Overview Chapters 2. Atoms & Molecules Element - pure substance made up of only one kind of atom Compound - pure substance made up of only one kind of.

Overview Chapters 2

• Atoms & Molecules• Element - pure substance made up of

only one kind of atom• Compound - pure substance made up of

only one kind of molecule, but two or more different kinds of atoms

• Mixture - not a pure substance

Elementary Chemistry

• Atomic number – number of protons• Atomic mass - # protons + # neutrons• Isotopes – extra neutrons

NEUTRONS DON’T AFFECT CHEMISTRY !

Elementary Chemistry

Particle location charge massProton nucleus positive 1 amuNeutron nucleus neutral 1 amuElectron orbitals negative approx.

0

Sub-Atomic Particles

• Affinity for electrons• Will determine type(s) of bonds• Will determine bond distances

Electronegativity

• Atoms can be grouped into molecules because of the way they attract and join other atoms. There are three kinds of bonds between atoms:–Covalent bonds–Ionic bonds–Hydrogen bonds

Chemical Bonds

• Covalent bonds are formed when two atoms share a pair of electrons between them. Each is attracted to the pair of electrons, and therefore to each other.

Chemical Bonds

• Two smallest atoms• Hydrogen has one

proton and one electron• Helium has two protons,

two neutrons, and two electrons.• Helium’s orbital is full; it

is not reactive...

Hydrogen and Helium

HYDROGEN

HELIUM

• Lithium, Beryllium, Boron…the next three elements...• Carbon has 6 protons, 6

neutrons, 6 electrons. Its outer orbital has 4 electrons;it needs 4 more to make 8...

Next Elements

CARBON

• Nitrogen has 5 outer electrons; needs 3 more• Oxygen has 6 outer electrons;

needs 2 more• Fluorine has 7 outer electrons;

needs only 1 more (not shown here)• Neon is full; it’s non-reactive.

Next Elements

NITROGEN

OXYGEN

NEON

• The hydrogen atoms on the left each need an electron to complete the outer orbital. If they overlap their orbitals, they can share one electron each and form the hydrogen molecule on the right.

Sharing ElectronsHYDROGEN

ATOMHYDROGEN

ATOMHYDROGENMOLECULE

The stick in our model represents the bond, a shared pair of electrons:

• The sodium atom on the left needs 7 electrons to complete its outer orbital. There’s just no way. The chlorine on the right needs only 1. Chlorine is so strongly attracted to the electron, and sodium is so weakly attracted, that the electron is transferred from one to the other, resulting in charged atoms, which attract each other. (Opposite charges attract.)

Ionic Bonds

CHLORINESODIUM

• that the electron is transferred from one to the other, resulting in charged atoms, which attract each other. (Opposite charges attract.)

Ionic Bonds

CHLORINESODIUM

CHLORI DESODIUM

• Hydrogen bonding is a result of slightly positive and slightly negative charges on parts of a molecule attracting each other.

• Water’s cohesive properties come from the fact that it is a polar molecule ...

Hydrogen Bonds

(-)

(+)

(-)

(+)

Hydrogen Bonding(-)

(+)

• Synthesis - small molecules into larger ones (Energy: anabolic - energy in)

• Decomposition- large molecules to small ones (Energy: catabolic - energy out)

• (Rearrangement…) combined reaction of both of the above. (reaction coupling)

Chemical reactions

• Dehydration - removal of water (usually in a synthesis reaction) e.g. dehydration synthesis

• Hydrolysis - using water to break down large molecules (usually in a decomposition reaction)

Chemical reactions

• Inorganic molecules - those that do not contain Carbon

• Organic - Carbon-containing molecules

• (Some chemists do not consider Carbon dioxide to be organic. They say there must be at least one Carbon-Hydrogen bond in the molecule…)

Inorganic/Organic

• Chemical properties of water– Polar molecule– Will dissolve polar molecules (hydrophilic)– Ionizable - dissociates in itself!

• Physical properties of water– Clear, liquid (0° C - 100°C)– Solid form less dense (ice floats)– High capacity for heat

Properties of Water

• Surface tension - a measure of how difficult it is to stretch or break the surface of a liquid.

• Cohesion – attraction between molecules of the same kind.

• Adhesion – attraction between different kinds of molecules.

Hydrogen Bonding

• Energy required for phase changes.

• Heat of vaporization (evaporate/condense).

• Heat of fusion (freeze/melt)

Physical Properties

Hydrogen Bonding(-)

(+)

• Hydrophilic – water seeking• Hydrophobic – water “fearing”

Membranes

• Water molecules will arrange themselves about ions in solution. This will buffer the charges in solution.

