Comprehensive Biochemistry Study Notes: Inorganic and Organic Compounds

Fundamentals of Biochemistry and Subatomic Structure

• Biochemistry is defined as the chemistry of life.

• Subatomic particles that form the foundation of atomic structure include neutrons, protons, and electrons.

• Chemical compounds in living systems are categorized into inorganic and organic compounds based on carbon-hydrogen bonding:

  • Inorganic compounds: Generally do not contain carbon bonded to hydrogen. Primary biological examples include water, acids, bases, and salts.

  • Organic compounds: Explicitly contain carbon bonded to hydrogen. Primary biological examples include carbohydrates, lipids, proteins, and nucleotides/nucleic acids.

Inorganic Compounds: Water

• Water is the most important and abundant inorganic compound in all living systems.

• Water constitutes $50\%$ to $75\%$ of total human body weight.

• Molecular Structure and Polarity:

  • Composed of two hydrogen atoms and one oxygen atom held together by covalent bonds.

  • Exhibits intrinsic molecular polarity, characterized by a partial positive charge ($\delta^+$) on the hydrogen atoms and a partial negative charge ($\delta^-$) on the oxygen atom.

  • Polarity allows water molecules to form hydration spheres around charged ions and dissolved polar molecules.

• Physiological Properties of Water:

  • Solvency: The ability to dissolve other chemical substances. Water is recognized as the universal solvent because it dissolves more substances than any other solvent. All metabolic reactions in the body depend directly on the solvency of water.

  • Cohesion: The tendency of water molecules to adhere to one another via hydrogen bonding.

  • Adhesion: The tendency of water molecules to cling to other polar surfaces and biological membranes.

  • Chemical Reactivity: The capacity to actively participate in metabolic chemical reactions, notably hydrolysis and dehydration synthesis.

  • Thermal Stability: Characterized by a high heat capacity, enabling water to absorb or release significant amounts of thermal energy with minimal changes in temperature.

Inorganic Compounds: Acids, Bases, and pH

• Acids and bases are defined according to their specific behaviors in aqueous solution with respect to hydrogen ions ($H^+$):

  • Acid: A proton donor that releases hydrogen ions ($H^+$) when dissolved in water ($H_2O$).

  • Base: A proton acceptor that either accepts hydrogen ions ($H^+$) or releases hydroxide ions ($OH^-$) in water ($H_2O$).

• Definition of pH:

  • pH measures the concentration of hydrogen ions in a solution.

  • Mathematically defined as the negative logarithm of hydrogen ion molarity:     $pH = -\log[H^+]$

Buffer Systems and Physiological pH Regulation

• Buffer: A chemical system that resists dramatic changes in pH when acids or bases are added.

• Consists of a weak acid and its corresponding conjugate anion.

• Carbonic Acid–Bicarbonate Buffer System: The chief physiological buffer system responsible for stabilizing blood and extracellular fluid pH.

• Homeostatic pH values in human physiology:

  • Normal Blood pH Range: Maintained strictly between $7.35$ and $7.45$.

  • Intracellular pH: Maintained at approximately $7.2$.

Quantitative Measures of Solution Concentration

• Solutions are measured based on the concentration of solute dissolved in a solvent:

• Weight per Volume:

  • Expresses the mass of solute present within a given total volume of solution.

  • Standard biological unit: milligrams per deciliter ($\text{mg/dl}$).

  • Example: Normal human serum cholesterol concentration is measured as $200\,\text{mg/dl}$.

• Percentage:

  • Expressed as the weight of solid solute per total volume of solution.

  • Example: A $5\%$ dextrose solution contains $5\,\text{g}$ of solute in $100\,\text{ml}$ of total solution.

• Milliequivalents per Liter ($\text{mEq/L}$):

  • Used to express electrolyte concentration.

  • Factors in both the millimolar concentration of the solute and the net electrical charge of its dissolved particles.

• Molarity ($M$):

  • Defined as the number of moles of solute per liter of total solution ($\text{mol/L}$).

  • One mole is defined as the mass in grams equal to the molecular weight of the substance.

  • Represents the most physiologically meaningful measure of solution concentration.

  • Concentrations in human body fluids are typically quantified in millimolar ($\text{mM}$) units.

Salts and Electrolytes

• Salt: An inorganic compound composed of any metal cation and nonmetal anion held together by ionic bonds.

• Electrolytes: Substances that dissociate into individual ions in solution and are capable of conducting an electrical current.

Organic Biomolecules and Chemical Reactions

• Organic biomolecules in the human body are polymers constructed from repeating monomer subunits:

  • Carbohydrates (built from monosaccharides)

  • Lipids (built from fatty acids and glycerol components)

  • Proteins (built from amino acids)

  • Nucleic Acids (built from nucleotides)

• Properties of Carbon Atoms:

  • Carbon possesses four valence electrons, allowing it to form four covalent bonds with other atoms.

  • Readily bonds with other carbon atoms to construct stable linear, branched, or cyclic carbon backbones.

  • Readily forms covalent bonds with hydrogen, oxygen, nitrogen, sulfur, and other elements.

