Chapter 2- Biochemistry, Cells, and Homeostasis

Water and Hydrogen Bonding

Water molecules have polar covalent bonds due to unequal sharing of electrons around the oxygen atom; oxygen becomes partially negative, hydrogens become partially positive.
Hydrogen bonds form between the hydrogen of one water molecule and the oxygen of another; individually weak but numerous, contributing to key properties.
These hydrogen bonds help explain surface tension and the formation of a meniscus in glass due to adhesive and cohesive forces.

Water as a Multifacted Substance in Physiology

Water is a solvent, a medium for reactions, a lubricant, and has a high heat capacity.
Solvent: dissolves solutes to form a solution; aqueous solutions can dissociate ionic compounds into ions (electrolytes).
We are largely water-based: the body is ~70% water; many dissolved substances exist as ions in solution.
Ionization in water enables electrolytes, which are essential for physiology (e.g., Na^+, K^+, Ca^{2+}, Cl^-).
Electrolytes are ions present in aqueous solution; an electrolyte is an ion in solution.
Water follows electrolytes (osmotic/rehydration principles) and sodium is especially important in muscle contraction and neural conduction.
Water acts as a medium for physiological reactions inside the body; a large proportion of biochemical processes occur in aqueous environments.
Water contributes to lubrication, e.g., synovial fluid in joints.
Blood composition: about 55% plasma, and plasma is ≈ 91% water.

Calorimetry, Heat, and Phase Changes

Calorie vs kilocalorie: a calorie (lowercase c) is the energy to raise 1 g of water by 1°C. Food energy is measured in kilocalories (uppercase C): 1 kcal = 1000 cal.
Phase changes of water involve energy input without temperature change:
- Melting (fusion): 1 g of ice at 0°C needs about 80 cal to turn into liquid water at 0°C (latent heat of fusion).
- Vaporization (boiling): 1 g of liquid water at 100°C needs about 540 cal to become steam (latent heat of vaporization).
- Heating the same water from 0°C to 100°C requires sensible heat (1 cal/g·°C) per degree rise; once at 100°C, phase change occurs.
For example, the text discusses an ice cube at 0°C absorbing energy to melt and then eventually to vaporize; these energy changes explain why water holds heat well and resists temperature fluctuations.
Fahrenheit conversion (mentioned): to convert Celsius to Fahrenheit, use the relation F = 1.8°C + 32.
Water is capable of existing in all three common states (solid, liquid, gas) under Earth-like conditions, making it unique in biological systems.
Evaporation as cooling: when water evaporates from the body, it takes heat energy with it, producing a cooling effect (thermoregulation via sweating).
High heat capacity and high heat of vaporization help organisms absorb or lose large amounts of energy with relatively small changes in temperature.

Key Electrolytes and Ions

Major electrolytes in the body include: Na^+, K^+, Ca^{2+}, Cl^-, HCO_3^-, and others; these ions are essential for muscle contraction, neural transmission, and fluid balance.
An electrolyte is an ion in aqueous solution; ions carry electrical charge and influence cellular processes.
Na^+ is a paramount ion in muscle contraction and neural conduction; others also play critical roles.
Ionization around solutes occurs via hydration shells (hydrospheres) that facilitate dissolution and subsequent biochemical activity.

Acids, Bases, and pH Homeostasis

pH scale (potential hydrogen): ranges from acidic (<7) to basic (>7), with 7 being neutral.
Blood pH is tightly regulated: arterial blood ~7.45 and venous blood ~7.35; small shifts in pH can have large physiological effects.
Carbon dioxide and carbonic acid buffer system:
- Cellular respiration yields CO2; CO2 combines with water to form carbonic acid, which dissociates into H^+ and HCO_3^-.
- Equilibrium: $CO2 + H2O \rightleftharpoons H2CO3 \rightleftharpoons H^+ + HCO_3^-$
Higher CO2 in blood increases H^+ → lower pH (acidemia); removing CO2 via respiration raises pH (alkalemia).
Buffers resist pH changes; main buffers include the bicarbonate system and protein buffers.
Acidosis vs alkalosis: uncontrolled acidity or basicity can be life-threatening; kidneys and lungs are major compensators.
Strong acids and bases differ in their causticity; strong acids (e.g., HCl) and strong bases (e.g., NaOH) are highly corrosive.
pH and safety of acids/bases are context-dependent; even a strongly acidic substance (pH ~3) can be harmful, while a basic substance with pH ~10-11 can also be dangerous.
Buffers and acid-base balance are essential to maintaining enzyme function and metabolic stability.

