PHA6112 - Lec - Amino Acids and Peptides

UNIVERSITY OF SANTO TOMAS
FACULTY OF PHARMACY BATCH 2025

PHA6112_LEC: PHARMACEUTICAL BIOCHEMISTRY
PROFESSOR CRISLEE M. TORIO, MSPh, PhD
OUTLINE
I. Biochemical functions of protein ● Peptides are amino acids joined together
systems ○ If longer, it is called polypeptide
II. Amino acid structure and classification ● Protein - at least 40 amino acids in a peptide
III. Amino acid interactions ● When proteins are hydrolyzed, they will have
amino acid residues
a. Acid-base behavior of amino acids
b. Oxidation ● Prefixes are used to name peptides
IV. Peptide bond formation, structural ○ E.g.: monopeptide, dipeptide,
features and stability tripeptide…
V. pI calculation of amino acids and ○ Dodecapeptide: 20 amino acids
peptides ○ Oligopeptide (few): 20-40 amino
acids
UNIT 1: Amino Acids & Peptides BIOCHEMICAL STRUCTURE OF PROTEINS

Structural
BIOCHEMICAL FUNCTIONS OF PROTEIN ● For supporting of structures and tissues
SYSTEMS ○ E.g.: collagen (bones and skin),
elastin (skin)
PROTEINS
Catalytic
● Naturally occurring, unbranched (Continuous)
● For hastening biochemical reactions
polymers in which the monomer units are
● Also called as enzymes
amino acids
○ E.g. amylase (saliva), lipase
● The 2nd most abundant substance in nearly all
(pancreas)
cells (15% of a cell’s overall mass)
Transport
● Contain C, H, O, N, S and sometimes contain
● For transport of other substances
Fe, P and some metals (specialized proteins)
○ E.g. hemoglobin (blood)
● Are peptides in which at least 40 amino acids
Regulation
are present
● For regulation/coordination of bodily activities
○ Several proteins with >10,000 AA
○ E.g. insulin (Beta cells pancreas),
residues are known
glucagon (Alpha cells pancreas)
○ Common proteins have 400-500 AA
Receptor
residues
● For response of cell to external stimuli
○ Small proteins have 40-100 AA
○ E.g. neuron receptors in nerve cells
residues
Contractile
● More than one polypeptide chain may be
● For movement
present in a protein
○ E.g. myosin, actin (muscles)
○ Monomeric (one polypeptide chain)
Defensive
○ Multimeric (2 or more polypeptide
● For protection against disease
chain)
○ E.g. antibodies (blood)
Additional notes:
Additional notes:
● Polymers: made up of many molecules to
make up a macromolecule REGULATION
● Water is the most abundant substance in all ● Insulin: to put the sugar levels DOWN
cells ● Glucagon: to put the sugar levels UP
● Every part of your body is made up of
proteins. AMINO ACID STRUCTURE AND
○ Glycoprotein - sugar + protein
CLASSIFICATION
○ Lipoprotein - lipid + protein
● Iron (hemoglobin): a transport protein AMINO ACIDS
responsible for carrying oxygen
● The building blocks for proteins
ABSALUD, BARROGA, CUISIA, DE PABLO, GATAPIA, MANGANTI, VIZ 1 I 2BPH (A.Y. 2022-2023)
General Structure of Amino Acids

Additional notes:
● Chiral - non-superimposable mirror images

● If you cannot easily determine whether an
amino acid has an L/D designation, use the
CORN rule (based on atomic number)
● Number groups based on priority:
1. CO = Carbonyl group
2. R = R-group
3. N = Nitrogen
4. H = Hydrogen
● Laevus: Clockwise (to the left)

● Contains the following Functional Groups:
● Dexter: Counter clockwise (to the right)
○ Amino group (-NH2)
○ Carboxyl group (-COOH)
○ Side chain group (-R) PRACTICE EXERCISE NO. 1: Given the amino acids, name
the correct designation for the enantiomer.
● All the known amino acids are α-amino acids
ANSWER:
L-Isoleucine
Additional notes: D-Cysteine
L-Tyrosine
● Amino acids are amphoteric. They can
function as either acid or base ● R side chain vary in size, shape, charge, acidity,
○ Amino group is basic functional groups present; and H-bonding
○ Carboxyl group is acidic
ability and chemical reactivity
● CH3CH2NH2 - Ethanamine ● Based on common “R” groups, there are 20 AAs
● COOH has higher priority compared to NH2 that are proteinogenic
Hence, NH2 usually functions as a ● Proteinogenic: 20 proteins that makes up our
substituent body
● α - attached to a major functional group

