notes
Biochemistry Notes – Explained From Scratch
What even is an enzyme?
Think of your body as a giant chemistry lab running thousands of chemical reactions every second — digesting food, making energy, building muscles, etc. The problem is most of those reactions are way too slow on their own. Your body doesn't have time to wait.
That's where enzymes come in. Enzymes are proteins that act as biological catalysts — they speed up chemical reactions without getting used up themselves. They grab molecules, help them react, then let go and do it again. Over and over.
A molecule that an enzyme works on is called a substrate. The enzyme has a special pocket called the active site where the substrate fits in, kind of like a lock and key.
Chapter 13 – How Enzymes Work
Catalytic Power
This is just a way of measuring how much faster an enzyme makes a reaction go compared to no enzyme at all. Some enzymes make reactions happen 10²⁶ times faster. That's a 1 followed by 26 zeros. For reference, the enzyme urease speeds up its reaction 100 trillion times (10¹⁴). Without enzymes, you simply could not be alive.
Specificity
Enzymes are picky. Each enzyme usually only works on one specific substrate, or a very small group of similar ones. The shape and chemistry of the active site only matches certain molecules — like how a specific key only opens one lock. This is called specificity.
Regulation
Your body doesn't want enzymes running at full speed all the time — that would be wasteful or even harmful. So enzymes can be turned up or down depending on what the cell needs. Think of it like a dimmer switch rather than just on/off.
Coenzymes and Cofactors
Some enzymes need a little helper to work. These helpers are called coenzymes (if they're organic molecules, like vitamins) or cofactors (if they're metal ions like zinc or magnesium). Without their helper, the enzyme doesn't function.
Enzyme Kinetics – How We Measure Enzyme Speed
The Saturation Effect
Imagine an enzyme as a single cashier at a grocery store. If only a few customers (substrate molecules) show up, the cashier handles them easily and the line moves quickly. As more customers arrive, the cashier gets busier. Eventually there are so many customers that the cashier is working as fast as humanly possible — adding more customers doesn't speed things up anymore. The cashier is saturated.
That's exactly how enzymes behave:
At low substrate concentration: the more substrate you add, the faster the reaction (first-order kinetics)
At high substrate concentration: the enzyme is maxed out, adding more substrate does nothing (zero-order kinetics)
The Michaelis-Menten Equation
Scientists made a formula to describe this behavior:
V₀ = Vmax[S] / (Km + [S])
Here's what each piece means in plain English:
V₀ — the speed of the reaction right now
Vmax — the maximum possible speed (when the enzyme is fully saturated)
[S] — how much substrate is present
Km — the amount of substrate needed to reach half of Vmax
Km is really important. A low Km means the enzyme reaches half speed even with very little substrate around — meaning it has a high affinity (love) for its substrate. A high Km means the enzyme needs a lot of substrate to get going — low affinity.
Turnover Number (kcat)
This tells you how many substrate molecules one single enzyme molecule can convert to product per second when it's working at full speed. Some enzymes do a few per second. Some do millions. It's a measure of how productive one enzyme molecule is.
Catalytic Efficiency (kcat/Km)
This is the ultimate measure of how good an enzyme is. It combines speed AND affinity into one number. The highest possible value is set by how fast the enzyme and substrate can physically bump into each other in solution (the diffusion limit). Enzymes that reach this limit are considered "perfect" enzymes.
Enzyme Inhibition – Ways to Slow an Enzyme Down
Sometimes molecules can block or slow down an enzyme. This is called inhibition and it's actually really useful — many drugs work this way.
Competitive Inhibition
The inhibitor looks similar to the real substrate and tries to sneak into the active site. It's literally competing with the substrate for the same spot. If you add more substrate, you can out-compete the inhibitor and the enzyme gets back to normal speed.
Km goes up (enzyme seems less attracted to substrate)
Vmax stays the same (you can still reach full speed with enough substrate)
Uncompetitive Inhibition
The inhibitor doesn't touch the free enzyme at all. It only grabs onto the enzyme after the substrate has already bound. It locks the substrate in and makes everything worse.
Both Km AND Vmax decrease
You can't overcome this by adding more substrate
Pure Noncompetitive Inhibition
The inhibitor binds to a completely different spot on the enzyme (not the active site) and it doesnds't matter if the substrate is there or not. It just makes the enzyme work worse overall.