Acids, Bases, and Buffers in the Body

Buffers: substances that resist strong changes in pH when acids or bases are added.
In the body, carbonic acid buffering and protein buffering help maintain pH within narrow limits.
If pH shifts too far, proteins (including enzymes) can denature, disrupting metabolism.
Fever and temperature: high temperatures can denature proteins and enzymes, altering their function.
The body’s compensatory mechanisms include respiratory adjustments and renal adjustments to balance pH.

Organic vs Inorganic Molecules in Biology

Inorganics: essential small molecules like O2, CO2, H2O, CO2, vitamins, minerals; act as cofactors and structural components.
Organics: carbon-based molecules including carbohydrates, lipids, proteins, nucleic acids; contain C, H, O, and often N (and sometimes S, P).
Vitamins and minerals serve as cofactors/coenzymes, enabling enzyme-catalyzed reactions.
The statement that inorganic does not matter is false; they are essential to life processes.

Carbohydrates (Carbs)

General formula:
- Carbohydrates have the CHO elements in a 1:2:1 ratio: $ext{C:H:O} = 1:2:1$ for monosaccharides (e.g., glucose: $ext{C}6 ext{H}{12} ext{O}_6$ ).
Monosaccharides (e.g., glucose, ribose) are the simple sugar units; ribose is a pentose (5 carbons) used in nucleic acids; glucose is a hexose (6 carbons).
Disaccharides and polysaccharides form via dehydration synthesis (condensation) and are broken by hydrolysis.
Energy yield: carbohydrates provide ~4 kcal per gram; glucose in cellular respiration yields about 36 ATPs, metabolic water, and heat.
Glucose can exist in ring or chain forms; in nursing contexts, IV glucose is called dextrose (glucose in solution).
Monosaccharide examples: glucose, ribose; disaccharides: sucrose (table sugar); lactose (milk sugar); maltose; polysaccharides: starch (plants), glycogen (animals).
Glycogen is the storage form of glucose in animals; starch is the storage form in plants. Excess glucose can be converted to lipids (lipogenesis).
Glycogen is branched (e.g., branches every ~10-15 units in glycogen) and stored in liver and muscle tissue.
Carbohydrates can also serve as cell surface markers (antigens) and as components of glycoproteins and glycolipids involved in cell recognition and transport.

Dehydration Synthesis and Hydrolysis (Carbohydrate Context)

Dehydration synthesis (condensation) forms glycosidic bonds between monosaccharides and builds larger carbohydrates, releasing water (H_2O).
Hydrolysis breaks glycosidic bonds by adding water, using water to split larger carbohydrates into monosaccharides.
This process is anabolic (building up) for dehydration synthesis and catabolic (breakdown) for hydrolysis.
Example: glucose + fructose → sucrose via dehydration synthesis.

Lipids

Lipid categories: oils, fats, steroids, cholesterol, waxes; all are hydrophobic or amphipathic and energy-dense.
General formula: CHO, but not in a fixed 1:2:1 ratio; energy yield is ~9 kcal per gram for lipids.
Fats vs oils: fats are solid at room temperature (saturated fats); oils are liquid (often unsaturated fats).
Saturated fats (e.g., butter): all carbon bonds are saturated with hydrogens, linear chains, pack tightly, higher solidification tendency.
Unsaturated fats (e.g., olive oil): contain double bonds (kinks) that prevent tight packing; liquid at room temperature.
Trans fats (partially hydrogenated oils): industrially altered fats with trans double bonds; longer shelf life but health risks; read nutrition labels.
Fat storage: triglycerides are the primary storage form of lipids in adipose tissue; can also be stored around organs (pericardial, omental fat) and subcutaneously.
Phospholipids and diglycerides: backbone (glycerol) with fatty acids and a phosphate group; essential components of plasma membranes.
Cholesterol and steroids: cholesterol is a backbone for steroid hormones and is embedded in cell membranes; cholesterol is required for hormone synthesis but excess can contribute to atherosclerosis.
Lipids serve multiple roles beyond energy: insulation, protection of core organs, membrane structure, and signaling.
Diets and metabolism: when carbs are scarce, the body can metabolize lipids (lipolysis) and produce ketones for brain energy; prolonged excess ketone production can lead to ketoacidosis.
Exercise and lipid metabolism: aerobic vs anaerobic exercise differences influence fat utilization and HDL/LDL ratios; exercise on an empty stomach can raise HDL and lower LDL.

