AP BIOLOGY EXAM: CONTENT REVIEW PAGE 1 Unit 0: Biological Skills and Experimental Design Scientific Method: 1. Define the Problem 2. Formulate a Hypothesis 3. Carry out a Controlled Experiment - Control Group and Experimental Group - Independent, Dependent, and Controlled Variables 4. Collect, Organize, and Analyze Data - Tables, Graphs, Charts, Etc 5. Draw Conclusions - Relate to Hypothesis 6. Identify sources of error and suggestions for future and/or repeated procedures. Definitions: Independent Variable - The manipulated (changing) variable in an experiment. Dependent Variable - The responding (measured) variable in an experiment. Experimental Group - The group that is acted upon by the independent variable. Control Group - The group that is not acted upon by the independent variable. Constants - The factors that must remain the same between the experimental and control group in an experiment. Hypothesis - A testable statement that includes information about the independent and dependent variables with a directionality prediction. Collecting and Organizing Data: D - Dependent Variable R - Responding Variable Y - Graph information on Y axis M - Manipulated Variable I - Independent Variable X - Graph information on X axis Title - “The effects of [independent variable] on [experimental group] as measured [by the dependent variable / over time].” Labels - Variable / time (units) Scale - Scale must be uniform and follow ⅔’s rule for provided graph space. Bar Graph - Snapshot of multiple groups (Usually an average at the conclusion of an experiment) AP BIOLOGY EXAM: CONTENT REVIEW PAGE 2 Line Graph - Overview of a single measurement over a range of time, distance, temperature, etc Double-Y Axis - Allows you to compare trends in the variables/groups in relation to each other. Log-Based Y-Axis - Allows you to graph a large range of values and still analyze trends in the data. Graphing analysis: Comparing Two Data Points: “How many times greater is point A than point B?” - Point A / Point B Analyzing Trend: “What is the rate of change?” - Y2 - Y1 / X2 - X1 Comparing Trends: “What is the relationship?” - As X (Increases, decreases, or remains constant), Y (Increases, decreases, or remains constant). Drawing Conclusions: Standard Error of the Mean: - “The give or take / room for error” - +/- 2 SEM = 95% confidence interval - Overlapping of SEM’s at +/- 2 SEM is not acceptable for drawing conclusions. Chi Square: - Used to determine if the difference that is noted can be attributed to random chance, or does there have to be an external factor affecting the outcome - “Is what we observed significantly different from that which we would expect” Null Hypothesis: - A prediction of the outcome based on the most simple set of circumstances. - The development of a Null hypothesis is used to know what we should be “expecting” - “The [independent variable] will have no impact on the [dependent variable], thus there will be no significant difference between the measurements of [the experimental] and [control groups].” Chi Square Process: 1. Development of a Null Hypothesis 2. Using the formula for Chi-Square calculate the numerical value known as “X Stat” 3. Compare “X Stat” to “X Critical” using the chart provided in your formula sheet - P = 0.05 - df = Number of categories minus one Analyzing Chi Square Results: - “X Stat” > “X Critical” = Rejection of null hypothesis = Cannot be random chance AP BIOLOGY EXAM: CONTENT REVIEW PAGE 3 - “X Stat” < “X Critical” = Fail to reject null hypothesis = Could be random chance. Limitations of Statistical Analysis: - Sample size bias AP BIOLOGY EXAM: CONTENT REVIEW PAGE 4 Unit 1: Chemistry of Life Elements of Life - CHNOPS (COHN) - Organisms must exchange matter with the environment to grow, reproduce, and maintain organization Inorganic Chemistry - Living systems depend on properties of water that result from its polarity and hydrogen bonding - Cohesion, Adhesion, and Surface Tension. Organic Molecules Overview - Dehydration synthesis and hydrolysis - Monomer vs Polymer Macromolecules - Carbohydrates - Monosaccharide monomers; short term energy - Nucleic Acids - Nucleotide monomers; DNA vs RNA - Lipids - Saturated vs Unsaturated Fats, Phospholipids; multiple functions - Proteins - Amino Acid monomers (Levels of organization); multiple functions - Enzyme Structure - Active Site / Substrate Compatibility - Structure - Chemical Compliance - Enzyme Catalysts - Lowering Activation Energy to Speed Up Reactions - Environmental Impacts on Enzyme Function - Change in Structure = Change in Function - Denaturing (Temperature and pH) - Regulation - Competitive vs Non-Competitive Chemistry In Biology: Primary Components and Elements: - All living things are composed of five primary components: - Water, Carbohydrates, Lipids, And Nucleic Acids - The following elements are considered essential for life: - Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorous, and Sulfur. (CHNOPS) AP BIOLOGY EXAM: CONTENT REVIEW PAGE 5 Law of Conservation of matter: - The elements for life cannot be made and therefore must be recycled. (Cycles) - Biotic Component (Food