AP Biology Study Guide PDF

Unit 0: Introduction to AP Biology Water: - Polar molecules with polar covalent bonds - Its oxygen end is a partial negative with hydrogen and it is also partially positive - cohesive Polar Covalent bonds - opposite ends of the molecule have opposite charges Cohesion: - H bonding be...

Unit 0: Introduction to AP Biology Water: - Polar molecules with polar covalent bonds - Its oxygen end is a partial negative with hydrogen and it is also partially positive - cohesive Polar Covalent bonds - opposite ends of the molecule have opposite charges Cohesion: - H bonding between H20 creates a sticky feeling - Allows for the movement of water against gravity - High surface tension - Allows water to move the opposite way up a tree for transpiration Adhesion: - H20 molecules form bonds with other substances - Capillary action (liquid flowing in narrow spaces without assistance against gravity) Hydrophilic - Some molecules have a natural liking for water (Polar and ionic) Hydrophobic - Substances that do not like water (non polar and non ionic) Specific Heat - the amount of heat for a substance to change by a certain temperature like 1 degree The scientific method Observation - Hypothesis - Experiment - Data Collection - Conclusion Experimental Design Constants: Conditions that are kept the same throughout the experiment Replication: Repeating experiments to ensure the variability Data Analysis: Use the results to determine the outcome Types of Data Qualitative Data - Descriptive Data Ex, color, behavior) Quantitative Data - Numerical Data Ex, Height, mass) Structure of an atom - consists of protons, neutrons and electrons Types of chemical bonds - covalent (strong) sharing of electrons - Ionic - transfer of electrons - Hydrogen - weak bonds between polar molecules Macromolecules Carbohydrates - short term energy storage (ex, glucose starch) Proteins - structures, enzymes, cell signaling Lipids - Long term Energy storage, insulation, cell membranes (Hydrocarbons are non-polar) Nucleic Acids - Stores genetic information (DNA/RNA) Cell theory - All living things are made up of cells - Cells are the basic units of life - All cells are made up of pre-existing cells Organelles and their functions Nucleus - stores genetic information (DNA) Mitochondria - Produces ATP Chloroplasts - Used for photosynthesis to capture light energy (plants) Ribosomes - used for Protein Synthesis Endoplasmic Reticulum - Protein and Fats processing Golgi Apparatus - Packaging and distribution of molecules Lysosomes - used for digestion and recycling Theory of Revolution - Organisms change over time and through genetic variation and natural selection Evidence includes: - Fossil Records - Comparative Energy - Molecular Biology Speciation - Formation of new species (The process by which new species are formed) Eukaryotic - Nucleus and membrane-bound organelles (ex, plants and animals) Prokaryoric - No nucleus (Bacteria) *Water's ability to dissolve many substances and transfer nutrients makes it a great solvent that is essential for biological processes. Unit 1: Properties of water: - Cohesion, adhesion, surface tension - High specific heat - Ice has a lower density than liquid - Solvent capabilities due to polarity To further expand, waters solvent capabilities vary and can range from many things like - Its ability to dissolve many substances becoming the reason for it being named the universal solvent - Partial positive charge of hydrogen and partial negative charge of oxygen attracts ions and polar molecules Examples - Ionic compounds disassociate themselves in water molecules as water molecules surround and separate the ions - Polar molecules form hydrogen bonds with water which adds to their factors of dissolution Hydrogen Bonding - the true basis of water's unique properties and its intermolecular forces that occur between water molecules - Weak interaction - Occurs when a hydrogen atom is covalently bonded to a highly electronegative - Gives rise to Cohesion, Adhesion, High specific heat, High heat of vaporization, expansion upon freezing and solvent capabilities (Acts as a universal solvent) - Lower concentrations of Hydrogen bonds cause certain segments of DNA to denature at lower temperatures Essential Elements CHNOPS - Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, and sulfur Carbons properties include: - Being able to form 4 covalent bonds which enables organic diverse molecules - Hydrocarbons with functional groups like (Hydroxyl, carboxyl, amino and phosphate) - Isomers (Structural, geometric and enatiomers) Dehydration Synthesis - Removal of water to form bonds between monemers (ex, creating polymers like proteins and polysaccharides) - Uses covalent bonds to form the new bonds Hydrolysis - Addition of water to break bonds (ex, digestion of polymers in to monomers) Enzymes and Their functions Structure & Function - Catalysts that lower activation energy - Specific to substrates (The lock and key model) - They are affected by pH, temperature and substrate concentration Enzyme Inhibitors Competitive v Noncompetitive inhibitors Competitive inhibition - Inhibitors that compete directly with the substrate for the binding of the active site - Ends up reducing the enzyme's ability to catalyze the reaction because the active site is being occupied by the inhibitor - The effects can be mitigated by increasing substrate concentration - Some examples can be represented as drugs that block enzyme production in metabolic pathways Noncompetitive inhibition - The inhibitors bind to another