Chapter 3: Amino Acids, Peptides,
Proteins
HLY-JU-JS-CD
Amino Acids (AA) are the building
blocks of peptides and proteins
Peptides generally contain 2-10 AA
 Polypeptides contain 10-100 AA
 Proteins contain >100 AA
General structure of AA:
at pH ~7.4:

L-Amino Acids are the biologically
relevant enantiomer
Of the 20 common AA, 10 of them
are considered essential

see page 67 of your book
Of the 20 common AA, 10 of them
are considered essential
see page 67 of your book
 Mnemonics: MILK FTW RHV
 “ESSENTIAL” = cannot be produced de
novo by the body
 Some AA are conditionally essential
 Note though that there are now more
than 20 AA! (but we will only focus on
the 20)

Selenocysteine is a derivative of Cys
used to derive protein structures
The 20 AA can be grouped
according to functional classes
Aliphatic (GAVLIMP)
 Aromatic (WYF)
 Polar, uncharged (CHNQST)
 Polar, charged – acidic (DE)
 Polar, charged – basic (RK)
*Histidine is basic but uncharged

See structures on page 70 of your book.
There are 7 AA With Aliphatic Side
Chains
Pro is an aliphatic AA with the amino and
the acid group in one 5-membered ring
There are 3 AA with Aromatic Side
Chains
Of the 6 polar uncharged AA, 2 have
Hydroxyl Side Chains (except Tyr)
One AA has a Sulfhydryl (-SH) Side Chain
There are 3 AA With Basic Side Chains, 2
of them ccharged (RK)
Two AA have acidic side chains (DE). Their
amide counterparts (NQ) are polar, uncharged
Chemical reactivity of AA are
dependent on their “R group”
AA structures and reactivity will be
important in understanding protein
structures and functions
 AA electric charges also affects protein
structure and function

Isoelectric point (pI) of an AA (or
peptide/protein) is equal to the pH
when net charge = 0
Isoelectric point (pI) of an AA (or
peptide/protein) is equal to the pH
when net charge = 0
pK1: -COOH  -COO- + H+
pK2: -NH3+  -NH2 + H+
pKR: -RH  -R- + H+
AA net charge is (-) if pH > pI,
and (+) if pH < pI

pI is estimated to be the AVERAGE of the
two pK values representing neutral
species.
AA net charge is (-) if pH > pI,
and (+) if pH < pI
CASE I: ONLY TWO IONIZABLE
GROUPS:
Ex. Alanine:

AA net charge is (-) if pH > pI,
and (+) if pH < pI
Case II: MORE THAN TWO IONIZABLE
GROUPS.
Ex. Aspartic Acid
Activity, open book/notes BUT no
talking (20 points)
1.
2.
3.
Determine the pI of Lysine. Show ALL
conformations and the net charges at
different pH’s.
Draw the titration curve for Lysine.
Determine the inflection points, and
draw the structure/s of Lysine at each
interval (i.e., before pK1, at pK1, after
pK1 but before pK2, etc.)
AA can link together via AMIDE
BOND to form peptides
• Two ends are form: amino or N terminus and
carboxyl or C terminus
• Peptide formation is a condensation reaction
(loss of H2O)
AA can link together via AMIDE
BOND to form peptides

VIDEO!
Peptides are cleaved via hydrolysis
Acids, bases or enzymes can be used to
facilitate the hydrolysis
 In our stomach or intestine, peptidases or
proteases are present
 Enzymes specific to some AA are used for
protein analysis (more of this later )

Proteins in our body play different
important roles
Biological functions of proteins depend on
the AA sequence (central dogma!)
 Six major classes of protein functions:

◦
◦
◦
◦
◦
◦
Enzyme
Transport and Storage Proteins
Structural Proteins
Muscle Contraction and Mobility Proteins
Regulatory and Receptor Proteins
Immune or Defense Proteins
There are six major classes of functions
of proteins
1.
Catalysts (Enzymes)
•The largest class of proteins, accelerate rates of reactions
DNA Polymerase
2.
CK2 Kinase
Catalase
Transport & Storage
Hemoglobin
Serum albumin
Ion channels
Ovalbumin
There are six major classes of functions
of proteins
3.
Structural
Collagen
4.
Keratin
Silk Fibroin
Generate Movement
Actin
Myosin
There are six major classes of functions
of proteins
5.
Regulation of Metabolism and Gene Expression
Lac repressor
Insulin
6.
Protection
Immunoglobulin
Thrombin and
Fibrinogen
Venom Proteins
Proteins have four levels of
structure