathy plot predict protein orientation in a membrane?

• Signal sequences and hydrophobic regions help determine which parts of a protein are embedded in the membrane and which face the cytosol or extracellular space.

What is Tm in membrane biology?

Transition temperature, where the membrane is optimally fluid and functional.

• Below Tm → Membrane becomes too rigid.

• Above Tm → Membrane becomes too fluid.

How do cells regulate membrane fluidity?

By altering membrane lipid composition (fatty acid length, saturation).

What is homeoviscous adaptation?

Cells adjust membrane fluidity by changing fatty acid length or introducing double bonds in response to temperature changes.

Compare diffusion, facilitated diffusion, active transport, and bulk transport.

• Diffusion: Passive movement from high to low concentration, no energy required.

• Facilitated Diffusion: Uses transport proteins for large/polar molecules, no energy required.

• Active Transport: Moves substances against concentration gradient, requires energy (ATP).

• Bulk Transport: Moves large molecules or large amounts via vesicles (endocytosis/exocytosis).

What factors affect membrane permeability?

• Size: Small molecules (<100 Da) pass easily.

• Polarity: Nonpolar molecules cross more easily.

• Charge: Charged molecules have low permeability.

Define osmolarity and calculate it.

Osmolarity = Molarity × Number of Dissociated Particles

Predict cell reactions in different tonicities.

• Hypertonic: Water leaves the cell → shrinks.

• Isotonic: No net water movement → stable.

• Hypotonic: Water enters the cell → swells.

How does a Paramecium regulate osmosis?

Lives in a hypotonic environment → contractile vacuole pumps water out to prevent bursting.

How do transport proteins facilitate diffusion?

Help move large, polar, or charged molecules (e.g., glucose transporters) across the membrane without energy.

What is the difference between direct and indirect active transport?

• Direct Active Transport: Uses ATP (e.g., Na+/K+ pump).

• Indirect Active Transport: Uses ion gradients to drive movement of other substances.

Explain the Na+/K+ pump mechanism.

1. 3 Na+ bind inside the cell (E1 conformation).

2. ATP phosphorylates the pump → switches to E2 conformation.

3. Na+ is released outside.

4. 2 K+ bind outside.

5. Dephosphorylation shifts pump back to E1 → K+ enters the cell.

How does the Na+/Glucose symporter work?

Uses Na+ gradient (created by the Na+/K+ pump) to bring glucose into the cell against its concentration gradient.

What is membrane potential (V_m)

The charge difference across a membrane.

• Inside the cell: Negative

• Outside the cell: Positive

• Electrochemical gradient: Combines membrane potential & concentration gradient to drive ion movement.

How does a CFTR defect cause cystic fibrosis?

CFTR normally moves Cl⁻ out of cells, driving water movement.

• Defective CFTR → Cl⁻ and Na⁺ stay inside → no water movement → thick mucus buildup.

What are the types of bulk transport?

• Exocytosis: Vesicles fuse with membrane to export substances (e.g., mucus, enzymes).

• Endocytosis: Membrane engulfs substances to import them.

  • Receptor-Mediated Endocytosis: Selective uptake using receptors (e.g., LDL uptake).

  • Pinocytosis: "Cell drinking" (fluid uptake).

  • Phagocytosis: "Cell eating" (engulfing large particles).

How are LDLs taken up by cells?

LDL receptors bind LDL, triggering receptor-mediated endocytosis.

What causes familial hypercholesterolemia (FH)?

Defective or missing LDL receptors → LDL cannot be removed from blood → high cholesterol levels (~650 mg/dL).

What is ACE2, and what does it do?

Angiotensin-Converting Enzyme 2 (ACE2) hydrolyzes angiotensin II to angiotensin 1-7, which lowers blood pressure.

What is the difference between vasoconstriction and vasodilation?

• Vasoconstriction: Narrows blood vessels → increases BP.

• Vasodilation: Widens blood vessels → decreases BP.

• ACE2 promotes vasodilation.

How does SARS-CoV-2 enter cells?

Binds to ACE2 receptors, tricking the cell into endocytosing the virus.