AP Bio Notes PDF

Unit 1: Chemistry of Life Chapter 1 Big Idea 1 - Evolution Characteristics of Life 1. Living things are organized - Made of cells 2. They acquire materials and energy 3. They maintain homeostasis 4. They respond to stimuli 5. They reproduce 6. They grow and develop...

Unit 1: Chemistry of Life Chapter 1 Big Idea 1 - Evolution Characteristics of Life 1. Living things are organized - Made of cells 2. They acquire materials and energy 3. They maintain homeostasis 4. They respond to stimuli 5. They reproduce 6. They grow and develop 7. They adapt 8. They die LUCA - Last Universal Common Ancestor - All organisms share same basic characteristics - Organized similarly - Genes composed of DNA - Same metabolic reactions to acquire energy and maintain organization - Evolution = Common descent with modification - Natural selection = Environment selects which traits go on because organisms with this traits reproduce - Selection agents = Temperature, pH, salinity, predators, illness, altitude, competition - Adaptations = Modifications that make organisms able to function better in a certain environment Big Idea 2 - Energy and Molecular Building Blocks - Energy = Capacity to do work - Metabolism = All chemical reactions that occur in a cell - Chemical cycling = Chemicals move through living organisms and are broken back down to inorganic molecules - Energy flow = Energy, starting from the sun, flows through organisms and dissipates as heat - Homeostasis = Biological balance / Maintaining a constant internal environment despite fluctuations in external environment Big Idea 3 - Info Storage, Transmission, and Response - Reproduce = Make more organisms + Pass info to next gen - Development = Become an adult + Use the info  - Genes = Genetic instructions (DNA) - Mutations = Inheritable changes in genetic info + Source of variation - Behavior = Coordinated responses to environmental stimuli Big Idea 4 - Interdependent Relationships Levels of Organization (Small to Big) - Atom - Molecule - (*Organelle) Cell - Tissue - Organ - Organ system - Organism - Population - Community - Ecosystem - Biosphere - Emergent properties = Each higher level of organization acquires new properties - Cooperation and competition (EXAMPLES BELOW) - Chemical reactions in a cell - Community structure in a forest - Circulatory system helps respiratory system and vice versa Science Practices 1. Models 2. Mathematics 3. Question scientifically 4. Collect diet responsibly 5. Analyze and evaluate collected data 6. Justify conclusions and theories with evidence to support a claim 7. Expand understandings and connections (THE FOUR BIG IDEAS) Scientific Method 1. Ask a question - Research your question = Get background information 2. Form a hypothesis (testable statement about the relationship between the independent / tested variable and dependent / data collection variable a. NULL = No relationship between 3. Predictions and experiment a. Deductive reasoning = If/then logic to make a prediction b. Independent / tested variable c. Responding / dependent variable = Data  d. Control = Not exposed to variable - Collect data 4. Analysis a. Stats b. Significance c. Scientific publications - Conclusion 5. Scientific theory = Join together related hypotheses that are well-supported by many observations, experiments, data, etc. Chi-Square Test - Used to accept or reject a null hypothesis 2 (𝑂𝑏𝑠𝑒𝑟𝑣𝑒𝑑 − 𝐸𝑥𝑝𝑒𝑐𝑡𝑒𝑑) - 𝑆𝑢𝑚 𝑜𝑓 𝐸𝑥𝑝𝑒𝑐𝑡𝑒𝑑 - Large number = Reject hypothesis - Degrees of Freedom = # of outcomes - 1 Chapter 2 Chemical Elements Atoms - Atomic structure = Smallest part of an element + Displays properties of element - Atomic number = Number of protons in a neutral atom + # of protons same as # of electrons - Atomic mass = Number of protons and neutrons in nucleus - Isotopes = Atoms of the same element with different numbers of neutrons - Electrons per ring = 2, 8, (OCTET RULE), 18, 32 - Change number of valence electrons = Chemical reaction Periodic Table - Groups = Vertical columns arranged by number of valence elections (same # of valence electrons = Similar chemical properties!) - Periods = Horizontal rows and equal to the electron energy level (number of rings) - Periodicity = Trends in the periodic table Electrons and Energy - Key / Focus = Number of electrons and the outermost energy level - When electrons absorb energy, they are boosted to higher energy levels - Electrons want to be comfortable / At lowest energy level - Release energy / Calm down = Doing work (Kinetic energy) Molecules and Compounds Ionic Bonding - Molecules bond for stability - Form an ion (Atom[s] with positive or electric charge due to losing or gaining electrons) - Have attraction between oppositely charged ions Covalent Bonding - SHARING electrons for stability - Nonpolar = Sharing equally - Polar = Unequal sharing – Electrons pulled to one element (stronger electronegativity) than another - Electronegativity = Atom’s ability to attract / pull - Three-dimensional shape - CRITICAL TO ITS FUNCTION? - Protein’s shape in enzymes determines functionality - Diatomic molecules = Element able to bond with itself to get stability - 3 important inorganic molecules 1. Oxygen 2. Carbon dioxide 3. Water Hydrogen Bonding - Weak attractive force between two differently charged molecules (POSITIVE H and NEGATIVE O) or two different polar molecules - Strong together - Found in DNA, protein structure, and bodies of water Chemistry of Water - Living things are made of 70-90% water - Water is liquid between 0-100 degrees Celsius Property Bio Benefits 1. High heat capacity = Hydrogen - Protect organisms from rapid temp bonds hold lots of energy changes - Help maintain homeostasis (Sweating so sweat absorbs heat instead) 2. High heat vaporization = Polar - Moderate Earth’s surface temperature covalent H bonds hold water as a - Permits living things to exist liquid = Need a lot of energy to - Oceans and rain ? evaporate 3. Solvent = Can have dissolved - Water can arrange itself around polar / substances (solute) in it + Hydrophilic charged molecules (Has both  and hydrophobic molecules act negative / O and positive / H charges!) differently - Blood plasma is mostly water 4. Cohesive and adhesive = Bond with - Allow water to move up through trees itself and other polar surfaces (TATC THEORY = Transpiration, a. Cohesion = Water to water Adhesion, Tension, Cohesion) b. Adhesion = Water to something else 5. High surface tension - Water striders 6. Frozen water is less dense than - Ice acts as insulation to protect life in liquid water = Hydrogen bonds body of water below expand to equal / uniform distance when water freezes (Arranged less densely to liquid water) Acids and Bases - Acid = Put in water and releases hydrogen (H) ions - Base = Put in water and releases hydroxide (OH) ions - pH scale = Measure amount of hydrogen ions - Low pH = High hydrogen ions - Each change = 10x concentration - Buffers = Chemical or combo of chems that keep pH within normal limits by taking up excess ions - Bio benefit = Regulate blood pH Chapter 3 Organic Molecules Carbon - # of bonds = 4 - Hydrocarbons = Chains of carbon atoms bonded exclusively to hydrogen atom - Can form branched and ringed compounds with single, double, and triple bonds - Good for fuel (WHY? Bonds = Energy) - Functional group = Cluster of specific atoms bonded to carbon skeleton with characteristic properties - Group Structure Compound Significance Hydroxyl R-OH Alcohol as in ethanol Polar Hydrogen bonds Present in sugars and some amino acids Carboxyl (acidic) O Carboxylic acid as in Polar // acetic acid Acidic R-C Present in \ fatty acid and OH amino acid Amino H Amine as in Polar / tryptophan Basic R-N Hydrogen \ bonds H Present in amino acids Sulfhydryl R-SH Thiol as in Disulfide ethanethiol bonds Present in some amino acids Phosphate O Organic phosphate Polar || as in phosphorylated Acidic R-O-P-OH molecules Present in | nucleotides OH and phospholipids Carbonyl O Aldehyde as in Polar // formaldehyde Present in R-C sugars \ H O Ketone as in acetone || R-C-R - Isomer = Molecules of identical formulas with different arrangements of atoms in space which result in different biological activities Macromolecules - Built with monomers via dehydration / condensation synthesis (Remove one water collectively from monomers + NEEDS an enzyme) - Break down bonds via hydrolysis (Add in water / Opposite of dehydration synthesis + NEEDS an enzyme) - Enzyme = Molecules (proteins) that bring reactants together to speed up chemical reactions - Enzyme participates in reaction but remains unchanged Carbohydrates / Sugars Monosaccharides - Quick energy - Most contain 6 carbons (Glucose, galactose, fructose) Disaccharides - Quick energy 1. Lactose (Milk sugar) = Glucose + Galactose 2. Maltose (Form during starch digestion) = Glucose + Glucose 3. Sucrose (Table sugar) = Glucose + Fructose Polysaccharides - Too large to pass through cell membranes - Not soluble in water - Function #1: Energy storage - Starch in plants - Glycogen in animals - Function #2: Structural molecules - Not digestible for humans - Cellulose in plant cell walls = Most abundant molecule on Earth - Chitin in exoskeletons and fungal cell walls Lipids / Fats and Steroids Triglycerides - Glycerol = Three carbons - Fatty acid chains = 16-18 carbons in a chian Saturated Unsaturated NO double bonds YES double bonds Straight Kinks SOLID at room temperature LIQUID at room temperature Animals Plants Phospholipids - Third fatty acid chain (hydrophobic) replaced with charged phosphate group (hydrophilic) - Main component of cell membranes - Modified lipid Steroids - 4 fused rings of carbon - Cholesterol in animal cell membranes and precursor to steroid hormones Waxes - Long chain alcohol + Long chain fatty acid - High melting point - Water proof  - Resist degradation - Examples in plants = Protective covering that slows water loss - Examples in animals = Maintain skin / fur, trap dust / first, and form honeycombs Proteins Functions in the Body - Enzymes - Muscles - Hormones - Antibodies - Hemoglobin - Carriers / channels Amino Acid (monomer) Structure - Central (alpha) carbon - Amino Group / Amino-terminus / N-terminus - Carboxyl Group / Carboxyl-terminus / C-terminus - New amino acids of polypeptide ALWAYS added here via dehydration synthesis - Bond between amino acids = Peptide bond - Hydrogen atom - R-group - 20 different groups - Determine identity of amino acid - Determine chemical properties (Acidic, basic, polar, nonpolar) Peptides - Covalent bond between two amino acids (Amino group and carboxyl group_ - Directionality = Amino acids have two ends that are chemically distinct from each other - New amino acids ALWAYS added to C-terminus end - Polypeptide = Chain of amino acids Shape - Primary structure = Sequence of amino acids - Interactions between R groups - Secondary structure = Alpha helix or Beta pleated sheet - Interaction between amino acid and carboxyl group (Attraction of opposite charges) - NOT dependent on R groups - Tertiary structure = Folding pattern imposed on secondary - Ultimately dependent on primary (Interactions between R groups) - Quaternary structure = More than one chain - Disulfide bond = Proteins with a sulfur R group tend to bond with each other to achieve the lowest level of energy  - Protein domain = Distinct functional and / or structural parts / units in a protein + Responsible for a particular function or interaction - Activation - DNA Binding Folding - Chaperone proteins = Help fold proteins into correct shape when built - Denaturation = Proteins exposed to extreme heat and PH and have irreversible change - Prion = Misfolded protein and therefore cause certain diseases Nucleic Acids / Nucleotides General - Nucleotide = Monomer - Nucleic acid = Polymer - DNA = Store genetic code - RNA = Translate genetic code of DNA into amino acid sequence using mRNA, tRNA, and rRNA - Directionality = 3’ vs 5’ - New nucleotides ALWAYS added to 3’ end of chain - Nucleic acids are ALWAYS ANTIPARALLEL (One chain 3’ to 5’ and the other 5’ to 3’) Components 1. Nitrogen base - Purine = Two rings - Adenine - Guanine - Pyrimidines - Thymine - ONLY IN DNA - Uracil - ONLY IN RNA - Cytasine 2. Sugar - Pentose = Deoxyribose - Ribose 3. Phosphate DNA RNA Sugar: deoxyribose ribose Bases: Adenine Instead of thymine, there is uracil  Thymine Guanine Cytosine Chains: 2 chains held together by hydrogen Single stranded bonds Complementary Base Pairing - Two nucleic acids strands held together via hydrogen bonds between a purine (TWO CARBON RINGS – A and G) and a pyrimidine (T and C) - Adenine and Thymine = 2 hydrogen bonds - Guanine and Cytosine = 3 hydrogen bonds ATP 1. Adenosine = Ribose + Adenine 2. Triphosphate = Three phosphate groups - Function = High energy molecule (Last two phosphate bonds release lots of energy when broken) - Used for synthetic reactions, muscle contraction, and transmission of nerve impulses Unit 2: Cell Structure and Function Chapter 4 Cellular Level of Organization Cell Theory 1. Living things are organized – Made of cells 2. Cells are the basic [ structural and functional ] unit of organisms 3. Cells come from ONLY preexisting cells Cell Size - The plasma membranes of cells NEED a large surface area - Exchange materials - Eliminate waste products - Acquire or dissipate thermal energy - Smaller cells have a larger surface area-to-volume ratio - Increase surface area = Increase ratio + Diffusion / Exchange - More surface area = Most efficient - Decrease surface area = Decrease ratio + Diffusion / Exchange - Prokaryotic = 1-10 um - Eukaryotic = 10-100 um - Surface area and volume REQUIRES cells to be SMALL  - Modification to increase surface area - Microvilli = Fold out - Mesosomes = Fold in - Examples in mammals: Elephants vs. Whales - Cells compensate for larger size with compartmentalizing Nutritional Modes CO2 or Related Compounds Organic Compounds Light ✩ Photoautotroph Photoheterotroph Chemical Compounds Chemoautotroph ✩ Chemoheterotroph (i.e. humans) Prokaryotic Cells The Gist 1. Lack a nucleus 2. Smaller and simpler than eukaryotic 3. Two domains = Bacteria and Archaea Outside - Plasma membrane = Decides what goes in or out - Cell wall made of peptidoglycan + Maintain cell shape + Structural and permeability for essential molecules (i.e. gasses) - Glycocalyx = Layer of polysaccharides (Carbohydrates) - Flagella / Flagellum = Whip-like tail for movement - Fimbriae = Small bristle-like structures for bacteria attach to surfaces - Sex pili = Tubes to pass DNA from cell to cell - Bacteria can have multiple - Bacteria tend to use when desperate to survive Inside / Cytoplasm - Nucleoid = Single chromosome - Plasmids = Small accessory / extra rings of DNA - Ribosomes = Workbench for protein synthesis - Cytosol contains water, inorganic / organic molecules, and enzymes Cyanobacteria - “Poster child” - Functions: Photosynthesis + Nitrogen fixation Domains 1. Bacteria = Everywhere  2. Archaea = Extremophiles 3. Eukarya / Eukaryotes - Fungi - Animalia - Plantae - Protista Archaea - Cell wall made of polysaccharides (Carbohydrates) - Cell membranes made with hydrocarbons instead of fatty acids = Different from bacteria - DNA and RNA structure more similar to eukaryotes - Found in extreme conditions Eukaryotic cell has membrane enclosed nucleus Thery it folded in to create a double fond to protect DNA Large prokaryotic engulf another prokaryotic cell Eukaryotic Cells The Gist - Members of domain Eukarya - Have membrane bound organelles - Larger = Less surface area to volume - Compartmentalized = Organelles perform certain functions - Plants have cell walls made of cellulose Evolution: Endosymbiosis Theory / Hypothesis - Smaller prokaryotic went to live in another - Form symbiotic relationship - Nuclear envelope evolved to protect important DNA - Ribosomes same size as prokaryotic = More proof - Ancestral mitochondria and chloroplasts were once free living prokaryotes - Same size as free living aerobic and photosynthetic bacteria - Have their own DNA (circular and not packaged on histones) - Self replicate with binary fission - Have two membranes (outer like eukaryotes and inner like prokaryotes) - Membrane organelles resulted from infolding of cell membrane Structure/Biochemistry - Nucleus communicates with ribosomes in cytoplasm - Organelles of endomembrane system communicate with each other - Energy-related organelles contain their own DNA and are self sufficient  - Cytoskeletal lattice of protein fibers that maintain shape of cell and assist in organelle movement Nucleus and Ribosomes Nucleus - Chromatin = Threadlike material that forms into chromosomes for cell division - DNA, proteins, and some RNA - Nucleolus = Form ribosomes - Nuclear envelope = Contain nuclear pore to permit passage of substances in and out of the nucleus Ribosomes - Site of protein synthesis - Free ribosomes synthesize proteins that are used within the cell - Peroxisomes = Small membrane-enclosed organelles that contain enzymes involved in metabolic reactions - Bound ribosomes attached to ER make proteins destined for export - Form two subunits = Large and small - Comprised of rRNA and protein - Ribosomes found in all forms of life = Common ancestry of all life (Evidence of Evolution) Endomembrane System - Series of intracellular membranes that compartmentalize the cell Endoplasmic Reticulum - System of membrane channels connected with nuclear envelope - Inside = Cisternal space - Provide mechanical support - Carry out protein synthesis on membrane-bound ribosomes - Intracellular transport - Rough ER = Contain ribosomes for protein synthesis + Proteins enter for packaging to be sent to Golgi - Smooth ER = Continuous with rough ER + Form lipids and metabolism of carbohydrates + Detoxify drugs and poisons Golgi Apparatus - Postal system - Has polarity - Receive protein / lipid vesicles from ER (cis side) - Do correct folding and chemical modification of newly synthesized proteins and packaging for protein trafficking - Active in synthesis, modification, sorting, and secretion of cell products (trans side) Lysosomes - Digestive (intracellular) organelle where macromolecules are hydrolyzed (broken apart) - Recycling of cell’s organic material - Apoptosis = Programmed cell death / suicide - Examples = WBC, bateria, and autodigestion of parts of cells - Not found in plant cells - Vacuoles - Large membranous sacs 1. Contractile vacuoles in protists = Water regulation 2. Digestive vacuoles 3. Storage vacuoles 4. Central vacuoles in plants - Maintain turgor - Contained within tonoplast (membrane) - Can make up 80% of a plant cell Energy-Related Organelles The Gist - Double membrane - Contain their own DNA as a ring shape (like prokaryotes) + Their own ribosomes - Self replicating Chloroplasts - Double outer membrane - Site of photosynthesis - Found in photosynthetic algae and plants - Grana and stroma = Stacks of thylakoids in chloroplast - Grana = Light dependent reactions of photosynthesis - Stroma = Carbon fixation (Calvin-Benson cycle) reactions of photosynthesis - Membranes and thylakoids contain chlorophyll pigments and electron transport proteins that comprise photosynthesis Mitochondria - Site of cellular respiration - Generate most of the cell’s ATP - Matrix = Inner compartment where Kreb’s cycle (citric acid cycle) reactions happen - Folded inner membrane and cristae = Increase surface area for electron transport and ATP synthesis for cellular respiration - Smaller and more varied shape compared to chloroplasts - Over 40 different diseases that can affect mitochondria Cytoskeleton - Network of connected filaments and tubules that extends from nucleus to plasma membrane Microfilaments / Actin - Function = Dense web of structural support under cell membrane or dynamic movement - Form tracts for chloroplasts to stream along - Interact with moto molecules (myosin) for muscle contraction Intermediate Filaments - Dynamic support - Important in maintaining shape of cell + Fix position of certain organelles Microtubules - Small hollow cylinders made from protein tubulin - Cellular railway - Form cilia / flagella - Separate chromosomes in cell division - Formed from MTOC (microtubule-organizing center / centrosome) near the nucleus Centrioles - Short cylinders (9 +0) = Nine triplet sets of microtubules - Perpendicular pairs in centrosomes of animal cells and most protists - Not in plant and fungal cells (Only have centrosome) - Basal bodies - Same structure as centrioles - May have originated from centrioles (EVO) - Anchor cilia and flagella Cilia / Flagella - Hairlike projections with a 9 + 2 arrangements of microtubules (9 doublets around 2 singles) - Cilia = Shorter + Movement of organisms or fluids - Flagella = Longer + Propel some organisms, sperm of animals, algae, and some plants Chapter 5 Plasma Membrane Structure and Function Membrane Components - Phospholipids = Molecules that are amphipathic (have both hydrophilic and hydrophobic regions - Hydrophilic heads point out towards aqueous medium or to interior of cell  - Hydrophobic tails point inward towards interior of cell membrane - Cholesterol (ONLY animal cells) = Fill in gaps of phospholipid bilayer + Modify fluidity of membrane over range of temperatures - Too hot = Keep membrane from being too fluid and breaking - Too cold = Keep membrane from freezing - Protein = What makes membranes different and determines their functions - Integral = Completely embedded and span cell membrane (i.e. channel / carrier) - Peripheral = One side of membrane (i.e. G protein) - Transport - Recognition - Enzymatic - Communication - Connections - Extracellular Matrix / ECM (ONLY animal cells) - Contain protein fibers and glycocalyx - Function = Support and communication - May anchor some proteins - Membrane is asymmetrical - Inside / Cytoskeleton may anchor some proteins - Outside = ECM - Emergent Properties = Whole is greater than sum of parts - Cell membrane responsible for dynamic homeostasis between external and internal environment of cells Fluid-Mosaic Model - Membrane components interact and are flexible - Fluid = Phospholipid bilayer which has consistency of olive oil - Mosaic = Scattered proteins Glycoproteins and Glycolipids - Unique to each cell = “Fingerprint” / I.D. - Glycoprotein = Carbohydrate side-chain attached to protein >>> Reception of signaling molecules - Glycolipid = Carbohydrate side-chain attached to lipid >>> Adhesion and recognition Glycoprotein Glycolipid Protein with carbohydrate group attached to Lipids with carbohydrate attached by polypeptide chain (protein) glycosidic / covalent bond In cell membrane and blood In cell membrane (mainly)  More diverse Less diverse Receptors for chemical signals Facilitate cellular recognition Functions of the Proteins - Channel protein = Allow particular molecule to cross freely - Cystic fibrosis = Inherited disorder that clogs airways, pancreas, and liver ducts with mucus due to faulty Cl / chloride channel - Carrier protein = Selectively interact with a specific molecule (temporarily bond) so it CAN cross membrane - In ability to use sodium-potassium (Na-K) pump / carrier = Possible cause of obesity - Cell recognition protein = Glycoproteins part of MHC (major histocompatibility complex) that help cells recognize outside / nonself cells - Rejection of organ donations in body - Receptor protein = Shaped so specific molecule (i.e. hormone) can bind - Wrong shape = Unable to receive growth hormones = Some forms of dwarfism - Enzymatic protein = Carry out specific metabolic functions - Cholera = Bacterial disease that releases a toxin preventing the enzymatic protein – adenylate cyclase – from metabolizing ATP - Junction protein = Join cells to work / perform a function together as a tissue Permeability of the Plasma Membrane - Only certain molecules can pass through - What passes through phospholipid bilayer = Water, gasses, small non-charged usually non-polar molecules, and hydrocarbons - What needs help to pass (channel or carrier) = Large or charged molecules - Passive transport = Does not need energy + Lower concentration gradient - Diffusion and facilitated diffusion using channel or carrier proteins using thermal or random motion energy intrinsic to the molecule - Aquaporins = Channel protein for water molecules for faster transport than straight through phospholipids - Active transport = Need energy, against concentration gradient - Pump = Carrier that requires ATP - Endo and exocytosis Cell Communication - Cells need to respond to signal to coordinate cellular activities, metabolize, and improve response to changing environment (maintain homeostasis) 1. Chemical messenger = Dial out on phone / Send a call / signal 2. Receptor protein = Different combinations in different cells - Like the receiver after the call bounces off a satellite  3. Signal-transduction pathway = Series of events / relay proteins triggered by receptor 4. Response = Proteins trigger cellular response - Activate enzyme - Trigger gene expression - Alter metabolism - Shape or movement - AND MORE Passive (no energy) Transport Across a Membrane Intro - Diffusion = High concentration to lower concentration (Distribution) - Solution = Solute (solid) + Solvent (liquid) - Diffusion affected by temperature, pressure, electrical current, and molecular size Osmosis - Diffusion of water (or other solvent) across a semipermeable membrane - Osmoregulation = Maintain water balance and allow organisms to control internal solute composition / water potential - Osmotic pressure = Tendency of water to move across membrane - Higher osmotic pressure = More solutes and water will flow into solution Solution Solute Solven Water flow Examples/Terms around t cell Water must into cell - Cytolysis - animal cells, burst as water enters (In flow from cell hemolysis, a RBC bursts) the becomes Turgor Pressure - plant cell wall pushes back again HYPOtonic larger pressure of water entering - prevents bursting Hypertonic out of cell - Crenation - animal red blood cell shrinks (hyper = cell Plasmolysis - plant cell membrane pulls away from wall more) becomes because vacuole becoming smaller smaller (i.e. wilting) Isotonic Osmotic No net Requires a 0.9% NaCl solution to be isotonic to a red pressure is equal change blood cell on both sides of the membrane Facilitated Transport - Carrier protein used for specific substance to transport - Protein may undergo conformational change during transport Active (energy) Transport Across a Membrane Active Transport - Molecules move against concentration gradient - Need carrier proteins (pumps) and ATP - Na+/K+ ATPase (sodium-potassium pump) = Use ATP to pump 3 sodium molecules OUT + Pump 2 potassium ions IN - Set up electro-chemical gradient = Membrane becomes polarized + All neurons / nerve cells need this to function Bulk Transport - Exocytosis / OUT = Vesicle formed by golgi fuses with plasma membrane to secrete substances (i.e. hormones, neurotransmitters, and enzymes) - Endocytosis / IN - Phagocytosis / “Cellular Eating” = Large molecules engulfed - White blood cell engulfing a pathogen - Pinocytosis / “Cellular Drinking” = Vesicles formed around fluids - Plant root cells and capillaries - Receptor-mediated endocytosis = Form of pinocytosis where specific macromolecules bind to receptors - Selective and more efficient than pinocytosis - Move substances like maternal to fetal blood Modification of Cell Surfaces *Animals 1. Extracellular matrix (ECM) outside of cells - Matrix of proteins and polysaccharides - Examples of support = Collagen and elastin - Examples of communication = Fibronectin (external protein) binds to integrin (membrane protein) which binds to actin (internal cytoskeleton) in order to influence shape of cell, etc. - Examples of control = Proteoglycans influence what substances can move through EMC to bind receptors on cell membranes - Variability affects structure (solid like bone or flexible like cartilage) 2. Junction between cells - Adhesion junction = Attach adjacent cells with plaques and sharing of cytoskeletons = Sturdy and flexible - Connect skin cells - Tight junction = Adjacent plasma membranes stitched together by shared proteins - Connect cells of intestine - Gap junction = Share channels between adjacent cells for communication and strength - Permit ion flow to contract as a unit for heart muscles Plant Cell Walls - Porous - Vary in thickness depending on function 1. Primary wall - Formed first - Contain cellulose - Pectins for flexibility - Polysaccharides later harden mature cells 2. Secondary wall - Form TO interior of primary wall in woody plants - More cellulose and lignin - Plasmodesmata = Narrow membrane-lined channels that pass through cell walls of neighboring cells and connect their cytoplasm Unit 3: Cellular Energetics Chapter 6 Cells and the Flow of Energy Energy - The ability to do work or bring about change - All energy is ultimately dependent on the sun - Kinetic energy = Anything moving - Potential energy = Stored - Chemical energy = Form of potential energy stored in a molecule’s chemical bonds Laws of Thermodynamics - The study of energy transformations that occur in matter 1. The Law of Conservation of Energy: Energy cannot be created or destroyed, but it can be transferred and transformed - Solar energy used to form carbohydrates by autotrophs 2. Energy transfer or transformation increases entropy OR the amount of disorder / randomness in the universe = Some energy is lost as heat - Heat generated by working out - No transfer of energy is 100% efficient - Energy cannot be created and can only be converted with some energy becoming less useful and lost as heat Entropy - Relative amount of disorganization - Glucose breaking down into carbon dioxide and water - Energy conversions result in heat = Entropy of the universe is always increasing  - Need constant input of energy to fight entropy = Maintain homeostasis Metabolic Reactions and Energy Transformations - Metabolism = Sum of all chemical reactions in the body / cell - Anabolism / Anabolic pathway = Consume energy to build complicated molecules from simpler ones - Building muscle in response to exercise - Catabolism / Catabolic pathway = Release of energy by the breakdown of complex molecules - Reactants = What you need