AP BIO NOTES MASTER

Unit 0: Statistics

• Quantitative data: Numerical data.
• Qualitative data: Data collected by senses, usually should be converted into quantitative.
• Inductive reasoning: Specific to general conclusions.
• Deductive reasoning: General to specific conclusions.
• Hypothesis: Testable idea about how something works.
• Scientific law: Universal scientific fact.
• Theory: Summarizes a group of hypotheses.
• Null hypothesis: Hypothesis that research aims to disprove; claims there is no correlation between variables.
• Alternative hypothesis: Hypotheses that explore different relationships between variables.
• Variables: Things that change.
• Constants: Things that don’t change.
• Independent variable: Factor deliberately changed.
• Dependent variable: Factor being measured, changes depending on independent variable.
• Controls: Eliminates error in experiments, increases reliability. Positive = exposed to treatment known to produce a certain effect; Negative = no treatment, known to produce no effect.
• Mean: Average value.
• Median: Middle-most value.
• Mode: Most frequent value.
• Standard deviation (s): How data is spread from the mean; high SD = more spread out; low SD = less spread out.
• Standard error of the mean (SEM): Confidence in the mean - how precise is it? Low SE = more confidence.
• Bar graph and error bars: Overlapping error bars = difference isn’t significant.
• Chi-square: Determines if there is a statistically significant relation between two variables.
• How to find standard deviation:
  1. Find mean.
  2. Mean - each data point.
  3. Square (mean - data point).
  4. Add up all values of step 3.
  5. Divide by degrees of freedom (n-1).
• How to find chi-square:
  • Expected given:
    1. Each observed - expected.
    2. Square each (observed - expected).
    3. Divide each by each expected.
    4. Add up all values.
    5. Compare with critical value.
  • No expected given:
    1. Find expected value by \frac{(column \ total \ * \ row \ total)}{total \ total} for each value.
    2. Continue as normal.
• Results of chi-square:
  1. Larger chi-square value: reject null, there is a significant relationship between variables.
  2. Smaller chi-square value: accept null, there is no significant relationship between variables.

