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Organic Chemistry and
Biochemistry
Lecture Text Chapter 2
Organic Molecules
• Molecules containing
both carbon and
hydrogen
• Carbon
– 4 valence electrons in
outer orbital
– Needs 8 total for full
complement
Carbon
• Can form 4 covalent bonds
• Can form 1-2 bonds with
multiple atoms, including
other carbon atoms
– Form chains of carbons,
rings, etc.
Reactive Groups
• Hydrocarbon chains may
be linked to more reactive
elements
– E.g., oxygen, nitrogen
Chemical Formulas
• Molecular Formulas
– Number of atoms of each element in the
molecule
• E.g. water = H2O
• E.g. methane = CH4
• E.g. glucose = C6H12O6
– Does not indicate how atoms bond together
Chemical Formulas
• Structural Formulas
–
–
–
–
Indicate bonds among atoms within molecules
Single line indicates single covalent bond
Double line indicates double covalent bond
E.g. Acetone (C3H6O)
Chemical Formulas
• Condensed Structural Formulas
– Not all bonds drawn
– Central atoms shown with atoms bonded to
them
– E.g. Acetone (C3H6O)
(CH3)CO(CH3)
O
or
(CH3)2CO
or
CH3CCH3
Chemical Formulas
• Line-Angle Formulas
– Bonds represented by lines
– Carbon atoms assumed to be present at the end of any
line
– Oxygen and Nitrogen shown, Hydrogen is not
– Each carbon is assumed to have enough hydrogens
bonded to it by single bonds to give it four bonds total
Chemical Formulas
• Line-Angle Example
Line-Angle
Structural Formula
Biomolecules
•
•
Complex organic molecules used in biological
systems
Polymers
– Made up of repeated subunits
•
Major Groups
1. Carbohydrates – energy sources, cell communication
2. Lipids – energy storage, cell membrane structure,
cushioning, cell communication
3. Proteins – structure, cell function (enzymes) , cell
communication
4. Nucleic Acids – information storage
Carbohydrates (Sugars)
• molecules that contain H, O and C
• relative amounts of each are the same in all
simple carbohydrates
– #C atoms = #O atoms
– #H atoms = 2x the number of either C or O
• general formula = (CH2O)n
– e.g. glucose – C6H12O6
Carbohydrates (Sugars)
• monosaccharide - individual
unit
• basic CH2O formula
• name possesses the suffix –ose
– e.g. glucose, galactose, fructose,
ribose
• Monosaccharides can have the
same formula but different
arrangements of atoms
– Isomers – molecules of same
formula but different structures
Carbohydrates (Sugars)
• Disaccharide
– two monosaccharides linked
together
• e.g. sucrose
= glucose + fructose
• e.g. maltose
= glucose + glucose
Carbohydrates (Sugars)
• Polysaccharide
– Many monosaccharides
linked together
• E.g. glycogen
– Polymer of glucose
Carbohydrate Synthesis
• Monosaccharides are linked
together by dehydration
synthesis
– employs specific enzymes
– H is removed from one
monosaccharide, an -OH group
from the other
– covalent bond (glycosidic bond)
formed between the two
– water formed as an end-product
Carbohydrate Digestion
• polysaccharides are
broken apart via
hydrolysis
– a water molecule is split
– H+ added to one of the
free monosaccharides
– OH group added to the
other
Lipids (Fats, Oils, Waxes)
• very general category
• contain compounds
that are not soluble in
water (hydrophobic)
• Major classes
– Triglycerides
– Phospholipids
– Steroids
Triglycerides
• fats and oils
• formed by dehydration
synthesis
• combine glycerol with
three molecules of
fatty acid
Triglycerides
• different types of fatty acids
• Saturated
– all carbons in chain linked by
single bonds
• Unsaturated
– one or more carbons in chain
linked by double bonds
• Unsaturated fatty acids tend
to be more fluid
Phospholipids
• contain a phosphate group
(PO4)
• commonly a combination of
a phosphate group to a
glycerol molecule attached
to two fatty acids
– e.g. lecithin
Phospholipids
• possess both polar an
nonpolar ends (amphipathic)
• nonpolar ends aggregate
together
• form micelles when mixed
in water
– interact with water – lowers
surface tension of water
Steroids
• Consist of 3 six-carbon rings and a
single five-carbon ring interlocked
together
• different functional groups
attached to basic structure
– e.g. sex steroids – produced by
gonads (testosterone, progesterone)
– e.g. corticosterones – produced by
adrenal glands
– e.g. cholesterol – precursor for
hormones, regulation of cell
membrane fluidity
Proteins
• Diverse in structure and
function
• Polymers of amino acids
• 20 common amino acids
each with:
– an amino group
– a carboxyl group
– a functional side-group
(differs among a.a.’s)
Peptide Bonds
• Amino acids are joined
together by dehydration
synthesis
• NH3 group of one joined to
the COOH group of another
to form a peptide bond
– two joined amino acids =
dipeptide
– many joined amino acids =
polypeptide
Protein Structure:
Primary Structure
• Sequence of amino acids in
a polypeptide chain
• From free amino end (Nterminus) to the free
carboxyl end (C-terminus)
• May be 1000’s of a.a.’s
long
Protein Structure:
Secondary Structure
• Formation of helix or sheet
shape in a protein chain
• due to hydrogen bonds
forming between the amino
group of one peptide bond
and the carboxyl group
from another peptide bond
Protein Structure:
Tertiary Structure
• Twisting and folding
of a single protein
chain
• due to chemical
interactions among the
different sidechain
groups
Protein Structure:
Quaternary Structure
• Bonding and
interactions of multiple
polypeptide chains
– e.g. insulin = two
separate chains
– e.g. hemoglobin = four
separate chains
Conjugated Biomolecules
• Combinations of two or more types of
biomolecules
– Glycoprotein = carbohydrate + protein
– Lipoprotein = lipid + protein
– Glycolipid = carbohydrate + lipid