to make something - Sunlight, carbon dioxide, and water are the reactants for photosynthesis - Products = Formed as a result of reaction between reactants - Photosynthesis produces glucose and oxygen - Free energy 𝚫G = The amount of energy left to do work after a chemical reaction has occurred - Exergonic reaction -𝚫G = Loss / Release / Exit of usable energy = Reactants have more energy - Spontaneous reaction - Endergonic reaction +𝚫G = Input / Gain of energy required = Products have more energy - NOT spontaneous reaction ATP - Energy currency of the cell - Hydrolyze bond connecting the third phosphate group and release 7.3 kcal of energy - Adenosine (adenine + ribose) + 3 phosphate groups - Coupled reaction = Using energy released from initial reaction towards another reaction / process = Minimize loss of energy - ATP hydrolysis can be coupled with an endergonic reaction so energy loss is minimized - ATP can be synthesized from ADP and inorganic phosphate - Only 39% efficient while the other 61% is lost as heat 1. Chemical work = Synthesis macromolecules (anabolism reaction) 2. Transport work = Pump substances across a membrane 3. Mechanical work = Permit movement (flagella, chromosomes, cytoskeleton, etc) Metabolic Pathways and Enzymes Basics - Metabolic pathways = Orderly sequence of linked reactions with each step catalyzed by a specific enzyme - Metabolic energy is captured more easily if it is released in small increments - Catalysts = Substances that can changed the rate of a reactions without:  - Being altered in the process - Changing the free energy change / difference of the reaction - Enzyme = Organic (carbon) catalysts, usually a protein, that can increase reaction rate by more than 1o million times - Ribozymes = Made of RNA, involved in synthesis of RNA and proteins on ribosomes - Substrate = Reactant of enzymatic reaction Enzyme-Substrate Complex - Active site = Part of enzyme that binds temporarily with the substrate - Any factor that alters the active site (temperature, pH, inhibitor) can change the shape of the enzyme and therefore change functionality - Enzymes can be denatured - Induced-Fit Model = When a substrate binds to an enzyme, the active site undergoes a slight change in shape that facilitates the reaction - Enzymes are not consumed by the reaction so only a small amount is required - Enzymes are specific to their substrate = Often named for their substrate - Commonly add -ase to substrate name - i.e. Lactase digests lactose Energy of Activation - Defined as Ea = Energy that must be added to cause molecules to react - Benefit = Hurdle of energy prevents molecules from spontaneously degrading - Enzymes speed up reactions by lowering the inherent activation energy = They don’t change the final energy content Factors Affecting Enzymatic Activity - Substrate concentration = Increase substrate or enzyme and increase reaction rate - Optimal pH = Where enzyme maintains its structural configuration and therefore its active site - Temperature = Typically as temperature increases, enzyme activity rises until the enzyme is denatured and loses functionality - Cofactors = Inorganic ions (i.e. zinc or iron) - Not carbon-based - Coenzymes = Nonprotein organic molecules (i.e. NAD+) - Vitamins are often components Enzyme Inhibition - When a molecule (the inhibitor) binds to an enzyme and decreases its activity - Noncompetitive inhibition = Inhibitor binds to the enzyme at a location other than the active site - This other / allosteric site directly changes the shape of active site if bound to the inhibitor  - End-Product inhibition = Final product inhibits initial reaction of metabolic pathway from occurring - Negative feedback - Increase efficiency by turning pathway off when end product is accumulated - Competitive inhibition = Inhibitor and substrate compete for active site Oxidation-Reduction Reactions and Metabolism - Oxidation-Reduction (redox) Reactions = Transfer of electrons (negative charge) between reactants - Oxidation = Loss of electrons / hydrogen + Gain oxygen - Reduction = Gain of electrons / hydrogen + Loss of oxygen - MNEMONIC || OIL RIG = Oxidation Is Loss, Reduction Is Gain - i.e. Na + Cl → NaCi - Sodium is oxidized and chlorine is reduced Couple Reaction Chloroplasts and Photosynthesis - Capture solar energy and convert into chemical energy - Initially ATP and reduced NADP is formed - Molecules used to reduce carbon dioxide into glucose - Electron transfer molecule = NADP Mitochondria and Cellular Respiration - Glucose gets oxidized into carbon dozed - ATP molecules are produced - Electron transfer molecule = NAD Electron Transport Chain and ATP Production - High energy electrons delivered to system and low energy electrons leave - Series of redox reactions - Energy released to pump hydrogens to one side of a membrane every time electrons transfer to a new carrier Chapter 7 Photosynthesis and Organisms Basics - Photosynthesis = Conversion of solar energy into chemical energy as a carbohydrate (glucose) - Carbohydrate for structure or fuel  - Autotroph = Organisms that produce their own food by converting the inorganic to organic - Heterotroph = Organisms that consume pre-formed organic molecules (plants, animals, fungi) as building blocks and sources of energy - Consumers - Oxygen is a second product of photosynthesis = Allow aerobic respiration Reactants = Solar energy + Water + CO2 - Water through the roots - CO2 through stomatal openings in leaves - Water and CO2 both diffuse into chloroplast Chloroplast Anatomy - Double membrane - Stroma = Semifluid interior where CO2 is fixed into a carbohydrate (glucose) - Thylakoid membrane increase surface area and generate ATP / NADPre - Form interconnected spaces where hydrogen ions can be concentrated - Pigments embedded in membrane - Grana / Granum = Membrane stacks Process of Photosynthesis Overall Reaction = Solar Energy + 6CO2 + 6H2O → C6H12O6 + 6O2 Role of NADP / H - Water provides electrons / energy to NADP+ in light dependent reaction - “Mule” / Man in the middle - NADP pass to CO2 in light independent reaction to reduce in to glucose - Ways to write it as reduced: (1) NADP + H+, (2) NADP + H+ (3) NADP- (4) NADPre - Ways to write it as oxidized: (1) NADP, (2) NADP+ (3) NADPox Light Dependent Reaction - Split water - Products = NADPH, ATP, and oxygen Light Independent Reaction - AKA Calvin Cycle or Dark Reaction - Use ATP and NADPH from light dependent reactions to reduce CO2 into glucose Plants Convert Solar Energy - Light Dependent Reaction Intro - Most light that hits Earth is visible light - Higher energy screened OUT by ozone layer  - Lower energy screened OUT by water vapor and CO2 Pigments and Photosynthesis - Light is either (1) absorbed, (2) transmitted, or (3) reflected - If you can see it (reflected), it is not being used! - Chlorophyll A and B = Absorb violet, blue and red + Reflect green - Carotenoid = Accessory pigment - Absorb violet, blue, and green + Reflect yellow and red (orange) - Photosystem = Pigment complex (a, b, and carotenoids) and electron acceptor molecules within the thylakoid membrane Noncyclic Electron Flow in Light Reaction PHOTOSYSTEM II 1. Water split = Form oxygen and hydrogen 2. “IN” = Hydrogen atoms donate electrons 3. Hydrogen gets concentrated inside thylakoid membrane 4. Electrons excited by solar energy - Solar energy concentrated in chlorophyll a molecules of “reaction center” 5. Electrons so excited that they escape to neighboring electron acceptor molecules as they continue through the electron transport chain (ETC) 6. Energy captured by PQ (plastoquinone) while electrons move through ETC = Used to concentrate hydrogen ions inside thylakoid spaces 7. Electrons passed onto PHOTOSYSTEM I - “OUT” = Reduced NADP PHOTOSYSTEM I - Electrons excited a second time by solar energy - Electrons passed to NADP+ to form NADPH (which is used by the Calvin Cycle) Cyclic Electron Flow in Light Reaction - Not as efficient as non-cyclic - Back-up option - Used by prokaryotes AND when there are high oxygen levels in eukaryotes - Avoid photorespiration - Water is NOT split - ONLY ATP is formed ATP Production - Interior of thylakoid membranes are reservoirs for hydrogen ions from splitting water and PQ - Generate electro-chemical gradient to generate ATP via chemiosmosis - Hydrogen ions move from higher to lower concentration in the stroma using an ATP synthase complex channel - Hydrogen moves through ATP synthase complex channel = Form ATP THE SONG Water, water, water, water, water What are we gonna do? Break it in half What do we get? Oxygen and electrons (2) ○ Photosystem II, 2 electrons from hydrogen Sweep sweep ○ Hydrogen ions / protons in thylakoid membrane Here comes the Sun traveling in waves – Particles of light are called photons And it gets the electrons excited Nanananananana ○ ETC PQ ○ Bring in hydrogen ions And you make some ATP mph ○ Photosystem I Here comes the Sun traveling in waves – Particles of light are called photons And it gets the electrons excited Nanananana ○ ETC Who catches it? NADP Forming reduced NADP Then you take some ATP and some reduced NADP To the dark reaction OR the Calvin cycle or the light independent reaction Plants Fix Carbon Dioxide - Light Independent Reaction / Calvin Cycle / Dark Reaction Overview - Series of reactions producing carbohydrates - Required reactants = CO2 from atmosphere + ATP and NADPH from light dependent reaction - Calvin cycle / Light independent reaction / Dark Reaction 1. Fixation of Carbon Dioxide - CO2 binds to 5C molecule (RuBP) via the rubisco enzyme (RuBP carboxylase) = 6C molecule - Repeat 3 times - Rubisco is most common protein in the biosphere - Each 6C molecule break in half = 6 3PG / PGA - Gas to solid 2. Reduction of Carbon Dioxide - Each (6) 3PG / PGA gets a phosphate group from ATP - ATP turns into ADP - Energy transfer  - NADPH reduces each (6) 3PG / PGA = Form (6) G3P / PGAL - Siphon off (1) G3P / PGAL = Half of a glucose molecule 3. Regeneration of RuBP - 3 ATP used to rearrange remaining (5) G3P / PGAL into 3 RuBP = Cycle can continue - Cycle occur 2x = 