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LECTURE 2
CHEMISTRY
Ch. 2
MATTER
Anything that occupies space and has
mass
-- mass is a measure of how much
matter there is
-- units are usually in kilograms (kg)
--there are 92 different kinds of
natural matter, called elements
120 ELEMENTS ON MODERN PERIODIC
CHARTS BUT EVERYTHING AFTER THEM
HAS BEEN MADE BY HUMANS
ATOM
Atom – the smallest division
of an element that has all the
chemical and physical
properties of that element.
Has a nucleus containing
protons and neutrons.
ELECTRONS IN A CLOUD
(shells) around the nucleus.
PROTONS + CHARGE
ELECTRONS – CHARGE
NEUTRONS - NEUTRAL
Isotopes
The mass of Hydrogen is 1.0.
The mass stated is 1.0078
because it represents the
average of all the isotopes.
Isotope – an atom that has a
different number of neutrons
from protons
Covalent bonds are formed when electrons are shared.
Methane and Ammonia represented three different ways:
Polar Covalent Bonds: form when there is unequal sharing of
electrons between two atoms in a covalent bond.
Oxygen is electronegative,
which means that it attracts
electrons.
When oxygen bonds with
hydrogen, it pulls negative
charge towards it, leaving
the positively charged
hydrogen.
IONIC BONDS
These are formed when
one atom donates an
electron to another atom.
Sodium has one electron in
its outer shell, so it donates
the electron to Chlorine,
forming Sodium-Chloride,
NaCl.
Ionic compound
How NaCl dissolves in water:
Ionic compounds easily dissociate (separate) when they are
dissolved in water. In water, NaCl becomes Na+ and Cl-
Fig. 2.6 in text
Opposite charges attract
Molecules that can
form hydration spheres
are polar and
hydrophilic.
HYDROGEN BONDS
Caused by an attraction between
the hydrogen on one water
molecule and an oxygen on
another water molecule.
They form between
electronegative elements
(F, N, O) and hydrogen
Hydrogen bonds hold DNA strands together.
Student Activity
Are these molecules polar or not?
1. Water H2O
2. Methane CH4
3.
4.
5.
6.
Amino acid
Oils
glucose
steroids
#3
If you’re not sure,
check here
Acids, Bases, and the pH Scale
Pure water ionizes to form equal amounts
of OH- and H+. This solution is neutral.
OH- and H+ are in a concentration of 10-7M
or .0000001 moles/liter.
Acid – a solution with a higher [H+]
Base – a solution with a lower [H+]. A base removes H+ from
solution. For example, NaOH is a base.
NaOH + H+  Na+ + H2O
pH = The Power of
Hydrogen
The concentration of H+ in a
solution is indicated in pH units on a
pH scale.
Click
here for
pH = - log [H+]
a video
- log[H+] = -log[10-7] = 7.0
Due to the logarithmic
aspect of the pH scale, each
pH value is ten-fold different
than the next.
ACIDS
STRONG
ACID
WEAK
ACID
BUFFERS
Click here for a video
A buffer is a chemical that minimizes changes in pH.
It reduces the excess acidity or alkalinity.
E.g. HCl + NaHCO3 
strong acid
pH 1.0
Na- bicarbonate
[baking soda]
buffer
NaCl + H2CO3
Or here
CO2 + H2O
carbonic*
acid
(a weak acid, pH 3-4)
*carbonated drinks contain carbonic acid, which then dissociates into
fizz (carbon dioxide)
Bicarbonate Buffer in the Blood
In blood plasma, the pH is stabilized by this reversible reaction:
Bicarbonate ion (HCO3-) + H+
Carbonic acid (H2CO3)
In other words, a strong acid, H+, is made into a weak acid,
H2CO3.
In this reaction, a proton H+ is taken out of solution.
Blood pH is maintained by the bicarbonate ion/carbonic acid buffer pair
If blood pH goes down, e.g. due to lactic acid releasing H+:
Bicarbonate ion (HCO3-) + H+
Carbonic acid (H2CO3)
If blood pH goes up, e.g. excessive vomiting and loss of gastric HCl,
then:
Carbonic acid (H2CO3)
Bicarbonate ion (HCO3-) + H+
Blood pH is maintained between pH 7.35 – 7.45
Acidosis/alkalosis are prevented.
ORGANIC MOLECULES
Molecules that contain carbon and
hydrogen (hydrocarbons)
Carbon bonds to four things and
therefore it forms chains and rings
through either single or double
bonds
Classes of organic compounds can
be named according to their
functional groups.
Functional Groups
Fig. 2.10 Various functional
groups of organic molecules:
Fig. 2.11 Categories of Organic
molecules based on functional groups.
Stereoisomers are molecules that have the same atoms in the same
sequence, but differ from each other in the way their atoms are
arranged three-dimensionally in space.
Examples:
1) Cis (two functional groups located
on the same side of the molecule),
and trans (two functional groups located
on opposite sides of the molecule). See
cis-2-butene and trans-2-butene.
