Molecular Biology and Biological Processes Study Guide

Molecular Biology Fundamentals

Definition: A field of study focusing on biological activity at a molecular level. This involves elucidating the structure and function of chemical substances and determining their interactions as integral parts of living processes.
Regulation of Processes: Biological processes are tightly regulated by enzymes, whose expression is controlled by gene activation via DNA. Changes in activity are typically determined by signaling molecules, which can be endogenous (originating within) or exogenous (originating outside) in origin.
Organic Compounds: A compound containing carbon found in living things.
Exceptions to Organic Classification: Compounds that contain carbon but are not classified as organic include: - Carbides (e.g., $CaC_2$ ) - Carbonates ( $CO_3^{2–}$ ) - Oxides of carbon ( $CO$ , $CO_2$ ) - Cyanides ( $CN^–$ )
Carbon Properties: Carbon serves as the basis of organic life due to its ability to form large, complex molecules via covalent bonding. - Carbon atoms can form four covalent bonds. - Bonds between carbon atoms are particularly stable, a property known as catenation. - These properties allow for a wide variety of chemically stable organic compounds.

Main Classes of Carbon Compounds

Carbohydrates: - Most abundant organic compound in nature. - Composed of $C$ , $H$ , and $O$ atoms in a common ratio of $(CH_2O)_n$ . - Functions: Principally a source of energy and short-term energy storage; also acts as a recognition molecule (e.g., glycoproteins) and a structural component (part of DNA and RNA).
Lipids: - Non-polar, hydrophobic molecules existing in simple, complex, or derived forms. - Functions: Major component of cell membranes (phospholipids and cholesterol); long-term energy storage (fats and oils); signaling molecules (steroids).
Nucleic Acids: - Genetic material of all cells; determines inherited features of an organism. - DNA: Functions as a master code for protein assembly. - RNA: Plays an active role in the manufacturing of proteins.
Proteins: - Make up over $50\%$ of the dry weight of cells. - Composed of $C$ , $H$ , $O$ , and $N$ atoms (some include $S$ ). - Functions: Major regulatory molecules in catalysis (all enzymes are proteins); structural molecules; cellular signaling (transduction pathways).

Complex Macromolecules and Monomers

Monomeric Subunits: Complex macromolecules are comprised of smaller, recurring subunits called monomers. - Carbohydrates, nucleic acids, and proteins are comprised of monomeric subunits that join to form polymers. - Lipids do not contain recurring monomers, though some (e.g., triglycerides) are composed of distinct subunits.
Carbohydrate Structure: Composed of monosaccharides ("single sugar units"). - Two sugar units form disaccharides; many form polysaccharides. - Most monosaccharides form ring structures and exist as various 3D configurations (stereoisomers).
Lipid Structure: No common recurring monomer. Many (triglycerides, phospholipids, waxes) contain fatty acid chains. - Fatty acids: Long chains of hydrocarbons that can be saturated (no double bonds) or unsaturated (contain double bonds).
Protein Structure: Composed of amino acid monomers joining to form polypeptide chains. - Amino acid structure: A central carbon connected to an amine group ( $NH_2$ ), a carboxyl group ( $COOH$ ), and a variable group ( $R$ ) that determines chemical properties (e.g., polarity).
Nucleic Acid Structure: Composed of nucleotides joining to form polynucleotide chains. - Nucleotide components: A pentose sugar, a phosphate group, and a nitrogenous base.

Molecular Bonding and Organization

Polysaccharide Variation: Structure varies based on monomer composition and bonding arrangement. Glucose can form glycogen, cellulose, and starch.
Lipid Classification: - Simple (neutral) lipids: Esters of fatty acids and alcohol (e.g., triglycerides, waxes). - Compound lipids: Esters of fatty acids, alcohol, and additional groups (e.g., phospholipids, glycolipids). - Derived lipids: Substances derived from simple or compound lipids (e.g., steroids, carotenoids).
Peptide Formation: Amino acids join via peptide bonds between the amine and carboxyl groups of adjacent acids. A dipeptide is formed from two; further additions create a polypeptide chain. Folding depends on the amino acid sequence order.
Polynucleotide Formation: Nucleotides bond between the pentose sugar and phosphate group. In DNA, two complementary chains pair via hydrogen bonding between nitrogenous bases to form double strands in a double helical arrangement.

Vitalism and the Synthesis of Urea

Doctrine of Vitalism: Alleged that organic molecules could only be synthesized by living systems because they possessed a "vital force" and a non-physical element lacking in inorganic molecules.
Disproof: Frederick Woehler (1828) heated an inorganic salt (ammonium cyanate) and produced urea. Urea is a waste product of nitrogen metabolism eliminated by kidneys in mammals. This proved organic molecules are not fundamentally different from inorganic ones.

