Introduction to Biochemistry

Biomolecules

Biochemistry focuses on the chemical processes within and related to living organisms. Understanding the structure and function of biomolecules is foundational to the field.

• Trace elements: Essential elements required in minute quantities for biological processes (e.g., Fe, Zn, Cu).

• Amino acids: Organic compounds containing both amino (-NH2) and carboxyl (-COOH) groups; building blocks of proteins.

• Carbohydrates: Organic molecules composed of carbon, hydrogen, and oxygen; serve as energy sources and structural components.

• Monosaccharide: The simplest form of carbohydrate (e.g., glucose, fructose).

• Nucleotide: Monomeric units of nucleic acids, consisting of a nitrogenous base, a sugar, and phosphate group(s).

• Lipid: Hydrophobic or amphipathic molecules, including fats, oils, and steroids.

• Monomer: A single molecular unit that can join with others to form a polymer.

• Polymer: Large molecules composed of repeating monomer units (e.g., proteins, nucleic acids, polysaccharides).

• Residue: A single monomer unit within a polymer chain.

• Peptide bond: Covalent bond linking amino acids in proteins.

• Phosphodiester bond: Covalent bond joining nucleotides in nucleic acids.

• Glycosidic bond: Covalent bond joining monosaccharides in carbohydrates.

Most abundant elements in biological molecules: Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N), Phosphorus (P), Sulfur (S).

Major classes of biological molecules: Proteins, nucleic acids, carbohydrates, lipids.

Major functions of biological polymers:

• Proteins: Catalysis (enzymes), structure, transport, signaling.

• Nucleic acids: Information storage and transfer (DNA, RNA).

• Carbohydrates: Energy storage, structure, recognition.

• Lipids: Energy storage, membrane structure, signaling.

Water and Its Properties

Key Terms and Interactions

• Polarity: Distribution of electrical charge leading to partial positive and negative regions.

• Hydrogen bond: Weak interaction between a hydrogen atom covalently bonded to an electronegative atom and another electronegative atom.

• Electrostatic interaction: Attraction or repulsion between charged particles.

• Van der Waals radius: The effective size of an atom for non-covalent interactions.

• Electronegativity: Atom's tendency to attract electrons in a bond.

• Van der Waals interaction: Weak, non-covalent interactions due to transient dipoles.

• Dipole-dipole interaction: Attraction between polar molecules.

• London dispersion forces: Weakest intermolecular forces due to temporary dipoles.

• Hydrophilic: Water-attracting (polar) molecules.

• Hydrophobic: Water-repelling (nonpolar) molecules.

• Hydrophobic effect: Tendency of nonpolar substances to aggregate in aqueous solution, driven by entropy.

• Amphiphilic/Amphipathic: Molecules with both hydrophilic and hydrophobic regions (e.g., phospholipids).

• Micelle: Spherical aggregate of amphipathic molecules in water.

Major types of electrostatic forces: Ionic interactions, hydrogen bonds, van der Waals interactions.

Relative strengths of bonds: Covalent > Ionic > Hydrogen bond > van der Waals.

Hydrophobic effect and entropy: Aggregation of hydrophobic molecules increases the entropy of water, making the process thermodynamically favorable.

Identifying hydrophobic/hydrophilic molecules: Polar groups (e.g., -OH, -NH2) indicate hydrophilicity; hydrocarbon chains indicate hydrophobicity; amphipathic molecules contain both.

Nucleotides and Nucleic Acids

Nucleotides

• Purine bases: Adenine (A), Guanine (G); double-ring structures.

• Pyrimidine bases: Cytosine (C), Thymine (T), Uracil (U); single-ring structures.

• Sugars in nucleotides: Ribose (RNA), 2'-deoxyribose (DNA).

• Nucleoside: Base + sugar; Nucleotide: Base + sugar + phosphate.

• Deoxynucleoside: Nucleoside with deoxyribose sugar.