Chain) -> Decomposition -> Abiotic Component -> Repeat - Example: Water Cycle - Evaporation -> Condensation -> Precipitation - Transpiration: - Water evaporates through the leaves of plants - Cohesion and Adhesion allow capillary action to occur pulling water from roots to leaves. - Example 2: Carbon Oxygen Cycle - Photosynthesis -> (Food Chain) -> Cell Respiration Inorganic Chemistry: Importance of Water: - Water is the most important inorganic substance (Lacking Carbon) to life on earth. - Water provides a matrix (a surrounding medium) for chemical reactions and is essential for energy production in ecosystems. (Photosynthesis) Properties of Water: - The properties of water stem from its polarity - Water has a partial negative charge on the “oxygen side” and a partial positive charge on the “hydrogen side” due to oxygen’s electron sharing with the two hydrogens. - Water molecules bond via Hydrogen bonding. - Cohesion: Water sticks to itself - High Specific Heat (Doesn’t change temperature easily) - Adhesion: Water bonds to other polar molecules - Universal Solvent - Things that bond to water are considered Hydrophilic - Things that do not bond to water are considered Hydrophobic AP BIOLOGY EXAM: CONTENT REVIEW PAGE 6 Definitions: Organic - Containing Carbon Carbohydrates - Energy Source Lipids - Energy, Insulation, Etc Proteins - Structure, Function, Energy Nucleic Acids - Genetic Material Monomer: A molecule that can be bonded to other identical molecules to form a polymer. Polymers: A large molecule that is composed of many repeated subunits. Organic Polymers: Structure Follows Function: - How monomers are arranged determines the function of the polymer - Type, Number, Orientation, Etc Important Processes: Dehydration Synthesis: Removing water to combine monomers - Requires Energy Input Hydrolysis: Adding water to split apart monomers - Process of breaking polymers back into its base monomers - Releases energy through breaking of chemical bonds. AP BIOLOGY EXAM: CONTENT REVIEW PAGE 7 Carbohydrates: Functions of Carbohydrates: - The primary biological function of carbohydrates is energy production. - Breaking down carbohydrates in the process of cellular respiration produces energy required for different metabolic processes.- - The secondary function of carbohydrates is structure - Cellulose (Plant cell wall) - Chitin (Exoskeleton) Monosaccharides (Isomers): - Glucose, Fructose, and Galactose - All have the same chemical make up (C6H12O6) but differ in structure. Disaccharides: - Two monosaccharides joined together by the process of dehydration synthesis and held together by a Glycosidic Linkage - Maltose = Glucose + Glucose - Sucrose = Glucose + Fructose - Lactose = Glucose + Galactose Glycosidic Linkage: A bond between two monosaccharides formed by dehydration synthesis. Polysaccharides: More than two monosaccharides joined together to form larger chains. - Plant Starch, Glycogen, and Cellulose - All are glucose polymers. Plant Starch: - Plants produce glucose during photosynthesis using what they need and then storing the rest in the form of starch. - Stored heavily in plant’s seeds, roots, and fruits in cell organelles called plastids. Glycogen: - Animals consume glucose using what they need and storing the rest away in the form of Glycogen. - Stored in muscles and liver cells. AP BIOLOGY EXAM: CONTENT REVIEW PAGE 8 Cellulose: - Structural carbohydrate found in plants - “Green” plants are high in cellulose - Due to the structural differences seen in cellulose (Alternating monomers are rotated from one another), heterotrophs don’t have the ability to digest cellulose. - To digest cellulose, heterotrophs rely on bacteria in their intestinal tract to break down polysaccharides into their usable monosaccharides. Carbohydrates in the diet: - Once glycogen reserves are full, extra carbohydrates are converted into fats. - 4 calories per 1 gram of carbohydrates - Makes up roughly 60% of daily caloric intake - 3,500 additional calories from carbohydrates equals one pound of fat storage Lipids: Types of Lipids: - Fats, Oils, Waxes - Phospholipids - Cholesterol - Steroids Properties of Lipids: lipids are hydrophobic because they do not have polar or ionic properties Fats: Are not true polymers, they are large molecules formed by smaller molecules joined by dehydration synthesis. - Components = Glycerol + Fatty Acid Tails Ester Linkage: 3 Bonds that hold fatty acids to the glycerol backbone. - Formed from dehydration synthesis - Forms one fat molecule known as a triglyceride (tri = 3, glyceride = chains of glucose.) Saturated Fats: - No double bonds between carbons in the fatty acid tails. - Straight chain, Solid at room temperature, typically found in animal fats and butter - Healthier Unsaturated Fats: - At least one double bond in the carbon chain causing a kink. - Bent chain, Liquid at room temperature, typically found in plant fats or fish fats, and are usually called “oils” - Diets rich in saturated fats typically leads to atherosclerosis (a buildup of plaque in arteries) making them less healthy AP BIOLOGY EXAM: CONTENT REVIEW PAGE 9 Hydrogenated Oils: - Makes saturated