Biochemistry Notes (Chapter 2): Inorganic Compounds, Organic Compounds, and ATP

Inorganic Compounds

  • Biochemistry studies chemical composition and reactions of living matter; chemicals are either inorganic or organic

  • Inorganic compounds

    • Water, salts, and many acids and bases

    • Do not contain carbon (generally) for inorganic compounds

    • Organic compounds contain carbon (carbohydrates, fats, proteins, nucleic acids) and are covalently bonded

    • Both inorganic and organic compounds are essential for life

Water (Inorganic Compound)

  • Most abundant inorganic compound

    • Accounts for 60%−80%60\% - 80\% of the volume of living cells

  • Important properties of water

    • High heat capacity: absorbs/release heat with little temperature change

    • High heat of vaporization: evaporation requires large amounts of heat

    • Polar solvent properties: dissolves and dissociates ionic substances; forms hydration layers around large charged molecules (e.g., proteins)

    • Reactivity: participates in hydrolysis and dehydration synthesis

    • Cushioning: protects certain organs from trauma (e.g., cerebrospinal fluid cushions nervous system organs)

  • Water (details)

    • High heat capacity prevents sudden temperature changes in organisms

    • High heat of vaporization provides cooling mechanism through evaporation

    • Polar solvent dissolves ionic substances and facilitates transport in the body

    • Hydration layers around macromolecules help stabilize structures and interactions

    • Water participates directly in chemical reactions (hydrolysis, dehydration synthesis)

    • Cerebrospinal fluid as a cushioning fluid protecting brain and spinal cord

Salts (Inorganic Compound)

  • Salts are ionic compounds that dissociate into ions in water

    • Separate into cations (positively charged) and anions (negatively charged)

    • Do not include H+ or OH− ions in the salt itself

  • In solution, all ions are electrolytes because they can conduct electrical currents

  • Ions have specialized roles in body functions

    • Examples: sodium (Na+), potassium (K+), calcium (Ca2+), iron (Fe2+/Fe3+)

  • Common body salts

    • NaCl, CaCO3, KCl, calcium phosphates

Acids and Bases (Chemical Balance in Water)

  • Both acids and bases are electrolytes that ionize/dissociate in water

  • Acids

    • Proton donors: release hydrogen ions (H+) in solution

    • Examples: HCl (hydrochloric acid), HC2H3O2 (acetic acid, HAc), H2CO3 (carbonic acid)

  • Bases

    • Proton acceptors: pick up H+ in solution

    • When dissolved, bases often release hydroxide ions (OH−)

    • Examples: HCO3− (bicarbonate), NH3 (ammonia)

  • pH: acid-base concentration

    • pH scale measures [H+] concentration in solution

    • pH = −log⁡[H+]-\log\bigl[\mathrm{H^+}\bigr]; ranges from 0 to 14

    • Scale is logarithmic: each unit represents a 10-fold change in H+ concentration

    • Example: a solution with pH 5 is 10 times more acidic than a solution with pH 6

  • Solutions by pH range

    • Acidic solutions: high [H+], low pH (0–6.99)

    • Neutral solutions: equal [H+] and [OH−]; pH 7 (pure water) with [H+] = 10⁻⁷ M

    • Alkaline/basic solutions: low [H+] but high pH (7.01–14)

  • Neutralization

    • Acid-base reaction forms water and a salt

    • Neutralization reactions balance H+ and OH− to form H2O

  • Buffers

    • Buffers resist abrupt/large changes in pH

    • They can release H+ if pH rises or bind H+ if pH falls

    • They convert strong acids/bases (completely dissociated) into weaker ones (slightly dissociated)

    • Clinical example: carbonic acid–bicarbonate system in blood

    • Acid-base equation for buffer system: H<em>2CO</em>3↔H++HCO3−\mathrm{H<em>2CO</em>3 \leftrightarrow H^+ + HCO_3^-}

  • Clinical – Homeostatic Imbalance 2.1

    • Enzymes in the body work within a very narrow pH range

    • Arterial pH of 7.0 during cardiopulmonary resuscitation predicts a poor outcome