● Only the R-group varies in every amino acid
● All amino acids have at least one stereocenter

(α-C) and are chiral (except Glycine)
● 2 Stereoisomers (enantiomers)
○ Laevus or L-
○ Dexter or D-
Additional notes:
● R-group determines the characteristics of
the polypeptide chain 2-Amino-3-merc

Cysteine Cys C aptopropanoic
acid
20 COMMON AMINO ACIDS:
NOMENCLATURE 2-Amino-4-carba
Trivial Names Glutamine Gln Q moylbutanoic
● Assigned names acid
Systematic Names
● Amino-carboxylic acid Glutamic 2-Aminopentane
Glu E
Acid dioic acid
Additional notes: Aminoethanoic

Glycine Gly G
acid
● Glycine is achiral because it has two
hydrogen atoms attached to the α-carbon 2-Amino-3-(1H-i
○ H functions as the R-group Histidine His H midazol-4-vl)pro
● α-carbon is a stereogenic center, and could panoic acid
therefore not rotate
● To avoid confusion in nomenclature: 2-Amino-3-meth
○ Aspartic Acid- Asp Isoleucine Ile I
ylpentanoic acid
○ Asparagine- Asn
2-Amino-4-meth
○ Glutamic acid-Glu Leucine Leu L
ylpentanoic acid
○ Glutamine-Gln
2,6-Diaminohex
○ Tryptophan-Trp Lysine Lys K
anoic acid
Three-letter Abbreviations 2-Amino-4-(met

● Used for naming Methionine Met M hylthio)butanoic
acid
● First letter of AA name is compulsory and
capitalized followed by the next two letters not Phenylalani 2-Amino-3-phen
capitalized except for Asparagine (Asn), Phe F
ne ylpropanoic acid
Glutamine (Gln) and Tryptophan (Trp)
One-letter Symbols Pyrrolidine-2-car
Proline Pro P
● Used for comparing AA sequences in proteins boxylic acid
● Usually the first letter of the name
2-Amino-3-hydro
● When more than one AA has the same letter,
Serine Ser S xypropanoic
the most abundant AA gets the first letter acid
2-Amino-3-hydro
One-letter Threonine Thr T
Trivial Name Symbol
Symbol
Systematic Name xybutanoic acid
2-Aminopropano 2-Amino-3-(1H-i
Alanine Ala A Tryptophan Trp W ndol-3-yl)propan
ic Acid
oic acid
2-Amino-5-guani
Arginine Arg R dinopentanoic 2-Amino-3-(4-hy
acid Tyrosine Tyr Y droxyphenyl)pro
panoic acid
2-Amino-3-carba
Asparagine Asn N moyl propanoic 2-Amino-3-meth
Valine Val V
acid ylbutanoic acid
Aspartic 2-Aminobutaned
Asp D
Acid ioic acid
Legend: Small Medium Large
CLASSIFICATION OF AMINO ACIDS:

BASED ON R GROUP
1. Non-polar (9)
● Hydrophobic, found in the interior of a protein
● These are F, L, I, P, V, M, A, W, G
4. Polar Basic (3)

● Contain –NH2 as part of the side chain.
● These are R, H, K
2. Polar-neutral (6)
● Uncharged, contain polar but neutral side
chains
● These are S, C, T, Q, Y, N
OTHER CLASSES
1. The ‘Aromatic’ WYF
3. Polar-acidic (2)
● Contain –COOH as part of the side chain
● These are E, D
2. The ‘Lonesome’ G ○ Can lead to glucose or ketone bodies

