Bio 11 Lecture- Chemistry II
Chemical reactions, Ions, pH,
functional groups, organic molecules
Lecture outline
• Chemical Bonds review
5. Ions
6. pH
7. Functional groups
8. Organic molecules
4. Chemical Reactions
9. Carbohydrates
What part(s) of an element’s atoms
determines its mass?
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A. Protons
B. Neutrons
C. Electrons
D. Protons + Neutrons
E. Electrons/Protons
What part(s) of an element’s atoms
define the element?
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A. Protons
B. Neutrons
C. Electrons
D. Protons + Neutrons
E. Electrons/Protons
What part(s) of an element’s atoms
differentiate its isotopes?
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A. Protons
B. Neutrons
C. Electrons
D. Protons + Neutrons
E. Electrons/Protons
What part of atoms determine how
they bond with other atoms?
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A. Protons
B. Neutrons
C. Electrons
D. Protons + Neutrons
E. Electrons/Protons
Basic atomic structure- protons,
neutrons, and electrons
The periodic table logically arranges
and describes all matter
Molecules, compounds, chemical
reactions, and bonding
Elements combine in chemical
reactions to form compounds
• Molecules- 2 or more atoms combined in a specific way
• Compounds- different elements in a molecule, in exact,
whole-number ratios, joined by a chemical bond
• 2 major means of intramolecular chemical bonding:
Covalent (incl. polar and nonpolar) and Ionic
Valence electrons determine bonding
Atoms seek complete valence electron
shells (the octet rule)
In Ionic bonding, atoms strip valence
electrons from partners, forming ions
Atoms are stable when their outer
shells are filled with electrons
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Shell 1: Holds 2 electrons
Shell 2: Holds 8
Shell 3: Holds 8
Hydrogen- 1p, 1e, seeks a
second electron in its
outermost shell
• Carbon seeks 4
• The electrons in the
outermost shell are called
valence electrons
Noble gases have a stable electron
structure
• Their outer orbitals
have a full complement
of electrons
• Noble gases are very
unreactive
LE 2-7
In ionic bonding, an atom takes an
electron from another atom, forming 2
ions
Transfer of
electron
Na+
Sodium ion
Na
Sodium atom
Cl
Chlorine atom
ClChloride ion
Sodium chloride (NaCl)
5. Ions
• Ions- Charged atoms or
molecules
• Anion- negative ion
• Cation- positive ion
• Ionization- reaction
producing ions
• Salt- a neutral
compound comprised
of ions
LE 2-7a-2
Na+
Sodium ion
ClChloride ion
Sodium chloride (NaCl)
LE 2-7b
Na+
Cl-
Water dissolves many ionic
compounds (“like dissolves like”)
Individual soluble ions are not physically bound to
each other
In covalent bonding, pairs of valence electrons are
shared, and molecules are formed
LE 2-17a
+
2 H2
+
O2
2 H2 O
LE 2-6b
Nitrogen (N)
Atomic number = 7
Oxygen (O)
Atomic number = 8
In neutral molecules, carbon always
forms 4 bonds
Structural
formula
Ball-and-stick
model
Space-filling
model
Methane
The 4 single bonds of carbon point to the corners of a tetrahedron.
LE 3-1b
Ethane
Propane
Carbon skeletons vary in length.
LE 3-1c
Butane
Isobutane
Skeletons may be unbranched or branched.
Butane and Isobutane are _______________of each
other.
LE 3-1d
1-Butene
2-Butene
Skeletons may have double bonds, which can vary in location.
LE 3-1e
Cyclohexane
Benzene
Skeletons may be arranged in rings.
