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The Molecules of Life
Biochem!
Chapter 9
Biochemistry
 Carbohydrates,
lipids, proteins,
and the nucleic acids
 All built from simple precursors
 How they are put together is the
key to their activity 
Carbohydrates
 Polymers
built from repeating
sugar molecules
Carbohydrates
 Glucose
– most common
• Assembled one way = starch – our
main E source
• Assembled a different way =
cellulose – main ingredient in wood
and most plentiful organic
substance on earth!
Lipids

Polymers built
from long
hydrocarbon
chains of fatty
acids
Proteins

Constructed
from 20 different
kinds of amino
acids
• Great structural
and functional
variability
Types of Proteins
– major component of
tendons, skin, and bones
 Hemoglobin – transports O2 in
the blood stream
 Enzymes – catalyst that speeds
up rxn’s in all living organisims
 Collagen
Biochem History


Until early 19th century, it was thought that
living things had something called “vital
forces” that was unique to only living things.
1828 – German Scientist Freidrich Wöhler
synthesized Urea from ammonium cyanate (a
mineral)
• Urea is a waste product of animal metabolism
• NH4OCH H2NCONH2
Current Realizations
 Any
compound that exists in a
living organism can be
synthesized in a lab
 Rxn’s of biomolecules depend
on the functional groups
Functional Groups
 Table
of functional groups
 Also, carbon containing
derivatives of phosphoric acid
[esters and anhydrides of
phosphoric acid  ADP, ATP
Amino Acids
 20
A.A’s - usually found in proteins
 General structure in common with
variations in side chains
 Amino acids contins amino groups
(RNH2, R2NH, R3N) and a carbonyl
group (RCOOH)
Amino Acids
 Both
groups are
bonded to the
same carbon atom
and labeled α
carbon = the one
next to the
carbonyl group
Amino Acids
 Carbon
atoms in the R group are
labeled using the Greek alphabet
starting w/the C adjacent to the
carbonyl group
α
β
γ
δ
ε
Alpha beta gama delta epsilon
Amino Acids
 Identity
of the amino acids
depends on the nature of the Rgroup.
Monosaccharides

Carbohydrates have the general formula
Cn(H2O)n
• All carbohydrates are not just hydrates of
water

Simple sugars (monosaccharides) are
cmpds that contain a single carbonyl
group & 2 or more hydroxyl groups
• Either polyhydroxyaldehydes or
polyhydroxyketones
Monosaccharides
The ones that contain aldehydes=aldases
 The ones that conatin ketones = ketoses
 6 Carbon sugars are most abundant in
nature but 2, 5 carbon sugars (ribose and
deoxyribose) occur in the structures of
RNA and DNA

The Structure of Nucleic Acid
Monomers
The 2 kinds of nucleic acids are DNA
and RNA
 There are diffs and sims b/t the two
 They are macromolecules (very large
molecules) formed by polymerizing
monomer units (nucleotides = monomer
units of nucleic acids)

The Structure of Nucleic Acid
Monomers

Nucleotides have a base, a sugar,
and a phosphoric acid residue
covalently bonded together
 Nucleic acids can be hydrolyzed to
their constituent nucleotides by acids,
bases, or enzymes
The Structure of Nucleic Acid
Monomers
 The
main distinction between the
nucleotide monomers of DNA and RNA
is the sugar portion
DNA = deoxyribose
RNA = ribose
Nucleotide Base
The Structure of Nucleic Acid
Monomers

1.
2.
Nucleic acid bases (aka nucleobases)
= nitrogen-containing aromatic
compounds that fall into 2 categories
Pyrimidines – cytosine (in
RNA&DNA)/thymine (DNA in rarely in
RNA)/uracil (only in RNA)
Purines  adenine
(RNA/DNA)/guanine (RNA/DNA)
Lipid Examples
Insoluble in H2O and soluble in
organic solvents
 Glycerol esters of fatty acids (long
chain carbox.acids) & derivatives of
these esters are imoportant
examples of lipids
 Another example = steroids

Biochem
Part II
Amino Acids

We know that proteins are long chain of
amino acids linked together by peptide
bonds between a + charged N (amino)
group at one end and a – charged
carbonyl group at the other end.
• Along the chain is a series of side chains
that are different for each of the 20 amino
acids
Amino Acids
Dipeptide = 2 amino acids
 Tripeptide = 3
 The sequence of the amino acids is
most important

• There are 8,000 ways to arrange them
• In a protein chain of 100 amino acids, there
are more ways to arrange them than there
are atoms in the universe
Of all the possible AA’s, only 20
are usually found in proteins!

General structure of an AA involves an
amino group, a carboxyl group & both
are bonded to the α C
• The α C is also bonded to a H
•
and an R group (side chain)
The R group determines the
identity of the AA
Amino Acids
 One
of the most important
properties of a AA is its 3-d shape
(stereochemistry)
• Mirror images that are superimposable = achiral
• Mirror images that aren’t superimposable = chiral
• Many important molecules are chiral
• Frequently, chiral center is a C atoms bonded to
4 different groups
Amino Acids
Glycine is the only AA that doesn’t have
a chiral center (it’s R group is a single
H, giving it 2H’s out of 4 groups)
 All other AA have
2 stereoisomers

Amino Acids

Dashed lines show behind the plane,
solid triangles show out of the plane
Amino Acids
In biochemistry, we don’t use R&S
designations, instead D & L are used
 L (laevus) and D (dexter) meaning left
and right
 For AA, D=amino group on right side,
L = amino group on the Left side

Amino Acids

AA in proteins are all L
Structures and Properties of the
Individual AA’s
R group (thus the amino acids) are
classified according to several criteria
(two very important)
 Polar or nonpolar nature of the side
chain
 Presence of an acidic or basic group in
the side chain

Group 1 – AA
Nonpolar side chains
 Alanine, valine, leucine, isoleucine,
proline, phenylalanine, tryptophan,
methionine

Group 2 - AA
With electrically neutral polar side
chains (neutral pH)
 Serine, threonine, tyrosine,
cysteine

Group 3 – AA - carboxyl groups in
their side chains
Glutamic acid and aspartic acid
 Carbonyl group can lose H+ (forming
carboxylate ion) so they are – charged
at neutral pH
 They frequently bond to –NH2 to form
side chain amide groups yielding
analogous AA glutamine & asparagine

Group 4 – AA
With basic side chains [+ charged
at or near neutral pH
 Histidine
 Lysine
 Arginine

Others
Some other AA’s are known to
occur in some, but not all proteins
 Derived from common AA and are
produced by the modification of the
parent AA after the protein is
synthesized by the organism

Others
Hydroxyproline and hydroxylysine have
extra –OH groups on the side chain
 Thyroxine (from tyrosine) has an extra
Iodine containing aromatic group on the
side chain (found only in thyroglobuin, a
protein in the thyroid)

The Peptide Bond
AA are linked by covalent bonds joining
the α – carboxyl group with the α-amino
group) splitting out an H2O
 After the H2O elimination, the groups are
linked amino acids residues
 A bond formed this way is called a
peptide bond (aka: amide bond)

Peptide Bond
The Peptide Bond

In a protein many AA (usually more than
100) are linked by peptide bonds to form
a polypeptide chain
• A peptide is a compound formed by liking smaller
#’s of amino acids (two  several dozen)
• The bond is a single bond with partial double
bond character (resonance)