Review_Chapters_1.2.3_students_updated
Chapter 1: Principles of Life
1.1 Living Organisms Share Common Aspects of Structure, Function, and Energy Flow
Learning Objectives
1.1.1 Understand the single origin of life.
1.1.2 Know the main steps in the history of life.
1.1.3 Understand the evolutionary tree of life.
1.1.4 Understand the concept of generalization.
1.1.1 Single Origin of Life
All living things are descended from a single common ancestor, sharing similar characteristics.
1.1.2 Main Steps in the History of Life
Earth Formation: Between 4.6 to 4.5 billion years ago.
Nucleic Acids: Evolution of life began with the formation of nucleic acids.
Cell Formation: Biological molecules were enclosed in a membrane (fatty acids) leading to the formation of prokaryotic cells in the ocean.
Photosynthesis: Evolved resulting in the accumulation of oxygen; first photosynthetic organisms were cyanobacteria.
Aerobic Organisms: Development of organisms that utilize oxygen.
Ozone Layer Formation: Accumulation of oxygen produced a protective layer of ozone (O3) from harmful UV radiation, allowing organisms to inhabit land.
1.1.3 Evolutionary Tree of Life
Evolution can be traced through species with mutations (genetic changes).
Species Naming: Genus species is the format used.
Genomic Comparison: Can reveal evolutionary relationships among species.
Three Domains of Life:
Bacteria
Archaea
Eukarya
1.1.4 Concept of Generalization
Discoveries in one type of organism can often be generalized to others due to common ancestry.
Importance of model organisms in scientific research.
Chapter 2: Life's Chemistry and the Importance of Water
2.1 An Element’s Atomic Structure Determines Its Properties
Learning Objectives
2.1.1 Describe the structure of an atom.
2.1.2 Relate atomic structure to element identity.
2.1.3 Use chemical characteristics to group elements in the periodic table.
2.1.1 Structure of an Atom
Components:
Proton (+)
Neutron (0)
Electron (-) around the nucleus.
2.1.2 Atomic Structure and Identity
Atomic Number: Number of protons is equal to the number of electrons.
Isotopes: Atoms with the same number of protons but different numbers of neutrons (e.g., C12, C14).
2.1.3 Electrons and the Periodic Table
Electrons in atomic orbitals determine chemical behavior and properties.
Octet Rule:
1st shell: 2 electrons
2nd shell: 8 electrons
3rd shell and beyond: 8 electrons.
2.2 Atoms Bond to Form Molecules
Learning Objectives
2.2.1 Predict element reactions based on electronegativity.
2.2.2 Describe covalent bonds in terms of electronegativity.
2.2.3 Recognize polar and nonpolar covalent bonds.
2.2.4 Describe hydrogen bonds and van der Waals interactions.
2.2.1 Chemical Reactions
High Electronegativity: Transfer of electrons leads to ionic bonds.
Low/Medium Electronegativity: Covalent bonds formed are nonpolar if equal and polar if different.
2.2.2 Covalent Bonds
Properties:
Nonpolar: Electrons shared equally.
Polar: Electrons pulled closer to the nucleus of the more electronegative atom.
2.2.3 Typical Covalent Bonds in Biological Molecules
Polar: H2O, NH3
Nonpolar: C-C bonds, C-H bonds.
2.2.4 Hydrogen Bonds and van der Waals Interactions
Hydrogen Bonds: Attraction between slightly charged hydrogen and negatively charged atoms (O or N).
van der Waals Interactions: Weak attractions between oppositely charged atoms.
2.3 Chemical Transformations Involve Energy and Energy Transfers
Learning Objectives
2.3.1 Define energy and its capabilities.
2.3.2 Discuss energy transformation principles.
2.3.3 Relate energy to thermodynamics laws.
2.3.1 Definition of Energy
Energy: Capacity to produce a change.
Forms of Energy:
Potential Energy
Kinetic Energy
2.3.2 Energy Conservation
1st Law of Thermodynamics: Energy cannot be created or destroyed; it only changes form.
2.3.3 Usable Energy and Entropy
2nd Law of Thermodynamics: Energy transformations increase entropy (disorder) in a system, leading to some energy becoming unavailable for work.
2.4 Chemical Reactions Transform Substances
Learning Objectives
2.4.1 Define chemical reaction.
2.4.2 Energy changes in reactions.
2.4.3 Factors affecting reaction rate.
2.4.1 Chemical Reaction Defined
Chemical reactions involve reconfiguration of atomic bonds and varying energy between reactants and products.
2.4.2 Energy Changes in Reactions
Exergonic Reaction: Releases energy (Gibbs free energy, G) is negative.
Endergonic Reaction: Requires energy to occur (G positive).
2.4.3 Factors Influencing Reaction Rate
Activation Energy (Ea): Minimum energy needed for a reaction.
Factors affecting rate include activation energy, temperature, and concentration of reactants and products.
2.5 The Properties of Water Are Critical
Learning Objectives
2.5.1 Hydrogen bonding effects on water properties.
2.5.2 Interactions of molecules in water.
2.5.3 Self-ionization of water.
2.5.4 Buffer effects on pH.
2.5.1 Hydrogen Bonding in Water
Water's hydrogen bonds lead to high specific heat, high heat of vaporization, cohesion, and adhesion which are crucial for life.
2.5.2 Molecular Interactions in Water
Ionic compounds dissolve due to hydration and polar molecules form hydrogen bonds. Nonpolar molecules do not dissolve well.
