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
http://www.johnkyrk.com/aminoacid.html
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):
non-polar and neutral,
2. polar and neutral,
3. acidic and polar,
4. basic and polar.
1.
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
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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
functional group (not amidethese are not polar enough to
ionize).
Acidic R groups contain a
carboxylic acid functional group
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 pH),
amino acid zwitterions
accept protons on their
basic –COO- groups to
leave only the positively
charged –NH3+ groups.
As the pH increases, the
carboxyl group will lose
the proton, and both
groups will be charged
At high pH – basic
conditions, both groups
become deprotonate
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:
• Having right- or lefthandedness
• non superimposable
mirror images
• Achiral:
• superimposable mirror
images and thus no
right- or left
handedness
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 threedimensional 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)
–
–
3.
Interactions between acidic R group and basic R group on different
subunits
generally buried in the interior of a protein
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.