  • Carbon backbones carry specific functional groups that dictate the chemical properties and behavior of organic molecules.

• Biomolecular Chemical Reactions:

  • Synthesis Reactions (Anabolism): Building complex molecules from simpler components. Driven by Dehydration Synthesis, where an $-OH$ group is removed from one monomer and an $-H$ group is removed from another, linking monomers together and generating a water molecule:     $A + B \rightarrow AB + H_2O$

  • Decomposition Reactions (Catabolism): Breaking down complex molecules into simpler monomers. Driven by Hydrolysis, where a water molecule is consumed ($H_2O \rightarrow H^+ + OH^-$) to cleave the covalent bond linking monomers:     $H_2O + AB \rightarrow A + B$

Carbohydrates: Structures and Physiological Roles

• Carbohydrates are the most abundant organic biomolecules in living organisms.

• Defined by a characteristic atomic ratio of two hydrogen atoms for every one oxygen atom ($2:1$ ratio of $H:O$).

• Nomenclature: Carbohydrate names typically contain the root "sacchar-" and the suffix "-ose", both meaning sugar or sweet.

• Categories of Saccharides:

  • Monosaccharides: Simple single-sugar carbohydrates. Examples include glucose, fructose, and ribose.

  • Disaccharides: Carbohydrates formed by linking two monosaccharides together. Examples include sucrose (composed of glucose and fructose) and lactose (composed of glucose and galactose).

  • Oligosaccharides and Polysaccharides: Complex polymers composed of longer sugar chains ("oligo-" = few, "poly-" = many). Examples include glycogen, starch, and cellulose.

  • Conjugated Carbohydrates: Carbohydrate molecules covalently bound to proteins or lipids:

  • Glycolipids and Glycoproteins: Cell membrane lipids and membrane proteins attached to sugar chains up to 12 units long.

  • Proteoglycans: Macromolecules composed primarily of carbohydrates with a minor protein portion. Proteoglycans form structural gels within the extracellular matrix (ECM) of connective tissues and provide essential joint lubrication.

  • Moiety: Term denoting each individual functional component or structural part of a conjugated macromolecule.

• Functions of Carbohydrates:

  • Serve as a rapidly mobilized primary energy source for cellular functions.

  • All digested dietary carbohydrates are converted to glucose.

  • Glucose molecules are oxidized inside cells to generate adenosine triphosphate (ATP).

Lipids: Structural Diversity and Biological Functions

• Lipids are hydrophobic organic molecules featuring a high ratio of hydrogen to oxygen.

• Contain significantly more energy per gram (higher caloric density) than carbohydrates.

• Five Primary Classes of Lipids in the Human Body:

  1. Fatty Acids: Hydrocarbon chains consisting of $4$ to $24$ carbon atoms, bounded by a carboxyl group ($-COOH$) at one end and a methyl group ($-CH_3$) at the opposing end.

  • Essential Fatty Acids: Fatty acids that cannot be synthesized by human cells and must be ingested in the diet.

  • Saturated Fatty Acids: Lack double bonds between carbon atoms; saturated with hydrogen. Typically solid at room temperature.

  • Unsaturated Fatty Acids: Contain one or more double bonds ($C=C$) within the carbon chain. Typically liquid at room temperature.

  • Polyunsaturated Fatty Acids: Contain multiple carbon-carbon double bonds in their hydrocarbon chains.

  • Omega-3 Fats: Polyunsaturated fats found in flaxseed oil and fish oil; essential dietary fats with documented positive effects on cardiovascular health.

  • Saturated Fats: Dietary fats found in animal fats, palm oil, and coconut oil; elevated consumption may increase risk for cardiac disease.

  • Trans Fats: Produced industrially by adding hydrogen atoms to unsaturated plant oils ("partially hydrogenated oils"); have no safe level of consumption and significantly elevate heart disease risk.

  1. Triglycerides (Neutral Fats): Storage molecules consisting of three individual fatty acids linked via dehydration synthesis to a 3-carbon carbohydrate backbone, glycerol. Dietary fats and oils are composed of triglycerides. Saturated triglycerides remain solid at room or body temperature.

  2. Phospholipids: Amphipathic lipids consisting of a glycerol molecule attached to a polar, hydrophilic head (containing a phosphate group) and two non-polar, hydrophobic fatty acid tails. Spontaneously assemble into lipid bilayers when placed in water.

  3. Eicosanoids: $20$-carbon signaling molecules derived from the essential fatty acid arachidonic acid. Serve as hormone-like chemical messengers between cells and include prostaglandins.

  4. Steroids: Nonpolar lipids defined by a core four-ring hydrocarbon structure termed the steroid nucleus.

  • Cholesterol: The foundational steroid from which all other functional steroids in the body are synthesized.

Membrane Fluidity and Environmental Adaptation

• Cellular membrane function depends on maintaining precise lipid fluidity.

• Cells adjust the proportion of saturated versus unsaturated fatty acids in their plasma membranes to adapt to temperature changes:

  • Higher growth temperatures: Cells reduce unsaturated fatty acids and increase saturated fats to keep the membrane stable and prevent excess fluidity.

