Comprehensive Review

biocum

Two cardinal rules of biochemistry

• Living systems obey the laws of thermodynamics

• Life is organized and compartmentalized

1st Law of Thermodynamics

Energy is conserved

2nd Law of Thermodynamics

Reactions proceed toward increased entropy

Function of membranes

Define compartments and regulate transport (selectively permeable)

Membrane composition

Phospholipids, cholesterol, proteins

Function of organelles

Specialized structures with distinct functions (e.g., nucleus, mitochondria)

Difference: Eukaryotes vs. Prokaryotes

• Eukaryotes have membrane-bound organelles

• prokaryotes do not

Two ways to target molecules in cells

• Signal sequences

• vesicular transport

Central dogma of molecular biology

DNA → RNA → Protein

Three processes of the central dogma

Replication, Transcription, Translation

Van der Waals force strength

0.4–4 kJ/mol

Ionic bond strength

40–200 kJ/mol

Hydrogen bond strength

4–20 kJ/mol

Hydrophobic effect

Nonpolar molecules aggregate in water to reduce entropy loss

Hydrogen bond donor

Hydrogen bonded to electronegative atom (N or O)

Hydrogen bond acceptor

Lone pair on electronegative atom (N or O)

Four major biomolecule classes

Proteins, Carbohydrates, Lipids, Nucleic Acids

Primary protein structure

Amino acid sequence

Secondary protein structure

α-helices and β-sheets (H-bonding)

Tertiary protein structure

3D folding (hydrophobic effect, disulfide bonds)

Quaternary protein structure

Multiple subunits (e.g., hemoglobin)

Anfinsen’s experiment

Found that protein folding is determined by amino acid sequence

Apoenzyme vs. Holoenzyme

• Apoenzyme = protein only

• Holoenzyme = protein + cofactor

Catalytic strategies

Acid-base, covalent, metal ion, proximity/orientation

Michaelis-Menten equation

v = (Vmax[S]) / (Km + [S])

Competitive inhibition effect on Vmax and Km

• Vmax unchanged

• Km increases

Noncompetitive inhibition effect on Vmax and Km

• Vmax decreases

• Km unchanged

Uncompetitive inhibition effect on Vmax and Km

Both Vmax and Km decrease

Glycolysis key activators

Insulin, AMP, F2,6BP

Gluconeogenesis key activators

Glucagon, acetyl-CoA, cortisol

Glycolysis vs. Gluconeogenesis

• Glycolysis = Glucose → Pyruvate

• Gluconeogenesis = Pyruvate → Glucose

Main link between TCA and ETC

NADH and FADH₂ donate electrons to ETC

Purpose of PPP

Produces NADPH and ribose-5-phosphate

Examples of second messengers

cAMP, Ca²⁺, IP₃

Insulin function

Lowers blood glucose

Glucagon function

Raises blood glucose

Epinephrine function

Stimulates glycogen breakdown

Urea cycle purpose

Removes excess nitrogen as urea

First product of purine synthesis

IMP (inosine monophosphate)

Cause of gout

Uric acid buildup from purine metabolism

Cause of sickle cell anemia

Hemoglobin mutation (Glu → Val)