CLASS: Fundamentals 1
DATE: August 8, 2011
PROFESSOR: Dr. DeLucas
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Amino Acids
Scribe: Pearl Shin
Proof: Vinh Duong
Page 1 of 3
AMINO ACIDS USED IN LIVING ORGANISMS [S1]
a. There are 20 unique amino acids that are used to form proteins.
AMINO ACIDS: BUILDING BLOCKS OF PROTEIN [S2]
a. What is so important about amino acids is that they have a tetrahedral nature to them.
i. This allows branching of amino acids in different direction when you join two or more together, or
polymerize, that can make long polypeptides, or proteins, that have a variety of structures.
ii. Structure determines function in biology and biochemistry.
b. A typical amino acid has an α-carbon that connects to:
i. A hydrogen atom
ii. An amino group
iii. A carboxyl moiety
iv. Another moiety, called the “R” side chain, which distinguishes one amino acid from another because, with
the exception of proline, all amino acids have similar structures.
AMINO ACIDS CAN JOIN VIA PEPTIDE BONDS [S3]
a. Dipeptide is two amino acids joined together.
b. Tripeptide is three joined
c. Polypeptides are multiple amino acids joined together.
d. Proteins are unbranched polymers of amino acids.
i. The amino acids join the nitrogen to the carbon in a head-to-tail formation.
ii. The peptide bond releases water when formed, a reaction called hydrolysis.
1. This reaction needs energy because the spontaneous and favorable reaction goes in the other
direction to split the two amino acids.
iii. The peptide backbone consists of a repeat of N, α-carbon, and carbonyl C.
WHAT IS THE FUNDAMENTAL STRUCTURAL PATTERN IN PROTEINS? [S4]
a. When forming a peptide bond, the carboxyl group of one amino acid and the amino group of another amino
acid join together in an amide bond.
i. Although this amide bond is usually depicted as the carbon having a double bond with the oxygen (C=O),
there is actually a sharing of that electron with the nitrogen to give the C-N bond a partial double bond
character.
1. The partial positive charge on the N is what pulls electrons and helps share them.
2. This ends up in a partial negative charge on the O.
ii. If there wasn’t a partial double bond between the C-N, the moiety bound to the nitrogen would have 360°
freedom of rotation, provided that the R group doesn’t get large enough to bump into something else.
iii. The partial double bond character constrains the rotation of the N-R bond.
1. As a result, there is a plane of the six atoms in the amide group that does not exhibit rotation.
2. When a peptide bond is configured how it should be with the shared electrons, the rotation occurs at
the corners where the α-carbon would connect to the next nitrogen or carbon.
iv. Usually, the peptide bond will adopt a trans conformation to reduce steric interference as opposed to a sis
conformation.
THE PEPTIDE BOND [S6]
a. Hydrogen bond length for a C-O bond is usually 0.120nm, which is close to the carbonyl in a peptide bond
(C=O) with 0.123nm.
b. A C-N bond is usually has a hydrogen bond length of 0.145nm, but because there is a partial double bond in
a peptide bond that imparts some of the electrons, it shortens the length to 0.133nm.
20 AMINO ACIDS IN PROTEINS [S11-S17]
a. How do you distinguish the 20 different amino acids?
i. Nonpolar amino acids
1. Example: Lucine- Doesn’t have a charged group on it or a polar moiety. As a result, it has several
carbons attached to the R group that are pretty insoluble in aqueous solution.
2. Most nonpolar/hydrophobic amino acids aren’t very soluble.
a. Nonpolar amino acids in proteins are usually found buried deep within the protein.
ii. Polar amino acids without a charge
1. These amino acids have groups on them that can hydrogen bond, so they interact with each other
mechanistically.
2. These are usually not very deep within a protein and available to the aqueous medium.
3. There is one moiety on tryptophan, a nonpolar amino acid, that can hydrogen bond, but it is a pretty
weak acid at a high pKa.
CLASS: Fundamentals 1
Scribe: Pearl Shin
DATE: August 8, 2011
Proof: Vinh Duong
PROFESSOR: Dr. DeLucas
Amino Acids
Page 2 of 3
4. Histidine is very important in how many proteins function because its pK a is close to neutrality so it
can release or grab hydrogen much more easily than any other amino acid.
a. You will see Histidine involved in reactions like Schiff base reactions.
iii. Polar amino acids with a negative charge
1. Negatively charged, acidic amino acids include Aspartate and Glutamic acid.
2. At neutral pH, they lose the hydrogen ion, and as a result, they have a negative charge.
a. These amino acids’ R groups frequently bind to positively charged ions.
3. These acidic amino acids are involved in critical biological functions of a protein.
4. Are seen on the surface of proteins or on an active site of an enzyme either through their charge or
through hydrogen bonding with a substrate.
iv. Polar amino acids with a positive charge
1. Same is true for basic acids as it is for acidic acids such as Lysine, Arginine, and Histidine.
VII.
AMINO ACID R GROUPS [S18]
a. The principle mechanism of nonpolar amino acids is protein folding.
i. Hydrophobic interactions dominate in determining protein folding.
b. Polar, charged and uncharged, groups can be in charge of folding patterns, like nonpolar amino acids,
especially with fibrous proteins. Promotes specific interactions due to the types of substituents on them.
VIII.
SEVERAL AMINO ACIDS OCCUR IN PROTEINS AS A RESULT OF POSTTRANSLATIONAL
MODIFICATIONS [S19]
a. Unusual amino acids, such as Hydroxylysine, Hydroxyproline, GABA, Histamine, and Serotonin are important
biologically and clinically.
i. Hydroxylysine is important for structural reasons in collagen, which is a triple-helical structure.
