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Proteins are about 50% of the dry weight of most cells, and are the most structurally complex
molecules known. Each type of protein has its own unique structure and function.
Polymers are any kind of large molecules made of repeating identical or similar subunits called
monomers. The starch and cellulose we previously discussed are polymers of glucose, which in that
case, is the monomer. Proteins are polymers of about 20 amino acids monomers.
The amino acids all have both a single and triple letter abbreviation. Here is an example.
Alanine = A = Ala
Each amino acid contains an "amine" group, (NH 2) and a "carboxylic acid" group (COOH)
(shown in black in the diagram).
The amino acids vary in their side chains (indicated in blue in the diagram).
The eight amino acids in the orange area are nonpolar and hydrophobic.
The other amino acids are polar and hydrophilic ("water loving").
The two amino acids in the magenta box are acidic ("carboxylic" group in the side chain).
The three amino acids in the light blue box are basic ("amine" group in the side chain).
H O
NH2
C C OH
CH3
H O
NH2
CH
H3C CH3
alanine
ala A
C C OH
NH2
C C OH
NH2
C C OH
CH2
CH2
leucine
leu L
NH2
H O
NH2
tryptophan
trp W
C C OH
H O
NH2
C C OH
CH OH
CH2
CH3
SH
OH
tyrosine
tyr Y
threonine
thr T
H O
NH2
C C OH
C C OH
CH2
O C
OH
aspartic acid
asp D
cysteine
cys C
C C OH
H O
NH2
CH2
O C
OH
glutamic acid
glu E
OH
glycine*
gly G
H O
C C OH
O C
NH2
NH2
C C OH
CH2
CH2
CH2
NH2
histidine
his H
H O
NH2
lysine
lys K
C C OH
CH2
CH2
O C
NH2
asparagine
asn N
CH2
NH
serine
ser S
CH2
CH2
NH2 C C OH
CH2
C C OH
CH2
H O
C C OH
H O
H O
NH2
H O
NH2
C C OH
proline
pro P
*
NH2
methionine
met M
H O
NH
isoleucine
ile I
CH2
CH3
CH2
CH3
C C OH
NH
H O
CH2 CH2
CH2
CH2
H O
NH2
C C OH
CH CH3
CH
H3C CH3
CH2
phenylalanine
phe F
NH2
CH2
valine
val V
H O
H O
NH2
C C OH
H O
H O
glutamine
gln Q
H O
NH2
C C OH
CH2
CH2
CH2
NH
NH C
NH2
arginine
arg R
Amino acids are named as such because each amino acid consists of an amine portion and a
carboxylic acid part, as seen below.
H O
NH2
C C OH
R
Compare this structure to the above structures of each of the amino acids. Each amino acid has this
general structure.
The side chains are sometime shown as R-groups when illustrating the backbone.
In the approximately 20 amino acids found in our bodies, what varies is the side chain. Some side
chains are hydrophilic while others are hydrophobic. Since these side chains stick out from the
backbone of the molecule, they help determine the properties of the protein made from them.
The amino acids in our bodies are referred to as alpha amino acids. The reason is that the central
carbon is in an alpha position in relation to the carbonyl carbon. The carbon adjacent to the carbonyl
carbon is designated the alpha carbon. Each carbon in the chain will be designated with a different
letter of the Greek alphabet. See the example below.
carbonyl carbon
beta
delta
epsilon
gamma
alpha
H O
+
NH3
C C O
R
zwitter ion
You may have noticed that the general form for the amino acid is often drawn with the acidic
hydrogen attached to the amine group. This occurs because amine groups are basic. So, the amino
acid has performed an acid-base reaction on itself. When the amino acid is in this form it is referred
to as a Zwitter ion. When amino acids are in solution this is the form that they will be found.