Vmax decreases
Km stays the same
Irreversible Inhibition
The inhibitor permanently destroys the enzyme. No coming back. Penicillin works this way — it permanently disables an enzyme bacteria need to build their cell walls. No cell wall = dead bacteria.
Chapter 14 – How Enzymes Actually Speed Things Up
The Energy Barrier Problem
For any chemical reaction to happen, molecules need to get over an energy hump first — called the activation energy. Think of it like pushing a boulder over a hill. Enzymes lower that hill, making it much easier for the reaction to happen.
Transition State Stabilization
At the top of that energy hill, molecules are in a weird, unstable, high-energy shape called the transition state. Enzymes are specially shaped to grip and stabilize this transition state — they essentially hold the molecule in the shape it needs to be in to react. The better the enzyme grips the transition state, the faster the reaction goes.
Transition State Analogs (TSAs)
These are drugs designed to look like the transition state. Since the enzyme's active site is perfectly shaped to grab the transition state, these drugs bind incredibly tightly and block the enzyme. Many blockbuster drugs are TSAs:
Statins — block an enzyme in cholesterol production
Tamiflu — blocks a flu virus enzyme
Protease inhibitors — block HIV enzymes (AIDS drugs)
Covalent Catalysis
Sometimes the enzyme temporarily forms a chemical bond with the substrate to help the reaction along. The enzyme and substrate literally stick together briefly, react, then separate. The enzyme comes out unchanged and ready to go again.
General Acid-Base Catalysis
The enzyme donates or accepts a proton (H⁺) at exactly the right moment to help the reaction happen. This is incredibly precise chemistry happening inside the enzyme's active site.
Serine Proteases
These are a family of enzymes (trypsin, chymotrypsin, etc.) that cut proteins. They have three amino acids that work as a team called the catalytic triad: His57, Asp102, and Ser195. These three residues work together like a molecular machine to attack and cut peptide bonds. Ser195 is the one that actually does the cutting — the other two help set it up.
Chapter 15 – How the Cell Controls Enzyme Activity
Why Regulation Matters
Your cells are constantly changing what they need. Sometimes you need more energy, sometimes less. Sometimes you need to build things, sometimes break things down. Enzyme regulation lets the cell respond to these changing needs in real time.
Allosteric Regulation
Some enzymes have a second binding site (not the active site) called the allosteric site. Molecules can bind here and change the shape of the entire enzyme — either activating it or inhibiting it. This is like having a remote control for the enzyme.
MWC Model (Concerted Model)
This explains how multi-subunit enzymes (enzymes made of multiple protein chains) are regulated. Imagine a team of workers that all have to be in the same mood — either all motivated (R state = relaxed = active) or all lazy (T state = taut = inactive). They all switch together at the same time. No mixed states allowed.
KNF Model (Sequential Model)
This is the alternative explanation. Here, one worker changes mood first, and that gradually influences the others. Changes happen one subunit at a time. This model can also explain negative cooperativity — where binding of one substrate makes it harder for the next one to bind.
Phosphorylation Regulation
This is the most common way cells control enzymes using covalent modification. A protein kinase enzyme adds a phosphate group to your enzyme, which changes its shape and either turns it on or off. A phosphatase enzyme can remove that phosphate group and reverse the change. It's like a molecular on/off switch that can be flipped back and forth.
Glycogen Phosphorylase – A Perfect Example
This enzyme breaks down glycogen (your body's glucose storage) to release energy. It's regulated in two ways:
Allosterically: AMP (low energy signal) turns it ON. ATP and glucose-6-phosphate (high energy signals) turn it OFF. Makes total sense — break down glycogen when energy is low, stop when you have plenty.
Covalently: Phosphorylation converts it from the b form (less active) to the a form (more active and no longer sensitive to allosteric signals). This is used in stress/emergency situations.
Hemoglobin – A Famous Example of Cooperative Binding
Hemoglobin (Hb) is the protein in your red blood cells that carries oxygen. It has four subunits, each capable of binding one oxygen molecule.