Metabolism: Anabolism and Catabolism

Metabolism: The totality of enzyme-catalyzed chemical processes within a living organism to maintain life. - Functions: Provides energy for cellular processes (growth, reproduction); enables synthesis and assimilation of new materials.
Anabolism: Metabolic reactions that build complex molecules from simpler ones (e.g., protein synthesis). - Process: Synthesis occurs via condensation reactions, where monomers covalently join and water is produced. - Glycosidic linkages: Join monosaccharides into disaccharides/polysaccharides. - Peptide bonds: Join amino acids into polypeptides. - Ester linkages: Join glycerol and fatty acids into triglycerides. - Phosphodiester bonds: Join nucleotides into polynucleotides.
Catabolism: Metabolic reactions that break complex molecules into simpler ones (e.g., digestion). - Process: Occurs via hydrolysis reactions, requiring the consumption of water molecules to break polymer bonds.

Properties of Water

Molecular Structure: Two hydrogen atoms covalently bonded to one oxygen atom ( $H_2O$ ). Electrons are shared unequally due to oxygen's higher electronegativity.
Polarity: Water is dipolar. Oxygen is slightly negative ( $\delta–$ ) and hydrogens are slightly positive ( $\delta+$ ).
Hydrogen Bonding: Weak associations between the $\delta+$ hydrogen of one molecule and a $\delta–$ atom (F, O, N) of another. These bonds are strong relative to other polar associations.
Thermal Properties: Water can absorb significant heat before changing state because hydrogen bonds must be broken first. This requires energy (heat). - Medium for life: Resists temperature change, supporting internal and external homeostasis.
Comparison with Methane ( $CH_4$ ): - Similarities: Comparable size/weight ( $H_2O = 18\,\text{dalton}$ , $CH_{4} = 16\,\text{dalton}$ ); similar valence structure (tetrahedral orbitals). - Differences: Water is polar (forms H-bonds); methane is non-polar (only weak dispersion forces). Methane has lower melting/boiling points, specific heat capacity, heat of vaporization, and heat of fusion. - Energy: Each H-bond in water has an average energy of $20\,kJ/mol$ .
Cooling Mechanism: Sweat evaporation on skin cools the body. High specific heat capacity and heat of vaporization mean water absorbs significant thermal energy before turning to vapor.
Cohesion and Adhesion: - Cohesion: Like molecules sticking together. Explains surface tension, allowing organisms to move on water surfaces. - Adhesion: Dissimilar molecules sticking together. Explains capillary action, allowing water to flow against gravity (e.g., transpiration in plant stems).
Solvent Properties: Known as the "universal solvent." It dissolves polar and ionic substances by forming hydration shells around ions, weakening intramolecular forces. - Hydrophilic: Water-loving substances (polar molecules/ions). - Hydrophobic: Water-hating substances (large non-polar molecules like fats).
Blood Transport Solubility: - Sodium Chloride ( $NaCl$ ): Ionic; travels freely. - Oxygen: Low solubility; transported by hemoglobin. - Glucose: Soluble due to hydroxyl ( $–OH$ ) groups. - Amino Acids: Transported in ionized states. - Lipids (fats/cholesterol): Insoluble; form complexes with proteins (lipoproteins).

Carbohydrate Specifics

Types: - Monosaccharides: Immediate energy (e.g., glucose, galactose, fructose). - Disaccharides: Transport form (e.g., lactose, maltose, sucrose). - Polysaccharides: Energy storage/structure (e.g., cellulose, glycogen, starch).
Key Polysaccharides: - Cellulose: Structural (cell walls), linear $\beta$ -glucose (1-4 arrangement). Indigestible for most except ruminants (bacteria) and caecotrophs (re-ingestion). - Starch: Energy storage in plants, $\alpha$ -glucose (1-4 arrangement). Forms include amylose (linear/helical, preferred for storage) and amylopectin (branched, 1-6 linkages). - Glycogen: Energy storage in animals (liver), highly branched $\alpha$ -glucose (1-4 and 1-6 linkages every 10 subunits).

