Amino Acids and Proteins
Protein Structure and Function:
An Overview
What We Will be Learning
1. Amino acid and Protein Structure and Function:
2. Types of Amino Acids and properties
3. Acid Base Properties of Amino Acids, zwitterions
& isoelectric points
4. Molecular Handedness and Amino Acids,
identifying enatiomers
5. Peptide bonding
6. Mechanism and properties for higher levels of
protein organization
Amino Acid Structure
Amino acid refers to the presence of two
specific functional groups:
An amine
group
A carboxylic acid
Dipeptide bond
When the carbonyl carbon atom
loses an oxygen atom, and the
second amino acid contributes
two hydrogen atoms, a dipeptide
bond forms joining the two amino
acids.
Polypeptide Chains
A chain of amino acids that contains more than about
5 amino acids is called a polypeptide.
Ser-Leu-Thr-Ser-Val.
Variations of Amino Acids
• This central carbon is bound to 4 distinct groups
• While each amino acid has an amine group and a
carboxylic acid, there is variation in the side chain
Glycine
variation in the side chain
The R Group
There are four different classes of amino
acids determined by different side chains
(R group):
1. non-polar and neutral,
2. polar and neutral,
3. acidic and polar,
4. basic and polar.
Non Polar Amino Acids
Aliphatic side chains of hydrocarbon give non polar amino acids
Even though the Sulfur is electronegative, the length of the chain
makes methionine non polar and hydrophobic
Identifying Side Chains
http://www.johnkyrk.com/aminoacid.html
Non polar Amino Acids with Aromatic Rings
Tyrosine
Phenylalanine
Tryptophane
Polar Amino Acid
R groups that give polar amino acids:
– Amides
– Hydroxyl
– Sulfur in a short chain
Amino Acids with Charged Side chains
• Basic R groups contain an amino Acidic R groups contain a
functional group (not amide- these carboxylic acid functional group
are not polar enough to ionize).
Acid Base Properties of Amino Acids
• The carboxyl group of an
amino acid can lose a
hydrogen ion
– R-COOH <——> R-COO– + H+
• The amine group can accept a
hydrogen ion
• R-NH3+ <——> R-NH2 + H+
Neutral dipolar ions are known as zwitterions.
Amino acids share
many of the
properties we
expect from salts:
– can form crystals
– have high melting points
– are soluble in water
– not soluble in hydrocarbon solvents
Ionization state of the Zwitterions depends on pH
At neutral pH, amino acids in solution exist as dipolar ions
The amino group is protonated -NH3+
carboxyl group is deprotonated (-COO-)
In acidic solution (low As the pH increases,
pH), amino acid At high pH – basic
the carboxyl group
zwitterions accept conditions, both
will lose the proton,
protons on their basic groups become
and both groups
–COO- groups to leave deprotonate
will be charged
only the positively
charged –NH3+ groups.
Isoelectric point
The pH at which the net positive
and negative charges are evenly
balanced
Each amino acid has at least two pKa values (the pH at which the weak acid and its
conjugate base are present in equal amounts), one for the alpha carboxyl group and
one for the alpha amino group
PKa– 9.7
Pka = 2.4
Handedness
Chiral: • Achiral:
• Having right- or left- • superimposable mirror
handedness images and thus no
• non superimposable right- or left handedness
mirror images
Handiness in Molecules
• Like the mirror image
of the hand – these
molecules can not be
superimposed – they
have “handiness”
• If a molecule has an
atom bonded to four
different groups, it is
chiral
Alanine is Chiral
• The mirror-image forms of a chiral molecule like
alanine are called enantiomers or optical isomers.
R & S Nomenclature
• Identify the group
with the lowest
priority (low atomic
number as #4 –
highest priority as
#1
• Draw an arrow
from low number
to high number
If the arrow traces a clockwise movement, the
enantiomer is the R enantiomer.
If it is counterclockwise, it is the S enantiomer.
Archiral – lacking in handiness
• Propane is an
achiral molecule.
