Download Lecture #13 – Introduction to Amino Acids and Proteins

An Introduction
to the Study of Biomolecules
Factors to Consider in the Study of Biomolecules
What are the features of the basic building blocks ?
(ex: monosaccharides, alcohols, fatty acids, amino acids)
1) General structure and functional groups
2) Polar and non-polar portions
3) Hydrogen bonding capabilities
4) Acid-Base properties
5) Optical activity
6) Other chemical properties
Factors to Consider in the Study of Biomolecules
Do the small building blocks function by themselves ?
Are the building blocks put together into larger structures ?
What are the physical properties of these larger structures ?
How are the various types of biomolecules suited for their
individual functions ?
Introduction to the Study of Proteins
Proteins - the most plentiful organic compounds in the body,
making up more than half its dry weight
Proteins can be categorized by function.
Catalytic proteins, or enzymes:
Catalyze the synthesis and utilization of
proteins, carbohydrates, lipids, nucleic
acids, and almost all other biomolecules.
Transport proteins:
Bind and carry specific molecules from
place to place.
Regulatory proteins:
Structural proteins:
Control cellular activity.
Give physical shape, and the strength to
maintain it, to structures in animals.
Contractile proteins:
Protective proteins:
Provide cells and organisms with the
ability to change shape and move.
Storage proteins:
Defend against invaders and prevent or
minimize damage after injury.
Provide a reservoir of nitrogen and other
nutrients, especially when external sources
are low or absent.
Proteins are Made of α-Amino Acids
Hydrolysis
Proteins ---------------------------->
Amino Acids
Mammals require all 20 amino acids for protein synthesis but can synthesize
only 10 of them.
There are 10 essential amino acids that must be obtained from the diet.
Phenylalanine, Valine, Tryptophan, Threonine, Isoleucine, Methionine,
Histidine, Arginine, Lysine, Leucine
Peptides
Peptide Bond Formation
How are amino acids joined together ?
H3C
CH
O
H2N
H
H
C
CH
CH3
CH
N
O
Alanine
H
C
H
CH3
O
The two amino acids
are joined
through a
dehydration reaction.
O
Valine
O
H2N
H3C
CH3
CH
C
CH
O
CH
N
C
CH3
H
O
H
Alanylvaline (Ala-Val)
peptide bond
Peptide Bond Formation
Peptides
Amino Acids
An α-amino acid
Twenty Standard Amino Acids
The amino acids are
categorized chemically
by the behavior of their
R-groups:
Neutral side chains
Aliphatic
Polar
Aromatic
Basic - Positively charged
Acidic - Negatively charged
The amino acids are categorized
chemically by the behavior of their
R-groups.
Non-polar, Neutral Side Chains
Polar, Neutral Side Chains
Basic Side Chains
Acidic Side Chains
Amino Acids with Nonpolar, Uncharged Side Chains
Amino Acids with Polar, Uncharged Side Chains
Amino Acids with Polar, Charged Side Chains
Charges on Amino Acids
α-Amino Acids May Exist in a Zwitterionic Form
The actual structure of a neutral amino acid in neutral solution and in the
solid is a charged molecule, containing a -COO- group and an –NH3+ group,
called a zwitterion. The net charge on the molecule is zero.
The presence of the
charged groups in the
zwitterion result in very
strong secondary forces
between the positive and
negative charges:
MP = 314°C
MP = 53°C
Amino Acids in Solution
1) Amino acids are also soluble in water due to the
strong secondary forces between the zwitterionic charge
centers of the amino acids and the dipolar water
molecules.
2) Free amino acids exist exclusively in the zwitterionic
form in the solid state.
3) In solution, amino acids assume a charged form
based on the pH of the solution.
Amino Acids in Solution
How do carboxylic acids and amines behave in acidic,
neutral, and basic solutions ?
O
R
C
O
OH
R
pH =1
R
NH3
C
O
O
pH = 7
R
NH3
R
C
O
pH = 12
R
NH2
The behavior of the carboxylic acid and amine functional groups
DOES NOT CHANGE when they are in the same molecule.
