General Biology: Thermodynamics, Biochemistry, Cell Organization, Communication, and Energetics Study Guide

Unit 1: Thermodynamics & Biochemistry

Thermodynamics

Thermodynamics is the study of energy transformations in biological systems. The first and second laws of thermodynamics are fundamental to understanding how energy flows and is conserved in living organisms.

• 1st Law of Thermodynamics: Energy cannot be created or destroyed, only transformed.

• 2nd Law of Thermodynamics: Every energy transfer increases the entropy (disorder) of the universe.

Gibbs Free Energy

Gibbs free energy determines whether a reaction is spontaneous. The equation is:

• $\Delta G = \Delta H - T\Delta S$

• Spontaneous reactions: Occur when $\Delta G$ is negative.

Enzymes

Enzymes are biological catalysts that speed up chemical reactions by lowering activation energy.

• Activation Energy: The energy required to start a reaction.

• Enzyme Activity: Influenced by substrate concentration, temperature, and pH.

• Active Site: The region on the enzyme where the substrate binds.

• Lock & Key Hypothesis: Substrate fits exactly into the active site.

• Induced Fit Hypothesis: Enzyme changes shape to fit substrate.

• Inhibition: Competitive (binds active site) vs. Non-competitive (binds elsewhere).

Water

Water is essential for life due to its unique chemical properties.

• Polarity: Water molecules have a partial positive and negative charge.

• Adhesion vs. Cohesion: Adhesion is attraction to other substances; cohesion is attraction between water molecules.

• Surface Tension: Caused by cohesion at the water's surface.

• High Heat of Vaporization: Water requires a lot of energy to change from liquid to gas.

• Temperature Regulation: Water stabilizes temperature due to hydrogen bonding.

• Density of Water: Ice is less dense than liquid water due to hydrogen bonds.

pH & Buffers

pH measures the concentration of hydrogen ions in a solution. Buffers help maintain stable pH in biological systems.

• pH Scale: Ranges from 0 (acidic) to 14 (basic); 7 is neutral.

• Calculation: $\text{pH} = -\log[\text{H}^+]$

• Buffers: Substances that minimize changes in pH.

Macromolecules

Macromolecules are large, complex molecules essential for life, including carbohydrates, lipids, proteins, and nucleic acids.

• Carbohydrates: Provide energy; monomers are monosaccharides; polymers are polysaccharides. Functional groups include aldehyde and ketone.

• Lipids: Store energy; include fats, phospholipids, and steroids. Saturated vs. unsaturated fatty acids.

• Proteins: Functions include catalysis, structure, and transport. Monomers are amino acids; polymers are polypeptides. Structure: primary, secondary, tertiary, quaternary.

• Nucleic Acids: Store genetic information; monomers are nucleotides.

Chemical Reactions

• Catabolic: Break down molecules.

• Anabolic: Build up molecules.

• Coupling Reactions: Link exergonic and endergonic reactions.

Bonds

• Glycosidic, Ester, Peptide, Hydrogen, Ionic

Unit 2: Cellular Organization and Transport

Transport Across Membranes

Cells regulate the movement of substances across membranes to maintain homeostasis.

• Passive Transport: Movement without energy input (diffusion, osmosis, facilitated diffusion).

• Active Transport: Requires energy (ATP) to move substances against their concentration gradient.

• Water Potential: Determines the direction of water movement; calculated using solute and pressure potential.

Endosymbiotic Theory

• Explains the origin of mitochondria and chloroplasts in eukaryotic cells.

• Supported by evidence such as double membranes and unique DNA.

Unit 3: Cellular Communication

Cell Signaling

Cells communicate through chemical signals to coordinate activities.

• Local vs. Long Distance Signaling: Paracrine, synaptic, endocrine.

• Signal Transduction Pathways: Involve receptors (G-proteins, ligand-gated ion channels, tyrosine kinase receptors).

• Feedback Loops: Negative feedback maintains homeostasis.

Apoptosis

• Programmed cell death; involves mitochondria and caspases.

Secondary Messengers

• Include cAMP, Ca2+, and IP3.

Endocrine Hormones

• Examples: Testosterone, Oxytocin, Prolactin, ADH, HGH.

Unit 4: Energetics

Photosynthesis

Photosynthesis converts light energy into chemical energy in plants.

• Structure of Chloroplast: Site of photosynthesis.

• Light-Dependent Reactions: Occur in thylakoid membranes; produce ATP and NADPH.

• Calvin Cycle: Uses ATP and NADPH to fix carbon dioxide into glucose.

• Role of Pigments: Absorb light at specific wavelengths.

• Photorespiration: Occurs when O2 is used instead of CO2.

Cellular Respiration

Cellular respiration breaks down glucose to produce ATP.

• Structure of Mitochondria: Site of aerobic respiration.

• Glycolysis: Occurs in cytoplasm; splits glucose into pyruvate.

• Krebs Cycle: Occurs in mitochondrial matrix; produces NADH and FADH2.

• Electron Transport Chain: Uses NADH and FADH2 to produce ATP via oxidative phosphorylation.

• Fermentation: Anaerobic process producing lactic acid or ethanol.

REDOX Reactions

• Involve transfer of electrons; oxidation is loss, reduction is gain.

Macromolecule	Monomer	Polymer	Main Function
Carbohydrate	Monosaccharide	Polysaccharide	Energy storage, structure
Lipid	Fatty acid	Triglyceride, phospholipid	Energy storage, membrane structure
Protein	Amino acid	Polypeptide	Catalysis, structure, transport
Nucleic Acid	Nucleotide	DNA/RNA	Genetic information

Example: ATP is produced during cellular respiration and used as the energy currency of the cell.

Additional info: Some details, such as the specific steps of glycolysis and the Calvin cycle, were expanded for clarity and completeness.