1 glucose (C6H12O6) - Start with CO2 both times - 6 carbons - 18 ATP - 12 NADPH - 2 G3P = 1 glucose Importance - G3P is the first reactant of several different plant products - Glucose and other sugars - Starch - Cellulose - Fatty acids - Amino acids - You get to be alive (food and oxygen) THE SONG 3 C5 + 3 C1 makes 3 C6 breaks down to 6 C3 Use some ATP, use some reduced NADP on your 6 C3 Take one away – PGL or G3P And you’re left with 5 C3 Use some ATP to build 3 C5 + 3 C1 makes 3 C6 breaks down to 6 C3 Use some ATP, use some reduced NADP on your 6 C3 Take one away – Glucose And you’re left with 5 C3 Use some ATP to build 3 C5 Other Types of Photosynthesis Photorespiration - Stomata close to conserve water when it is hot - CO2 is used up = Levels decrease - Photorespiration = Oxygen build up in leaf competes with CO2 for RuBP - Use as much as 50% of the carbon that would be fixed C4 Plants - Adaptation to avoid photorespiration via structural and biochemical partition in space  - Light-dependent reactions occur in one cell and light-independent reactions occur in another more isolated cell that has CO2 escorted to it using PEP - Bundle-sheath cells surrounding leaf veins are larger and photosynthetic - Surrounded by mesophyll cells - Arranged in a ring - Form layer of insulation - Mesophyll cells use PEP to fix Co2 while not bonding to O2 - PEP escorts CO2 to bundle-sheath cells = Release it to RuBP and return to bundle-sheath cell for another load - Costs energy - Advantageous in hot, dry climates CAM - Adaptation to avoid photorespiration via partition in time - Fix CO2 to PEP at night when stomata can afford to open - Release stored CO2 during the day once light-dependent reactions begin - Photosynthesis is minimal - Allow plants to live with stomata closed during the day Photosynthesis Adaptations in Different Environments - C4 plants best in high light intensities, high temps, and limited rainfall - More sensitive to cold - C3 plants better in colder conditions - CAM plants better than both C3 and C4 when conditions are extremely dry Chapter 8 Overview of Cellular Respiration Basics - Break down carbohydrates to build ATP - Consume oxygen - Produce carbon dioxide - Equation = C6H12 —> 6CO2 + 6H2O + 30-32 ATP - Some of initial 36-38 ATP lost as heat (2nd Law of Thermodynamics) Energy - High energy = Glucose - Low energy = CO2 and H2O - Electron pathway is aerobic (has oxygen) - Glucose gets oxidized - Electrons passed to enzymes (NAD / FAD) - Drop electrons at electron transport chain (ETC) - Reduce oxygen into water  - Energy harvested from ETC used to makes ATP - Reactions of cellular respiration allow energy in glucose to be released slowly = ATP produced gradually - 39% efficient Coenzymes - NAD and FAD accept electrons temporarily to form NADre and FADre - Not consumed - Recycled / reused Steps - Aerobic respiration with oxygen - Glycolysis - Preparatory reaction (transition) = Formation of acetyl coenzyme A - Citric acid cycle - ETC = Oxygen is the final electron acceptor - Anaerobic respiration options without oxygen 1. Fermentation (+ Glycolysis) 2. Alter final electron acceptor at bottom of ETC - Some bacteria / microorganisms use ions (nitrate or sulfate) or even carbon diozide Phosphorylation Overview - Substrate-level phosphorylation = Hand over a phosphate group from one molecule to another - Example of process = Glycolysis - Does not involve ETC - Does not generate too much ATP - Oxidative phosphorylation - Requires oxygen - Oxygen = Final electron acceptor at bottom of the ETC in _ - Most efficient way to generate ATP of the types of phosphorylation - Photophosphorylation = Associated with light and ETC of chloroplasts (photosynthesis) Glycolysis – Outside the Mitochondria Overview - Occur in cytoplasm by all cells - Break down glucose into 2 pyruvate or pyruvic acid molecules via 10 steps - Universal reaction = Probably evolved ??? Energy Investment - Break down glucose using 2 ATP  - Glucose split into three-carbon molecules called G3P (same as Calvin Cycle product in photosynthesis) Energy Harvest - Oxidize G3P into pyruvate - Reduce NAD - Substrate-level phosphorylation of 4 ATP - Enzyme pass high-energy phosphate to ADP = Form ATP - Net gain of 2 ATP, 2 NADre and 2 pyruvate - Spent 2 of the initial 4 during energy investment stage Fermentation – Outside the Mitochondria Overview - Anaerobic process of glycolysis + reduction of pyruvate to lactate OR alcohol and CO2 - Depends on the organism 1. Alcoholic fermentation by yeast = Alcohol and CO2 2. Lactic acid fermentation by bacteria / fungi / animalia = Produce lactic acid - Purpose = Oxidize NADH to be reused in glycolysis again - Nets 2 ATP Advantages - Quick burst of energy for organisms (i.e. sprinting) - Used in food production (i.e. cheese, yogurt, bread rising, alcohol, etc…) Disadvantages - Only produce 2 ATP (from glycolysis) - Oxygen debt causes us to use fermentation - i.e. breathing heavy - Body trying to get required amount of O2 necessary in order to rid of lactate - Lactate is toxic to cells - Changes pH - Need to oxidize back to pyruvic acid / glucose in the liver Efficiency of Fermentation = 2.1% of potential energy of glucose Facultative Anaerobes - Make ATP by aerobic respiration IF oxygen is present - Can switch to fermentation under anaerobic conditions - i.e. muscle cells - OPPOSITE = Obligate anaerobes cannot survive in the presence of oxygen Inside the Mitochondria Structure Review - Intermembrane space between outer and inner membrane = Where hydrogen ions are pumped / concentrated - Matrix = Location of prep reaction and citric acid cycle - Cristae = Folds on inner membrane and location of ETC Preparatory Reaction - Connect glycolysis to citric acid cycle - Each pyruvate is converted into acetyl coenzyme A - Remove a carbon group (-COOH) as CO2 and a hydrogen from each pyruvate - Use electron from hydrogen to reduce NAD+ - Molecule of CoA binds where the -COOH group was located Citric Acid / Krebs / TCA Cycle - Completes the oxidation of the original glucose - Cycle occurs 2 times for each glucose molecule = Need 2 acetyl CoA) 1. Acetyl group binds to a C4 group to get a C6 group which is citric acid 2. Remove a carbon as CO2 and reduce an NAD+ = C6 becomes C5 3. Remove a carbon as CO2 and reduce an NAD+ = C5 becomes C4 4. Substrate-level phosphorylation = Make 1 ATP 5. Reduce 1 FAD+ 6. Reduce 1 NAD+ Electron Transport Chain (ETC) - Purpose = Reduced NADH / FADH2 bring electrons to the ETC = Become oxidized and return to other steps of cellular respiration - NADH entering at the top generate 3 ATP (or 2.5 ATP due to heat loss) - FADH2 enter just before second reductase = Generate 2 ATP (1.5 ATP due to heat loss) - NADH from glycolysis sometimes passes electrons to FAD+ = Why there is variability in ATP from 36-38 to 30-32 ATP - Electrons go down ETC = Go from high energy to low energy - Energy captured to pump hydrogen ions into intermembrane space - Ions move away from space - Ions move into matrix through ATP synthase complex (a channel enzyme) due to proton-motive force = Generate ATP - Chemiosmosis = When ATP production is tied to H+ gradient - ETC in the cristae of mitochondria - Includes three protein complexes and two carriers 1. (NADH) Reductase 2. (Cytochrome) Reductase 3. Cytochrome oxidase  - Oxygen is the final acceptor - Binds to hydrogen = Form water = Oxidative phosphorylation Energy Yield – OLD NUMBERS WITHOUT CONSIDERATION OF HEAT LOSS Substrate level phosphorylation - Glycolysis = 2 ATP - Citric Acid Cycle (2x) = 2 ATP ETC - Prep / Citric Acid = 8 NADH = 24 ATP - Glycolysis = 2 NADH = 4-6 ATP - Prep = 2 FADH2 = 4 ATP Efficiency = 39% CELLULAR RESPIRATION SONG What’s it all called? Cellular respiration (jogging) First step? Glycolysis Who does it? All cells Where? In the cytoplasm What do you start with? Glucose How many carbons? 6 What do we do with it? Break it in half Steps? 10 Enzymes? 10 What is it called? 2 pyruvic acid ○ AKA pyruvate Oh no! We don’t have any oxygen. What are we gonna do? Fermentation How many choices? 2 You and I make lactic acid – Makes our muscles sore Yeast and plants make (exhale) alcohol ○ Exhale + 3 fingers to 2 = Also making 2CO2 Either way you reduce your NAD and make some ATP – 2 We have plenty of oxygen. What are we gonna do? Aerobic respiration What’s the first step? Transition prep ○ 3 fingers to 2 = Taking out a carbon group as a CO2 from each of the 2 pyruvates and replacing with CoA to make acetyl CoA 2 acetyl CoA Take one away 2 and 4 is 6 Do the bit get 5 Do the bt get 4 Make some ATP  Reduce an FAD Reduce a NAD Gather all your reduced NADs and FADs Take them to the top of the ETC Uh uh - FAD does not go all the way Nanananana - NAD goes all the way Reductase, reductase, cytochrome oxidase And you make some ATP – A lot of it, a lot of it, a lot of it – Who catches it at the bottom? Oxygen - Oxidative phosphorylation And you make water Metabolism Catabolism - Degradative - Tends to be exergonic - Glucose can use x at all three steps of cellular respiration - Glucose can us pyruvate (glycerol) by snipping the long chains (acetyl CoA) Anabolism = ATP produced during catabolic reactions drive endergonic anabolic reactions Energy Organelles - Similarities between chloroplasts and mitochondria - Use of a membrane - Chloroplasts have thylakoid membranes - Mitochondria have cristae - ETC and electrochemical gradient of H+ followed by production of ATP via chemiosmosis - Chloroplasts bring H+ IN - Mitochondria bring H+ OUT - Enzymes in Calvin Cycle are the same / similar to the Citric Acid Cycle - Flow of energy = Sun → Chloroplast → Mitochondria Phosphofructokinase (PFK) – Excellent Example of Negative Feedback - Allosteric enzyme that is active early in the pathway of glycolysis - Inhibited by high levels of ATP= Stop catalytic pathway of glycolysis - Considered the pacemaker of respiration. Fitness Introduction - Fitness = Ability / Chance / Likelihood of passing on genes - Diversity naturally occurs among and between components within biological systems that affects their interactions with