BIOL 141 Test 1 Study Notes: Chapters 1–3

Chapter 1: The Science of Biology

• Characteristics of Life:

  • Living organisms display 7 fundamental characteristics:

  • Cellular organization: All living organisms consist of one or more cells.

  • Ordered complexity: Living things are organized from simple parts into complex systems.

  • Sensitivity: Organisms respond to stimuli in their environment.

  • Growth, development, and reproduction: Organisms grow, change, and produce offspring.

  • Energy utilization: Organisms obtain and use energy.

  • Homeostasis: Maintaining a stable internal environment despite external changes.

  • Evolutionary adaptation: Populations change over generations; helpful heritable traits can become more common.

  • Memory Trick: C-O-S-G-E-H-E — say the letters in order.

• Hierarchical Organization:

  • Living systems are organized hierarchically from smallest to largest: Atoms $\rightarrow$ Molecules $\rightarrow$ Organelles $\rightarrow$ Cells $\rightarrow$ Tissues $\rightarrow$ Organs $\rightarrow$ Organ Systems $\rightarrow$ Organism $\rightarrow$ Population $\rightarrow$ Community $\rightarrow$ Ecosystem $\rightarrow$ Biosphere.

  • Emergent Property: A system possesses a property that its individual constituent parts do not have when isolated.

  • Example: Individual heart cells cannot pump blood through the whole body on their own, but the organized structure of the entire heart can.

• Inductive vs. Deductive Reasoning:

  • Inductive Reasoning: Moving from specific observations to a general conclusion. Involves observing many individual examples and then forming a general conclusion.

  • Deductive Reasoning: Moving from a general rule or law to make a specific prediction.

  • Memory Trick: INDUCTIVE = individual observations $\rightarrow$ general idea. DEDUCTIVE = general idea $\rightarrow$ specific prediction.

• Hypothesis-Driven Science:

  • Scientific inquiry follows a structured process: Observation $\rightarrow$ Question $\rightarrow$ Hypothesis $\rightarrow$ Prediction $\rightarrow$ Experiment $\rightarrow$ Results $\rightarrow$ Conclusion.

  • Hypothesis: A proposed explanation that can be tested.

  • Scientific Theory: A well-supported explanation backed by substantial evidence; it is not simply a guess.

  • Basic Research: Seeks knowledge and general understanding.

  • Applied Research: Uses knowledge to solve practical problems.

  • Memory Trick: BASIC = knowledge. APPLIED = application.

• Darwin and Natural Selection:

  • Charles Darwin traveled on the HMS Beagle and studied organisms including Galápagos finches.

  • Thomas Malthus: Proposed that populations can produce more offspring than available resources can support, leading to competition for limited resources.

  • Natural Selection: Process wherein individuals possessing advantageous heritable traits are more likely to survive and reproduce, making those traits more common over generations.

• Evidence for Evolution:

  • Fossil Record: Shows changes in organisms through geological time.

  • Earth's Age: Earth is old enough for evolutionary change to occur.

  • Heredity: Traits can be passed from parents to offspring.

  • Homologous Structures: Similar underlying structure and common evolutionary ancestry, though they may serve different functions.

  • Analogous Structures: Similar function but different evolutionary origins.

  • Molecular Evidence: DNA and protein similarities can reveal evolutionary relationships.

  • Memory Trick: HOMO = same underlying origin. ANALOGOUS = similar function.

• 5 Core Concepts in Biology:

  1. Life is subject to chemical and physical laws.

  2. Structure determines function.

  3. Living systems transform energy and matter.

  4. Living systems depend on information — especially DNA and cellular processes.

  5. Evolution explains the unity and diversity of life.

Chapter 2: Molecules and Properties of Water

• Atoms and Subatomic Particles:

  • Proton: Positive charge (+$+$), located in the atomic nucleus.\n * **Neutron**: Neutral / no charge (0), located in the atomic nucleus.\n * **Electron**: Negative charge (-$+$), located outside the nucleus in orbitals.

  • Memory Trick: Proton = Positive • Neutron = Neutral • Electron = Negative.

• Atomic Number and Atomic Mass:

  • Atomic Number: Number of protons in an atom. This uniquely identifies the element.

  • Mass Number: Approximately equal to protons plus neutrons ($\text{Mass Number} \approx \text{Protons} + \text{Neutrons}$).

  • Memory Trick: Change protons $\rightarrow$ different element. Change neutrons $\rightarrow$ isotope.

• Ions and Redox Reactions:

  • Cation: A positive ion formed when an atom loses electrons.

  • Anion: A negative ion formed when an atom gains electrons.

  • Oxidation: The loss of electrons.

  • Reduction: The gain of electrons.

  • Memory Trick: OIL RIG = Oxidation Is Loss, Reduction Is Gain.

  • Memory Trick: CATion = PAWsitive. ANion = gains/ADDS electrons.

• Isotopes and Half-Life:

  • Isotopes: Atoms of the same element with different numbers of neutrons.