site besides the active site(allosteric site) which causes a conformational change in the enzyme - This change will reduce the enzymes activity regardless of substrate concentration - Example: Heavy metal ions that inactivate enzymes Which Macromolecules interact with water and other solutions? Carbohydrates Interaction with water - highly hydrophilic due to its abundance of hydroxl groups that always end up forming bonds with water - Carbohydrates ability to interact with water to help in nutrient passage and storage - They occur as monomers, chains of monomers and branched structures Proteins Interaction with water: Proteins can be hydrophilic or hydrophobic depending on the R - groups(side chains) of the amino aci L/ds - An example being enzymes ability to dissolve in water to catalyze reactions - Amino acids are the building blocks Lipids Interaction with water: Lipids are largely hydrophobic due to their long non-polar hydrocarbon chains Phospholipids are an exception beacuse they have hydrophilic heads and hydrophobic tails. An example being lipids do not dissolve in water water but can interact with other non polar solvents Nucleic Acids (DNA & RNA) Interaction with water: Highly hydrophilic due to their sugar-phosphate backbones and polar nitrogen bases An example being DNA & RNA dissolving in water which enables their roles in genetic information and storage In sum, Carbohydrates, Proteins and Lipids specifically take in water. DNA’s backbone contains deoxyribose RNA’s backbone contains ribose Different structures of DNA Primary structure - The linear sequence of nucleotide bases (Adenine, Thymine, Cytosine, Guanine) linked by phosphodiester bonds in a singe strand of DNA - Encodes genetic information in the specific sequence of bases - The order of nucleotides determines the genetic instructions for synthesizing proteins Secondary Structure - The double helix formed by two complementary DNA strands held together by hydrogen bonds between base pairs like (A-T and C-G) - Anti parallel orientation (5’ - 3’ & vice versa) - Major and minor grooves provide access for protein interactions (ex, transcription & enzymes) - Double helix protects genetic info by shielding the bases - Complementary base pairing allows for easy replication and repair Tertiary structure - The higher-order folding and supercoiling of DNA in the cell to fit into the nucleus - Supercoiled DNA: overwound or underwound DNA - Chromatins, DNA wrapped around histone proteins - Allows DNA to fit inside the nucleus - Interactions between R-groups and with their environment determine tertiary structure Quaternary Structure - Interactions of DNA with other molecules (proteins, RNA) to form functional complexes - DNA Protein complexes like chromatins and nucleosomes - Higher level chromosomal organization - Organizes and stabilizez the genome - Enables processes like transcription, replication and DNA repair Anaerobic and Aerobic Respiration Aerobic Respiration - Requires oxygen to produce energy - Takes place in the cytoplasm and mitochondria (eukaryotes) - Produces high amounts of ATP - Prodocues CO2 and H20 as byproducts Anaerobic respiration - occurs in the absence of oxygen  - Occurs only in the cytoplasm - Produces a lower amount of ATP - Produces lactic acid & CO2 *If molecules are packed more closely together, they have a better chance at becoming a solid *An electron state of potential energy is called its energy level or electron shell How is the chemical behavior of an atom determined? - Distribution of electrons in electron shells - The periodic table of elements shows the electron distribution of elements Valence electrons - Those in the outermost shell or valence shell - Elements with a full valance shell are chemically inert - Typically found in orbitals & each shell consists of a specific number of orbitals Subatomic particles - Atoms are composed of subatomic particles Most relevant subatomic particles include: - Neutrons (No electrical charge) - Protons (positive charge) - Electrons (Negative charge) *Electrons form a cloud of negative energy around the nucleus *Neutron and Proton mass are almost identical and are typically measured in daltons Isotopes - are two atoms of an element that differ in number of neutrons All atoms of an element have the same number of protons but may differ in number of neutrons *Radioactive isotopes decay spontaneously, giving rise to particles and energy Radioactive tracers are often used as diagnostic tools in medicine and can be used to track atoms through the metabolism *Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms A covalent bond is the sharing of a pair of valence electrons by two atoms to form a molecule In a nonpolar covalent bond, atoms share electrons equally (hydrophobic molecules) Weak chemical reactions - Most of the strongest bonds in organisms are covalent bonds that form a cells molecules - Many large molecules are held in their functional form by weak bonds - The reversibility of weak bonds can be used as an advantage Van der waals interactions - If electrons are not evenly distributed, they may accumulate by chance in one part of a molecule - Van der waals interactions are attractions between molecules that are close together as a result of these charges Photosynthesis chemical equation Sunlight powers the conversion of carbon dioxide and water to glucose and oxygen 6CO2 + 6H2O to create C6H12O6 + 6O2 All chemical reactions are reversible, theres always a reversible reaction *Chemical reactions are the making and breaking of chemical bonds