Biochemistry

Biochemistry - The molecules of Life Chapters - Campbell 2-5
 * Complete Activities Quizzes for Chapters 3-5 in Campbell 8th ed. (you can review the activities first and take thesed as many times as you like.)
 * Select 8th Editions AP Campbell Site
 * Be sure you are logged into MY class
 * If you complete the LONGER Practice Tests on these chapters, it will be EC :)

EL - Chapters 4, 5

Basic Chemistry[[image:http://www.revisionworld.com/files/atomicnumber.jpg width="586" height="390" align="right" caption="external image atomicnumber.jpg"]]

 * Elements - Atoms and Subatomic Particles
 * Calculating number of protons, neutrons, and electrons
 * Valence electrons involved in bonding
 * Isotopes and neutrons

Bond Video - what kinds of bonds are these
 * Bonding
 * [[image:hhsbiology:02_06_stable_arrangement.jpg width="478" height="406" align="left" caption="02_06_stable_arrangement.jpg"]]Octet Rule
 * Types of Bonds
 * Ionic Bonds - transfer of electrons (ions formed); can dissolve in water
 * Covalent Bonds - sharing electrons
 * polar vs. non-polar
 * non-polar bonds share electrons equally or nearly equally
 * polar bonds share them unequally, so create areas of "partial" charge
 * polar bonds are soluble
 * Hydrogen Bonds - attraction of a partially + Hydrogen in one polar molecule to an N or O on another molecule
 * this is a relatively weak bond, but VERY important in biology

Chemistry of Water[[image:hhsbiology:water.gif width="222" height="226" align="right" caption="water.gif"]]

 * ===water is a polar molecule===
 * Since O is more electronegative than H, the electrons are more often found near O than H
 * This makes a molecule with positive and negative "ends" or poles
 * The H of one water molecule is attracted to the O of a neighboring water molecule.
 * Hydrogen bonds are formed, which are weak attractive forces.
 * Because water is a polar molecule, it has "special" properties that are essential to life on earth
 * ====Water is less dense as a solid than a liquid.====
 * as water cools, its molecules slow down and begin to contract, but at 4°C, the substance is the most dense
 * as water cools from 4°C to 0°C (freezing), H-bonds begin to form and the molecules begin to "space out" in arrangement
 * since the volume is greater, while the mass remains the same, the density is less
 * this causes ice to float.
 * Biological implications: bodies of water don't freeze solid/ice acts as an insulator/movement of water brings nutrients and ozygen to lower depths
 * ====Water is cohensive and adhesive====
 * Because water is polar, it forms H-bonds with itself (cohesion) and other polar substances (adhesion)
 * Biological implications: water sticks together, allowing it to be "pulled" up the veins of leaves
 * Surface tension - cohesiveness of water molecules at surface: insects can walk across water
 * ====Water has a high specific heat====
 * Because it takes energy to break H-bonds, it takes a relatively large amount of energy to raise the temperature of water.
 * specific heat is defined as the amount of energy needed to raise the temperature of 1 kg of water 1°C
 * Biological implications: water ecosystems have stable temperatures/water can help regulate temperature in all organisms (they are primarily water)/ecosystems near water have more stable climates (they don't heat up as fast in summer nor cool down as quickly in the winter since forming H-bonds releases energy (heat) to the environment, and breaking them requires energy (heat)
 * ====Water has a high heat of vaporization====
 * the heat of vaporization is defined as the amount of energy (heat) needed to convert 1 mole of a substance from a liquid to a gas.
 * Since H-bonds must be broken to vaporize water, this takes a LOT of energy compared to other substances.
 * This energy acts as an EVAPORATIVE COOLANT (think - when sweat evaporates, you feel cooler because energy from you (heat) is used to convert water from liquid to gas
 * [[image:hhsbiology:nacl2.gif width="350" height="182" align="right" caption="nacl2.gif"]]

Water is a good solvent

 * Since water is polar, it has partial positive (H) and partial negative (O) ends.
 * These "poles" are attracted to oppositely charged particles (other polar and ionic substances)
 * Water surrounds the particles, breaking them apart
 * SOOO... polar and charged (ionic) solutes will dissolve in water.