Cooperative Binding
When the first oxygen binds, it changes the shape of hemoglobin slightly, making it easier for the second oxygen to bind, and so on. This means hemoglobin picks up oxygen very efficiently in the lungs (where oxygen is abundant) and drops it off very efficiently in your tissues (where oxygen is scarce). A lone oxygen-carrying protein without cooperativity couldn't do this nearly as well.
The Bohr Effect
When you exercise, your muscles produce CO₂ and acid (H⁺). These H⁺ ions bind to hemoglobin and change its shape, making it release oxygen. This is perfect — the harder your muscles are working (more CO₂ and acid), the more oxygen gets released right where it's needed. In the lungs, CO₂ gets exhaled and H⁺ is consumed, so hemoglobin goes back to holding oxygen tightly.
2,3-BPG
This molecule lives inside red blood cells and fits into a pocket in the middle of hemoglobin. It locks hemoglobin in the "let go of oxygen" shape, tuning how much oxygen gets released in tissues. Fetal hemoglobin has a slightly different structure that doesn't grip BPG as well, so it holds onto oxygen more tightly — allowing the fetus to steal oxygen from mom's blood. Clever.
Sickle-Cell Anemia
One tiny change in hemoglobin — a single amino acid swap (glutamate → valine at position 6 of the β chain) — causes the whole disease. Valine is hydrophobic (water-avoiding), so it creates a sticky patch on the outside of the protein. Hemoglobin molecules start sticking to each other and forming long fibers, warping red blood cells into crescent shapes. These sickle-shaped cells get stuck in capillaries and cause all kinds of damage.
Chapter 18 – Glycolysis (Breaking Down Glucose for Energy)
The Big Picture
Glycolysis is the first step in getting energy from glucose. It happens in the cytoplasm (no special organelle needed) and doesn't require oxygen. You take one glucose molecule and break it into two smaller molecules called pyruvate, and in the process you make a small amount of ATP (energy currency) and NADH (electron carrier).
Net result: 1 glucose → 2 pyruvate + 2 ATP + 2 NADH
Why Glucose Gets Phosphorylated First
The very first thing that happens is glucose gets a phosphate group added to it (hexokinase does this, using one ATP). This traps glucose inside the cell — phosphorylated glucose can't cross the cell membrane. Smart.
Two Phases
Phase 1 (investment): You spend 2 ATP to activate and split glucose. Think of it as spending money to make money.
Phase 2 (payoff): You get 4 ATP back. Net gain = 2 ATP.
What Happens to Pyruvate?
Oxygen available (aerobic): Pyruvate goes into the mitochondria and gets fully broken down for a lot more ATP
No oxygen (anaerobic): Pyruvate gets converted to lactate (in your muscles — this is what causes the burn) or to ethanol and CO₂ (in yeast — this is how beer and bread are made)
Regulation
Glycolysis is controlled at three key steps where the reactions are essentially irreversible. These are the "checkpoints" — hexokinase, phosphofructokinase (PFK), and pyruvate kinase. PFK is the most important — it's the main throttle of glycolysis. High ATP signals "we have enough energy, slow down." High AMP signals "we're running low, speed up."
Chapter 19 – The TCA Cycle (The Cell's Energy Hub)
The Big Picture
After glycolysis, pyruvate enters the mitochondria and gets converted to acetyl-CoA. This acetyl-CoA then enters the TCA cycle (also called the citric acid cycle or Krebs cycle). The TCA cycle's main job is not to make ATP directly — it's to harvest high-energy electrons in the form of NADH and FADH₂, which then go power the real ATP-making machinery.
Pyruvate Dehydrogenase Complex (PDC)
This is the gateway. Before entering the TCA cycle, pyruvate is converted to acetyl-CoA by a massive enzyme complex (three enzymes working together). This reaction is irreversible — once you make acetyl-CoA from pyruvate, there's no going back. This is why you can't make glucose from fat (fats break down to acetyl-CoA, and you can't reverse this step to make pyruvate).
What the TCA Cycle Does
The 2-carbon acetyl group from acetyl-CoA gets attached to a 4-carbon molecule (oxaloacetate), making a 6-carbon molecule (citrate). That 6-carbon molecule gets processed, releasing 2 CO₂ and harvesting electrons as NADH and FADH₂, until you're back to the 4-carbon molecule ready to accept another acetyl group. It's a cycle.
