Principles of Biology: Unit 1 Study Guide – Biological Molecules, Chemistry, and Membranes

Biology as a Science

Proximate vs. Ultimate Explanations

Biological phenomena can be explained at different levels: proximate (mechanistic) and ultimate (evolutionary).

• Proximate explanations: Address the immediate mechanisms underlying a process (e.g., how cells divide).

• Ultimate explanations: Address the evolutionary reasons for a process (e.g., why cell division is advantageous).

• Example: Proximate: Cells divide by mitosis. Ultimate: Cell division enables growth and reproduction.

Experimental Design

Scientific experiments require careful planning to ensure valid results.

• Key features: Control groups, variables (independent, dependent), replication, randomization.

• Application: Design experiments to test hypotheses, identify flaws, and suggest improvements.

• Hypotheses: Must be testable and falsifiable; predictions should logically follow from hypotheses.

Chemistry Fundamentals

Atomic Structure and Bonding

Atoms are the basic units of matter, composed of protons, neutrons, and electrons.

• Atomic structure: Nucleus (protons, neutrons), electron shells.

• Bond types: Ionic, covalent, hydrogen bonds.

• Bond prediction: Based on electronegativity differences between elements.

Properties of Water

Water's unique properties arise from its structure and hydrogen bonding.

• Structure: Two hydrogen atoms covalently bonded to one oxygen atom.

• Bonding: Covalent bonds within molecule; hydrogen bonds between molecules.

• Partial charges: Oxygen is partially negative, hydrogens are partially positive.

• Hydrogen bonding effects: High specific heat, heat of vaporization, cohesion, adhesion.

• Biological relevance: Sweating, climate moderation.

Acids, Bases, and pH

Acids and bases affect hydrogen ion concentration and pH in solutions.

• Acid: Donates H+ ions.

• Base: Accepts H+ ions.

• pH: Measures hydrogen ion concentration.

• Relationship: $\text{pH} = -\log_{10}[\text{H}^+]$

• Calculation: Changes in [H+] alter pH logarithmically.

Carbon-Based Molecules and Energy

Functional Groups

Functional groups determine the chemical properties of organic molecules.

• Amino (-NH2): Acts as a base.

• Carbonyl (C=O): Found in aldehydes and ketones.

• Carboxyl (-COOH): Acts as an acid.

• Hydroxyl (-OH): Increases solubility.

• Methyl (-CH3): Nonpolar.

• Phosphate (-PO4): Energy transfer.

• Sulfhydryl (-SH): Forms disulfide bonds.

Energy and Thermodynamics

Energy transformations are essential for life; governed by thermodynamic laws.

• First Law: Energy cannot be created or destroyed.

• Second Law: Entropy (disorder) increases in spontaneous processes.

• Gibbs Free Energy: Determines spontaneity of reactions.

• Equation: $\Delta G = \Delta H - T\Delta S$

• Endergonic: $\Delta G > 0$ (requires energy).

• Exergonic: $\Delta G < 0$ (releases energy).

• Coupled reactions: Exergonic reactions can drive endergonic ones.

Graphical Analysis of Reactions

Graphs of free energy changes illustrate reactants, products, activation energy, and enzyme effects.

• Activation energy: Energy barrier to reaction.

• Enzymes: Lower activation energy, increase reaction rate.

• Effect on graph: Enzyme lowers peak of activation energy.

Biological Molecules

Comparison of Macromolecules

Biological macromolecules include proteins, nucleic acids, carbohydrates, and lipids.

Macromolecule	Monomer	Polymerization Bond	Function
Protein	Amino acid	Peptide bond	Enzymes, structure, signaling
Nucleic Acid	Nucleotide	Phosphodiester bond	Information storage, transfer
Carbohydrate	Monosaccharide	Glycosidic bond	Energy, structure
Lipid	Fatty acid, glycerol	Varies (ester bond in fats)	Membranes, energy storage

Protein Structure and Function

Proteins are essential for cell function, with diverse roles.

