b.
carboxyl group
A. The Chemistry of Life.
1. Classifying matter- 3 types of matter: elements, compounds & mixtures
Matter- anything that has mass and occupies space
a. Atom - basic unit of matter- smallest piece of matter that retains all characteristics of that matter
1.Composed of :
i. proton- positive unit found in nucleus; 1 a.m.u
ii. neutron- neutral unit found in nucleus; 1 a.m.u
iii. electron- negative unit found outside of nucleus; 1/1837 a.m.u.
2. atomic number- number of protons in an atom
3. mass number- number of protons + number of neutrons
4. Isotope- atom which has different number of neutrons
- atomic mass- average of all known isotopes atomic mass and their occurrence in nature
- half life- time in which it takes 50% of an active isotope to decay into a more stable form
Carbon 14 --------> Carbon 12 5770 years
Potassium 40 1.3 billion years
Uranium 235 730 million years
** half lives are used in determining the relative age of fossils and/or remains
Practice: Isotopes, atomic numbers & mass numbers
b. Element- A pure substance composed solely by one type of atom
1.chemical symbol - shorthand notation used to identify certain elements
2. Periodic Table- table used to classify elements in accordance to their properties
family of elements- elements in the same column that possess similar chemical/physical properties
Dmitri Mendeleev- Russian to establish early periodic table
c. Compound- a pure substance composed of two or more elements that are chemically combined
1. molecule - the smallest particle of an element or compound
2. Atomic Structure
a. Nucleus- central positive core of an atom; composed of protons and neutrons
b. Electron cloud- electrons exist in defined space; position is dependent upon energy
1. shell (energy level) - set of orbitals (determined by period number)
2. subshell - specific orbital type within a particular shell (determined by family position)
3. orbital - region around the nucleus where an electron has the highest probability of being
located
c. valence shell - the outermost shell in an atom; contains "reactive" electrons (highest energy)
d. valence electrons - the most reactive electrons; determine how an atom will react
( number of electrons is determined by the family number for main group elements)
e. Lewis Dot Structure- Shorthand representation used to identify atom and valence electrons
* Octet Rule- all atoms strive to have 8 electrons in the outermost shell
Resource: Structure of Atoms and Biomolecules
3. Chemical Bonding
a. Ionic bonds- bonds between atoms that occur due to a transfer of electrons
1. ion- an atom which has either gained or lost electrons
i. cation- an atom which has lost electrons -- positive ion
ii. anion- an atom which has gained electrons-- negative ion
b. Covalent bonds - bonds between atoms which occur because of a sharing of electrons
-found most commonly within biomolecules
1. single covalent- share one pair of electrons
2. double covalent - share two pairs of electrons
3. triple covalent- share three pairs of electrons
*Electronegativity- the amount of pull on electrons by certain atoms.
Periodicity- periodic trends on the period table (fluorine vs. francium & nobles gases)
4. nonpolar covalent- covalent bond where electronegativities are the same
5. polar covalent- covalent bond where electronegativities are different; one is usually larger.
Creates a dipole moment in the molecule.
i. molecular structure of water
6. hydrogen bond- an attraction between a hydrogen atom which is polar covalently bonded to an atom and another polar covalently bonded atom -gives structure to many biologically compounds
i. adhesion properties of water- Water attracts to other materials that are polar- like glass
ii. cohesion properties of water- Water attracts to itself creating surface tension and drops
iii. capillary properties of water- water can move up a small glass tube against gravity due to adhesive properties.
Virtual Lab. Properties of Water.
7. Hydrophobic interactions- molecules which associate due to a mutual exclusion of water
4. Chemical Reactions-the breaking and remaking of chemical bonds producing new substances
a. signs of a chemical change- (10 signs)
b. reactant(s) - the substance whose bonds will be broken
c. product(s)- the substance which is produced from the chemical reaction
d. chemical equilibrium- a reaction which reproduces the reactants in the same ratio as products
e. catalyst - a substance which assists a reaction but does not become altered itself
f. balanced chemical equation- shows the formulas for each reactant & product involved in a
chemical reactions with the appropriate numbers to satisfy the Law of Conservation of Matter.
Tutorial: Balancing Equations Game.