Per acetyl-CoA that enters: 3 NADH, 1 FADH₂, 1 GTP (≈ATP), 2 CO₂
Anaplerotic Reactions
"Anaplerotic" just means "filling up." The TCA cycle intermediates get drained off constantly to make amino acids, porphyrins, and other molecules. Anaplerotic reactions replenish these intermediates so the cycle keeps running. The most important one: pyruvate carboxylase converts pyruvate → oxaloacetate.
Regulation
Just like glycolysis, three enzymes control the pace of the TCA cycle. The common theme: high energy (lots of ATP, NADH) slows it down. Low energy (lots of ADP, AMP, NAD⁺) speeds it up.
Chapter 20 – Making ATP (Oxidative Phosphorylation)
The Big Picture
This is where the majority of your ATP comes from. All that NADH and FADH₂ collected from glycolysis and the TCA cycle gets used here. It happens on the inner membrane of the mitochondria and requires oxygen.
The Electron Transport Chain (ETC)
Think of this as a series of relay runners passing a baton (electrons). NADH drops off electrons at the start (Complex I). The electrons get passed along through several protein complexes (I → III → IV for NADH, or II → III → IV for FADH₂). At each handoff, energy is released. That energy is used to pump H⁺ ions (protons) across the inner mitochondrial membrane, building up a concentration gradient. At the very end, the electrons are handed off to oxygen, making water. That's why you need oxygen — it's the final electron acceptor.
The Proton Gradient
You've now got a huge buildup of H⁺ on one side of the membrane (like water backed up behind a dam). That concentrated H⁺ desperately wants to flow back across. The only way it can is through a protein called ATP synthase.
ATP Synthase
This is one of the most amazing molecular machines in biology. As H⁺ flows through ATP synthase (down its concentration gradient), it physically rotates part of the protein like a turbine. That rotation powers the making of ATP from ADP and phosphate. There are three active sites on ATP synthase that cycle through three conformations — open, loose, and tight — as the protein spins. Each rotation makes ATP.
The Cost of Exporting ATP
ATP is made inside the mitochondria but used all over the cell. A transporter protein (ATP-ADP translocase) swaps ATP out for ADP in. But this transport costs energy — about 1 extra H⁺ per ATP exported. So the total cost is about 4 H⁺ per usable ATP.
NADH Shuttle Systems
NADH made in the cytoplasm during glycolysis can't cross the inner mitochondrial membrane. So the cell uses shuttle systems to smuggle the electrons in:
Malate-aspartate shuttle: Transfers electrons as NADH inside — makes more ATP. More efficient.
Glycerophosphate shuttle: Transfers electrons to FADH₂ inside — makes less ATP. Less efficient, but always works in one direction.
Here are flashcards for everything — just cover the answer and test yourself!
Chapter 13 – Enzymes & Kinetics
Q: What is an enzyme? A: A protein that acts as a biological catalyst — it speeds up chemical reactions in the body without being used up itself.
Q: What is a substrate? A: The molecule an enzyme works on. It fits into the enzyme's active site like a key into a lock.
Q: What is catalytic power? A: The ratio of the enzyme-catalyzed rate to the uncatalyzed rate. It measures how much faster an enzyme makes a reaction go. Some enzymes have a catalytic power of 10²⁶.
Q: What is specificity? A: An enzyme's selectivity for its substrate. Each enzyme usually only works on one specific molecule because only that molecule fits the active site.
Q: What is Km and what does it tell you? A: Km is the substrate concentration at which the reaction runs at half of its maximum speed (½ Vmax). Low Km = high affinity (enzyme works well even with little substrate). High Km = low affinity (needs a lot of substrate to get going).
Q: What is Vmax? A: The maximum speed of an enzyme-catalyzed reaction — reached when every enzyme molecule is fully occupied with substrate (fully saturated).
Q: Write out the Michaelis-Menten equation and explain each part. A: V₀ = Vmax[S] / (Km + [S]) V₀ = current reaction speed, Vmax = maximum speed, [S] = substrate concentration, Km = substrate concentration at ½ Vmax.
Q: What is the saturation effect? A: At low [S] the reaction speeds up as you add more substrate (first-order). At high [S] the enzyme is maxed out and adding more substrate doesn't help (zero-order). The enzyme is saturated — like a cashier with too many customers.