– PITTT
● (Exclusively) Glucogenic
○ Can lead to glucose – all else
Additional notes:
● Valine(isopropyl)
● Leucine(sec butyl)
● Isoleucine(isobutyl)
3. The ‘Sulfurated’ MC
● Proline: fused with the amine; involves the
alpha amino group
○ Not aromatic ring
● Phenylalanine(aromatic)
● Thioether (R-S-R)
● Tryptophan: looks like a W (indole ring)
PRACTICE EXERCISE NO. 2: Classify the following AAs

based on the polarity of the R-groups.
4. The ‘Branched’ VIL
ANSWER:
NP, PN, PA, PB
PA-Asp (Aspartine)
NP-Ala (Alanine)
CLASSIFICATION OF AMINO ACIDS: PN-Tyr (Tyrosine)
BASED ON NUTRITIONAL REQUIREMENTS PB-Arg (Arginine)
1. Essential (10) NP-Phe (Phenylalanine)
● A standard AA needed for protein synthesis,
obtained from dietary sources because the AMINO ACID SOURCES
body cannot synthesize it in adequate Complete Dietary Protein
amounts from other substances ● Contains all essential AAs in the amounts the
● F, V, T, W, I, M, H, R, L, K body needs
● R is required in children but is not essential Incomplete Dietary Protein
for adults ● Does not contain adequate amounts of AAs the
Standard Pneumonic: body’s needs
● Limiting AAs is an essential amino acid that is
missing, or present in inadequate amounts, in
an incomplete dietary protein
Complementary Dietary Protein
● (Exclusively) Ketogenic ● Inc dietary protein + inc dietary protein =
○ Can lead to ketone bodies – LL adequate amount of all essential AAs
● Both glucogenic and ketogenic
2. Nonessential (10) ● An unbranched chain of amino acids

● A standard AA needed for protein synthesis but ● Classified based on number of amino acids
can be synthesized by the body present
● A, R, N, D, C, E Q, G, P, S, Y ○ Dipeptide (2AAs), Tripeptide (3AAs),
● R is required in children but is not essential for Oligopeptide (10 to 20 AAs), &
adults Polypeptide (long chain of
unbranched AA)
Additional notes: ● AAs are joined together by peptide bonds
● When we eat FOOD to supply ENERGY to

our body
● Glucose => source of fuel and energy
● Glycogen will be used if you do not eat ● In the same way peptide bonds are formed
● Then, fats will be used for glucose ○ Individual amino acids can be linked
● Proteins will be used after fats by forming covalent bonds between
the –COOH and the –NH2 group
DERIVED AMINO ACIDS ○ Water is eliminated
● Known as “nonstandard” amino acids
● Formed by enzyme-facilitated reaction on a Additional notes:
common AA after that AA has been
incorporated in a protein structure How are amides formed?
○ E.g. cystine (dipeptide), desmosine ● An acid with organic amine to create AMIDE
and isodesmosine hydroxyproline and Amino acids will join together and there is
hydroxylysine found in collagen production of H2O
gamma-carboxylglutamate found in
prothrombin PEPTIDE BONDS
● Represented beginning with the AA with a free
Note: Dopamine, Norepinephrine, Epinephrine, Histamine, NH2 group (N-terminal end) and the other end
Serotonin, and Melatonin are neurotransmitters in contains free carboxyl group (C-terminal end)
psychiatric conditions, other pathologies and drug action
and will be discussed in other subjects (closest one being
Medicinal Chemistry).
● An amino acid residue is the portion of an

amino acid structure that remains after the
release of water when it dissociates from a
peptide chain
BASIC PEPTIDE ANATOMY
Additional notes:
The following structures that are almost similar to each

other:
● Tyrosine = Dopamine, Norepinephrine,
Epinephrine ● This tripeptide has 2 peptide bonds
● Histidine = Histamine (Amine group) ○ Name: Glycylalanylserine
● Tryptophan = Serotonin and Melatonin
PEPTIDES
● Are a chain of covalently linked amino acids
NOMENCLATURE OF PEPTIDES ● Alanylglycine (GA)

● Each amino acid beginning from the N-terminal
end that has the -ine or -ic acid is replaced by
-yl
● The last amino acid at the C-terminal end of the
peptide has its full name
○ E.g Serine-Asparagine-Aspartic
acid-Glutamic acid (Ser-Asn-Asp-Glu)
○ SerylAsparaginylAspartyl Glutamic
acid
Additional notes:
● No functionality is need to be considered

when naming peptides
ACTIVITY NO. 1: Draw the dipeptides, glycylalanine, and

alanylglycine Isomeric Peptides
● Glycylalanine (GA)
● The two dipeptides are constitutional isomers,
i.e. made up of the same AA but different order.
● Are they one and the same protein? No! They
are totally different in chemical and physical
properties. Thus, the sequence of AA in
peptides and peptides in proteins are very
important.
Additional notes:
● Amino terminal and Carboxy terminal should

not be interchanged
● Cysteine can create disulfide bond
● Differ in position 3 and 8
● Oxytocin: ends with Glycine(NH2)
SMALL PEPTIDE HORMONES