2.5.3 Self-Ionization of Water
Water molecules can ionize into H3O+ and OH-.
Acids Increase H+ concentration whereas Bases Increase OH- concentration.
2.5.4 Buffers and pH Changes
Buffers minimize pH changes by reacting with H3O+ and OH- when acids or bases are added.
Chapter 3: Macromolecules
3.1 Lipids Are Characterized by Their Insolubility in Water
Learning Objectives
3.1.1 Define lipids.
3.1.2 Identify triglycerides and phospholipids.
3.1.3 Differentiate saturated and unsaturated fatty acids.
3.1.4 List functions of lipids.
3.1.1 Definition of Lipids
Nonpolar, hydrophobic molecules due to nonpolar C-C and C-H bonds.
3.1.2 Triglycerides and Phospholipids
Triglyceride: 3 fatty acids + 1 glycerol.
Phospholipid: 2 fatty acids + 1 glycerol + phosphate group (amphipathic).
3.1.3 Saturated vs. Unsaturated Fatty Acids
Saturated: All single bonds; solid at room temp.
Unsaturated: One or more double bonds; liquid at room temp.
3.1.4 Functions of Lipids
Membranes, energy storage, insulation, waterproofing, light absorption, and intracellular signaling.
3.2 Carbohydrates Are Made from Simple Sugars
Learning Objectives
3.2.1 Draw ring forms of carbohydrates.
3.2.2 Distinguish structural isomers and stereoisomers.
3.2.3 Define monosaccharides, disaccharides, oligosaccharides, and polysaccharides.
3.2.4 Discuss linear vs branched polysaccharides.
3.2.1 Ring Forms of Carbohydrates
Ring closure occurs between carbon 1 and 5 or 1 and 4 in pentose and hexose sugars.
3.2.2 Isomers of Monosaccharides
Structural Isomers: Same atoms, different bonds.
Stereoisomers: Same atoms, same bonds, different 3D orientations.
3.2.3 Types of Carbohydrates
Monosaccharides: 5-6 carbons, e.g., glucose.
Disaccharides: 2 monosaccharides linked by a glycosidic bond.
Oligosaccharides: 3-10 monosaccharides.
Polysaccharides: Polymers of hundreds to thousands of monosaccharides.
3.2.4 Linear vs. Branched Polysaccharides
Linear: Cellulose (plant structure), Chitin (arthropod skeleton).
Branched: Starch (plant energy storage), Glycogen (animal energy storage).
3.3 Nucleic Acids Are Informational Macromolecules
Learning Objectives
3.3.1 Recognize nucleotide structure.
3.3.2 Describe base pairing rules.
3.3.3 List differences between RNA and DNA.
3.3.4 Define replication, transcription, and translation.
3.3.1 Structure of a Nucleotide
Components: Sugar (pentose), nitrogenous base, phosphate group (1 to 3).
Phosphodiester Bonds: Connects nucleotides, oriented 5' to 3'.
3.3.2 Base Pairing Rules
Purine pairs with Pyrimidine:
A-T (DNA), A-U (RNA), G-C (both).
3.3.3 RNA vs. DNA
DNA: Deoxyribose, double-stranded, bases A, T, C, G.
RNA: Ribose, single-stranded, bases A, U, C, G.
3.3.4 Processes
Replication: Copying DNA.
Transcription: DNA information into RNA.
Translation: RNA information into proteins.
3.4 Proteins Are Polymers with Variable Structures
Learning Objectives
3.4.1 Describe amino acid diversity.
3.4.2 Explain peptide bonds.
3.4.3 Distinguish protein structures.
3.4.4 Define denaturation.
3.4.1 Amino Acid Structure
Components: Amino group, Carboxyl group, and side chain (R group).
Differences include charge, polarity, size, shape (e.g., Glycine, Cysteine).
3.4.2 Peptide Bonds
Formed through condensation reactions between amino and carboxyl groups, linking amino acids from N terminus to C terminus.
3.4.3 Protein Structures
Primary: Sequence of amino acids.
Secondary: Local folding into alpha-helices and beta-sheets.
Tertiary: Overall 3D shape.
Quaternary: Assembly of multiple polypeptide chains.
3.4.4 Denaturation of Proteins
Disruption of secondary and tertiary structure due to heat or chemicals.
Proteins can revert when normal conditions return, as the primary structure holds information.
3.5 Function of Proteins
Learning Objectives
3.5.1 List protein functions.
3.5.2 Describe factors altering protein shape.
3.5.3 Define cofactors.
3.5.4 Define enzymes and their functions.
3.5.5 Discuss regulation and inhibition.
3.5.1 Functions of Proteins
Key Roles:
Enzymes, structure, transport, signaling, defensive, motion, and storage.
3.5.2 Factors Affecting Protein Shape
Ligand binding, R group modifications, cofactor presence, and proteolysis.
3.5.3 Cofactors
Nonprotein molecules essential for enzyme function, including inorganic ions (e.g., Iron, Zn) and organic cofactors (e.g., coenzymes like NADH).
3.5.4 Enzymes
Catalyze reactions by lowering activation energy; bind specifically to substrates at active sites.
3.5.5 Regulation and Inhibition
Active Site Regulation: Irreversible inhibitors permanently bind; competitive inhibitors bind reversibly.
Allosteric Regulation: Molecules bind elsewhere and influence enzyme activity.