Proteins

Proteins are composed of amino acids (20 standard types) with a central carbon, amino group, carboxyl group, a hydrogen, and a variable side chain (R group).
Essential vs nonessential amino acids:
- Essential amino acids: eight cannot be synthesized by the body and must be obtained from diet.
- Nonessential amino acids: liver can synthesize them via transamination.
Peptide bonds link amino acids (carboxyl group of one amino acid to the amino group of the next): this forms dipeptides, tripeptides, and polypeptides.
Protein structure levels:
- Primary: linear sequence of amino acids.
- Secondary: alpha helix or beta pleated sheet stabilized by hydrogen bonds.
- Tertiary: three-dimensional folding stabilized by various interactions, including disulfide bonds between sulfur atoms.
- Quaternary: complex of multiple polypeptide chains (e.g., hemoglobin has two alpha and two beta chains).
Disulfide bonds (between sulfur atoms) help stabilize tertiary and quaternary structures and thus protein shape.
Enzymes are proteins that catalyze biochemical reactions; all enzymes are proteins, but not all proteins are enzymes.
Enzyme specificity:
- Each enzyme catalyzes one type of reaction; substrate compatibility is described by the lock-and-key model or induced fit; active site binds substrate, forming enzyme-substrate complex and producing product.
- Enzymes are not consumed in reactions and can be reused.
Factors affecting enzyme activity: temperature, pH, salinity, substrate availability; enzymes have optimal conditions under which they function best.
Protein roles in the body (examples): enzymatic catalysis, structural support (collagen, keratin), transport channels, recognition and binding (receptors, antibodies), immunological defense, contractile proteins in muscle.
Hemoglobin example: hemoglobin carries oxygen; sickle cell anemia can result from a single amino acid substitution (glutamic acid replaced by valine at a specific position), causing abnormal shape under hypoxic conditions and vascular occlusion.
Collagen is the most abundant protein in the body, providing structural support across tissues.
Controls on protein function include sequence accuracy and correct folding; misfolding can lead to disease.

Nucleotides, Nucleic Acids, and Genetic Information

Nucleotides consist of three parts: a nitrogenous base, a sugar (ribose in RNA or deoxyribose in DNA), and a phosphate group.
Two main nucleic acids:
- DNA: deoxyribonucleic acid, double-stranded, contains thymine (T); sugar is deoxyribose.
- RNA: ribonucleic acid, single-stranded, contains uracil (U) instead of thymine; sugar is ribose.
Nitrogenous bases:
- Purines: adenine (A) and guanine (G) with two rings.
- Pyrimidines: cytosine (C), thymine (T, in DNA), and uracil (U, in RNA) with one ring.
Base pairing in DNA: A pairs with T; C pairs with G (complementary base pairs).
RNA base pairing differs: RNA uses A-U, C-G.
DNA is double-stranded and forms a helix, which remains in the nucleus; RNA is typically single-stranded and transits to the cytoplasm for protein synthesis.
Transcription: the language of DNA is transcribed into RNA, which leaves the nucleus to participate in protein synthesis.
The language and structure of nucleic acids are essential for preserving genetic information and directing protein synthesis.
ATP (adenosine triphosphate): a nucleotide with adenine, ribose, and three phosphate groups; the primary energy currency of the cell.
- ATP hydrolysis releases energy used for cellular work; ADP and inorganic phosphate (Pi) form when ATP is hydrolyzed.
- ATP is also involved in signaling via cyclic AMP (cAMP), a second messenger in hormonal signaling.

Cellular Biology: Cells and Membranes

The cell is the basic unit of life; organisms can be unicellular or multicellular.
Animal cells have a plasma membrane; plants have a plasma membrane and a cell wall.
Plasma membrane structure: a phospholipid bilayer with hydrophilic heads facing aqueous environments and hydrophobic tails forming the interior; this arrangement creates a fluid mosaic model with membrane fluidity.
Cholesterol within the membrane maintains integrity and fluidity.
Glycolipids and glycoproteins on the membrane surface act as markers for cell recognition and interactions (e.g., immune recognition).
The membrane is selectively permeable and regulates exchange with the environment via concentration gradients, molecule size, charges, and receptor-mediated processes.
The membrane also provides structural support and participates in cell signaling.
Red blood cells: ~35 trillion RBCs, each RBC contains roughly 250–300 million hemoglobin molecules; Hb carries oxygen via iron-containing heme groups.
Carbon monoxide (CO) can bind hemoglobin with high affinity, displacing oxygen and impairing oxygen transport; this is hazardous in high exposure.
Membrane composition and function are critical for cellular homeostasis and organism health.