Chemical Equilibrium - reached when the forward and reverse reactions occur at the same time - At equilibrium, the relative concentrations of reactants and products do not change - The two opposite headed arrows indicate that the reaction is reversible Unit 2 Histology - study of cells and tissues Cell Fractionation - Method to separate organelles by size - Heavier organelles precipitate out first All cells have cytoplasm, genetic material, ribosomes and plasma membrane Eukaryotic cells Specialized structures - Specialized functions, cilia or flagella Containers - Partition cell into compartments - Creates different local environments (separates pH, or concentrations of materials) Distinct & incompatible functions Lysosomes and its digestive enzymes Membranes as sites for chemical reactions - Unique combinations of lipids and proteins - Embedded enzymes & reaction centers Chloroplasts & mitochondria Plasma membrane - selective barrier that allows sufficient passage of oxygen, nutrients, and waste to service the volume of every cell - Small, non polar molecules can pass through - Large polar molecules can enter using channels and carriers Phospholipids - Amphipathic molecule - hydrophobic and hydrophillic ends - Notice double bond is one of the fatty acid tails which prevents clumping at low temperatures - Weak hydrophobic interactions lone holds membrane together - lipids and proteins can move sideways (rarely, lipids can flip flop through layers) Nucleus Nuclear Envelope - the bilayer membrane covering Nuclear Pores - tiny openings in the membrane that allow communication with the cytoplasm Nucleolus - the site of ribosome synthesis Chromatin - the tightly coiled thread-like DNA Ribosomes - Made in the nucleus - Free ribosomes in cytoplasm to make intracellular cytosolic proteins Bound of ER - to make proteins for plasma membrane and lysosomes to send out of the cell Endoplasmic Reticulum - ER Rough ER/Membrane Factory - Ribosomes;glycoproteins folded in lumen and secreted as vesicles; destined for plasma membrane Smooth ER - makes lipids, hydrolyze glycogen in liver, stores calcium ions, detox drugs by adding hydroxyl group which increases solubility Golgi Apparatus - Consists of flattened membranous sacs called cisternae - Modifies products of the ER - Manufactures certain macromolecules - Sorts and packages materials into transport vesicles Lysosomes - Membranous sac of hydrolytic enzymes to digest macromolecules (only in animals) - Works best in acidic pH 5 hence it is compartmentalized; lysosome mebrane pumps H+ into lysosomes - Stomach of the cell, digests materials - Made in the ER and processed in the golgi apparatus Autophagy - recycle organelles and macromolecules within cells When they do not work well.. - Lysosomal storage disorders like (Tay Sachs, Gaucher disease, Fabry disease) - Birth defects Vacuole Large vesicles derived from ER and golgi apparatus for storage Food vacuole - formed by phagocytosis Contractile Vacuoles - pump out excess water Central Vacuoles - mature plant cells to store organic compounds and water Chloroplasts Capture of light energy and conversion to chemical energy (Photosynthesis) In leaves, other green organs in plants and algae Consists of ribosomes, chloroplasts, thylakoids, stroma and intermembrane space Mitochondrion 1-100s in a cell according to energy needs Helps convert chemical energy in food to useable energy for cells in the form of ATP Cristae has many folds for high SA area - increase ATP - increase synthesis capacity - powerhouse of the cell Endosybiont Theory - an early ancestor of eukaryotic cells engulfed an oxygen using non-photosynthetic prokaryotic cell, involved a symbiotic relationship, this engulfed cell became the mitochondria One of these new cells later engulfed a photosynthetic prokaryotic cell. This became the ancestor of plant cells Cytoskeleton - provides mechanic support and shape (especially in animal cells) Microtubules - are hollow rods that shape the cell, move organelles and separate chromosomes in cell division Cilia and Flagella share a common structure Cell Wall  - Plant Cells, prokaryores, fungi, some unicellular eukaryotes - Protection, maintain shape, prevent excess uptake of water - Made of cellulose fibers embedded in other polysaccharides and proteins - Primary layer - thin, laid first - Secondary - thicker, closer to the plasma membrane - Middle lamella - between the two - Plasmodesmata are communication bridges in the cell wall Extra Cellular Matrix (ECM) - Animal cells have elaborate ECM - Made of glycoproteins like collagen - Binds to receptor proteins in the plasma membrane called intergrins - Communicates with cell and regulates cell behavior through integrins Phospholipids and Cholesterol - Membranes can solidify at low temperatures, depends on ratio of unsaturated to saturated lipids in the membrane - Cholesterol has different effects at different temperatures - Changes to lipid composition is a species-specific evolutionary adaptation Proteins in the Membrane - Proteins embedded in fluid matrix of lopid bilayer - Phospholipids - structural component Proteins - responsible for most of the functions of the membrane - Peripheral proteins, bound to the surface - Integral proteins, have hydrophobic core of one or more - Transmembrane proteins - integral proteins that span the membrane Unit 3 Selective Permability Hydrophobic non polar molecules (hydrocarbons) - dissolves in the lipid bilayer and passes through quickly Hydrophilic ions and polar molecules need membrane proteins for transport Receptor