CHEMISTRY OF AMINO ACIDS, PEPTIDES, AND PROTEINS PART 1 DR.

SANTOS

CHEMISTRY OF AMINO ACIDS, PEPTIDES, AND PROTEINS PART 1 VITAMIN C is important in the synthesis of collagen
Dr. Remedios Santos Without Vitamin C, you cannot produce a good collagen.
Keratin
I. PROTEINS
5. Immune Protection
Proteins = third major nutrient that the body needs
Among all the nutrients that our body needs, proteins are the most ANTIBODIES are derived from gamma globulins, which are
important -- we cannot live without proteins proteins.

Proteins: 6. Generation and Transmission of Nerve Impulses

- Complex, organic nitrogenous substances with very high molecular
weight
- Found in all plant and animal cells
- Consists largely or entirely of alpha-amino acids united in peptide
linkages
AMINO ACIDS = basic unit by which proteins are made of
They are joined together through the PEPTIDE BONDS
There are 21 amino acids
Amino Acids are alphabets of proteins
Comparable to the letters in the alphabet
Out of the 26 letters in the alphabet, you can form all the
words in the dictionary. By changing the sequence of the
letters, you could come up with different words. Same thing
goes with amino acids the amount/number or the sequence
of amino acids could vary and would come up with proteins.
Sickle Cell Hemoglobin VS Normal Hemoglobin
Differ in one amino acid
Sickle Cell Hemoglobin = ABNORMAL
Normal Hemoglobin = NORMAL
This goes to show that the difference between a normal
protein and an abnormal protein could just be because of one
amino acid.
There are neurotransmitters that are derived from different
amino acids.
Serotonin
Derived from Tryptophan
It is a neurotransmitter and at the same time a
vasoconstrictor, and a GIT regulator (regulates GI tract
motility).
7. Control of Growth and Differentiation
REPRESSOR PROTEINS are important control elements that
silence a specific DNA of a cell This is essential for the
orderly growth and differentiation of cells.
8. Cell Signalling
MEMBRANE RECEPTORS such as Insulin Receptors.
9. Hormones
PROTEIN HORMONES includes Insulin, Thyrotropin,
Somatotropin (Growth Hormone), Luteinizing Hormone, and
Follicle Stimulating Hormone

- Derived from the Greek word proteios = primary or holding first 10. Proteins are one of the major components of biological membranes
place or of first importance proteins are among the most
important substances which make up the human body CLASSIFICATION OF PROTEINS:
- G. J. Mulder = Dutch chemist who coined the word protein in 1893 A. Classification Based on Composition, Physical and Chemical Properties
of the Protein
FUNCTIONS OF PROTEINS: 1. SIMPLE PROTEINS = made up of AMINO ACIDS ONLY
1. Enzymatic Catalysts a. Albumin
- Soluble in water
Enzymes, which are important in the different metabolic - Dilute aqueous salt solution
processes in the body, are protein in nature. - Heat coagulable
Enzymes are needed to digest our food Without b. Globulin
enzymes, we cannot get the nutrients from the food that - Insoluble in water
you eat. (If we cannot digest our food We become - Soluble in aqueous solution
malnourished We die - Heat coagulable
Enzymes are also needed in the different metabolic c. Glutelin
pathways Without enzymes, the pathways will not work - Soluble in dilute acids and alkalies
If the pathways will not work, we wont have energy. - Heat coagulable
2. Transport and Storage
ORYZENIN
One example would be Hemoglobin HEMOGLOBIN Protein found in rice
transports oxygen. Incomplete Protein

3. Coordinated Motion COMPLETE PROTEIN VS INCOMPLETE PROTEIN

Complete Protein
These are the proteins involved in muscle contraction ACTIN Contains all the essential amino acids
and MYOSIN. Can sustain life by itself you can live just by eating
Complete Protein
4. Mechanical Support Examples: Protein found in milk (that is why babies
can live and grow just by drinking milk alone), meat,
Collagen
and eggs
Most abundant protein in the body
Incomplete Protein
Without collagen, there wouldnt be any support to the
Lacks one or more of the essential amino acids (even
different tracts in the body
if it just lacks one amino acid)
Lining of blood vessels has collagen
Cannot sustain life by itself

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 CHEMISTRY OF AMINO ACIDS, PEPTIDES, AND PROTEINS PART 1 DR. SANTOS

d. Prolamine C. Classification Based on Biologic Functions

- Alcohol-soluble protein 1. ENZYMES = Dehydrogenases, Kinases, etc.