  • Radioactive Isotope: An unstable isotope that undergoes decay over time.

  • Half-Life: Time needed for half of a radioactive sample to decay.

  • Example: $100\,\text{g} \rightarrow 50\,\text{g} \rightarrow 25\,\text{g} \rightarrow 12.5\,\text{g}$ after 1, 2, and 3 half-lives, respectively.

• Electrons, Valence, and the Octet Rule:

  • Orbitals / Energy Levels: Regions where electrons are found.

  • Valence Electrons: Outermost electrons; strongly influence bonding and reactivity.

  • Octet Rule: Atoms tend to become more stable with 8 valence electrons.

  • Memory Trick: CHON = Carbon, Hydrogen, Oxygen, Nitrogen — four major elements in living systems.

• Chemical Bonds:

  • Ionic Bonds: Electrons are transferred completely from one atom to another; opposite charges attract.

  • Covalent Bonds: Electrons are shared between atoms.

  • Nonpolar Covalent Bonds: Electrons are shared fairly equally.

  • Polar Covalent Bonds: Electrons are shared unequally.

  • Electronegativity: An atom’s ability to pull shared electrons toward itself.

  • Memory Trick: Ionic = transfer. Covalent = share. Bigger electronegativity difference = more polar.

• Chemical Reactions:

  • Reactants $\rightarrow$ Products. Reactants start the reaction; products are formed.

  • Reaction Rate: Can be influenced by temperature, concentration, and catalysts.

  • Catalyst: Speeds a reaction by lowering activation energy and is not consumed.

• Water and Hydrogen Bonding:

  • Water Polarity: Water is polar; oxygen is slightly negative ($\delta^-$) and hydrogens are slightly positive ($\delta^+$).

  • Hydrogen Bonds: Attraction between slightly positive H and slightly negative O on nearby molecules.

  • Cohesion: Water sticks to water $\rightarrow$ helps create surface tension.

  • Adhesion: Water sticks to other substances.

  • Capillary Action: Movement of water in narrow spaces due to cohesion + adhesion.

  • Memory Trick: COHESION = water with water. ADHESION = water with another substance.

• 6 Important Properties of Water:

  1. High specific heat: Resists temperature changes.

  2. High heat of vaporization: Takes a lot of heat to turn liquid water into gas.

  3. Solid water is less dense than liquid water: Ice floats on top of liquid water.

  4. Excellent solvent: Dissolves polar and ionic substances easily.

  5. Organizes nonpolar molecules: Forces hydrophobic molecules together.

  6. Can form ions: Dissociates into $\text{H}^+$ and $\text{OH}^-$ ions.

  • Memory Trick: H-H-S-S-O-I = High specific heat • High heat of vaporization • Solid less dense • Solvent • Organizes nonpolar molecules • Ion formation.

• Acids, Bases, pH, and Buffers:

  • Acid: Increases $H^+$ concentration; generally low pH.

  • Base: Decreases $H^+$ concentration / accepts $H^+$; generally high pH.

  • pH Scale: pH 0–6 = acidic; 7 = neutral; 8–14 = basic.

  • Buffer: Resists changes in pH; biological buffers help maintain safe pH in living systems.

  • Memory Trick: LOW pH = HIGH $H^+$. BUFFER = pH shock absorber.

Chapter 3: Chemical Building Blocks of Life

• Carbon Chemistry:

  • Carbon can form 4 covalent bonds, allowing it to build many complex biological molecules.

  • Biological molecules commonly contain carbon bonded to O, N, S, P, or H.

  • Hydrocarbons: Molecules containing carbon and hydrogen.

  • Memory Trick: Carbon = the flexible framework of biological molecules because it can make 4 bonds.

• Functional Groups and Isomers:

  • Functional Groups: Specific atom groups attached to carbon skeletons that affect molecular behavior.

  • Isomers: Same molecular formula but different structures/arrangements.

  • Structural Isomers: Atoms are connected differently.

  • Stereoisomers: Same connections but different 3-D arrangement.

  • Chiral: A molecule that is not superimposable on its mirror image.

  • Memory Trick: Chiral = like left and right hands: mirror images that do not perfectly overlap.

• Monomers, Polymers, and Chemical Reactions:

  • Monomer: One building block.

  • Polymer: Many repeating monomers connected together.

  • Dehydration Synthesis: Removes $H_2O$ to build/connect molecules.

  • Hydrolysis: Adds $H_2O$ to break molecules apart.

  • Memory Trick: MONO = one. POLY = many. DEHYDRATION = remove water/build. HYDROLYSIS = add water/break.

• The 4 Major Biomolecules:

  • The four categories are Carbohydrates, Nucleic Acids, Proteins, and Lipids.

  • Memory Trick: Carbs = energy • Nucleic acids = information • Proteins = work • Lipids = hydrophobic/energy/membranes.

• 1. Carbohydrates:

  • Main Roles: Quick energy, energy storage, and structure.