• Major bases: Adenine, Guanine, Cytosine, Thymine (DNA), Uracil (RNA).

• Hydrogen bonding: Purines and pyrimidines form specific hydrogen bonds (A-T/U: 2 bonds; G-C: 3 bonds).

Primary Structure of Nucleic Acids

• Nucleic acid: Polymer of nucleotides (DNA or RNA).

• RNA vs. B-DNA: RNA is usually single-stranded; B-DNA is the common double-helical form of DNA.

• Bonds: Ester, phosphoester, and phosphodiester bonds link nucleotides.

• Directionality: Nucleic acids have 5' (phosphate) and 3' (hydroxyl) ends; sequences are written 5' to 3'.

• RNA susceptibility: RNA is more prone to alkaline hydrolysis due to the 2'-OH group.

• Base stacking: Stabilized by van der Waals forces and hydrophobic interactions.

Secondary Structure of Nucleic Acids

• Mononucleotide, dinucleotide, oligonucleotide: Molecules with one, two, or a few nucleotide units, respectively.

• Chargaff’s rules: In DNA, %A = %T and %G = %C.

• Antiparallel: DNA strands run in opposite directions (5' to 3' and 3' to 5').

• B-DNA double helix: Two antiparallel strands, right-handed helix, stabilized by hydrogen bonds and base stacking.

• Grooves: Major and minor grooves allow protein binding and recognition.

• RNA vs. DNA 3D structure: RNA can form complex secondary/tertiary structures; DNA is typically a double helix.

Denaturation of Nucleic Acids

• Denaturation: Separation of double-stranded DNA into single strands by heat, pH, or chemicals.

• Melting: The process of DNA denaturation; Tm: Temperature at which half the DNA is denatured.

• Hypochromic effect: Double-stranded DNA absorbs less UV light than single-stranded (hyperchromic effect upon melting).

• Renaturation/annealing: Reformation of double-stranded DNA from single strands.

• Tm and GC content: Higher GC content increases Tm due to more hydrogen bonds.

• Effect of pH and ionic strength: Extreme pH or low ionic strength destabilizes DNA.

• RNA melting: RNA can denature, but its structure is more variable.

Protein Structure and Function

Amino Acids and Their Properties

• Generic structure: Central (α) carbon, amino group, carboxyl group, hydrogen, and variable side chain (R group).

• 20 amino acids: Each with unique side chains; classified as nonpolar, polar, or charged.

• Charge states: At physiological pH (~7), amino acids are zwitterions (both + and - charges).

• Chirality: All except glycine are chiral (asymmetric α-carbon).

• Special side chains: Ser, Thr, Tyr (can be phosphorylated); Cys (forms disulfide bonds); His (buffering); Gly (flexibility); Pro (rigid structure).

Peptide Bonds and Protein Primary Structure

• Primary structure: Linear sequence of amino acids in a polypeptide.

• Residues: Amino acids within a polypeptide chain.

• Peptide bond: Planar and rigid due to partial double-bond character.

• Polypeptide backbone: Repeating N-Cα-C units.

Secondary Structure of Polypeptides

• Levels of structure: Primary, secondary (α-helix, β-sheet), tertiary, quaternary.

• α-helix: Right-handed coil stabilized by hydrogen bonds.

• β-sheet: Parallel or antiparallel strands stabilized by hydrogen bonds.

• Regular vs. irregular structure: Regular (α-helix, β-sheet); irregular (loops, turns).

• Stabilization: Mainly by hydrogen bonds.

Tertiary and Quaternary Structure

• Tertiary structure: 3D folding of a single polypeptide.

• Quaternary structure: Association of multiple polypeptide chains.

• Surface vs. core: Hydrophobic residues in core; polar/charged on surface.

• Stabilization: Hydrophobic interactions, hydrogen bonds, ionic interactions (salt bridges), disulfide bonds.

• Prosthetic group: Non-protein component required for function (e.g., heme).

