Biochemistry II Exam Study Notes: Metabolism, Glycolysis, and Population Genetics

Introduction to Metabolism

Overview of Metabolic Pathways

• Metabolism refers to the sum of all chemical reactions in the body, divided into catabolism (breakdown of molecules to release energy) and anabolism (synthesis of complex molecules from simpler ones).

• Catabolic pathways generate ATP and reduced cofactors (e.g., NADH), while anabolic pathways consume ATP and reducing equivalents.

• Major metabolic fuels: carbohydrates, fats, proteins.

• Catabolism produces CO2, H2O, NH3; anabolism builds amino acids, sugars, fatty acids, nucleic acids.

Metabolic Fuels & Dietary Components

Energy Density of Macronutrients

• Fat: 9 kcal/g

• Carbohydrates: 4 kcal/g

• Protein: 4 kcal/g

• Alcohol: 7 kcal/g

Essential vs. Non-Essential Amino Acids

• Essential amino acids (cannot be synthesized by the body): PVT TIM HALL

  • Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine, Arginine, Leucine, Lysine

• Non-essential amino acids can be synthesized by the body.

Vitamins

• Fat-soluble: A, D, E, K

• Water-soluble: B, C

Nitrogen Balance

• Positive nitrogen balance: Growth (intake > loss)

• Negative nitrogen balance: Starvation (loss > intake)

Fed, Absorptive, Fasting, and Starvation States

Fuel Utilization by Tissue

Tissue	Fuel
Brain	Glucose → Ketones (during prolonged fasting)
RBC	Glucose ONLY
Muscle	Glucose & Fatty acids
Adipose	Triglycerides stored
Liver	Produces glucose/ketones

Metabolic States and Hormonal Regulation

State	Insulin	Liver	Muscle	Brain	Fat
Fed (0–2 h)	↑↑	Glycogenesis, Glycolysis, Lipogenesis	Glucose uptake, Glycogen/protein synthesis	Glucose	TG storage
Basal (2–12 h)	↓	Glycogenolysis	Fatty acid use	Glucose	Lipolysis (slight)
Fasting (1–2 days)	↓↓	Gluconeogenesis, β-oxidation	Fatty acid use, β-oxidation	Glucose	↑↑ Lipolysis
Starve (>3–5 days)	Very low	Ketogenesis, Gluconeogenesis	Fatty acid use	Ketones	Lipolysis

Key Pathways in Fasting

• Glycogenolysis: Breakdown of glycogen to glucose (lasts ~30 hours)

• Gluconeogenesis: Synthesis of glucose from non-carbohydrate sources

• Lipolysis: Breakdown of triglycerides to fatty acids

• β-oxidation: Fatty acid breakdown for energy

Important Glucose Transporters

• Muscle: GLUT4

• Liver: GLUT2

• RBC: GLUT1

• Pancreas: GLUT2

• Brain: GLUT1

Bioenergetics

Gibbs Free Energy

• Gibbs free energy (ΔG) determines whether a reaction is spontaneous.

• If ΔG < 0: Reaction is exergonic, releases energy, and is spontaneous.

• If ΔG > 0: Reaction is endergonic, requires energy input, and is non-spontaneous.

Equation:

$\Delta G = \Delta H - T\Delta S$

• Where ΔH is enthalpy change, T is temperature (Kelvin), and ΔS is entropy change.

Glycolysis

Overview and Importance

• Glycolysis is the metabolic pathway that converts glucose into pyruvate, generating ATP and NADH.

• Occurs in the cytoplasm of all cells, does not require oxygen (anaerobic or aerobic conditions).

• Critical for tissues lacking mitochondria (e.g., RBCs) and during hypoxia.

Overall Reaction

$\text{Glucose} + 2\,\text{P}_i + 2\,\text{ADP} + 2\,\text{NAD}^+ \rightarrow 2\,\text{Pyruvate} + 2\,\text{ATP} + 2\,\text{NADH} + 2\,\text{H}^+ + 2\,\text{H}_2\text{O}$

Key Features

• Occurs in the cytoplasm

• Can proceed with or without O2

• Contains irreversible steps (1, 3, 10)

• RBCs depend entirely on glycolysis for ATP

• Warburg effect: Cancer cells favor glycolysis even in the presence of oxygen

Regulation of Glycolysis

• Key regulatory enzymes: Hexokinase/Glucokinase (step 1), Phosphofructokinase-1 (PFK-1, step 3), Pyruvate kinase (step 10)

• Regulated by ATP, AMP, citrate, and hormonal signals (insulin, glucagon)

Mnemonic for Intermediates

• "Girls Get Fine Food, Gentlemen Dine, Boys Prefer Picking Pepperoni Pizza"

Substrate-Level Phosphorylation

• ATP is generated directly in glycolysis at steps 7 and 10 (phosphoglycerate kinase and pyruvate kinase reactions)

Protein Digestion: Exo- and Endopeptidases

Protease Types

• Exopeptidases: Cleave amino acids from the ends of peptide chains (aminopeptidase, carboxypeptidase)

• Endopeptidases: Cleave peptide bonds within the chain (e.g., trypsin, chymotrypsin)

Population Genetics and Molecular Tools

Hardy-Weinberg Principle

• Describes allele and genotype frequencies in a population not subject to evolutionary forces.

Allele frequency:

$p + q = 1$

Genotype frequency:

$p^2 + 2pq + q^2 = 1$

Mutation rate:

$\mu = \frac{n}{2N}$

Carrier Frequency Example

• If 4% of a population shows a recessive trait ($q^2 = 0.04$), then $q = 0.2$, $p = 0.8$

• Carrier frequency ($2pq$): $2 \times 0.8 \times 0.2 = 0.32$ (32%)

Molecular Biology Techniques

• Southern blot: Detects DNA

• Northern blot: Detects RNA

• Western blot: Detects protein

• Mnemonic: SNOW DROP (Southern-DNA, Northern-RNA, Western-Protein)

Additional info: Some diagrams and mnemonics were interpreted and expanded for clarity. Regulatory steps and enzyme names in glycolysis were inferred from standard biochemistry knowledge.