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Basic Chemistry
Matter is anything that takes up space and
has mass.
3 states solid, liquid, and gas
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Percent by Weight
60
Earths crust
organisms
40
20
0
Fe
Ca
Si Al Mg Na
Element
Only 92 naturally occurring elements serve as the building blocks of all matter.
Other elements have been human-made and are not biologically important.
Carbon
Hydrogen
Nitrogen
Oxygen
Phosphorus
Sulfur
Atomic Structure
An atom is the smallest part of an element
that displays the properties of the element.
Atoms are made up of subatomic particles.
Protons - positively charged, found in nucleus
Neutrons - uncharged, found in nucleus
Electrons - negatively charged, move around
nucleus
Helium (He)
= proton
= neutron
= electron
a.
b.
Subatomic Particles
Particle
Atomic Mass
Location
+1
Nucleus
Neutron
Nucleus
Electron
~0
Proton
c.
Electric
Charge
Electron orbital
VIII
He
1.008
II
III
IV
VI
VII
4.003
10
Li
Be
Ne
12.01
14.01
16.00
19.00
20.18
6.941
Periods
9.012 10.81
11
12
13
14
15
16
17
18
Na
Mg
Al
Si
Cl
Ar
22.99
24.31
26.98
28.09
30.97
32.07
35.45
39.95
19
20
31
32
33
34
35
36
Ca
Ga
Ge
As
Se
Br
Kr
39.10
40.08
69.72
72.59
74.92
78.96
79.90
83.60
Groups
Isotopes
Atoms of the same element with a differing
numbers of neutrons
Radioactive isotopes emit various types of
energy as they decay.
12
13
14
*radioactive
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larynx
thyroid gland
trachea
a.
b.
a: Biomed Commun./Custom Medical Stock Photo; b(left): Mazzlota et al./Photo Researchers, Inc; b(right): Hank Morgan/Rainbow
Electrons
In an electrically neutral atom, the positive
charges of the protons in the nucleus are
balanced by the negative charges of electrons
moving about the nucleus.
Energy levels (electron orbitals)
*1st contains 2 electrons
*Every one after that can contain 8 electrons
- Octet rule
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hydrogen
1
H
1
electron
electron orbital
nucleus
carbon
12
C
6
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nitrogen
14
N
7
Oxygen
16
O
8
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Phosphorus
31
P
15
Sulfur
32
S
16
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hydrogen
1
H
1
electron
electron orbital
nucleus
carbon
12
C
6
nitrogen
14
N
7
Phosphorus
31
P
15
Sulfur
32
S
16
Oxygen
16
O
8
Ionic Bonding
Ions form when electrons are
transferred from one atom to
another.
Ionic compounds are held together
by an attraction between oppositely
charged ions called an ionic bond.
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Cl
Na
Electron transfer
creates charge
imbalance
Ionic bond held
together by
attraction of ions
+
Na
Cl
sodiumion (Na+)
chlorideion (Cl+)
Covalent Bonding
A covalent bond results when two atoms
share electrons in such a way that each
atom has an octet of electrons in the outer
orbit.
{An atom may share electrons with one or more
atoms}
Covalent Bonding
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Electron Model
Structural
Formula
Molecular
Formula
H2
a. Hydrogengas
Covalent Bonding
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O2
b. Oxygen gas
Shape of Molecules
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H
H
H
C H
H
c. Methane
CH4
Shape of Molecules
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Space-filling Model
Ball-and-stick Model
H
hydrogen
carbon
covalent bond
H
109
d. Methanecontinued
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Structural
Formula
Electron Model
If the sharing
between two
atoms is fairly
equal, the
covalent
bond is
described as
nonpolar.
Molecular
Formula
H2
C H
CH4
a. Hydrogen gas
H
H
H
H
H
c. Methane
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Structural
Formula
Electron Model
Molecular
Formula
H2
O2
a. Hydrogen gas
b. Oxygen gas
H
C
CH4
c. Methane
Ball-and-stick Model
hydrogen
Space-filling Model
carbon
covalent bond
H
d. Methanecontinued
109
Electron Model
Ball-and-stick Model
Space-filling Model
Oxygen attracts the shared
electrons and is partially negative.
O
O
O
H
104.5
H
+
H
+
Hydrogen Bonding
Polarity
within a
water
molecule
causes the
hydrogen
atoms in one
molecule to
be attracted
to the oxygen
atoms in
other water
molecules.
Weak
individually
but quite
strong
collectively.