Proteins Intracellular receptors Introduction to Metabolism: Metabolism is the totality of an organism's chemical reactions - How energy is captured and utalized - It is an emergent property of life that arises from orderly interactions between molecules Metabolic Pathways - A specific molecule is altered in a series of steps to produce a product - Each step is catalyzed by a specific enzyme Catabolic Pathways release energy by breaking down complex molecules into simpler compounds in “Downhill” reactions like cellular respiration Laws of thermodynamics - Energy use/transfer by living things demonstrates the first law of thermodynamics  (Energy can be transferred or transformed, but not created or destroyed) - The conversion of energy to thermal energy released as heat by living things demonstrates the second law of thermodynamics (Every energy transfer or transformation increases entropy (disorder) of the universe Spontaneous vs Non-Spontaneous Processes - Processes that increase the entropy of the universe can occur spontaneously, needs no energy input; they can also happen quickly or slowly - Processes that decrease entropy are non spontaneous; they require an input of energy DeltaG = change in free energy DeltaH = change in enthalpy (total energy) DeltaS = change in entropy T = temperature in kelvin(k) *changes in free energy during a reaction is related to temperature, changes in enthalpy and entropy DeltaG for a process can be used to determine wether it is spontaneous or not *DeltaG represents the difference between free energy of the final state and free energy of the intial state Higher G = more stable Lower G = less stable Dehydration Synthesis - Anabolic reaction, Endergonic - needs energy input Hydrolysis - Catabolic reaction, Exergonic - Energy released and can be spontaneous How does ATP provide energy that preforms work? Phosphorylation, the transfer of a phosphate group from ATP to another molecule which is typically used to power endergonic reactions Enzymes Induced fit model - Enzymes are highly specific to the substrate - The reactant that an enzyme acts on is called the enzymes substrate - The enzyme binds to its substrate, forming an enzyme-substrate complex - While bound, the catalytic activity of the enzyme converts substrate to product - The active site is the region on the enzyme, often a pocket or groove, that binds to the substrate - The complementary fit between the shape of the active site and the shape of the substrate is responsible for enzyme specificity - When the substrate enters the active site, the enzyme changes slightly, tightening around the substrate like a handshake - This induced fit results from interactions between chemical groups on the substrate and active site. It brings the chemical groups of the active site into positions that enhance catalysis of the reaction  - The substrate is typically held in the enzymes active site by weak bonds, such as hydrogen bonds - The conversion of substrate to product happens rapidly, and the product is released form the active site Enzymes use a variety of mechanisms to lower the activation energy - Substrates may be oriented to facilitate the reaction - Substrates may be stretched to make the bonds easier to break - The active site may provide a microenvironment that factors the reaction - Amino Acids in the active site may participate in the reaction The rate of an enzyme-catalyzed reaction can be sped up by increasing the substrate concentration - When all enzyme molecules have their active sites engaged, the enzyme is saturated - If the enzyme is saturated, the reaction rate can only be sped up by adding more enzyme Factors that affect enzyme activity: - Enzyme concentration - Substrate concentration - Temprature - pH - Salinity Factors Affecting Enzyme Action - Activators (Molecules that turn on and increase enzyme activity) Cofactors - Non-protein, small inorganic compounds &i ion s - Bound within enzyme molecule - Mg, L, Ca, Zn, Fe, Cu Coenzymes - Non- proteins - Bind temporarily or permanently to enzyme near active site - Many vitamins - NAD, FAD, coenzyme Inhibitors (molecules that reduce enzyme activity) - Competitive inhibition - Noncompetitive inhibition (allosteric inhibitor) - Irreversible inhibition (competitor or alosteric) - Feedback inhibition Regulating Enzyme Action Allosteric Regulation - through conformational change Inhibitors - keeps enzyme in inactive form Activators - Keeps enzyme in active form Cooperativity - substrate itself acts as an activator substrate causing a conformational change in enzyme (induced fit) Cellular Respiration Overview of Cellular Respiration - Glucose is oxidized and oxygen is reduced in cellular respiration - Eukaryotes (plant and animal cells) break down organic molecules by cellular respiration in the mitochondria - In prokaryotes, cellular respiration reactions take place in the cytoplasm or cell membrane - The chemical energy in food is transformed into chemical energy in ATP - Some energy is released (or lost) to the environment as heat Energy flow and Matter cycling - Energy enters ecosystems as light and exits as heat - The chemical elements essential to life are recycled - In cellular respiration: - Catabolic pathways break down complex molecules to release stored energy - exergonic reactions Fermentation (anaerobic partial degradation) Aerobic (with oxygen) - Electron transfer from food to other carrier molecules - Catabolic pathways do not directly power work in the cell; they are linked to work by ATP *transferring energy during chemical