Organic Chemistry
• The chemistry of carbon
• Hydrocarbons are the
most basic example
– Combustible
– Can form rings
The variety of carbon compounds is
limitless
inorganic - lack carbon atoms
organic - with carbon (plus hydrogen)
biochemical - organic molecule in life
• carbohydrates • proteins
• lipids
• nucleic acids
Covalent bonds hold together the
macromolecules of life
• Living things create
macromolecular products for
structure:
• 6CO2(g)+ 6H2O(l) + hν  C6H12O6(s)
+ 6O2(g)
• Macromolecules as reactants are
broken down for energy:
C6H12O6(s) + 6O2(g)  6CO2(g)+ 6H2O(l)
All the reactions of a living thing are
called its metabolism
Electronegativity determines properties
of covalently bonded molecules
Electronegativity = “electron
greediness”
• Atoms in covalently bonded
molecules do not always
share electrons equally
• This creates polar molecules
• Polar regions of water
molecules interact to form
hydrogen bonds
• Hydrogen bonds:
weak/temporary
intermolecular forces
Some electronegativity values
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Hydrogen: 2.20
Oxygen: 3.44
Carbon: 2.55
Chlorine: 3.16
Sodium: 0.93
• Difference between:
• H and O: 1.22
• H and C: 0.35
Hydrogen bonding in water determine
many of water’s unique properties
• H-bonds can form a
lattice (ice)
• H-bonds require much
energy to break
• H-bonds give water
surface tension
Hydrogen bond
Water dissolves many ionic
compounds (“like dissolves like”)
Intermolecular Hydrogen bonds give water its
surface tension
Intermolecular Hydrogen bonds require
much heat in order to be broken
Water also forms ions sometimes
H2O
↔ H+ + OH• Spontaneously happens to water
molecules
• 1/ 107 water molecules are
ionized in distilled water
• In dH2O, [H+ ]= [OH-]
salt - neutral molecule releases ions
acid releases hydrogen H+, burns
base releases hydroxide OH–, slimy
pH is a measure of acidity/basicity
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pH = -log [H+] (logarithmic scale)
pH 1 6.9: acid
pH 7.114: base
pH 7 neutral
buffers - absorb excess H+ or OH–
- stomach 2, urine 5-7.8, blood 7.4
Acids donate [H+] to water
Bases remove [H+] from water (or donate [OH-] to
water)
• Proteins are very sensitive to small changes in pH
LE 2-15
pH scale
H+
H+
H+
H+ OH
+
OH- H
H+
H+
Lemon juice, gastric juice
H+
Grapefruit juice, soft drink
Acidic solution
Tomato juice
Human urine
OH-
OH-
-
H+
H+ OH
OH OHH+
H+
H+
Neutral solution
NEUTRAL
[H+[
-
Pure water
Human blood
Seawater
Milk of magnesia
Household ammonia
OHOHOH-
OHH+
H+
OH-
Household bleach
OH-
Basic solution
Oven cleaner
7. FUNCTIONAL GROUPS
hydroxide group
– OH
amino group – NH2
carboxyl group
– COOH
phosphate group – PO4
methyl group – CH3
The physical/
chemical
properties of
carbon skeletons
can be modified
by functional
groups
figure 02-20b.jpg
2.20 –
Part 2
Figure 2.20 – Part 2
Functional groups can radically change the
function of a molecule
Estradiol
Female lion
Testosterone
Male lion
• The six functional groups that are most important in
the chemistry of life:
– Hydroxyl group (alcohols)*
– Carbonyl group
– Carboxyl group (carboxylic acids)*
– Amino group*
– Sulfhydryl group
– Phosphate group*
– Methyl group
LE 4-10aa
STRUCTURE
(may be written HO—)
Ethanol, the alcohol present in
alcoholic beverages
NAME OF COMPOUNDS
Alcohols (their specific names
usually end in -ol)
FUNCTIONAL PROPERTIES
Is polar as a result of the
electronegative oxygen atom
drawing electrons toward itself.
Attracts water molecules, helping
dissolve organic compounds such
as sugars (see Figure 5.3).
LE 4-10ab
Acetone, the simplest ketone
STRUCTURE
EXAMPLE
Acetone, the simplest ketone
NAME OF COMPOUNDS
Propanal, an aldehyde
Ketones if the carbonyl group is
within a carbon skeleton
FUNCTIONAL PROPERTIES
Aldehydes if the carbonyl group is
at the end of the carbon skeleton
A ketone and an aldehyde may
be structural isomers with
different properties, as is the case
for acetone and propanal.
LE 4-10ac
STRUCTURE
EXAMPLE
Acetic acid, which gives vinegar
its sour taste
NAME OF COMPOUNDS
Carboxylic acids, or organic acids
FUNCTIONAL PROPERTIES
Has acidic properties because it is
a source of hydrogen ions.
The covalent bond between
oxygen and hydrogen is so polar
that hydrogen ions (H+) tend to
dissociate reversibly; for example,
Acetic acid
Acetate ion
In cells, found in the ionic form,
which is called a carboxylate group.
LE 4-10ba
STRUCTURE
EXAMPLE
Glycine
Because it also has a carboxyl
group, glycine is both an amine and
a carboxylic acid; compounds with
both groups are called amino acids.
NAME OF COMPOUNDS
Amine
FUNCTIONAL PROPERTIES
Acts as a base; can pick up a
proton from the surrounding
solution:
(nonionized)
(ionized)
Ionized, with a charge of 1+,
under cellular conditions
LE 4-10bb
STRUCTURE
EXAMPLE
(may be written HS—)
Ethanethiol
NAME OF COMPOUNDS
Thiols
FUNCTIONAL PROPERTIES
Two sulfhydryl groups can
interact to help stabilize protein
structure (see Figure 5.20).
LE 4-10bc
STRUCTURE
EXAMPLE
Glycerol phosphate
NAME OF COMPOUNDS
Organic phosphates
FUNCTIONAL PROPERTIES
Makes the molecule of which it
is a part an anion (negatively
charged ion).
