Bellringer 9/11/17 Go to your next blank left and right pages (have to be side by side) and label it Unit 1.1: Biochemistry and decorate it.

Bet you wish you were able to spin fibers from your bum! The Chemistry of Life Domains of Study Domain of BioMolecules Domain of Cells Domain of Organisms Domain of Populations Domain of Communities

Why are we studying chemistry? Chemistry is the foundation of Biology link

Everything is made of matter Matter is made of atoms Hydrogen 1 proton 1 electron Oxygen 8 protons 8 neutrons 8 electrons Proton + Neutron Electron –

Atomic Structure Electron: -1, “0” dalton Mass number= #p+#N Atomic mass is average abundance of isotopes Proton: +1, 1 dalton Neutron: 0, 1 dalton Showed mostly “empty space”! Rutherford’s gold foil experiment

Higgs Bosun= God Particle Higgs Bosun= God Particle? With super colliders, scientists discover particles beyond known 3 link

The World of Elements link Arranged by increasing protons Elements in the same group/family have same therefore, chemically similar properties. valence electrons

Compound Element A combination of elements bonded to other elements. the most basic form of any pure material. Example: Hydrogen (H) Example: Potassium (K) Compound A combination of elements bonded to other elements. Examples: H2O, CO2, C6H12O6

Life requires ~25 chemical elements About 25 elements are essential for life Four elements make up 96% of living matter: • carbon (C) • hydrogen (H) • oxygen (O) • nitrogen (N) Four elements make up most of remaining 4%: • phosphorus (P) • calcium (Ca) • sulfur (S) • potassium (K)

How does this atom behave? Bonding properties Effect of electrons electrons determine chemical behavior of atom depends on number of electrons in atom’s outermost shell valence shell How does this atom behave?

Bonding properties Effect of electrons What’s the magic number? Bonding properties Effect of electrons chemical behavior of an atom depends on number of electrons in its valence shell Sulfur on the LEFT Magnesium on the RIGHT How does this atom behave? How does this atom behave?

Elements & their valence shells Elements in the same row have the same number of shells Moving from left to right, each element has a sequential addition of electrons (& protons)

Elements & their valence shells Elements in the same column have the same valence & similar chemical properties Remember some food chains were built on reducing O to H2O & some on reducing S to H2S Oxygen has medium electronegativity so doesn’t pull electrons all the way off hydrogen whereas chlorine would. So oxygen forms a polar covalent bond. Carbon has only a weak electronegativity so forms a nonpolar covalent bond

Natural Nuclear Decay: spontaneous disintegration of nucleus by particle emission. Transmutation-change of because of loss of a which identifies an element. element proton

Carbon-14 incorporated in organisms can be used to date fossils. How does it work?? 1/2 LIFE!

1/2 Life: The time it takes for ½ of the material to decay into another material. Can be seconds, minutes, days, years, until a stable isotope is made. 100% - 50% - 25% - 12.5% - 6.25% 1 – 1/2 – 1/4 - 1/8 – 1/16 – 1/32

Medical Uses of Radioactive Isotopes: Cesium filled seeds for radiation therapy Xe133 shows organ blood flow PET Positron emission tomography

This tendency drives chemical reactions… Chemical reactivity Atoms tend to complete a partially filled valence shell or empty a partially filled valence shell This tendency drives chemical reactions… and creates bonds – –

Bonds in Biology Bonds between molecules Bonds between atoms Hydrogen bond H2O Bonds between molecules hydrogen bonds attraction between + and – hydrophobic & hydrophilic interactions van derWaals forces Bonds between atoms covalent bonds share electrons Ionic transfer electrons – H2 (hydrogen gas) Covalent bond

COVALENT BONDING: H2O O H H Nonmetal-nonmetal Pair of electrons shared unequally = polar bond H2O (molecular formula) O Polar molecule H H (structural formula) Electronegativity: the ability to attract electrons

BellRinger: 9/12/17 Write down the question and draw the graph that is the correct answer.

Covalent bonds Why is this a bond? Forms molecules two atoms share a pair of electrons both atoms holding onto the electrons very stable Forms molecules H Oxygen – H O H — H H2 (hydrogen gas) H2O (water)

Multiple covalent bonds 2 atoms can share >1 pair of electrons double bonds 2 pairs of electrons triple bonds 3 pairs of electrons Very strong bonds More is better! H H–C–H –

Polar covalent bonds Pair of electrons shared unequally by 2 atoms Water = O + H oxygen has stronger “attraction” for the electrons than hydrogen oxygen has higher electronegativity water is a polar molecule + vs – poles leads to many interesting properties of water… H Oxygen + – – – – +

IONIC BONDING: Metal-nonmetal Transfer of electrons always results in a polar bond and a polar molecules. Cation: (+) loss of electrons Na+ Anion (-) gain of electrons Cl-

Polarity determines solubility: “like dissolves like” Water is a polar molecule Cell membranes have both hydrophilic and hydrophobic lipids.

shape Bonding and Polarity drives molecular CH4 methane Bent shape Nonpolar bond, nonpolar molecule, linear shape Tetrahedral shape

PH Scale (p.165) Acids Bases PH Scale Buffers

Copyright Cmassengale Water About 60-90 percent of an organism is water Water is used in most reactions in the body Water is called the universal solvent Copyright Cmassengale

Copyright Cmassengale Water Properties Polarity Cohesiveness Adhesiveness Surface Tension Copyright Cmassengale

Carbon-based Molecules Although a cell is mostly water, the rest of the cell consists mostly of carbon-based molecules Organic chemistry is the study of carbon compounds Copyright Cmassengale

H A R E Structure determines Function ormone ntibody eceptor nzyme Determines how molecules recognize and respond to each other

HIV infecting a body cell

Intermolecular forces VanDerWaals forces unbalanced electrical charges around nonpolar molecules attract each other. What do Spiderman and geckos have in common? How do they do it?

Hydrogen bonding Polar water creates molecular attractions positive H atom in one H2O molecule attracted to negative O in another H2O also can occur wherever an -OH exists in a larger molecule stronger bond than van der waals Hydrogen bonded to F, O, N APBio/TOPICS/Biochemistry/MoviesAP/03_02WaterStructure_A.swf James is the only BOND!

CHEMICAL REACTIONS Reactants Products will proceed to dynamic equilibrium whereby forward and reverse reaction occur at same rate.

Biologists in the Chemistry Lab!