reactions releases energy Redox Reactions: Oxidation and Reduction - Chemical reactions that transfer electrons between reactants are called oxidation-reduction reactants are called oxidation-reduction reactions, or redox reactions In redox reactions, the loss of electrons from a substance is called oxidation - The electron donor is called the reducing agent - The addition of electrons to a substance is called reduction - the electron acceptor is called the oxidizing agent, it oxidizes the electron donor *An electron loses potential energy when it shifts from a less electronegative atom toward a more electronegative one *Redox reactions that move electrons closer to electronegative O atoms release energy Oxidation = loss of electrons Reduction = gain of electrons Electron Transport Chain (ETC) If NADH transferred electrons directly to oxygen, energy would be released in one explosive reaction - Instead, cellular respiration uses an electron transport chain to break the fall of electrons to O2 into several energy - releasing steps An electron transport chain consists of a series of molecules built into the inner membrane of the mitochondria (or cell membrane of prokaryotes)  - NADH (electron carrier) passes electrons to the electron transport chain where they are transferred in a series of redox reactions, each releasing a small amount of energy - O2 is the final electron acceptor - Energy yielded in the ETC is used to regenerate ATP Role of ATP - The free energy used for starting reactions (activation energy) - ATP is energetically unstable; like a tightly coiled spring Example: Phosphorylation of glucose in cell respiration, Na/K pump ATP hydrolysis is energetically favorable/ exergonic It is paired with an energetically unfavorable/ endergonic reaction usually with a shared intermediate Overview of cellular respiration Glycolysis pyruvate oxidation Citric Acid Cycle Oxidative Phosphorylation Glucose to pyruvate to acetyl coA to to Stages of cellular respiration Harvesting energy from glucose bu cellular has three stages: - Glycolysis breaks down glucose into two molecules of pyruvate - Pyruvate oxidation and the citric acid cycle complete the breakdown of glucose to CO2 - During Oxidative phosphorylation the electron transfer chain and chemiosmosis facilitate the synthesis of most of the cells ATP Phosphorylation Oxidative - 90% ATP generated this way - Powered by stepwise redox reactions - ETC and chemiosmosis Substrate level - Limited ATP produced - Glycolysis and TCA cycle - An enzyme transfers a phosphate group directly from a substrate to ADP Glycolysis Harvest chemical energy by oxidizing glucose to 2 molecules of pyruvate Glycolysis occurs in the cytoplasm and has two major phases 1. Energy investment phase, 2 ATP are used to split glucose in to 2 three-carbon sugar molecules 2. Energy payoff phase, 4 ATP are synthesized, 2NAD+ are reduced to NADH, the small sugars are oxidized to form 2 pyruvate and 2 H2O A new of 2 ATP are produced by substrate-level phosphorylation during glycolysis Pyruvate Oxidation If O2 is present, - Pyruvate enters a mitochondrion to complete glucose oxidation in eukaryotic cells - Occurs in the cytosol for aerobic prokaryotes Pyruvate is concerted to acetyl coenzyme A The citric acid cycle (TCA cycle/krebs cycle) TCA cycle oxidizes organic fuel derived from pyruvate, generating 1 ATP, 3 NADH and 1 FADH per turn 2 Co2 are produced as waste products Chemiosmosis The energy released as electrons are passed down the ETC and that is used to pump H+ protons from the mitochondrial matrix to the intermembrane space H+ then moves down its concentration gradient back across the membrane, passing through the protein complex ATP synthase During cellular respiration, most energy flows in this sequence Glucose to NADH to ETC to proton-motive force to ATP *An appropriate negative control for repeating an experiment with enzymes is a denatured enzyme Factors that influence Photosynthesis Light intensity Effect: photosynthesis increases as light intensity increases, up to a certain point where it plateaus Why: Light provides the energy needed to split water molecules and power the Calvin cycle Carbon dioxide Effect: Higher CO2 levels generally increase photosynthesis rates, as CO2 is the key reactant Limitation: Beyond a certain concentration, the rate stabilizes as other factors become limiting Temperature Effect: Photosynthesis is a temperature dependent, as enzymes involved function optimally within a certain temperature range Extremes: Excessively high temperatures and low temperatures can denature the enzyme though Factors that influence Cellular Respiration Oxygen Availability Effect: oxygen is essential for aerobic respiration (final electron acceptor in the ETC) Limitation: In low oxygen conditions, cells switch to anaerobic respiration Glucose (or substrate) Availability Effect: Glucose is the main fuel for cellular respiration. Low glucose levels reduce the rate of respiration Alternative Fuels: Lipids and proteins can also be used when glucose is scarce Temperature Effect: Enzymes involved in glycolysis, the Krebs cycle, and the electron transport chain operate optimally within specific pH ranges Extremes: Too high or too low of temperatures can denature the enzymes involved in the process. Unit 4 How do cells communicate with each other? Cells communicate with each other through chemical signals sent between signaling and target cells. Communication can also occur between short and long distances - Short-distance communication: Signals (ex, neurotransmitters) travel