• Amino acid structure: Central carbon, amino group, carboxyl group, hydrogen, R-group.

• R-group properties: Determine solubility and acid/base behavior.

• Levels of structure:

  • Primary: Sequence of amino acids (peptide bonds).

  • Secondary: Alpha helices, beta sheets (hydrogen bonds).

  • Tertiary: 3D folding (hydrophobic interactions, disulfide bonds).

  • Quaternary: Multiple polypeptides (not always present).

• Enzyme function: Active site binds substrate; lowers activation energy; specificity due to shape.

• Reaction rates: Influenced by pH, temperature, substrate concentration.

Nucleic Acids

Nucleic acids store and transmit genetic information.

• Nucleotide structure: Sugar, phosphate, nitrogenous base.

• DNA: Double helix; stores genetic information.

• RNA: Single-stranded; mRNA (messenger), tRNA (transfer), rRNA (ribosomal).

• Replication: Structure enables copying.

• RNA world hypothesis: RNA may have been the first self-replicating molecule.

Carbohydrates

Carbohydrates provide energy and structural support.

• Monosaccharides: Simple sugars (glucose).

• Disaccharides: Two monosaccharides (sucrose).

• Polysaccharides: Many monosaccharides (starch, cellulose).

• Structural polysaccharides: Cellulose (plants), chitin (fungi, insects).

• Storage polysaccharides: Starch (plants), glycogen (animals).

• Digestibility: Depends on enzyme presence.

• Energy storage: Polysaccharides preferred over monomers for stability.

Lipids

Lipids are hydrophobic molecules important for membranes and energy storage.

• Categories: Phospholipids, fats (triglycerides), steroids.

• Phospholipids: Form cell membranes.

• Fats: Energy storage.

• Steroids: Signaling molecules (e.g., cholesterol).

• Saturated vs. unsaturated: Saturated have no double bonds; unsaturated have double bonds (cis/trans).

• Cis vs. trans: Cis double bonds cause kinks; trans are straighter.

Membranes and Membrane Transport

Phospholipid Bilayer Formation

Phospholipids spontaneously form bilayers in water due to their amphipathic nature.

• Hydrophilic heads: Face water.

• Hydrophobic tails: Face inward, away from water.

Membrane Fluidity and Permeability

Membrane properties depend on lipid composition and cholesterol content.

• Fatty acid saturation: Unsaturated increases fluidity.

• Fatty acid length: Shorter increases fluidity.

• Cholesterol: Modulates fluidity.

Cell Membrane Components

Cell membranes contain proteins, carbohydrates, and lipids.

• Integral proteins: Span membrane.

• Peripheral proteins: Attached to membrane surface.

• Carbohydrates: Cell recognition.

• Lipids: Structural component.

Membrane Transport

Substances cross membranes by different mechanisms.

• Diffusion: Passive movement down concentration gradient.

• Osmosis: Diffusion of water.

• Facilitated diffusion: Passive, via proteins.

• Passive transport: No energy required.

• Active transport: Requires energy; moves substances against gradient.

• Channels: Allow specific ions/molecules to pass.

• Carriers: Bind and transport molecules.

• Pumps: Use energy to move substances.

• Co-transport: Coupled movement of substances.

Permeability and Transport Prediction

Ability of substances to cross membranes depends on size, polarity, and concentration gradients.

• Small, nonpolar molecules: Cross easily.

• Large or charged molecules: Require transport proteins.

• Direction: Movement from high to low concentration unless actively transported.

Summary Table: Membrane Transport Mechanisms

Mechanism	Energy Required	Example
Diffusion	No	O2 movement
Osmosis	No	Water movement
Facilitated Diffusion	No	Glucose transport
Active Transport	Yes	Na+/K+ pump

Additional info: These notes expand on the learning objectives by providing definitions, examples, and context for each topic, suitable for exam preparation in introductory biology.