fats by adding hydrogen bond to fatty acid chain “unbending it” but also makes a trans double bond or Trans Fat. These have a greater effect on cardiovascular disease. Function of Fats: - Energy Dense storage. - Can store two times as much energy compared to carbohydrates. - Density is favorable due to the mobile nature of animals versus plants that can afford to store energy as large starch compounds because they are immobile. - Stored in adipose tissue - Cushioning Vital organs, - Body insulation, - Dissolving important vitamins. Waxes: - One fatty acid tail joined to a long chain alcohol. - Exhibits extremely hydrophobic properties. Phospholipids: - Composes cell membranes - Only 2 fatty acid tails instead of 3 (one saturated, one unsaturated) - The final hydroxyl group is joined to a phosphate group giving the “head” of a phospholipid a slightly negative charge making them hydrophilic and the tails hydrophobic - Head = Hydrophilic - Tail = Hydrophobic - In a aqueous environment phospholipids assemble into bilayer (Cell membrane) because of their hydrophobic/hydrophilic properties Cholesterol: - Common in animal cell membranes and is synthesized in the liver - Precursor from which many steroid hormones are made - Too much can lead to atherosclerosis. - HDL = Good cholesterol - LDL = Bad cholesterol (Causes plaque buildup in arterial pathways) - Prevents blood flow to the heart = heart attack - Prevents blood flow to the brain = stroke - Prevents blood flow to limbs = Peripheral Artery Disease Steroids: - Characterized by a Carbon Skeleton consisting of four fused rings - Many hormones, like estrogen and testosterone, are steroids - Steroid variation depends on the chemical group joined to the four ring structure derived from cholesterol. AP BIOLOGY EXAM: CONTENT REVIEW PAGE 10 Structural Models of Lipids: Unsaturated Fats: AP BIOLOGY EXAM: CONTENT REVIEW PAGE 11 Saturated Fats: Hydrogenated Oils: AP BIOLOGY EXAM: CONTENT REVIEW PAGE 12 Phospholipids: Phospholipid Bilayer Example: AP BIOLOGY EXAM: CONTENT REVIEW PAGE 13 Cholesterol: Nucleic Acids: Adding Nitrogen to CHOP: - So far Carbohydrates and Lipids have only included CHO and P of CHNOPS. Proteins and Nucleic Acids introduce Nitrogen. Structure of Nucleic Acids: - True polymers made of nucleotide monomers - Nucleotide Structure: - Phosphate Group - 5 Carbon Sugar (Deoxyribose (DNA) / ribose (RNA) - Nitrogenous Base Purines: 2 Carbon Rings - Adenine (A) and Guanine (G) Pyrimidines: 1 Carbon Ring - Thymine (T), Cytosine (C), and Uracil (U)* - Uracil is only found in RNA, while Thymine is found only in DNA. AP BIOLOGY EXAM: CONTENT REVIEW PAGE 14 Phosphodiester bonds: - Similar to Ester Linkages in fats, phosphodiester bonds hold nucleotides together between phosphate groups and the next adjacent sugar, formed through dehydration synthesis. - Leaves a phosphate attached to the 5’ carbon of one end, and has an OH bonded to the 3’ carbon of the other end. - The two distinct ends (5’ end and 3’ end) give the molecule directionality. - The numbers come from the carbons composing the sugar. DNA: Deoxyribose Nucleic Acid - Double strand of nucleic acid chains - Strands are antiparallel (Run in opposite directions) - Uses ATGC (A=T and G=C) - Must stay in the nucleus of cell - Serves as storage for genetic code AP BIOLOGY EXAM: CONTENT REVIEW PAGE 15 RNA: Ribose Nucleic Acid - Single strand of nucleic acid chain - Uses AUGC (A=U and G=C) - Freely moves from nucleus to the ribosomes - Transports a copy of genetic code Proteins: Central Dogma of genetics: DNA -> RNA -> Protein Functions of Proteins: - Enzymes, Structure, Storage, Transport, Hormones, Receptors, Motor, Defense, Energy - Proteins account for about 50% of the dry mass of any given cell. Polypeptides: - Proteins are true polymers composed of 20 monomers called amino acids of which there are 11 essential and 9 non essential. - A protein consists of one or more polypeptides folded and coiled into specific 3-D structures. Amino Acid Structure: - All Amino Acids have the same structure with one differing group (R-Group) - Each consists of an alpha carbon joined to an Amine (Amino) group, a Carboxyl group, a single hydrogen, then a variable known as the R group. AP BIOLOGY EXAM: CONTENT REVIEW PAGE 16 Bonding of Amino Acids: - Amino acids join together by a carboxyl group bonding with a amine group through dehydration synthesis to form a peptide bond. - This leaves a free amino group at one end (N-Terminus) and a free carboxyl group at the other (C-Terminus) 3D Structure of Proteins: - The function of a protein is directly tied to its 3D shape that results from intricate folding of the chain. (STRUCTURE FOLLOWS FUNCTION) Primary Structure: Unique sequence of Amino Acids (from inherited genetic information) Secondary Structure: Folding due to hydrogen bonding between the backbone of the chain. - Alpha helix every 4th amino acid - Beta Pleated Sheets: Two or more regions of the chain lying side by side that are hydrogen bonded to each other. Tertiary Structure: The overall 3D shape of the protein resulting from interactions between the side chains - R-Groups interacting