Amino Acids in Solution
CH3CH
How does the amino acid alanine behave
in acidic, basic, and neutral solutions ?
O
CH3 CH
NH3
pH =1
C
O
NH2
O
OH
CH3 CH
NH3
pH = 7
C
C
O
O
CH3CH
C
O
NH2
pH = 12
At low pH, the functional groups have accepted all of the
protons possible, and at high pH, the functional groups have
donated all of the protons possible.
OH
Amino Acids in Solution
1) Each amino acid has a pH at which almost all of the molecules are
present in a neutral form (0 net charge), called the isoelectric point.
2) At a pH below that of the isoelectric point, the cation
concentration increases (net positive charge).
3) At a pH above that of the isoelectric point, the anion
concentration increases (net negative charge).
4) Most neutral amino acids have isoelectric points in the
range 5 - 6.
5) “Neutral” amino acids include 15 of the 20 common amino
acids.
Amino Acids in Solution
Compounds with the ability to both release protons (acids)
and absorb protons (bases) are called
amphoteric compounds*.
Amino acids are least soluble in their zwitterionic form,
although even this form is fairly soluble.
*Is there a common chemical application
for such compounds??
O
Amino Acids in Solution
H
How does the amino acid aspartic acid behave ?
C
OH
C
NH2
CH2
C OH
O
O
H
O
C
OH
C
NH3
H
O
O
C
O
C
NH3
H
C
O
C
NH3
H
C
O
C
NH2
CH2
CH2
CH2
CH2
C OH
C OH
C O
C O
O
O
O
O
pH =1
pH = 3
pH = 7
pH 12
Amino Acids with Polar, Charged Side Chains
O
Amino Acids in Solution
H
How does the amino acid lysine acid behave ?
C
OH
C
NH2
CH2
CH2
CH2
CH2
O
H
O
C
OH
C
NH3
H
O
C
O
C
NH3
H
NH2
O
C
O
C
NH2
H
C
O
C
NH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
NH3
NH3
CH2
CH2
NH3
NH2
pH =1
pH = 7
pH = 10
pH 12
Amino Acids with Polar, Charged Side Chains
Electrophoresis of Amino Acids
Electrophoresis can be used to analyze mixtures of α-amino acids.
In this procedure, a strong electric field causes anions (acidic amino acids)
to move towards the anode (positive electrode) and cations (basic amino
acids) to move towards the cathode (negative electrode).
Amino acids whose isoelectric pH is close to the pH of the solution remain
stationary in the electric field.
A form of electrophoresis called
paper electrophoresis is often
used for this analysis:
Electrophoresis of Amino Acids
Stereochemistry - Review of Isomerism
Isomers
Structural Isomers
Stereoisomers
Stereochemistry - Review of Isomerism
Isomers
Structural Isomers
Cis-trans Isomers
Stereoisomers
Isomers with
chiral centers
Stereochemistry - “Handedness” in Everyday Objects
We can imagine the mirror image of an object.
In some cases, the mirror image and
the original object are identical.
In some cases, the mirror image and
the original object are not identical.
Stereochemistry - “Handedness” in Everyday Objects
Stereochemistry - “Handedness” in Organic Compounds
Enantiomers - compounds that have the following characteristics:
1) Molecules of two compounds are mirror images of each other.
2) Molecules of two compounds are nonsuperimposable.
The characteristics of
enantiomers are often the
result of a single
“chiral” carbon atom.
Stereochemistry
All tetrahedral carbons are not chiral.
Stereochemistry - A Chiral Tetrahedral Carbon
1, 2, 3, and 4 must be different groups.
What are “different” groups?
Stereochemistry - Examples of Enantiomers
bromochlorofluoromethane
Stereochemistry - Examples of Enantiomers
2-bromobutane
Stereochemistry - Examples of Enantiomers
L-carvone
D-carvone
Stereochemistry - Examples of Enantiomers
Stereochemistry - Chirality in Amino Acids
O
OH
O
C
H2N
C
H
R
OH
H
NH2
R
What would be the
consequences of this
chirality of amino acids if a
long chain of amino acids
were joined in a polymer ??