ZEIN = Protein found in corn Enzymes are called CATALYTIC PROTEINS because they are
involved in catalysis.
e. Albuminoid or Scleroprotein
- Least soluble 2. STORAGE PROTEINS = Ferritin, Myoglobin
3. REGULATORY PROTEINS = DNA-Binding Proteins, Peptide
Protein found in exoskeletal structures HAIR AND NAILS Hormones
4. STRUCTURAL PROTEINS = They are said to function in brick and
f. Histone
mortar roles. Example: Collagen, Proteoglycans, Elastin
- Basic protein Contains a lot of basic amino acids
5. PROTECTIVE PROTEINS = Blood Clotting Factors, Immunoglobulins,
- Soluble in water
Interferon
- Dilute acid and alkali
6. TRANSPORT PROTEINS = Hemoglobin, Plasma Lipoproteins,
- Found in combination with DNA
Transferrin
g. Protamine
7. CONTRACTILE OR MOTILE PROTEINS = Actin, Myosin
- Simplest protein
- Basic
Some proteins have functions that are rather exotic and not easily
- Soluble in water
classified. Examples of these proteins are:
- Dilute ammonia, acid and alkali
1. MONELLIN
- Found in spermatozoa
- Protein of an African plant which has an intensely sweet taste
- Being studied as a non-fattening, nontoxic food sweetener for
2. CONJUGATED PROTEINS = made up of AMINO ACIDS + OTHER
human use
SUBSTANCE (PROSTHETIC GROUP)
2. ANTI-FREEZE PROTEIN
a. Nucleoprotein = has NUCLEIC ACIDS as prosthetic group
- Found in the blood plasma of some Antarctic fish which protects
b. Glycoprotein and Mucoprotein = has CARBOHYDRATES as
their blood from freezing
prosthetic group
3. RESILIN
c. Phosphoprotein = has PHOSPHORIC ACID RESIDUES as
- Where wing hinges of some insects are made of
prosthetic group
- Has nearly perfect elastic properties
- Example: CASEIN Protein found in milk
d. Chromoprotein = contains PROSTHETIC GROUPS THAT GIVE
COLOR
II. AMINO ACIDS
- Example: Hemoglobin
Group of relatively simple building block molecules which proteins are
e. Lipoproteins = contains LIPIDS
built
- Example: LDL, HDL, Chylomicrons
All proteins are constructed from the same basic set of 20 amino acids,
f. Metalloproteins = contains METALS
covalently linked in characteristic sequences
- Example: Insulin, Cytochrome
Each of these amino acids have a distinctive side chain Responsible
3. DERIVED PROTEINS for its chemical individuality
a. Primary Derived May be regarded as the alphabet of protein structure
b. Secondary Derived
Again, AMINO ACIDS are the basic unit by which proteins are made of.
Whatever is the characteristic of the amino acid found in the protein
B. Classification Based on the Shape and Certain Physical Characteristics
will have an impact on the function of the protein.
of the Protein
1. FIBROUS PROTEINS = elongated STANDARD, PRIMARY, OR NORMAL AMINO ACIDS = 20 amino acids of
- Tough proteins; Referred to as such to distinguish them from other kinds of
- Insoluble in water amino acids present in living organisms but not in proteins
- Arranged around a single axis to form a fiber NONSTANDARD AMINO ACIDS = consists of amino acid residues that
- Involved in structural functions have been chemically modified after they have been incorporated into a
- Examples: polypeptide and amino acids that occur in living organisms but are not
Collagen and Keratin > They form the matrix of bone and found in proteins
ligaments and provide structural and elasticity to organs and Examples:
the vascular system 1. Conversion of peptidyl proline and lysine to 4-hydroxyproline and
Keratin = It is the chief structural component of hair, scales, 5-hydroxylsine
horns, wool, nails, and feathers. It is also the principal 2. Conversion of peptidyl glutamate to gamma carboxyglutamate
component of the tough armor of the tortoise (turtle) 3. Methylation, formation, acetylation, and phosphorylation of
certain aminoacyl residues
2. GLOBULAR PROTEINS = circular *These modifications extend the biologic diversity of proteins by
- Involved in mobile and dynamic functions altering their solubility, stability, and interaction with other proteins.
- Examples: Enzymes, Hemoglobin, Plasma Proteins
Each amino acid has a central carbon, called the ALPHA-CARBON, to
The shape of the protein is based on its function. which 4 different groups are attached:
Hemoglobin 1. A basic amino group (-NH2)
Rounded 2. An acidic carboxyl group (-COOH)
Found inside the red blood cells 3. A hydrogen atom (-H)
The reason why it is rounded is for it to be accommodated 4. A distinctive side chain (-R)
inside the red blood cell It follows the shape of the RBC. Common amino acids are known as ALPHA-AMINO ACIDS (-AMINO
ACIDS) Because they have a primary amino group and a carboxylic
acid group as substituents of the same alpha-carbon atom.

