Download CHEMISTRY AND ORGANIC MOLECULES Matter: Has mass and

CHEMISTRY AND ORGANIC MOLECULES
Matter: Has mass and takes up space; stuff
Three states of matter: solid, liquid, gas
All Matter composed of Elements
Element: cannot be broken down into simpler forms with different properties
Density, solubility, melting point, reactivity
Six Elements basic to life: Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, Sulfur
CHNOPS
However, other elements are essential (necessary) for life
Atomic Theory (John Dalton, early 1800s):
Atom (Greek, indivisible): smallest part of an element that displays properties of that element
Unit of matter
Atomic Symbol
Atomic Particles: more than 100 different kinds, but three stable kinds
Protons, Neutrons in nucleus
Electrons spin around nucleus
Electrons negatively charged, protons positively charged
Protons and neutrons have same mass (about 2000X that of electron)
So electrons really don’t figure into atomic mass
Proton, electron equal, but opposite, charges
Protons, neutrons equal masses
Atomic Number: at lower left of atomic symbol = number of protons
Atomic Weight: protons plus neutrons
Isotopes: any atom of a given element has the same number of protons, atomic number, but
isotopes of that element are forms with numbers of neutrons different than the number of
protons. Therefore, isotopes don’t have the same mass as the elemental atom with equal
numbers of protons and neutrons.
C12 is most common form of Carbon, but C13 and C14 also exist
C13 is stable, but C14 is radioactive, or unstable, meaning it decays into something else
Both stable and radioactive isotopes can be very useful in biological experiments, as tracers
Atoms are mostly empty space. If the nucleus is golf ball sized, the electrons would be ~1km
away
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Valence shell electrons: those on the outermost orbital, important in chemical bonding
Chemical Bonds: Covalent, Ionic, Hydrogen
Covalent: outer shell (valence) electrons are shared, but not necessarily equally
O is ~8X bigger than H, so even though there are 2 H’s, O gets more of the
valence shell e- of the shared e-‘s, resulting in Polarity
Ionic: transfer of electrons resulting in two, oppositely charged, ions: opposites attract
Ion: charged atom
Hydrogen: the H portion of an electronegative molecule is shared with another
electronegative molecule (e.g. H20 and NH3). A very weak bond.
H bonds very biologically important within and between molecules
H bonds hold the two strands of DNA together, but are easily separated
Molecular Shapes: think of these things in three dimensions
C has 4 valence e-, forms a tetrahedron, not linear
Acids and Bases:
Acids: donate H+ (proton)
Tomato, lemon, vinegar, coffee = acidic
Bases: donate OH- (hydroxide)
Chalk, baking soda, lye = caustic, basic, alkaline
Measured by pH (parts of Hydrogen)
Ranges 0 – 14 with 7 as neutral and extending on log scale in both directions
Low pH is acid, 7 is neutral, high pH is basic
Acids and bases have “strengths” as they dissociate more
High alkalinity is as potentially harmful as high acidity
Buffers: resist changes in pH by taking up both excess H+ and OHRemember homeostasis
In Human blood Carbonic Acid, H2CO3
Dissociates as H+ and HCO3- (bicarbonate)
Add H+ + HCO3 -> H2CO3
Add OH- + H2CO3 -> HCO3- + H2O
Water
There’s a lot of it. 70 – 90% of organisms are water (similar to earth’s surface)
Cal = E to raise 1g liquid H20 1C
Solid to liquid and liquid to gas takes even more E
E required for liquid to gas is what makes sweat effective at cooling
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This is a relatively large amount of required E and is due to the huge number of H
bonds
10X that of iron, almost 2X that of alcohol
A lot of E is absorbed breaking H bonds before molecules move faster (heat)
A lot of E is lost as H bonds form (consuming E) before motion slows
Nutritional c are kcal.
This is Specific Heat; water takes a lot of E to warm up and then cools very slowly
Remember homeostasis, this property of water helps in that
Maritime moderate climates
Cohesion: water sticks to itself, H bonds
As water evaporates from a tree, it is replaced by water moving up from roots
Adhesion: water sticks to other stuff,
Put a drop of water, and a drop of soapy water on the table.
Surface Tension: leaves, water striders, float on water
Ice floats; think about what that means, ponds, lakes, polar ice caps
The crystalline lattice of ice takes up 10% more space than liquid water
Insulation, turnover
Densest at 4C, ocean currents, e.g.
Solvent: stuff dissolves in it to form a an aqueous Solution (Solvent dissolves the Solute)
Polar or ionic substances dissolve in water: Hydrophilic
Non-ionic and non-polar substances do not: Hydrophobic
Q: why don’t cell membranes dissolve?
Organic Molecules
Organic chemistry involves carbon based molecules
Hydrocarbons = only C and H
Inorganic chemistry is pretty much everything else (e.g. batteries)
Carbon chains, saturated, unsaturated, rings
Functional groups: bonded atoms attached to carbon or carbon chains rather than
H (OH- hydroxyl, CO carbonyl, COOH carboxyl, -NH2 amino, -SH sulfhydryl, -PO4 phosphate
C (four valence shell e-) can attach four ways resulting in a tetrad, any part of which can
be H or functional group
This can change the molecule to Hydrophilic or Hydrophobic
Cells (and organisms) are largely water, so hydrophilia is important
(again, why don’t membranes dissolve?)
Organic Macromolecules (big)
Carbohydrates, Lipids, Proteins, Nucleic Acids
Carbohydrates (CHO)
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C, H, O that’s it
Includes sugars (monosaccharides (now, glucose), di- (sucrose, lactose), poly (storage;
starch, structural CO (glycogen; cellulose, chitin indigestible)
Cellulose: animals cannot digest. Symbiotes can (ruminants, termites)
Glycogen is stored energy and released as glucose by liver as commanded by
release of insulin (hormone (homeostasis) from pancreas.
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