Chirality:
A chiral compound must contain a carbon that is bonded to four different atoms/groups. If you look at
the above amino acids you will see that, with the exception of glycine, each structure is chiral around
the carbon with the R group. Each amino acid will come in two structural formats, called
enantiomers, an L and a D. You were given two tables of all the amino acids, the tables are only
different in the format that the amino acids are drawn. The first format is the one used to show the
chirality of the amino acid. To determine which enantiomer you have you look to the location of the
hydrogen on the chiral carbon. If the hydrogen is on the left, then the amine group is on the right, this
is the D enantiomer. If the hydrogen is on the right, then the amine group is on the left, this is the L
enantiomer. See the below structural diagrams:
COOH
COOH
COOH
COOH
NH2 C H
H C NH2
NH2
C H
H C NH2
CH2
CH2
CH3
CH3
OH
OH
D-alanine
L-serine
L-alanine
D-serine
The importance of chiral compounds is that their chemical reactivity is different. Sometimes the
difference means the compound will have an adverse effect on a person. Sometimes the difference
means the person simple can not metabolize the compound. The latter is the case with amino acids.
Meaning we can consume both L and D amino acids, but our bodies will only metabolize the D form.
The enzymes used in the metabolism of amino acids are built to fit this D form but not the L form.
The L form will pass through your body unused.
Buffering:
-amino acids contain both acidic -COOH and the basic NH 2 groups, these two functional groups
allow them to act as a buffer. Unfortunately, though, the picture is not as simple as this. In the
solid crystalline state the a-amino acids exist as Zwitter ions, as discussed before they are formed
by the transfer of protons, H+ from the -COOH to the NH2 groups. For -amino acids without
acidic or basic side chains these zwitter ions have charged groups but are neutral overall. Amino
acids are found in the Zwitter form even as solids, they form an ionic matix similar to salts.
H O
+
NH3
C C O
R
Zwitter ions remain when the -amino acid is dissolved in water at pH 7. Addition of an acid,
supplying more protons, produces ions with an overall positive charge. The amino acid forms the
below structure in an acid environment.
H O
H O
+
NH3
C C O
H+
NH3
C C OH
R
R
Addition of a base, removes the acidic hydrogens, producing ions with an overall negative charge.
The amino acid forms the below structure in a basic environment.
H O
H O
+
NH3
C C O
OH
NH2
C C O
H2O
R
R
We can describe -amino acids as amphoteric as they can react with both acid and alkali. They
are effective buffers in biological systems. The situation is more complicated in a-amino acids that
have acidic or basic R groups , e.g. glu or lys.
At very low pH all -amino acids exist as ions with an overall positive charge, while at high pH
they exist as ions with an overall negative charge. For each -amino acid there is a pH between
these extremes at which its molecules are neutral overall. This value is called the isoelectric
point for the -amino acid. At its isoelectric point the -amino acid molecules will not move when
placed in an electric field. The separation technique called electrophoresis relies on molecules
with different isoelectric points moving at different speeds when kept at a fixed pH and placed in
an electric field.
The isoelectric point is calculated by averaging the pKa values for the carboxylic acid and the
amine group. pK1 applies to the carboxylic acid and pK2 applies to the amine.
pK 1 pK 2
pI
2
This formula does not take into account acidic or basic side chains. If an acidic side chain is
present you average the side chain pKa and pK1. For a basic side chain you average the side
chain pKa and pK2.
Protein Functions:
Type of Protein
Structure
Function
structural support
Contractile
Transportation
Storage
muscle movement
movement of compounds
nutrient storage
Hormone
Enzyme
chemical communication
Catalyze biological reactions
Protection
Examples
collagen in tendons and cartilage
keratin in hair and nails
actin, myosin, tubulin and kinesin proteins
hemoglobin carries O2 and lipoproteins carry lipids
ferritin stores iron is spleen and liver
casein stores proteins in milk
insulin regulates blood sugar
lactase breaks down lactose
trypsin breaks down proteins
immunoglobulins stimulate immune system
A longer polypeptide is shown above. Each peptide chain will have an amine end and a carboxylic
acid end and each amino acid is referred to as a residue. So, the ends are named, n-terminal residue
and c-terminal residue or the n-terminus and c-terminus.