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 CHEMISTRY OF AMINO ACIDS, PEPTIDES, AND PROTEINS PART 1 DR. SANTOS
(Picture Above) PARTS OF AN AMINO ACID:
Center = ALPHA CARBON
3 Reactive Parts:
1. Amino Group (-NH2)
2. Carboxyl Group (-COOH)
3. Side Chain (-R)
*ALPHA-AMINO ACID = both the amino group and carboxyl group are
attached to the alpha-carbon
*BETA-AMINO ACID = amino group is attached to the beta-carbon
not found in the body
EXEMPTION: PROLINE Have a second amino group (-NH-)
Referred to as -IMINO ACID Since its nitrogen is bonded to the -
carbon and the side chain group.
Gives a polypeptide important structural features Because of its
usual structure
All protein amino acids share the absolute configuration of L-
GLYCERALDEHYDE L--AMINO ACIDS
WHY DO YOU CALL IT L-ALPHA-AMINO ACIDS?
Different from Levotatory small letter L (l) or (-) sign
Same concept with D-Glucose and L-Glucose:
Reference Point: Position of the OH at the penultimate
carbon
*Penultimate Carbon = carbon next to the last; for example,
you have 6 carbons, so you will look at carbon number 5
- -OH on the RIGHT of the penultimate carbon = D-Glucose
- -OH on the LEFT of the penultimate carbon = L-Glucose
Likewise, in amino acids, it depends on the position of the amino
group relative to the alpha-carbon.
Amino group is on the LEFT of alpha-carbon = L-Amino Acid
- All amino acids is the body are L-Amino Acids
Amino group is on the RIGHT of alpha-carbon = D-Amino Acid
- There are only 2 D-Amino Acids in the body: D-ASPARTATE
AND D-SERINE Found in the brain
- Can be found in bacterial cell walls
D-AMINO ACIDS = usually found in non-mammalian peptides an certain
antibiotics
D-SERINE and D-ASPARTATE = can be seen in human brain tissue
D-ALANINE and D-GLUTAMATE = abundant in the cell walls of gram-
positive bacteria
SIDE CHAINS = functional groups that are the major determinants of the
conformation and function of proteins, as well as the electric charge on
the molecule
Properties of each amino acid are dependent on its side chain (-R)
Knowledge of the properties of these side chains Important for
understanding methods of analysis, purification, and identification of
proteins
CHARGED, POLAR OR HYDROPHILIC SIDE CHAINS = usually exposed
on the surface of proteins
NONPOPLAR HYDROPHOBIC RESIDUES = usually buried in the
hydrophobic interior of a protein and are out of contact with water
IF YOU WANT TO WRITE THE FORMULA OF THE AMINO ACIDS:
An amino acid will always have:
Alpha Carbon
Amino Group
Carboxyl Group
Hydrogen Group
The only one that changes is the R-Group.
For example: If you make the R-Group CH3 Alanine; If you
make the R-Group CH2OH Serine
You always have to take note of the R-Group attached
R-Group distinguishes an amino acid from the other amino
acids. It is also responsible for the specific characteristic of the
amino acid.
-------------------------------------------------------------------------------------------
AMINO GROUP can accept a Hydrogen ion (H+)/a proton.
When you add another Hydrogen, it becomes positively
charged NH2 will become NH3+
Proton Acceptor (Bronsted-Lowry Definition) = BASE
Amino group is the BASIC part of the amino acid.
CARBOXYL GROUP can dissociate.
Can become a carboxylate ion (-COO-) + hydrogen ion (H+)
Proton Donor (Bronsted-Lowry Definition) = ACID
Carboxyl group is the ACIDIC part of the amino acid.
AMPHOTERIC PROPERTY = An amino acid can act as a base at the
same time because it has both a basic part and an acid part.
All amino acids are amphoteric.
NEUTRAL AMINO ACID
If you look at the R-group and you do not find another amino
group and carboxyl group
MONOAMINO-MONOCARBOXYLIC AMINO ACID
Only one amino group and only one carboxyl group = NEUTRAL
Base (amino group) will neutralize the acid (carboxyl group)
All are neutral EXCEPT Aspartic Acid/Aspartate, Glutamic
Acid/Glutamate, which are acidic, and Lysine, Arginine and
Histidine, which are basic.
ACIDIC AMINO ACID
If you look at the R-group and you find another carboxyl group
2 (acid) carboxyl groups versus 1 amino group (base) = ACIDIC
2 Acidic Amino Acids:
- Aspartic Acid/Aspartate
- Glutamic Acid/Glutamate
*(Picture Below) PINK BOX = Carboxyl Group
MONOAMINO-DICARBOXYLIC AMINO ACID
BASIC AMINO ACID
If you look at the R-group and you find another amino group
2 amino groups (base) versus 1 carboxyl group (acid) = BASIC
3 Basic Amino Acids:
- Lysine
- Arginine
- Histidine
*(Picture on 1st Box on the Next Page) PINK BOX = Amino
Group
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 CHEMISTRY OF AMINO ACIDS, PEPTIDES, AND PROTEINS PART 1 DR. SANTOS
*Sorry, Im not sure kung saan yung other amino group sa
Histidine
DIAMINO-MONOCARBOXYLIC AMINO ACID
FUNCTIONS OF AMINO ACIDS:
1. Building blocks of proteins PRIMARY FUNCTION
2. Amino acids are precursors of a variety of complex, nitrogen-
containing molecules:
a. Glycine Heme, Purines, Creatine, Glutathione, Hippuric Acid
HEME = Glycine + Succinyl-CoA
PURINES (Picture Below: Adenine)
N3 and N9 = comes from
Glutamine
N1 = comes from Aspartic Acid
C4, C5, N7 = comes from
Glycine
When you synthesize purines,
you need those amino acids.
Purines are found in DNA.
No amino acids No purines No DNA No cell
growth, cell multiplication and cell maturation
Impossible for you to live
CREATINE = tripeptide; GlAM Glycine, Arginine,
Methionine
GLUTATHIONE = tripeptide; GCG Glycine, Cysteine,
Glutamic Acid
b. Glutamic Acid GABA (Gamma Aminobutyric Acid)
GABA are our natural tranquilizers. If you cannot synthesize
GABA, you will have convulsive seizures.
c. Phenylalanine and Tyrosine Melanin, Dopamine, Thyroxine,
Epinephrine, and Norepinephrine
Thyroxine = Thyroid Hormone
Melanin = Pigment responsible for your complexion
Epinephrine = Important hormone for the control of your
blood sugar level
Stimulates Glycogenolysis and Gluconeogenesis
Increases Blood Sugar Levels
Hyperglycemic Hormone
d. Tryptophan Niacin, Serotonin, Indole and Skatole, Melatonin
Niacin = Vitamin B3
Pellagra = Niacin Deficiency Manifested by the 3 Ds:
Dermatitis, Diarrhea, and Dementia
Serotonin = Neurotransmitter
Melatonin = Hormone that induces sleep
Substance found in sleeping tablets (Sleepasil)
Indole and Skatole = Responsible for the odor of the stool
e. Histidine Histamine
f. Lysine and Methionine Carnitine
3. Source of energy
Just like your Carbohydrates and your Lipids, your Proteins can
also be sources of energy.
1 gram of Carbohydrates = 4 calories
1 gram of Fats = 9 calories
1 gram of Protein = 4 calories
4. Special amino acids as components of certain types of proteins
These amino acids arise post-translational modifications of an
amino acid that has previously been incorporated into a peptide
protein.
When you say special amino acids, these are amino acids that
have been modified post-translationally.
a. Hydroxyproline and Hydroxylysine Present in Collagen
Proline and Lysine have been modified by hydroxylation to
produce Hydroxyproline and Hydroxylysine.
These two amino acids are important components of
Collagen.
Structure of Collagen:
Made up of Glycine, and X and Y amino acids: (Gly-X-Y)n
Gly-X-Y- Gly-X-Y-Gly-X-Y
Glycine comes every 3rd in the composition of collagen
Glycine is the most abundant amino acid in collagen.
X and Y could be any amino acids, but majority of these
X and Y are Hydroxyproline, Hydroxylysine, or Proline
- These 3 amino acids (Hydroxyproline, Hydroxylysine,
or Proline) are responsible for the tensile strength of
Collagen Collagen is a structural protein, so it must
be strong. What makes it strong and hard is its high
composition of these 3 amino acids.
For you to be able to form Hydroxylysine and
Hydroxyproline, you need to have VITAMIN C.
If you dont have Vitamin C You cannot synthesize
Hydroxyproline and Hydroxylysine You will come up
with a Collagen that is abnormal.
- This could happen on your BLOOD VESSELS. The
lining, which is made up of Collagen, is an abnormal
Collagen. Your blood vessels become fragile. That is
why the earliest sign of Vitamin C Deficiency is NOSE
BLEEDING (EPISTAXIS).
b. N-Methyllysine Found in Myosin
c. Gammacarboxyglutamic Acid Component of Prothrombin
Gammacarboxylglutamic Acid is found in Prothrombin. It is a
special type of Glutamic Acid that has undergone
gammacarboxylation.
VITAMIN K = Necessary for gammacarboxylation to take
place
That is why Vitamin K is important for the synthesis of
Prothrombin
d. Desmosine Derivative of Lysine; Found in Elastin
e. N-Acetyllysine Found in Histones that are associate with
chromosomes
5. Phosphorylation and dephosphorylation of Serine, Threonine and
Tyrosine play a major role in the signal transduction pathways by
which cells communicate with and respond to their environment.
Hydroxyl (-OH) containing amino acids, such as SERINE,
THREONINE, and TYROSINE, undergo Phosphorylation and
Dephosphorylation.
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 CHEMISTRY OF AMINO ACIDS, PEPTIDES, AND PROTEINS PART 1 DR. SANTOS

CLASSIFICATION OF AMINO ACIDS BASED ON POLARITY:

You can attach Phosphate to OH Becomes CH2O-
A. Amino Acids with NONPOLAR or Hydrophobic R Groups
Phosphate
- Referred to as NEUTRAL amino acids containing hydrocarbon R
In Carbohydrate Metabolism:
groups The term NEUTRAL is used because these R groups do
Enzyme activated by Phosphorylation = GLYCOGEN
not bear positive or negative charges
PHOSPHORYLASE (Glycogenolysis)
- Interact poorly with water Play an important role maintaining
Enzyme activate by Dephosphorylation (Remove
the 3-dimenstional structure of proteins.
Phosphate) Enzyme is activated) = GLYCOGEN
- Two Types of Hydrocarbon Side Chains:
SYNTHETASE
1. AROMATIC
6. L--amino acids in low molecular weight peptides play additional a. Phenylalanine = Benzene Ring
roles as hormones. b. Tryptophan = Indole Ring
7. Both D- and L--amino acids are present in polypeptide antibiotics *Phenylalanine and Tryptophan contain aromatic ring structure
elaborated by microorganisms. *The other aromatic amino acid, Tyrosine, is polar.
- Examples: Bacitracin, Gramicidin A 2. ALIPHATIC
8. Several -amino acids or their derivatives act as chemical messengers. a. Glycine
- Example: Glycine, GABA, Serotonin and Melatonin are b. Alanine
neurotransmitters (substances released from one nerve cell that c. Valine
influence the function of a second nerve cell or a muscle cell) d. Leucine
9. Hormones can be deprived from amino acids e. Isoleucine Branched-Chain Amino Acids
- Thyroxine, Epinephrine, and Norepinephrine are derived from f. Methionine
Phenylalanine and Thyrosine g. Proline
10. Several standard and non-standard amino acids act as metabolic - Nonpolar or Hydrophobic Amino Acids:
intermediates. Alanine
- Arginine, Citrulline, and Ornithine are components of the Urea Glycine
Cycle - Simplest amino acid R-Group is another Hydrogen ion
- Smallest amino acid Can be accommodated in places
ABBREVIATIONS OF AMINO ACIDS inaccessible to other amino acids (particularly where
peptides bend sharply)

