Basic Chemistry

Matter Elements. Atoms Compounds Molecules

A. Matter
Material that takes up space.

1. Elements
Pure chemical substances composed of atoms. Examples? How many elements exist? How many of these elements are essential to life?

Periodic Table of Elements

2. Atom
The smallest piece of an element that retains the characteristics of that element.

Composed of 3 subatomic particles:

Protons Neutrons Electrons

Characteristics of Subatomic Particles

Model of an Atom

ATOMS
Atomic symbol Atomic number Atomic mass (weight).

CHEMICAL REACTIONS
Electron

shells Valence (outer) shell Octet rule Ionic bonds Covalent bonds

Atoms will strive to fill their outer (valence) orbitals

If

an atom has 1 valence e-, its happy to give it away Example: Sodium

1 valence e-

Atoms will strive to fill their outer (valence) orbitals

ANDIf an atom has 7 valence e-, its happy to pick up one Ex. Chlorine

7 valence e-

Ionic Bonds

Ions can have important biological functions.

Covalent Bonding
Each pair of electrons represents the formation of a covalent bond.

C
H

Carbon (C) 4

Hydrogen (H) 1

Methane CH4

Aside from single covalent bonds, double, or triple covalent bonds can form.

Review
Ionic

bonds occur when e- are shared in a +/- arrangement Covalent bonds exist when one atom shares 1 or more e- with another atom. One covalent bond means 2 e- are involved.

Always involves a pair of e-

Oxidation/Reduction
Oxidation----loss

of electron Reduction----Gain of electron Examples?

Water and Life

Water

is the most abundant molecule in living things. Water has special traits that make it important to life.

Water molecules: 2-H covalently bonded to 1-O. Covalent=shared e-. But is sharing equal?

Chemistry of Water
Amazing stuff!!! Should not be a liquid at room temp Highly Polar molecule.

WATER
Hydrogen

bonds

Polarity

Hydrogen Bonding
Positively charged hydrogen end Covalent bonds between hydrogen and oxygen

Negatively charged oxygen end

Hydrogen Bonds

Characteristics of water:
1. 2. 3. 4.

5.
6. 7. 8.

liquid at room temperature universal solvent for polar molecules water molecules are cohesive water molecules are adhesive temperature of water changes slowly absorbs heat upon vaporization releases heat upon freezing frozen water is less dense

B. The Importance of Water 1. Properties

Cohesion

- the attraction of water molecules for each other. Adhesion - the attraction of water molecules for other compounds. High heat capacity takes a great deal of heat to raise the temperature of water.

 High

heat of vaporization - a lot of heat is required to evaporate water. Exists as solid, liquid or gas - solid (ice) is less dense than liquid.

2. Solutions
A solution is a mixture of one or more solutes dissolved in a solvent. If solvent is water, then it is an aqueous solution. Water is a strong solvent because it separates charged atoms or molecules.

Water as a Solvent How it Works

Dissociation of Water Molecules

Water dissociates and releases hydrogen ions (H+) and hydroxide ions (OH-).

Acids

ACIDS AND BASES

- release hydrogen ions + (H ) in solution.

HCl H+ + Cl-

Bases

- take up hydrogen ions + (H ) or give off hydroxide ions (OH ) in solution.

NaOH Na+ + OH-

pHa Measure of Acidity

If ph<7, acid

7=neutral

If pH>7, base

Buffers

--substances that help to resist change in pH. Why important?

WaterFinal Notes
Hydrophilic--polar Hydrophobic

non-polar Amphipathic---contain hydrophilic and hydrophobic parts

Organic Moleculescarbon based

Organic molecules are found in living things. The chemistry of carbon accounts for the chemistry of organic molecules. Macromolecules (Polymers)

Organic Molecules
organic

monomer

polymer

Macromolecules (polymers) and monomers.

Polymer carbohydrate protein nucleic acid Monomer monosaccharides amino acid nucleotide

Dehydration Synthesis or Condensation Reactions vs Hydrolysis

Dehydration (condensation) builds. Hydrolysis breaks down.
covalent bonds Condensation

OH

B
Hydrolysis

If the reaction is carried out multiple times you create a polymer!

+ HOH or H2O

+ H2O molecules

Proteins
What do they do? Structure Act as enzymes to speed reactions Serve as carriers Act as antibodies Transporters and channels

Proteins --polymers of amino acids.