2)Enantiomers (optical isomers) that are
mirror images of each other. They are like
left- and right-handed gloves: if the palms
are facing the same direction, they cannot be superimposed on each
other. See D- and L-glyceraldehyde
Four Main Classes of Macromolecules
POLYMERS
Carbohydrates (complex)
MONOMERS
simple sugars, monosaccharides
Proteins
amino acids
Lipids
fatty acids + glycerol
Nucleic acids
nucleotides
Carbohydrates
Simple structure - CH2O
Most simple carbohydrates in our bodies are
hexoses. Hex = 6, and –ose means sugar
C6H12O6 Most common ones are glucose,
fructose, galactose.
Pentoses have 5 carbons.
Forming a bond while losing water
Dehydration Synthesis
Hydrolysis
Hydrolysis is the breakdown of polymers by the addition of water.
HYDRO - LYSIS
Polysaccharides are Polymers
GLYCOGEN
Monomers are glucose, specifically.
Glycogen is sometimes called “animal starch”
Glycogen is more branched than starch
FOR COMPARISON…
GLYCOGEN is animal
starch, α-1,4 glycosidic bonds;
HIGHLY BRANCHED
STARCH IS FROM PLANTS, α-1,4GLYCOSIDIC BONDS
CELLULOSE IS FROM PLANTS, β-1,4GLYCOSIDIC BONDS. NO HUMAN
ENZYMES WILL DIGEST IT.
CHITIN HAS LINKAGES SIMILAR
TO CELLULOSE.
(POLY-N-ACETYLGLUCOSAMINE)
Student Activity:
WHICH IS A POLYSACCHARIDE AND WHICH IS A
MONOSACCHARIDE?
WHAT IS THE RATIO OF C:H:O IN A CARBOHYDRATE?
Lipids:
SOURCES OF Ω3’S
Liquids are called oils. Solids are called fat,
lard, butter
Lipids are ALL insoluble in polar solvents. They’re nonpolar.
Fatty acids:

Omega-3
Cis and trans fatty acids
Oleic acid –
hydrogen atoms
on the same side
(cis-configuration)
Elaidic Acid –
hydrogen atoms
on opposite sides
(trans-configuration)
Triglycerides are formed by Dehydration Synthesis:
Draw a triglyceride
simplified:
Triglycerides are the most common
lipid.
KETONE BODIES
Ketone Bodies
Four-carbon molecules that are
breakdown products of fatty acids.
PHOSPHOLIPIDS
They make up cell
membranes
The phosphates are
polar, (hydrophilic –
water-loving)
but the fatty acids are
nonpolar (hydrophobic –
water-fearing)
“like dissolves in like”
“amphipathic”
Fig. 2.22
WHAT HAPPENS IF YOU PUT PHOSPHOLIPIDS INTO WATER?
Micelles form when
you drop phospholipids
into water
Simplified drawing
of a phospholipid:
Steroids
are
Lipids
STEROIDS
We can convert
cholesterol into
steroid hormones
These are nonpolar
MINIQUIZ: do this and then check it with your neighbor
DRAW THE BASIC STRUCTURES (cartoons) OF
STEROIDS
PHOSPHOLIPIDS
TRIGLYCERIDES
Prostaglandins
They are regulatory molecules.
e.g. they regulate blood vessel
diameter, ovulation, uterine
contractions during labor,
inflammation, blood clotting
AMINO ACIDS
MAKE
UP PROTEINS
THERE ARE
20 AMINO
ACIDS
8 ARE ESSENTIAL
12 ARE NONESSENTIAL
Peptide Bonds are formed by dehydration synthesis
The amino acid sequence of a protein is its primary structure.
Primary structure is
determined by the sequence
of a.a. chains
Secondary structure is due to
weak hydrogen bonds. α-helix
and β-sheets
Tertiary structure – due to the
interaction of R-groups on amino
acids (most important for
function; affected by
denaturation).
The bonds responsible for the tertiary structure of a protein
Tertiary structure
can be destroyed
by pH or
temperature
extremes
(denaturation)
Deoxyribonucleic
Acid (DNA)
FORMS A DOUBLE HELIX DUE
TO BASE PAIRING (RULES) WHICH
ARE DUE TO H BONDS
DNA Structure – double helix
RNA:
Uses A, G, C, U
Uses ribose sugar
Is shorter than DNA
Is single-stranded
RNA vs. DNA
DNA:
uses A, G, C, T
Uses deoxyribose sugar
Is longer than RNA
Is double-stranded
Types of RNA
a.Four types of RNA are used to take information for
assembling a protein out of the nucleus and to actually
assemble it:
1)Pre-MRNA, 2)Messenger RNA (mRNA)
2)Transfer RNA (tRNA)
3)Ribosomal RNA (rRNA)
b.Other RNA-related molecules serve important
functions in the body
1)ATP, GTP – energy carriers
2)cAMP - regulation
3)NAD, FAD – co-enzymes
end