final bio exam senior
Chapter 2: The Chemical Context of Life
Matter, Elements, and Compounds
Matter: Anything that takes up space and has mass.
Elements: Substances that cannot be broken down to other substances by chemical reactions.
Essential elements for life: C, H, O, N (make up 9696\% of living matter).
Trace elements: Required in only minute quantities (e.g., Fe, I).
Compounds: Substances consisting of two or more different elements combined in a fixed ratio (e.g., H2OH2O, NaCl).
Atomic Structure
Atom: The smallest unit of matter that still retains the properties of an element.
Subatomic particles:
Protons: Positively charged, located in the nucleus. Mass ≈≈ 11 dalton.
Neutrons: No charge, located in the nucleus. Mass ≈≈ 11 dalton.
Electrons: Negatively charged, orbit the nucleus. Mass ≈≈ 1/20001/2000 dalton.
Atomic number: Number of protons (defines the element).
Mass number: Sum of protons + neutrons.
Atomic mass: The atom's total mass, can be approximated by the mass number.
Isotopes: Atoms of the same element with different numbers of neutrons (e.g., 12C12C, 13C13C, 14C14C).
Radioactive isotopes: Decay spontaneously, giving off particles and energy.
Chemical Bonds
Valence electrons: Electrons in the outermost shell, determining chemical behavior.
Covalent bonds: Sharing of a pair of valence electrons by two atoms.
Nonpolar covalent bond: Electrons shared equally (e.g., O2O2).
Polar covalent bond: Electrons shared unequally due to differences in electronegativity (e.g., H2OH2O).
Ionic bonds: One atom transfers an electron to another, forming ions (charged atoms).
Cation: Positively charged ion.
Anion: Negatively charged ion.
Hydrogen bonds: Weak attraction between a hydrogen atom covalently bonded to an electronegative atom and another electronegative atom.
Van der Waals interactions: Weak, transient interactions between molecules due to temporary dipoles.
Chapter 3: Water and Life
Polarity of Water
Water (H2OH2O) is a polar molecule due to oxygen's high electronegativity, leading to partial negative charge on oxygen and partial positive charges on hydrogens.
Forms hydrogen bonds with other water molecules and polar substances.
Four Emergent Properties of Water
Cohesive and Adhesive Behavior
Cohesion: Water molecules sticking to each other via hydrogen bonds.
Adhesion: Water molecules sticking to other surfaces.
Contributes to surface tension and transport in plants (transpiration).
Ability to Moderate Temperature
High specific heat: Water absorbs and releases large amounts of heat with only slight temperature change.
High heat of vaporization: Large amount of energy needed to change liquid water to gas.
Evaporative cooling: Helps organisms cool down.
Expansion upon Freezing
Ice is less dense than liquid water because hydrogen bonds form a stable, crystalline lattice when frozen, spreading molecules farther apart.
Insulates aquatic environments.
Versatile Solvent
Solvent: Dissolving agent.
Solute: Substance being dissolved.
Aqueous solution: Water is the solvent.
Hydrophilic: Substances that have an affinity for water (polar or ionic).
Hydrophobic: Substances that do not have an affinity for water (nonpolar).
Acids, Bases, and pH
Dissociation of water: 2H2O⇌H3O++OH−2H2O⇌H3O++OH− or H2O⇌H++OH−H2O⇌H++OH−
pH scale: Measures hydrogen ion concentration ([H+][H+]).
pH=−log[H+]pH=−log[H+]
Acidic solutions: [H+]>[OH−][H+]>[OH−], pH <7<7
Basic solutions: [H+]<[OH−][H+]<[OH−], pH >7>7
Neutral solutions: [H+]=[OH−][H+]=[OH−], pH =7=7
Buffers: Substances that minimize changes in pH.
Chapter 4: Carbon and the Molecular Diversity of Life
Carbon: The Backbone of Life
Organic chemistry: Study of carbon compounds.
Valence of carbon: Can form four covalent bonds due to having four valence electrons.
Diversity of carbon skeletons:
Length: Varies (e.g., methane to long carbon chains).
Branching: Can be unbranched, branched, or ring structures.
Double bond position: Can vary (e.g., 1-butene vs. 2-butene).
Presence of rings: Carbon atoms can form rings.
Hydrocarbons: Organic molecules consisting only of carbon and hydrogen.
Are nonpolar and hydrophobic.
Isomers
Compounds with the same molecular formula but different structures and properties.
Structural isomers: Differ in the covalent arrangements of their atoms.
Cis-trans isomers (geometric isomers): Differ in arrangement about a double bond.
Cis: Same side.
Trans: Opposite sides.
Enantiomers: Isomers that are mirror images of each other (chiral molecules).
Often differ in biological activity.
Functional Groups
Small chemical groups that affect molecular function by being directly involved in chemical reactions.
Hydroxyl group (−OH−OH): Polar, forms hydrogen bonds, found in alcohols.
Carbonyl group (C=OC=O): Found in sugars.
Ketone: Carbonyl group within a carbon skeleton.
Aldehyde: Carbonyl group at the end of a carbon skeleton.
Carboxyl group (−COOH−COOH): Acidic, donates H+H+; found in carboxylic acids (e.g., amino acids).
Amino group (−NH2−NH2): Basic, accepts H+H+; found in amino acids.
Sulfhydryl group (−SH−SH): Forms disulfide bridges; found in thiols.
Phosphate group (−OPO32−−OPO32−): Contributes negative charge, stores energy; found in ATP, phospholipids, nucleic acids.
Methyl group (−CH3−CH3): Nonpolar, affects gene expression and shape of sex hormones.
Chapter 5: The Structure and Function of Large Biological Molecules
Macromolecules
Large molecules essential to life: carbohydrates, proteins, nucleic acids, lipids.
Polymers: Long molecule consisting of many similar building blocks (monomers).
Dehydration reaction: Synthesizes a polymer by removing a water molecule.
Hydrolysis: Breaks down a polymer by adding a water molecule.
Carbohydrates
Sugars and polymers of sugars.
Monosaccharides: Simplest sugars (e.g., glucose, fructose).
Sources of immediate energy, building blocks for other molecules.
Disaccharides: Two monosaccharides joined by a glycosidic linkage (e.g., sucrose, lactose).
