Chapter 1: Evolution, the Themes of Biology, and Scientific Inquiry

Properties of Living Organisms

Living organisms share a set of fundamental properties that distinguish them from non-living matter.

• Order: Highly organized structure, such as cells and tissues.

• Regulation: Ability to maintain internal stability (homeostasis).

• Growth and Development: Increase in size and change in form, directed by genetic information.

• Energy Processing: Use of energy to power activities (e.g., metabolism).

• Response to the Environment: Ability to sense and react to stimuli.

• Reproduction: Production of new organisms.

• Evolutionary Adaptation: Populations change over generations to become better suited to their environment.

Hierarchy of Biological Organization

Biological systems are organized from the smallest to the most complex levels:

• Atom

• Molecule

• Organelle

• Cell

• Tissue

• Organ

• Organ System

• Organism

• Population

• Community

• Ecosystem

• Biosphere

Definitions: Population, Community, Ecosystem

• Population: Group of individuals of the same species in a given area.

• Community: All populations of different species in a given area.

• Ecosystem: The community plus the non-living (abiotic) environment.

Experimental Controls and Variables

• Negative Control: Group where no response is expected.

• Positive Control: Group where a known response is expected.

• Independent Variable: The variable changed or controlled by the experimenter.

• Dependent Variable: The variable measured or observed.

Energy Flow in Ecosystems

• Energy enters as sunlight, is converted by producers (plants), passes through consumers, and exits as heat.

Steps in Scientific Study

1. Observation

2. Question

3. Hypothesis

4. Prediction

5. Experiment/Test

6. Conclusion

Hypothesis: An explanation based on observations and assumptions, leading to testable predictions.

Chapter 2: The Chemical Context of Life

Chemical Reactions and Atomic Structure

• Reactants: Starting molecules in a chemical reaction.

• Products: Molecules produced by the reaction.

• Atomic Number: Number of protons in the nucleus.

• Atomic Mass (Mass Number): Number of protons plus neutrons.

• Protons: Positive charge, mass ≈ 1 Dalton.

• Neutrons: Neutral, mass ≈ 1 Dalton.

• Electrons: Negative charge, negligible mass, found in electron shells.

Calculating Neutrons:

• Neutrons = Mass Number − Atomic Number

• Example: Atomic Number = 8, Mass Number = 16 → Neutrons = 8

Isotopes

• Atoms of the same element with the same number of protons but different numbers of neutrons.

Chemical Bonds

• Covalent Bond: Atoms share electrons (strong bond).

• Ionic Bond: Atoms transfer electrons, forming ions that attract each other (strong bond).

• Polar Covalent Bond: Electrons shared unequally, creating partial charges (e.g., water).

• Nonpolar Covalent Bond: Electrons shared equally, no partial charges.

• Hydrogen Bond: Weak attraction between a hydrogen atom and an electronegative atom (e.g., O or N).

• Van der Waals Interactions: Weak attractions due to temporary uneven electron distribution.

Bonding Capacity of Elements

• Carbon: 4 bonds

• Nitrogen: 3 bonds

• Oxygen: 2 bonds

• Hydrogen: 1 bond

Chemical Inertness

• Elements with a full valence shell are chemically inert (non-reactive).

Major and Trace Elements in Living Organisms

• Major Elements: Carbon, Hydrogen, Oxygen, Nitrogen (CHON).

• Trace Elements: Required in minute quantities (e.g., iron, iodine).

Chapter 3: Water and Life

Polarity and Properties of Water

• In water, oxygen is δ− (delta negative), hydrogen is δ+ (delta positive).

• Water is polar because oxygen is more electronegative than hydrogen.

• Cohesion: Hydrogen bonds hold water molecules together.

• Surface Tension: Caused by cohesion at the surface.

• Ice Floats: Ice is less dense than liquid water due to hydrogen bonding.

Evaporation and Cooling

• Evaporation causes the remaining liquid to cool (evaporative cooling).