Unit 1: Chemistry of Life and Properties of Water

Chemistry of Life

• Macromolecule:
  • Four types: carbohydrates, proteins, lipids, and nucleic acids.
  • Organic compound: Molecules containing carbon.
  • Protein: Made of CHONS (remember disulfide bond for S and Amino/N terminus for N).
  • Carbohydrate: Made of CHO, ring structures.
  • Lipid: Made of CHOP (remember phospholipids), all nonpolar, no specific monomers/polymers.
  • Nucleic acid: Made of CHONP (remember phosphate group for P and nitrogenous base for N).
  • Monomer: Single unit of a macromolecule.
  • Polymer: More than one unit of a macromolecule.
  • Dehydration synthesis: Removes a water molecule to bond two monomers together.
  • Hydrolysis: Breaks down polymer by adding a water molecule.
• Carbohydrates:
  • Glycosidic linkage: The covalent bond between monosaccharides.
  • Monosaccharide: Monomer of carbohydrates.
  • Disaccharide: Two monosaccharides.
  • Polysaccharide: Polymer of carbohydrates.
  • Linear: Chain of monomers.
  • Branched: When a nonlinear chain of monomers bonds to create a tree-like structure.
  • Rings: Many simple sugars exist in this form, usually monosaccharides.
  • Cellulose: Structural carbohydrate found in cell wall, hard to break down because linear chain.
  • Starch: Storage carbohydrate in plants, easier to break down because it’s slightly branched.
  • Glycogen: Storage carbohydrate in animals, easy to break down because it’s very branched.
• Lipids:
  • Fatty acid: A long chain of hydrocarbons.
  • Saturated fatty acid: With no double bond, solid at room temperature.
  • Unsaturated fatty acid: That has a double bond, non solid at room temperature.
  • Glycerol: A carbohydrate involved in fatty acids and phospholipids.
  • Triglyceride: A fat, made of glycerol and three fatty acids.
  • Phospholipid: Hydrophilic head, hydrophobic fatty acid tails, glycerol backbone. Amphipathic = having both hydrophilic and hydrophobic parts.
  • Cell membrane (phospholipid bilayer): Made of phospholipids, the hydrophobic tails face each other and the heads face outward.
  • Ester bond: Bond between lipids.
  • Steroid: Lipid, four rings.
  • Cholesterol: A lipid in the bilayer that allows for fluidity.
• Proteins:
  • Amino acid: Monomer for protein.
  • Amino or N terminus: One functional group of an amino acid.
  • Carboxyl or C terminus: The other functional group of an amino acid where new amino acids are added.
  • Central carbon: Middle part of an amino acid.
  • R group / side chain: Variable group, several options, makes the amino acid unique.
  • Dipeptide: Two amino acids.
  • Polypeptide: Polymer of proteins.
  • Peptide bond: The covalent bond between amino acids.
  • Protein backbone: Chain of amino acids.
  • Primary structure: Chain of amino acids, peptide bonded.
  • Secondary structure: Backbone held together with hydrogen bonds, slight bending due to interactions between the carboxyl and amino terminus.
    • Alpha helix: Spiral of amino acid chain, found in secondary structure.
    • Beta sheet: Pleated chain, found in secondary structure.
  • Tertiary structure: 3D shape, determined by polarity of R group.
    • Disulfide bond: Bond between cysteine chains, seen in protein folding.
    • Hydrophobic interactions: When the R groups are hydrophobic, they fold inside the structure, away from an aqueous solution.
  • Quaternary structure: Not all have this, only when a protein has more than one chain; large 3D structure as amino acids interact.
  • Antibody: A type of protein that targets antigens.
  • Enzyme: Types of proteins that catalyze (or speed up) reactions.
• Nucleic Acids:
  • Nucleotide: Monomer for nucleic acids, pairs are held together by hydrogen bonds.
  • Phosphodiester bond: Bond between nucleotides.
  • Sugar: The five-carbon sugar (either ribose or deoxyribose).
  • Phosphate: One part of a nucleotide, is negatively charged which gives DNA a negative charge.
  • Nitrogenous base: Adenine, guanine, thymine, cytosine, and uracil.
  • Deoxyribose: DNA sugar base.
  • Ribose: RNA sugar base.
  • DNA: Double-stranded.
  • RNA: Single-strand.
  • 5’ Phosphate group: end.
  • 3’ Hydroxyl group: end/near sugar.
  • Antiparallel: DNA runs 5’ to 3’ prime in both directions.
  • Pyrimidine: One ring, Thymine, Uracil, and Cytosine.
  • Purine: Double ring, Adenine and Guanine.
  • Cytosine: Pairs with Guanine, pyrimidine base, has 3 hydrogen bonds and is harder to break.
  • Guanine: Pairs with Cytosine, pyrimidine base, has 3 hydrogen bonds and is harder to break.
  • Adenine: Pairs with Thymine/Uracil, purine base, has 2 hydrogen bonds and is easier to break.
  • Thymine: Pairs with Adenine, purine base, has 2 hydrogen bonds and is easier to break.
  • Uracil: Pairs with Adenine, purine base, has 2 hydrogen bonds and is easier to break.
  • ATP: RNA monomer.
  • Aqueous: Water solvent.