The sequence of amino acids will cause the protein to have areas of its shape conforming to one of 3
shapes, alpha-helical, beta-pleated sheet or woven (sometimes called turns). These are secondary
structures.
The two most common secondary structures are shown above, alpha helical and beta sheet.
These structures are created by molecular interactions between amino acids. Normally the
interactions are hydrogen bonds. Other interactions will form as well.
Hydrogen bonds, in the most simple explanation, from between hydrogens attached to an oxygen
or nitrogen and the lone pairs found on an oxygen or nitrogen.
Disulfide bridges form between cysteine and methionine amino acids.
Salt bridges are interactions between the ends of the Zwitter ion, the NH 3+ and the COO-.
Hydrophobic interactions are formed between those amino acids with hydrophobic R groups.
The above picture shows an entire protein, this is called its tertiary structure. The tertiary
structure gives the protein its function. If the tertiary structure is deformed the protein will not
function. The primary structure is sequenced in a way as to form the tertiary structure. The side
chains of the amino acids cause them to interact with the other parts of the chain. These interactions
include hydrogen bonding, hydrophobic interactions, electrostatic interactions and van der Waals
forces. An egg white is all protein, when it comes out of the shell it is clear, when you cook the egg
you destroy its Tertiary Structure and the protein unfolds and becomes white, this destroys the
proteins secondary, tertiary and quaternary structures. The primary structure will normally stay intact
if the food is cooked..
Some proteins have a quaternary structure. The quaternary structure occurs in proteins composed of
more than one peptide chain. Meaning two or more proteins come together to form one large protein.
We have mentioned hemoglobin a couple of time. This large protein has a quaternary structure as it
is composed of four myoglobin subunits. Each subunit is a separate polypeptide chain.
This picture is showing each of the four structure types and the order of their formation. First the
primary structure is formed, as this structure forms secondary structures take shape. Once the
protein sequence is completed the protein folds into its tertiary structure. If the protein has a
quantanary structure, two or more proteins will come together to complete the quantanary structure.
Destroying a Protein:
When a protein is destroyed it is said to be denatured. Remember that the purpose of a primary
structure is so the secondary and tertiary structures will form. Certain conditions will cause the
protein to unfold, leaving only the primary structure.
heat breaks hydrogen bonds by causing the atoms to vibrate too radically
UV light breaks hydrogen bonds by exciting bonding electrons
organic solvents breaks hydrogen bonds
strong acids and bases breaks hydrogen bonds and can hydrolyze the peptide bonds, breaking
the primary structure
detergents disrupt hydrophobic interactions
heavy metal ions forms bonds to sulfur groups and can cause proteins to precipitate out of
solution.
C C OH
CH2
CH2
O C
H O O
H C C C OH
H
pyruvic acid
NH2
CH2OH
H
HO
O
H
OH
glutamic acid
H O
NH2
C C OH
CH2
O C
O
H
HO C C C C OH HO C C
H
oxaloacetic acid
aspartic acid
H O
CH2
NH2
C C OH
CH2
phenylalanine
OH
serine
O H H O O
O H O O
C C OH
OH
H
HO
alpha -D-glucose
H O
H O
NH2
C C OH
C C C OH
H H
oxoglutaric acid
H O
NH2
C C OH
CH2
H O
NH2
C C OH
H C OH
CH2
CH2
H C H
CH2
H
threonine
CH3
methionine
SH
homocysteine
1.
2.
3.
4.
5.
6.
7.
8.
9.
Histidine
Isoleucine
Leucine
Lysine
Methionine
Phenylalanine
Threonine
Tryptophan
Valine
must be consumed
Protein Nutrition:
Protein in our diets comes from both animal and vegetable sources. Most animal sources (meat, milk,
eggs) provide what's called "complete protein," meaning that they contain all of the essential amino
acids. Vegetable sources usually are low on or missing certain essential amino acids. For example,
rice is low in isoleucine and lysine. However, different vegetable sources are deficient in different
amino acids, and by combining different foods you can get all of the essential amino acids throughout
the course of the day. Some vegetable sources contain quite a bit of protein -- things like nuts, beans,
soybeans, etc. are all high in protein. By combining them you can get complete coverage of all
essential amino acids.