• Apoprotein: Protein without prosthetic group; Holoprotein: Protein with prosthetic group.

Myoglobin and Hemoglobin

• Structures: Myoglobin (monomer), hemoglobin (tetramer).

• Functions: Myoglobin stores O2 in muscle; hemoglobin transports O2 in blood.

• Oxygen binding curves: Myoglobin (hyperbolic), hemoglobin (sigmoidal, cooperative binding).

• Histidine roles: Proximal and distal histidines stabilize O2 binding.

• Allosteric effectors: Molecules that modulate protein activity (e.g., BPG, H+ for hemoglobin).

• Bohr effect: Lower pH (higher H+) stabilizes T state, promoting O2 release.

• Fetal vs. adult hemoglobin: Fetal hemoglobin has higher O2 affinity due to structural differences.

Enzymes

What are Enzymes?

• Enzyme: Biological catalyst, usually a protein, that accelerates reactions without being consumed.

• Specificity: Enzymes act on specific substrates.

• Substrate: Molecule upon which an enzyme acts.

• Regulation: Enzyme activity can be modulated by various mechanisms.

How Do Enzymes Work?

• Free energy diagrams: Show energy changes during reactions; enzymes lower activation energy ().

• Spontaneity: A reaction is spontaneous if .

• Mechanisms of catalysis: Proximity/orientation, transition state stabilization, acid-base catalysis, covalent catalysis.

• Active site: Region where substrate binds and reaction occurs.

• Induced fit: Enzyme changes shape upon substrate binding.

• Cofactor, cosubstrate, prosthetic group: Non-protein components required for activity.

Regulating Enzyme Activity

• Regulation mechanisms: Allosteric regulation, covalent modification (e.g., phosphorylation), proteolytic activation, gene expression, compartmentalization, substrate availability.

• Competitive inhibition: Inhibitor competes with substrate for active site; can be overcome by increasing substrate concentration.

• Allosteric regulation: Effectors bind at sites other than the active site, altering enzyme activity.

• Protein phosphorylation: Addition/removal of phosphate groups by kinases/phosphatases modulates activity.

Biological Membranes

Fatty Acids, Triacylglycerols, and Membrane Lipids

• Lipid classification: Based on hydrophobicity/amphipathic nature.

• Types of lipids: Fatty acids, triacylglycerols (TAGs), phospholipids, sterols (e.g., cholesterol).

• Fatty acid structure: Long hydrocarbon chain with terminal carboxyl group; α and β carbons are adjacent to the carboxyl group.

• Amphipathic: Fatty acids have hydrophobic tails and hydrophilic heads.

• Saturated vs. unsaturated: Saturated (no double bonds), monounsaturated (one double bond), polyunsaturated (multiple double bonds).

• Cis/trans double bonds: Cis bends the chain; trans is straighter.

• Melting point: Increases with chain length, decreases with unsaturation.

• Triacylglycerol vs. glycerophospholipid: TAGs are storage fats; phospholipids are membrane components.

• Cholesterol: Modulates membrane fluidity; fits between phospholipids in bilayer.

Structure of Biological Membranes

• Lipid bilayer: Fluid, dynamic structure; dimensions vary with composition.

• Cholesterol: Increases membrane stability and modulates fluidity.

• Membrane proteins: Integral, peripheral, and lipid-anchored; integral proteins span the bilayer.

• Protein structures in membranes: α-helices and β-barrels.

Transport Across Membranes

• Passive transport: No energy required; includes simple diffusion and facilitated diffusion.

• Active transport: Requires energy (e.g., ATP hydrolysis).

• Transporters vs. channels: Transporters bind and move substances; channels form pores.

• Uniport, symport, antiport: Uniport moves one substance; symport moves two in same direction; antiport moves two in opposite directions.

• Na+/K+ ATPase: Pumps Na+ out and K+ in, using ATP.