Key Concepts/Skills

• Describe the role of carbon in biological systems.
• For each type of biological macromolecule:
  • Identify the monomer, polymer, general structure, functions, examples, and the elements that typically make up that type of macromolecule.
    • Carbs: Monosaccharides, polysaccharides, rings or branched chains, usually acts as sugars, examples glucose and starch, CHO.
    • Proteins = amino acids, polypeptides, four types of structures, have specific functions throughout the body, example enzyme, CHONS.
    • Lipid = CHOP.
    • Nucleic Acid = CHONP
  • Identify the type of macromolecule when given its chemical structure:
    • Carbs = CHO.
    • Proteins = CHONS.
    • Lipid = CHOP.
    • Nucleic acid = CHONP.
  • Explain what dehydration synthesis is and the types of covalent bonds formed between monomers of the different types of macromolecules.
    • Dehydration synthesis = when a water molecule is removed to bond two monomers; Proteins = peptide bonds; Carbs = glycosidic linkages; Nucleic acids = phosphodiester bonds; Lipids = ester bonds.
  • Explain what hydrolysis is: When a water molecule is added to a polymer and the bond between monomers is broken.
  • Identify the parts of a nucleotide: There is a sugar base (either ribose or deoxyribose), a phosphate group, and a nucleotide.
  • Describe the differences between DNA and RNA: DNA is double stranded, with nucleotides A, T, G, C; it has deoxyribose sugar base. RNA is single-stranded, with nucleotides A, U, G, C; it has ribose sugar.
  • Explain how DNA and RNA store information: Information is stored in DNA and RNA’s nucleotide sequences; they store the codes needed to translate proteins.
  • Identify the parts of an amino acid: There is an Amino or N terminus, a Carboxyl terminus, a central carbon, and an R group. The Amino and Carboxyl terminuses dictate the polarity of the protein, and the R group makes the Amino Acid unique.
  • Explain the effect of a change in the amino acid sequence on the structure and function of a protein: Amino acid sequences code for proteins, so if the sequence changes, an entirely different protein may be created.
  • Explain the effect of a change in the chemical environment on the structure and function of a protein (ex. If the pH of a solution changes, what may happen): A protein, specifically an enzyme, will denature when no longer in its optimal environment. This means that if the pH of a solution changes, the protein will lose its function and denature altogether.
  • Describe what happens to the stability of a protein as the number of disulfide bonds increases: As the number of disulfide bonds increases, the stability of the protein increases.
  • When given chemical properties of a molecule (or parts of a molecule), predict how the molecule will interact in an aqueous solution. A hydrophilic or polar property means the molecule will directly interact with the solution, whereas a hydrophobic or nonpolar property means the molecule will not want to interact with the solution.
  • Compare and contrast unsaturated and saturated fats.
    • Unsaturated:
      • Double bond kink.
      • Liquid at room temperature.
    • Saturated:
      • No double bonds.
      • Solid at room temperature.

Properties of Water

• Polarity: When there is an unequal sharing of electrons in a molecule.
  • Polar (AKA hydrophilic): When there is an overall charge in a molecule.
  • Nonpolar (AKA hydrophobic): When charges in a molecule cancel out and the molecule is left with no overall charge.
  • Covalent bond: When more than one molecule shares valence electrons.
  • Hydrogen bond: Weak bond between hydrogens and oxygens of different water molecules.
  • Intermolecular bond: Bonds between molecules (not within).
• Solvent: A solution where things are dissolved in.
• Solute: Something that dissolved in a larger liquid.
• Solution: When two or more things are mixed together, usually liquid
• Universal solvent: Water’s ability to act as a solvent for most polar substances.
• Adhesion: Water molecules are attracted to other polar substances.
• Cohesion: Water molecules attracted to other water molecules due to hydrogen bonding.
  • Xylem: Part of plant involved in capillary action; water climbs up xylem walls due to adhesion.
• Surface tension: Cohesion develops on the surface of water and it’s harder to break those hydrogen bonds.
• Capillary action: (A mix of cohesion and adhesion) When water moves up through the roots to the leaves of a plant. Water at leaves evaporates, so the next water molecules are pulled up, climbing the sides of the plant (xylem).
• High specific heat: It takes more energy to change water’s temperature.
• Evaporative cooling: When sweat is released from an organism so that it can break the hydrogen bonds and release hot water vapor and cool the organism.
• Elements of life: CHONPS.
• pH: As pH increases, the amount of H+ decreases. Higher pH = more basic; lower pH = more acidic.
• Functional groups: Hydroxyl, Carbonyl, Carboxyl, Amino, Sulfhydryl, Methyl, Phosphate.