Polysaccharides: Long chains of monosaccharides.
Storage polysaccharides:
Starch: Storage in plants (amylose, amylopectin).
Glycogen: Storage in animals (liver, muscle).
Structural polysaccharides:
Cellulose: Major component of plant cell walls; cannot be digested by most animals.
Chitin: Found in exoskeletons of arthropods and cell walls of fungi.
Lipids
Diverse group of hydrophobic molecules.
Fats (Triglycerides):
Glycerol + three fatty acids.
Saturated fatty acids: No double bonds, solid at room temperature (e.g., butter).
Unsaturated fatty acids: One or more double bonds (cis or trans), liquid at room temperature (e.g., olive oil).
Energy storage, insulation, organ protection.
Phospholipids:
Glycerol + two fatty acids + a phosphate group.
Amphipathic: Hydrophilic head (phosphate) and hydrophobic tails (fatty acids).
Major component of cell membranes.
Steroids:
Lipids characterized by a carbon skeleton consisting of four fused rings (e.g., cholesterol, hormones).
Cholesterol is a precursor for other steroids and a component of animal cell membranes.
Proteins
Diverse functions: structural support, transport, enzymes, defense, movement, communication.
Polymers of amino acids (polypeptides).
Amino acids: Consist of an alpha carbon, amino group, carboxyl group, hydrogen atom, and a variable R-group.
2020 different amino acids, classified by R-group properties (nonpolar, polar, electrically charged).
Peptide bonds: Covalent bond between the carboxyl group of one amino acid and the amino group of another.
Protein structure:
Primary structure: Unique sequence of amino acids.
Secondary structure: Coils ($\alpha$-helix) and folds ($\beta$-pleated sheet) due to hydrogen bonds between backbone constituents.
Tertiary structure: Overall 3D shape due to interactions between R-groups (hydrogen bonds, ionic bonds, hydrophobic interactions, disulfide bridges).
Quaternary structure: Overall structure when two or more polypeptide chains interact (e.g., hemoglobin).
Denaturation: Loss of a protein's native structure due to changes in pH, temperature, or salt concentration, leading to loss of function.
Nucleic Acids
Store, transmit, and help express hereditary information.
Polymers of nucleotides.
Nucleotides: Consist of a nitrogenous base, a pentose sugar, and one or more phosphate groups.
Nitrogenous bases: Adenine (A), Guanine (G), Cytosine (C), Thymine (T) in DNA, Uracil (U) in RNA.
Sugars: Deoxyribose in DNA, Ribose in RNA.
DNA (Deoxyribonucleic Acid):
Double helix structure.
Sugar-phosphate backbone.
Base pairing: A with T, G with C.
Stores genetic information.
RNA (Ribonucleic Acid):
Single-stranded.
A with U, G with C.
Involved in gene expression (mRNA, tRNA, rRNA).
now can you give me chapters 6-9 from the same textbook?
Chapter 6: A Tour of the Cell
How Biologists Study Cells
Microscopy:
Light Microscope (LM): Uses visible light, magnifies up to 1,0001,000 times, resolves down to 0.20.2 micrometers (μmμm).
Electron Microscope (EM): Uses electron beams, much higher resolution.
Scanning Electron Microscope (SEM): Focuses a beam of electrons onto the surface of a specimen, providing 3D images.
Transmission Electron Microscope (TEM): Focuses a beam of electrons through a specimen, used to study internal ultrastructure.
Cell Fractionation:
Breaks up cells and separates organelles based on size and density, often using a centrifuge.
Eukaryotic Cells
Eukaryotic cells: Have a nucleus and membrane-bound organelles. Larger and more complex than prokaryotic cells.
Animal Cell Organelles and Structures:
Nucleus: Contains most of the cell's DNA.
Nuclear envelope: Double membrane, perforated by nuclear pores.
Nucleolus: Site of rRNA synthesis and ribosomal subunit assembly.
Chromatin: DNA and proteins.
Ribosomes: Sites of protein synthesis; can be free in the cytosol or bound to the ER/nuclear envelope.
Endoplasmic Reticulum (ER): Network of membranes.
Smooth ER: Lacks ribosomes; synthesizes lipids, metabolizes carbohydrates, detoxifies drugs and poisons, stores calcium ions.
Rough ER: Studded with ribosomes; synthesizes secretory proteins, membrane proteins, and phospholipids; produces new membrane.
Golgi apparatus: Modifies, stores, and packages proteins and lipids from the ER.
Cis face: Receiving side.
Trans face: Shipping side.
Lysosomes: Membranous sacs of hydrolytic enzymes; digest macromolecules, old organelles, and food particles.
Vacuoles: Large vesicles derived from the ER and Golgi.
Food vacuoles: Formed by phagocytosis.
Contractile vacuoles: Pump excess water out of cells.
Central vacuole (plants): Stores water, nutrients, wastes; maintains turgor pressure.
Mitochondria: Sites of cellular respiration; produce ATP.
Inner membrane: Folded into cristae to increase surface area.
Mitochondrial matrix: Contains enzymes for respiration.
Peroxisomes: Contain enzymes that transfer hydrogen atoms from various substrates to oxygen, producing hydrogen peroxide as a byproduct (H2O2H2O2), which is then converted to water.
Plant Cell Organelles and Structures (in addition to animal cell structures):
Cell wall: Rigid outer layer; maintains shape, protects cell, prevents excessive water uptake. Primarily cellulose.
Chloroplasts: Sites of photosynthesis.
Thylakoids: Sacs often stacked into grana.
Stroma: Fluid outside the thylakoids.
Plasmodesmata: Channels through cell walls connecting the cytoplasm of adjacent plant cells.
The Cytoskeleton: Network of fibers extending throughout the cytoplasm; organizes structures and activities.
Microtubules: Thickest; shape the cell, guide organelle movement, separate chromosomes in cell division.
Microfilaments (actin filaments): Thinnest; muscle contraction, cell division (cleavage furrow), cell shape changes.
Intermediate filaments: Intermediate diameter; maintain cell shape, anchor organelles (e.g., nucleus).
Extracellular Matrix (ECM) of Animal Cells:
Made of glycoproteins (e.g., collagen) and other carbohydrate-containing molecules.
Provides support, adhesion, movement, and regulation.
