Comprehensive Biochemistry, Cell Biology, and Genetics Study Notes

Atoms and the Foundations of Atomic Theory

• John Dalton, an English chemist, developed the atomic theory in 1803. The core tenets are:

  • All matter is composed of atoms.

  • Atoms are indivisible and indestructible.

  • Compounds are formed by a combination of two or more different kinds of atoms.

• Niels Bohr, a Danish physicist, proposed the planetary model of atomic structure. This model posits that electrons orbit the nucleus in specific energy levels, similar to planets orbiting a sun.

• Subatomic Particles:

  • Protons (represented as $p^+$): Carry a single positive charge and have a mass of approximately $1\,amu$.

  • Neutrons (represented as $n^0$): Have no charge and a mass of approximately $1\,amu$.

  • Electrons (represented as $e^-$): Carry a single negative charge and have very low mass. They reside in concentric clouds (energy levels) surrounding the nucleus and determine chemical properties.

• Atomic Number and Mass:

  • Atomic Number: The number of protons in the nucleus. The atom is electrically neutral because the number of electrons equals the number of protons.

  • Atomic Mass: The sum of protons and neutrons. Examples from the transcript include:

  • Nitrogen (N): $7p^+$, $7e^-$, $7n^0$. Atomic number = 7; Atomic mass = 14.

  • Sodium (Na): $11p^+$, $11e^-$, $12n^0$. Atomic number = 11; Atomic mass = 23.

  • Potassium (K): $19p^+$, $19e^-$, $20n^0$. Atomic number = 19; Atomic mass = 39.

The Chemical Elements and Minerals of Life

• Element: The simplest form of matter to have unique chemical properties.

• Atomic Weight: Relative weights measured in atomic mass units (AMU). One AMU is defined as $1/12^{th}$ the mass of a Carbon-12 atom (approximately $1.66 \times 10^{-24}\,g$).

• The Periodic Table:

  • Groups: Columns of elements with the same valence (outer shell) electron count.

  • Periods: Rows indicating the number of energy levels (shells).

  • Categories: Includes Noble Gases, Major Elements, Lesser Elements, and Trace Elements.

• Biological Role of Elements:

  • 24 elements have a biological role.

  • Major Elements (98.5% of body weight):

  • Oxygen (O): $65.0\%$

  • Carbon (C): $18.0\%$

  • Hydrogen (H): $10.0\%$

  • Nitrogen (N): $3.0\%$

  • Calcium (Ca): $1.5\%$

  • Phosphorus (P): $1.0\%$

  • Lesser Elements (0.8% of body weight): Sulfur (S) $0.25\%$, Potassium (K) $0.20\%$, Sodium (Na) $0.15\%$, Chlorine (Cl) $0.15\%$, Magnesium (Mg) $0.05\%$, Iron (Fe) $0.006\%$.

  • Trace Elements (0.7% of body weight): Chromium (Cr), Cobalt (Co), Copper (Cu), Fluorine (F), Iodine (I), Manganese (Mn), Molybdenum (Mo), Selenium (Se), Silicon (Si), Tin (Sn), Vanadium (V), Zinc (Zn).

• Minerals: Ca, P, Cl, Mg, K, Na, Fe, Zn, and S constitute about 4% of body weight. They are vital for structure (teeth, bones), enzymes, and electrolytes.

Isotopes, Radioactivity, and the Contributions of Madame Curie

• Madame Marie Curie:

  • First woman to receive a Nobel Prize (1903) and the first woman to receive a Ph.D.

  • Coined the term "radioactivity."

  • Discovered the radioactivity of polonium and radium.

  • Trained physicians in X-ray use and pioneered radiation therapy for cancer.

  • Died of radiation poisoning at age 67.

• Isotopes: Varieties of an element that differ only in the number of neutrons, which increases atomic weight. Isotopes are chemically similar because they have the same number of valence electrons.

• Radioisotopes and Radioactivity:

  • Radioisotopes: Unstable isotopes that decay into stable isotopes while releasing radiation.

  • Physical half-life: The time needed for 50% of a radioisotope to decay into a stable state.

  • Biological half-life: The time required for 50% of a radioisotope to be cleared from the body (via decay and physiological clearance).

• Isotopes of Hydrogen:

  • Hydrogen ($^{1}H$): $1p^+$, $0n^0$, $1e^-$.

  • Deuterium ($^{2}H$): $1p^+$, $1n^0$, $1e^-$.

  • Tritium ($^{3}H$): $1p^+$, $2n^0$, $1e^-$.