between cells that are close together, like across a synapse or via gap junctions - Long-distance communication: Signals (ex, hormones) are transported through the bloodstream or other fluid systems to reach distant target cells *Local signaling is especially important in embryonic development, immune response, and maintaining adult stem cell populations Components of a signal transduction pathway A signal transduction pathway allows a cell to convert an extracellular signal into a response involving three steps: 1. Reception - A signaling molecule (ligand) binds to a specific receptor on the target cell - Receptors can be on the cell membrane (G-coupled Receptors) or intracellular 2. Transduction - The binding of the ligand activates the receptor, initiating a series of intracellular events - This often involves a cascade of molecular interactions, where proteins or second messengers relay the signal 3. Response - The signal triggers a specific cellular response like gene response, enzyme activation or changes in cell behavior Cell communication and feedback in homeostasis Feedback Mechanisms: Negative feedback: reduces the process of maintaining homeostasis Example: insulin reduces blood glucose levels when they are too high, bringing them back to a normal stage - Negative feedback brings systems back to a set point or homeostasis Positive Feedback: Amplifies a process until a specific event occurs - Positive feedback moves systems away from set point or causes homeostatic imbalance Maintaining homeostasis: Communication pathways ensure that cells detect and respond to the changes in the environment correcting deviations from the opposite states Example: Temperature regulation via hypothalamus-meditated feedback loops Types of cellular respiration 1. Gene Expression: - Activating or repression of specific genes to produce proteins necessary for a function of adaptation Example: Hormones like estrogen trigger gene expression changes 2. Enzyme Activation - Modulation of an enzyme activity to increase or decrease metabolic reactions Example: Activation of glycogen phosphorylase during flight or fight response 3. Changes in cell behavior - Alternation of movement, growth or apoptosis Example: immune of cells migrating toward infection sites in response to cytokinase signals Role of the Environment - External signals: Environmental factors like temperature, light or chemical signals (ex, phermones) can trigger cell communication - Internal Signals: Signals from within the organism, such as blood glucose levels, direct cellular activity - Structural Changes in Signaling Molecules Receptor Mutations: - Mutations in receptors can prevent ligand binding or after reception function - Example: Insulin receptor mutations can lead to diabetes by disrupting the glucose uptake Ligand Modifications: - Changes in the shape or chemical structure of a ligand can affect the binding affinity and signaling - Example: A defective epinephrine analog might fail to activate the receptor, reducing the fight-or-flight response Pathway Disruption: - Mutations in downstream signaling molecules can amplify, reduce or entirely block signal transduction pathways External Signals are converted to response within the cell - Cell signaling is critical to prokaryotes even though they are unicellular - A concentration of signaling molecules allows bacteria to sense local population density in a process called quorum sensing More info on Cell Reception - The binding between a signal molecule(ligand) and receptor is highly specific - A shape in a receptor is generally the initial transduction of the signal - Most signal receptors are plasma membrane proteins, but others are located inside the cell  - Receptors in the plasma membrane - G protein-coupled receptors are the largest family of cell surface receptors - Most water-soluble signal molecules bind to specific sites on receptor proteins that transmit information from the extracellular environment to the inside of the cell Three main types of receptors: - G protein-coupled receptors - Receptor tyrosine kinases - Ion Channel receptors Intracellular Receptors - Intracellular receptor proteins are found in the cytoplasm or nucleus of target cells - Small or hydrophobic chemical messengers can readily cross the membrane and activate receptors - Examples of hydrophobic messengers are the steroid and thyroid hormones of animals - An activated hormone-receptor complex can act as a transcription factor, turning on or off specific genes *Protein phosphates rapidly remove the phosphates from proteins, a a process called dephosphorylation *Ca2+ can function as a second messenger because its concentration in the cytosol is normally much lower than the concentration outside the cell Regulation of the response A response to a signal may not be simply on or off There are four aspects of signal regulation: 1. Amplification of the signal 2. Specificity of the response 3. The overall efficiency of response, enhanced by scaffolding proteins 4. Termination of the signal Signal Amplification - Enzyme cascades amplify the cell's response to the signal - At each step, the number of activated products can be much greater than in the preceding step The specificity of cell signaling and coordination of the response - Different kinds of cells have different collections of proteins - These different proteins allow cells to detect and respond to different signals - The same signal can have different effects in cells with different proteins and pathways - Pathway branching and “cross