AP Biology Study Guide- Biochemistry Notes PDF

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Notes for AP Biology Chapter 2, AP Biology Chapter 2 Biochemistry Notes for AP BIology Chapter 2 Biochemistry Notes AP Biology Study Guide...

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AP Biology Study Guide- Biochemistry By Charlotte Nour Kastoun Table of Contents: 1. The Scientific Method 2. Atomic Structure 3. Interactions and Properties of Atoms 4. Properties of Water 5. Organic Compounds 6. pH The Scientific Method ● The scientific method is used to answer questions posed in science. ● It’s not a rigid procedure- certain steps can be switched around ● The steps are as follows: ○ Define the problem ■ What question is being asked? ● This question has to be: ○ Answerable ○ Objective ○ Specific ○ Collect information ■ This includes reading articles and making observations ○ Form a hypothesis ■ This must be testable, in the form of a statement, and based on observations and background research/knowledge ○ Test the hypothesis/create an experiment ■ Independent variable: what affects the dependent variable ■ Dependent variable: what is affected by the independent variable ■ Controlled variables: variables that remain constant throughout the experiment ■ Control group: a group of test subjects who have no variables affecting them (ex. Rats receiving a sugar pill- placebo- instead of the medication)

○ Draw a conclusion ■ The conclusion either supports or refutes/does not support the hypothesis ○ Edit your hypothesis, elaborate on it, ask more questions, conduct more experiments, publish/share your results, etc. ● Theories: ○ A hypothesis that has been repeatedly supported and never refuted. ● Statistical Tests ○ These help determine the validity of your results ○ Quantify: to turn observations into explicit counts or measures ○ Chi-Squared Statistical Test: ■ Measures how the expected results compare to the observed ones ■ Can only be used for raw counts (not measurements or percentages) ■ The greater the amount of data collected, the more accurate the test ■ Null Hypothesis (H0): A hypothesis that states that there is no difference between groups of data, and that all variation is due to chance ● Ex. Woodlice have no preference between a humid and a dry atmosphere. Any variation in the data is due to chance. ■ Alternate Hypothesis (HA): A hypothesis that states the predicted results ● Ex. Woodlice have a preference for a humid atmosphere over a dry one. ■ Formula: ● x2 = Σ((O-E)2/E) ○ O = observed data ○ E = expected data (calculated by dividing the sum of the observed values by the number of categories) ● Create a table in which you calculate: ○ The sum of the observed data ○ The expected data ○ The difference between the observed and expected data, and then the square of that ○ (O-E)2/E ○ The sum of all the values found through (O-E) 2/E ● Calculate the degrees of freedom: number of categories - 1 ● Use the x2 table:

○ Find the critical p value at 0.05 and the appropriate number of degrees of freedom. ○ If your x 2 value is greater than the p value, then you can reject the null hypothesis. ○ If your x 2 value is less than the p value, then you cannot reject the null hypothesis. ● Conclusion: ○ With ______ degrees of freedom I have an x2 value of _______ which has a p value of ________. I therefore reject/fail to reject the null hypothesis.

Atomic Structure ● All matter is made up of atoms (the smallest particle of matter with the element still being itself). ○ Never trust an atom. They make up everything! ● An element is a pure substance made up of only one kind of atom ● Elements form compounds ● Atoms are made of: ○ Protons: positively charged subatomic particles. They are found in the nucleus and determine the atomic number of an atom. ○ Neutrons: neutral subatomic particles (they have no electrical charge). They are found in the nucleus. Protons + neutrons = atomic mass. ■ Isotopes have different amounts of neutrons but the same amount of protons. ● In other words, they have the same atomic number but a different atomic mass ● An isotope is still an atom ○ Electrons: negatively charged particles. They are found in shells around the nucleus. Number of electron shells = period number. ■ An atom has the same number of protons and electrons. It has no charge. ■ An ion has more or less electrons than protons ● A cation is a pawsitively charged ion ● An anion is a negatively charged ion ■ Octet Rule: atoms want a full valence shell (8 electrons in their valence shell, except for hydrogen and helium, which only need 2) ■ Valence shell: The outer electron shell ■ Valence electrons: The electrons in the valence shell