Lipids and Health

Fatty Acids: - Saturated: No double bonds, linear, animal sources, solid at room temp. - Unsaturated: Double bonds, bent, plant sources, liquid. Can be monounsaturated ( $1$ bond) or polyunsaturated (>1 bond). - Cis: Hydrogens on the same side of double bond. - Trans: Hydrogens on opposite sides; linear despite being unsaturated; produced by industrial hydrogenation; solid at room temp.
Triglycerides: Formed by condensation of one glycerol and three fatty acids via ester linkages; releases three $H_2O$ molecules.
Cholesterol and Lipoproteins: - Low Density Lipoproteins (LDL): Carry cholesterol from liver to body ("bad"); raise blood cholesterol. - High Density Lipoproteins (HDL): Scavenge excess cholesterol to the liver ("good"); lower blood cholesterol. - Effects: Saturated fats increase LDL; Trans fats increase LDL and decrease HDL; Cis unsaturated fats increase HDL.
Health Risks: High LDL leads to atherosclerosis (hardening/narrowing of arteries via plaques). Blockage of coronary arteries causes Coronary Heart Disease (CHD), heart attacks, and strokes.
Health Claims: Saturated/trans fats correlate positively with CHD, while cis fats decrease risk. Exceptions exist (e.g., Maasai tribe).
Lipids vs. Carbohydrates (SODAS): - S (Storage): Lipids better for long-term. - O (Osmolality): Lipids have less effect on osmotic pressure. - D (Digestion): Carbohydrates easier to digest. - A (ATP Yield): Lipids store more energy per gram. - S (Solubility): Carbohydrates easier to transport in blood.
Energy Analogy: ATP is "cash." Carbohydrates (glycogen) are a "wallet" (accessible, low capacity). Lipids (triglycerides) are a "safe" (hard to access, high capacity).

BMI and Body Mass

Formula: $\text{BMI} = \frac{\text{mass (kg)}}{(\text{height (m)})^2}$ .
Use: Screening tool for sedentary adults. Not valid for pregnant women or professional athletes (atypical muscle/fat ratios).
Nomograms: Alignment charts using weight and height axes to assign color-coded BMI values.

Protein Structure and Function

Amino Acids: 20 universal types; two variants (selenocysteine, pyrrolysine). Linked at ribosomes.
Structural Levels: - Primary: Amino acid sequence; determines folding. - Secondary: $\alpha$ -helices (coils) or $\beta$ -pleated sheets (staggered strands) via hydrogen bonds between non-adjacent amine and carboxyl groups. - Tertiary: 3D configuration via side chain ( $R$ group) interactions (H-bonds, disulphide bridges, etc.). - Quaternary: Multiple polypeptide chains or inorganic prosthetic groups (e.g., Hemoglobin with four chains and haeme groups).
Denaturation: Structural change causing loss of biological properties. Caused by high temperature (disrupts H-bonds) or extreme pH (alters protein charge/solubility).
Genes and Proteomes: - One Gene – One Polypeptide rule: DNA sequence encodes polypeptide via transcription (mRNA) and translation (ribosome). Exceptions: alternative splicing, tRNA genes, mutations. - Proteome: Totality of expressed proteins. Larger than the genome due to alternative splicing and post-translational modifications (glycosylation, phosphorylation).
Protein Functions (SHITS ME): - S (Structure): Collagen (connective tissue), spider silk. - H (Hormones): Insulin (lowers blood glucose), glucagon (raises blood glucose). - I (Immunity): Immunoglobulins (target antigens). - T (Transport): Hemoglobin ( $O_2$ transport), cytochrome (electron transport chain). - S (Sensation): Rhodopsin (light detection in retina). - M (Movement): Actin (thin filaments), myosin (thick filaments). - E (Enzymes): Rubisco (photosynthesis), catalase.

Enzymes and Catalysis

Mechanism: Globular proteins; biological catalysts. Substrate binds to the Active Site.
Collision Frequency: Catalysis rate increases with molecular motion (thermal energy) and concentration (substrate/enzyme).
Enzyme-Substrate Complex: Substrate + Enzyme $\rightarrow$ Enzyme-Substrate Complex $\rightarrow$ Enzyme-Product Complex $\rightarrow$ Enzyme + Product.
Factors Affecting Activity: - Temperature: Low energy = slow rate. Increasing temp increases collisions until the optimal point, after which heat disrupts H-bonds leading to denaturation. - pH: Moving outside the optimal range alters enzyme charge/shape and diminishes function. - Substrate Concentration: Activity rises until saturation ( $V_{max}$ ) where all active sites are occupied.
Immobilized Enzymes: Fixed to static surfaces. Advantages: enzymes conserved/reused, product separation easier. Uses: biofuels (ethanol), medicine (pregnancy tests), biotechnology (gene splicing), food (dairy), textiles, paper.
Lactose-Free Milk: Lactase (from yeast/bacteria) immobilized on alginate beads. Milk passed over it breaks lactose into glucose and galactose. Advantages: dairy for intolerant individuals, increased sweetness, reduced ice cream crystallization, faster cheese production.

