Lecture #1
Chapter 2 & 3:
Basic Chemistry
Water and the Fitness of
the Environment
Chemical Context of Life
 Matter (space & mass)
 Element; compound
 The atom
 Atomic number (# of
protons); mass number
(protons + neutrons)
 Isotopes (different # of
neutrons); radioactive
isotopes (nuclear decay)
 Energy (ability to do work);
energy levels (electron
states of potential energy)
Covalent Bonding
 Sharing pair of valence
electrons
 Number of electrons
required to complete an
atom’s valence shell
determines how many
bonds will form
 Ex: Hydrogen & oxygen
bonding in water;
methane
Polar/nonpolar covalent bonds
Electronegativity
attraction for electrons
Nonpolar covalent
•electrons shared equally
•Ex: diatomic H and O
Polar covalent
•one atom more
electronegative than
the other (charged)
•Ex: water
Ionic bonding
 High electronegativity
difference strips
valence electrons away
from another atom
 Electron transfer
creates ions (charged
atoms)
 Cation (positive ion);
anion (negative ion)
 Ex: Salts (sodium
chloride)
Molecular Shape & Function
Each molecule has a characteristic size
and shape.
Relates directly to its function in the cell
Molecular shape determines how
molecules recognize one another
Ex: Pain Receptors in the brain
Water
 Polar ~ opposite ends, opposite
charges
 Cohesion ~ H+ bonds holding
molecules together
 Adhesion ~ H+ bonds holding
molecules to another substance
 Surface tension ~ measurement of
the difficulty to break or stretch the
surface of a liquid
Water
 Specific heat ~ amount of heat absorbed or lost to
change temperature by 1oC
Water has one of the highest at 4.18 J/goC
 Heat of vaporization ~ quantity of heat required to
convert 1g from liquid to gas states
Because of the shc, this is a large amount of energy
 Universal solvent
Almost everything dissolves in water
Density
Less dense as solid
than liquid
Due to hydrogen
bonding
Crystalline lattice
keeps molecules at a
distance
Acid/Base & pH
 Dissociation of water into a
hydrogen ion and a hydroxide
ion
 Acid: increases the hydrogen
concentration of a solution
 Base: reduces the hydrogen
ion concentration of a solution
 pH: “power of hydrogen”
 Buffers: substances that
minimize H+ and OHconcentrations (accepts or
donates H+ ions)
 Ex : Blood
Lecture #2
Chapter 4 & 5
Carbon & The Molecular
Diversity of Life
The Structure & Function
of Macromolecules
Organic chemistry
 Biological thought:
 Vitalism (life force outside physical
& chemical laws) Berzelius
 Mechanism (all natural
phenomena are governed by
physical & chemical laws) Miller
 Carbon
tetravalence
tetrahedron
shape determines function
Hydrocarbons
 Only carbon & hydrogen
(petroleum; lipid ‘tails’)
 Covalent bonding; nonpolar
 High energy storage
 Isomers (same molecular
formula, but different structure &
properties)
 Structural : differing covalent
bonding arrangement
 Geometric : differing spatial
arrangement
 Enantiomers : mirror images;
pharmacological industry
(thalidomide)
Functional Groups, I
 Attachments that replace
one or more of the
hydrogens bonded to the
carbon skeleton of the
hydrocarbon
 Each has a unique
property from one
organic molecule to
another
Hydroxyl Group
H bonded to O;
alcohols;
polar (oxygen);
solubility in water
Carbonyl Group
C double bond to O;
At end of chain:
aldehyde Otherwise:
ketone
Functional Groups, II
Carboxyl Group
O double bonded to C to
hydroxyl; carboxylic acids;
covalent bond between O and
H;
polar;
dissociation, H ion
Amino Group
N to 2 H atoms; amines;
acts as a base (+1)
Sulfhydral Group
sulfur bonded to H;
thiols
Phosphate Group
phosphate ion; covalently
attached by 1 of
its O to the C
skeleton;
Functional Groups,
Chart 1
Hydroxyl
Carbonyl
Carboxyl
Functional Groups,
Chart 2
Amino
Nitrogen
Sulfhydryl
Sufur
Phosphate
Phosphorous
Polymers
 Covalent monomers
 Condensation reaction
(dehydration reaction):
One monomer provides a
hydroxyl group while the other
provides a hydrogen to form a
water molecule
 Hydrolysis:
bonds between
monomers are broken by
adding water (digestion)
Carbohydrates, I
Monosaccharides
√ CH2O formula;
√ multiple hydroxyl (-OH)
groups and 1 carbonyl
(C=O) group:
aldehyde (aldoses) sugar
ketone sugar
√ cellular respiration
√ raw material for amino acids
and fatty acids
Carbohydrates, II
Disaccharides
√ glycosidic linkage (covalent
bond) between 2
monosaccharides;
√ covalent bond by
dehydration reaction
Sucrose (table sugar)
√ most common disaccharide
Disaccharides
Carbohydrates, III
 Polysaccharides
Storage: Starch - glucose
monomers
Plants: plastids
Animals: glycogen
 Polysaccharides
Structural:
Cellulose - most abundant
organic compound
Chitin - exoskeletons; cell