The digestive system breaks all proteins down into their amino acids so that they can enter the
bloodstream. Cells then use the amino acids as building blocks.
From this discussion you can see that your body cannot survive strictly on carbohydrates. You must
have protein. According to this article, the RDA (Recommended Daily Allowance) for protein is 0.36
grams of protein per pound of body weight. So, a 150-pound person needs 54 grams of protein per
day.
Athletes will need more in their diets. Many studies have recommended protein levels of 1 gram of
protein per kilogram of body weight per day. Which is near three times that of a non-active person.
If you would like to read some good sports nutrition texts, try "The Athlete's Kitchen" by Nancy Clark
MS RD or "Sports Nutrition" by Dan Benardot Ph.D., RD. Sports nutrition for children, try "Play Hard
Eat Right" by Debbi Sowell Jennings MS RD and Suzanne Nelson Steen D.Sc. RD.
Above are pictures of gel electrophoresis. The protein is denatured so that it loses all secondary
and tertiary structure. This means you have the protein as a string of amino acids. It is because
of this string-like form that you can separate proteins based on their molecular weight alone. A
protein standard solution, a mixture of proteins of known molecular masses, is loaded into lane
spot #1. The protein samples that are your unknowns are loaded into other adjacent lanes #2 &
#3.
In electrophoresis an electric potential difference is applied across a plate of gel. Molecules
separate on the gel since they move at speeds that depend on their size. Smaller proteins move
at a faster rate than larger proteins. When the protein bands have migrated down the gel one can
compare the molecular weights of the unknown proteins to the standard protein molecular
masses.
nitroprusside
Biuret Test:
positive test for peptide bonds
Biuret Reagent is made of sodium hydroxide and copper sulfate
blue reagent turns violet in the presence of proteins
pink color persists with short-chain polypeptides
color intensity varies with concentration of peptides
Ninhydrin Test:
positive test for amino acids, not peptides
all amino acids give blue
except proline which gives a yellow color
Sanger Reagent:
Reagent for the determination of the N-terminal amino acid in a peptide.
In the first step the amino group is coupled to 1-fluoro-2,4-dinitirobenzene (by a nucleophilic
aromatic substitution).
Then the peptide is hydrolytically cleaved. If the hydrolysis is mild enough (which can be quite
annoying), then the whole peptide can be degradated via this reaction.
After the cleavage the dinitrophenyl residue is still connected to the N-terminal amino acid. That
can easily be separated and analyzed by e.g. chromatography
Edman Degradation:
Degradation of the N-terminal amino acid of a peptide.
Then the amino acid can be identified e.g. with chromatographic methods or melting point.
Vegan Vegetarians
PHENYLALANINE
Main Functions:
Precursor to Tyrosine, which, in turn, is the precursor to the neurotransmitters: Dopamine and the
excitatory neurotransmitters Norepinephrine and Epinephrine.
Precursor to the hormone, Thyroxin.
Enhances mood, clarity of thought, concentration, and memory.
Suppresses appetite.
Major part of collagen formation.
While the L-form of all of the other amino acids is the one that is beneficial to people, the
D and DL forms of Phenylalanine have been useful in treating pain.
DL-Phenylalanine is useful in reducing arthritic pain.
Powerful anti-depressant.
Used in the treatment of Parkinson's Disease.
Phenylalanine Excessive Seen In:
Pregnancy
pigmented melanoma
PKU (phenylketonuria)
panic disorder/anxiety attacks.
Phenylalanine Deficiency Seen In:
Depression
Obesity
Cancer
AIDS
Parkinson's Disease
Note:
Phenylalanine should be avoided if you suffer from High blood pressure, as it has hypertensive.
THREONINE
Main Functions:
Required for formation of collagen.
Helps prevent fatty deposits in the liver.
Aids in production of antibodies.
Can be converted to Glycine (a neurotransmitter) in the central nervous system.
Acts as detoxifier.