• Glucose transport: Involves both active and facilitated transport mechanisms.

Introduction to Metabolism

Purposes and Concepts

• Major purposes: Energy production and biosynthesis.

• Catabolic vs. anabolic pathways: Catabolic break down molecules (release energy); anabolic build molecules (require energy).

• Amphibolic: Pathways that function in both catabolism and anabolism (e.g., citric acid cycle).

• Anapleurotic: Reactions that replenish intermediates of metabolic cycles.

Essential Concepts in Metabolism

• Free energy change (): Determines reaction direction; negative is spontaneous.

• Standard free energy () and biochemical standard (): Reference values for comparing reactions.

• Electron carriers: NAD+, NADP+, FAD; shuttle electrons in redox reactions.

• High-energy intermediates: ATP, GTP, phosphocreatine; store and transfer energy.

• ATP hydrolysis: Releases large, negative free energy; drives endergonic processes.

• Coupled reactions: Energetically unfavorable reactions are driven by coupling to favorable ones (e.g., glucose phosphorylation).

• Phosphocreatine: Serves as a rapid ATP buffer in muscle.

• Regulation: Rate-limiting steps, reciprocal regulation, product and feedback inhibition.

Nucleotides as High-Energy Molecules and Electron Carriers

• Phosphoanhydride bond: High-energy bond in ATP and other nucleoside triphosphates.

• Hydrolysis of phosphoanhydride bonds: Highly favorable due to relief of electrostatic repulsion and resonance stabilization.

• NAD+, NADP+, FAD: Dinucleotides functioning as electron carriers.

• Reduction equations:

Oxidative Phosphorylation

• Location: Inner mitochondrial membrane.

• Electron transport chain (ETC): Series of complexes that transfer electrons from NADH/FADH2 to O2, pumping protons to generate a gradient.

• ATP synthase: Uses proton gradient to synthesize ATP; Fo (membrane channel), F1 (catalytic).

• Terminal electron acceptor: O2; equation:

• Uncouplers: Increase O2 consumption by dissipating the proton gradient.

• Brown adipose tissue: Generates heat via uncoupling protein (thermogenin).

• ATP yield: Fewer ATP per FADH2 than NADH due to entry points in ETC.

Glycolysis and Glucose Metabolism

• Purpose: Breakdown of glucose to pyruvate, generating ATP and NADH.

• Location: Cytoplasm.

• Key steps: Three regulated steps catalyzed by hexokinase, phosphofructokinase-1 (PFK-1), and pyruvate kinase.

• ATP yield: Gross: 4 ATP; Net: 2 ATP per glucose.

• Regulation: Allosteric effectors, feedback inhibition, feed-forward activation.

• High-energy intermediates: 1,3-bisphosphoglycerate, phosphoenolpyruvate.

Fates of Pyruvate

• Aerobic fate: Conversion to acetyl-CoA (enters citric acid cycle).

• Anaerobic fates: Conversion to lactate (muscle), ethanol (yeast).

• Lactate: Dead-end in muscle; can be transported to liver for gluconeogenesis (Cori cycle).

• Acidotic damage: Accumulation of H+ during anaerobic glycolysis.

• Pyruvate dehydrogenase: Converts pyruvate to acetyl-CoA; tightly regulated by energy status and covalent modification.

The Citric Acid Cycle (CAC)

• Location: Mitochondrial matrix.

• Functions: Oxidizes acetyl-CoA to CO2, generates NADH, FADH2, GTP/ATP.

• Regulation: By substrate availability, product inhibition, allosteric effectors.

• Amphibolic: Functions in both catabolism and anabolism.

• Anapleurotic reactions: Replenish CAC intermediates (e.g., pyruvate carboxylase forms oxaloacetate).

Table: Comparison of Major Biological Polymers

Additional info: This guide expands on the syllabus learning objectives with academic context, definitions, and examples to serve as a comprehensive study resource for foundational biochemistry topics.