Connects to cells via integrins.
Cell Junctions:
Tight junctions: Prevent leakage across cell layers.
Desmosomes: Fasten cells together into strong sheets.
**Gap junctions: Provide cytoplasmic channels between adjacent cells.
Prokaryotic Cells
Prokaryotic cells: Lack a nucleus and membrane-bound organelles. Bacteria and Archaea.
Nucleoid: Region where the cell's DNA is located (not enclosed by a membrane).
Cell wall: Present.
Plasma membrane: Inner boundary.
Cytoplasm: Contains ribosomes.
Capsule: Sticky outer layer in some prokaryotes.
Pili: Attachment structures.
Flagella: For locomotion.
Chapter 7: Membrane Structure and Function
Membrane Models
Fluid Mosaic Model: The membrane is a fluid structure with a "mosaic" of various proteins embedded in or attached to a double layer (bilayer) of phospholipids.
Membrane Components
Phospholipids: Form the bilayer.
Amphipathic: Have both a hydrophilic (water-loving) head and hydrophobic (water-fearing) tails.
Bilayers assemble spontaneously in aqueous environments, with heads facing water and tails away from water.
Membrane fluidity:
Cholesterol: Reduces fluidity at warm temperatures, hinders solidification at cold temperatures.
Saturated vs. unsaturated fatty acids: Unsaturated tails with kinks prevent tight packing, enhancing fluidity.
Proteins:
Integral proteins: Span the membrane (transmembrane).
Peripheral proteins: Loosely bound to the surface of the membrane.
Functions of membrane proteins:
Transport (channels, carriers)
Enzymatic activity
Signal transduction (receptors)
Cell-cell recognition
Intercellular joining
Attachment to cytoskeleton and ECM
Carbohydrates: On the exterior surface, often attached to proteins (glycoproteins) or lipids (glycolipids).
Important for cell-cell recognition.
Membrane Permeability
Selective permeability: Membranes allow some substances to pass more easily than others.
Permeable: Small, nonpolar molecules (e.g., O2,CO2O2,CO2, hydrocarbons).
Less permeable: Large, polar molecules, and ions (e.g., glucose, ions, water).
Transport Across Membranes
I. Passive Transport: Movement of substances down their concentration gradient, no energy required.
Diffusion: Movement of molecules from an area of higher concentration to an area of lower concentration.
Applies to substances directly across the lipid bilayer.
Osmosis: Diffusion of water across a selectively permeable membrane.
Tonicity: The ability of a surrounding solution to cause a cell to gain or lose water.
Isotonic solution: Solute concentration same as inside the cell; no net water movement.
Hypertonic solution: Solute concentration greater than inside the cell; cell loses water and shrivels.
Hypotonic solution: Solute concentration less than inside the cell; cell gains water and lyses (bursts) or becomes turgid (in plant cells).
Facilitated diffusion: Transport proteins (channels or carriers) speed up the movement of molecules down their concentration gradient.
Channel proteins: Provide corridors for specific molecules/ions (e.g., aquaporins for water, ion channels).
Carrier proteins: Bind to molecules and change shape to shuttle them across.
II. Active Transport: Movement of substances against their concentration gradient, requires energy (usually ATP).
Example: Sodium-potassium pump (Na+Na+/K+K+ pump) moves 3Na+3Na+ out and 2K+2K+ into the cell, creating an electrochemical gradient.
Membrane potential: Voltage difference across a membrane, created by unequal distribution of ions.
Electrochemical gradient: Combination of voltage and concentration gradient.
III. Bulk Transport (requires energy):
Exocytosis: Cells secrete macromolecules by fusing vesicles with the plasma membrane.
Endocytosis: Cells take in macromolecules by forming new vesicles from the plasma membrane.
Phagocytosis: "Cellular eating"; engulfs large particles.
Pinocytosis: "Cellular drinking"; takes in extracellular fluid containing solutes.
Receptor-mediated endocytosis: Specific binding of solutes to receptors triggers vesicle formation.
Chapter 8: An Introduction to Metabolism
Metabolism, Energy, and Life
Metabolism: The totality of an organism's chemical reactions.
Catabolic pathways: Release energy by breaking down complex molecules into simpler compounds (e.g., cellular respiration).
Anabolic pathways: Consume energy to build complex molecules from simpler ones (e.g., protein synthesis, photosynthesis).
Energy: The capacity to cause change.
Kinetic energy: Energy of motion.
Thermal energy (heat): Kinetic energy associated with random movement of atoms or molecules.
Potential energy: Energy that matter possesses because of its location or structure.
Chemical energy: Potential energy available for release in a chemical reaction.
Laws of Thermodynamics
First Law of Thermodynamics (Principle of Conservation of Energy): Energy can be transferred and transformed, but it cannot be created or destroyed.
Second Law of Thermodynamics: Every energy transfer or transformation increases the entropy (SS) (disorder or randomness) of the universe.
Free Energy (GG): Energy that can do work when temperature and pressure are uniform, as in a living cell.
ΔG=ΔH−TΔSΔG=ΔH−TΔS
ΔGΔG: Change in free energy.
ΔHΔH: Change in enthalpy (total energy).
TT: Absolute temperature in Kelvin.
ΔSΔS: Change in entropy.
Exergonic reaction: Proceeds with a net release of free energy; ΔG<0ΔG<0 (spontaneous).
Endergonic reaction: Absorbs free energy from its surroundings; ΔG>0ΔG>0 (non-spontaneous, requires energy input).
ATP: The Cell's Energy Shuttle
Adenosine Triphosphate (ATP): Powers nearly all cellular work.
Composed of adenine, ribose, and three phosphate groups.
Energy is released when the terminal phosphate bond is hydrolyzed (ATP→ADP+PiATP→ADP+Pi), an exergonic reaction.
Energy coupling: The use of an exergonic process (ATP hydrolysis) to drive an endergonic one.
ATP is regenerated by adding a phosphate group to ADP, an endergonic process fueled by catabolic reactions.
Enzymes: Catalysts of Life
Enzyme: A macromolecule (usually a protein) that acts as a biological catalyst, speeding up a biochemical reaction without being consumed.
Activation energy (EAEA): The initial energy needed to start a chemical reaction.
Enzymes lower the activation energy, but do not change the ΔGΔG of a reaction.