    • Arterial pH < 6.85: patients rarely survive

Organic Compounds: Synthesis and Hydrolysis

  • Organic molecules contain carbon (exceptions: CO2 and CO are inorganic)

  • Carbon characteristics

    • Electrically neutral (electroneutral)

    • Covalent bonding; forms four covalent bonds

    • Central to living systems

  • Major organic classes

    • Carbohydrates, lipids, proteins, nucleic acids

  • Polymers and monomers

    • Many organics are polymers composed of repeating monomer units

    • Synthesized by dehydration synthesis (loss of water) and broken down by hydrolysis (addition of water)

  • Dehydration synthesis and hydrolysis (general)

    • Dehydration synthesis: monomer1 + monomer2 → dimer + H2O

    • Hydrolysis: dimer + H2O → monomer1 + monomer2

  • Figure references (for context): Dehydration synthesis and hydrolysis concepts illustrated in diagrams

Carbohydrates (1 of 4)

  • Carbohydrates include sugars and starches; contain C, H, O

    • Hydrogen and oxygen in 2:1 ratio (CH2O)n

  • Classes of carbohydrates

    • Monosaccharides: one sugar (monomer)

    • Disaccharides: two sugars

    • Polysaccharides: many sugars; polymers of monosaccharides

  • Monosaccharides

    • Simple sugars with 3–7 carbon atoms

    • General formula: (CH<em>2O)</em>n(CH<em>2O)</em>n where n = number of carbon atoms

    • Important monosaccharides: pentose sugars (ribose, deoxyribose) and hexose sugars (glucose)

  • Carbohydrate molecules important to the body

    • Carbohydrates provide energy and structural roles

  • Disaccharides

    • Double sugars; too large to pass through cell membranes

    • Important disaccharides: sucrose, maltose, lactose

    • Formation: dehydration synthesis of two monosaccharides (e.g., glucose + fructose → sucrose + water)

  • Polysaccharides

    • Polymers of monosaccharides formed by dehydration synthesis

    • Important storage polysaccharides: starch (plants), glycogen (animals)

    • Generally not very soluble in water

Lipids (1 of 9)

  • Lipids contain C, H, O, and sometimes P; less O than carbohydrates

  • Insoluble in water

  • Main types: triglycerides, phospholipids, steroids, eicosanoids

  • Triglycerides

    • Fats (solid) and oils (liquid)

    • Structure: glycerol backbone with three fatty acids via dehydration synthesis

    • Functions: energy storage, insulation, protection

  • Triglycerides structure (visuals in figures)

    • Glycerol + three fatty acids

  • Fatty acids: saturated vs unsaturated

    • Saturated: all C-C bonds are single; maximum H atoms; linear; pack tightly; solid at room temperature (e.g., animal fats, butter)

    • Unsaturated: one or more C=C double bonds; kink; cannot pack tightly; liquid at room temperature (e.g., olive oil)

    • Trans fats: modified trans fat oils; resemble saturated fats and considered unhealthy

    • Omega-3 fatty acids: heart-healthy fats

  • Phospholipids

    • Modified triglycerides: glycerol + two fatty acids + a phosphorus-containing group

    • Head (polar, hydrophilic) and tails (nonpolar, hydrophobic)

    • Important in cell membrane structure

  • Steroids

    • Four interlocking hydrocarbon rings

    • Most important steroid: cholesterol

    • Cholesterol is made by liver and found in animal products; basis for synthesis of vitamin D, steroid hormones, and bile salts; important in cell plasma membrane structure

  • Eicosanoids

    • Derived from arachidonic acid in cell membranes

    • Prostaglandins are examples; roles in blood clotting, blood pressure, inflammation, labor contractions

    • Inflammation and other actions can be blocked by NSAIDs (e.g., aspirin, ibuprofen)

Proteins (2 of 9 sections; 2/3 in content)

  • Proteins constitute 20–30% of cell mass; have the most varied functions

    • Structural, chemical (enzymes), contraction (muscles)

  • Composition

    • Contain C, H, O, N, and sometimes S and P

    • Polymers of amino acid monomers held together by peptide bonds

  • Structural levels determine shape and function

    • Primary structure: linear sequence of amino acids (order)