● Oxytocin and vasopressin produced by the
pituitary gland; nonapeptides with 6 AA held in
a loop by S-S (disulfide) bond from 2 Cysteine
residues; differ in position 3 and 8
○ Take note that the OH of the COOH
at the terminal (Glycine residue) was
replaced by -NH2
SMALL PEPTIDE ANTIOXIDANT

Additional notes:
● Glutathione is a tripeptide that regulates
● When cells are damaged, a polypeptide re-dox reactions; protects cells from oxidizing
called Bradykinin is released which agents; Glu (E) is bonded to Cys (C) through the
stimulates the release of prostaglandins -COOH side chain and not at the α-COO-
● When you are injured, the defense
mechanism will be released
SMALL PEPTIDE NEUROTRANSMITTERS

● Enkephalins are pentapeptides produced by
the brain; natural analgesics
○ Two best known are Met-enkephalin
and Leu-enkephalin
○ The two differ only in the last AA
residue as their names imply
SMALL PEPTIDE
● Aspartame
○ L-aspartyl-L-phenylalanine methyl
ester
IONIZATION (pH SHIFTS)

Additional notes:
● Net charge: the charge in the species will be

equal to 0 (cancelling each other)
● The ionized form of NH2 is NH3

● NH2 can actually acquire a positive charge
● The ionized form of COOH, if it is Acidic Basic

deprotonated, oxygen will be given the bond. Condition Group Group Process
Thus, it will result to negative charge (-COOH) (-NH2)
Ionized
AMINO ACID INTERACTIONS Neutral to
pH < pKa Protonated
(COOH) Positive
ACID-BASE BEHAVIOR OR AMINO ACIDS (NH3+)
● In pure from, AAs are white crystalline solids
● Most decompose before melting Ionized to
Neutral
● Not very soluble in water pH > pKa Negative Deprotonated
(NH2)
● Under physiological conditions, exists as (COO-)
zwitterions
● For an AA with R group that is either acidic or

basic, where the side chain can acquire a
charge, and thus may have several forms.
○ The species with ZERO net charge is

○ Aspartic Acid
called Zwitterion or Double ion
(hybrid ion - one positive and one
negative canceling each other) Additional notes:
● pKa = dissociation constant; innate and

Additional notes: never changing
● pH: measure of acidity; [H+] concentration ● pH < pKa: pH less: acidic; ionized to positive
● It will turn to Zwitterion, It happens when it (NH3+); Protonated (nothing happens)
is in a solution or inside our body
● pH > pKa: ionized to negative; Neutral; base
● If a given AA is exposed in low pH, it is group
protonated
● Net charge is +1
PRACTICE EXERCISE NO. 1: Draw the structure form of
● If a given AA is exposed in high pH, it is the amino acid valine that predominates in solution at
deprotonated each of the following pH values.
● Net charge is -1
● AAs can exist in 3 forms (zwitterion and ionized

- positive ion and negative ion) when in solution
● Equilibrium shifts with change in pH
a. pH = 7.0 b. pH = 12.0 c. pH = 2.0
ANSWER:
Note: Out of the 20 common amino acids, 7 have ionizable

groups. Specifically, α-carbonyl, α-amino, Asp | Glu, Arg,
His, Lys, Cys, and Tyr.
pI CALCULATION OF AMINO ACIDS AND

PEPTIDES
ISOELECTRIC POINT (pI OR ipH)

● pH at which the concentration of zwitterion is
at its maximum
● Different AAs have different ipH (refer to ANSWER:
Stoker) a. Proline-6.30
○ Nonpolar or polar neutral have ipH b. Methionine-5.75
4.8-6.3
○ Polar basic - high ipH What are the amino acids with R groups that are
○ Polar acidic - low ipH ionizable?
● At ipH, AAs are not attracted to applied electric
fields because they carry net zero charge
Additional notes:
● R-group ionization
● Asp
● Glu
● His
● Cys
● Tyr
● Lys
● Arg
● Asp and Glu
● Side Chain: have RCOOH
● His, Lys and Arg
● Side chain:have NH2(basic side)
● Cys and tyr(Pn):
● Side chain: have phenol
● CYDERHK: AA that has side chain that can

be ionized
Note: For these amino acids, the R group ionization
occurs before the α-NH3+ ionization.
PRACTICE EXERCISE NO. 2: How do you determine ipH?