More Key Concepts/Skills

• Draw a water molecule and label the partial charges. Oxygen has a partial negative and the two hydrogens have partial positives.
• Explain why a water molecule has partial charges. There is an unequal sharing of electrons within the molecule, causing oxygen to have a partial negative charge and the two hydrogens to have a partial positive.
• Draw several water molecules and the hydrogen bonds between the water molecules. The hydrogen atoms will be attracted to the oxygen atoms; the hydrogen bonds will be between hydrogen atoms and oxygen atoms of different molecules.
• Explain what a hydrogen bond is and what causes them to form. Hydrogen atoms in a water molecule have a partial positive charge, and oxygen atoms in a water molecule have a partial negative charge, so the hydrogens and oxygen from different water molecules attract when they’re near each other.
• Explain how each of the following properties of water works and one example of how each can help life on Earth.
  • Surface tension: When hydrogen bonding at the surface of water makes it hard to penetrate surface (ex. spiders walking on water).
  • Cohesion: Hydrogen bonding and polarity leads to water molecules being attracted to each other (ex. capillary action).
  • Adhesion: Water’s polarity makes it attracted to other polar molecules (ex. capillary action).
  • Capillary action: When hydrogen bonds cause water molecules to be attracted to other water molecules (ex. plants can stay hydrated).
  • Universal solvent: Water’s polarity allows other polar substances to dissolve in it (ex. water can carry nutrients and chemicals within an organism’s body).
  • Density: When stable hydrogen bonds are more spread out in ice than liquid water, so there’s more space between molecules (ex. helps sea organisms survive under a layer of ice).
  • High heat capacity (temperature control): When it takes a large amount of energy for water to change temperature (ex. allows sea organisms to survive despite fluctuations in air temperature).
• Identify the elements that make up nearly all living matter. CHONPS, the elements of the macromolecules.
• Explain the properties of carbon that allow it to make such diverse molecules. Carbon can form up to 4 bonds, it can single, double, and triple bond, and it can bond with itself.
• Identify the functional groups in the vocabulary list. Use the graph and memorize it. All you need to know are which ones are polar and be able to identify them if you see a molecular diagram of it (elements and arrangement).