Interactions and Properties of Atoms ● Electronegativity: the atom’s attraction to its electrons ○ The greater this attraction, the greater the electronegativity of the atom ○ Electronegativity depends on the number of protons an atom has and on the distance between the valence shell and the nucleus ■ For instance, iodine is less electronegative than oxygen because even though iodine has more protons, there is a greater distance between its nucleus and its valence shell in iodine than in oxygen ○ Oxygen and Nitrogen are the most electronegative biological atoms ○ Chlorine, Oxygen, and FLUORINE are the most electronegative atoms on the Periodic Table ○ When bonding, if the electronegativity difference is less than 0.5, then a nonpolar covalent bond is formed. If it’s between 0.5 and 2, then a polar covalent bond is formed. If it’s greater than 2, then an ionic bond is formed. ● Chemical bonds and interactions ○ Ionic Bond ■ A very electronegative atom steals an electron from another atom (electron transfer) ● Both their valence shells are full ■ The ion with an extra electron has a negative charge (anion). The ion(s) missing an electron has a positive charge (cation). The opposite charges of these ions causes them to be attracted to each other. ■ This attraction causes them to stick together in an ionic bond ● These are called ionic compounds or salts ○ Ex. NaCl ○ Covalent Bond ■ Electrons are shared between atoms, resulting in full valence shells for all atoms involved ■ Covalent bonds are strong. It takes a lot of energy to break them. ■ Polar Covalent Bonds ● Electrons are shared unevenly. This is due to the difference in electronegativity of the atoms bonded together. ● The more electronegative atom will hold the “shared” electrons closer to itself

● The molecule must have asymmetry to be considered polar because if the molecule is linear, the slight opposite charges of the molecules balance each other out ● There are partial charges on opposite sides of the bond ● As a general rule, polar molecules are hydrophilic, meaning they like to interact with water (which is polar) ○ If a compound is hydrophilic depends on the individual molecules that make it up and their [partial] charges ○ For instance, phospholipids contain hydrophobic fatty acids and hydrophilic phosphate groups ● A permanently polar molecule is a dipole ○ Dipole moment - the charge around a molecule is separated into a more positive and a more negative area ● “Like dissolves like”- polar molecules dissolve polar molecules and nonpolar molecules dissolve nonpolar molecules ■ Nonpolar Covalent Bonds ● Electrons are shared equally ● Most of the molecules in the compound must be nonpolar for the molecule to be considered nonpolar ● Most nonpolar molecules are hydrophobic, or water-hating ■ Covalent Bonds in Organic Compounds ● Peptide bond- in amino acids ● Glycosidic linkage- in carbohydrates ● Ester bonds- in lipids ● Disulfide bridges- found in the tertiary structure of a protein ○ Hydrogen Bond ■ A partially negatively charged atom in a polar molecule is attracted to another molecule’s slightly positively charged hydrogen atom ■ These can occur within a molecule as well ■ These are a type of van der Waals interaction ○ Hydrophobic Interactions ■ The interactions between nonpolar molecules in the presence of polar substances (ex. oil in water) ○ van der Waals Interactions

● Functional Groups ○ What do they do? ■ They attach to/are part of a molecule. They give it specific properties. ○ What are they? ■ Methyl: -CH3 ● Nonpolar ● Hydrophobic ● Used for DNA and regulation ■ Hydroxyl: -OH ● Polar ● Hydrophilic ● Alcohol (sometimes) ■ Carboxyl: -COOH ● carbon double bonded to an oxygen and single bonded to a hydroxyl group ○ Polar ○ Hydrophilic ○ Acidic* ■ Amino/Amine: -NH2 ● Basic* ■ Phosphate** ● Phosphate is a “bad atom”. It forms more bonds than it needs to (5 bonds instead of 3) ● It will ALWAYS have negatively charged energy ● Used in lipids ○ Polar ○ Hydrophilic ○ Acid *see pH section for more information **see “Functional Groups” notes for more information/clarification

