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Week 1 Lecture 3, Basics of Chemistry:

Chemistry Review
-Atoms
-Subatomic particles
-Elements
-Valence
-Energy (photosynthesis, fluorescence, heat)
-Ions-atoms or molecules
-Cation-positively charged (missing electrons)
-Anion-negatively charged (extra electron)
-Compounds
-Molecules
-Bonding
-Covalent
-Hydrogen
-Ionic
-Van der Waals
-Biologically important molecular properties
-Chemical reactions
Elements
-A substance that cannot be broken down into smaller parts by
chemical reactions.
-Most abundant elements in biology:
-Hydrogen (H)
-Carbon (C)
-Nitrogen (N)
-Oxygen (O)
-These elements make up more than 93% of a humans body weight.
-Several other elements are crucial for life.
Atoms
-Smallest unit of an element that still retains the properties of that
element.
-Subatomic particles: protons (positive), neutrons (neutral), electrons
(negative)
Electron Shells
-Each electron shell corresponds to a certain energy.
-Shell further from the nucleus have a higher energy.
-Each shell contains electron orbitals.
-Two electrons for each orbital.
Valence Shell
-Outermost electron shell.

-Electrons in this shell are valence shells.


-Atoms prefer to have a full valence shell.
-Will determine an elements atomic properties.
-Will determine bonding between atoms.

Ions
-Change the number of electrons.
-Cations-atom or molecule with a postive charge (fewer electrons than
protons).
-Anions-atom or molecule with a negative charge (more electrons than
protons).
-Crucial for biological processes.
-Examples:
-Electrical impulses in the brain (action potentials) require Na+,
K+, and
Ca2+
-Regulation of blood pressure (people with high blood pressure
eat a low sodium diet)
Ionic Bonds: Attraction between ions (which were formed by gaining or
losing electrons entirely)
Covalent Bonds: Atoms share electrons to fill their valence shells.
-Hydrogen likes to form one bond.
-Oxygen likes to form two bonds.
-Nitrogen likes to form three bonds.
-Carbon likes to form four bonds.
Molecule: Two or more atoms held together covalently.

Hydrogen Bonding:
-Weaker than covalent bond, but crucial to biology.
-Holds DNA together in double helix.
-Helps keep proteins properly folded.
-Works due to electronegativity.
Van der Waals Interactions:
-Weakest bond individually but their culumative effect is very strong.
-Helps keep proteins properly folded.
-Butter and vegetable oil (shapes of fat determine which one it is).
Structure Determines Function
-Shape-interacting molecules fit together.
-Charge and Polarity-opposites attract.
-Molecular properties determine how molecules will interact which
determnes the function of the molecule.
Chemical Reactions
-Cannot create or destroy matter.
-Change matter through reactions.
Reversible Chemical Reactions
-Reaction can go in either direction.
-Reaches dynamic equilibrium.
-not equal concentration but concentrations not changing
-reaction does not stop, but forward and reverse ractions occur
at the same
rate
-Example: 3 H 2+ N 2< 2 N H 3
Week 1 Lecture 4, Water:
Water makes biology work!
-Cells are 70-95% water
-Earths surface is 75% water
-Water is more necessary than food for water
-Required or generated in many chemical reactions.
-Required for proper protein folding and for lipid bilayer (membrane)
formation.
-Required for transport of molecules across a membrane.
-Surrounds every moleucle in the cell!
Properties of Water
-3 states
-density of solid
-polarity

-moderates temperature
-specific heat
-evaporative cooling
-insulation by ice
-solvent
-pH
Water as the 3 states of matter:
-3 states of matter are solid, liquid, gas
- H 2 O is ice, water, and steam
-only common substance that exists in all 3 states in nature
-unlike most substances, water is less dense as a solid than as a liquid
Water is Polar
-Oxygen is more electronegative than hydrogen.
-Shared electrons spend more time with oxygen.
-Oxygen has partial negative charge.
Hydrogen has partial positive charge.
-Polar molecule.
Hydrogen Bonds
-Waters polarity allows it to form hydrogen bonds between water
molecules and with other polar molecules.
-Hydrogen bonds make water
cohesive (binds other water molecules) and
adhesive (binds molecules other than water)
Surface Tension
-Surface tension is a measure of how difficult it is to break the surface
of a liquid.
-Water has a high surface tension due to its cohesiveness.
Temperature of Water
-Heat is the total kinetic energy of molecules in a body of matter.
-Temperature is the average kinetic energy of molecule in a body of
matter.
Specific Heat-the amount of heat that must be absorbed or lost for 1 g
of that substance to change its temperature by 1 degree Celcius.
-Water has a high specific heat.
-Resists changes in temperature.
-Large change sin heat result in small changes in temperature.
-Stabilizes ocean and coastal temperatures.
Evaporation: kinetic energy increases hydrogen bonds more likely to
break liquid water becomes gaseous.

Evaporative Cooling: Molecules with high kinetic energy leave liquid


average kinetic energy (temperature) decrease
-Organisms use evaporative cooling to regulate their temperature.
-Sweating
-Evaporation from leaves
Ice as Insulation
-Ice floats because frozen water is less dense than liquid water.
-Prevents liquid below from freezing.
-Organisms can continue living on the liquid.
The Solvent of Life
-Solution-homogeneous mixture of two or more substances.
-Solvent-substance that does dissolving.
-Solute-substance that is dissolved.
syrup=water+sugar
solution=solvent+solute
-Hydrophilic-loves interacting with water.
-Hydrophobic-hates interacting with water.
-Determines how biological molecules are organized (lipids and
protein).
Disociation of Molecules
Water

hydroxide ion

-results in more


++C
l
HCL

H
+

H than O H when added to water.

-results in more

NaOH

O H than

Acid

Base

pH


++O H
H 2 O< H
hydrogen ion

N a
+O H
+
H when addd to water.

+
-pH is proportionate to the concentration of H in solution.
+

-In an aqueous solution, [ H ] x [ O H ] = 1014


+

-At neurtal pH, [ H ] = 1017 and [ O H ] = 107

+
-pH = -log [ H ]
-At neutral pH, pH = -log 107 = 7
+
+
-Acid=More H , [ H ] > 107 , lower pH
+
+
-Basic=Less H , [ H ] < 107 , higher pH
Buffers
-Resist changes to pH

+ + HC O3
H 2 C O3 < H
carbonic acid
hydrogen ion
bicarbonate
-Bicarbonate is a buffer in human blood.
+
+<
N H 4
-Weak base
N H3+ H
ammonia
hydrogen ion
ammonium ion
-Level of ammonium in water is crucial for acquatic life.
-Weak acid