talk” further help the cell coordinate incoming signals Termination of the signal - Inactivation mechanisms are an essential aspect of cell signaling - If the concentration of external signaling molecules falls, fewer receptors will be bound - Unbound receptors revert to an inactive state Role of Integrins - Principal receptor proteins used by animal cells to bind the extracellular matrix - Heterodimers that function as transmembrane linkers between the extracellular matrix and the actin cytoskeleton  - A cell can regulate the adhesive activity of its integrins from within - Also function as signal transducers, activating various intracellular signaling pathways when activated by matrix binding Apoptosis requires the integration of multiple cell signaling pathways Cells that are infected, damaged, or at the end of their functional lives often undergo “programmed cell death” (apoptosis) - Apoptosis is the best-understood type - Components of the cell are chopped up and packaged into vesicles that are digested by scavenger cells - Apoptosis prevents enzymes from leaking out of a dying cell and damaging neighboring cells *Apoptosis can be triggered by signals from outside the cell or inside it - Internal signals can result from irreparable DNA damage or excessive protein misfolding The cell cycle - The ability of organisms to produce more of their own kind is the one characteristic that distinguishes living things from nonliving matter - Continuity of life is based upon the reproduction of cells or cell division - Cell division is remarkably accurate in passing DNA from one generation to the next - All the DNA in a cell constitutes the cell's genome - A genome consists of a signal DNA molecule - DNA molecules are packaged into chromosomes Chromatin vs chromosome vs chromatid Chromatin - all the DNA/proteins in the nucleus condense to form chromosomes during mitosis Chromatid - Sister chromatids derived from daughter cells after cell division before chromosome duplication Chromosomes - condensed chromatin.. Either 2 sister chromatids or 1 chromatid In 1882, the German anatomist walther flemming developed dyes to observe chromosomes during mitosis and cytokinesis The cell cycle consists of - Mitotic (M) phase (Mitosis and cytokinesis) - Interphase (cell growth and copying of chromosomes in preparation for cell division The mitotic spindle - The mitotic spindle is a structure made of microtubules that controls chromosome movement during mitosis - The centrosome replicates during the interphase(S) phase, forming two centrosomes that migrate to opposite ends of the cell during prophase and prometaphase - The spundle includes the centrosomes, the spindle microtubules, and the asters - Each sister chromatid has a kinetochore In anaphase, the cohesins are cleaved by an enzyme called separase  - Sister chromatids separate and move along the kinetochore microtubules towards opposite ends of the cell *Prokaryotes reproduce by a type of cell division called binary fission Meiosis & Sexual LIfe Cycles Describe the similarities and/or differences between the phases and outcomes of mitosis and meiosis Similarities: Fundamental Processes - Both involve the division of parent cell in to daughter cells - Both follow the same stages of prophase, metaphase, anaphase and telophase - Both involve DNA replication during the S phase of the cell cycle prior to division Chromosome Behavior - Chromosomes condense, align and separate using spindle fibers in both processes - Sister chromatids are pulled apart during anaphase of mitosis and anaphase 2 of meiosis Cytokinesis - Both processes typically end with cytokinesis, dividing the cytoplasm to produce separate cells Feature Mitosis Meiosis Growth, repair, and asexual Purpose Production of gametes for sexual reproduction. reproduction. Number of Divisions One division. Two divisions (Meiosis I and Meiosis II). Number of Daughter Two daughter cells. Four daughter cells. Cells Ploidy of Daughter Diploid (2n), identical to Haploid (n), containing half the chromosomes of the Cells parent cell. parent cell. No variation; cells are Genetic variation due to crossing over and Genetic Variation identical. independent assortment.  Homologous Do not pair or exchange Pair during prophase I (synapsis) and exchange Chromosomes segments. genetic material (crossing over). Homologous chromosomes separate during Sister chromatids separate Chromatid Separation anaphase I, and sister chromatids separate during during anaphase. anaphase II. Occurs in Somatic (body) cells. Germ (sex) cells. Phases and their differences 1. Prophase Mitosis: Chromosomes condense, and spindle fibers form Meiosis 1: Homologous chromosomes pair up (synapsis) and undergo crossing over 2. Metaphase Mitosis: Individual chromosome lines align at the metaphase plate Meiosis 1: Homologous pairs align at the metaphase plate Meiosis 2: Individual chromosomes align similarly to mitosis 3. Anaphase Mitosis: sister chromatids are pulled apart Meiosis 1: Homologous chromosomes are pulled apart Meiosis 2: Sister chromatids are pulled apart 4. Telophase Mitosis: Two identical nuclei form Meiosis 1: Two haploid nuclei form, but each still contains duplicated chromosomes Meiosis 2: Four haploid nuclei form Outcomes of the processes Mitosis: - Two genetically identical diploid cells - Maintains chromosome number (2n) - No genetic variation Meiosis: - Four genetically unique haploid cells - Reduces chromosome number (2n to n) - Introduces genetic variation via crossing over and independent assortment Offspring/Heredity The