Substrate: The reactant an enzyme acts on.
Active site: The region on the enzyme where the substrate binds.
Induced fit: The enzyme changes shape slightly upon substrate binding to enhance the fit.
Factors affecting enzyme activity:
Temperature and pH: Each enzyme has an optimal temperature and pH at which it functions most effectively.
Cofactors: Nonprotein helpers for catalytic activity.
Inorganic cofactors: Metal ions (e.g., Zn2+Zn2+, Fe2+Fe2+).
Coenzymes: Organic cofactors (e.g., vitamins).
Enzyme Inhibitors:
Competitive inhibitors: Bind to the active site, competing with the substrate.
Noncompetitive inhibitors: Bind to another part of the enzyme (allosteric site), causing a shape change that makes the active site less effective.
Regulation of Enzyme Activity:
Allosteric regulation: Regulatory molecules bind to an allosteric site, affecting enzyme activity.
Activators: Stabilize the active form.
Inhibitors: Stabilize the inactive form.
Feedback inhibition: The end product of a metabolic pathway acts as an inhibitor of an enzyme earlier in the pathway.
Chapter 9: Cellular Respiration and Fermentation
Catabolic Pathways That Yield Energy
Cellular Respiration: The process that converts the chemical energy in glucose into ATP.
Overall equation: C6H12O6+6O2→6CO2+6H2O+Energy (ATP + heat)C6H12O6+6O2→6CO2+6H2O+Energy (ATP + heat)
Redox reactions: Chemical reactions that involve the transfer of electrons.
Oxidation: Loss of electrons.
Reduction: Gain of electrons.
Electron carriers: NAD+NAD+ (nicotinamide adenine dinucleotide) and FADFAD (flavin adenine dinucleotide).
NAD++2e−+H+→NADHNAD++2e−+H+→NADH
FAD+2e−+2H+→FADH2FAD+2e−+2H+→FADH2
Stages of Cellular Respiration
1. Glycolysis (occurs in the cytosol)
Breaks down glucose (6-carbon) into two molecules of pyruvate (3-carbon).
Energy investment phase (2ATP2ATP consumed) and energy payoff phase (4ATP4ATP produced by substrate-level phosphorylation).
Net gain: 2ATP2ATP, 2NADH2NADH, 2pyruvate2pyruvate per glucose molecule.
Can occur with or without O2O2.
2. Pyruvate Oxidation (occurs in the mitochondrial matrix)
Pyruvate is converted to acetyl CoA.
Each pyruvate releases one CO2CO2 and one NADHNADH. Acetyl CoA (22-carbon) enters the citric acid cycle.
Total per glucose: 2CO22CO2, 2NADH2NADH, 2AcetylCoA2AcetylCoA.
3. Citric Acid Cycle (Krebs Cycle) (occurs in the mitochondrial matrix)
Completes the breakdown of glucose by oxidizing acetyl CoA to CO2CO2.
For each acetyl CoA entering the cycle: releases 2CO22CO2, produces 3NADH3NADH, 1FADH21FADH2, and 1ATP1ATP (by substrate-level phosphorylation).
Total per glucose (two acetyl CoA's): 4CO24CO2, 6NADH6NADH, 2FADH22FADH2, 2ATP2ATP.
4. Oxidative Phosphorylation (occurs at the inner mitochondrial membrane)
Electron Transport Chain (ETC): Electron carriers (NADHNADH and FADH2FADH2) donate electrons to a series of protein complexes.
Electrons pass from higher to lower energy levels, releasing energy.
This energy is used to pump protons (H+H+) from the mitochondrial matrix to the intermembrane space, creating a proton gradient.
Oxygen (O2O2) is the final electron acceptor, forming water (H2OH2O).
Chemiosmosis: The H+H+ gradient drives ATP synthesis.
Protons flow back into the matrix through ATP synthase, a protein complex that uses the energy of the flow to phosphorylate ADP to ATP.
Generates the vast majority of ATP (about 26−28ATP26−28ATP) during cellular respiration.
Overall ATP Yield (approximate, per glucose):
Glycolysis: 2ATP2ATP
Citric Acid Cycle: 2ATP2ATP
Oxidative Phosphorylation: 26−28ATP26−28ATP
Total: About 30−32ATP30−32ATP
Fermentation and Anaerobic Respiration
Fermentation: A catabolic process that makes a limited amount of ATP from glucose without an electron transport chain and produces a characteristic end product, such as ethyl alcohol or lactic acid.
Occurs when O2O2 is not present.
Glycolysis still produces 2ATP2ATP.
NADHNADH generated during glycolysis is used to reduce pyruvate or its derivatives, regenerating NAD+NAD+ so glycolysis can continue.
Alcohol fermentation: Pyruvate is converted to ethanol (e.g., in yeast).
Pyruvate →→ Acetaldehyde +CO2+CO2
Acetaldehyde +NADH→+NADH→ Ethanol +NAD++NAD+
Lactic acid fermentation: Pyruvate is reduced directly by NADHNADH to form lactate (e.g., in muscle cells during strenuous exercise).
Pyruvate +NADH→+NADH→ Lactate +NAD++NAD+
Anaerobic Respiration: Uses an electron transport chain with a final electron acceptor other than oxygen (e.g., sulfate). Primarily occurs in some prokaryotes.
now can i get chpaters 10-13 from the same
textbook
Chapter 10: Photosynthesis
Photosynthesis: The process that converts light energy into chemical energy, creating sugar and oxygen from carbon dioxide and water.
Overall equation: 6CO2+6H2O+Light Energy→C6H12O6+6O26CO2+6H2O+Light Energy→C6H12O6+6O2
Chloroplasts: Sites of photosynthesis in plant cells. Contain thylakoids (stacked into grana) and stroma.
Two Stages of Photosynthesis:
Light Reactions (photo part)
Occur in the thylakoid membranes.
Convert solar energy to chemical energy (ATP and NADPH).
Water (H2OH2O) is split, releasing O2O2 as a byproduct.
Pigments (e.g., chlorophyll a, chlorophyll b, carotenoids) absorb light energy.
Photosystems: Protein complexes that contain light-harvesting complexes and a reaction-center complex.
Photosystem II (PSII): P680680 (absorbs light best at 680680 nm).