Ions, Electrolytes, and Free Radicals

• Ions: Charged particles with unequal numbers of protons and electrons.

  • Ionization: The transfer of electrons from one atom to another to achieve valence shell stability.

  • Anion: An atom that gains electrons and acquires a net negative charge.

  • Cation: An atom that loses an electron and acquires a net positive charge.

• Electrolytes: Substances that ionize in water and form solutions capable of conducting electricity. Examples of dissociation:

  • Calcium chloride ($CaCl_2 \rightarrow Ca^{2+} + 2Cl^-$)

  • Disodium phosphate ($Na_2HPO_4 \rightarrow 2Na^+ + HPO_4^{2-}$)

  • Sodium bicarbonate ($NaHCO_3 \rightarrow Na^+ + HCO_3^-$)

• Free Radicals: Chemical particles with an odd number of electrons. They are produced by radiation, chemicals, and normal metabolic reactions. They cause tissue damage, cancer, and aging.

• Antioxidants: Chemicals that neutralize free radicals.

  • Endogenous: Superoxide dismutase (SOD) converts superoxides into water and oxygen.

  • Dietary: Selenium, Vitamin E, Vitamin C, and carotenoids.

Molecules, Chemical Bonds, and Isomers

• Definitions:

  • Molecule: Chemical particles composed of two or more atoms united by chemical bonds.

  • Compound: Molecules composed of two or more different elements.

  • Molecular Formula: Identifies constituent elements and the number of atoms (e.g., $C_6H_{12}O_6$).

  • Structural Formula: Shows the location of each atom.

• Isomers: Molecules with identical molecular formulae but different arrangements of atoms (e.g., Ethanol and Ethyl ether both share $C_2H_6O$).

• Molecular Weight (MW): The sum of the atomic weights of all atoms in a compound.

  • Calculation for Glucose ($C_6H_{12}O_6$):

  • $6\,C \times 12\,amu = 72\,amu$

  • $12\,H \times 1\,amu = 12\,amu$

  • $6\,O \times 16\,amu = 96\,amu$

  • Total MW = $180\,amu$.

• Types of Chemical Bonds:

  • Ionic Bond: Relatively weak attraction between an anion and a cation; easily disrupted in water (e.g., salt dissolving).

  • Covalent Bond: Sharing of one or more pairs of electrons between nuclei.

  • Single Covalent: Sharing one electron pair.

  • Double Covalent: Sharing two electron pairs (e.g., between Carbon atoms).

  • Nonpolar Covalent: Electrons are equally attracted to both nuclei; the strongest type of bond.

  • Polar Covalent: Electrons are more attracted to one nucleus, resulting in slightly positive and negative regions.

  • Hydrogen Bond: Weak attraction between polarized molecules or regions of a large molecule. Important for protein folding; easily disrupted by pH and temperature changes.

  • Van der Waals Forces: Weakest of all bonds; brief attractions due to random disturbances in electron clouds.

Water: The Universal Solvent and Biological Mixtures

• Water Properties: Water constitutes 50% to 75% of body weight. Its polar covalent bonds and V-shape provide unique properties:

  • Solvency: The ability to dissolve chemicals (Universal Solvent).

  • Hydrophilic: Substances (polarized or charged) that dissolve in water.

  • Hydrophobic: Substances (nonpolar or neutral like fat) that do not dissolve.

  • Cohesion and Adhesion: Water sticks to itself and other surfaces.

  • Chemical Reactivity: Participates in metabolic reactions.

  • Thermal Stability: High heat capacity. $1\,cal$ is the amount of heat needed to raise $1\,g$ of water by $1^{\circ}C$. Hydrogen bonds inhibit molecular motion; $1\,mL$ of perspiration removes $500\,calories$.

• Types of Mixtures:

  • Solution: Particles <$1\,nm$; clear; do not scatter light or settle (e.g., glucose in blood).

  • Colloid: Particles $1$-$100\,nm$; often cloudy; do not settle (e.g., proteins in blood, milk protein).

  • Suspension: Particles >$100\,nm$; cloudy or opaque; particles settle out (e.g., blood cells in plasma, cornstarch in water).

Measures of Concentration, Acids, and Bases

• Concentration Measures:

  • Weight per Volume: grams per liter ($g/L$) or milligrams per deciliter ($mg/dL$).

  • Percentage: Weight/volume of solute in solution (e.g., $D5W$ is $5\,g$ dextrose in $100\,mL$ water).

  • Molarity (M): Moles of solute per liter of solution. One mole is the MW in grams or $6.023 \times 10^{23}$ molecules (Avogadro’s number).

