Download Chapter 3: The Chemistry of Organic Molecules

Chapter 3: The Chemistry of
Organic Molecules
3.1 Organic Molecules
• Organic Molecule= A molecule that
contains carbon and hydrogen; it may also
have O, N, P, or S.
Carbon
• Has four electrons in
outer shell, therefore
make up to four
covalent bonds with
four other atoms.
• It can also bond itself
to form both chains
and rings. Carbon
chains make up the
skeleton or “backbone”
of organic molecules.
Functional Groups
• Functional groups= clusters of certain
atoms, attached to the carbon back bone
(see figure 3.2).
• Differences in the
carbon backbone and
attached functional
groups cause an
organic molecule to
have different chemical
properties.
– (ex) molecules
composed of only
carbon and hydrogen
are hydrophobic (not
attracted to water). But
the addition of a
functional group like –
OH makes the
molecule polar, or
hydrophilic (attracted
to water).
• 4 classes of organic molecules:
carbohydrates, lipids, proteins, and nucleic
acids.
• Each of these 4 types of macromolecules
is a polymer, which is a long chain of
covalently bonded unit molecules called
monomers.
Monomers and Polymers
• Carbohydrates: polymer = polysaccharide
monomer= monosaccharide
• Proteins: polymer= polypeptide
monomer= amino acid
• Nucleic acids: polymer= nucleic acid
Monomer= nucleotide
• Condensation synthesis: when a water
molecule is removed in order to form a
bond between two monomers. (an –OH
group is removed from one molecule and
a hydrogen (H) is removed from the other.)
• Hyrdolysis: The means by which
polymers are broken down. A water
molecule is added to break the bond
between monomers.
3.2 Carbohydrates
• Energy storage compounds & building materials.
• Monosaccharides: simple sugars, carbon back
has 3-7 atoms.
– Glucose (C6H12O6) and fructose are both hexoses: 6-carbon
sugars; glucose found in blood of animals, fructose found in
fruits. (isomers)
– Ribose and deoxyribose are both pentoses: 5-carbon sugars;
found in DNA and RNA.
Disaccharides
• Two monosaccharides joined by
condensation.
• Lactose: contains galactose and glucose; found in
milk.
• Maltose: two glucose molecules; result in starch
digestion.
Polysaccharides
• Long polymers of monosaccharides
• Glycogen- have many branches of Glucose.
Storage vessel for animals. Liver and Muscles.
Allows for breakdown to happen at many points.
• Starch- have many branches of glucose. Storage
vessel of carbohydrates for plants. Seeds and
roots. Allows for breakdown to happen at many
points.
Polysaccharides
• Cellulose: Straight and Fibrous (structure
support) glucose.
– Hydrogen bonds.
– Plant cell walls (cotton) (wood)
Polysaccharides Cont’d
Chitin: Exoskeletons, amino group attached to each
glucose.
– Sutures
3.2 Lipids
• Lipids: organic molecules that are
generally insoluble in water; used as longterm energy storage compounds in plants
and animals.
Fats and Oils
Glycerol: compound with
3 hydroxyl groups (OH); hydroxyl groups
are polar which makes
glycerol soluble in
water.
Fatty Acids: Long
hydrocarbon chain
with carboxyl group (COOH)at one end
Formation of a fat/oil:
Condensation
synthesis involving 3
fatty acids and one
glycerol, forming a
triglyceride.
Fatty acids: carboxyl group
is polar which makes fatty
acid soluble in water.
Types:
» Saturated: no double
bonds between carbon
atoms, causes
molecule to be more
rigid.
» Unsaturated: have
double bonds in carbon
chain, causes molecule
to be more fluid.
Waxes
• Waxes are long-chain fatty acid bonded to
a long-chain alcohol.
• Solid at room temp., hydrophobic, usually act as a
protective coating in plants and animals. (ex.: ear
wax in humans for trapping dirt and dust particles,
preventing them from reaching the eardrum.)
Phospholipids
• Soluble in water; contains a glycerol molecule, 2
fatty acids, and one phosphate group.
• Phosphate group is the “polar head” of molecule.
• Fatty acid chains are “nonpolar tails” of molecule.
• Plasma membrane in eukaryotic cells is a phospholipid bilayer.