the environment - Variation at the molecular level = Organisms given ability to respond to a variety of environmental stimuli - Number and type of molecules within cells determine ability to survive and reproduce in different environments Illustrative Examples - Variety = Better adaptation to a cell’s environment or stages of development 1. Variety in phospholipids depends on the environment and what is needed for climate variations 2. Variety in hemoglobin - Protein responsible for transporting oxygen within red blood cells - Hemoglobin F = Fetus pull on oxygen more and hang onto it (increased “stickiness”) when the environment is relatively low in oxygen - Oxygen coming from mother’s Hemoglobin A - Hemoglobin A = No longer have “stickiness” of Hemoglobin F when grown up because it becomes too difficult to get the oxygen to various tissues that need it 3. Variety in Chlorophyll: better at absorbing different wavelengths of light, different types of day/year - Chlorophyll a = violet / blue and red / infrared - Chlorophyll b = blue / green and orangish red Unit 4: Cell Communication and Cell Cycle Chapter 40 Animal Hormones Introduction - Hormones = Chemicals that affect the behavior of other glands or tissues - Influence (1) metabolism of cells, (2) growth and development of body parts, and (3) homeostasis - Endocrine glands = Secrete hormones into bloodstream via tissue fluid - Exocrine glands = Secrete products into ducts that take them outside the body or to the lumens of other organs - i.e. salivary glands Hormones and Homeostasis Nervous System Endocrine System Composed of Neurons Usually glands Delivery Nerve impulse and Hormone neurotransmitter How it is delivered Axon and synapse Usually bloodstream Target Muscles and glands Cells throughout body Response Rapid and short-lived Slow and long-lasting Controlled by Negative feedback Negative feedback - Act slowly but has longer lasting effects compared to the nervous system - Controlled by feedback loops - Negative feedback = Level of hormone itself, or of some chemical induced by the hormone, inhibits further secretion of the hormone - Many examples - Positive feedback = Output intensifies and increases output of system - Few examples - Antagonistic hormones = Contrary hormones that have opposite effects - Hypersecretion = Too much - Hyposecretion = Too little Hormones are Chemical Signals - Can only impact target cells that have protein receptors for that hormone - Pheremones = Chemical signals that act between individuals - Important in many animal species - Example 1 = Women prefer men who have different MHC molecules than themselves - Example 2 = Axillary excretions may affect the menstrual cycles of other women - Example 3 = Men had lower testosterone levels when they smelled a jar full of tears from a woman than when they smelled a jar of saline solution Action of Hormones - Peptide hormones = Water soluble and triggers second messengers 1. Hormone (first messenger) binds to receptor in plasma membrane because it can’t cross the membrane - Epinephrine binds to a receptor protein in target cell’s plasma membrane 2. Binding triggers second messenger - Binding activates enzyme (G protein) that activates another enzyme (adenylate cyclase)  - Change ATP to cAMP - cAMP is the second messenger 3. Second messenger triggers metabolic cascade of events - cAMP activates enzyme cascade that ultimately leads glycogen to break down into glucose and become available to tissues - Steroid hormones = Lipid soluble and affect gene expression 1. Diffuse through plasma membrane 2. Bind to intracellular receptor 3. Reach nucleus 4. Hormone-receptor complex acts as a transcription factor and activates a gene - Testes, ovaries, and adrenal cortex Similarities to Nervous System - Different types of receptors BUT all have ion channels that trigger a membrane potential change - Taste receptors located in other spots of the body G-Protein Coupled Receptors - Snakes through membrane 7 times - One end outside (receptor for ligands) - One end inside cell - (1) Alpha unit, (2) Beta unit, and (3) Gamma unit - GDP bonds to Alpha unit = Inactive protein - GTP bonds to Alpha unit = Active protein - Alpha unit able to separate and interact with other things Gs - Stimulates adenylate cyclase (enzyme) - Remove two phosphate molecules from ATP to get cAMP - cAMP binds to regulatory unit of kinase A = Pull the pin so regulatory and catalytic units separate - Catalytic unit able to trigger cellular response Gi - Inhibitory - Opposite of GS Gq Enzyme-Coupled Receptors - 3 main types Receptor Tyrosine Kinase - Most common 1. Ligands bond to receptor domain 2. Dimerize 3. Cross-phosphorylation = S Ion Channel - 3 kinds (photo, something, and something) Hypothalamus and Pituitary Gland Introduction - Help regulate internal environment through autonomic nervous system and glandular secretions of pituitary gland - Pituitary controls many other glandular secretions = Master gland - Pituitary has two portions that are controlled differently by the hypothalamus Posterior Pituitary - Controlled indirectly by the hypothalamus who has neurosecretory cells extending into the posterior pituitary - Oxytocin = Uterine contractions (baby out) and milk release out of mammary glands (milk out) - ADH = Cause / control water reabsorption in kidneys Anterior Pituitary - Thyroid - Controlled indirectly through double capillaries - First set extend into stalk (stimulating hormones) Second set extends to anterior pituitary where hormones released from hypothalamus trigger stimulating hormones from anterior pituitary - TSH stimulates thyroid gland - ACTH stimulated adrenal (cortex) gland - Prolactin stimulates mammary glands to encourage milk production (not release) - Growth hormones stimulate bones and muscles - FSH and LH stimulate ovaries / testes Disorders - Diabetes insipidus = Too little ADH secreted so not enough water is reabsorbed - Pituitary dwarfism = Too little GH - Gigantism = Too much GH too early - Acromegaly = Too much GH as an adult  - Cushing syndrome = Too little ACTH so too much cortisol is secreted which increases fat production **Other Endocrine Glands and Hormones Thyroid - Large glands in neck - Thyroid Hormone (TH) = Multiple targets, regulates metabolism, requires iodine to form TH - Calcitonin = lowers blood calcium level - Goiter = Hyposecretion of TH due to of lack of iodine which causes the thyroid gland to swell - Cretinism = Hyposecretion of TH since birth Parathyroid - PTH raises blood calcium - Contrary to calcitonin Adrenal Glands - Sit on top of kidneys - Adrenal medulla - Controlled by ANS - Short-term response to stress - Adrenaline / Epinephrine = Fight or flight - Noradrenaline / norepinephrine = Anger - Adrenal cortex - Controlled by ACTH - Steroid hormones - Long term response to stress - Glucocorticoids = Raise blood glucose levels and metabolism while suppressing inflammatory response - Cortisol - Mineralocorticoids = Regulate salt and water balance by increasing sodium reabsorption by the kidneys - Aldosterone - Contrary hormone is ANH (atrial natriuretic hormone) which is secreted by the heart when the atria is stretched - Small amount of cortical sex hormones Pancreas - Act as exocrine gland in digestion - Islets of Langerhans act as endocrine gland secreting hormones - Insulin lowers blood glucose - Glucagon raises blood glucose - Type 1 Diabetes = Not producing enough insulin, hyposecretion  - Type 2 Diabetes = Body tissues do not respond to insulin Testes and Ovaries - Steroid hormones affect gamete development, development, hair growth, and function of sex organs - Ovaries = Estrogen / Progesterone, fat distribution, and uterine cycle The Ovarian Cycle: (FOL) - Follicular phase (days 1-13): - Follicle maturation occurs as a result of FSH (anterior pituitary), which causes the developing follicle (jacket around developing oocyte/egg) to secrete estrogen. - Estrogen gives positive feedback to the hypothalamus/pituitary - Ovulation (day 14): egg is released from follicle as a result in a spike in LH (anterior pituitary) - Luteal phase (days 15-28): - Corpus luteum develops from empty follicle. The corpus luteum secretes progesterone - Progesterone gives negative feedback to the hypothalamus/pituitary The Uterine Cycle: (MPS) 1. Menstruation (days 1-5): as a results of low progesterone levels, uterine lining is shed 2. Proliferative phase (days 6-13): uterine lining builds due to rising levels of estrogen 3. Secretory phase (days 14-28): endometrium layer thickens and is maintained as a result of progesterone Menstruation: menses, endometrial lining broken down and released out the vagina - lasts 3-10 days Fertilization and Pregnancy: - Egg fertilized in oviduct - Travels to uterus and embeds in endometrium - Zygote produces hCG: which maintains the corpus luteum (so progesterone is continued to be made) until the placenta takes over in production of progesterone at about 10 weeks Estrogen and Progesterone: - Hormones are responsible for secondary sex characteristics - Menopause: ovarian and uterine cycles cease, likely to occur between ages 45-55, are often accompanied by hot flashes, dizziness, headaches and insomnia, sleepiness and depression. - Testes = Testosterone, muscular strength, vocal odors, acne, body odor, and baldness - GnRH: secreted by hypothalamus, stimulates the anterior pituitary gland - From Pituitary: - FSH: stimulates sperm production (seminiferous tubules) - LH: stimulates testosterone production (interstitial cells) - From Testes: - testosterone (interstitial cells) needed for normal development and functioning of the reproductive organs and the secondary sex characteristics as well. - inhibin: feedback - Both testicular hormones exert negative feedback on both the hypothalamus and pituitary Pineal Gland - Melatonin - Gland in brain - Circadian rhythms - Daily behaviors - Reproductive organs Thymus Gland - Thymosin - Gland above heart - Larger in children - Stimulate T cell maturation Hormones from other Tissues - Leptin = Produced by fat tissues, fullness - EPO = Secreted