Carbon at the center of all amino acids is called a CHIRAL

CARBON.
What is a CHIRAL CARBON?
This is carbon to which you have 4 different groups
attached.
Also called ASYMMETRIC CARBON
Capable of optical rotation Can be
Dextrolevotatory or Levotatory
EXEMPTION: GLYCINE
The R group of Glycine is another
Hydrogen ion You only have 3
different groups
Glycine has no dextrolevotatory and
levotatory because it has no chiral
carbon
-----------------------------------------------------------------------------
Solubility in water of the amino acid if they are nonpolar
depends upon their R group.
Longer R Group = Less soluble in water
Shorter R Group = More soluble in water

Proline
- Referred to as the helix breaker

For all the amino acids, the R-group is

attached to the alpha carbon, but for
PROLINE, the R-group is not only
attached to the alpha carbon but also
to the amino group.
We MUST know how to abbreviate amino acids. There are 2 ways *That is why Proline is cyclic in appearance and structure.
on how to abbreviate: It is also the reason why Proline is sometimes referred to
1. 3-Letter-Abbreviation usually the first 3 letters of the amino as an Imino Acid.
acid
*EXEMPTIONS: Ile = Isoleucine, Asn = Asparagine, Gln = Phenylalanine
Glutamine, and Trp = Tryptophan Tryptophan
*This will be the one used by Dra. Santos sa exam daw Methionine
2. 1-Letter-Abbreviation NO NEED TO MEMORIZE Unless you - Source of SAM (S-adenosylmethionine) = active methyl donor
want to take the US MLE or you want to, i-push mo lang yan. Leucine
Haha! Isoleucine
Valine

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 CHEMISTRY OF AMINO ACIDS, PEPTIDES, AND PROTEINS PART 1 DR. SANTOS

C. Amino Acids with POSITIVELY CHARGED POLAR R Groups (Basic

Amino Acids)
Positively Charge R Groups (Basic Amino Acids):
Lysine
Arginine
- R-group is called GUANIDO GROUP
Histidine
- R-group is called IMIDAZOLE GROUP
*pK of its imidazole proton = permits it to function at neutral
pH as either a base or an acid catalyst
- Responsible for the buffering capacity of haemoglobin
- Plays unique roles in enzymatic catalysis

3 TYPES OF POLAR AMINO ACIDS:

1. Uncharged Polar D. Amino Acids with NEGATIVELY CHARGED POLAR R Groups (Acidic
2. Positively Charged Polar Amino Acids)
3. Negatively Charged Polar Negatively Charged R Groups (Acidic Amino Acids)
Aspartic Acid
Glutamic Acid
B. Amino Acids with UNCHARGED POLAR R Groups
Uncharged Polar Amino Acids:
1. Hydroxyl-containing Amino Groups:
a. Serine
b. Threonine
c. Tyrosine
2. Amide (CONH2) Derivatives of Glutamate and Aspartate
a. Glutamine
- Derivative of Glutamate
- Primary source of urinary ammonia All amino acids have trivial or common names. In some cases, it is
b. Asparagine derived from the source from which they were first isolated:
- Derivative of Aspartate ASPARAGINE
3. Other: - First amino acid to be discovered
a. Cysteine - Found in asparagus in 1806
- Thiol group GLUTAMATE
- Polar because of its sulfhydryl group - First isolated from wheat gluten
Have functional groups capable of hydrogen bonding so they easily TYROSINE
interact with water - First isolated from cheese Name is derived from the Greek
SERINE, THREONINE, and TYROSINE tyros meaning cheese
Hydroxyl-containing Amino Acids GLYCINE
Contain polar hydroxyl groups Enables them to participate in - Greek glykos means sweet So named because of its sweet
hydrogen bonding, which is an important factor in protein taste
structure
-OH groups of Serine and Threonine = points for attaching SELENOCYSTEINE = 21st L--amino acid
carbohydrates A selenium atom replaces the sulfur of
Sites of Phosphorylation reactions its structural analog, cysteine
Site of Glycosylation reactions It is a rare amino acid residue that is
GLUTAMINE and ASPARAGINE = important in detoxification of inserted into polypeptide during
ammonia translation rather that created
through postsynthetic modification
Unlike the other 20 genetically
encoded amino acids, it is not
specified by a simple 3-letter codon
It is present at the active site of
several human enzymes that catalyse Red-Ox reactions
(Thioredoxin, Glutathione Peroxidase, Deiodinase)
Impairment in human selenoproteins have been implicated in
tumorigenesis and atherosclerosis, and are associated with
selenium deficiency cardiomyopathy (Keshan Disease)
- KESHAN DISEASE
Fatal, congestive cardiomyopathy (Abnormality of the cardiac
muscles due to selenium deficiency)
Primarily affects children and women of childbearing age

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 CHEMISTRY OF AMINO ACIDS, PEPTIDES, AND PROTEINS PART 1 DR. SANTOS

Occurs in areas with low soil trace elements (Parts of China, PHYSICAL PROPERTIES OF AMINO ACIDS:
New Zealand and Finland) 1. Solubility
All amino acids are soluble in water
TYPES OF INTERACTION ENTERED INTO BY THE DIFFERENT SIDE CHAINS - R-groups of Polar, Uncharged Amino Acids = more soluble in
OR R-GROUPS OF AMINO ACIDS: water/more hydrophilic
1. Hydrogen Bonding
POLARS (Most soluble in water) NONPOLARS with SHORT R-
R-group with an OH VS an R-group with a COOH: GROUP NONPOLARS with LONG R-GROUPS (Least soluble in
Amino Acids with OH in the R-group: SERINE, THYROSINE, water)
and THREONINE -----------------------------------------------------------------------------------
Amino Acids with COOH in the R-group: ASPARTIC ACID ARRANGE FROM MOST SOLUBLE TO LEAST SOLUBLE IN WATER:
and GLUTAMIC ACID Arginine, Alanine, and Isoleucine
Example: Serine Glutamic Acid Arginine Alanine Isoleucine
R-group with an OH VS another R-group with an OH
Example: Serine Serine, Serine Threonine
R-group with an SH VS an R-group with an OH
Amino Acids with SH in the R-group: CYSTEINE
Example: Cysteine Serine