• Hydrogen bonds must be broken for water to evaporate.

pH and Buffers

• pH: Negative logarithm of hydrogen ion concentration:

• Lower pH = higher [H+]. pH 5 has 100× more H+ than pH 7.

• Buffers: Substances that minimize changes in [H+] and [OH−].

Acidification

• Acidification lowers water pH, harming aquatic organisms and disrupting biological processes.

Chapter 4: Carbon and the Molecular Diversity of Life

Organic Chemistry and Carbon

• Organic chemistry studies carbon-containing compounds.

• Carbon forms four covalent bonds, allowing for diverse molecules.

Isomers

• Isomers: Compounds with the same molecular formula but different structures.

• Structural Isomers: Different covalent arrangements.

• Cis-trans (Geometric) Isomers: Same covalent bonds, different spatial arrangements.

• Enantiomers: Mirror images of each other.

Functional Groups

• Groups of atoms attached to carbon skeletons, involved in chemical reactions.

Chapter 5: The Structure and Function of Large Biological Molecules

Polymers and Their Synthesis/Degradation

• Polymers (e.g., polysaccharides, proteins, nucleic acids) are built by dehydration reactions (removal of water) and broken down by hydrolysis (addition of water).

Carbohydrates

• Monosaccharide: Single sugar molecule (e.g., glucose).

• Disaccharide: Two sugars joined (e.g., sucrose).

• Polysaccharide: Many sugars joined (e.g., starch, glycogen, cellulose).

Lipids

• Triacylglycerol (Triglyceride): Glycerol + 3 fatty acids.

• Saturated Fatty Acids: No double bonds, solid at room temperature.

• Unsaturated Fatty Acids: One or more double bonds, liquid at room temperature (oils).

• Phospholipids: Glycerol, two fatty acids, phosphate group; main component of cell membranes.

• Steroids: Lipids with four fused carbon rings (e.g., cholesterol).

Proteins

• Made of 20 amino acids, differing in R groups (side chains).

• Primary Structure: Sequence of amino acids.

• Secondary Structure: Coils (α-helix) and sheets (β-pleated sheet).

• Tertiary Structure: 3D shape of a single polypeptide.

• Quaternary Structure: Association of multiple polypeptides.

• Denaturation: Loss of protein's native structure due to disruption of bonds.

Nucleic Acids

• Polymers of nucleotides (nitrogenous base, sugar, phosphate group).

• DNA: Deoxyribose sugar, thymine, double helix, stores genetic information.

• RNA: Ribose sugar, uracil, single-stranded, involved in protein synthesis.

• Base Pairing: Adenine (A) pairs with Thymine (T), Guanine (G) pairs with Cytosine (C) via hydrogen bonds.

Calculating Nucleotide Percentages: If T = 30%, then A = 30%, G + C = 40%, so G = 20%, C = 20%.

Chapter 6: A Tour of the Cell

Prokaryotic vs. Eukaryotic Cells

• Prokaryotic Cells: Lack nucleus and membrane-bound organelles (e.g., bacteria, archaea).

• Eukaryotic Cells: Have nucleus and membrane-bound organelles (e.g., plants, animals, fungi, protists).

Major Components of Animal and Plant Cells

• Nucleus

• Ribosome

• Rough Endoplasmic Reticulum (ER)

• Smooth ER

• Golgi Apparatus

• Lysosomes

• Vacuoles

• Mitochondria

• Plasma Membrane

• Plant cells also have: Chloroplasts, Cell Wall, Central Vacuole

Plant vs. Animal Cells

• Plant cells have cell wall, chloroplasts, and a large central vacuole; animal cells do not.

Functions of Organelles

Cytoskeleton Elements

• Microtubules: Largest, involved in cell division, organelle movement, cilia/flagella.

• Intermediate Filaments: Middle size, provide strength and support.

• Microfilaments: Smallest, involved in cell movement and muscle contraction.