Can transfer energy between
organic molecules.
Organic molecules are good energy sources
Energy is required to form covalent bonds;
energy is released when bonds are broken
Most molecules in living things fall into
four categories
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Carbohydrates
Lipids
Proteins
Nucleic acids
These all exhibit modular construction
Modular housing
Made of interchangeable parts
Freight trains have modular assembly
Modular assembly allows a wide
variety of products from a few pieces
Most biopolymers of life are formed by
dehydration synthesis
Hydrolysis is
the reverse
reaction
(Catabolic)
4. CHEMICAL REACTIONS
• metabolism
- all chemical reactions in body
- reactants ‹ products
synthesis - build larger molecule
CH3-OH + H-CH3 ‹ CH3-CH3 + H2O
hydrolysis - break down molecule
CH3-CH3 + H2O ‹ CH3-OH + H-CH3
exchange reaction
- example: AB + CD ‹ AD + CB
Carbohydrates
• “Carbon” + “Hydro”
• Formula (CH2O)n
• Different from
hydrocarbons
• Soluble in water
• Includes: table
sugar, honey, starch,
glycogen, cellulose,
high fructose corn
syrup
• Glucose is the
monomer
Glucose can cyclize to form a ring
structure
Atoms in bonds are free to rotate around the bonds
Glucose + Glucose = Maltose
Sugar dimer)
(A
Chain can be extended to thousands
9. Carbohydrates
• functions
- principle source of energy
(4 kcal/g)
- structure & energy storage
in plants
atoms - C H O
structure - ring or chain of 56 C’s
monosaccharide
- single sugars (example:
glucose)
disaccharide
- double sugars (example:
sucrose)
polysaccharide
- polymer or chain of 100’s
sugars
- starch & cellulose (mostly
plants)
- glycogen (animals, esp.
liver)
Proteins are polymers made of 20
different kinds of amino acid monomers
table 03-02bc.jpg
Table 3.2 – Part 2
Table 3.2 – Part 2
table 03-02d.jpg
Table 3.2 – Part 3
Table 3.2 – Part 3
Proteins: Polymers of Amino Acids
• Amino acids are covalently bonded
together by peptide linkages. Review
Figure 3.4
figure 03-04.jpg
Modular assembly
of amino acids
through
dehydration
synthesis
3.4
Proteins have an incredible variety of
structures
Proteins have an incredible variety of
functions
Hair, skin, fingernails, muscles, eye pigments, are all
made of protein
11. Proteins
functions - energy (4
kcal/g)
- structure in animals
(meat)
- enzymes (speed up & reg
chem rxs)
atoms - C H O N
amino acid
- central C, hydrogen –H
- amino group –NH2
- carboxyl group –COOH
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4 levels of structure - necessary
for protein function, esp.
enzymes
I° primary structure - sequence of
amino acids in
polypeptide chain
II° secondary structure
- coiling or folding of chain
- hydrogen bonds between regions
III° tertiary structure
- folding of coiled-folded chain
IV° quaternary structure
- linkage to other polypeptides
Lipids
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Non-polar
High-energy molecules
For energy storage
Forms cell membranes
Hormones
Members of family
include oils, fats, waxes,
and cholesterol
(steroids)
Lipids are non-polar
• Therefore, they are
hydrophobic
Triglycerides are a primary lipid structure
Dehydration synthesis links fatty acids to
glycerol
Fatty acids can be saturated and
unsaturated (cis and “trans”)
10. Lipids
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functions
- energy storage (9 kcal/g)
- also animal structure (blubber)
atoms - C H O
structure - glycerol + 3 fatty acids
oil - liquid, unsaturated (missing H’s)
fat - solid, saturated (maximum H’s)
- promotes heart disease
others
- steroids, phospholipids, waxes
Nucleic acids
• Informational molecules
in cells
• Include DNA, RNA, and
ATP/ADP
• Have other functions
Nulceotides are the subunits of nucleic
acids
• Consist of a sugar, a
phosphate, and a
nitrogen-containing
base
• Sugar can be
deoxygenated
12. Nucleic Acids
• function - not energy
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- genetics (genes &
chromosomes)
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• atoms - C H O N P S
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• structure - chain of 100’s
nucleotides
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• examples - DNA, RNA, ATP
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Review
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Atomic structure- protons, neutrons electrons
Valence electrons
Carbon
Functional groups
Carbohydrate structure
Protein structure
Lipid structure
Things left unsaid
• Isotopes of all elements exist (some of these are
radioactive)
• Electronegativity determines polarity of covalent
bonds, and thus solubility
• Water has important physical properties essential
to life on earth
• Isomers have the same molecular formula but
not the same shape in space
• Nucleic acids are comprised of nucleotide
monomers