with each other and water. AP BIOLOGY EXAM: CONTENT REVIEW PAGE 17 Quaternary Structure: Multiple polypeptide chains that are put together to form one macromolecule. (Not all proteins have a quaternary structure) Examples of 3D shape importance: - Antibodies, Enzymes, Receptor Proteins Denaturation: - Because structure follows function. The changing of the shape of a protein is to denature it. - pH, Salinity, Temperature, Etc can all affect denaturation. - Causes changes in the folding pattern which alters 3D structure. (Fevers) Other Changes In Shape: - A genetic mutation will change primary structure leading to a different 3D structure. - (Negative mutation) disease and (Positive mutation) adaptation Enzymes: Importance of Enzymes: - Enzymes act as biological catalysts. They lower the amount of activation energy needed in order to get a reaction to occur. Reactions can either be Catabolic (Break down) or Anabolic (Build up). - Named primarily after their substrates and tend to end in -ase. Enzyme Function: - An enzyme’s function is tied directly to its shape. In particular the shape of its active site. - In order to function, the substrate must fit structurally and comply chemically to the active site of the enzyme. AP BIOLOGY EXAM: CONTENT REVIEW PAGE 18 Theories of Enzyme Function: Lock and Key Model: There is only one enzyme for one substrate. Induced Fit Model: One enzyme may play a role in the reaction for more than one substrate, as long as they are very similar in shape. The enzyme has the ability to slightly change shape after the substrate binds making it slightly more versatile. Other Factors Affecting Enzyme Function: - Co-Factors: Inorganic compounds that bind to the enzyme and ain in the joining of the enzyme to its substrate. - Often are ionic elements and are more commonly known as minerals. - Co-Enzymes: Organic compounds that bind to the enzyme and ain in the joining of the enzyme to its substrate. - Non-Protein - More commonly known as vitamins. - Both of these must be present for many enzymes to function properly, facilitating chemical compliance of the substrate to the active site. - At the point of saturation increasing concentration does not affect reaction rate. AP BIOLOGY EXAM: CONTENT REVIEW PAGE 19 Enzyme Regulation: - There are two primary means of enzyme regulation. Competitive Inhibition and Non-Competitive Inhibition (Allosteric Regulation) Competitive Inhibition: Chemical blocks the active site and prevents substrate binding. Non-Competitive Inhibition: Chemical bound to a different site on the enzyme that makes the active site undergo conformational change (shape change), still preventing enzyme function. AP BIOLOGY EXAM: CONTENT REVIEW PAGE 20 Unit 2: Cell Structure and Transport Eukaryotic vs Prokaryotic: Endosymbiotic Theory: - The evolutionary process by which eukaryotic cells were derived from prokaryotic cells. Evidence for Endosymbiotic Theory: - Mitochondrial DNA - Circular Chromosome.(Similar to chromosomes found in prokaryotes) - Double Membrane - Shape Cell Size: - Surface area to volume ratio limits cell size. - There are many ways to increase this ratio. (Dividing/Folding) - The higher this ratio ( SA / V ), the more efficient the cell can function. AP BIOLOGY EXAM: CONTENT REVIEW PAGE 21 Organelles: - Specific structures used for specific purposes. Most are a part of the endomembrane system in that they are membrane bound and directly or indirectly connected - Use of membrane bound organelles localizes reactions and compartmentalizes function (minimizes competing creations), increases surface area for reactions, and thus is a reflection of a higher evolutionary state. Nucleus: - Double Membrane - Nuclear Pore - Regulates passage of molecules between the nucleus and cytoplasm - Nucleolus - Involved in assembly of ribosomes a nd modification of tRNA - Houses DNA. - DNA is typically stored as chromosomes made up of Chromatin - Chromatin: Protein whose function is packing long dna molecules into more compact dense structures and help with regulation. Ribosomes: - Complex made up of rRNA and protein (two subunits) - Involved in protein synthesis - Free vs Bound - Free = Proteins to be used in cell - Bound = Proteins to be shipped outside of the cell. Endomembrane System: - Endoplasmic Reticulum (Smooth and Rough) - Golgi Apparatus - Lysosomes - Vacuoles Endoplasmic Reticulum (ER): - Makes up more than half of the Endomembrane system. - Connected to the nuclear envelope - Smooth ER (SER) - Synthesis of lipids, detox of drugs and poisons - Originates from rough ER by shedding ribosomes. - Rough ER (RER) - Assists ribosomes with protein synthesis, Intracellular transport (Within Cell) via transport vesicles, production of phospholipids. - Has ribosomes bound to it AP BIOLOGY EXAM: CONTENT REVIEW PAGE 22 Secretory Pathway: Transport of proteins throughout the endomembrane system - ER > Golgi > Cell membrane > Exits cell - > = vesicle Golgi Apparatus: - Modifying, sorting and packaging of proteins for secretion - Transport of lipids around the cell - Creation of lysosomes - Cisternae: The stacks of folds of the golgi