    • Secondary structure: local folding patterns (α-helix, β-pleated sheets)

    • α-helix resembles a spring; β-pleated sheets resemble accordion ribbons

    • Tertiary structure: 3D shape formed by interactions of secondary structures

    • Quaternary structure: interaction of two or more polypeptide chains

  • Fibrous vs Globular proteins

    • Fibrous: structural, strand-like, water-insoluble, stable; often have tertiary or quaternary structure; provide mechanical support; examples: keratin, elastin, collagen, certain contractile fibers

    • Globular: functional, compact, water-soluble, sensitive to environment; often have tertiary or quaternary structure; active sites; examples: antibodies, hormones, molecular chaperones, enzymes

  • Protein Denaturation

    • Globular proteins unfold and lose their functional 3D shape; fibrous proteins are more stable

    • Active sites may be deactivated; typically reversible if conditions return to normal; irreversible if changes are extreme (cooking an egg is a common example)

  • Amino Acids and Peptide Bonds

    • 20 amino acids used to build proteins

    • Amino acids joined by covalent peptide bonds

    • Each amino acid has an amine group, a carboxyl group, and a unique R group

    • Amino acids can act as acids or bases (amphoteric)

    • R group variations determine properties and function of each amino acid

  • Enzymes (protein catalysts)

    • Enzymes are globular proteins acting as biological catalysts; they speed up reactions without being consumed

    • They lower activation energy, enabling reactions at body temperature; allow millions of reactions per minute

    • Functional enzymes (holoenzymes) consist of two parts:

    • Apoenzyme (protein portion)

    • Cofactor (metal ion) or coenzyme (organic molecule, often a vitamin)

    • Enzyme specificity: each enzyme acts on a specific substrate

    • Naming: many end with -ase; often named for the reaction they catalyze (e.g., hydrolases, oxidases)

  • Mechanism of Enzyme Action

    • Substrate binds to enzyme's active site, forming enzyme–substrate complex

    • Substrate undergoes rearrangement, forming final product

    • Product is released; enzyme is free to catalyze further reactions

  • Figure references (for context): Enzyme action and mechanisms illustrated in diagrams

  • Key concept: Enzymes reduce the energy barrier to chemical reactions, enabling efficient metabolism

Nucleic Acids (1–4 of 4)

  • Nucleic acids are the largest biomolecules in the body

  • Polymers built from monomers called nucleotides

    • Each nucleotide contains a nitrogenous base, a pentose sugar, and a phosphate group

  • Two major classes

    • DNA (deoxyribonucleic acid)

    • RNA (ribonucleic acid)

  • DNA features

    • Holds the genetic blueprint for the synthesis of all proteins

    • Structure: double-stranded helical molecule located in the cell nucleus (double helix)

    • Nitrogen bases: Purines (Adenine A, Guanine G); Pyrimidines (Cytosine C, Thymine T)

  • DNA base-pairing rules

    • A pairs with T; G pairs with C (complementary base pairing)

  • RNA features

    • RNA links DNA to protein synthesis; single-stranded and active mostly outside the nucleus

    • Sugar: ribose (not deoxyribose); Uracil (U) replaces thymine

    • Three major RNA types carry out protein synthesis: mRNA, tRNA, rRNA

  • Figures and animations referenced for structure and function (DNA/RNA visuals and animations)

ATP (1–3 of 3)

  • ATP (adenosine triphosphate) is the primary chemical energy carrier in cells

  • Source of energy: chemical energy released when glucose is broken down is captured in ATP

  • ATP structure

    • Adenine-containing RNA nucleotide with two additional phosphate groups (three total phosphates)

  • ATP usage and conversion

    • Terminal phosphate group can be transferred to other compounds to do work

    • ATP → ADP + P _i (energy released)

    • ADP → AMP + P _i (further energy release under successive dephosphorylation)

  • Three examples of cellular work driven by ATP

    • Muscle contraction, active transport across membranes, and chemical work (driving endergonic reactions)

  • Visuals: Structure and hydrolysis/energy transfer diagrams illustrate ATP use