  • Lower growth temperatures: Cells increase unsaturated fatty acids to prevent rigid packing and maintain adequate membrane fluidity.

Proteins: Structure, Folding, and Functions

• Proteins are polymers composed of amino acid monomers containing Carbon, Hydrogen, Nitrogen, Oxygen, and frequently Sulfur ($C, H, N, O, S$).

• All functional human proteins are assembled from a standardized pool of $20$ amino acids.

• Levels of Protein Structure and Folding:

  • Protein biological activity depends entirely on its three-dimensional shape. Changing even a single amino acid in a sequence can alter folding patterns and abolish biological function.

  • Secondary Structure: Localized coiling or folding stabilized by hydrogen bonds forming between slightly negative carbonyl oxygen atoms ($C=O$) and slightly positive amino hydrogen groups ($-NH$).

  • Tertiary Structure: Comprehensive three-dimensional folding into globular or fibrous shapes, driven by hydrophobic-hydrophilic interactions and van der Waals forces, and reinforced by covalent disulfide bridges between cysteine amino acid residues.

• Structural Classes of Proteins:

  • Fibrous Proteins: Long, extended, rope-like structural strands composed mainly of nonpolar amino acids. Add mechanical strength and durability to tissues.

  • Globular Proteins: Compact, spherical molecules composed mainly of polar amino acids. Function dynamically as enzymes, hormones, membrane channels, and signaling messengers.

• Protein Denaturation:

  • The loss of secondary and tertiary protein structure caused by exposure to hostile environmental conditions (such as extreme pH or high heat), resulting in permanent loss of biological function.

• Seven Major Functional Roles of Proteins:

  1. Structure: Structural components such as collagen and keratin.

  2. Communication: Peptide hormones and cell surface receptors.

  3. Membrane Transport: Transmembrane channel proteins, carriers, and active pumps.

  4. Catalytic Activity: Enzymes that accelerate metabolic chemical reactions.

  5. Recognition and Protection: Immunoglobulins (antibodies), clotting factors, and cell identity markers.

  6. Movement: Contractile motor proteins such as actin and myosin.

  7. Cell Adhesion: Cell adhesion molecules that bind adjacent cells together in tissues.

Nucleotides and Nucleic Acids

• Nucleotides are organic monomers composed of Carbon, Hydrogen, Nitrogen, Oxygen, and Phosphorus ($C, H, N, O, P$).

• Structural Components of a Nucleotide:

  1. A nitrogenous base with a hydrocarbon ring structure.

  2. A 5-carbon pentose sugar (ribose or deoxyribose).

  3. One or more attached phosphate groups.

• Classification of Nitrogenous Bases:

  • Purines: Double-ring nitrogenous bases comprising Adenine (A) and Guanine (G).

  • Pyrimidines: Single-ring nitrogenous bases comprising Cytosine (C), Uracil (U), and Thymine (T).

• Deoxyribonucleic Acid (DNA):

  • Double-stranded nucleic acid polymer arranged in a twisted double helix.

  • Contains genes, which hold the fundamental recipes (genetic code) for cellular protein synthesis.

  • Exhibits strict complementary base pairing:

  • Adenine pairs exclusively with Thymine ($A = T$).

  • Guanine pairs exclusively with Cytosine ($G = C$).

• Ribonucleic Acid (RNA):

  • Single-stranded nucleotide polymer that moves between the nucleus and the cytoplasm.

  • Contains the pentose sugar ribose and utilizes Uracil (U) in place of Thymine ($A = U$ pairing).

  • Protein Synthesis Steps:

  • Transcription: Process where ribosomal rRNA/transcriptional machinery transcribes a specific gene recipe from DNA.

  • Translation: Process where transfer RNA (tRNA) directs assembly of specific amino acids into a protein chain at the ribosome based on the RNA transcript.

High-Energy Compounds: Adenosine Triphosphate (ATP)

• Adenosine Triphosphate (ATP) serves as the primary chemical energy transfer molecule in human cells.

• Structure: Composed of adenine, ribose sugar, and three covalently bonded phosphate groups.

• Energy Dynamics and Synthesis:

  • Synthesized from adenosine diphosphate (ADP) and inorganic phosphate ($P_i$):     $ADP + P_i + \text{Energy} \rightarrow ATP$

  • Energy required for ATP synthesis is released by exergonic oxidation of biomolecules:     $C_6H_{12}O_6 + 6O_2 \rightarrow 6CO_2 + 6H_2O + \text{Energy}$

  • Energy is liberated from ATP via hydrolysis to drive endergonic cellular reactions:     $ATP \rightarrow ADP + P_i + \text{Energy}$

  • Cleavage of the terminal phosphate bond in ATP is highly exergonic because ADP is significantly more chemical stable than ATP.

• Cellular Functions Driven by ATP Hydrolysis:

  • Muscle contraction

  • Ciliary beating and movement

  • Active transport across membranes

  • Anabolic synthesis reactions