2. Ionic Interaction

R-group with a -COOH VS an R-group with an amino group

(NH3+)
Between an acidic (-COOH) amino acid and a basic (NH3+)
amino acid
2. Melting Points
Acidic Amino Acids: ASPARTIC ACID and GLUTAMIC ACID
Basic Amino Acids: LYSINE, ARGININE, and HISTIDINE Amino acids have a high melting point Usually 2000C and
Example: Aspartic Acid Arginine above
3. Hydrophobic Interaction 3. Taste

Interaction between Nonpolar R-groups Taste could either be sweet, bitter, or tasteless.
Nonpolar Amino Acids: ALANINE, GLYCINE, VALINE,
LEUCINE, ISOLEUCINE, METHIONINE, PROLINE, 4. Appearance
PHENYLALANINE, and TRYPTOPHAN
They are white-crystalline in appearance.
4. Disulfide Bond
5. Optical Property
Between sulfur and sulfur For all the standard amino acid, except Glycine, the -carbon is
Example: Cysteine Cysteine asymmetric, bonded to four different substituent groups:
- Carboxyl Group
If you are studying your amino acids, there are 4 things that you - Amino Group
must know: - R Group
1. How to write the structure - Hydrogen Atom
2. How to abbreviate (3-letter-abbreviation) -carbon is a CHIRAL CARBON
3. How to classify All molecules with a chiral center = OPTICALLY ACTIVE Can rotate
Is it Polar or Nonpolar? the plane polarized light either to the right (dextrolevotatory) or
If it is POLAR, is it Charged or Uncharged? to the left (levotatory)
If it is CHARGED, is it Positively Charged or Negatively 6. Ultraviolet Absorption Spectrum of Aromatic Amino Acids
Charged?
4. R-R Interaction Aromatic Amino Acids are responsible for ultraviolet
------------------------------------------------------------------------------------ absorption. They are absorb ultraviolet light.
IDENTIFY THE TYPE OF INTERACTION: Among the 3 Aromatic Amino Acids, TRYPTOPHAN exhibits
1. Aspartic Acid and Serine the most ultraviolet absorption.
Aspartic Acid = Amino acid with COOH in the R-group
Amino acids do not absorb visible light Colorless
Serine = Amino acid with OH in the R-group
TYROSINE, PHENYLALANINE, and especially TRYPTOPHAN = absorb
Type of Interaction = HYDROGEN BONDING (-OH VS -
high wavelength ultraviolet light
COOH)
- TRYPTOPHAN
2. Aspartic Acid and Lysine Absorbs ultraviolet light 10x more efficiently
Aspartic Acid = Acidic Amino Acid (-COOH) Makes the major contribution to the ability of most proteins
Lysine = Basic Amino Acid (NH3+) to absorb light in the region of 280 nm
Type of Interaction = IONIC BONDING (-COOH VS NH3+) 7. Acid-Base Properties

RECALL:
3. Methionine and Alanine
Amino Group = can become positively charged when it
Methionine = Nonpolar
accepts a proton
Alanine = Nonpolar
Carboxyl Group = can become negatively charged when it
Type of Interaction = HYDROPHOBIC BONDING (Nonpolar
VS Nonpolar) donates a proton

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 CHEMISTRY OF AMINO ACIDS, PEPTIDES, AND PROTEINS PART 1 DR. SANTOS

Amino and carboxylic acid groups of amino acids readily ionize 4. FULLY DISSOCIATED FORM
- pK values of the -carboxylic acid groups = usually lie in a small Fully dissociated means all hydrogen ions
range around 2.2 are removed
- pK values of the -amino groups = all near 9.4 - Carboxyl Group NEGATIVELY
Physiological pH (7.4) CHARGED
- Amino groups are protonated - Amino Group Not positively charged
- Carboxylic acid groups are in their conjugate base (carboxylate) Fully dissociated forms are ALWAYS
form NEGATIVE
- Amino acid can therefore act as both an acid and a base pH 11 and above ALKALINIC MEDIUM

Those -amino acids having a single amino group and a single carboxyl Does an amino acid carry a fixed charged? (Is it always positive?
group crystallize from neutral aqueous solutions as fully ionized Is it always negative? Is it always zwitterion?) NO. Amino acids
species known as ZWITTERIONS (German for hybrid ions), each does not carry a fixed charge.
having both a positive and a negative charge. These ions are What determines the charge of an amino acid? PH OF THE
electrically neutral and remain stationary in an electrical field. MEDIUM
It becomes FULLY PROTONATED if the medium is VERY
ISOELECTRIC POINT (pHI or pI or IpH) ACIDIC (Amino acids become positively charged.)
That pH at which an amino acid bears no net charge and hence does It becomes FULLY DISSOCIATED if the medium is VERY
not move in an electrical field BASIC/ALKALINIC (Amino acids become negatively charged.)
That pH exactly at the midpoint between the pK values on either In between the two, they become ZWITTERION
side of the zwitterion species Basis of PROTONIC EQUILIBRIUM of AMINO ACIDS
General Rule Regarding Isoelectric Points:
- IpH of neutral amino acids = in the neighborhood of 6.0
- IpH of acidic amino acids = very much below 6.0 TITRATION OF AMINO ACIDS -- Protonic Equilibria or Titration of Amino
- IpH of basic amino acids = very much above 6.0 Acids
Acid-base titration involves the gradual addition or removal of
Physical properties of amino acids are influenced by the ionic states protons
of the alpha-carboxyl and alpha-amino groups and any ionisable Step by step dissociation of amino acid Starting from the fully
groups in the side chains. protonated form (positive form) up to the fully dissociated form
Seven of the common amino acids have ionisable side chains with (negative form)
measurable pKa values.
Each amino acid has either two or three pKa values These values
differ among the amino acids
At a given pH, amino acids have different net charges
The ionic states of amino acid side chains strongly influence the
three-dimensional structures and biochemical functions of proteins. (Picture Above) When you do Protonic Equilibria, you start from
the most positive, pass through the zwitterion form, and you end
DIFFERENT FORMS OF AN AMINO ACID: up with the most negative form.
1. UNIONIZED FORM You start at pH 1 At pH 1, it will be at its most positive form
Carboxyl Group NOT NEGATIVE (Didnt
As you increase the pH, eventually it becomes negatively
donate any proton)
charged
Amino Group NOT POSITIVE (Didnt
At pH 11 and above, it is negatively charged
accept any proton)
Unionized form does not exist in the body
Uses:
Only used in writing the formula of the 1. It can predict the charge of the amino acid in a given solution with
amino acids known pH.
2. It can devise a procedure of separating amino acids based on their
2. DIPOLAR IONS or ZWITTERION FORM charges.
Forms that exist in the body Dipolar
3. From the titration curve of the amino acid, one can know the
Ions (ZWITTERION)
regions of buffering power of the amino acid. These are the
Amino Group POSITIVELY CHARGED relatively flat portions of the curve, extending for approximately 1
Carboxyl Group NEGATIVELY CHARGED
pH unit on either side of the pK values.
Equal amounts of positive charge and Amino acids contain ionisable groups Predominant ionic form of
negative charge = ELECTRICALLY NEUTRAL these molecules in solution depends on the pH
(ZERO CHARGE)
Titration of an amino acid illustrates the effect of pH on amino acid
When you place it in an electrical field (cathode and electrode), it side chains.
will not move Stay in the center because it is neutral in charge
A. Titration of NEUTRAL AMINO ACIDS (Example: ALANINE)
3. FULLY PROTONATED - During titration with a strong base (such as NaOH) Alanine loses
Fully protonated means all hydrogen ions are attached
two protons in a stepwise fashion
- Carboxyl Group INTACT - In a strongly acidic solution (pH 1) Alanine is present mainly in
- You have another hydrogen attached the form in which the carboxyl group is uncharged or undissociated
to the Amino Group POSITIVELY
Alanine has a net charge of +1 (Ammonium group is protonated)
CHARGED - Lowering H+ concentrations Results in carboxyl group losing its
Fully protonated forms are ALWAYS
proton to become a negatively charged carboxylate group (TAKE
POSITIVE NOTE: Protons are first lost from the group with the lowest pKa)
pH 1 ACIDIC MEDIUM - At this point, Alanine has no net charge and is electrically neutral
pH at which this occurs is called ISOELECTRC POINT (Because