apparatus. - Cis Side: Receving side - Trans Side: Shipping side (Think Trans = Transport) AP BIOLOGY EXAM: CONTENT REVIEW PAGE 23 Lysosomes: - Membranous sac of hydrolytic enzymes - The enzymes work best in acidic pH - Phagocytosis: Cell engulfs another cell to break it down (Immune cells) - Autophagy: Breaking down and recycling of dead organelles. Peroxisomes: - Uses oxygen to break down molecules like fatty acids - Produces Hydrogen Peroxide as a bi-product. - Contains Peroxidase within the organelle to break it down. - Shows importance of compartmentalization. Vacuoles: - Membrane bound vesicles - Food vacuoles: Storage of food source for the cell - Contractile Vacuoles: Pumps water out of cell to maintain suitable concentrations - Central Vacuoles: Helps maintain Turgidity in plants (Structure) Cytoskeleton: - Network of fibers extending throughout the cell which organelles move with. - Functions: - Support - Motility - Regulation Microtubules: - Small, made from tubulin, and serves as a monorail on which organelles can travel. - Resists pressure - Cilia and Flagella Mitochondria: - Not a part of the endomembrane system - Site of cellular respiration - Contains DNA - Semi-autonomous - Cristate: Folds - Matrix: Inside - Contains an outer and inner membrane as well as an intermembrane space to facilitate the creation of concentration gradients for cellular respiration. Chloroplasts: - Not a part of the endomembrane system - Site of Photosynthesis - Outer membrane > Inner membrane > Stroma > Granum > Thylakoid. - Contains DNA AP BIOLOGY EXAM: CONTENT REVIEW PAGE 24 Cell transport: Cell Membrane: - Fluid Mosaic Model: More accurate description than “Phospholipid Bilayer” - Phospholipids move around the membrane and shift places - Integral proteins: Pass into or all the way through the bilayer, hydrophobic and hydrophilic parts. - Peripheral proteins: appendages loosely bound to the surface. - Membrane proteins: attached to cytoskeleton or fibers of the ECM - Move, but very slowly and very little= - Protein Function: - Transport: Hydrophilic channel / conformational (shape) change - Enzymatic activity: - Receptors: - Cell-Cell Recognition: Glycoproteins, MHC (Major histocompatibility complex) - Intercellular joining: gap and tight junctions - Attachment to cytoskeleton and/or fibers of the ECM. AP BIOLOGY EXAM: CONTENT REVIEW PAGE 25 Selective Permeability: - Small, non-polar can pass freely through the cell membrane. - Polar, charged, and large molecules get stopped due to polar properties of phospholipids. (Small polar molecules can still pass through but slowly) - Large polar/charged molecules require help from proteins Passive Transport: - Simple Diffusion: movement of molecules (solutes) across a barrier in an attempt to reach dynamic equilibrium. - High to low concentration - Does not require energy - Facilitated Diffusion: Use of proteins to “facilitate” passage of solutes across a barrier. - Does not require energy - Aquaporins: transport water - Gated channels: Open and close in response to stimulus - Carrier proteins: Undergo conformational change to allow for passage - Osmosis: Diffusion of water - If solutes are unable to move water will move to even out the concentration Tonicity: - Hypotonic: Out < In (Bloating) - Isotonic: Out = In (Normal) - Hypertonic: Out > in (Shirvel) - Tonicity In plants: - Cell walls prevent some of the problems associated with hyper/hypotonicity (Cellulose,Chitin). - Tonicity in animals: - Require contractile vacuole to mitigate problems. - Factors: - Concentration difference - Type of solute - Temperature - Pressure applied to the system AP BIOLOGY EXAM: CONTENT REVIEW PAGE 26 Water Potential: Electrochemical Gradient: - Ions will move passively to balance out not only their concentration but also their relative charge. - This process is manipulated by many body systems (Cardiovascular, Digestive, Nervous) Active Transport: Uses energy to carry solutes against the concentration gradient or electrochemical gradient. - Uses ATP and potential energy of another substance's concentration gradient as sources of energy. (tag along) Phosphorylation: ATP breaks off a phosphate group adding it to the protein, allowing it to work. Sodium Potassium Pump: - Pumps 3NA+ out and 2K+ in every turn. - Creates a positive membrane potential outside the cell for late processes to exploit. (Electron Transport Chain) - Electrochemical gradient favors negative ions out and positive ions in Proton Pump: - Pumps hydrogen ions across the membrane to maintain the potential Co-Transport: Active transport driven by an electrochemical concentration gradient - Similar to pumping water uphill so that it can do work as it naturally flows back down. (Sodium-Glucose Symporter) AP BIOLOGY EXAM: CONTENT REVIEW PAGE 27 Endocytosis: Bulk intake of materials by forming a vesicle that is pinched off from the cell membrane (Into the cell) - Phagocytosis = Cell eating - Pinocytosis = Cell drinking - receptor -mediated endocytosis = receptor vs ligand Exocytosis: Bulk movement of materials out of the cell. - Transport vesicles made by the golgi exit the cell. Unit 3: Cellular