Photosystem I (PSI): P700700 (absorbs light best at 700700 nm).
Linear electron flow (noncyclic):
Electrons are passed from PSII to PSI via an electron transport chain.
Generates ATP (by chemiosmosis, photophosphorylation) and NADPH.
Cyclic electron flow: Electrons cycle back from Fd to the PSI reaction center, producing only ATP.
Calvin Cycle (synthesis part)
Occurs in the stroma.
Uses ATP and NADPH from the light reactions to convert CO2CO2 into sugar (G3P).
Three phases:
Carbon fixation: CO2CO2 is attached to RuBP (ribulose bisphosphate) by the enzyme RuBisCO.
Reduction: ATP and NADPH are used to convert 3-PGA to G3P (glyceraldehyde-3-phosphate).
Regeneration of RuBP: ATP is used to rearrange remaining G3P molecules back into RuBP.
Alternative Mechanisms of Carbon Fixation:
C4 plants: Minimize photorespiration by incorporating CO2CO2 into four-carbon compounds in mesophyll cells, before moving them to bundle-sheath cells where the Calvin cycle occurs (e.g., corn, sugarcane).
CAM plants: Open their stomata at night to take up CO2CO2 and store it as organic acids, then close stomata during the day and release CO2CO2 for the Calvin cycle (e.g., succulents, cacti).
Chapter 11: Cell Communication
Cell communication: The process by which cells detect and respond to signals from their environment.
Types of Signaling:
Local signaling:
Paracrine signaling: Signaling molecules secreted by a cell affect nearby target cells.
Synaptic signaling: Neurotransmitters released by neurons diffuse across a synapse to target cells.
Long-distance signaling:
Endocrine signaling (hormonal signaling): Hormones travel via the circulatory system to target cells far away.
Three Stages of Cell Signaling:
Reception: A signaling molecule (ligand) binds specifically to a receptor protein.
Most receptors are plasma membrane proteins.
Types of receptors:
G protein-coupled receptors (GPCRs): Work with the help of a G protein.
Receptor tyrosine kinases (RTKs): Ligand binding activates the tyrosine kinase domain, which then phosphorylates other proteins.
Ion channel receptors: Ligand binding opens or closes an ion gate.
Intracellular receptors: Found in the cytoplasm or nucleus; bind to ligands that can pass through the plasma membrane (e.g., steroid hormones).
Transduction: A series of steps that converts the signal into a form that can bring about a specific cellular response.
Often involves a phosphorylation cascade, where protein kinases transfer phosphate groups from ATP to proteins.
Second messengers: Small, nonprotein, water-soluble molecules or ions that relay signals (e.g., cyclic AMP (cAMP), calcium ions (Ca2+Ca2+)).
Response: The transduced signal triggers a specific cellular response.
Can involve activation of gene expression (nuclear response) or activity of proteins in the cytoplasm (cytoplasmic response).
Apoptosis (Programmed Cell Death): Cells undergo self-destruction in a controlled manner; essential for development and maintaining healthy tissues.
Chapter 12: The Cell Cycle
The cell cycle: The life of a cell from when it is first formed from a dividing parent cell until its own division into two daughter cells.
Phases of the Cell Cycle:
Interphase (about 9090"% of the cell cycle): Cell growth and copying of chromosomes in preparation for cell division.
G1 phase ("first gap"): Cell grows.
S phase ("synthesis"): DNA replication occurs; chromosomes are duplicated.
G2 phase ("second gap"): Cell grows further and prepares for mitosis.
M phase (Mitotic phase): Includes mitosis and cytokinesis.
Mitosis: Division of the nucleus, resulting in two genetically identical nuclei.
Prophase: Chromatin condenses into visible chromosomes; mitotic spindle begins to form.
Prometaphase: Nuclear envelope fragments; kinetochores (protein structures at the centromere) attach to microtubules.
Metaphase: Chromosomes align at the metaphase plate.
Anaphase: Sister chromatids separate and move to opposite poles of the cell.
Telophase: Daughter nuclei form; nuclear envelopes reform; chromosomes decondense.
Cytokinesis: Division of the cytoplasm.
Animal cells: Formation of a cleavage furrow.
Plant cells: Formation of a cell plate.
Regulation of the Cell Cycle:
Cell cycle control system: A cyclically operating set of molecules in the cell that triggers and coordinates key events.
Checkpoints: Critical control points where stop and go-ahead signals regulate the cycle.
G1 checkpoint: "Restriction point"; if passed, cell usually completes the rest of the cycle. If not, it may enter a G0 phase (nondividing state).
G2 checkpoint: Ensures DNA replication is complete and damage is repaired.
M checkpoint: Ensures all chromosomes are properly attached to the spindle before anaphase.
Cyclins and Cyclin-Dependent Kinases (CDKs): Regulatory proteins.
CDKs are only active when bound to cyclins. Different cyclin-CDK complexes regulate different checkpoints.
MPF (Maturation-Promoting Factor) is a cyclin-CDK complex that triggers a cell's passage from G2 to M phase.
Cancer: Results from a breakdown in cell cycle control, leading to uncontrolled cell division.
Chapter 13: Meiosis and Sexual Life Cycles
Heredity: The transmission of traits from one generation to the next.
Genetics: The scientific study of heredity and variation.
Genes: Units of heredity, segments of DNA.
Locus: A gene's specific location on a chromosome.
Types of Reproduction:
Asexual reproduction: A single individual is the sole parent and passes copies of all its genes to its offspring (e.g., mitosis).
Sexual reproduction: Two parents give rise to offspring that have unique combinations of genes inherited from the two parents.
Sets of Chromosomes:
Somatic cells: All body cells except gametes; diploid (2n2n).
Gametes: Reproductive cells (sperm and egg); haploid (nn).
Homologous chromosomes (homologs): A pair of chromosomes (one from each parent) that are similar in length, gene position, and centromere location.
Autosomes: Non-sex chromosomes.
Sex chromosomes: Determine an individual's sex (e.g., X and Y).
Diploid (2n2n): Two sets of chromosomes (e.g., human somatic cells have 2n=462n=46).
Haploid (nn): One set of chromosomes (e.g., human gametes have n=23n=23).
Meiosis: A type of cell division that reduces the number of sets of chromosomes from two to one in the gametes.