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 CHEMISTRY OF AMINO ACIDS, PEPTIDES, AND PROTEINS PART 1 DR. SANTOS

there is no net charge at the isoelectric point Amino acids are

pK VALUES OF ALANINE:
least soluble at this pH.
What does these pK values represent?
- Isoelectric point for alanine may be calculated as follows:
pH of pK1 = 2.3 This means that if the pH of the medium
is at exactly 2.3, the form of Alanine is 50% +1 and 50%
Zwitterion.
- At exactly the pK value, half of it will be fully protonated,
half of it will be dissociated.
- When you go above 2.3, there will be more of Zwitterion
The predominant form of Alanine is Zwitterion.
- When you go below 2.3, there will be more of +1 The
predominant form of Alanine is +1.
pH of pK2 = 9.7 This means that if the pH of the medium
**IpH of Alanine is therefore 6.0.
is at exactly 9.7, the form of Alanine is 50% Zwitterion and
- As the titration continues, the ammonium group loses its proton
50% -1.
Leaving an uncharged amino group Alanine then has a net
- When you go above 9.7, there will be more of -1 The
negative charge because of the carboxylate group
predominant form of Alanine is -1.
- When you go below 9.7 and above 2.3, there will be
more of Zwitterion The predominant form of Alanine
is Zwitterion.

ISOELECTRIC POINT (IpH):

pH wherein an amino acid is 100% Zwitterion

(Picture Above) TITRATION OF ALANINE (NEUTRAL AMINO

ACID)
When you titrate, you always start with the most positive
form. At pH 1 = Alanine is +1 (Refer to picture above --
Structure on the LEFT: MOST POSITIVE FORM OF ALANINE) This means that at pH 6, Alanine is 100% Zwitterion.
When you titrate, you add Sodium Hydroxide (NaOH). When Rule regarding Isoelectric Points:
you add NaOH to a medium that started from pH 1, you will Neutral Amino Acids = Have an IpH around 6 (6 = 5-7)
have a higher pH. Acidic Amino Acids = Have an IpH 5
pH 7 = Neutral Basic Amino Acids = Have an IpH 7
pH 7 = Acidic
pH 7 = Basic
NaOH has an OH that is negatively charged It will attract
a hydrogen ion.
It has 2 hydrogen ions that it can attract. Which one will it
attract first?
- It depends on the strength of the acids
DISSOCIATION CONSTANT The stronger the acid, the
higher the dissociation constant. The weaker the acid,
the lower is the dissociation constant. This means
that if the acid is stronger, it will dissociate faster.
- In this case, the CARBOXYL GROUP (-COOH) will donate
the proton first. The dissociation of this one is
designated as pK1.
- The higher the dissociation constant, the lower the pK
value. (If pH = more acidic If more acidic =
dissociation constant And if dissociation constant
= pK value)
- pK1 = always represents the dissociation of the ALPHA-
CARBOXYL GROUP (pH 2.3 for Alanine)
- Once the alpha-carboxyl group has dissociated (COOH
becomes COO-), this now becomes your ZWITTERION
(Refer to picture above -- Structure in the MIDDLE:
ZWITTERION)
- As you add more base, the hydrogen in the AMINO (Picture Above) TITRATION CURVE OF ALANINE
GROUP will now dissociate, and you designated that as Notice that the dots (pK values) are not connected by a
pK2. straight line Somehow flattened around the pK values
- pK2 = always represents the dissociation of the ALPHA- Indicate that there is a buffering capacity of the amino acids
AMINO GROUP (pH 9.7 for Alanine) at the pK values
- Once the alpha-amino group has dissociated (NH3+ Amino acids are good buffers They are good buffers at
becomes NH2), Alanine now becomes -1. (Refer to their pK values
picture above -- Structure on the RIGHT: MOST The is no buffer effect at the isoelectric point
NEGATIVE FORM OF ALANINE) Straight/Steep Line

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 CHEMISTRY OF AMINO ACIDS, PEPTIDES, AND PROTEINS PART 1 DR. SANTOS

RECALL (ALANINE):
pK1 = 2.3
pK2 = 9.7
IpH = 6.0

What is the predominant form of Alanine if it is placed in a IpH of Glutamic Acid is 3.2 (Di ko din sure kung bakit 3.2
medium with pH 4? lang. Not sure kung tatanggalin lang yung hundredth digit
ZWITTERION Because 4 is above 2.3 (pK1) and below 9.7 kasi di naman niya niround off @.@)
(pK2) - RECALL: ACIDIC Amino Acids should have an IpH 5.
- If you think you got a wrong pK value, you will know that
What are the exact values wherein Alanine is a good buffer? you are really wrong if it contradicts the rule. (For
2.3 and 9.7 Amino acids are good buffers at their pK example, you got an IpH value of 7 even if it is an acid
values. amino acid.)
------------------------------------------------------------------------------------
RECALL (GLUTAMIC ACID):
B. Titration of ACIDIC AMINO ACID (Example: Glutamic Acid)
pK1 = 2.2
pKr= 4.3
pK2 = 9.6
IpH = 3.2

What is the predominant form of Glutamic Acid if it is placed

in a medium with pH 5?
-1 Because 5 is above 4.3 (pKr) and below 9.6 (pK2)

What are the exact values wherein Alanine is a good buffer?