Nucleic Acids: DNA and RNA

Nucleotide Components: 5-carbon pentose sugar, phosphate group (attached to $5'$ carbon), nitrogenous base (attached to $1'$ carbon).
DNA: Store genetic blueprint; double-stranded; deoxyribose sugar; A, G, C, T bases.
RNA: Transfers information; single-stranded; ribose sugar; A, G, C, U bases.
Strand Formation: Nucleotides link via condensation reactions between phosphate and $3'$ hydroxyl group, forming phosphodiester bonds.
DNA Structure: Two antiparallel strands held by hydrogen bonds (A=T with $2$ bonds; G $\equiv$ C with $3$ bonds), forming a double helix (~10–15 bases per twist).
Scientific History: - Levene (1919): Nucleotide identification. - Chargaff (1950): Purines = Pyrimidines ( $A+G = C+T$ ). - Franklin (1953): X-ray crystallography confirmed helical structure. - Watson & Crick (1953): Proposed double helix model (triple helix and bases-out models were early faults).

DNA Replication and Protein Synthesis

Semi-conservative Replication: One original template strand and one newly synthesized strand. Confirmed by Meselson-Stahl experiment (1958) using $^{15}N$ and $^{14}N$ isotopes.
Enzymes: - Helicase: Unwinds helix and breaks H-bonds. - DNA Polymerase: Aligns free deoxynucleoside triphosphates opposite templates; cleaves excess phosphates for energy to link nucleotides.
Polymerase Chain Reaction (PCR): Artificial amplification. Steps: Denaturation ( $~90^{\circ}C$ ), Annealing ( $~55^{\circ}C$ ), Elongation ( $~75^{\circ}C$ utilizing heat-tolerant Taq polymerase).
Transcription: RNA polymerase produces RNA copy from antisense DNA strand ( $5' \rightarrow 3'$ ). Antisense is template; sense is identical to RNA (with T instead of U).
The Genetic Code: Set of rules for mRNA translation. Codons (base triplets) code for one amino acid. $64$ total possibilities ( $4^3$ ). Start codon is AUG. Code is universal.
Translation: Ribosome binds mRNA in cytoplasm; tRNA anticodons pair with mRNA codons; ribosome catalyzes peptide bonds between amino acids; continues until a stop codon.
Recombinant Gene Transfer: Human insulin produced in bacteria ( $E. coli$ ) by splicing the human gene into a plasmid vector.

Cell Respiration

Definition: Controlled release of energy from organic compounds (carbohydrates, lipids, proteins) to produce ATP.
ATP: Immediate power source. Reverts to ADP + Pi when hydrolyzed to release stored energy.
Glycolysis: Anaerobic breakdown of glucose in cytosol into two pyruvate (3C) molecules, yielding $2$ ATP and NADH.
Anaerobic Respiration: Absence of oxygen. Restores NAD+ for glycolysis. Animals: pyruvate $\rightarrow$ lactic acid. Plants/Yeasts: pyruvate $\rightarrow$ ethanol + $CO_2$ .
Aerobic Respiration: Presence of oxygen in mitochondria. Link reaction, Krebs cycle, electron transport chain. Yields $34–36$ ATP, $CO_2$ , and $H_2O$ .
Respirometer: Measures rate of $O_2$ uptake or $CO_2$ production. Carbon dioxide is absorbed by an alkali to measure pressure changes from oxygen consumption.

Photosynthesis

Definition: Anabolic synthesis of organic molecules from inorganic molecules ( $CO_2$ , $H_2O$ ) using sunlight.
Visible Spectrum: $400–700\,nm$ (Violet to Red). Chlorophyll absorbs blue and red most strongly; reflects green.
Spectra: - Absorption Spectrum: Wavelengths absorbed by pigments. - Action Spectrum: Rate of photosynthesis at each wavelength.
Process Steps: - Light Dependent: Photolysis of water ( $H_2O \rightarrow O_2 + H$ ); production of ATP. - Light Independent: ATP and Hydrogen fix carbon from $CO_2$ to form organic molecules (e.g., carbohydrates).
Chromatography: Separation of pigments (chlorophylls, xanthophyll, carotenes). Rf value = distance component travels $\div$ distance solvent travels. Forms: Paper chromatography, Thin layer chromatography.
Limiting Factors: Temperature (enzyme-driven), Light intensity (photo-activation), and $CO_2$ concentration (fixation rate).
Measuring Photosynthesis: Direct (uptake of $CO_2$ , production of $O_2$ ) or indirect (biomass change, starch levels via iodine staining).
Oxygen Evolution on Earth: Photosynthesis began saturating the environment $2.3$ billion years ago. Oceanic iron reacted to form Banded Iron Formations (BIFs). Atmosphere shifted from anoxic to $20\%$ oxygen. Resulted in extinction of obligate anaerobes and evolution of aerobically respiring organisms.