Properties of Water ● Hydrogen Bonds ○ They hold together the water molecules and are responsible for the majority of the properties of water

● Universal Solvent ○ Water dissolves almost every polar molecule ■ Hydrogen bonds are broken when water dissolves stuff ■ When dissolving an ionic compound, water separates the molecule into its ions and surrounds each individual ion so they don’t rejoin. The (partially positive) hydrogen parts of water surround the anion and vice versa. ■ When dissolving sugar, the water molecules separate the sugar into monosaccharides and surround the ring of the monomers in a similar manner as an ionic compound. ■ Examples of things that dissolve in water: ● Glucose ● Sucrose ● Table salt (NaCl) ■ Examples of substances that don’t dissolve in water: ● Sand ● Oil ○ Solvent: the substance in which stuff dissolves ○ Solute: what dissolves in the solvent ○ Aqueous Solution: a solution in which water is the solvent ● Polarity ○ This causes it to have a “Mickey Mouse” or “V” shape ○ It is also why water is such a great solvent ● High Heat Capacity/Specific Heat ○ It takes a lot of heat to heat up water ○ This is because the hydrogen bonds between water molecules must be broken before water can be heated up ○ Water can retain a lot of heat ● High Heat of Vaporization ○ A lot of heat is needed to turn liquid water into gas ○ This is a similar concept to the high heat capacity of water- many hydrogen bonds must be broken before the water can change its state of matter ■ An example of this is when we sweat, we take heat away from us and we are cooled down ● High Heat of Fusion ○ A lot of heat is required to change solid ice into liquid water ● Cohesion ○ The attractive force between water molecules and each other

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○ Water molecules form tight hydrogen bonds and stick together to cover the least surface area possible ■ This is shown when water is placed on wax paper and it beads up ○ Nonpolar, hydrophobic substances cannot break water’s cohesive forces, because unlike polar molecules, they are unable to break the hydrogen bonds. Surface Tension ○ Surface tension is very closely related to cohesion ○ It is because the attraction of water molecules to each other (cohesion) at the surface of water is very strong and the hydrogen bonds are very tightly packed as a result. ■ This is what causes water to not overflow when carefully poured into a cup, even if it is above the rim of the cup ■ This is also why, in the water stations lab, the needle floated on the surface of the water, which seemed to bend around it ● When the soap was added to the water, its polar ends caused the hydrogen bonds to break and as a result, the surface tension broke and the needle sank Adhesion ○ Adhesion is also related to cohesion ○ While cohesion is the attraction between water molecules, adhesion is the attraction between water molecules and solid surfaces around it. Capillary Action ○ This is related to cohesion and adhesion ○ Let’s use the example of water sliding up a straw: ■ Adhesion causes the water to be attracted to the straw, and to start sliding up it. ■ Then, the cohesive forces between the water molecules cause them to follow each other and push each other up the straw Density ○ Unlike any other substance, the density of ice (solid water) is less than the density of liquid water ■ This is due to the hydrogen bonds spreading out when water is freezing ○ As a result, ice will float on water ■ This is important to living things because in a lake, the floating ice serves as thermal insulation and prevents the rest of the lake from freezing or getting colder. This helps ensure the survival of aquatic ecosystems.