transmission of traits from one generation to the next is called inheritance, or heredity Meiosis - 2n to 2n to 1n & 1n to 1n & 1n & 1n &1n Mitosis - 2n to 2n to 2n & 2n *Each chromosome has two chromatids Karyotype - An ordered display of the pairs of chromosomes from a cell The fertilized egg is called a zygote and the zygote produces somatic cells by mitosis and develops into an adult Mutations (changes in a organisms DNA) are the original source of genetic diversity - Mutations create different versions of different alles - Reshuffling of alleles during sexual reproduction produces genetic variation Three mechanisms contribute to genetic variation - Independent assortment - Crossing over - Random Fertilization Crossing Over - Crossing over produces recombinant chromosomes, which combine DNA inherited from each parent - Crossing over contributes to genetic variation by combining DNA from two parents into a single chromosome - In humans, an average of one to three crossover events occur per chromosome Random Fertilization Random fertilization adds to genetic variation because any sperm can fuse with any ovum (unfertilized egg) Natural Selection results in the accumulation of genetic variations favored by the environment Unit 5 Autosomal Dominant (each gen has the disease, each individual has an affected parent) - Vertical Pattern: Multiple generations affected - Males and females equally like to be affected - See male-to-male transmission - Each child of an affected individual has a 50% chance to be affected - Every affected child has an affected parent Autosomal Recessive (Parents, grandparents and great have normal phenotype) - Horizontal pattern: single generation affected - Males and Females equally like to be affected - Parents of affected children are unaffected gene carriers and have a 1 in 4 or 25% recurrence risk - Unaffected siblings have a 2/4 or 67% chance to be carriers - Children of affected individuals are obligate carriers X-Linked Recessive (Male only, skips generations) - Males are more often affected than females - Affected males pass the gene to all of their daughters and none of their sons (NO male-to-male transmission)  - Daughters of carrier females have a 50% chance to be unaffected carriers. Sons of carrier females have 50% chance to be affected - Affected males in the family are related to each other through carrier females X-Linked Dominant - For rare conditions, females ar about 2x as likely to be affected than males. May be lethal in males and usually milder, variable in females. - Affected males pass the gene to all of their daughters, who will be affected, and none to their sons. - Sons and daughters of affected females have a 50% chance of being affected Mitochondrial Inheritance - Maternal inheritance, is passed down only by egg cell which has mitochondria with a mutation on mtDNA - Affected males do not pass on genes to offspring, because sperm does not contribute to mitochondria - Not lethal, since there are many mitochondria in each cell, and there will be some other normal mitochondria with functional mtDNA. Mendels Principles 1. Alternate versions of genes (alleles) cause variations in inherited characteristics among offspring 2. For each character, every organism inherits two alleles, one allele from each parent 3. If 2 alleles are different, the dominant allele will be fully expressed; the recessive allele will have no noticeable effect on offsprings appearance 4. Law of segregation: the 2 alleles for each heritable character separate during gamete formation Complete dominance - Heterozygous phenotype same as that of homozygous dominant( (PP or Pw) Incomplete dominance - Heterozygous phenotype intermediat between the two homozygous phenotypes (C*R C*R or C*R C*W) Codominance - Both phenotypes expressed in heterozygous (I*A I*B) Pleiotropy - One gene is able to affect multiple phenotypic characteristics Chromosome theory of inheritance - Genes have specific locations (loci) on chromosomes - Chromosomes segregate and assort independently *Drosophilia melanogaster - fruit fly - Fast breeding with short-generation time - Only 4 pairs of chromosomes - Produce many offspring *Fathers pass X-linked genes to daughters but not sons X-inactivation Barr Body - Inactive X chromosome; regulates gene dosage in females during embryonic development SRY gene - sex-determining region of Y chromosome Genetic Recombination - Production of offspring with new combo of genes from parents If they look like their parents, they are parental types If they look different, they are recobinants *If results do not follow mendels law of independent assortment, then the genes are probably linked Linked genes:located on the same chromosome and tend to be inherited together during cell division *crossing over explains why some linked genes get separated during meiosis Genomic Imprinting Genomic imprinting: phenotypic effect of gene depends on wether from M or F parent Methylation: Silence genes by adding methyl groups to DNA Methylation: Silence genes by adding methyl groups to the DNA Nondisjunction - Aneuploidy: Incorrect # of chromosomes - Polyploidy: 2+ complete sets of chromosomes *Can end up leading to down syndrome *karyotypes can detect non disjunction Alterations of chromosome structure Breakage of a chromosome can lead to four types of changes in chromosome structure - Deletion: removes a chromosomal fragment - Duplication: repeats a segment - Inversion: reverses orientation of a segment within a chromosome - Translocation: moves a segment from one chromosome to another