Unit 2: Cell structure and Function

• Cell: Basic unit of life.
• Prokaryote: Bacteria/archaea.
• Eukaryote: Animals/plants.
• Organelle: Smaller specialized structures within a cell.
• Endomembrane system: The network of internal membranes within a eukaryote.
• Nucleoid: Where the nucleus is in a prokaryote.
• Nucleus: Stores the cell’s genetic information.
• Nuclear envelope: Where the nucleus is in a eukaryote.
• Rough endoplasmic reticulum: Has ribosomes on it, synthesizes proteins.
• Smooth endoplasmic reticulum: No ribosomes on it, function varies but usually synthesizes lipids.
• Golgi complex/apparatus: Receives vesicles from ER and modifies them, sending them to other organelles or outside the cell.
• Cisternae: The sacs that hold synthesized proteins while in the rough ER.
• Cis face: The receiving part of the Golgi apparatus.
• Trans face: The part of the Golgi apparatus where the modified proteins and lipids leave in vesicles.
• Lysosome: Contains hydrolytic enzymes and undergo digestion, important for autophagy, only found in animals.
• Autophagy: Cells break down and reuse old material, done by lysosomes.
• Apoptosis: When a cell triggers its own death.
• Secretory vesicles: Release molecules outside the cell by exocytosis.
• Food vacuole: Stores food, not commonly found.
• Central vacuole: Only in plants, water storage.
• Contractile vacuole: When some cells are hypotonic, the contractile vacuole will fill with water and then expel it out so that the cell doesn’t burst.
• Mitochondria: Convert food energy to ATP.
• Cristae: The folds in the membrane of the mitochondria.
• Matrix: Cytoplasm of mitochondria.
• Chloroplast: Organelles that undergo photosynthesis, only in plants.
• Stroma: Fluid inside chloroplasts.
• Chlorophyll: The green pigment in a chloroplast’s thylakoid membrane that receives light photons.
• Thylakoids: Their membranes hold chlorophyll and are important for light-dependent reactions.
• Grana: Stacks of thylakoids.
• Ribosomes: They are made in the nucleus (in nucleolus) and assemble proteins by reading mRNA.
• Cell wall: Found in all cells except animals, structurally support the cell.
• Cytosol: Jelly-like part of the cytoplasm.
• Cytoplasm: Substance within the cell.
• Cytoskeleton: Part of the cytoplasm that holds all the organelles in place.
• Compartmentalization: When cells have several smaller sections within.
• Endosymbiont: When one organism lives inside another.
• Endosymbiont theory: Explains origin of eukaryotes and mitochondria/chloroplasts.
• Binary fission: How prokaryotes asexually reproduce; how mitochondria and chloroplast replicate, supporting endosymbiont theory.
• ATP: Energy molecule.
• Phospholipid: Amphipathic lipids that make up the bilayer of the cell membrane.
• Phospholipid bilayer: The two rows of phospholipids that make up the cell membrane.
• Fluid mosaic model: Membrane contains phospholipids, cholesterol, and proteins that are all moving around.
• Self-sealing: Cell membrane can mend tears in itself.
• Semi-permeable: Allows some molecules to pass but not others.
• Integral proteins: Proteins embedded in the cell membrane.
• Peripheral proteins: Proteins that attach to the sides of the cell membrane.
• Surface area: volume ratio: A smaller surface area to volume ratio is most efficient.
• Homeostasis: The process by which organisms maintain stable internal environments.
• Diffusion: Molecules move from high concentration to low.
• Concentration gradient: Goes from high concentration to low.
• Facilitated diffusion: Requires no energy, polar molecules, and ions.
• Passive transport: Molecules go down the concentration gradient, requires no energy, nonpolar molecules.
• Active transport: Pumping molecule/ion against the concentration gradient, requires ATP.
• Membrane potential: Electrical charge across a membrane, created by pumping ions.
• Carrier protein: Transport specific molecules through the membrane, sometimes require ATP.
• Channel protein: Channel through the membrane for ions, facilitated diffusion.
• Aquaporin: The pump that transfers water across the membrane, doesn’t require energy.
• Endocytosis: Vesicle attaches to membrane to take in a molecule, requires ATP.
• Exocytosis: Vesicle attaches to membrane to release a molecule, requires ATP.
• Dialysis: The movement of a solute across a membrane.
• Osmosis: Diffusion of water along the concentration gradient.
• Tonicity: The ability of a solution to cause water to move across a membrane.
  • Hypertonic: More solute than water.
  • Hypotonic: More water than solute. Plants prefer to be hypotonic so that water will flow inside.
  • Isotonic: When water flows in and out of the cell at the same rate, animals prefer this.
• Osmoregulation: Regulating osmotic balance.
• Plasmolysis: When plant cells are in a hypotonic environment, the membrane shrinks away from the cell wall, vacuole shrinks, and the plant wilts.
• Turgid: When a plant cell is swelled and full of water.
• Flaccid: When a plant cell is hypotonic to its environment, water will leave the cell and the cell will shrink.
• Turgor pressure: The pressure exerted on the cell wall due to an influx of water inside the cell, only applicable to plant cells.
• Water potential: Water’s tendency to move from where it is to where it’s not. High = a bigger concentration of water than solute, meaning the water is likely to move. Low = not a lot of water and it’s unlikely to move. Adding solute decreases the WP, adding pressure increases the WP.
• Solute potential: Adding solute decreases the WP.
• Pressure potential: Adding pressure increases the WP.
• Hydrophilic: Polar, interacts with water.
• Hydrophobic: Nonpolar, doesn’t like to interact with water.
• Glycolipids: Lipids attached to cell membrane.
• Glycoproteins: Proteins attached to cell membrane.
• Transpiration: The process by which water evaporates in plants. Capillary action brings water up to leaves where it evaporates, and hydrogen bonding pulls more water up from the roots.