1. Involved in intramolecular interactions via hydrogen bonding, intercollagen strands interacting with
each other and interacting with surrounding carbohydrate that are a part of various tissue matrices.
ii. Hydroxyproline is also important for structural reasons in collagen.
1. Intracollagen interactions
2. Marfan’s Syndrome: Pete Marovich- basketball player with Marfan’s.
a. Very skinny, flexible and lanky.
b. Dominant trait, genetic disorder- a protein that is important in terms of structural areas in
connective tissues called fibrillin.
i. When this protein is mutated, there’s a secondary mutation that leads to an excess of
growth factor TGF-β, which causes a weakening of tissue-muscle tissue, tissue around
your aorta, vessel tissue, tendons, etc.
c. Dentistry: clinically 20% of patients have narrow jaws and high arch palate.
d. Optometry: 80% of patients have “subluxated” lens, which makes eye artificially near or
farsighted.
e. 200,000 people have this.
iii. GABA (Gamma-Aminobutyric Acid)
1. Are not in proteins, unlike other amino acids.
2. The inhibitory neurotransmitter in central nervous system. Responsible for muscle tone. If a patient
has damage in neural cortex, can have hypertonic muscle tone.
iv. Histamine
1. Everyone has histamines.
2. Released if you are allergic to something.
3. If release too much due to severe allergy, can go into anaphylactic shock.
a. Remedy is epinephrine, which causes the overproduction of histamine to be extruded.
b. Benadryl doesn’t work because it blocks the histamine receptor but only a part of it.
4. There are some people that naturally release too much histamine, and the body responds by
releasing as much adrenaline.
a. So this type of person will be really energetic in the day and lethargic by night.
b. This is treated by diet- eat foods with high or low content of Histadine, which is what
Histamine comes from.
b. Dr. DeLucas said he wouldn’t test us on the unusual amino acids, but it was on the slide of test
objectives.
IX.
ACID-BASE PROPERTIES OF AMINO ACIDS [S32]
a. Acid/base character of amino acids:
i. Depending on R groups, can have a transition where all amino acids have a negative charge at neutral pH,
and as you go up higher and higher in pH, you find a point where charges are neutral, which is called
isoelectric point or zwittionic situation.
CLASS: Fundamentals 1
Scribe: Pearl Shin
DATE: August 8, 2011
Proof: Vinh Duong
PROFESSOR: Dr. DeLucas
Amino Acids
Page 3 of 3
1. This is the point where proteins are least soluble.
b. All amino acids are weak polyprotic acids.
i. They aren’t strong strong acids, but they have more than one moiety that can be protonated depending on
environmental pH.
ii. Take all pKas for amino acids with a grain of salt because they are not going to be that way in the protein
due to interaction.
iii. Each amino acid has at least two chemical groups capable of acting as an acid or base but at different pHs,
will be either protonated or not.
1. Can change pH up to a full pH unit depending on what the interactions are.
X.
PKA VALUES OF THE AMINO ACIDS [S33]
a. If you look at the α-carboxyl group, the H group on the -OH moiety, it has pKa of 2.
i. A carboxyl group on an aliphatic chain has a higher pKa.
ii. This increase in acidity is due to the N pulling some of the negative charge, which makes the protein easier
to strip off.
iii. The pKa also changes for the α-amino group.
XI.
PKA VALUES OF THE AMINO ACIDS CON’T [S34]
a. There is a equilibrium between cationic, zwittionic, and anionic forms of amino acids.
i. The moieties will change depending on the pH.
XII.
PKA VALUES OF THE AMINO ACID R GROUPS [S35]
a. Arginine has a guanidino group which raises pKa to 12, so you have to get pretty high in pH to affect it.
b. Aspartic Acid is not as acidic as the carboxyl H group, but is still pretty acidic.
i. Glutamic acid is similar.
c. Cysteine at physiological pH won’t be deprotonated very much, but in a protein, the pK a can lower to around
7.5 and play a more prominent role.
i. Histidine is similar.
XIII.
REACTIONS OF AMINO ACIDS [S41]
a. Amino acids form Schiff bases which play a very important role in biology, and side chains have unique
reactions.
XIV.
SPECTROSCOPIC PROPERTIES [S44]
a. Aromatic amino acids absorb UV light at a maximum around 280 nm.
i. Can use this to detect proteins, so when purifying proteins or when looking specifically the aromatic amino
acids, it’s an easy way to not only see that they are there but to see how many are there as well.
b. Proteins can also be detected as a result of absorbance at the peptide, double bond area, which is close to
190-200 nm.
i. It’s more sensitive than the other, but because most proteins have these amino acids, this is where we
usually monitor proteins.
c. Purifying amino acids:
i. Can purify amino acids similarly to how one can purify proteins.
ii. Ion Exchange Chromatography:
1. All amino acids have different charges at different pHs, so they will stick to different affinity mediums.
Separate based on charge affinity.
iii. Reverse Phase Chromatography:
1. This method uses a medium that is hydrophobic. Each amino acid has some sort of hydrophobic
character, and if you have noncharged, nonpolar amino acids, they will bind/interact much more
tightly than those that are charged and polar.
d. To separate the different amino acids within a chromatography column, you must change a variable such as
changing the pH or hydrophobicity
XV.
THE SEQUENCE OF AMINO ACIDS IN A PROTEIN [S51]
a. The sequence of amino acids is critical because it shows how a protein will fold.
i. Every protein has unique biological characteristics, and it is all based on its sequence of amino acids.
1. Tryptophan is odd where it sits on proteins.
a. It can hydrogen bond and interact with water.
b. You can find Tryptophan and even Tyrosine, which is somewhat hydrophobic, close to the
membrane interacting with both the membrane and the aqueous environment.
c. Due to its unique role, Tryptophan is not as common as other amino acids.
[End 48:19 mins]