Organic Compounds ● Basics ○ Monomers: building blocks of complex molecules ○ Polymers: made up of monomers bonded covalently ○ Macromolecules: large molecules formed by covalent bonds between smaller molecules ■ Important to living things: proteins, lipids, carbs, nucleic acids ○ Condensation/Dehydration Synthesis: removes water to form bonds ○ Hydrolysis: adds water to break bonds and separate molecules ○ Organic Compounds: carbon-based compounds found in living things ■ Carbon can form covalent bonds with up to four other atoms ○ In a chemical reaction, the reactants go through a process to yield the products ● Carbohydrates ○ What are they made of? ■ Carbo: carbon ■ Hydrate: water ■ So, carbohydrates are made up of carbon, hydrogen, and oxygen molecules. The hydrogen and oxygen atoms are in a 2:1 ratio ● For every carbon there is a water molecule (in a simple sugar) ○ Functions of carbohydrates: ■ Energy storage and transport ■ Structural: cellulose and chitin ■ Signals/communication ○ Monosaccharides: the building blocks of carbohydrates ■ Glucose, fructose, and galactose are monosaccharides ● They are hexoses- they contain 6 carbons ● Their formula is: C6H12O6 ● They are isomers- they have the same molecular formula, but different structural formulas (they are arranged differently) ● Glucose is neutral (in electrical charge) but polar ■ Ribose and deoxyribose are pentoses (5 carbons) ■ Numbering carbons: find the oxygen and then go counterclockwise. The carbon sticking out should be the last carbon.

○ Disaccharides: when two monosaccharides bond together through a glycosidic linkage ■ Sucrose ● Glucose + Fructose ■ Maltose ● Glucose + Glucose ■ Lactose ● Galactose + Glucose ■ These disaccharides are isomers as well ● Formula: C12H22O11 ○ This is because 1 water molecule was removed ○ Polysaccharides: when several monosaccharides are bonded together ■ Starch ● Energy storage in plants ■ Cellulose ● Structure of cell wall ■ Glycogen ● Store energy/glucose in animals and humans ■ Chitin ● Exoskeleton of insects ■ These four polysaccharides are isomers ● Lipids ○ What are they? ■ Fats, oils, and waxes ■ When stating the molecular formula for a lipid, go carbon by carbon ■ Most lipids are made up of an alcohol and fatty acids ● Alcohols: carbon atoms bonded to hydrogen atoms and hydroxyl groups ● Fatty acids: long hydrocarbon (H + C) chains and a carboxyl (COOH) group ○ Saturated fats: as much hydrogen as possible ○ Unsaturated fats: 1 or more double-bonded carbons ■ Has kinks and is not as tightly packed as saturated fats ■ This results in them being liquid at room temperature, while saturated fats are solid ■ van der Waals interactions hold hydrocarbons together in water

■ Lipids have no ratio of oxygen to hydrogen atoms. However, there are more hydrogen atoms than oxygen atoms. ○ Functions: ■ Long-term energy storage (triglycerides) ■ Cell membrane structure (phospholipids) ■ Hormones and steroids ■ Thermal insulation ○ Important lipids: ■ Cholesterol ● Makes sex hormones and steroids ● Controls fluidity/stiffness of cell membrane ○ More cholesterol = more stiffness ○ Prevents the membrane from “freezing up” ■ Triglycerides ● Made of glycerol (backbone) and 3 fatty acids ■ Phospholipids ● Made of 1 glycerol + 2 fatty acids + 1 phosphate group ● Makes up the cell membrane ○ The polar and hydrophilic phosphate group is the “head” and is on the outside of the bilayer, so it can interact with the aqueous solutions inside and outside the cell ○ The nonpolar and hydrophobic fatty acid tails are on the inside of the bilayer ○ This results in only nonpolar molecules being able to diffuse through a membrane ● They are amphipathic: they are partly hydrophobic and party hydrophilic ● Nucleic Acids ○ Made of nucleotides ■ Made of: ● Nitrogen base ○ DNA: adenine, thymine, cytosine, guanine ○ RNA: adenine, uracil, cytosine, guanine ○ Attached to carbon 1 in sugar ○ Purine ■ Has two rings ■ “Purine is as s old” ○ Pyrimidine