  • Monosaccharide: One sugar. Examples: glucose, fructose, galactose.

  • Disaccharide: Two sugars. Examples: sucrose, lactose, maltose.

  • Polysaccharide: Many sugars.

  • Starch: Energy storage in plants.

  • Glycogen: Energy storage in animals.

  • Cellulose: Structural component of plant cell walls.

  • Chitin: Structural component of arthropod exoskeletons and fungal cell walls.

  • Memory Trick: PLANTS STORE = STARCH • ANIMALS STORE = GLYCOGEN • PLANTS STRUCTURE = CELLULOSE • BUGS/FUNGI = CHITIN.

• 2. Nucleic Acids:

  • Function: Store/transmit genetic information. Main examples: DNA and RNA.

  • Nucleotide Composition: Sugar + phosphate + nitrogenous base.

  • 5 Nitrogenous Bases: Adenine (A), Guanine (G), Cytosine (C), Thymine (T), Uracil (U).

  • DNA Bases: A, T, C, G.

  • RNA Bases: A, U, C, G.

  • Phosphodiester Bonds: Connect nucleotides in the nucleic-acid backbone.

  • DNA Base Pairing: A–T and C–G.

  • RNA Function: Uses U instead of T; helps use genetic information to make proteins.

  • Memory Trick: SPB = Sugar + Phosphate + Base. DNA = ATCG. RNA = AUCG.

• 3. Proteins:

  • Monomer & Polymer: Monomer = amino acid; Polymer = polypeptide/protein.

  • Amino Acid Components: Central carbon + amino group + carboxyl group + H + variable R group.

  • R Group: Varies among amino acids and helps determine their properties.

  • Peptide Bonds: Covalent bonds connecting amino acids; formed by dehydration synthesis.

  • 4 Levels of Protein Structure:

  • Primary: Amino acid sequence.

  • Secondary: Local $\alpha$-helices and $\beta$-sheets.

  • Tertiary: Overall 3-D shape of one polypeptide.

  • Quaternary: Multiple polypeptide chains together.

  • Memory Trick: 1 = sequence • 2 = coils/sheets • 3 = 3-D shape • 4 = multiple chains.

  • Chaperones & Denaturation:

  • Chaperones: Proteins that help other proteins fold correctly.

  • Denaturation: Loss/change of a protein’s normal shape, often from heat, extreme pH, or chemicals.

  • Memory Trick: STRUCTURE DETERMINES FUNCTION. Change the shape $\rightarrow$ function can change or stop.

• 4. Lipids:

  • Lipid Characteristics: Generally hydrophobic and poorly soluble in water.

  • Fats: Typically 1 glycerol + 3 fatty acids.

  • Saturated Fatty Acids: No C=C double bonds; straighter chains; often solid at room temperature.

  • Unsaturated Fatty Acids: One or more C=C double bonds; bends/kinks; often liquid at room temperature.

  • Memory Trick: SATURATED = STRAIGHT. UNSATURATED = BENT.

  • Phospholipids:

  • Components: Glycerol + 2 fatty-acid tails + phosphate head.

  • Phosphate Head: Hydrophilic (likes water).

  • Fatty-Acid Tails: Hydrophobic (avoid water).

  • Bilayer Formation: Phospholipids arrange into a bilayer that forms the basic structure of cell membranes.

  • Micelles: Lipid structures that arrange hydrophilic portions toward water and hydrophobic portions away from water.

  • Memory Trick: HEADS like water. TAILS avoid water.

High-Priority Test Review

• Key Concepts Checklist:

  • List the 7 characteristics of life.

  • Put the levels of biological organization in order from smallest to largest.

  • Explain an emergent property with an example.

  • Tell inductive reasoning from deductive reasoning.

  • Explain hypothesis vs. scientific theory.

  • Explain natural selection and the role of Malthus.

  • Distinguish homologous from analogous structures.

  • Know proton, neutron, electron: charge and location.

  • Know atomic number and how to calculate neutrons from mass number.

  • Know cation vs. anion and OIL RIG.

  • Know isotopes and half-life.

  • Know CHON, valence electrons, and the octet rule.

  • Distinguish ionic, nonpolar covalent, and polar covalent bonds.

  • Explain water polarity, hydrogen bonds, cohesion, adhesion, and capillary action.

  • Know the six properties of water.

  • Know acids, bases, pH, and buffers.

  • Know carbon’s ability to form 4 covalent bonds.

  • Distinguish monomer vs. polymer and dehydration synthesis vs. hydrolysis.

  • Know the 4 major biomolecules and their basic functions.

  • Know carbohydrate examples: glucose, starch, glycogen, cellulose, chitin.

  • Know nucleotide components and DNA/RNA base pairing.

  • Know amino-acid structure, peptide bonds, and the 4 protein-structure levels.

  • Know denaturation and why protein shape matters.

  • Know saturated vs. unsaturated fats.

  • Know phospholipid structure and hydrophilic vs. hydrophobic.