General Biology: Foundations, Chemistry, Macromolecules, and Experimental Design

Chapter 1 – Introduction

Control Variables vs. Control Experiments

Understanding experimental design is essential in biology to ensure valid and reliable results.

• Control variable: A factor kept constant to ensure only the independent variable affects the results.

• Control experiment: A setup where the independent variable is not applied, used as a baseline for comparison.

Importance of Experimental Controls (Isopod Example)

Controls help isolate the effect of one variable, such as moisture or light, in behavioral studies.

• They prevent confounding factors from influencing results, ensuring observed effects are due to the tested condition.

Standard Error of the Mean (SEM)

SEM quantifies how much the sample mean is likely to differ from the true population mean.

• Smaller SEM: Indicates more precise estimates of the mean.

95% Confidence Interval

The confidence interval provides a range that likely contains the true mean with 95% certainty.

• Helps assess the reliability of sample estimates.

Calculating SEM from Standard Deviation (SD)

SEM is derived from the standard deviation and sample size.

• $SEM = SD / \sqrt{n}$

True Mean (μ) vs. Sample Mean (x̄)

Distinguishing between population and sample statistics is fundamental in biology.

• True mean (μ): Actual average of the entire population (usually unknown).

• Sample mean (\bar{x}): Average from your dataset, used to estimate μ.

Chapter 2 – Chemistry Review

Bond Types

Chemical bonds determine molecular structure and properties.

• Nonpolar covalent: Equal sharing of electrons (e.g., C–H, O2).

• Polar covalent: Unequal sharing of electrons (e.g., O–H in water).

• Ionic: Electron transfer (e.g., Na+Cl–).

Hydrogen Bonds and Van der Waals Interactions

Weak interactions play crucial roles in biological systems.

• Hydrogen bonds: Form between polar molecules (e.g., H2O).

• Van der Waals interactions: Weak attractions due to temporary dipoles (important in gecko feet adhesion).

Chapter 2 – Water

Water Polarity

Water's polarity underlies its unique properties.

• Oxygen is more electronegative than hydrogen, creating partial negative (O) and partial positive (H) charges.

Properties from Hydrogen Bonding

Hydrogen bonds give water its biological significance.

• Cohesion/adhesion: Water sticks to itself and other surfaces.

• Temperature stabilization: High specific heat buffers temperature changes.

• Ice expansion: H-bonds hold molecules apart, making ice less dense than liquid water.

• Solvent: Polar nature dissolves many substances.

Thermal Energy and H-Bonds

Thermal energy affects hydrogen bonding in water.

• More energy breaks H-bonds (liquid → gas); less energy strengthens H-bonds (ice formation).

Hydrophilic vs. Hydrophobic

Water interactions affect biological molecules.

• Hydrophilic: Polar/charged, form H-bonds with water.

• Hydrophobic: Nonpolar, repel water.

Gecko Feet and Van der Waals Forces

Geckos use Van der Waals forces for adhesion between setae and surfaces.

• Allows climbing on smooth surfaces.

pH Scale

pH measures hydrogen ion concentration.

• $pH = -\log[H^+]$

• Acidic: pH < 7; Basic: pH > 7.

• $pH + pOH = 14$

Chapter 3 – Carbon

Carbon's Versatility

Carbon forms diverse organic molecules due to its bonding properties.

• 4 valence electrons allow formation of chains, rings, and branching structures.

Isomers

Isomers are molecules with the same formula but different structures.

• Structural isomers: Different covalent arrangements.

• Cis-trans isomers: Same bonds, different spatial arrangement.

• Enantiomers: Mirror images.

Phosphate Groups

Phosphate groups are hydrophilic due to negative charges and interact with water.

• Important in energy transfer (e.g., ATP).

Carbon Cycling

Carbon cycles through ecosystems via various processes.

• Photosynthesis, respiration, decomposition, and fossil fuel use.

Chapter 3 – Polymers

Dehydration vs. Hydrolysis

Polymer formation and breakdown involve water.

• Dehydration: Removes water to build polymers.

• Hydrolysis: Adds water to break polymers.

CHNOPS Elements in Macromolecules

Major biological macromolecules contain specific elements.

Macromolecule	Main Elements
Carbohydrates	C, H, O
Lipids	C, H, O (few O)
Proteins	C, H, O, N, S
Nucleic acids	C, H, O, N, P

Carbohydrates

Carbohydrates are energy sources and structural components.

• Building blocks: Monosaccharides (e.g., glucose, fructose).

• Bond: Glycosidic linkage.

• Nomenclature: Mono = 1 sugar, di = 2, poly = many.

• Functions: Energy storage (starch, glycogen), structure (cellulose, chitin).

• Formulas: Dehydration removes H2O; hydrolysis adds H2O.

Lipids

Lipids are hydrophobic molecules important for energy storage and membranes.

• Not polymers (built from glycerol + fatty acids, but no repeating monomer chain).

• Unsaturated fatty acids: Double bonds, kinked, liquid at room temperature.

• Trans fats: Straight double bonds, behave like saturated fats.

• Steroids: Four fused rings, hydrophobic, grouped as lipids due to nonpolarity.

Proteins

Proteins perform diverse functions and are made from amino acids.

• Nitrogen cycle: Nitrogen fixed into NH3 → nitrates → taken up by plants → animals → returned via decomposition.

• Building blocks: Amino acids.

• Dehydration to make 500 aa protein: 499 reactions.

• Polypeptide backbone: Repeating N–C–C pattern.

• Protein structure:

  1. Primary: Amino acid sequence (peptide bonds).

  2. Secondary: α-helix, β-sheet (H-bonds).

  3. Tertiary: 3D folding (disulfide bridges, ionic, H-bonds, hydrophobic interactions).

  4. Quaternary: Multiple polypeptides.

• Denaturation: Heat, pH, salt break bonds (H-bonds, ionic, hydrophobic); primary structure stays intact.

• Hydrophilic vs. hydrophobic side chains: Polar/charged = hydrophilic; nonpolar = hydrophobic.

Nucleic Acids

Nucleic acids store and transmit genetic information.

• DNA vs. RNA: DNA = double helix, deoxyribose, thymine, nucleus; RNA = single-stranded, ribose, uracil, cytoplasm/nucleus.

• Nucleotide: Sugar + phosphate + nitrogen base.

• Base pairing: A–T (DNA), A–U (RNA), G–C (H-bonds).

• 5' and 3': Refer to carbon positions in sugar backbone; strands run antiparallel.

Nutrient Cycles

Carbon Cycle

Carbon cycles through photosynthesis and respiration.

• Photosynthesis captures carbon; respiration releases it.

Nitrogen Cycle

Nitrogen is fixed, assimilated, and returned to the environment.

• Fixation, nitrification, assimilation, denitrification.

Phosphorus Cycle

Phosphorus cycles through weathering, absorption, and decomposition.

• Recycled through biotic/abiotic reservoirs; lacks a gas phase.

Isopod Lab

Taxis vs. Kinesis

Animal movement can be directed or random in response to stimuli.

• Taxis: Directed movement toward/away from a stimulus.

• Kinesis: Random movement; rate changes with stimulus intensity.

Types of Taxis

• Phototaxis: Movement in response to light.

• Thigmotaxis: Movement in response to touch/contact.

Agonistic Behaviors

Agonistic behaviors include threatening, submissive, or fighting actions to resolve conflict (e.g., aggression, defense).