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AP Biology

This text covers the fundamental concepts of basic chemistry, including elements, compounds, atomic structure, chemical bonds, and chemical reactions. It also explores the unique properties of water and its role in biological systems.

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AP Biology

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  1. AP Biology Exam Critical Concepts Chapters 2-5 Biochemistry

  2. Chapter 2 Basic chemistry • C, H, O, N = Essential elements • Ca, P, K, S = Trace elements • Protons, neutrons, electrons • Element: substance that cannot be broken down to other substances by chemical reactions • Compound: substance consisting of two or more elements in a fixed ratio • Atomic number: # of protons in nucleus • Mass number: sum of protons + neutrons

  3. Chapter 2 Basic chemistry cont. • Atoms are the smallest unit of matter

  4. Chapter 2 Basic chemistry cont. Helium 2He Hydrogen 1H Atomic number 2 He 4.00 Atomic mass Element symbol First shell Electron- distribution diagram Lithium 3Li Beryllium 4Be Fluorine 9F Boron 5B Nitrogen 7N Neon 10Ne Carbon 6C Oxygen 8O Second shell

  5. Chapter 2 Basic chemistry cont. • Atomic mass: atom’s total mass/mass number • Isotopes: two atoms of an element that differ in number of neutrons • Radioactive isotopes: decay spontaneously, giving off particles and energy • Valence electrons: electrons in the outermost shell, or valence shell • Chemical bonds: Attraction between atoms

  6. Chapter 2 Basic chemistry cont. • Covalent bond: sharing of valence electrons by two atoms • Single bond: sharing of one pair of valence electrons • Double bond: sharing of two pairs of valence electrons • Valence: Bonding capacity Electron- distribution Diagram Lewis Dot Structure and Structural Formula Name and Molecular Formula Space- filling Model Hydrogen (H2) Oxygen (O2)

  7. Chapter 2 Basic chemistry cont. • Electronegativity: an atom’s attraction for the electrons in a covalent bond • Nonpolar covalent bond: the atoms share electron equally • Polar covalent bond: one atom is more electronegative, atoms do not share electron equally • Unequal sharing of electrons causes a partial positive or negative charge for each atom or molecule – O H H + + H2O

  8. Chapter 2 Basic chemistry cont. • Ionic Bonds: Atoms sometimes strip electrons from their bonding partners • Ion: Charged atom or molecule Cl Cl Cl Na+ Cl– Na Sodium ion (a cation) Chloride ion (an anion) Sodium atom Chlorine atom Sodium chloride (NaCl)

  9. Chapter 2 Basic chemistry cont. • Cation: positively charged ion • Anion: negatively charged ion • Ionic bond: attraction between an anion and a cation • Hydrogen bond: a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom • Chemical reactions: the making and breaking of chemical bonds • Reactants: starting molecules of a chemical reaction

  10. Chapter 2 Basic chemistry cont. • Products: final molecules of a chemical reaction • Chemical equilibrium: reached when the forward and reverse reaction rates are equal

  11. Chapter 3 Water Chemistry • Polar molecule: opposite ends have opposite charges • Hydrogen bonds: polarity allows water molecules to form with each other water molecules • Properties of water: contribute to Earth’s fitness for life • Surface tension/Cohesive behavior: • Adhesion: water sticks something (water drop) • Cohesion: water sticks to itself (movement of water in plants) • Hydrophilic substance that has an affinity for water

  12. Chapter 3 Water Chemistry cont. • Hydrophobic substance without an affinity for water • Formation of water droplets & • Ability to moderate temperature: • Water has a high specific heat • Specific heat is the amount of energy required to change the temperature of a substance. • Water can absorb large amounts of heat energy before it begins to get hot • Water releases heat energy slowly when situations cause it to cool

  13. Chapter 3 Water Chemistry cont. • Expansion upon freezing • Ice floats in liquid water because hydrogen bonds in ice are more “ordered,” making ice less dense • Versatility as a solvent • Solution: a liquid that is a homogeneous mixture of substances • Solvent is the dissolving agent of a solution • Solute: substance that is dissolved • Aqueous solution: water is the solvent • Hydrophilic substance that has an affinity for water • Hydrophobic: substance that does not have an affinity for water

  14. Chapter 3 Water Chemistry cont. • Colloid : a stable suspension of fine particles and water • Hydronium ion (H3O+): molecule with an extra proton • Hydroxide ion (OH–): molecule that lost the proton. • pH scale: Measure of the OH– and H+ ions • 0-6.9 Acid (more H+ ions) • 7.0 Neutral (ratio of ions balanced) • 7.1-14 basic (more OH– ions)

  15. Chapter 3 Water Chemistry cont. • Buffers: substances that minimize changes in concentrations of H+ and OH– in a solution • Carbonicacid: Regulates pH changes in animals

  16. Chapter 4 Carbon Chemistry • Organic Compounds: contain carbon • Major elements in life: CHNOPS • Four valence electrons: carbon can form four covalent bonds with a variety of atoms • Carbon chains: the skeletons of most organic molecules • Carbon chains vary in length and shape • Hydrocarbons: organic molecules consisting of only carbon and hydrogen • can undergo reactions that release a large amount of energy • Fats: have hydrocarbon components