• pH and Acids/Bases:

  • Acid: Proton donor (releases $H^+$ in water).

  • Base: Proton acceptor (accepts $H^+$ or releases $OH^-$).

  • pH Scale: Invented by Sören Sörensen in 1909. $pH = -\log[H^+]$. A change of 1 on the scale is a 10-fold change in concentration.

  • Neutral: $pH = 7.0$ ($H^+ = OH^-$).

  • Acidic: $pH < 7.0$ ($H^+ > OH^-$).

  • Basic: $pH > 7.0$ ($OH^- > H^+$).

  • Blood pH: Ranges from $7.35$ to $7.45$. Deviations cause tremors, paralysis, or death.

Energy, Chemical Reactions, and Metabolism

• Energy: Capability to do work (moving something).

  • Potential Energy: Stored energy due to position or state.

  • Chemical Energy: Potential energy in molecular bonds.

  • General Kinetic Energy: Energy of motion.

  • Free Energy: Available to do useful work.

  • Heat: Kinetic energy of molecular motion.

• Reaction Classes:

  • Decomposition: $AB \rightarrow A + B$ (e.g., starch to glucose).

  • Synthesis: $A + B \rightarrow AB$ (e.g., amino acids to protein).

  • Exchange: $AB + CD \rightarrow ABCD \rightarrow AC + BD$.

  • Reversible Reactions: Can go in either direction depending on the Law of Mass Action (proceeds to the side with lesser concentration).

• Metabolism:

  • Catabolism: Exergonic (energy-releasing) decomposition reactions. Breaks covalent bonds.

  • Anabolism: Endergonic (energy-storing) synthesis reactions. Requires energy input.

  • Oxidation: Removal of electrons. Reduction: Addition of electrons.

Monomers, Polymers, and Carbohydrates

• Macromolecules: Large organic molecules like proteins or DNA.

• Polymerization: Joining monomers together.

  • Dehydration Synthesis (Condensation): A hydroxyl ($-OH$) and a hydrogen ($-H$) are removed to form water, creating a covalent bond.

  • Hydrolysis: Water is ionized into $-OH$ and $-H$ to break a covalent bond (lysis).

• Carbohydrates: Hydrophilic molecules with general formula $(CH_2O)_n$.

  • Monosaccharides: Glucose, Galactose, Fructose (all isomers of $C_6H_{12}O_6$).

  • Disaccharides: Sucrose (Glucose + Fructose), Lactose (Glucose + Galactose), Maltose (Glucose + Glucose).

  • Polysaccharides:

  • Glycogen: Energy storage in animals (liver, muscles, uterus).

  • Starch: Energy storage in plants (only significant digestible polysaccharide in human diet).

  • Cellulose: Structural fiber in plants; not digested by humans.

  • Conjugated Carbohydrates: Glycoproteins (cell surface/mucus), Glycolipids (cell surface), Proteoglycans (adhesion/lubrication).

Lipids: Fats, Phospholipids, and Steroids

• Characteristics: Hydrophobic; high ratio of $H$ to $O$; highly calorie-dense.

• Fatty Acids: Chains of 4-24 carbons with a carboxyl and methyl end.

  • Saturated: No double bonds (saturated with H).

  • Unsaturated: Contains $C=C$ bonds.

  • Essential Fatty Acids: Must be obtained from diet (e.g., alpha-linolenic and linoleic acid).

• Triglycerides (Neutral Fats): Three fatty acids bonded to one glycerol via dehydration synthesis. Used for energy storage and insulation.

• Phospholipids: Amphiphilic molecules with a hydrophilic phosphate "head" and hydrophobic fatty acid "tails." Form the structural foundation of cell membranes.

• Steroids: Lipids with 17 carbon atoms in four rings.

  • Cholesterol: The parent steroid for cortisol, progesterone, estrogen, testosterone, and bile acids. 85% is synthesized internally by the liver.

• Lipoproteins: Droplets of complexes (HDL is "good" with high protein-to-lipid ratio; LDL is "bad" with high lipid-to-protein ratio).

Proteins and Enzymes

• Protein: Polymer of amino acids. 20 identical types of amino acids differ only by their radical (R) group.

• Structures:

  • Primary: Sequence of amino acids encoded in genes.

  • Secondary: Coiled (Alpha helix) or folded (Beta sheet) shapes held by hydrogen bonds.

  • Tertiary: Folding into globular (suited for cell membranes) or fibrous (suited for muscle/skin) shapes.

  • Quaternary: Association of two or more polypeptide chains.

• Conformation: The unique 3D shape essential for function. Denaturation is an extreme change in shape (due to heat or pH) that destroys function.