by kidneys in response to low blood oxygen levels - Growth factors = Released by many tissues and stimulate cell division - Prostaglandins = Act locally, both promote and inhibit inflammation Chapter 26 Plant Hormones Introduction - Plant stimuli includes light, gravity, COs levels, pathogen infections, water levels, and touch - Signal transduction = Process of responding to stimuli - Receptor = Proteins activated by a specific signal - Transduction pathway = Series of relay proteins that add and convert the original signal into one that affects the cellular machinery - Cellular response = An activated metabolic pathway that is most often a change in gene expression or a cellular process that affects plant growth and development - Hormones = Chemical signals that coordinate cellular responses - Generated in one part of a plant - Active in a different part of a plant Auxin - IAA / Indole Acetic Acid = Most common - Required for embryo survival - Phototropism - Towards light = Positive - Away from light = Negative 1. Auxin concentrates in cells on the shady side of the plant  2. Hydrogen ions pumped into cell walls = Weaken - Change in pH activates enzymes that break down cellulose fibers - Cells forced to rebuild bigger = Asymmetrical elongation - Gravitropism - Roots grow down = Positive - Shoots go up = Negative - Promote growth of roots and fruit - Prevent loss of leaves and fruit - Apical dominance = Encourage plant to grow up instead of branching out / laterally - Auxin moves down from shoot tips to inhibit branching = Positive - Grow like a bush (low and lateral) = Negative - Auxin sprays can be used to develop fruit that will be seedless - “Agent Orange” = Synthetic auxin that can be used as an herbicide Gibberellins - GA3 = Most common - Causes cell elongation - 136 types - Break bud and seed dormancy - Larger fruit (grapes) - Earlier flowering - Beer making (break dormancy of barley seed and produce sugar) Cytokinin - Required for embryo survival - Promote cell division and organ formation - Interact with cytoplasm - Responsible for root nodule formation in nitrogen-fixing bacteria - Prevent senescence (aging of plant) - Leaves change colors and eventually die when cytokinin levels are low - Genetically modified lettuce produce cytokines at the onset of aging = Do not wilt / turn brown Abscisic Acid (ABA) - Produced in chloroplasts - Stress hormone - Promote dormancy or cease growth in response to adverse conditions - Close stomata under water stress Ethylene - Gas hormone = Travel through air and affect different fruit  - Abscission of leaf, fruits, and flowers - Promote fruit ripening - Commercial use Responding to Biotic Environment - Biotic factors = herbivory, parasitism, and competition from other plants - Hormones help biotic factors response to abiotic conditions like light and water - Plants need more than epidermic to be chewed through → Plants produce secondary metabolites to prevent and discourage competition - Direct defenses = Traits that increase plant’s resistance to attacking insect herbivores by affecting their physiology or behavior - Indirect defenses = Attract natural enemies of herbivores to reduce plant loss and provide food and shelter to carnivores Plant Growth and Movement Responses Introduction - Internal movement and stimulus = Turgor pressure and movements, electrical impulses, and hormones - External movement and stimulus = Responses to light and water - Tropisms = Growth responses towards or away from unidirectional external stimuli - Positive = Towards - Negative = Away Phototropism - Positive in shoots - Neutral or negative in roots - Phototropin = Receptor - Gets phosphorylated + Changes shape in presence of blue light (400-500m) Thigmotropism - Some part of the plant responds to contact with another object - Cells on opposite side (not point of contact) elongate - Thigmomorphogenesis = Whole plant changes its shape Gravitropism - Negative in shoots - Positive in roots - Organelles called amyloplasts contain statoliths that settle to the bottom because of gravity and signal downwards growth Movement Caused by Internal Stimuli - Nastic movements = When a cell swells due to turgor pressure / movements  - Touch, shaking, and thermal stimulation can cause turgor responses - Cause leaves to fold within a second to shake off an attacking / feeding insect - May be an electrical mechanism Plant Responses to Phytochrome Introduction - Plants are aware of light - Can sense time of day (amount of light) to adjust metabolic processes like photosynthesis - Can sense time of year = Affect seasonal responses like flowering - Dependent on wavelengths of light using phototropin and phytochrome Phytochrome - Blue-green pigment found in cytoplasm - Can detect light - On / Off switch to initiate signal transduction pathway - Distinguish between red wavelengths and interconvert (whatever light it absorbs will eventually convert to the other form) - Inactive Pr = Absorb red light and become active Pfr - Active Pfr = Absorb far-red light in the evening and concert back to Pr during the night / in darkness - Photoperiodism = Physiological response due to light in a 24 hour period - Short day / Long night = Minimum / critical number of night hours - Poinsettia - Long day / Short night = Maximum / critical number of night hours - Wheat - Flashes of light can disrupt a long night and make it short = No flowering - Different seed have different light requirements = germination - Photomorphogenesis = When plant shoots are exposed to red light, accumulate Pfr, expand their leaves, and become green - Etiolated = When the plant shoot increases in length but has no photomorphogenesis because it grows in the dark - Plants grown closer together experience more far-light (shade) - Plants grow taller in response to compete better and receive more light Circadian Rhythm - When metabolic processes cycle (high vs. low activity) during a 24 hours period regardless of light levels and can be reset due to external clues - Stomata opening in the morning - NEctar secreting at the same time every day - Leaves closing at night  - Biological clock = Internal mechanism in which circadian rhythm is maintained in the absence of external stimuli - Phytochrome sets this clock in plants Chapter 9 Cell Increase and Decrease Cell Cycle - Cell Cycle = Starts the moment the cell forms until its own division into two cells - Interphase (I) = Most (90%) of cell life spent here - G1 = Cell grow larger and organelles increase - G0 = Branch off from G1 for muscles and nerves + No longer enter mitotic stage - S = DNA synthesis (duplication of chromosomes / replication) - G2 = Synthesize proteins - Mitotic Stage (M) - Mitosis = Nuclear division into two nuclei containing the same exact DNA as the parent cell - Cytokinesis = Division of cytoplasm to form two cells Control - Controlled by external growth factors and internal signals (DNA damage) - Signal = Molecule that either stimulate or inhibits a metabolic event - 3 CHECKPOINTS = G1, G2, and M - Apoptosis if any one checkpoint is not passed 1. G1 = Critical + Cell stays in G0 if it doesn’t get the signal to move onto S - Cell is checked for DNA damage, inability to be repaired, or for chromosomes not lining up correctly - CHECK THAT MITOSIS WAS DONE CORRECTLY - GROWTH SIGNALS = Encourage means CDK add phosphate to RB protein (major regulator) release E2F which binds to DNA and triggers cell cycle proteins - Availability of nutrients = RB losses phosphate if no pass - Asses integrity of DNA = Poor = Phosphorylate and goes to work 2. G2 = Check that DNA was replicated / synthesized properly - Checking for damage that can’t be repaired - Check the cell can move onto mitosis 3. M = Check that chromosomes are properly aligned - Cyclins = Protein that controls the cell cycle - Must build up and be present to move into the S and M stages - CDK (Cyclin Dependent Kinases) = Enzymes activated by cyclins - Become inactive when cyclins deteriorate Apoptosis - Apoptosis = Programmed cell death 1. Caspases (enzymes) normally kept in check by inhibitors 2. Internal or external signals deactivate inhibitors - Balance with mitosis helps maintain the normal cell level of somatic cell = Prevent tumors Eukaryotic Chromosome Structure - Organize / prepare for mitosis after S and G2 stages of interphase - Chromatin (DNA and proteins) coil up into two rod shapes (2 copies of DNA) joined by a centromere - DNA winds around histone protein spools to form nucleosomes - Nucleosomes condense into chromosomes Appearance - Solid nucleus and unwound DNA during interphase - Replicate during S stage - No noticeable shape under microscope - Chromosomes form and appear as doubled, sister chromatids that are held together by a centromere during the mitotic stage Mitosis and Cytokinesis Diploid vs. Haploid - Duploid (2n) = 2 full sets of chromosomes - One set from each parent - Somatic cells - Haploid (n) = Only 1 set of chromosomes - Gametes = i.e. sperm or egg Mitosis - Mitosis = Generate 2 identical cells 1. Prophase - Chromosomes become visible - Nuclear envelope and nucleolus breaks down - Centrosomes with spindle fibers move to poles (“ends” of the cell) - Microtubules extend from centrosomes = Aster 2. Metaphase - Chromosomes meet in the middle - Microtubule complex = Spindle 3. Anaphase - Sister chromatids split apart  - Motor molecules, kinesin, and dynein assist - Cells begin destroying cyclin to inactivate CDK and end mitosis 4. Telophase - Nuclear membranes with a nucleus reform - Sister chromatids become chromosomes and unwind Cytokinesis - Cytokinesis = Division of the cell to form 2 cells - Cleavage furrow indents the plasma membrane in animal cells - Cell plate forms to become cell wall in plate cells - Cell wall does not permit cleavage furrowing Function - Mitosis by somatic cells is for growth and repair - Stem cells and red bone marrow can continue to replicate and form new cells - M MITOSIS SONG What’s the whole thing called? Mitosis What’s the first step? Prophase The chromosomes become visible Meet in the middle for metaphase