Spheres of Hydration

• Below is a phospholipid. It is made of two fatty acid chains (green), which are neutral, and a phosphate head (purple), which is negative.

Membrane Composition

-neutral

neutral

• Here’s how the phospholipids will arrange themselves with respect to water:

MICELLECELL MEMBRANE

• Solution–Aqueous solution– Solvent = what is doing the dissolving– Solute = what is being dissolved

Solutions

• Ionization of salt…

NaCl Na+ + Cl -

Ionization

• Ionization of water in solution…

Ionization of Water

H2O H+ + OH-

-1 +1

• A proton comes off the molecule… H+

• Measure of the hydrogen ion concentration:

[H+]

pH

H2O H+ + OH-

1x10-7 1x10-7

pH = - (exponent of [H+])pH = -(-7) = 7

• Thousands of protein “words” • Functions–Cell structures–Chemical messengers–receptors on cell membranes–Immunity–ENZYMES

• Thousands of protein “words” • Functions–Cell structures–Chemical messengers–receptors on cell membranes–Immunity–ENZYMES

Proteins

• smallest unit of proteins (monomer)• Contains:• smallest unit of proteins (monomer)• Contains:

Amino Acids

Aminogroup

Acidgroup

“R” group N CH

C

H

O

OH

H

• To form larger molecules the acid end of one amino acid and the amino end of another dehydrate to form a larger molecule...

• To form larger molecules the acid end of one amino acid and the amino end of another dehydrate to form a larger molecule...

Dehydration Synthesis

• That is called a dipeptide. The bond between the two original amino acids is a covalent bond called a peptide bond.

• That is called a dipeptide. The bond between the two original amino acids is a covalent bond called a peptide bond.

Dipeptide

• A string of amino acids is called a polypeptide. The backbone (NCCNCCNCCNCC) is made of covalent bonds. This backbone is called the primary structure of a protein.

• A string of amino acids is called a polypeptide. The backbone (NCCNCCNCCNCC) is made of covalent bonds. This backbone is called the primary structure of a protein.

Primary Structure

• The polypep-ide is coiled into its secondary structure.• The coil is held in shape

by hydrogen bonds...

• The polypep-ide is coiled into its secondary structure.• The coil is held in shape

by hydrogen bonds...

Secondary StructureAlpha Helix

• There is another way to organize primary protein chains. These are parallel primary chains linked by hydrogen bond.

• There is another way to organize primary protein chains. These are parallel primary chains linked by hydrogen bond.

Another SecondaryBeta Pleated Sheet

2ndary Structure Combinations within Tertiary Structure

Alphahelixes

Beta pleated sheet

Sulfurbridge

• Next the secondary structure is wrapped on itself in the tertiary (globular) form. This is held together by–Hydrogen bonds–Sulfur bridges–Weak electrostatic bonds

• Next the secondary structure is wrapped on itself in the tertiary (globular) form. This is held together by–Hydrogen bonds–Sulfur bridges–Weak electrostatic bonds

Tertiary Structure

• Finally, some tertiary proteins are joined with others to form quaternary proteins.

• Finally, some tertiary proteins are joined with others to form quaternary proteins.

Quaternary Structure

This one is hemo-globin. The red disks are heme.

• Numerous diagrams of tertiary and quaternary proteins

• Several types of chaperonins• “Molecules of the year”• What do you mean biologists are geeks?

Web Sites - Proteins

A.P. Biology Salesianum School PDV / 2004

http://www.rcsb.org/pdb/molecules/molecule_list_2002.html

http://kuchem.kyoto-u.ac.jp/kozo/home/structure.html

Enzymes - Active Site• Enzyme specificity allows for binding of

substrate at active site.• Active site = “groove / pocket” on enzyme.• Enzyme interaction with substrate causes

a conformational change in which the enzyme changes shape slightly - active site fits “snugly” around substrate

• “Induced Fit”

INACTIVE ENZYME

Induced fit

ACTIVE ENZYME

A

B

B

Environment & Enzyme Activity

• Temperature affects 3D shape of enzyme (structure) / bonding• Salt concentration affects chemical

bonds within protein structure• pH affects protein structure -> [H+]

Other Factors Affecting Enzyme Activity

• Cofactors = non-protein “helpers”• Coenzyme = organic molecule

Allosteric Inhibition

ACTIVE ENZYMEINACTIVE ENZYME

A B

Inhibition: Permanent or Temporary?

• Irreversible = covalent bonding• Reversible = weak/hydrogen

bonds• Depends on Concentrations–Substrate vs. Inhibitor molecule

Inhibition and Cell Metabolism

• Use of reversible inhibitors• “Negative feedback”= metabolic

reaction is blocked by its products.• Energy saving device–Ex: ATP