The molecule and
its mirror image
are identical and it
has no left- and
right-handed
isomers
Amino Acids are Chiral
Only glycine is achiral
• The naturally occurring amino acids are classified
as left-handed or L-amino acids
• In nature, only one enantiomer of most chiral
biological compounds, such as amino acids is
present.
• As a result, different enantiomers of a compound
may have substantially different biological effects.
Enantiomers
• Enantiomers of a compounds have the same
formula and atomic connections but different
spatial arrangements.
• The same physical properties except they
always differ in their effect on polarized light
• They differ in how they react with other chiral
molecules.
• Pairs of enantiomers often differ in their
biological activity, odors, tastes, or activity as
drugs.
Amino Acids are Chiral
Spearmint leaves and
caraway seeds have very
different flavors - imparted
by a pair of enantiomers
Pairs of Enantiomers often differ in their biological
activity, odors, tastes, or activity as drugs.
Levels of Protein Structure
Primary protein structure: The sequence in which amino
acids are linked by peptide bonds in a protein.
Convention in Writing Peptide Chains
1.Peptides are always written with the N-
terminal on the left, and the carboxyl
terminal on the right
2. Individual amino acids joined in the chain
are referred to as residues
Proteins have four levels of structure
1. Primary structure is the sequence of amino acids in a
protein chain
2. Secondary structure is the regular and repeating
spatial organization of neighboring segments of single
protein chains
3. Tertiary structure is the overall shape of a protein
molecule produced by regions of secondary structure
combined with the overall bending and folding of the
protein chain.
4. Quaternary structure refers to the overall structure of
proteins composed of more than one polypeptide
chain
Intermolecular forces determine the shapes
and functions of proteins
• The non-polar hydrophobic
side chains are pushed and
pulled into clusters within a
large protein molecule
• Hydrophilic groups on the
surface of folded proteins
impart water solubility to
the proteins.
Myoglobin has hydrophobic amino acid R groups packed into the interior , while
those on the surface are hydrophilic – making the molecule water soluble
Link
Intermolecular Forces In Proteins
Secondary Protein Structure
• The secondary structure includes two kinds of
repeating patterns known as the a-helix and the
b-sheet.
• In both, hydrogen bonding between backbone
atoms holds the polypeptide chain in place.
Alpha-helix Secondary Structure
The stabilizing hydrogen
bonds of the alpha helix
point to the C-terminus and
are nearly parallel to the
long axis of the spiral of the
helix.
Beta-sheet secondary structure.
The protein chains
usually lie side by
side.
the R groups point
above and below
the sheets
Tertiary Protein Structure
• The three-dimensional shape that results from
the folding of a protein chain is the protein’s
tertiary structure.
• Depends on interactions of amino acid side
chains that are far apart along the same
backbone.
Quaternary Protein Structure
• The way in which two or
more polypeptide
subunits associate to
form a single three-
dimensional protein
unit.
Protein Structure in Review
Quaternary structure
This is found in proteins that have multiple polypeptide subunits.
1. Noncovalent interactions:
– hydrophobic interactions :
interactions between nonpolar R groups on different subunits
– hydrophilic interactions (electrostatic)
interactions between polar R groups on different subunits
2. salt bridges (electrostatic)
– Interactions between acidic R group and basic R group on different
subunits
– generally buried in the interior of a protein
3. Covalent interactions:
– disulfide bridges between two cysteine residues that have been oxidized
• (form after protein has folded to further stabilize structure)
What is it all For?
Goals Recaped
1. Recognize an amino acid and describe the
basic structure
2. illustrate how amino acids link together to
form peptide chains and proteins.
3. Use the structure and size of side chains to
predict polarity and charge in acid and basic
conditions
4. Understand amino acids as zwiterions and
the concept of isoelectric point.
5. Be able to identify chiral molecules and chiral
carbon atoms
6. Be able to identify enatiomers
7. Draw and name a simple protein structure
from the amino acid sequence
8. The importance and meaning of disulfide
bonds, hydrogen bonds, and non covalent
interactions in determining secondary,
tertiary and higher levels of protein structure
9. Be able to describe protein hydrolysis and
denaturation, and give some examples of
agents that cause denaturation.