Key Concepts/Skills

• Compare and contrast prokaryotic and eukaryotic cells.
  • Prokaryotes= smaller, simpler, no nucleus, circular DNA, found in archaea/bacteria.
  • Eukaryotes= larger, more complex, nucleus, several linear chromosomes, have a mitochondria, have membrane-bound organelles.
• Describe similarities and/or differences in compartmentalization between prokaryotic and eukaryotic cells: Prokaryotes have simpler structures, so there is less compartmentalization, while eukaryotes have several internal sections.
• Which organelles are in eukaryote vs. prokaryote?
  • Eukaryote:
    • Mitochondria.
    • Chloroplast (only plants).
    • Nucleus (nuclear envelope).
    • Cytoplasm.
    • Vacuoles.
    • Cell membrane.
    • Cell wall (excluding animals).
    • Ribosomes.
    • Lysosomes.
    • Rough & smooth ERs.
    • Golgi apparatus.
  • Prokaryote:
    • Cyanobacteria.
    • Nucleus (nucleoid).
    • Cytoplasm.
    • Cell membrane.
    • Cell wall.
    • Ribosomes.
• Predict the effect(s) of a malfunctioning organelle on a cell’s ability to work properly.
• Understand the functions of each organelle so that if it stops functioning properly, you will know what effect it has.
• When given information about a cell not functioning properly, explain which organelle(s) is likely causing the problem.
• Understand the functions of each organelle so that when there is a specific problem, you can predict which organelle isn’t functioning properly.
• Describe the structural features of a cell that allow organisms to capture, store, and use energy: Mitochondria turn food energy into ATP, and chloroplasts turn light energy into ATP.
• Identify organelles when given diagrams of cells.
• Explain what compartmentalization is and two ways that it is helpful to eukaryotic cells. When cells are divided into sections, which helps certain parts of the cell to have individual chemical properties and increases internal surface area.
• Explain what the endosymbiont theory is and four pieces of evidence supporting it. Ancient bacteria was consumed by ancient archaea and became an inner mitochondrion and started to secrete vesicles which would later become organelles. Then, free-living cyanobacteria entered a eukaryote and evolved into a chloroplast. For evidence: mitochondria and chloroplasts both have their own circular DNA, undergo binary fission, produce their own proteins, and they have their own double membranes.
• Describe how a protein is formed and finally packaged and secreted from the cell.
• Explain why cells are small: Smaller cells have larger SA:V ratios, which allows them to be more efficient than if they were larger.
• Calculate surface area-to-volume ratios for different shapes when given the formulas \frac{SA}{V}, SA = 6s^2, V = s^3
• Explain the effect of surface area-to-volume ratios on the exchange of materials between cells or organisms and the environment. A higher SA:V ratio increases the efficiency of the exchange of materials.
• Explain how specialized structures and strategies are used for the efficient exchange of molecules to the environment. Mitochondria and chloroplasts have inner folds that allow them to be extra efficient. Because their cellular processes are incredibly important to the survival of the organism, mitochondria and chloroplasts need to maximize their surface area in order to be efficient.
• Describe the Fluid Mosaic Model of cell membranes. There are proteins and cholesterol in the membranes. The cholesterol helps keep the membrane fluid, and the proteins and other molecules scattered within it create a “mosaic”.
• Explain how the structure of biological membranes influences selective permeability. The amphipathic nature of phospholipids means the inside of the membrane is nonpolar. This means that only certain molecules can pass through and others cannot and require pumps and channel proteins.
• Describe the role of the cell wall in maintaining cell structure and function. Composed of cellulose, prevents over-expansion in response to increased water take.
• Describe the characteristics of the cell (plasma) membrane.
  • It’s semi-permeable, meaning not everything can pass through.
  • It’s self-healing, meaning it can heal its own tears.
  • It’s fluid, as the cholesterol keeps the membrane from hardening, meaning the proteins and molecules on it are always moving.
  • It’s a mosaic, so there are several different types of molecules within it, such as proteins, lipids, and cholesterol.
• Describe the mechanisms that organisms use to transport large molecules across the plasma membrane: Endocytosis and exocytosis help large molecules pass through.
• Explain how the structure of a molecule affects its ability to pass through the plasma membrane. Whether it passes through or not depends on its polarity and size.
• Compare and contrast diffusion and osmosis: Diffusion is the movement of molecules along the concentration gradient. Water moves along this concentration gradient. But osmosis refers specifically to the movement of water.
• When given the water potential of two solutions, determine the movement of water. Water will always move to hypertonic environment, the one with more solution than water.
• Explain how concentration gradients affect the movement of molecules across membranes. Molecules will usually move along the concentration gradient to where there is a lower concentration of molecules.
• Explain how osmoregulatory mechanisms contribute to the health and survival of organisms. They help regulate the internal balance of water and maintain homeostasis.
• Describe the processes that allow ions and other molecules to move across membranes.
  • Nonpolar molecules use passive diffusion.
  • Ions and small polar molecules use facilitated diffusion or active transport.
  • Large molecules use endo/exocytosis.

