Metabolism, Enzymes, and Bioenergetics: GOB Chemistry Study Guide

Enzymes

Enzyme Structure and Function

Enzymes are biological catalysts that speed up chemical reactions in living organisms. They are highly specific for their substrates and can be described by different models of substrate binding.

• Lock and Key Model: The enzyme's active site is a perfect fit for the substrate, like a key fitting into a lock.

• Induced Fit Model: The enzyme's active site molds itself around the substrate upon binding, allowing for a better fit.

• Key Terms: Cofactors (non-protein helpers), Coenzymes (organic cofactors), Holoenzyme (enzyme with its cofactor), Apoenzyme (enzyme without its cofactor).

Enzyme Activity and Regulation

• Effect of Temperature and pH: Enzyme activity is affected by temperature and pH. Each enzyme has an optimal temperature and pH where it functions best.

• Substrate Concentration: Increasing substrate concentration increases reaction rate until the enzyme is saturated.

• Graphical Representation: Enzyme activity vs. substrate concentration typically shows a hyperbolic curve.

• Inhibitors: Molecules that decrease enzyme activity. Competitive inhibitors bind to the active site, while noncompetitive inhibitors bind elsewhere, changing the enzyme's shape.

Enzyme Kinetics and Regulation

• Reversible vs. Irreversible Inhibition: Reversible inhibitors can dissociate from the enzyme, while irreversible inhibitors form covalent bonds and permanently inactivate the enzyme.

• Allosteric Regulation: Enzymes can be regulated by molecules that bind to sites other than the active site, causing conformational changes that affect activity.

Carbohydrate Metabolism: Glycolysis, Gluconeogenesis, Glycogen Metabolism

ATP and Metabolic Pathways

Metabolism is divided into catabolic (breaking down molecules to release energy) and anabolic (building molecules using energy) pathways. ATP (adenosine triphosphate) is the main energy currency of the cell.

• ATP Structure: Composed of adenine, ribose, and three phosphate groups.

• ATP Hydrolysis: Releases energy for cellular processes.

Glycolysis

• Definition: The breakdown of glucose into pyruvate, producing ATP and NADH.

• Key Steps: Glycolysis occurs in the cytoplasm and consists of 10 steps, divided into energy investment and energy payoff phases.

• Feeder Pathways: Galactose and fructose can enter glycolysis after conversion to intermediates.

• Fate of Pyruvate: Under aerobic conditions, pyruvate enters the mitochondria and is converted to acetyl-CoA. Under anaerobic conditions, it is converted to lactate (in animals) or ethanol (in yeast).

Gluconeogenesis and Glycogen Metabolism

• Gluconeogenesis: The synthesis of glucose from non-carbohydrate sources, such as amino acids and lactate. Occurs mainly in the liver.

• Glycogenolysis: The breakdown of glycogen to glucose.

• Glycogenesis: The synthesis of glycogen from glucose.

• Regulation: Hormones such as insulin and glucagon regulate these pathways based on blood glucose levels.

Energy Production: Citric Acid Cycle, Oxidative Phosphorylation, Electron Transport Chain

Citric Acid Cycle (Krebs Cycle)

The citric acid cycle is a series of reactions in the mitochondrial matrix that oxidizes acetyl-CoA to CO2, generating NADH and FADH2 for use in the electron transport chain.

• Main Purpose: To harvest high-energy electrons from acetyl-CoA.

• Key Products per Turn: 3 NADH, 1 FADH2, 1 GTP (or ATP), and 2 CO2.

Electron Transport Chain (ETC) and Oxidative Phosphorylation

• Location: Inner mitochondrial membrane.

• Complexes: The ETC consists of four protein complexes (I-IV) and ATP synthase (Complex V).

• Electron Carriers: NADH and FADH2 donate electrons, which pass through the complexes, pumping protons to create a gradient.

• ATP Synthesis: Protons flow back through ATP synthase, driving the phosphorylation of ADP to ATP.

• Oxygen: The final electron acceptor, forming water.

Summary Table: ATP Yield from Glucose Oxidation

Pathway	ATP (or GTP)	NADH	FADH2
Glycolysis	2	2	0
Pyruvate to Acetyl-CoA	0	2	0
Citric Acid Cycle	2	6	2
Total (after ETC)	~32-38	-	-

Additional info: The exact ATP yield varies depending on the cell type and shuttle systems used.

Lipid and Amino Acid Metabolism

Fatty Acid Oxidation (Beta-Oxidation)

• Definition: The breakdown of fatty acids in the mitochondria to produce acetyl-CoA, NADH, and FADH2.

• Steps: Activation of fatty acids, transport into mitochondria, repeated cycles of oxidation, hydration, oxidation, and thiolysis.

• Energy Yield: Fatty acids are more reduced than carbohydrates, so their oxidation yields more ATP.

• Equation for Palmitic Acid (C16):

$\text{Palmitoyl-CoA} + 7 \text{FAD} + 7 \text{NAD}^+ + 7 \text{CoA} + 7 \text{H}_2\text{O} \rightarrow 8 \text{Acetyl-CoA} + 7 \text{FADH}_2 + 7 \text{NADH} + 7 \text{H}^+$

Amino Acid Catabolism

• Deamination: Removal of the amino group, producing ammonia and a carbon skeleton.

• Glucogenic Amino Acids: Amino acids whose carbon skeletons can be converted to glucose.

• Ketogenic Amino Acids: Amino acids whose carbon skeletons are converted to acetyl-CoA or ketone bodies.

Key Definitions and Concepts

• Oxidation vs. Reduction: Oxidation is the loss of electrons (or hydrogen), reduction is the gain of electrons (or hydrogen).

• ATP Production: Fatty acid oxidation produces more ATP per carbon than carbohydrate oxidation.

Summary Table: Comparison of Carbohydrate and Fatty Acid Oxidation

Substrate	ATP Yield (per molecule)
Glucose	~32-38
Palmitic Acid (C16)	~106

Additional info: The higher ATP yield from fatty acids is due to their greater degree of reduction compared to carbohydrates.