The Phopholipid Bilayer of Plasma
Membranes
Steriods
• Backbone of 4 fused carbon rings, vary
according to the types of functional groups
bonded to the rings.
• Cholesterol- component of animal cell membrane,
precursor for other types of steroids (estrogen,
testosterone).
Cholesterol is the
molecule from which
other steroids, including
the sex hormones, are
synthesized.
3.4 Proteins
• Polymers of amino acids
• Functions:
– Support / structure: Keratin in hair and nails,
collagen in ligaments, skin, tendons.
– Regulation: Enzymes that speed up reactions
(catalyze), Hormones like insulin regulates
levels of glucose in blood
Protein Functions contd
• Defense: Antibodies, and antigens
• Motion: contractile proteins (actin and
Myosin) in muscles.
• Transport: Channel and carrier proteins in
plasma membrane, hemoglobin (O2)
Monomers Of Proteins
• Amino Acids: Carbon
Atom bonded to 3
functional groups.
– Animo group (-NH2)
– Carboxyl group (COOH) (acidic)
– R group = “remainder”
of molecule;
determines the 20
different amino acids
found in life; unique
properties.
Polymers of proteins
• Polypeptides: two or
more amino joined
by condensation
– Peptide bond:
between Carbon of
one amino acid and
the nitrogen of
another.
– Most proteins are at
least 150 A.A. long.
– Some proteins can
contain more than
one polypeptide
chain
Protein Structure
• Primary Structure: The sequence of amino
acids joined by peptide bonds.
• Secondary Structure: Coiling or folding of
polypeptide chain due to properties of A.A.
w/in primary structure. (H-bonds b/w
different A.A.)
– Beta sheets
– Alpha helix
Protein Structure Contd
• Tertiary Structure: The folding and twisting
that results in the 3-D shape of
polypeptide.
– H-bonds, disulfide links (fxnl group?), Ionic
bonds, and other molecular interactions
between R groups.
• Quaternary Structure: arrangement of
more than one polypeptide chain
– Hemoglobin: globular protein with 4 peptide chains
– Some proteins
Protein Structure: 2 models
Denaturation
• When a protein loses its 40/30/20 structure.
• Renders a protein inactive.
• Caused when the environment that protein
is in changes (temperature, pH)
– Causes interactions/bonds to break
– Proteins have optimal environments.
• Renaturation: when protein is place back
into optimal environment it will reform into
proper structure.
High temperatures or various chemical treatments will denature a protein, causing
it to lose its conformation and hence its ability to function. If the denatured protein
remains dissolved, it can often renature when the chemical and physical aspects of
its environment are restored to normal.
Importance of Denaturation /
Renaturation
• Regulation: This is a way for cells to
regulate which chemical reactions will
happen and when they will occur.
• Not very efficient if cells are undergoing all
reaction all at once.
Nucleic Acids
Three types of nucleic acids:
1) DNA
1. DNA (deoxyribonucleic acid) – the genetic material that store
information for replicating itself and the sequence of amino acids
to make all of an organisms proteins
• Monomers = nucleotide
• There are three molecules that make up a nucleotide:
1. Phosphate functional group
2. Nitrogen containing base
3. Pentose monosaccharide = deoxyribose
• There are four types of nucleotides that are determined by the
type of base each has: Cytosine, Thymine, Adenine, and
Guanine
DNA Continued
The different nucleotides are joined together
by a bond between the phosphate of one
nucleotide and the sugar of another.
(Sugar–Phosphate Backbone) Process?
DNA has two strands of nucleotides that are
joined together by hydrogen bond between
different bases (A-T, T-A, C-G, G-C)
This results in the double-helix
2) RNA
• RNA (ribonucleic acid) – involved in the
process of making proteins form DNA.
– Similar to DNA except:
1. Single Stranded
2. Ribose instead of Deoxyribose
3. Uracil instead of Thymine
3) ATP
• ATP (Adenosine Triphosphate) – supplies energy for
synthetic reactions and for all energy requiring processes in
cells. (a cell’s energy currency)
– Adenosine = ribose + adenine
– Triphosphate = three phosphates bonded together
ATP Contd
High energy molecule due to the instability of phosphates.
ATP → ADP + P + H20 (energy) Reversible reaction constantly
recycled in cells