Q: What is kcat (turnover number)? A: The number of substrate molecules one enzyme molecule converts to product per second when fully saturated. It measures how productive a single enzyme molecule is.
Q: What is kcat/Km and why does it matter? A: Catalytic efficiency — measures how well the enzyme works at low substrate concentrations. The upper limit is set by the diffusion rate (~10⁸–10⁹ M⁻¹s⁻¹). Enzymes near this limit are considered "perfect."
Q: What is competitive inhibition? A: The inhibitor looks like the substrate and competes for the active site. You can overcome it by adding more substrate. Km increases, Vmax stays the same.
Q: What is uncompetitive inhibition? A: The inhibitor only binds to the enzyme-substrate complex (ES), not the free enzyme. It locks the substrate in and makes everything worse. Both Km and Vmax decrease. Cannot be overcome with more substrate.
Q: What is pure noncompetitive inhibition? A: The inhibitor binds a site other than the active site, on both free enzyme and ES complex. Slows the enzyme down no matter what. Vmax decreases, Km stays the same.
Q: What is irreversible inhibition? Give an example. A: The inhibitor permanently destroys the enzyme — no recovery. Example: penicillin permanently disables the enzyme bacteria use to build their cell walls, killing the bacteria.
Q: What is the difference between sequential and ping-pong bisubstrate reactions? A: Sequential: both substrates must bind before any product is released. Ping-pong: first substrate binds, first product is released, then second substrate binds. The enzyme acts as a temporary carrier between the two substrates.
Chapter 14 – Mechanisms of Catalysis
Q: What is the activation energy and how do enzymes deal with it? A: The energy barrier molecules must overcome for a reaction to happen. Enzymes lower this barrier, making the reaction happen much faster — like lowering a hill the boulder has to roll over.
Q: What is the transition state? A: The unstable, high-energy arrangement of atoms at the peak of the activation energy barrier. It exists for only a tiny fraction of a second during a reaction.
Q: How do enzymes stabilize the transition state? A: The enzyme's active site is shaped to grip the transition state tightly, holding the molecule in the exact shape it needs to react. The better the grip, the faster the reaction.
Q: What is a transition state analog (TSA)? A: A drug designed to look like the transition state. Since the enzyme grips transition states tightly, TSAs bind extremely tightly and block the enzyme. Examples: statins (cholesterol), Tamiflu (flu), protease inhibitors (HIV/AIDS).
Q: What is covalent catalysis? A: The enzyme temporarily forms a covalent bond with the substrate during the reaction. The enzyme-substrate pair reacts, then the enzyme is released unchanged and ready to go again.
Q: What is general acid-base catalysis? A: The enzyme donates or accepts a proton (H⁺) at exactly the right moment to help the reaction proceed. Very precise chemistry happening inside the active site.
Q: What are serine proteases and what is their catalytic triad? A: Enzymes that cut proteins (trypsin, chymotrypsin, elastase, thrombin, etc.). Their catalytic triad is His57, Asp102, and Ser195 — three amino acids that work as a team to attack and cut peptide bonds. Ser195 does the actual cutting.
Q: What are aspartic proteases and how do they work? A: Enzymes that cut proteins using two Asp residues (pepsin, renin, HIV-1 protease, etc.). Their main mechanism is general acid-base catalysis — the two Asp residues donate and accept protons to drive the reaction.
Q: What is the oxyanion hole in serine proteases? A: A part of the active site formed by N-H groups of Ser195 and Gly193 that stabilizes the negatively charged tetrahedral intermediate formed during the cutting reaction.
Chapter 15 – Enzyme Regulation
Q: What is allosteric regulation? A: Control of enzyme activity by molecules binding to a site other than the active site (the allosteric site). This changes the enzyme's shape and either activates or inhibits it. Like a remote control for the enzyme.
Q: What is the MWC (concerted) model? A: A model for allosteric regulation where all subunits of an enzyme must be in the same state — either all R (relaxed, active) or all T (taut, inactive). They all switch together at once. T state dominates without substrate.
Q: What is the KNF (sequential) model? A: A model where ligand binding changes one subunit at a time, and that change can spread to neighboring subunits. Changes are ligand-induced. Explains negative cooperativity (where binding of one substrate makes the next bind less easily).