(Picture Above) TITRATION OF GLUTAMIC ACID (ACIDIC AMINO 2.2, 4.3 and 9.6 Amino acids are good buffers at their pK
ACID) values. (No matter how many pK values there are, they are
Difference is that, you have another carboxyl group at the R- all buffering zones.)
group There will now be 3 groups that could dissociate.
At pH 1 = Glutamic Acid is +1 Fully Protonated Form (Refer
to picture above 1st Structure on the Left: MOST POSITIVE
FORM OF GLUTAMIC ACID)
When you add NaOH, the ALPHA-CARBOXYL GROUP ALWAYS
DISSOCIATE FIRST.
It is designated as pK1. In the case of Glutamic Acid, pK1 =
2.2
When the alpha-carboxyl group gets dissociated (-COOH
becomes COO-), Glutamic Acid now becomes ZWITTERION
(Refer to picture above 2nd Structure from the Left:
ZWITTERION)
As you add more base (NaOH), it can either be the R-Group or
the amino group that will get dissociated.
Between those 2, the CARBOXYL GROUP from the R-
GROUP will now get dissociated (Remember: Acids
dissociate first.)
The dissociation of your R-Group is designated as your pKr.
In the case of Glutamic Acid, pKr = 4.3. (Picture Above) HOW TO USE THE pK VALUE TABLE:
When the carboxyl group of the R-group gets dissociated (- If you look at the pK value:
COOH becomes COO-), Glutamic Acid now becomes -1 pK1 = Always for the ALPHA-CARBOXYL GROUP
(Refer to picture above 3rd Structure from the Left: -1) pK2 = Always for the ALPHA-AMINO GROUP
The last one that will get dissociated is the ALPHA AMINO pKr = Always for the R-GROUP
GROUP. pK value it will dissociate first
It is designated as pK2. In the case of Glutamic Acid, pK2 = In the case of your BASIC AMINO ACIDS, pK of Alpha-Amino
9.6 Group is than pK of the R-Group = Alpha-Amino Group
When the amino group gets dissociated NH3+ becomes dissociates first.
NH2), Glutamic Acid now becomes -2 (Refer to picture In the case of your ACIDIC AMINO ACIDS, pK of R-Group is
above 4th Structure from the Left: -2) than pK of Alpha-Amino Acids = R-Group dissociates
For all the amino acids, ONLY THE ACIDIC AMINO ACID CAN first.
BECOME -2 Because it is only them who have 2 carboxyl For all the amino acids, the ALPHA-CARBOXYL GROUP has
groups. the lowest pK value It is always the Alpha-Carboxyl
When you compute for the IpH of Glutamic Acid, you only add Group that dissociates first.
the pK values before and after the zwitterion ion. In this case,
you only add pK1 and pKr.
C. Titration of BASIC AMINO ACID (Example: Lysine)
This was not included sa lecture ni Dra. Ininclude ko nalang din kasi
magkaiba pa din pag ACIDIC and BASIC. Ginamit ko lang yung mga