  17. Chapter 4 Carbon Chemistry cont • Isomers: compounds with the same molecular formula but different structures and properties: • Structural isomers: have different covalent arrangements of their atoms • Geometric isomers: have the same covalent arrangements but differ in spatial arrangements • Enantiomers: (stereo or right and left hand) are isomers that are mirror images of each other

  18. Chapter 4 Carbon Chemistry cont Structural isomers: Geometric isomers: Enantiomers:

  19. Chapter 5 Biological Molecules • Isomers: same molecular formula but different arrangement. • Polymers: long chains of repeating molecules • Dehydrationreaction: create polymers • Remove water

  20. Chapter 5 Biological Molecules cont. 1 Dehydration reaction in the synthesis of a polymer HO 1 2 3 H H 3 OH Unlinked monomer Short polymer Dehydration removes a water molecule, forming a new bond H2O HO 1 2 H 4 2 3

  21. Chapter 5 Biological Molecules cont. H 1 • Hydrolysis reaction: break polymers • Need water HO 3 2 4 1 H HO H2O H 4 2 3 H2O 2 1 3 4 H H OH HO H Unlinked monomer Short polymer

  22. Chapter 5 Biological Molecules cont. • Carbohydrates: sugars and polymers of sugars • Monosaccharaides: single sugars • molecular formulas that are usually multiples of CH2O • Glucose (C6H12O6): the most common • Disaccharide: formed when a dehydration reaction joins two monosaccharaides • Polysaccharides: polymers composed of many sugar building blocks • Glycogen: storage polysaccharide in animals • Starch: storage polysaccharide of plants • Cellulose: plant cell wall structure • Chitin: Skeleton of arthropods

  23. Chapter 5 Biological Molecules cont. Carbohydrates

  24. Chapter 5 Biological Molecules cont. • Lipids: large biological molecules that do not form polymers • Energy storage • Fats: constructed from two smaller molecules: • Glycerol: three-carbon alcohol with a hydroxyl group attached to each carbon Fatty acid: a carboxyl group attached to a long carbon skeleton • Saturated fatty acids: maximum number of hydrogen atoms possible and no double bonds • Unsaturated fatty acids: one or more double bonds

  25. Chapter 5 Biological Molecules cont. • Hydrogenation: process of converting unsaturated fats to saturated fats by adding hydrogen • Phospholipid: two fatty acids and a phosphate group are attached to glycerol • Component of all cell membranes • Steroids: characterized by a carbon skeleton consisting of four fused rings • Estrogen and testosterone • Cholesterol: component in animal cell membranes

  26. Lipids Chapter 5 Biological Molecules cont. Fatty Acids Phospholipids Steroids

  27. Chapter 5 Biological Molecules cont. • Protein:polymers of amino acids (polypeptides) • Functions include: structural support, storage, transport, cellular communications, movement, and defense against foreign substances • built from the same set of 20 amino acids Shape dictates function: • Primary structure: unique sequence of amino acids in a chain • Secondary structure: coils and folds in the polypeptide chain • Tertiary structure: determined by interactions among various side chains (R groups) • Quaternary structure: consists of multiple polypeptide chains

  28. Proteins structure Chapter 5 Biological Molecules cont.

  29. Chapter 5 Biological Molecules cont. Protein Structure: Secondary Protein Structure: Primary Protein Structure: Tertiary Protein Structure: Quaternary

  30. Chapter 5 Biological Molecules cont. Proteins Because their shape is held together by weak hydrogen bonds, proteins are easily denatured by heat, acids/bases or shaking.

  31. Chapter 5 Biological Molecules cont. • Enzymes: protein that acts as a catalyst to speed up chemical reactions • perform functions repeatedly as workhorses temperature and pH dependent • binds to the reactants, called the substrate, of a chemical reaction • Substrate joins with the enzyme at the enzymes activesite forming an enzyme-substrate complex • enzyme releases the product(s) and the enzyme is ready to bind to more substrate

  32. Chapter 5 Biological Molecules cont. Enzyme Structure: • Chaperonins: protein molecules that assist the proper folding of other proteins

  33. Enzymes lower activation energy Chapter 5 Biological Molecules cont. Active Site Enzyme Substrate Complex If it happens in a cell, an enzyme does it! S1 + S2 E New Material + Enzyme

  34. Chapter 5 Biological Molecules cont. • Nucleic acids: store and transmit hereditary information • Two types of nucleic acids: • Deoxyribonucleic acid (DNA) • Ribonucleic acid (RNA) • DNAprovides directions for its own replication • directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis • Gene: amino acid sequence of a polypeptide is programmed by this unit of inheritance composed of a nucleic acid

  35. Chapter 5 Biological Molecules cont. • Nucleotides: monomers of nucleic acids • consists of a • nitrogenous base • bases pair up and form hydrogen bonds: • adenine (A) always with thymine (T) • guanine (G) always with cytosine (C) • pentose sugar • DNA: sugar is deoxyribose • RNA: sugar is ribose • Phosphate group

  36. Chapter 5 Biological Molecules cont. • Polynucleotides: polymers of nucleic acids • Nucleotides are joined by covalent bonds that form between the –OH group on the 3 carbon of one nucleotide and the phosphate on the 5 carbon on the next • Antiparallel: the DNA double helix in which the two backbones run in opposite 5 → 3 directions from each other

  37. DNA and RNA Chapter 5 Biological Molecules cont. • RNA usually 1 strand • DNA usually a double helix • RNA in both nucleus and cytoplasm • DNA in nucleus

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