Peptide Bonds

Proteins--Levels of Organization.

structure and environment FactorsR-groups

TERTIARY (3) STRUCTURE3D

Hydrogen bonding Hydrophobic interactions Ionic (salt) bridges Disulfide bonds

Native

vs Denatured REMEMBER: A PROTEINS FUNCTION IS A RESULT OF ITS FORM!!

EnzymesBiological Catalysts
Catalyst?

Speeds up reaction Proteins The Model:

E=Enzyme
S=Substrate

P=Product

E+S

ES

E+P

Enzymes Lower Energy of Activation

Enzymes-- lower the energy barrier

Reactants

Products

Figure 5.5A

Enzyme

EA barrier

Enzyme-Substrate Complexes
Every

reaction in a cell requires a specific enzyme. Enzymes are named for their substrates: Substrate Enzyme Lipid Lipase Urea Urease Maltose Maltase Ribonucleic acid Ribonuclease

Cell Chemistry
Enzymesinvolved

chemical reactions. AnabolismThe building reactions. EX. Protein synthesis CatabolismThe breakdown reactions. EX. Protein digestion Metabolismsum of all reactions

in almost all

Enzyme Cofactors
Cofactors

---may be necessary for some enzymes to carry out their functions. Two types: Metal ions. EX copper (Cu+2) or iron (Fe+2) Coenzymes Organic molecules, must be present for other enzymes to function. EX vitamins

Levels of Protein Structure Quaternary (4) Structure

Multiple chains: interactions of more than one polypeptide chain to form the complete, functional protein. Ex. Hemoglobin and antibodies

Carbohydrates

Generally, C:H:O in a 1:2:1 ratio (CH2O)n Functions quick energy and short-term energy storage. EX glycogen, starch Structure. EX. Cellulose Polymer=polysaccharides EX. Starch Monomers= monosaccharides EX. glucose

NOMENCLATURE
Based

on number of carbons 3C==triose 4C==tetrose 5C==pentose, etc

Structure of Glucose

Disaccharides

Polymerization of Carbohydrates

POLYSACCHARIDES
STARCH

GLYCOGEN

CELLULOSE

LIPIDS
NON-POLAR

BIOLOGICAL MOLECULES

FUNCTIONS

Energy storage: Fats and oils. Waterproofing: Waxes and oils Insulation: Fat layers (blubber) Cushioning: Fat layers (soles of your feet) Regulating metabolism: Steroids Component of cell membranes: Phospholipids

Lipid structure (Triglyceride)

Glycerol backbone Fatty acid tails Fats vs oils

X3

Triglyceride formation

H H-COH H-COH H-COH

H
GLYCEROL

O HHHHH HO-C-C-C-C-C-C-H HHHHH O HHHHH HO-C-C-C-C-C-C-H HHHHH O HHHHH HO-C-C-C-C-C-C-H HHHHH

O HHHHH H-CO-C-C-C-C-C-C-H + H20 HHHHH O HHHHH H-CO -C-C-C-C-C-C-H + H20 HHHHH O HHHHH H-CO -C-C-C-C-C-C-H + H20 HHHHH H TRIGLYCERIDE + 3 H20 Dehydration Synthesis

FATTY ACIDS

What type of reaction forms a triglyceride?

Saturated vs. Unsaturated Fats

Saturated vs. Unsaturated Fats

Fatty Acids: cis vs. trans

-linolenic acid

Trans -linolenic acid

Phospholipids
The major structural component of cell membranes

Phospholipid Behavior

Phospholipids

Soaps and Emulsifiers

Steroids-Hormones and Structure

Nucleic Acids
Polymers:

DNA and RNA Monomers: nucleotides Functions Information storage and transmission ATP is energy currency of cell

Nucleotide Structure

DNA vs RNA

The Double Helix of DNAComplementary base pairing

The Central Dogma

Replication---

DNA-gene

ATGAGTAACGCG TACTCATTGCGC

duplication of DNA using DNA as the template

DNA

ATGAGTAACGCG TACTCATTGCGC

+
ATGAGTAACGCG TACTCATTGCGC

Transcription--synthesis of RNA using DNA as the template

RNA

mRNA-message

AUGAGUAACGCG

Translation--synthesis of proteins using RNA as the template

Protein

MetSerAsnAla Protein--end product

Mutation-DNA Change

Adenosine Triphosphate-ATP
Adenosine triphosphate (ATP) is
the energy currency of cells