Enzyme Kinetics and Protein Function in Physiology

Enzymes catalyze reactions but are not consumed; they have specific substrates and products; each enzyme typically catalyzes a single reaction.
Substrate and enzyme fit denote specificity; the active site is the binding region that facilitates reaction.
Temperature, pH, and ionic strength (salinity) affect enzyme activity; extreme conditions can denature enzymes and halt metabolic processes.
The concept of isomers and enzyme-substrate specificity explains why different enzymes catalyze distinct reactions even if substrates are similar.
Isomers and conformations are crucial for enzyme function and protein folding extends beyond primary sequence to tertiary and quaternary structure.

Practical and Real-World Contexts and Metabolism

Diet, exercise, and health:
- Lipids provide a dense energy source but can contribute to cardiovascular disease if dietary fats are not managed properly.
- Exercise improves lipid profiles by increasing HDL and reducing LDL; different exercise intensities affect fat metabolism and energy use.
- Ketosis as an energy pathway during carbohydrate restriction; excessive ketone production can cause ketoacidosis, especially in diabetics.
Antibiotic use and resistance:
- Completing antibiotic courses is important to eradicate weak and strong bacteria; stopping early can allow resistant strains to persist and proliferate.
Public health and education implications:
- Understanding basic biochemistry and physiology supports healthier lifestyle choices, disease prevention, and informed medical decisions.

Quick Reference and Key Equations

Water and phase changes:
- Latent heat of fusion: $ext{LHF} \approx 80 \, \text{cal/g}$
- Latent heat of vaporization: $\text{LHV} \approx 540 \, \text{cal/g}$
- Specific heat of water: $c = 1 \, \text{cal/g} \cdot ^\circ C$
Cellular respiration (summary):
- General form: $\text{C6H12O6} + 6 \; O2 \rightarrow 6 \; CO2 + 6 \; H2O + \text{ATP (and heat)}$
Carbonic acid buffering system:
- $CO2 + H2O \rightleftharpoons H2CO3 \rightleftharpoons H^+ + HCO_3^-$
Carbohydrate formula and energy:
- General monosaccharide ratio: $\text{CH}_2\text{O} \; (\text{1:2:1 ratio})$
- Glucose formula: $\mathrm{C6H{12}O_6}$
- Energy yield: $\approx 4\ \text{kcal/g}$
Lipid energy yield: $\approx 9\ \text{kcal/g}$
ATP components (nucleotide):
- Adenosine triphosphate: $\text{ATP} = \text{adenine} + \text{ribose} + 3\; \text{phosphate groups}$
- ATP hydrolysis can form ADP and Pi; energy released powers cellular work.

Connections to Foundational Principles

Structure determines function across molecules: bonding patterns (ionic, covalent, hydrogen, disulfide, peptide) and higher-order folding determine biological activity.
Thermodynamics and energy flow govern metabolism: endergonic vs exergonic reactions, energy coupling, and the role of ATP.
Homeostasis emerges from integrated systems: buffers, respiratory and renal compensation for acid-base balance, and regulation of temperature and fluid balance.
Evolutionary and physiological relevance of macromolecules: carbohydrates for energy and signaling, lipids for energy storage and membranes, proteins for catalysis and structure, nucleic acids for genetic information and protein synthesis.
Clinical relevance: diseases arising from protein misfolding (e.g., certain enzyme deficiencies, sickle cell disease), acid-base disturbances, cholesterol-related cardiovascular risk, and the importance of dietary balance and physical activity.

Summary Takeaways

Water’s unique properties underpin life: solvent capabilities, high heat capacity, lubricating functions, and the formation of hydrogen bonds.
Biomolecules (carbs, lipids, proteins, nucleic acids) follow fundamental chemical rules but enable diverse biological roles through structure and interactions.
Enzymes catalyze specific reactions; protein structure and folding are essential for function; misfolding or denaturation disrupts biology.
The body maintains chemical and electrical homeostasis through buffers, membrane transport, and organ systems (lungs and kidneys) that manage pH and metabolic waste.
Diet, metabolism, and physical activity dramatically influence energy balance, cardiovascular risk, and overall health, illustrating the practical relevance of these biochemical principles.