Consists of two consecutive cell divisions: Meiosis I and Meiosis II.
Results in four haploid daughter cells, each genetically distinct from the parent cell and from each other.
Meiosis I (Reductional Division):
Prophase I:
Chromosomes condense.
Synapsis: Homologous chromosomes pair up, forming a tetrad.
Crossing over: Non-sister chromatids exchange DNA segments at chiasmata.
Metaphase I: Homologous pairs (tetrads) align at the metaphase plate.
Anaphase I: Homologous chromosomes separate and move to opposite poles.
Telophase I and Cytokinesis: Two haploid cells form; each chromosome still consists of two sister chromatids.
Meiosis II (Equational Division):
Prophase II: Spindle apparatus forms.
Metaphase II: Sister chromatids align at the metaphase plate.
Anaphase II: Sister chromatids separate and move to opposite poles.
Telophase II and Cytokinesis: Four haploid daughter cells are formed, each with unduplicated chromosomes.
Comparison of Mitosis and Meiosis:
Mitosis: Conserves the number of chromosome sets; produces genetically identical daughter cells.
Meiosis: Reduces the number of chromosome sets from two to one; produces genetically different daughter cells.
Origins of Genetic Variation:
Independent assortment of chromosomes: Random orientation of homologous pairs at metaphase I.
Crossing over: Exchange of genetic material between homologous non-sister chromatids in Prophase I.
Random fertilization: Any sperm can fuse with any egg.
Evolutionary Significance: Genetic variation is the raw material for evolution by natural selection.
Chapter 14: Mendel and the Gene Idea
Genetics: The scientific study of heredity and variation.
Heredity: The transmission of traits from one generation to the next.
Variation: Differences among individuals of a species.
Mendel's Experiments:
Character: A heritable feature that varies among individuals (e.g., flower color).
Trait: Each variant for a character (e.g., purple or white flowers).
True-breeding: Organisms that produce offspring of the same variety over many generations of self-pollination.
Hybridization: Crossing two true-breeding varieties.
P generation: True-breeding parents.
F1 generation: Hybrid offspring of the P generation.
F2 generation: Offspring of the F1 generation self-pollinating or interbreeding.
Mendel's Model of Inheritance:
Alternate versions of genes (alleles) account for variations in inherited characters.
For each character, an organism inherits two alleles, one from each parent.
If the two alleles at a locus differ, then one (dominant allele) determines the organism's appearance, and the other (recessive allele) has no noticeable effect.
Law of Segregation: The two alleles for a heritable character segregate (separate) during gamete formation and end up in different gametes.
Homozygous: An organism with two identical alleles for a character (e.g., or ).
Heterozygous: An organism with two different alleles for a character (e.g., ).
Phenotype: An organism's physical appearance or observable traits (e.g., purple flowers).
Genotype: An organism's genetic makeup (e.g., ).
Testcross: Breeding an organism of unknown genotype with a recessive homozygote to determine the unknown genotype.
Law of Independent Assortment: Each pair of alleles segregates independently of each other pair of alleles during gamete formation.
Probability rules:
Multiplication Rule: The probability that two or more independent events will occur together is the product of their individual probabilities.
Addition Rule: The probability that any one of two or more mutually exclusive events will occur is calculated by adding their individual probabilities.
Beyond Mendelian Inheritance:
Complete dominance: Phenotypes of the heterozygote and dominant homozygote are identical.
Incomplete dominance: Phenotype of F1 hybrids is somewhere between the phenotypes of the two parental varieties (e.g., red and white flowers produce pink).
Codominance: Two dominant alleles affect the phenotype in separate, distinguishable ways (e.g., MN blood group, and alleles for blood type).
Multiple alleles: Most genes exist in more than two allelic forms (e.g., blood groups have alleles).
Pleiogeny: One gene has multiple phenotypic effects (e.g., cystic fibrosis, sickle-cell disease).
Epistasis: A gene at one locus alters the phenotypic expression of a gene at a second locus (e.g., labrador retriever coat color).
Polygenic inheritance: Multiple genes individually affect a single phenotypic character, resulting in a continuous variation (e.g., human skin color, height).
Norm of reaction: The phenotypic range of a genotype influenced by the environment.
Multifactorial characters: Characters influenced by both genetic and environmental factors.
Pedigree analysis: A family tree that describes the interrelationships of parents and children across generations.
Recessively inherited disorders: Cystic fibrosis, sickle-cell disease, Tay-Sachs disease.
Dominantly inherited disorders: Achondroplasia, Huntington's disease.
Chapter 15: The Chromosomal Basis of Inheritance
The Chromosome Theory of Inheritance: Mendelian genes have specific loci (positions) on chromosomes, and chromosomes undergo segregation and independent assortment.
Thomas Hunt Morgan's Experiments:
Working with fruit flies (Drosophila melanogaster), Morgan provided evidence that genes are located on chromosomes.
Wild type: The phenotype most commonly observed in natural populations (e.g., red eyes).
Mutant type: Alternative traits to the wild type (e.g., white eyes).
Morgan discovered that the gene for eye color is located on the X chromosome, demonstrating sex-linked inheritance.
Sex Chromosomes:
Hoff (XY System): Females are XX, males are XY. The Y chromosome is much smaller and carries fewer genes.
Sex-linked genes: Genes located on either sex chromosome (usually on the X chromosome).
Inheritance of X-linked genes:
X-linked recessive disorders are much more common in males than in females (e.g., color blindness, hemophilia, Duchenne muscular dystrophy).
Carrier: A heterozygous female for an X-linked recessive trait, usually phenotypically normal.
Random X-inactivation in female mammals:
Barr body: The inactive X chromosome in each cell of a female condenses into a compact object.
Mosaicism: Females are a mosaic of two types of cells, those with the active X from the father and those with the active X from the mother.
Linked Genes: Genes located on the same chromosome that tend to be inherited together.
Genetic recombination: The production of offspring with combinations of traits that differ from those found in either P generation parent.
Parental types: Offspring with a phenotype matching one of the parental phenotypes.
Recombinant types (recombinants): Offspring with nonparental phenotypes.
Crossing over: The exchange of segments of non-sister chromatids during meiosis I (Prophase I).