Q: What is the key difference between MWC and KNF models? A: MWC: all subunits switch states simultaneously, no ligand-induced changes. KNF: ligand induces conformational changes one subunit at a time.
Q: What is phosphorylation regulation and how is it reversed? A: A protein kinase adds a phosphate group to the enzyme, changing its shape and turning it on or off. A phosphoprotein phosphatase removes the phosphate and reverses the change. It's a reversible molecular on/off switch.
Q: How does PKA (protein kinase A) work? A: PKA is a R₂C₂ tetramer (2 regulatory + 2 catalytic subunits). When cAMP binds to the R subunits, they release the C (catalytic) subunits, which are then active and go phosphorylate target proteins.
Q: What is acetylation regulation? A: Adding an acetyl group to a lysine residue on the enzyme, changing it from positively charged to neutral. This alters the enzyme's shape and function. KATs add acetyl groups; KDACs remove them.
Q: How is glycogen phosphorylase regulated? A: Two ways — allosteric: AMP activates it (low energy = need glucose); ATP and glucose-6-P inhibit it (high energy = don't need more glucose). Covalent: phosphorylation converts it from the less-active b form to the more-active a form, used in emergency/stress situations.
Q: What does cooperative binding mean in hemoglobin? A: When the first oxygen binds to hemoglobin, it slightly changes the shape, making it easier for the next oxygen to bind, and so on. This makes hemoglobin very efficient at picking up O₂ in the lungs and dropping it off in tissues.
Q: What is the Bohr effect? A: H⁺ (acid) decreases hemoglobin's affinity for oxygen, causing it to release O₂. Active tissues produce CO₂ → CO₂ + H₂O → H⁺ + HCO₃⁻ → the H⁺ triggers O₂ release right where it's needed most. Reversed in the lungs.
Q: What does 2,3-BPG do to hemoglobin? A: It binds in the central cavity of hemoglobin and stabilizes the T state (low O₂ affinity), promoting O₂ release in tissues. It interacts with 8 positive charges in the cavity (2 Lys, 4 His, 2 N-termini).
Q: Why does fetal hemoglobin have higher O₂ affinity than adult hemoglobin? A: Fetal Hb has γ-chains instead of β-chains. The γ-chains have serine instead of histidine at position 143, reducing positive charges in the BPG-binding cavity. BPG binds less tightly → fetal Hb holds O₂ more tightly → fetus can steal O₂ from mom's blood.
Q: What causes sickle-cell anemia at the molecular level? A: A single amino acid change — glutamate (charged, water-loving) → valine (hydrophobic, water-avoiding) at position 6 of the β-chains. Valine creates a sticky hydrophobic patch → Hb molecules clump into fibers → red blood cells warp into crescent shapes → get stuck in capillaries.
Chapter 18 – Glycolysis
Q: What is glycolysis in plain terms? A: The process of breaking one glucose molecule into two pyruvate molecules to extract a small amount of energy. Happens in the cytoplasm, no oxygen needed.
Q: What is the net yield of glycolysis? A: 2 ATP and 2 NADH per glucose. (4 ATP are made but 2 are spent in phase 1, so net = 2 ATP.)
Q: Why is glucose phosphorylated at the start of glycolysis? A: Adding a phosphate group (making glucose-6-phosphate) traps glucose inside the cell — phosphorylated glucose cannot cross the cell membrane and escape.
Q: What are the two high-energy intermediates in phase 2 of glycolysis? A: 1,3-bisphosphoglycerate (1,3-BPG) and phosphoenolpyruvate (PEP). These are used to make ATP by substrate-level phosphorylation.
Q: What happens to pyruvate when oxygen IS available? A: Pyruvate enters the mitochondria, gets converted to acetyl-CoA by the pyruvate dehydrogenase complex, and enters the TCA cycle for much more ATP production.
Q: What happens to pyruvate when oxygen is NOT available? A: It gets converted to lactate (in animals and most microbes) or to ethanol + CO₂ (in yeast). This regenerates NAD⁺ so glycolysis can keep running.