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 CHEMISTRY OF AMINO ACIDS, PEPTIDES, AND PROTEINS PART 1 DR. SANTOS
concepts na ginamit niya for neutral and acidic. Onti lang naman
yung difference niya. I-correct niyo nalang din pag may mali
Peptides perform prominent roles in the neuroendocrine system as
hormones,
neurotransmitters.
Peptides Which Have Significant Biologic Activities:
1. Glutathione
(Picture Above) TITRATION OF LYSINE (BASIC AMINO ACID)
You have another amino group at the R-group There will
be 3 groups that could dissociate.
At pH 1 = Lysine is +2 Fully Protonated Form (Refer to
picture above 1st Structure on the Left: MOST POSITIVE
FORM OF LYSINE)
When you add NaOH, the ALPHA-CARBOXYL GROUP ALWAYS
DISSOCIATE FIRST.
It is designated as pK1. In the case of Lysine, pK1 = 2.18
When the alpha-carboxyl group gets dissociated (-COOH
becomes COO-), Lysine now becomes +1 (Refer to picture
above 2nd Structure from the Left: +1)
As you add more base (NaOH), it can either be the R-Group or
the amino group that will get dissociated.
Between those 2, the ALPHA-AMINO GROUP from the R-
GROUP will now get dissociated
It is designated as pK2. In the case of Lysine, pK2 = 8.95
When the amino group gets dissociated (NH3+ becomes
NH2), Lysine now becomes ZWITTERION (Refer to picture
above 3rd Structure from the Left: ZWITTERION)
The last one that will get dissociated is the AMINO GROUP OF
2. Oxytocin and Vasopressin
THE R-GROUP.
The dissociation of your R-Group is designated as your pKr.
In the case of Lysine, pKr = 10.93.
When the Amino Group of the R-Group gets dissociated
NH3+ becomes NH2) Lysine now becomes -1 (Refer to
picture above 4th Structure from the Left: -1)
When you compute for the IpH of Lysine, you only add the pK
values before and after the zwitterion ion. In this case, you
only add pK2 and pKr.
IpH of Lysine is 9.94
- RECALL: BASIC Amino Acids should have an IpH 7.
3. Met-Enkephalin and Leu-Enkephalin
III. PEPTIDES
Definitions:
Peptides
- Has a low molecular weight
- Typically consists less than 50 amino acids
Protein
- Molecules with more than 50 amino acids
- Consists one or more polypeptide chains
Oligopeptides
- Polymers consisting of 2 to 10 amino acids
Dipeptide = 2 amino acids
Tripeptide = 3 amino acids
Polypeptides
- Have more than 10 amino acid residues (More than 10, Below 50)
hormone-releasing factors, neuromodulators or
Significant for its antioxidant property.
Glutathione must be reduced for it to function as an
antioxidant.
-glutamyl-L-cysteinylglycine
Contains an unusual -amide bond (wherein the -carboxyl group
of the glutamic acid residue, not the -carboxyl group, contributes
to the peptide bond)
Found in almost all organisms
Involved in many important biological processes like:
- Protein and DNA synthesis
- Drug and environmental toxin metabolism
- Amino acid transport
- *REDUCING AGENT reducing component is the SH group of
the cysteine residue (reduced glutathione GSH)
Protects cells from the destructive effects of oxidation Reacts
with substances such as peroxides (R-O-O-R, by products of O2
metabolism)
In red blood cells, Hydrogen Peroxide oxidizes the Iron of
haemoglobin to its ferric form (Fe+3)
- METHEMOGLOBIN = product of this reaction
- Glutathione protects against the formation of methemoglobin
by reducing H2O2 in a reaction catalysed by the enzyme
glutathione peroxidase
Differ only by two residues
Both contain 9 amino acid residues
Produced by the cleavage of polypeptide precursors within
different specialized cells in the hypothalamus
After synthesis, they are transported down the nerve tracts into the
Posterior Pituitary Gland (where they are stored)
Each peptide is secreted in response to specific signals from the
hypothalamus
OXYTOCIN
- Stimulates contraction of uterine muscles during childbirth
- Stimulates ejection of milk by the mammary glands during
lactation
- In males, Oxytocin may have a regulatory role in the synthesis of
Testosterone
- CYS-TYR-ILE-GLN-ASN-CYS-PRO-LEU-GLY-NH2
VASOPRESSIN
- Also known as Antidiuretic Hormone (ADH)
- Secreted in response to low pressure or high Na+ concentration
- Act by stimulating the kidneys to retain water Concentrated
urine
- CYS-TYR-PHE-GLN-ASN-CYS-PRO-ARG-GLY-NH2
Belong to a group of peptides called OPIOID CELLS
Found predominantly in the nervous tissue cells
OPIOID PEPTIDES
- Molecules that relieve pain and produce pleasant sensations
- Bind to receptors in certain cells of the brain and induce
analgesia (deadening of pain sensations)
- Represent one of the bodys own mechanisms for control of pain
Enkephalin receptors also bind to morphine, heroin and other
addicting opiate drugs (although these are not peptides)
Pentapeptides that only differ only in their C-terminal amino acid
residues
- Met-enkephalin = TYR-GLY-GLY-PHE-MET
- Leu-enkephalin = TYR-GLY-GLY-PHE-LEU
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 CHEMISTRY OF AMINO ACIDS, PEPTIDES, AND PROTEINS PART 1 DR. SANTOS
4. Atrial Natriuretic Factor
Peptide with 28 amino acid residues
Produced by specialized cells in the heart and the nervous system
Stimulates the production of a dilute urine (an effect opposed to
that of vasopressin)
5. Substance P and Bradykinin
Stimulate the perception of pain Opposed by Opioid Peptides
Pain = protective mechanism in animals that warns of tissue
damage
6. Glucagon
Pancreatic Hormone
Has 29 amino acid residues
Opposes the action of Insulin
7. Corticotropin
Contains 39 amino acid residues
Hormone of the Anterior Pituitary Gland Stimulates the Adrenal
Cortex
8. L-Aspartylphenylalanyl Methyl Ester
Commercially synthesized dipeptide
Artificial sweetener better known as ASPARTAME or NUTRASWEET
IV.STRUCTURE OF PROTEINS
A. Formation of the Peptide Bond
For example, you want to form the dipeptide Alanyl-Serine:
In the formation of the peptide bond:
- You need to react 1 carboxyl and 1 amino group.
- You remove water DEHYDRATION REACTION
*-OH comes from your COOH
*H+ come from your NH2
Of all the biochemical reactions of amino acids, the most important is
the formation of peptide bonds
Amino acid can be polymerized to form chains
Can be represented as a CONDENSATION REACTION (elimination of a
water molecule) Results to formation of CO-NH linkage
CO-NH Linkage = amide linkage known as the PEPTIDE BOND
After peptide bonds are incorporated into a peptide, an individual
amino acids (monomeric units) is now referred to as AMINO ACID
RESIDUES
Polypeptides are linear polymers Each amino acid participates in
two peptide bonds and is linked to its neighbors in a head-to-tail
fashion rather than forming branched chains
Residues at the two ends of the polypeptide each participate in just
one peptide bond
Residue with a free amino group (leftmost residue) = AMINO
TERMINUS/N-TERMINAL
Residue with a free carboxylate group (right) = CARBOXYL
TERMINUS/C-TERMINAL
Variations in the length and the amino acid sequence of
polypeptides contribute to the diversity of the shape and biological
functions of proteins.
When you name the chain, you always start with the LEFT
SIDE.
On the left side or at the start of the chain, you always have
a free amino group Amino group that did not participate
in peptide bond formation N-TERMINAL AMINO ACID
On the right side of the chain or at the end of the chain, you
always have a free carboxyl group Carboxyl group that did
not use C-TERMINAL AMINO ACID
B. Nomenclature How Peptide Chains are Named
When you name the chain, you always change the ending of the
amino acid into ly EXCEPT for the last amino acid.
Example: ALA-SER-LYS (Alanine-Serine-Lysine) Alanyl-Seryl-
Lysine
Peptides are named from the sequence of their constituent amino
acids Beginning at the left with the N-terminal residue and
proceeding towards the C-terminal residue at the right
Amino acid residues in polypeptides:
Drop the suffix ine or ate in the name of the amino acid
Replace it by yl except for the C-terminal amino acid (retains its
original name
-ine ending in amino acids indicates that its -carboxyl group is not
involved in peptide bond formation
Example: SER-ALA-LYS-PHE-GLU-TYR
Seryl-Alanyl-Lysyl-Phenylalanyl-Glutamyl-Tyrosine
C. Evidences that a Peptide Linkage Exist in Proteins
1. Positive reaction to Biuret Test
Biuret Test = general test for proteins
For as long as you have at least 2 peptide bonds, it will react
with the Biuret Test.
2. Relatively few titratable amino and carboxyl functions
There will be relatively few titratable amino and carboxyl
functions as you form the peptide chains
For every amino acid, there will be 1 amino group and 1
carboxyl group that is titratable For every amino acid, there
is atleast 2 titratable groups.
When you form the bonds, you always use either the amino
group and carboxyl group You expect to the number of
titratable groups to be less.
When you form the bonds, you always use the amino group
and LEA THERESE R. PACIS 12
 CHEMISTRY OF AMINO ACIDS, PEPTIDES, AND PROTEINS PART 1 DR. SANTOS

ALANYL-SERYL-LYSYL-ASPARTYL-METHIONINE:

When the amino acids are taken separately:

Alanine = 2 titratable groups (Carboxyl Group and Amino
Group)
Serine = 2 titratable groups (Carboxyl Group and Amino
Group)
Lysine = 3 titratable groups (Carboxyl Group, Amino Group,
and Amino Group at the R-Group)
Aspartic Acid = 3 titratable groups (Carboxyl Group, Amino
Group, and Carboxyl Group at the R-Group)
Methionine = 2 titratable groups (Carboxyl Group and
Amino Group)
Total Titratable Groups = 12

When you form the chain:

Total Titratable Groups = 4
Why 4?
- 4 Peptide Bonds X 2 (2 Titratable Groups Used = 1
Carboxyl Group + 1 Amino Group) = 8
- 12 Total Titratable Groups (when amino acids are taken
separately) 8 = 4

3. Hydrolyzed by enzymes which are specific for the peptide bond

Enzymes are specific when it comes to the type of bond that

react on.

4. X-ray diffraction studies proved the existence of peptide linkages

between amino acids in hemoglobin and myoglobin
5. Synthesis of Insulin

**To be continued

1-C ORANGE BALLS, you are missed. Huu

Lea

LEA THERESE R. PACIS 13