walls of fungi; surgical
thread
Polysaccharides
Lipids






No polymers; glycerol and fatty acid
Fats, phospholipids, steroids
Hydrophobic; H bonds in water exclude fats
Carboxyl group = fatty acid
Non-polar C-H bonds in fatty acid ‘tails’
Ester linkage: 3 fatty acids to 1 glycerol
(dehydration formation)
 Triacyglycerol (triglyceride)
 Saturated vs. unsaturated fats; single vs. double
bonds
Lipids, II
Phospholipids
2 fatty acids instead
of 3 (phosphate
group)
‘Tails’ hydrophobic;
‘heads’ hydrophilic
Micelle (phospholipid
droplet in water)
Bilayer (double layer);
cell membranes
Steroids
 Lipids with 4 fused carbon
rings
 Ex: cholesterol:
cell membranes;
precursor for other
steroids (sex hormones);
atherosclerosis
Nucleic Acids, I




Deoxyribonucleic acid (DNA)
Ribonucleic acid (RNA)
DNA → RNA → protein
Polymers of nucleotides
(polynucleotide):
 nitrogenous base
 pentose sugar
 phosphate group
 Nitrogenous bases:
 pyrimidines: cytosine (C), thymine (T),
uracil (U)
 purines: adenine (A), guanine (G)
Nucleic Acids, II
Pentoses:
√ ribose (RNA)
√ deoxyribose (DNA)
√ nucleoside (base + sugar)
Polynucleotide:
√phosphodiester linkages
covalent (phosphate +
sugar)
Nucleic Acids, III
Inheritance based on
DNA replication
Double helix (Watson &
Crick - 1953)
H bonds - between paired
bases
van der Waals - between
stacked bases
A to T; C to G pairing
Complementary
Proteins
 Importance:
Instrumental in nearly everything organisms do; 50% dry weight of
cells; most structurally sophisticated molecules known
 Monomer: amino acids (there are 20)
Each contains - carboxyl (-COOH) group, amino group (NH2), H atom,
variable group (R)….
 Variable group characteristics:
polar (hydrophilic), nonpolar (hydrophobic), acid or base
 Polypeptides (dehydration reaction):
peptide bonds: covalent bond
carboxyl group to amino group (polar)
Protein Structure
 Three-dimensional shape
Conformation
 Primary
Amino Acids
 Secondary
α-Helix, β-sheet
 Tertiary
Many secondary; β barrels
 Quartinary
Total binding; creates sites
for recognition
Primary Structure
Conformation:
Linear structure
Molecular Biology:
each type of protein has a unique
primary structure of amino acids
Ex: lysozyme
Amino acid substitution:
hemoglobin; sickle-cell anemia
Secondary Structure
 Conformation:
coils & folds (hydrogen bonds)
 Alpha Helix:
coiling; keratin
 Pleated Sheet:
parallel; silk
Tertiary Structure
 Conformation:
irregular contortions from R
group bonding
√ hydrophobic
√ disulfide bridges
√ hydrogen bonds
√ ionic bonds
Quaternary Structure
 Conformation:
2 or more polypeptide
chains aggregated
into 1 macromolecule
√ collagen (connective
tissue)
√ hemoglobin
Lecture #3
Chapter 6
An Introduction to
Metabolism
Metabolism/Bioenergetics
Metabolism: The totality of an organism’s
chemical processes; managing the material and
energy resources of the cell
Catabolic pathways: degradative process such
as cellular respiration; releases energy
Anabolic pathways: building process such as
protein synthesis; photosynthesis; consumes
energy
Thermodynamics
 Energy (E)~ capacity to do work; Kinetic energy~ energy of
motion; Potential energy~ stored energy
 Thermodynamics~ study of E transformations
 1st Law: conservation of energy; E transferred/transformed,
not created/destroyed
 2nd Law: transformations increase entropy (disorder,
randomness)
Combo: quantity of E is constant, quality is not
Free energy
 Free energy: portion of system’s E that can perform work
(at a constant T)
 Exergonic reaction: net release of free E to surroundings
 Endergonic reaction: absorbs free E from surroundings
Gibbs Free Energy
ΔG = ΔH – TΔS
ΔG = change in free energy
ΔH = the change in the enthalpy (heat/kJ)
T = temperature in Kelvin (K)
ΔS = change in entropy (disorder)
Energy Coupling & ATP
 E coupling: use of exergonic
process to drive an
endergonic one (ATP)
 Adenosine triphosphate
 ATP tail: high negative
charge
 ATP hydrolysis: release of
free E
 Phosphorylation
(phosphorylated
intermediate)~ enzymes
Enzymes
 Catalytic proteins: change
the rate of reactions w/o
being consumed
 Free E of activation
(activation E): the E
required to break bonds
 Substrate: enzyme reactant
 Active site: pocket or
groove on enzyme that
binds to substrate
 Induced fit model
Effects on Enzyme Activity
Temperature
pH
Cofactors:
inorganic, nonprotein
helpers; ex.: zinc, iron,
copper
Coenzymes:
organic helpers; ex.:
vitamins
Enzyme Inhibitors
 Irreversible (covalent);
reversible (weak bonds)
 Competitive: competes for
active site (reversible); mimics
the substrate
 Noncompetitive: bind to
another part of enzyme
(allosteric site) altering its
conformation (shape);
poisons, antibiotics