Lif101 6

LIFE 101A
INTRODUCTION TO
BIOLOGY – Lecture 6
Topic: Amino acids and protein structures
Structure dictates function
Amino Acids
There are 20 "standard" amino
acids that are specified by the
genetic code and polymerized into
proteins by ribosomal translation.
All amino acids contain an a carbon

to which typically 4 different
substituent groups are attached.
These groups are the α-amino

group, the α-carboxyl group,
hydrogen, and the variable R group
(side-chain).
Amino Acids
Glycine - [R = H]
In the other 19 amino
acids, the  carbon is a
chiral center.
There are two possible
configurations for
these four substituents.
Amino Acids: D and L
Amino acids are specified as D or L based on
comparison of their configurations to the
reference compounds, D- and L-glyceraldehyde.
Amino Acids: Classification
Amino acids are

classified based on the
characteristics of their
R groups.
The chemical
properties of the
standard 20 amino
acids are summarized
in next few slides.
[Nonpolar, Aliphatic Amino Acids]
Lack polar functional groups in their side chains.
[Polar, Uncharged Amino Acids]
R = contains polar functional groups that can
hydrogen bond with water.
[Aromatic Amino Acids]
The side-chains of the aromatic amino acids,
phenylalanine, tyrosine, and tryptophan, overall
are very hydrophobic.
[Aromatic Amino Acids]
R in tyrosine: contains a polar hydroxyl group.
Tryptophan: absorb UV light (λmax = 280nm)
[Positively Charged Amino Acids]
Lysine and Arginine: Positively charged R group
Histidine: Partially positively charged R group
[Negatively Charged Amino Acids]
R groups of aspartate and glutamate contain
carboxyl groups that are negatively charged.
Amino Acids: Three-Letter and
Single-Letter codes
Cysteine and Disulfide Bonds
Thiol groups of two cysteines are readily oxidized
to form a covalently linked disulfide bond.
Amino Acids: Numbering of Carbons
The conventions for labeling the carbon atoms
in amino acids is illustrated using lysine. The 
carbon is always carbon-2 of the amino acid.
The -carboxyl group is always carbon-1
Amino Acids: Ionization
When a simple amino acid [e.g. alanine] is dissolved in
water at neutral pH, its -carboxyl group is negatively
charged, and its -amino group is positively charged.
Such dipolar ions (total charge equals 0) are called
zwitterions. Substances having this dual (acid-base)
nature are amphoteric and are often called
ampholytes.
Amino Acids: Ionization
A zwitterion can act as either an acid (proton
donor) or a base (proton acceptor).
Ionization Behavior of Peptides
The -amino and -carboxyl
groups of amino acid residues that
are joined together in peptide
bonds do not undergo ionization
reactions near physiological pH.
The free -amino group at the N-
terminus of the peptide, and the
free -carboxyl group at the C-
terminus ionize as they do in
isolated amino acids. Likewise the
R groups that contain ionizable
functional groups continue to
ionize as in free amino acids.
These properties are exploited in
some of the separation techniques
discussed later in the chapter.
Amino Acids and Proteins
[Sizes and Molecular weight]
Average molecular weight of an amino acid is about

110 Da. A Dalton (Da) is defined as 1/12th the mass of
a carbon atom.
Some proteins consist of a single polypeptide chain,
whereas others called multisubunit proteins have two
or more associated polypeptides.
The individual polypeptide chains in a multisubunit
protein can be identical or different.
The amino acid

compositions of
proteins differ between
proteins and are highly
variable. Some amino
acids occur only once or
not at all in a given
protein and other
amino acids may occur
in large numbers.
The lengths of polypeptide chains in proteins vary
considerably. The largest known protein is titin
(26,926 amino acids), which is a component of
vertebrate muscle.
Conjugated Proteins
Some proteins contain other associated chemical
components in addition to amino acids. The non-
amino acid part of a conjugated protein is called its
prosthetic group.
Protein Structure
Peptide bond properties
Peptide bond properties
In a polypeptide chain, three dihedral angles are defined as φ (phi), ψ

(psi) and ω (omega).
Non-covalent interactions in protein structure
https://en.wikipedia.org/wiki/Protein_tertiary_structure
Secondary structure: α-Helix
- α-helix; a common motif in the secondary structure of proteins

- right hand-helix conformation (backbone N−H group hydrogen bonds to the backbone C=O
group of the amino acid located three or four residues earlier along the protein sequence)
Secondary structure: β-strand
Organization of protein structure
Structure dictates function

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LIFE 101A

All amino acids contain an a carbon

These groups are the α-amino

Amino acids are

Average molecular weight of an amino acid is about

The amino acid

In a polypeptide chain, three dihedral angles are defined as φ (phi), ψ

- α-helix; a common motif in the secondary structure of proteins

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