Energetics Photosynthesis: Function: - Take water and carbon dioxide and produce glucose and oxygen. Requirements: - Chlorophyll a (Blue-green) - Chlorophyll b (Olive green) - Carotenoids (Yellow/Orange) Two Phases of Photosynthesis: - Light Dependent reactions: - Takes place along the thylakoid membranes mostly in photosystems. - Consumes water and energy (sunlight) and produces ATP and NADPH. - Light Independent reactions: - Takes place in the stroma - Consumes CO2 and energy (ATP From LDR’s) produces glucose. Photosystems: - Photosystem II > Photosystem I - Named in order of discover not in order of process - Each photosystem consists of a reaction complex surrounded by a light absorbing complex. AP BIOLOGY EXAM: CONTENT REVIEW PAGE 28 Light Dependent Steps: 1. A photon of light is absorbed by chlorophyll a (P680) in the light absorbing complex of PSII which raises an electron to a higher energy state. However, this higher state renders the electron unstable and within a billionth of a second falls back down releasing energy. (Exergonic Reaction: Energy Is released) 2. At the same time one electron is falling down a juxtaposed pigment of chlorophyll is excited and this pathway continues until it reaches the reaction center of Photosystem II. 3. The electron does not drop back down in the reaction center. It is transferred to the primary electron acceptor, leaving behind P680+ 4. P680+ is one of the strongest oxidizing agents (Stealer of electrons), so it stimulates an enzyme to split water into its base components. 2 Hydrogen+, 2 Electrons, and 1 oxygen atom). The electrons are passed to P680+ pigments, stabilizing them and the oxygen molecules join together to create O2 5. The primary electron acceptor then passes the accepted electron down an electron transport chain to successively more electronegative electron acceptors (proteins) 6. The exergonic transfer of electrons causes hydrogen ions to be pumped across the thylakoid membrane. - Used to create an ion gradient to be later exploited during chemiosmosis which will activate ATP synthase. - ATP synthase: Enzyme that phosphorylates ADP to create ATP - Directionality of ATP production: ATP is synthesized on the outside of the thylakoid membrane into the stroma. 7. P700 chlorophyll is excited by photons of light in the in light absorption complexes of photosystem I, which in the same “wavelike” manner that was seen before passes the energy to successive P700 pigments until it reaches the reaction center of PS I thus creating P700+ 8. P700 now accepts the electron passed down the ETC from Photosystem II 9. The electron acceptor of PS I now sends an electron down a secondary ETC which does not create a gradient and so does not produce ATP. 10. NADP reductase (Adds electrons) stimulates the transfer of the electrons from the secondary ETC to the final electron acceptor NAD+ to create NADPH (an electron carrier) AP BIOLOGY EXAM: CONTENT REVIEW PAGE 29 Light Independent Steps: (Also called Calvin’s Cycle) - Cycle actually produces a product called G3P which is then converted by other metabolic pathways into many other materials, mostly glucose. - Requires 3 CO2 to produce a net gain of one G3P (Must run 3 times per 1 G3P) 1. Carbon fixation a. An enzyme called rubisco adds one CO2 molecule at a time to CO2 acceptors known as RuBP b. The addition of CO2 to RuBP forms an unstable product and causes it to split into two molecules of 3-Phosphoglycerate. (Creates 6 molecules by end of step, two per original one CO2) 2. Reduction a. ATP then phosphorylates these molecules creating Bisphosphoglycerate b. Each molecule then has an electron pair added to it by NADPH (Created during light dependent reactions) c. Each molecule then sheds its phosphate group becoming G3P i. Requires 6NADPH’s and produces a total of 6G3P’s 3. Regeneration a. In a series of complex steps 5 of the 6 G3P’s produced are rearranged to form 3 molecules of RuBP to continue the cycle. - Requires 3 ATP Reactants Overview: - 3 CO2 molecules (Atmosphere) - 6 NADPH (From LDR) - 9 ATP (From LDR) AP BIOLOGY EXAM: CONTENT REVIEW PAGE 30 Cellular Respiration: Aerobic Respiration: Occurs in the presence of oxygen (More energy) Anaerobic Respiration: Occurs regardless of whether oxygen is present or not. Does not require oxygen. (less energy) Steps of Aerobic Cellular Respiration: 1. Glycolysis: - Occurs in the cytoplasm of the cell. a. One glucose bond is broken into two pyruvates. However this requires activation energy in the form of 2 ATP. The process though produces 4 ATP which gives the reaction a net gain of 2 ATP b. The phosphates used to make the ATP come from Substrate-Level phosphorylation. Denoted with a Pi (Inorganic phosphate) it just means that the phosphate was taken by an enzyme from a substrate as opposed to the addition of a free phosphate. c. Finally glycolysis produces a total of 2 NADH that result from the oxidation of glucose. 