Q: What are the three regulatory enzymes of glycolysis? A: Hexokinase (HK), phosphofructokinase (PFK), and pyruvate kinase (PK). These catalyze irreversible steps and act as the main control points. PFK is the most important.
Chapter 19 – TCA Cycle
Q: What is the main purpose of the TCA cycle? A: To harvest high-energy electrons in the form of NADH and FADH₂, which will be used by the electron transport chain to make large amounts of ATP.
Q: What does the pyruvate dehydrogenase complex (PDC) do? A: Converts pyruvate → acetyl-CoA + CO₂ + NADH. This irreversible step links glycolysis to the TCA cycle. Three enzymes and five coenzymes are involved.
Q: Why is the PDC reaction so significant? A: It's irreversible — you can't go back from acetyl-CoA to pyruvate. This is why fat (which breaks down to acetyl-CoA) cannot be converted back to glucose.
Q: What does one turn of the TCA cycle produce? A: 3 NADH, 1 FADH₂, 1 GTP (≈ ATP), and 2 CO₂ per acetyl-CoA that enters.
Q: What are anaplerotic reactions? A: Reactions that refill TCA cycle intermediates when they get drained off for biosynthesis. Most important: pyruvate carboxylase converts pyruvate → oxaloacetate.
Q: How is the TCA cycle regulated? A: Three key enzymes are regulated. Common theme: high energy (lots of ATP/NADH) slows the cycle; low energy (lots of ADP/AMP/NAD⁺) speeds it up. The three enzymes: citrate synthase, isocitrate dehydrogenase, and α-ketoglutarate dehydrogenase.
Q: How is the pyruvate dehydrogenase complex (PDC) regulated? A: Allosterically: inhibited by ATP, NADH, and acetyl-CoA (products = slow down); activated by NAD⁺ and CoA. Covalently: phosphorylation (by PDK) turns it OFF; dephosphorylation (by PDP) turns it ON.
Chapter 20 – Electron Transport & Oxidative Phosphorylation
Q: What is the electron transport chain (ETC)? A: A series of protein complexes on the inner mitochondrial membrane that pass electrons from NADH and FADH₂ down to oxygen. Energy released at each step pumps H⁺ ions across the membrane, building a gradient.
Q: Why is oxygen essential for oxidative phosphorylation? A: Oxygen is the final electron acceptor at the end of the ETC. Without oxygen to accept the electrons, the whole chain backs up and stops. That's why lack of oxygen is lethal.
Q: What is the proton gradient and why does it matter? A: H⁺ ions get pumped across the inner mitochondrial membrane during electron transport, creating a concentration difference (high outside, low inside). This stored energy — like water behind a dam — drives ATP synthesis.
Q: How does ATP synthase work? A: H⁺ flows back through ATP synthase down its gradient, physically spinning part of the protein like a turbine (the γ subunit). This rotation drives three active sites (β subunits) through three conformations — O (open), L (loose), T (tight) — cycling to make and release ATP.
Q: What are the three conformations of the β subunits in ATP synthase? A: O (open) — nucleotides enter and leave freely. L (loose) — ADP and Pi are trapped inside. T (tight) — ATP is synthesized but can't be released until the subunit rotates back to O. No two subunits are ever in the same conformation at once.
Q: What does the ATP-ADP translocase do and why does it cost energy? A: It exports ATP out of the mitochondria and imports ADP in. It swaps ATP⁴⁻ for ADP³⁻ — a net negative charge moving out — which costs the equivalent of 1 H⁺. So making and exporting 1 ATP costs ~4 H⁺ total.
Q: Why do cells need NADH shuttle systems? A: NADH made in the cytoplasm during glycolysis cannot cross the inner mitochondrial membrane. Shuttle systems transfer the electrons across without actually moving NADH.
Q: What is the difference between the two NADH shuttle systems? A: Malate-aspartate shuttle: transfers electrons as NADH inside the mitochondria → more ATP, reversible. Glycerophosphate shuttle: transfers electrons to FAD → FADH₂ inside → less ATP, but works in one direction only.
Q: What is the difference in ATP yield between NADH and FADH₂ entering the ETC? A: NADH enters at Complex I and generates more ATP (~2.5 per NADH). FADH₂ enters at Complex II, bypassing Complex I, and generates less ATP (~1.5 per FADH₂).