(simply average the pKas) What is the ipH of the
following:
a. Proline b. Methionine
PEPTIDE ipH
PRACTICE EXERCISE NO.1: What is the ipH of the
dipeptide Gly-Asp?
Steps:
1. Draw the peptide with the ionizable groups
2. Protonate/deprotonate all ionizable groups.
3. Find the net charge (max charge)
4. Determine how many units away from zero is
What is the ipH of aspartic acid given the following pKas: the max charge
5. Find pKa before and after zero
COOH = 2.09 NH2 = 9.82 R = 3.86 6. Average the pKa between the no net charge
REFERENCES
● Campbell, Harper Voet, D. Voet, J.G, Pratt
C.W.(2013). Principles of Biochemistry 4th ed.
Singapore pte. Ltd.:John
● Lehninger’s Principles of Biochemistry 4th
What is the ipH of lYS acid given the following pKas: Edition
● Murray et.Harper’s Biochemistry 26th Edition
COOH = 2.18 NH2 = 8.95 R = 10.53 ● Stoker, H Stephen (2017). General, organic and
biological chemistry 3rd ed., Cengage learning
STOKER
What are the ipHs of tyrosine and cysteine given the

values? (Although tyrosine and cysteine are not classified
as acidic, their R groups are fairly acidic. Consider them
“acid-like” amino acids when computing for ipH)
Cys 1.71 10.78 8.33*

Tyr 2.20 9.11 10.07
AMINO ACIDS INTERACTIONS

Redox Reaction
a. Oxidation
● Addition of O and removal of H
b. Reduction
● Addition of H and removal of O

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UNIVERSITY OF SANTO TOMAS

FACULTY OF PHARMACY BATCH 2025

UNIT 1: Amino Acids & Peptides BIOCHEMICAL STRUCTURE OF PROTEINS

General Structure of Amino Acids

● Chiral - non-superimposable mirror images

● Laevus: Clockwise (to the left)

● α - attached to a major functional group

● All amino acids have at least one stereocenter

● R-group determines the characteristics of

the polypeptide chain 2-Amino-3-merc

Additional notes: Aminoethanoic

Three-letter Abbreviations 2-Amino-4-(met

Legend: Small Medium Large

CLASSIFICATION OF AMINO ACIDS:

4. Polar Basic (3)

2. The ‘Lonesome’ G ○ Can lead to glucose or ketone bodies

● Tryptophan: looks like a W (indole ring)

PRACTICE EXERCISE NO. 2: Classify the following AAs

2. Nonessential (10) ● An unbranched chain of amino acids

● When we eat FOOD to supply ENERGY to

● An amino acid residue is the portion of an

BASIC PEPTIDE ANATOMY

The following structures that are almost similar to each

NOMENCLATURE OF PEPTIDES ● Alanylglycine (GA)

● No functionality is need to be considered

ACTIVITY NO. 1: Draw the dipeptides, glycylalanine, and

● Amino terminal and Carboxy terminal should

SMALL PEPTIDE HORMONES

SMALL PEPTIDE ANTIOXIDANT

SMALL PEPTIDE NEUROTRANSMITTERS

IONIZATION (pH SHIFTS)

● Net charge: the charge in the species will be

● The ionized form of NH2 is NH3

● The ionized form of COOH, if it is Acidic Basic

● For an AA with R group that is either acidic or

○ The species with ZERO net charge is

● pKa = dissociation constant; innate and

● AAs can exist in 3 forms (zwitterion and ionized

a. pH = 7.0 b. pH = 12.0 c. pH = 2.0

Note: Out of the 20 common amino acids, 7 have ionizable

pI CALCULATION OF AMINO ACIDS AND

ISOELECTRIC POINT (pI OR ipH)

● CYDERHK: AA that has side chain that can

PRACTICE EXERCISE NO. 2: How do you determine ipH?

What are the ipHs of tyrosine and cysteine given the

Cys 1.71 10.78 8.33*

AMINO ACIDS INTERACTIONS

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