Recombination frequency: Percentage of recombinant offspring. Allows for the construction of genetic maps.
Genetic map: An ordered list of the genetic loci along a particular chromosome.
Linkage map: A genetic map based on recombination frequencies.
Map units (centimorgans): Distances between genes on a linkage map, with one map unit equivalent to a 1% recombination frequency.
Chromosomal Alterations:
Nondisjunction: Pairs of homologous chromosomes do not separate normally during meiosis I, or sister chromatids fail to separate during meiosis II.
Aneuploidy: Abnormal number of a particular chromosome.
Monosomy (): Missing one chromosome (e.g., Turner syndrome, XO).
Trisomy (): Having an extra chromosome (e.g., Down syndrome/Trisomy 21).
Polyploidy: More than two complete sets of chromosomes (common in plants, rare in animals).
Alterations of chromosome structure:
Deletion: Removes a chromosomal segment.
Duplication: Repeats a segment.
Inversion: Reverses a segment within a chromosome.
Translocation: Moves a segment from one chromosome to a nonhomologous chromosome.
Genomic imprinting: Phenomenon in which expression of an allele in offspring depends on whether the allele is inherited from the male or female parent.
Organelle genes: Genes located in mitochondria and chloroplasts are inherited maternally only.
Chapter 16: The Molecular Basis of Inheritance
DNA as the Genetic Material:
Frederick Griffith's experiment (1928): Discovered transformation in bacteria (converting harmless bacteria into pathogenic ones).
Oswald Avery, Maclyn McCarty, and Colin MacLeod (1944): Identified DNA as the transforming substance.
Hershey and Chase experiment (1952): Confirmed DNA is the genetic material in bacteriophages (viruses that infect bacteria).
Structure of DNA:
DNA (deoxyribonucleic acid) is a polymer of nucleotides.
Nucleotide: Consists of a nitrogenous base, a deoxyribose sugar, and a phosphate group.
Nitrogenous bases: Adenine (A), Guanine (G), Cytosine (C), Thymine (T).
Chargaff's Rules (1950):
The base composition varies between species.
In any species, the number of A and T bases are equal, and the number of G and C bases are equal.
Rosalind Franklin and Maurice Wilkins: Produced X-ray diffraction images of DNA, suggesting a helical structure.
Watson and Crick (1953): Deduced the double helix model of DNA.
Double helix: Two antiparallel sugar-phosphate backbones, with nitrogenous bases paired in the interior.
Base pairing: A pairs with T (two hydrogen bonds), G pairs with C (three hydrogen bonds).
DNA Replication:
Semiconservative model: Each new DNA molecule consists of one old strand and one newly synthesized strand.
Origin of replication: Where DNA replication begins.
Replication fork: A Y-shaped region where the parental DNA strands are being unwound.
Helicase: Enzyme that unwinds the DNA double helix at the replication forks.
Single-strand binding proteins: Bind to and stabilize single-stranded DNA.
Topoisomerase: Relieves strain ahead of the replication fork caused by unwinding.
DNA polymerase: Enzymes that synthesize new DNA strands by adding nucleotides to a pre-existing strand or RNA primer.
DNA polymerase III (in E. coli): Adds nucleotides to a new DNA strand.
DNA polymerase I (in E. coli): Replaces RNA primers with DNA.
Primer: A short RNA segment that provides a starting point for DNA polymerase.
Primase: Synthesizes the RNA primer.
Leading strand: Synthesized continuously in the direction toward the replication fork.
Lagging strand: Synthesized discontinuously in the direction away from the replication fork, forming Okazaki fragments.
Okazaki fragments: Short segments of DNA synthesized on the lagging strand.
DNA ligase: Joins the Okazaki fragments together.
Proofreading and Repair:
DNA polymerases proofread newly made DNA, replacing incorrect nucleotides.
Mismatch repair: Other enzymes correct errors that DNA polymerase missed.
Nucleotide excision repair: Nuclease cuts out and replaces damaged stretches of DNA.
Telomeres: Eukaryotic chromosomal DNA molecules have special nucleotide sequences at their ends.
Telomeres postpone the erosion of genes near the ends of DNA molecules.
Telomerase: Enzyme that catalyzes the lengthening of telomeres in germ cells and cancer cells.
Chromatin structure:
Chromatin: DNA combined with proteins.
Histones: Proteins around which DNA is wound, forming nucleosomes.
Nucleosome: DNA wrapped around a core of histones.
Euchromatin: Loosely packed chromatin, generally available for transcription.
Heterochromatin: Densely packed chromatin, typically not transcribed.
Chapter 17: From Gene to Protein
The Flow of Genetic Information:
Central Dogma: DNA RNA Protein.
Transcription: The synthesis of RNA using a DNA template.
Translation: The synthesis of a polypeptide using mRNA as a template.
Ribosomes: Sites of translation.
Genetic Code:
Triplet code: A series of three-nucleotide sequences (codons) in mRNA that specify amino acids.
Codon:
codons, for amino acids, stop codons.
Start codon: (methionine).
Genetic code is redundant (more than one codon per amino acid) but not ambiguous (no codon specifies more than one amino acid).
Genetic code is nearly universal across all life forms.
Transcription (Synthesis of RNA):
RNA polymerase: Enzyme that synthesizes RNA by unwinding DNA and adding RNA nucleotides.
No primer needed.
Prokaryotes: RNA polymerase directly binds to promoter.
Eukaryotes: Transcription factors mediate the binding of RNA polymerase to the promoter.
Stages of transcription:
Initiation: RNA polymerase binds to the promoter (DNA sequence that signals start of transcription).
Elongation: RNA polymerase moves along the DNA, unwinding the double helix and adding RNA nucleotides complementary to the DNA template strand.
Termination: RNA polymerase reaches a terminator sequence, and the RNA transcript is released.
RNA Processing (in eukaryotes only):
Pre-mRNA (primary transcript) is modified before leaving the nucleus.
5' Cap: A modified guanine nucleotide added to the 5' end.
Poly-A tail: adenine nucleotides added to the 3' end.
Functions of 5' cap and poly-A tail:
Facilitate export of mRNA from the nucleus.
Protect mRNA from hydrolytic enzymes.
Help ribosomes attach to the 5' end.
RNA splicing: Removal of introns and joining of exons.