Unit 3: Cellular Energetics. Enzymes & Cellular Energetics

• Metabolism: The process used to store or release energy in a cell.
• Metabolic pathway: Linked series of reactions in a cell, can be linear or cyclical.
• Intermediate: The middle products of a metabolic pathway that aren’t present in the end.
• Catabolism: Reaction that breaks something down.
• Anabolism: Reaction that builds something.
• Thermodynamics: How energy is transferred in a system.
• Entropy: Measures the amount of chaos/disorder in a reaction.
• Free energy: Measures the amount of work a thermodynamic system can perform.
• Enthalpy: Measures the amount of heat in a system.
• Exothermic: Releases heat, increases enthalpy.
• Endothermic: Requires heat, decreases enthalpy.
• Exergonic: Release energy, increase entropy.
• Endergonic: Require energy, decrease entropy.
• Product: The results of an enzyme-substrate reaction. Can either build two substrate pieces together or break a substrate apart.
• Activation energy: Amount of energy needed to initiate a reaction.
• ATP: Powers work within cells, usually built by connecting ADP and a phosphate group.
• Hydrolysis: When ATP is broken into ADP and a phosphate group by adding a water molecule.
• Enzyme: Proteins that catalyze (speed up) reactions and lower the activation energy.
• Catalyst: Something that speeds up a reaction.
• Active site: Place where substrates and other molecules can bind.
• Induced fit: Active site adjusts shape to fit substrate further.
• Optimal conditions: The conditions in which an enzyme can work efficiently.
• Denature / denaturation: Changes in environment cause an enzyme’s active site to change and can’t bind with substrate, enzyme loses function.
• Cofactor: Molecule that helps enzyme activity by binding to the enzyme.
• Coenzyme: A type of cofactor that binds directly to the active site.
• Inhibition: When an inhibitor binds to an enzyme and stops the reaction from happening, can be permanent or reversible.
  • Competitive inhibitor: Foreign molecule that blocks the active site.
  • Noncompetitive inhibitor: Foreign molecule binds to the allosteric site and changes the active site shape so that the substrate can’t bind (reversible).
• Allosteric site: Alternative site where other molecules can bind and affect enzyme activity.
• Allosteric regulation: How molecules that bind to the allosteric site either activate or inhibit the reaction.
  • Allosteric activator: When a molecule binds to the allosteric site and induces change in the active site that supports/furthers the reaction.
  • Allosteric inhibitor: When a molecule binds to the allosteric site and inhibits enzyme activity.
• Cooperativity: The binding of one substrate to one part of an enzyme affects the binding of other substrates to other parts of the enzyme.
• Feedback inhibition: When the products of a reaction pathway become inhibitors of the start to the pathway so that when too much product is produced, the pathway stops.

