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?” - Y 2 - Y 1 / X 2 - X 1 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 (C 6 H 12 O 6 ) 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 t wo 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.