Needed by the GI (gastrointestinal) tract for normal functioning.
Provides symptomatic relief in ALS (Amyotrophic Lateral Sclerosis, Lou Gehrig's Disease).
In laboratory experiments with animals, Threonine increases thymus weight.
Threonine is often low in depressed patients. In that group of patients, Threonine is helpful in treating
the depression.
Threonine Excess Seen In:
Alcohol ingestion
Those treated with sedative anti-convulsing medication (animal studies)
Vitamin B6 deficiency
Pregnancy
Liver cirrhosis
Threonine Deficiency Seen In:
Depression
AIDS
Muscle Spasticity
ALS (Amyotrophic Lateral Sclerosis)
Vegetarianism
Epilepsy
TRYPTOPHAN
Main Functions:
Precursor to the key neurotransmitter, serotonin, which exerts a calming effect.
Effective sleep aid, due to conversion to serotonin.
Reduces anxiety.
Effective in some forms of depression.
Treatment for migraine headaches.
Stimulates growth hormone.
Along with Lysine, Carnitine, and Taurine is effective in lowering cholesterol levels.
Can be converted into niacin (Vitamin B3).
Lowers risk of arterial spasms.
The only plasma amino acid that is bound to protein.
Tryptophan must compete with 5 other amino acids to pass through the blood-brain barrier and enter
the brain. Those 5 are: tyrosine, phenylalanine, leucine, isoleucine, and valine and are called Large
Neutral Amino Acids (LNAA).
Requires pyridoxal-5-phosphate (P5P) a form of vitamin B6 to be converted into serotonin. P5P
deficiency will lower serotonin levels, even if Tryptophan levels are normal.
Tryptophan Excess Seen In:
Increased intake of salicylates (aspirin).
Increased blood levels of free fatty acids.
Sleep deprivation.
Niacin intake.
Tryptophan Deficiency Seen In:
Depression
Insomnia
Chronic Fatigue Syndrome
ALS
FDA ban of Tryptophan
Note:
Simultaneous treatment with Tryptophan and Prozac (and other SSRI anti-depressants, such as Paxil
and Zoloft) can produce an irreversible brain disorder called Serotonin Syndrome. This treatment
combination is to be avoided.
Standard AMA, APA (American Psychiatric Association), FDA, and pharmaceutical industry position
has been that Tryptophan is not an effective treatment of serotonin-depletion depressions, when
compared to Prozac and other SSRI's.
Clinical experience has shown that some people respond well to Prozac while others respond well to
Tryptophan in treating serotonin-depleted depressions. When the FDA banned Tryptophan,
thousands of people who only had a positive response to Tryptophan (and not to Prozac)
decompensated psychologically and never recovered.
Tryptophan is again available, but only through prescription and compounding pharmacies.
VALINE
Main Functions:
One of the 3 major Branched-Chain Amino Acids (BCAA) . . .the other 2 being leucine and
isoleucine . . . all of which are involved with muscle strength, endurance, and muscle stamina.
BCAA levels are significantly decreased by insulin. High dietary sugar or glucose intake causes
release of insulin, which, in turn, causes a drop in BCAA levels.
Competes with Tyrosine and Tryptophan in crossing the blood-brain barrier. The higher the Valine
level, the lower the brain levels of Tyrosine and Tryptophan. One of the implications of this
competition is that Tyrosine and Tryptophan nutritional supplements need to be taken at least an hour
before or after meals or supplements that are high in branched chain amino acids.
Actively absorbed and used directly by muscle as an energy source.
Not processed by the liver before entering the blood stream.
Any acute physical stress (including surgery, sepsis, fever, trauma, starvation) requires higher
amounts of Valine, Leucine and Isoleucine that any of the other amino acids.
During period of Valine deficiency, all of the other amino acids (and protein) are less well absorbed by
the GI tract.
Valine Excess Seen In:
Ketotic Hypoglycemia
Visual and tactile hallucinations
Valine Deficiency Seen In:
Kwashiorkor
Hunger
Obesity
Neurological deficit
Elevated insulin levels