Key Concepts/Skills

• Compare and contrast anabolic and catabolic pathways: Anabolic pathways require energy to build things and are endothermic, while catabolic pathways release energy when they break things down and are exothermic.
• Describe the first and second laws of thermodynamics: 1st: Energy is conserved; 2nd: entropy increases over time.
• Explain why life, which requires a highly ordered system, does not violate the second law of thermodynamics: It’s converted from one form to another, never destroyed.
• Describe the energy conversions that occur when an organism consumes food: The food energy is broken down in catabolic pathways and energy is released, then that energy is used to build other molecules through anabolic pathways.
• Describe how living things increase the entropy of their environment: Organisms often release heat as a result of their metabolic pathways.
• Describe three kinds of work cells perform: Chemical work: building and breaking down molecules; Transport work: moving molecules across membranes; Mechanical work: physical movements.
• Explain under what conditions a reaction is spontaneous: Exothermic and increased entropy (disorder).
• Describe the structure and function of ATP: The ADP molecule and a phosphate group make up ATP.
• Explain how ATP is used for energy: When the phosphate group and ADP are broken apart through hydrolysis, energy is released.
• Describe the structure and function of an enzyme: Enzymes can catalyze reactions and have an active site that fits perfectly with a specific substrate, as well as an allosteric site that regulates the enzyme activity.
• Name the suffix of most enzymes: “-ase”.
• Describe what happens to an enzyme before, during, and after a reaction. An enzyme binds with its substrate, the enzyme and substrate interact, and products are the outcome.
• Explain why enzymes are specific to particular reactions: The active sites of enzymes are built to fit perfectly with its desired substrate.
• Explain how enzymes speed up a reaction: They lower the activation energy, or the energy needed for the reaction to start, so the process is conducted faster.
• Explain how enzymes lower the activation energy of a reaction: Enzymes provide an alternative reaction pathway for a substrate, which reduces the amount of energy needed to start to the reaction.
• Interpret a graph of energy vs. reaction progress to determine whether a reaction is exergonic or endergonic: Less energy to start and more energy at the end=endergonic, not spontaneous. More energy to start and less energy at the end=exergonic, spontaneous.
• Explain why enzymes have “optimal conditions.” Because enzymes are proteins and can have complex structures, if you change certain factors of the environment, the enzyme’s shape can change and won’t be able to interact with the substrate (denaturation).
• List factors that affect enzyme activity and predict or explain their effect. Factors include:
  • pH: Enzymes have an optimum pH level where they perform most efficiently. As the pH level decreases or increases, the enzyme loses efficiency.
  • Temperature: Enzymes can be more efficient as temperature increases due to increased kinetic energy, but after a peak temperature the enzyme will denature.
  • Salinity: High salinity can decrease enzyme function.
  • Substrate concentration: At low substrate concentration, the probability of the enzyme finding the substrate is low, and vice versa with high substrate concentration.
  • Enzyme concentration: High enzyme concentration speeds up a reaction and low enzyme concentration decreases the speed of reaction.
• Explain the effect of a mutation (change in the DNA sequence) on a segment of DNA that codes for an enzyme: This can lead to a modified or non-functional enzyme.
• Describe reversible and irreversible denaturation.
  • Reversible: Enzymes can function again when optimal conditions return.
  • Irreversible: Enzymes cannot function again after denaturation.
• Compare and contrast competitive inhibition and noncompetitive inhibition: Competitive inhibition is when a foreign molecule blocks the active site so the