• Protein Functions: include structure (Keratin, Collagen), communication (Hormones/Ligands), membrane transport (Channels, Carriers), catalysis, recognition, and movement.

• Enzymes: Biological catalysts that decrease activation energy to permit rapid reactions at body temperature. They are highly specific ("lock and key") and reusable.

  • Cofactors: Inorganic partners (Iron, Copper, Zinc, Mg, Ca) required for enzyme function.

  • Coenzymes: Organic cofactors derived from vitamins (e.g., $NAD^+$).

Nucleotides and Nucleic Acids

• Nucleotide Components: Nitrogenous base, Monosaccharide (sugar), and one or more phosphate groups.

• Adenosine Triphosphate (ATP):

  • Contains Adenine, Ribose, and 3 Phosphate groups.

  • Holds energy in high-energy covalent bonds (~).

  • Hydrolyzed by ATPases into $ADP + P_i + energy$.

  • Phosphorylation: Carried out by kinases.

  • Replenishment: Entire body supply lasts < 1 minute; Cyanide stops its synthesis.

• Other Nucleotides:

  • GTP (Guanosine triphosphate): Energy transfer.

  • cAMP (Cyclic adenosine monophosphate): "Second messenger" for hormones.

• Nucleic Acids: Polymers of nucleotides.

  • DNA (Deoxyribonucleic acid): Holds instructions for protein synthesis and hereditary information.

  • RNA (Ribonucleic acid): Three types (mRNA, rRNA, tRNA); carries out genetic instructions to assemble amino acids.

Cell Theory and the Interior of the Cell

• Cell Theory:

  • All organisms are composed of cells and cell products.

  • The cell is the simplest structural and functional unit of life.

  • Cells come only from preexisting cells.

  • Fundamental similarities exist in chemical composition and metabolism across species.

• The Plasma Membrane: A selectively permeable bilayer of phospholipids with proteins and cholesterol.

• Organelles:

  • Membranous: Nucleus (genetic center), Mitochondria (ATP synthesis), Lysosomes (digestion), Peroxisomes (detoxification), Endoplasmic Reticulum (Rough for protein synthesis, Smooth for lipid synthesis/calcium storage), Golgi complex (packaging).

  • Nonmembranous: Ribosomes (protein synthesis), Centrioles (cell division), Basal bodies.

• The Cytoskeleton: Includes Microfilaments (support), Intermediate filaments (shape), and Microtubules (transport tracks).

• Mitochondria Evolution: Possess mtDNA (circular like bacterial DNA). Inherited almost exclusively from the mother.

Membrane Transport and Tonicity

• Passive Transport (No ATP):

  • Filtration: Particles driven through a membrane by hydrostatic pressure (e.g., blood pressure).

  • Simple Diffusion: Net movement down a concentration gradient.

  • Factors: Temperature, molecular weight, gradient steepness, surface area, and permeability.

  • Osmosis: Net flow of water toward the side with higher solute concentration. Uses Aquaporins.

• Active Transport: Requires ATP.

• Tonicity: Ability of a solution to affect cell volume.

  • Hypotonic: Lower solute concentration than ICF; cells absorb water and may lyse (burst).

  • Hypertonic: Higher solute concentration than ICF; cells lose water and crenate (shrivel).

  • Isotonic: Same concentration as ICF; no change in cell volume.

Genetics: DNA Structure and Protein Synthesis

• DNA Discovery: Structure determined by Watson, Crick, and Wilkins in 1953 using X-ray data from Rosalind Franklin.

• DNA Components:

  • Nucleotides: Phosphate, 5-carbon sugar (Deoxyribose), Nitrogenous base.

  • Purines: Adenine (A), Guanine (G). Pyrimidines: Cytosine (C), Thymine (T) [Uracil in RNA].

  • Law of Complementary Base Pairing: $A-T$ (2 hydrogen bonds), $G-C$ (3 hydrogen bonds).

• Terms:

  • Gene: Information-containing segment of DNA coding for RNA and protein production.

  • Genome: All the genes of one person (approx. 20,000-25,000; 2% coding).

  • Human Genome Project: Found humans are 99.99% genetically identical; variation comes from single-nucleotide polymorphisms.

• Protein Synthesis:

  • Transcription: DNA structure is copied into mRNA in the nucleus.

  • Translation: Occurs at ribosomes. The nucleotide sequence of mRNA is translated into the amino acid sequence of a polypeptide using tRNA anticodons and the triplet code (Codon).

  • Splicing: Exons are joined and introns removed to allow one gene to code for multiple proteins.