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H
O
hydrogen
bond
Chemistry of Water
The first cell(s) evolved in water
All living things are 7090% water
Water is a polar molecule
Water molecules are hydrogen-bonded to one
another
Water is liquid at temperatures typical of the Earths
surface due to hydrogen bonding.
Properties of Water
Water has a high heat capacity.
A calorie is the amount of heat energy needed
to raise the temperature of 1g of water 1C.
The many hydrogen bonds that link water
molecules help water absorb heat without a
great change in temperature.
Because the temperature of water rises and
falls slowly, organisms are better able to
maintain their normal internal temperatures
and are protected from rapid temperature
changes.
Properties of Water
Water has a high heat of vaporization.
Converting 1 g of the hottest water to a gas
requires an input of 540 calories of heat energy.
Gives animals in a hot environment an efficient
way to release excess body heat.
Also helps moderate temperatures along coasts.
Properties of Water
Water is a solvent
Due to its polarity, water facilitates chemical
reactions, both outside and within living systems.
A solution contains dissolved substances, which
are then called solutes.
Hydrophilic molecules attract water.
Hydrophobic molecules do not attract water.
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+ H
O
H
Na+
H
Cl
O
H
H
O H
H
H
Properties of Water
Water molecules are cohesive and adhesive.
Water molecules cling together because of
hydrogen bonding (cohesion).
Waters positive and negative poles allow it to
adhere to polar surfaces (adhesion).
Water is an excellent transport system, both
outside and within living organisms.
Properties of Water
Water has a high surface tension
The stronger the force between molecules in
a liquid, the greater the surface tension.
This allows some insects to walk on the
surface of a pond or lake.
Properties of Water
Frozen water (ice) is less dense than liquid
water.
As liquid water cools, the molecules come closer
together.
Water expands as it freezes.
Ice floats.
Bodies of water freeze from the top down.
ice lattice
liquid water
water
hydrogen
ion
hydroxide
ion
HCl
H+ + Cl-
NaOH
Na+ + OH-
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oven
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sodium
hydroxide
(NaOH)
Buffers and pH
A buffer is a chemical or combination of
chemicals that keep pH within normal
limits.
Bicarbonate ions (HCO3-) and carbonic
acid (H2CO3) found in human blood buffers
the pH to 7.4
Buffers and pH
If hydrogen ions (H+) are added to the blood, this reaction occurs:
H+ + HCO3-
H2CO3
If hydroxide ions (OH-) are added to the blood, this reaction occurs:
Organic Molecules
Always contain:
Carbon (C) and Hydrogen (H)
A carbon atom may share electrons with
another carbon atom or other atoms.
H
Organic Molecules
Macromolecules contain many molecules joined
together
Monomers: Simple organic molecules that
individually
Dimers, Trimers, Oligomers:.
Polymers: Large organic molecules form by
combining monomers
exist
Organic Molecules
Polymer
Monomer
monosaccharide
amino acid
nucleotide
Organic Molecules
Cells have common mechanisms
Dehydration Reaction: an -OH and -H are
removed as a water molecule
Hydrolysis Reaction: the components of
water are added
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monomer
OH
dehydration
reaction
monomer
H2O
monomer
monomer
monomer
monomer
a.
H2O
hydrolysis
reaction
monomer
b.
OH
monomer
Carbohydrates
Simple Carbohydrates
Monosaccharides are sugars with 3 - 7
carbon atoms
Pentose refers to a 5-carbon sugar
Hexose refers to a 6-carbon sugar
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6 CH2OH
O
5C
CH2OH
H
C
4
H
OH
HO
C OH
C1
OH
H
OH
HO
OH
C6H12O6
OH
Carbohydrates
Disaccharides contain two monosaccharides.
Examples maltose, sucrose, lactose
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CH2OH
CH2OH
O H
+
OH
hydrolysis reaction
HO
dehydration reaction
CH2OH
O
O
glucose C6H12O6
monosaccharide
CH2OH
glucose C6H12O6
monosaccharide
maltose C12H22O11
disaccharide
H2O
water
water
Carbohydrates
Polysaccharides are long polymers that contain
many glucose subunits.
Starch is the storage form of glucose in plants.
Glycogen is the storage form of glucose in animals.
Cellulose can be found in the cell walls of plants.
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CH2OH
CH2OH
CH2OH
CH2OH
O
O
O
O H
H
H H
H H
H H
H
H
H
H
OH
H
OH
H
OH
H
OH
H
O
O
O
O
O
H
OH
OH
OH
OH
branched
nonbranched
starch
granule
cell wall
potato cells
Jeremy Burgess/SPL/Photo Researchers, Inc.
