BIOCHEMISTRY GUIDED NOTES - AP BIOLOGY-
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1 BIOCHEMISTRY GUIDED NOTES - AP BIOLOGY- ELEMENTS AND COMPOUNDS - anything that has mass and takes up space. - cannot be broken down to other substances. - substance containing two or more different elements in a fixed ratio. ELEMENTS OF LIFE Elements- required for an organism to live and healthy life and reproduce. o Four Elements,,,, make up 96% of all living matter. Elements- required by an organism, but only in very small quantities. THE ATOM - smallest unit of matter that retains the properties of an element. o - positively charged, found in nucleus o - neutral/no charge, found in nucleus o - negatively charged, found in electron cloud. - identifies an element. Equal to the number of. (and electrons if neutral) - protons + neutrons o Will vary for isotopes. - the average weighted mass of the isotopes. ISOTOPES Isotopes- different forms of the same element. Vary in the number of, which gives them a different number.
2 Isotopes- atom that has an unstable nuclei that decays and breaks down at a continuous rate. o Used to date life, follow atoms through chemical processes, etc. ENERGY LEVELS - found in the outermost shell, the valence shell. Atoms with the same number of electrons in their valence shell behave similarly. An atom with a completely filled valence shell is chemically, or inert. CHEMICAL BONDS Covalent Bond- electrons are shared,. o Single, Double, Triple Bonds- share 1, 2 and 3 pairs of electrons respectively. o - two or more elements held together by a covalent bond. o - the attraction of an atom for the electrons of a covalent bond. The more electronegative an atom is, the more strongly it pulls shared electrons toward itself. Covalent Bond- a bond where electrons are not shared equally. (varying degrees) Covalent Bond- a bond where electrons are shared equally. Ionic Bond- electrons are transferred, forming ions. - negatively charged ion, has gained electrons. - positively charged ion, has lost electrons. Ionic Compounds/Salts- the result of an ionic bond.
3 Hydrogen Bond- forms between,,,. Van der Waals Forces- formed by atoms that are very close together with positively and negatively charged regions. *Weak bonds help reinforce the of the molecule. INTERMOLECULAR AND INTRAMOLECULAR FORCES Intermolecular Forces- between atoms of two different molecules. o Ex: Intramolecular Forces- between atoms of the same molecule. o Ex: CHEMICAL REACTIONS Rate of Reaction can be affected by:,,,, and. Chemical Equilibrium- forward and reverse rate of reactions are. o - reactions are still going on, but do not affect the concentration of the reactants or products, and they remain equal. PROPERTIES OF WATER Molecule- has an overall charge that is unequally distributed. (due to unequal sharing of electrons). - the ability of like molecules to attract. - the clinging of one substance to another substance. o Adhesion and Cohesion are responsible for. - very high in water- as a result of cohesion.
4 - this allows water to stabilize temperatures. (how well a substance resists change in temperature) o High specific heat is a result of - amount of energy for evaporation to occur. - as liquid evaporates, the surface of the liquid that remains behind cools down C, water moves too slowly to break hydrogen bonds and starts to freeze. - water is a great solvent because of its polarity, allowing it to draw in and dissolve molecules with opposing charges. o Solute o Solvent o Solution HYDROPHILIC VS. HYDROPHOBIC Hydrophilic- substance that has an affinity for water. Hydrophobic- substance that seems to repel water. o These are nonpolar compounds. (ie: oils) CHEMISTRY CALCULATIONS Calculating Molecular Mass o Acetone- C3H6O Making Solutions?g/mol x 1mol/L = 1 molar solution?g/mol x 4 mol/l = 4 molar solution
5 ACIDS AND BASES Acid- increases the concentration of a solution. (lower OH- concentration). Base- increases the concentration of a solution. (lower H+ concentration). Neutral- solution where H+ and OH concentrations are equal. o ph = - log [H+] o Each ph unit represents a difference in H+ and OH- concentrations. - substances that minimizes changes in concentrations of H+ and OH- in a solution. o By accepting hydrogen ions when in excess and donating when they have been depleted. o Most buffers are weak acid- base pairs. ORGANIC CHEMISTRY Organic Chemistry- the study of - the number of covalent bonds an atom can form. (generally equal to the number of electrons required to complete the valence shell). HYDROCARBONS - organic molecules consisting of only carbon and hydrogen. (nonpolar) o Fats have long hydrocarbon tails attached to a non- hydrocarbon component. - no C=C (saturated w/ Hydrogen) - at least or more 1 C=C o Hydrocarbons can undergo reactions that release large amounts of. FUNCTIONAL GROUPS Functional Groups- participate in chemical reactions in a characteristic way.