2. Kreb’s Cycle. - Requires oxygen - Occurs in the matrix of the mitochondria - Acetyl CoA: a. The carboxyl group from each pyruvate is broken off and releases a molecule of carbon dioxide per pyruvate. b. The two carbon molecule left behind is oxidized to from acetate (electrons are transferred to NAD+ to form NADH) c. Coenzyme A (derived from B vitamins) is attached to the acetate by an unstable bond to form Acetyl CoA i. Intermediates are produced along the way. ii. Final products: Per one pyruvate. 1. 4 NADH 2. 1 FADH2 3. 1 ATP Pi iii. By-Products: 1. Carbon Dioxide - Electron Transport Chain: - Occurs in the cristae of the mitochondria - Electrons are brought to the cristae by NADH and FADH2 - The goal of the ETC is taking a huge energy release and breaking it down into smaller energy releases that can be used to power the production of ATP. - Includes 4 protein complexes. - FADH2 enters the chain a lower complex so the electron it carries releases less energy. AP BIOLOGY EXAM: CONTENT REVIEW PAGE 31 - Oxygen - Serves as final electron acceptor - Oxygen is reduced then binds with hydrogens to form water which is released as a waste product. - Chemiosmosis and Oxidative Phosphorylation: - Energy created by ETC is used to power chemiosmosis - H+ ions are pumped out creating potential energy to be pushed back in powering ATP synthase. - Phosphates come from enzymes and are therefore inorganic. (oxidative phosphorylation) AP BIOLOGY EXAM: CONTENT REVIEW PAGE 32 - ETC Products: - 32 ATP via oxidative phosphorylation. - Water released as a byproduct. - Oxidized electron carriers (Ready to be used again) Aerobic Respiration Summary: - Glycolysis: - 2 ATP via substrate level phosphorylation, 2 NADH, 2 Pyruvates. - Kreb’s Cycle: - 2 ATP via substrate level phosphorylation, 8 NADH, 2 FADH2, 6CO2 - ETC: - 32 ATP via oxidative phosphorylation, 6H2O, Oxidized electron carriers Anaerobic Respiration: - Can occur without the presence of oxygen - Obligate anaerobes: M ust carry out anaerobic respiration - Facultative anaerobes: Choose when to carry out anaerobic respiration - Goals of Fermentation: - Generate ATP - Recycle NAD+ so that glycolysis can keep running. - How it accomplishes these goals: - Pyruvates made during glycolysis are used to oxidize NADH to NAD+ so the cycle can continue. - Types of Fermentation: - Lactic Acid: Produces lactic acid as byproduct (Humans) - Alcoholic: Produces ethyl alcohol as byproduct - Alcoholic Fermentation: - Pyruvates are broken down releasing carbon dioxide. The resulting two carbon products are reduced by NADH which creates ethyl alcohol and allows NAD+ to be recycled. - Popular in bacteria like yeast - Lactic Acid Fermentation: - Pyruvates are directly reduced by NADH which creates lactic acid and recycles NAD+ - Used by Humans in response to low oxygen supplies - Excess lactic acid is broken down by liver to be converted back into pyruvates. AP BIOLOGY EXAM: CONTENT REVIEW PAGE 33 Unit 4: Cell Cycle and Regulation: Why do Cell Divide: - Larger cell means worse SA/V ratio - Replace damaged or dead cells - To make new organisms (Asexual Reproduction) Cell Cycle: Interphase: - G1 Phase: Growth cycle - S Phase: DNA replication - G2 Phase: Preparation for division Mitosis: (Shortest Phase) - Prophase: - Metaphase: - Anaphase: - Telophase: - Cytokinesis: - Remember the order by the saying “Pl ease Make A Telephone Call” AP BIOLOGY EXAM: CONTENT REVIEW PAGE 34 Control Factors: - Internal Factors: - Cyclin Dependent Kinases: - At checkpoints between G1 and S and G2 and M - Kinases hold a constant concentration however Cyclin fluctuates and unless cyclin levels are satisfactory to activate the kinases the cycle cannot progress. - MPF: (Mitosis Promoting Factor) - Name given to Cyclin dependent Kinase complex - Formed at checkpoint G2/M to allow the cell to progress into mitosis. - G0: (G-Zero) - Once cells specialize they go into a non-dividing state known as G0. - They may re-enter the cell cycle if needed. - Cells will enter G0 if they are not able to pass the checkpoint at the end of G1. - If any other checkpoint is failed, the cell will undergo apoptosis. - External Factors: - Usually growth factors such as hormones or another chemical like PDGF - Platelet Derived Growth Factor: - PDGF is made and released by platelets in response to injury. The growth factor is received by fibroblast cells pushing them past G1 into division state so the fibroblasts can divide and form a scab. - Density Dependent Inhibition: - Cells stop dividing when they come in contact with each other. - Anchorage Dependence: - Cells should not divide unless they are physically bound to a surface. Failure to regulate: - If a cell fails to regulate the cell cycle it becomes known as a cancer cell. - Move past checkpoints when shouldn’t be able to - Lost Density Dependent Inhibition - Lost Anchorage dependence AP BIOLOGY EXAM: CONTENT REVIEW PAGE 35 Chromosomes: - Made from DNA wrapped around a histone protein. - Chromatin: - Dense patches of lengthened chromosomes found in the nucleus. - Humans have 46 chromosomes in their somatic cells (Body cells) - This is called the diploid number. Mitosis: - Prophase: - Chromosomes form - Centrioles move to opposite poles - Nuclear envelope disappears - Spindle fibers form and attach to fibers at the centromere - Metaphase: - Chromosomes are lined