■ One ring ■ “ the (pie)” ● Phosphate group ○ Attached to carbon 5 in sugar ● Sugar ○ Ribose (in RNA) ■ C5H10O5 ○ Deoxyribose (in DNA) ■ C5H10O4 ■ Has one less oxygen than ribose ■ Nucleotides are linked together through phosphodiester bonds ○ DNA vs. RNA ■ DNA is double stranded. It forms a helix and is antiparallel. ■ RNA is single stranded ■ They have different sugars ■ DNA has thymine while RNA has uracil instead ■ DNA is less flexible than RNA ○ Functions: ■ DNA stores and transmits genetic information ■ RNA transmits information from DNA for protein synthesis ■ Transcription, Translation, and Replication ● Transcription: ○ DNA is copied into RNA ● Translation: ○ Nucleotides in RNA determine amino acids ● Replication: ○ DNA makes an exact copy of itself ■ Gene expression: transcription and translation of specific DNA sequences ● Genome: complete set of DNA in an organism ● Proteins ○ Functions ■ Carry out the instructions of DNA ■ Do literally everything in your body ○ Made in ribosomes ○ Made up of: amino acids ■ Amino acids are made up of: ● central/alpha carbon bonded to a hydrogen atom ● Amine group (NH3)

● Carboxyl group (COOH) ● Variable group/R group/side chain ○ Defines the amino acid & its properties ■ There are 20 different amino acids in your body, so there are 20 different variable groups ○ Levels of protein organization ■ Primary Structure ● Linear sequence of amino acids ● Determined by peptide bonds ■ Secondary Structure ● How the amino acid sequence in a polypeptide folds over itself ● Determined by backbone interactions, which are determined by hydrogen bonds ● Two patterns: ○ Alpha helix: coil shape ○ Beta pleated sheet: two chains of amino acids are joined together through hydrogen bonds ■ Parallel (amine and carboxyl groups line up) ■ Antiparallel (amine and carboxyl groups don’t line up) ■ Tertiary Structure ● Secondary structure folds even more over itself ● Depends on interactions between the R groups, stabilized by hydrogen bonds ● Other important bonds in this level are van der Waals, hydrophobic interactions, and disulfide bridges ○ Hydrophobic R-groups fold on the inside of the polypeptide to avoid aqueous solutions ■ Quaternary Structure ● Interactions between multiple polypeptides (subunits) ○ Important Proteins: ■ Hemoglobin ● Binds to oxygen and carries it through the bloodstream ■ Enzymes ● Speed up a reaction without being altered in it (biological catalysts) ○ Lowers the amount of activation energy/energy needed in a chemical reaction

○ Can be reused ● Enzymes are specific- they only work with a certain substrate ○ The function of an enzyme depends on its shape and on its chemical properties ● Substrates: reactants ● Active site: where the substrates bind ● Activating enzymes: ○ Cofactors- inorganic molecule ○ Coenzyme- organic molecule ○ Bind to the enzyme to activate it/make it work ● Reactions: ○ Anabolic reaction: join simple molecules to make more complex molecules ○ Catabolic reaction: split complex molecules into simple molecules ○ Part of metabolism: all reactions that involve energy ● Inhibitors ○ Irreversible inhibition ■ Binds to an amino acid side chain and blocks the active site ○ Reversible inhibition ■ Competitive inhibition ● Binds with active site but no reaction occurs ■ Noncompetitive/allosteric inhibition ● Binds at allosteric site, blocking the active site ● Binds at allosteric site, changing the shape of the enzyme/active site ○ Feedback Inhibition ■ When the end product binds to the first enzyme in the metabolic pathway ○ Denaturing proteins ■ Environmental factors can denature proteins ● pH: can affect how hydrophobic a protein region is and can change its shape ● Temperature: too much heat can break noncovalent bonds in polypeptides and denature proteins

■ Proteins can no longer function if they are denatured and their shape/tertiary structure is altered.

pH- Acids & Bases ● ● ● ●

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pH is the measure of t...