CH2OH
CH2OH
O
H
O
H
OH
OH
H
O
CH2OH
O
H
OH
OH
H
O
CH2OH
O
H
OH
OH
H
O
H
OH
OH
H
O
glycogen
granule
liver cells
Don W. Fawcett/Photo Researchers, Inc.
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plant
cell wall
cellulose
fiber
cellulose fibers
microfibrils
CH2OH
H
H
OH
CH2OH
H
H
OH
H
CH2OH
H
H
OH
CH2OH
OH
H
H
O
O
H
H
OH
O
H
H
O
O
OH
OH
H
CH2OH
OH
O
CH2OH
OH
H
CH2OH
OH
OH
CH2OH
H
H
OH
H
OH
CH2OH
OH
OH
O
H
H
OH
OH
H
H
OH
CH2OH
OH
H
H
OH
H
H
CH2OH
OH
H
H
H
OH
O
O
OH
OH
H
glucose
molecules
O
O
CH2OH
Lipids
Lipids are diverse in structure and function.
One common characteristic they do not
dissolve in water (hydrophobic)
Types
Fats and oils
Phospholipds
Steroids
Lipids
Fats
Usually of animal origin
Solid at room temperature
Oils
Usually of plant origin
Liquid at room temperature
Triglycerides
One glycerol and 3 fatty acid molecules
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H C OH
H C OH
HO
O
HO
O
H C OH
H
glycerol
HO
3 fatty acids
dehydration reaction
H
hydrolysis reaction
H C
H
H
fat molecule
3 H2O
3 water
molecules
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polar end
+
nonpolar end
emulsifier
fat
emulsification
Emulsification
Fat droplets disperses in water.
Emulsifiers contain molecules with a polar
and nonpolar end.
Polar Head
inside cell
CH2
Primary components of
cellular membranes
They spontaneously
form a bilayer in which
the hydrophilic heads
face outward toward
watery solutions and the
tails form the
hydrophobic interior.
CH2
CH2
CH2
CH2
outside cell
a. Plasma membrane of a cell
C
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH
CH
CH
CH
CH2
CH2
CH2
Fatty acids
CH2
CH O
glycerol
CH2 O
Comprised of 2 fatty
acids + a phosphate
group
Phospholipids
phosphate
R O P O 3CH2
Lipids
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CH2
CH2
CH2
CH2
CH2
CH2
CH2
Nonpolar Tails
CH2
CH2
CH2
CH3
b. Phospholipid structure
CH2
CH2
CH2
CH2
CH3
Lipids
Steroids
All have a backbone of four fused carbon
rings.
Examples: Cholesterol, Testosterone, Estrogen
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OH
OH
CH3
CH3
CH3
HO
a. Testosterone
b. Estrogen
Proteins
Proteins are polymers composed of amino
acid monomers.
Amino acids
Amino group (-NH2)
Acidic group (-COOH)
R group varies
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amino group
acidic group
C
R
O
C
OH
amino acid
OH
C
H
amino acid
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H
H3N+
H3N+
O
C
CH3
C
O
CH
CH3
H3C
H
H3N+
O
C
O
CH2
SH
H
H3N+
C
CH2
O
C
O
Proteins
Peptides
amino group
C
R
peptide bond
acidic group
O
C
OH
amino acid
OH
C
H
amino acid
dehydration reaction
hydrolysis reaction
R
N
dipeptide
OH
C
H2O
O
water
Proteins
Levels of Protein Organization
The structure of a protein has at least 3 levels of
organization.
Some can have four.
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H3N+
amino acid
COO
peptide bond
C
CH
C N
R
CH
CH
C N
R
hydrogen bond
C
CH
C N
hydrogen bond
CH
C
C
CH
C N
R
CH
CH
N R
(alpha) helix
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(alpha) helix
disulfide bond
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H3N+
amino acid
COO
peptide bond
C
C
C
CH
CH
N
CH
CH
N
C
C
CH
CH
N
hydrogen bond
R
hydrogen bond
C
C
CH
CH
N
(alpha) helix
disulfide bond
Nucleic Acids
DNA (deoxyribonucleic acid)
DNA stores genetic information in the cell and in the
organism.
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O
O
phosphate
C
O
5'
4'
1'
2'
3'
pentose sugar
Nucleotide structure
nitrogencontaining
base
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G
C
A
T
G
T
T
C
one nucleotide
S
P
S
P
A
P
a.
c.
b.
a: Radius Images/Alamy RF
Nucleic Acids
RNA is single stranded
Several types involved in carrying information
in DNA to make proteins
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H2O
P
+ energy