Chemistry of Carbon and its Compounds

 * valence electrons and bonding
 * carbon has 4 valence electrons so it MUST form FOUR covalent bonds
 * these can be single, double, or triple bonds
 * these can be with carbon or with other atoms
 * Valence of main CHONPS elements:
 * C = 4
 * H = 1
 * N = 3
 * O = 2
 * S = 2, 6
 * ===versatility of carbon===
 * can make single, double or triple bonds
 * can be with carbon or with other atoms
 * can form LONG chain molecules
 * can be straight chains
 * can be branched chains
 * can be cyclic (roughly circular)
 * infinite number of compounds to form...
 * ==functional groups==
 * ===hydroxyl -OH===
 * (increases solubility; is not reactive)
 * ===carbonyl - C=O===
 * (increases solubility)
 * ===carboxyl -COOH===
 * (this is carbonyl and hydroxyl on same carbon)
 * (these donate H + ions in water, so they are ACIDS)
 * the ionized form (once they lost the H + ) is - COO -
 * ===amino - NH 2 ===
 * these accept H+ ions so they are BASES
 * the ionized form is - NH 3 +
 * ===phosphate - PO 4 ===
 * these are negatively charged
 * they increase solubility
 * ===sulfhydryl - SH===
 * increase solubility
 * if two of these are near each other, they will covalently bond to each other.
 * this forms a "disulfide bridge"
 * it stabilizes the 3-D structure in proteins.
 * Supplemental Activity
 * Biocoach - Building Biomolecules ([|www.biology.com] Classic Biology Place)
 * Biocoach - Properties of Biomolecules ([|www.biology.com] Classiv Biology Place)

Macromolecules (Biological Polymers)
> Chapter 5 review > >
 * Carbohydrate
 * Lipids HHMI - Fat
 * Proteins You Tube Clip on Proteins
 * Nucleic Acids You tube clip on DNA
 * Function
 * information transfer
 * in protein synthesis (DNA to RNA to protein)
 * prior to mitosis/meiosis so genetic instructions go from original cell to daughter cell or gametes
 * information storage
 * code for making proteins
 * Examples
 * DNA
 * RNA
 * Made of nucleotides
 * Sugar
 * deoxyribose (DNA)
 * ribose (RNA)
 * Phosphate(s)
 * Nitrogen Base
 * Purine (2 rings)
 * Adenine
 * Guanine
 * Pyrimidine (1 ring)
 * Cytosine
 * Thymine (DNA)
 * Uracil (RNA)
 * Antiparallel nature
 * Base pairing rules
 * purine to pyrimidine
 * A-T (2 H-bonds)
 * C-G (3 H-bonds)
 * Essential Experiments
 * Hershey-Chase (Blender)
 * Griffith/Avery - transformation in pneumonia bacteria
 * Chargaff
 * Wilkins/Franklin
 * Watson/Crick
 * Here is a good overall link to a review:

**DNA Replication**

 * Overview
 * DNA unzips, semiconservative replication
 * Details
 * Direction of replication
 * Leading vs. Lagging Strand
 * Enzymes/Proteins/other molecules involved
 * Helicase
 * Single Stranded Binding Proteins
 * Primase
 * RNA primer
 * DNA polymerase I and III
 * ligase
 * How do we know this?
 * Meselson-Stahl experiment

Basic and Biochemistry Powerpoints
Basic Chemistry & Water from KIm Foglia Carbon from KIm Foglia Carbohydrates from KIm Foglia Lipids from KIm Foglia Proteins from Kim Foglia - remember secondary structure - NOT in R-groups. Nucleic Acids from Kim Foglia