Introns: Noncoding regions (intervening sequences).
Exons: Coding regions that are eventually expressed.
Spliceosomes: Complexes of proteins and small RNAs that carry out splicing.
Ribozymes: RNA molecules that function as enzymes (catalyze their own splicing).
Alternative splicing: A single gene can code for multiple proteins depending on which segments are treated as exons.
Translation (Synthesis of Polypeptide):
tRNA (transfer RNA): Carries specific amino acids to the ribosome.
Anticodon: Three-nucleotide sequence on tRNA that base-pairs with a complementary mRNA codon.
Aminoacyl-tRNA synthetase: Enzyme that correctly matches tRNA to its amino acid.
Ribosomes: Composed of rRNA and proteins.
Binding sites:
P site (peptidyl-tRNA binding site): Holds the tRNA carrying the growing polypeptide chain.
A site (aminoacyl-tRNA binding site): Holds the tRNA carrying the next amino acid to be added.
E site (exit site): Where discharged tRNAs leave the ribosome.
Stages of translation:
Initiation: mRNA, a tRNA with the first amino acid (methionine), and the ribosomal subunits assemble.
Elongation: Amino acids are added one by one to the preceding amino acid in a three-step cycle:
Codon recognition: Incoming aminoacyl-tRNA binds to A site.
Peptide bond formation: rRNA forms peptide bond between amino acid in A site and growing polypeptide in P site.
Translocation: Ribosome moves tRNA from A site to P site, and tRNA from P site to E site.
Termination: A stop codon reaches the A site, a release factor binds, leading to hydrolysis of the polypeptide from the tRNA in the P site, and ribosomal subunits dissociate.
Protein folding: Polypeptides fold into specific 3D shapes, often with the help of chaperonins.
Targeting polypeptides to specific locations: Signal peptides target proteins to the ER or other organelles.
Mutations:
Point mutations: Changes in a single nucleotide pair of a gene.
Substitutions: Replacement of one nucleotide with another.
Silent mutation: No effect on the amino acid sequence (due to redundancy of the genetic code).
Missense mutation: Codes for a different amino acid.
Nonsense mutation: Changes an amino acid codon into a stop codon, resulting in a prematurely terminated protein.
Insertions and deletions: Additions or losses of nucleotide pairs.
Frameshift mutation: Alters the reading frame of the genetic message, usually leading to a nonfunctional protein if not in multiples of three.
Mutagens: Physical or chemical agents that can cause mutations.
Chapter 18: Regulation of Gene Expression
Regulation in Bacteria (Operons):
Operon: A unit of genetic function found in bacteria and phages, consisting of a promoter, an operator, and a cluster of genes whose products function in a common pathway.
Operator: A segment of DNA within the promoter or between the promoter and the enzyme-coding genes that controls the access of RNA polymerase to the genes.
Repressor: A protein that binds to an operator and blocks RNA polymerase access to the genes.
Corepressor: A molecule that cooperates with a repressor protein to switch an operon off.
Inducer: A molecule that inactivates the repressor to turn on transcription.
Trp operon (
repressible operon
): Regulates the synthesis of tryptophan.
Normally on; can be turned off (repressed) when tryptophan (corepressor) is present, binding to the repressor and activating it.
Lac operon (
inducible operon
): Regulates the metabolism of lactose.
Normally off; can be turned on (induced) when lactose (inducer) is present, binding to the repressor and inactivating it.
Positive gene regulation:
Cyclic AMP (cAMP) and cAMP receptor protein (CRP, also called CAP):
When glucose levels are low, cAMP accumulates and binds to CRP.
Activated CRP-cAMP complex binds upstream of the lac operon promoter, increasing the affinity of RNA polymerase for the promoter, thus speeding up transcription (positive control).
Eukaryotic Gene Expression Regulation:
Differential gene expression: The expression of different sets of genes by cells with the same genome.
Chromosome structure:
Histone acetylation: Acetyl groups are added to histone tails, loosening chromatin structure and promoting transcription.
DNA methylation: Methyl groups are added to DNA bases, usually cytosine, often preventing gene expression.
Epigenetic inheritance: Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence.
Transcription initiation:
Control elements: Noncoding DNA segments that serve as binding sites for transcription factors.
Proximal control elements: Located close to the promoter.
Enhancers: Distal control elements, usually located far from a gene or even in an intron.
Transcription factors: Proteins that mediate the binding of RNA polymerase and initiation of transcription.
General transcription factors: Required for the transcription of all protein-coding genes.
Specific transcription factors: High-level transcription of particular genes.
Activators: Bind to enhancers and stimulate transcription.
Repressors: Bind to control elements or activators to inhibit transcription.
Coordinately controlled genes:
Associated with the same activator or repressor (same control elements).
RNA Processing:
Alternative RNA splicing: Different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and introns.
Translation and Protein Processing:
Regulation of mRNA degradation: The lifespan of mRNA molecules in the cytoplasm determines how much protein can be produced.
Initiation of translation: Regulatory proteins can bind to the 5' UTR of mRNA, preventing translation.
Protein processing and degradation: Polypeptides undergo modifications (cleavage, chemical modifications) to become functional.
Ubiquitin: Small protein tag added to proteins targeted for degradation.
Proteasomes: Protein complexes that recognize ubiquitin-tagged proteins and degrade them.
Noncoding RNAs: Play crucial roles in gene expression regulation.
miRNAs (microRNAs): Small, single-stranded RNA molecules that bind to complementary mRNA sequences and either block translation or degrade the mRNA.
siRNAs (small interfering RNAs): Similar to miRNAs, involved in RNA interference (RNAi), often leading to chromatin remodeling or mRNA degradation.
Cellular Differentiation:
Cell differentiation: The process by which cells become specialized in structure and function.
Morphogenesis: The development of the form of an organism and its structures.
Cytoplasmic determinants: Maternal substances in the egg that influence early development.
Induction: Signal molecules from embryonic cells cause transcriptional changes in nearby target cells.
Homeotic genes: Master regulatory genes that control pattern formation in the late embryo, larva, and adult (e.g., Drosophila development).
Cancer:
Oncogenes: Cancer-causing genes.
Proto-oncogenes: Normal versions of genes that promote cell growth and division; when mutated, they can become oncogenes