up on the metaphase plate (down the center) - Anaphase: - Sister chromatids are separated and pulled by spindle fibers to the poles. - Telophase: - Opposite of prophase in addition to the formation of a cleavage furrow - Cleavage Furrow: Indentation of the cell's surface that begins the progression of division. - Cytokinesis: - Physical separation of the two daughter cells. AP BIOLOGY EXAM: CONTENT REVIEW PAGE 36 Meiosis: - Reproduction from the combination of two gametes. - Gametes: Specialized sex cells. - Sperm: Male gamete - Formed through spermatogenesis - Takes place in testes - Ovum: Female gamete - Formed through oogenesis - Takes place in ovaries - Fertilization: Joining of an egg and sperm. (Zygote) Somatic vs Sex Cells - Somatic Cells: - 2 Daughter cells - 46 Chromosomes (Diploid) - 1 Division - Sex Cells: - 4 Daughter Cells - Females: 1 egg and 3 polar bodies. (Produced before birth) - Males: 4 viable sperm cells. (Constantly produced) - 23 Chromosomes (Haploid) - 2 Divisions AP BIOLOGY EXAM: CONTENT REVIEW PAGE 37 Unit 5: DNA Replication Central Dogma of Genetics: - DNA > RNA > Protein DNA Structure: - Complementary, Anti-Parallel, Double Helix composed of repetitions of four nucleotides. - Adenine, Guanine, Cytosine, Thymine Eukaryotic Cells: - Multiple, linear chromosomes. Prokaryotic Cells: - Single, circular chromosome - Plasmids: Extrachromosomal piece of DNA Semi-Conservative Model of Replication: - Proposed by Watson and Crick (1953) - Proven by Meselon and Stahl (1958) Replication Terms: Origin of Replication: A particular sequence in a genome at which replication is initiated. Replication Fork: Area in which replication of DNA occurs. (Replication goes into the fork) Leading Strand: Continuous replication strand, single RNA primer. Lagging Strand: Non-Continuous replication strand, m ultiple RNA primers. Okazaki Fragments: Discontinuous sections of nucleotides on the lagging strand Nucleotide Excision Repair: Cutting out damaged strings of nucleotides. Telomere: Region of repetitive nucleotide sequences at the end of a chromosome. AP BIOLOGY EXAM: CONTENT REVIEW PAGE 38 Enzymes: DNA Helicase: Separates strands of DNA to allow replication (Forms replication fork) SS Binding Proteins: Binds to single strand to assist in repair, protection, and replication. Topoisomerase: Prevents overwinding or underwinding of the DNA. RNA Primase: Creates RNA primers that allow for DNA polymerase to start replication. DNA Polymerase III: 1. Matches free nucleotides complementary to the DNA template strand. 2. Proof reads each nucleotide against the template strand and removes mismatched nucleotides. 3. Replaces RNA primers on the Leading strand: DNA Polymerase I: 1. Replaces RNA primers with DNA nucleotides on lagging strand DNA Ligase: Joins together Okazaki Fragments (assists in mismatch repair) Nuclease: Breaks phosphodiester bonds between nucleotides (assists in mismatch repair) Telomerase: Adds telomeres to the end of chromosome Base Proces Nucleotide Excision Repair: - Nuclease cuts out damaged sections of nucleotides and DNA Polymerase III adds in nucleotides and DNA ligase joins the sections together. Base Process 1. Helicase unwinds strands 2. SS Binding proteins stabilize the single stands. 3. Topoisomerase relieves tension beyond the replication bubble. 4. RNA primase adds RNA primers to provide free 3’ ends 5. DNA polymerase III adds nucleotides in the 5’ - 3’ direction 6. Leading strand is continuous and moves toward the replication fork, Lagging is discontinuous from the replication fork but replication still moves toward 7. DNA polymerase I removes RNA primers and adds matching nucleotides 8. DNA ligase joins okazaki fragments AP BIOLOGY EXAM: CONTENT REVIEW PAGE 39 Telomeres: - Due to the 5’ - 3’ rule of DNA polymerase, the 5’ end of daughter strands are not able to have DNA nucleotides added where the RNA primer was removed. This means as replication repeats the strands are continuously shortening. (Only occurs in Somatic Cells) - To avoid this humans have a nucleotide sequence that is non-coding and is repeated between 100 and 1000 times at the end of chromosome. (Telomeres) - Sex cells contain an enzyme called telomerase that lengthens the teleomeres in gametes avoiding this issue all together. - Telomeres are believed to be a protection against cancer. AP BIOLOGY EXAM: CONTENT REVIEW PAGE 40 Unit 5: Genetics Mendelian Genetics: Mendel’s Principles: 1. Principle of Independent Assortment - “Factors” are separately inherited 2. Principle of Dominance: - One “factor” has the ability to mask out the other (Heterozygous genotype) 3. Principle of segregation: - During gamete formation the two “factors” separate from each other (Anaphase I of meiosis) Where Mendel’s Principles Fail: Co-Dominance: Both alleles are equally expressed Incomplete Dominance: Neither allele is more dominant than the other Multiple Alleles: A single trait with two or more different versions. - Each allele may function differently in terms of dominance. (A and B are Co-Dominant, but are both completely dominant to O) Polygenic Trait: More than one gene controls a single trait.