Practice: Balancing Equations. Answers
5. Mixtures and Solutions
a. Mixture- a substance in which two or more materials are mixed but not chemically combined
1. homogeneous mixture- uniform composition
2. heterogeneous mixture- non-uniform composition
b. Solution- a type of mixture in which there exists uniform distribution (homogeneous mixture)
1. solvent- the substance in which "dissolves" another substance (greater amount)
2. solute- the substance which is "dissolved" (smaller amount)
3. solubility- the factor which defines the relationship between solute and solvent
i. insoluble- the solvent will not dissolve the solute (usually nonpolar molecules)
ii. soluble- the solvent will dissolve the solute (usually polar molecules)
iii. concentration & concentration gradients
-diffusion of solute particles in water by Brownian motion
-diffusion of solute particles across a membrane
c. Acids- solutions which donate hydrogen ions to the solution - (donate protons to solution)
d. Bases- solutions which donate hydroxide ions to the solution -(accept protons from solution)
*pH Scale- measures the solute concentration of an acid or base (concentration of ions)
resource: Biochemistry
6. macromolecules
a. Carbon & its bonding properties
1. multiple bond types (single, double, & triple)
2. ability to form long chains (polymerize)
3. ability to covalently bond with multiple nonmetals (H, N, O, F, S, Cl, Br, & I)
4. has the ability to form polar & nonpolar bonds (due to 2.5 electronegativity)
b. hydrocarbon- an organic compound composed of hydrogen and carbon
1. skeleton- the chain of carbon atoms
2. functional groups- a group of atoms which branch off the skeleton and changes properties of the molecule
a. hydroxyl - produces alcohols
b. carboxyl - produces carboxylic acids
c. amino - produces amines
d. phosphate - produces phosphates
e. carbonyl - produces aldehydes and ketones
3. Macromolecules-molecules which are composed of hundreds to thousands of atoms
*monomer- the principle component of a macromolecule
*polymer- a chain of monomers
c. Macromolecule Reactions
1. dehydration synthesis (condensation) - chemical reaction which builds polymers through a loss
of water
H-O-A-H H-O-B-H --------> H-O-A-B-H + H-O-H
monomers ------------------------> polymer
2. hydrolysis - chemical reaction which breaks polymers by adding water
H-O-C-D-H + H-O-H --------> H-O-C-H + H-O-D-H
polymer --------------------------------> monomers
d. Carbohydrates (carbon-based molecules with multiple hydroxyl groups)
1. monosaccharides. Simple sugars (general formula: CH2O)
a. pentose sugars: ribose & ribulose
b. hexose sugars: glucose, fructose, galactose
c. can exist in linear and ringed forms
2. dissacharides (glycosidic linkage via dehydration synthesis)
a. maltose- 2 glucose (sugar found in beer)
b. lactose- glucose & galactose (milk)
c. sucrose- glucose & fructose (table sugar)
d. cellobiose- 2 glucose (found in cellulose)
3. polysaccharides
a. starch- food storage in plants. image of starch
b. cellulose- structure molecule in plants
c glycogen- food storage in animals
** all three are large polymers of glucose**
d. chitin- polymers of N-acetylglucosamine- found in exoskeleton of arthropods
4. role of carbohydrates in the body
- energy source, cell-to-cell recognition, structure (cartilage/tendons, fingernails, etc.)
Resource: Comparison of Glucose-Fructose & Cellulose-Starch
e. Lipids. class of molecules that don’t mix with water
1. fatty acids- long hydrocarbons with a carboxyl group at C1.
a. saturated – contains no carbon-carbon double bonds
b. unsaturated – contains 1 or more carbon-carbon double bonds
2. fats & oils. a.k.a. triacylglycerols or triglycerides. image of triacylglycerol
-contain glycerol & 3 fatty acid chains bonded by an ester linkage formed via condensation
-glycerol is a 3 carbon trihydroxyl
-fatty acid chains are skeletal chains of carbons (16-18) with a carboxyl group
-fats are typically saturated, while oils are typically unsaturated
-role: fats store much more energy than sugars because of a more chemical bonds
3. others: & steroids (cholesterol)
a. phospholipids- fats that contain 2 fatty acid chains and a phosphate group
-produce a two layer molecule. image
i. hydrophilic head- portion of the molecule which is attracted to water (phosphate)
ii. hydrophobic tail- portion which repels water (fatty acids chains)
iii. role: function in cell membranes to produce a bilayer
b. steroids- lipids that contain 4 fused rings
-cholesterol- used in production of hormones and cell membrane
f. proteins. image
1.amino acids- monomers of proteins- 20 common amino acids
-each amino acid contains:
a. alpha carbon
b.
carboxyl group
c. amino group These 4 covalent bonds to the Alpha carbon
d. hydrogen
e. side chain (R)
2. polypeptides & peptide bonds- amide linkage between a carboxyl and amine of adjacent amino
acids
3. protein structure.
a. primary: chain of amino acids
b. secondary: common structure (alpha helices & beta sheets)
c. tertiary: random shapes caused from side-chain interactions
d. quaternary: interactions of separate polypeptide structures.
-denaturing proteins via heat and pH causes a change in the structure.
What happens to cooking egg whites (albumin in eggs).?
4. enzymes as biological catalysts- regulation of biochemical reactions.
a. active site- region where activity occurs on an enzyme
b. substrate- the chemical(s) that an enzyme works on
c. inhibitors (drugs, medicines & poisons)- all hinder the catalytic ability of an enzyme.
5. other roles:
a. regulatory- Insulin, transcription Repressors
b. transport- Hemoglobin, Serum Albumin
c. storage- Ovalbumin, Casein, Ferritin
d. contractile & Motile- Actin/Myosin, Tubulin/Dynein
e. structural- a-Keratin, Collagen, Elastin
f. scaffold- (used during cellular response mechanisms)
g. protective & exploitive- Immunoglobulins, Thrombin/Fibrinogen, Ricin, Venoms
h. exotic- Monellin, Glue Proteins
g. nucleic acids. image
1. nucleotide- (sugar, phosphate & nitrogenous base) adenine, cytosine, thymine, guanine
2. DNA- deoxyribonucleic acid.
a. complement base pairing- Chargaff’s rule
b. structure: double-helix; James Watson & Francis Crick.
c. role: information center: stores all genetic information for the body
3. RNA- ribonucleic acid
a. structure: single strands
b. 3 common types exist: mRNA, tRNA, rRNA
c. role(s): carrier of information, assist in protein synthesis
Resource: Ken Todar's Microbial World