6 ADENOSINE TRIPHOSPHATE (ATP) ATP is an BIOLOGICAL MOLECULES - made from thousand of smaller molecules. o A is a long molecule made of repeating units called. o - specialized macromolecules that speed up chemical reactions. SYNTHESIS AND BREAKDOWN OF POLYMERS Polymers are created and broken down by 2 reactions: o Reaction- creates a polymer from 2 or more monomers. Lose H2O. o - breaks down a polymer into its monomers. Form H2O
7 CARBOHYDRATES Carbohydrates- made up of monosaccharides, generally has molecular formula. (- ose). Carbohydrates provide for cellular processes. o Sugars frequently contain and. - covalent bond connecting two monosaccharides. Polysaccharides- hundreds or thousands of monosaccharides joined by glycosidic linkages. o - starch (plants) glycogen (animals) o - cellulose and chitin LIPIDS Lipids- hydrophobic compounds that include,,, and. Fats- energy molecules made of and. o - used to join fatty acid molecules to glycerol by connecting a hydroxyl group and a carboxyl group. Types of Fats o Fats- no double bonds o Usually solid at room temperature. o Fats- contains at least 1 double bond o Usually liquid at room temperature. (cis bonds) o Fats- unsaturated fats with trans double bonds.
8 Phospholipids- two fatty acids attached to a glycerol and includes a phosphate group (negative charge) which can link other small molecules. Contains and. Steroids- lipids characterized by a carbon skeleton of 4 fused rings. o Steroids are distinguished by the different chemical groups that attach to the 4 rings. o - found in animal cell membranes, template from which other steroids are synthesized (in the liver). PROTEINS Proteins- a biological molecule consisting of one or more polypeptides, folded in a specific 3D structure. o - a polymer of amino acids.
9 o - organic molecule containing an amino group and a carboxyl group. - covalent bond that connects 2 amino acids- forms a polypeptide. o The amino acid sequence of a polypeptide determines the of the protein. Four Levels of Protein Structure o - the series of amino acids in a unique sequence. Coded for in DNA. o - coils and folds in the polypeptide chain. Result from between polypeptide backbone - a coil held together by H- bonding between every 4 th amino acid. - 2 or more strands of a polypeptide chain laying side by side and connected by H- bonds. o - results from interactions between side chains (R groups). - align nonpolar side chains in the core of the protein- away from water. - covalent bonds between side chains. o - association between multiple polypeptide chains- forming a functional protein.
10 Protein Structure o - proteins that assist in the proper folding of other proteins. o - protein unravels and loses its shape. Because of change in,,, etc. Protein Function
11 NUCLEIC ACIDS - a short segment of DNA, located on a chromosome. Types of Nucleic Acids o Deoxyribonucleic Acid (DNA) o Ribonucleic Acid (RNA) DNA and RNA direct, which occurs on the ribosomes. Nucleic Acids- made of polynucleotides, which are composed of monomers called. 3 Parts of a Nucleotide o o o
12 Nitrogenous Bases o : 2 ring structure (6C and 5C). Includes Adenine and Guanine o : 1 ring structure (6C). Includes Cytosine, Uracil, and Thymine. o DNA contains Adenine,, Guanine, and Cytosine. o RNA contains Adenine,, Guanine, and Cytosine. - connects nucleotides by joining the sugars of 2 nucleotides with a phosphate group. o Creates a with repeating units - 2 polynucleotide strands that spiral around. (DNA) o These two strands run in opposite directions, and are referred to as. Base Pairing ( ) Rule- forms a complementary strand. o pairs with (DNA) or (RNA) o pairs with
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