Away in anaphase To nuclei in telophase Cytokinesis – Namaste The Cell Cycle and Cancer Intro - Qualities in normal cells and cell division - Density-dependent (contact) inhibition = Phenomenon where crowded cells stop dividing - Anchorage dependency = Normal cells must be attached to a substratum like the extracellular matrix (ECM) of a tissue in order to divide - Neoplasm = Abnormal growth of cells - Tumor = Mass of abnormal cells within otherwise normal tissue - Benign = Encapsulated + Is not cancerous and has not invaded adjacent tissue - Malignant 6= Has the ability to spread or already has - Metastasis = Cells separated from malignant tumors and enter blood or lymph vessels to travel to other parts of the body. - Cancer = Cellular growth disorder as a result of mutations of genes that regulate the cell cycle - Loss of control  - Carcinogenesis = Development of cancer - Usually gradual - Can take decades Characteristics of Cancer Cells 1. Lack of differentiation - Not specialized - “Immortal” 2. Abnormal nuclei = Enlarged size, abnormal numbers, or gene amplification (deleted or duplicated portions of chromosomes) 3. Lack of apoptosis despite abnormal cells or aged DNA - Cells typically stop after going through the cycle 50 4. No density-dependent inhibition = Form tumors 5. Undergo metastasis and angiogenesis - Metastasis = New tumors form away from the primary tumor - Angiogenesis = Tumors cells acquire additional mutations by directing the growth of new blood vessels into the tumor Origin of Cancer - Usually due to gene mutations 1. Proto-oncogene = Code proteins that promote the cell cycle and prevent apoptosis - Like the gas pedal - Stimulatory pathway - Mutation turns it into cancer-causing oncogenes - Over 40 potential oncogenes - ras gene family = cancers of the lung, colon, pancreas, and thyroid as well as leukemia / lymphoma - 30% of all cancers - BRCA1 = Breast cancer predisposition gene 1 → Breast and ovarian cancers - WNT, MYC, ERK, and TRK 2. Tumor suppressor genes = Code proteins that inhibit the cell cycle and promote apoptosis - Like the brakes - Prevent cell cycle and promote apoptosis when DNA is damaged - Over 1000 1. RB = Involved in retinoblastoma, breast, prostate, bladder, and small-cell lung carcinoma - Deletion of RB1 causes 91-100% of lung cancer, 72.2% of basal-like, 61.5% of luminal B breast cancer, 63% of osteosarcomas, 30% of non-small cell lung cancer (NSCLC), and 17-33% of castration-resistant prostate cancer 2. p53 = Suppress cancer in 4 different ways  i. Activate p21 gene to bind with CDKs and give time for DNA to repair ii. Activate a group of microRNA to inhibit the cell cycle iii. Turn on genes directly involved in DNA repair iv. Activate “suicide genes” / caspases to stimulate apoptosis - Estimate of over one-half (50%) of human cancers caused by abnormal or deleted p53 genes 3. BRCA1 and BRCA2 - More likely to cause breast and ovarian cancer when lacking 3. Failure of DNA repair systems 4. Telomeres (end of chromosomes) are no longer shortening with each replication due to telomerase (enzyme) Prokaryotic Cell Division Prokaryotic Chromosomes - Single circular chromosome located in the nucleoid region along with a few associated proteins - 1000x the length of the cell - Asexual reproduction = Offspring are genetically identical to the parent Binary Fission 1. Chromosome replicates 2. Cell elongates 3. Build cell membrane and wall between the two identical chromosomes Organism Cell Division Function Prokaryotes: bacteria and Binary Fission Asexual reproduction archaea Eukaryotes: Protists and Mitosis and cytokinesis Asexual reproduction some fungi Eukaryotes: other fungi, Mitosis and cytokinesis Development, growth and plants, and animals repair Chapter 33 Evolution of Immune System - Protect from all sorts of harmful invaders (i.e. bacterial and viral pathogens, various toxins, and maybe even cancerous cells) Examples - Cellular slime molds (protists)  - Can live independently when food is plentiful - Live as a group / multicellular slug when food is low - Cells called sentinels circulate throughout to engulf bacteria and toxins and then self-sacrifice = Precursors to neutrophils and macrophages - Drasophilia (fruit fly) - Can recognize pathogen-associated molecular patterns (PAMPs) such as dsRNA produced by viruses and other organic molecules on bacteria or fungi - Receptors for PAMPs have also been found in plants and humans - May be the earliest versions or receptors to recognize pathogens - Can recognize common microbial invaders quickly but do not increase response after repeated exposure to the same pathogen - TLDR innate immunity does not learn Adaptive Immunity = Immunological Memory - Diverse antigen receptors on the surfaces of specialized cells like B and T lymphocytes that bind to antigens which stimulate a cascade of cells to respond to a specific antigen - Binding similar to PAMPs - Increased responses upon second exposure - Diversity due to gene arrangement = Allow continual evolution of responses to ever-changing myriad of pathogens Lymphatic System Basics - Collect excess tissue fluid at capillaries - Protect body by producing lymphocytes - B and T white blood cells - Collect fat at villi of small intestines - Edema = Problem where accumulation of tissue fluid causes swelling Vessels - Close associate with cardiovascular system - Lymphatic capillaries →Venules → Lymph veins with valves → Subclavian veins - Movement dependent upon skeletal muscle contractions - Tissue fluid = Fluid around cells from the blood plasm not recovered at venous end of capillaries - Lymph = Tissue fluid now in lymphatic vessels Organs - Primary - Red bone marrow - All blood cells originate here - B cells mature here - Thymus gland  - T cells mature here - Secondary - Spleen filters blood - Lymph nodes filter tissue fluid - Patches of lymphoid tissues respond to pathogens entering via the mouth - Tonsils trap germs in throat - Peyer patches on intestinal walls - Vermiform appendix attached to cecum (start of large intestines) Innate Immune Defenses Barriers to Entry - Skin and hair - Oil glands = Inhibit growth of bacteria - Ciliated cells = Line respiratory tract to help get bacteria out - Stomach with low pH - Lysozyme = Antimicrobial enzymes to break down bacterial cell walls - Saliva, mucous secretions, and tears - Harmless bacteria living in intestines and vagina prevent pathogens from colonizing Inflammatory Reaction - Antigen = Any substance that causes the body to make an immune response against that substance - Toxins, chemicals, bacteria, viruses, or other substances outside of the body - Can be within own body tissues and cells - Can be used as markers in laboratory tests to identify tissues or cells with antigens (i.e. cancer cells) - Result of damaged tissues due to injury or invaders - Phagocyte and NKCs use TLRs (toll like receptors) to recognize damaged tissues and begin the fight - Neutrophils = Most numerous and first at the scene to eat - Monocytes = Migrate to infection scene and become macrophages (bigger eaters, alarms, and scavengers) - Dendritic cells = Eaters, display foreign antigen to activate the rest of the immune system, work with T-cells, clear up destruction - Natural Killer Cells (NKCs) = Recognize and remove diseased cells contain viruses or cancer cells - Swelling due to mast cells releasing histamine = Cause vasodilation - Redness / Higher temp due to enlarged capillaries - Pain due to swollen area triggering free nerve endings - Fever inhibits growth of microorganisms  - Pus is from dead phagocytic white blood cells - Leaky / dilated capillaries allow fighting cells, dendrites, neutrophils, and other white blood cells to access injury site more easily Protective Proteins - Complement proteins = Produced mainly by the liver and complement / aid certain immune responses - Always in blood but need to be activated by pathogens 1. Enhance inflammation – Trigger histamine release or attract phagocytes 2. Increase phagocytosis – Increase odd of binding to surface of pathogen 3. Membrane attack complexes – Produce holes in surface of bacteria and viruses so it will burst - Cytokines = Soluble proteins that affect the behavior of other cells when released - Interferon = Type of cytokine produced by virus-infected cell to warn neighboring cells to produce substance to slow metabolism in order to interfere with virus replication - Interleukin = Encourage cells to fights Adaptive Immune Defenses Introduction - AKA “acquired” immunity because we are not born with it - Can distinguish between self and non-self - Can take a week to develop BUT lasts for years - Primarily depend on activities of B and T cells with specific antigen receptors on their plasma membrane - Diversification of antigen receptors happens during maturation process = Create virgin B and T cells that can respond to any possible antigen through genetic recombination in posttranscriptional processes - Exon recombination of just three genes Antigens - Any foreign substance that triggers an immune response - Found on surface of virus, bacterial, or eukaryotic cells - Made of carbohydrates / proteins B Cells and Antibody-Mediated Immunity - Target free-floating virus, bacteria, or toxin - Need direct contact - BCRs = B Cell receptors that are usually activated in a lymph node or the spleen - Originate in mature in bone marrow - Virgin cell trigger by antigen and T Cell’s cytokines = Form two cells - Plasma cells mature and produce antibodies specific to one antigen  - Commit apoptosis to maintain homeostasis once done fighting - Memory cells recognize antigen in the future - Clones recognize and produce antibodies to (re)build army of cells that can do the same - Antibodies / Immunoglobulins (Ig) are Y shaped - Bind to and mark antigen for destruction - Mode of destruction / type of Ig determined by the pase of the Y - IgG = Blood, single Y - Most common - Complement phagocytosis - IgA = Milk, tears, and saliva - Prevent pathogen from attaching to digestive and respiratory tract - IgM = First to appear during B-cell r