Amino acids: building blocks
of proteins
1
Proteins
• All proteins are composed of amino
acids
• There are 20 common amino acids
• Not every protein contains all 20 amino
acids
2
Amino Acids:
Structure Overview
• 20 amino acids
a-Carbon:
4
2
1
3
1. Primary amino group
(exception is proline)
2. Carboxylic acid
3. Hydrogen atom
4. R group
•
Side chain
3
20 Standard Amino Acids
Know all names,
& 3-letter &
1-letter Abbrev.
4
Importance of side chain
characteristics
• In a biological system, we classify molecules on the
basis of their polarity, their interaction with water
– Polar vs. Non-Polar
• Polar side chains will form favorable interactions
with water and each other
– Hydrophilic interactions such as hydrogen bonds, ionic and
dipole interactions
• Non-polar side chains will interact with each other
rather than with water or polar side chains
– Hydrophobic interactions
Know and understand classifications (It will help
make easier the memorization of all amino acids)
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Classification of Amino acids
•
•
•
–
–
Based on R group, or side chain
The side chain, determines the structural range
and general physical characteristics of the amino
acids
The amino acids are generally grouped according
to the various characteristics of their R groups
Non-polar amino acids (hydrophobic)
Polar amino acids (hydrophilic)
•
•
•
uncharged (no charge at physiological pH, 7.4)
+ charged (+ charge at physiological pH, 7.4)
- charged (- charge at physiological pH, 7.4)
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Nonpolar Aliphatic R groups
Gly, G
Ala, A
Pro, P
Val, V
Ile, I
Met, M
• Form hydrophobic
interactions
• Will
– Minimize contact
with water
– Want to associate
with other
hydrophobic groups
• Will NOT
– form hydrogen
bonds
– participate in ionic
or dipole
interactions
Leu, L
7
Aromatic R Groups
Characterized by bulk and polarity
Phe, F
Tyr, Y
Trp,W
• Phenylalanine and Tryptophan are also classified as non-polar
• Tyrosine can be also be classified as polar uncharged
– Can participate in hydrogen bonds
8
Uncharged Polar R Groups :
Hydroxyl, Amide and Thiol Groups
Ser, S
Thr, T
Cys, C
• Uncharged at pH 7.4
• Hydrophilic
• These side chains like to
participate in hydrogen
bonds
– Contains polar atoms in side
chains
Asn, N
Gln, Q
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Polar Positively Charged R Groups:
• Positively charged at pH 7.4
– (Histidine ionizes around pH 7.4)
• These side chains are likely to
participate in ionic interactions
• Can be hydrogen bonds donors
H+
+
Lys, K
Arg, R
His, H
10
H
Polar Negatively Charged R Groups
• Negatively charged at
pH 7.4
• These side chains like to
participate in ionic
interactions
• Can be hydrogen bonds
acceptors
Asp, D
Glu, E
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Hydropathy scale for amino acid residues
• Hydropathy: A measure of
the combined
hydrophobicity and
hydrophilicity of an amino
acid
• Indicative of the
likelihood of finding
that residue in a
protein interior
• Highly hydrophobic
(interior of proteinavoid solvent)
• Slightly hydrophilic
• Highly hydrophilic
(exterior of proteinsolvent exposed)
DO NOT MEMORIZE – UNDERSTAND THE PRINCIPLE
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Amino Acids are Weak Acids
• Weak acids only partially dissociate
• Ka is the ionization constant for a weak acid, HA, in water
• HA  H+ + A-
[H+][A-]
Ka = ----------------[HA]
•
pKa = -log Ka
•
The smaller the pKa, the more acidic the weak acid
– The more likely the acid is to donate an H+
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Ionizable Groups in amino acids
• All amino acids have at least two acid – base groups
– a-carboxyl group (pKa ~2)
– a-amino group (pKa ~9)
pKa 9
pKa 2
• Dipolar ions- Molecules such as amino
acids that contain charged groups of
opposite polarity
– Also referred to as zwitterions
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Amino Acids
General
Structure
• Dipolar ions
– The amino and carboxylic acid
groups ionization state at
physiological pH (~ 7.4)
1. -NH2 has a pKa of ~ 9
pH < pKa, so [HA] > [A-]
7.4 < 9, so [-NH3+] > [-NH2]
Base
Conjugate Acid
2. -COOH has a pKa of ~2
pH > pKa, so [HA] < [A-]
7.4 > 2, so [-COOH] < [-COO-]
Acid
Conjugate Base
Dipolar AA
at pH 7.4
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Amino Acids at Physiological pH
Zwitterions- dipolar ions
- Amino group (+1)
- Carboxylate group (-1)
- Net charge (0)
• At physiological pH (~7.4):
– the amino groups are protonated
– the carboxylic acid groups are in their conjugate base
(carboxylate) form – deprotonated
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Ionization of Amino Acids
• All amino acids are weak polyprotic acids
• Undergo multiple ionization events
– Carboxyl group – pKa of ~2.2; readily ionizes, donating a proton
– Amino group – pKa of ~9.4, ionizes at higher pH
– Can contain other ionizable groups within the side chain
(denoted ‘R’ above)
• Based on your understanding of titration curves, draw a
titration curve for a simple diprotic amino acid
– Identify inflection points, important pKa values and label axis
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values
Titration curve for Diprotic
Acid: Example of Alanine
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Ionizable Groups in amino acids
• All amino acids have at least two acid – base groups
– a-carboxyl group
– a-amino group
• Those with ionizable side chains (R groups) have three
– Lysine
– Arginine
– Histidine
– Glutamic Acid
– Aspartic Acid
– Cysteine
– Tyrosine
– Serine
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– Threonine
pKa Values of Amino Acids
AA
pK (-COOH)
pK (-NH3+)
Gly
2
9
Ala
2
9
Pro
2
9
Val
2
9
Leu
2
9
Ile
2
9
Met
2
9
Phe
2
9
Trp
Gln
Asn
2
2
2
9
9
9
pK (side chain)
NON IONIZABLE
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SIDE CHAINS!
pKa Values of Amino Acids
pH is 7.4 (physiological pH)
AA
Asp
Glu
His
Cys
Tyr
Lys
Arg
Thr
Ser
pK (-COOH)
COO-
SH
OH
NH3+
OH
pK (-NH3+)
pK (side chain)
2
2
9
9
3.7
4.3
2
2
2
9
9
9
6
8
10
2
2
2
9
9
9
10
12
13
2
9
13
pH > pKa
H+ off
pH < pKa
H+ on
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Histidine (His, H)
• The pKa of the His
side chain is ~6
– It is ionizable at
physiological pH
R
His, H
pKa = 6
H+
R
His, H
• Can exist in protonated
and neutral from at
physiological pH
• Oftentimes the
ionization of the His
side chain plays an
important catalytic role
in many enzymes
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Structure varies with pH
• At low pH all ionizable groups are protonated – cationic form
• At mid pH range the zwitterionic form dominates
pH<pKa
H+ on
No net charge
• At high pH the ionizable groups are deprotonated – anionic form pH>pKa
H+ off
H+ on
-NH3+
-COOH
No net charge
-NH3+
-COO-
No H+
-NH2
-COO-
Charge range for amino acids with no charge on their
R-group is +1 → -1
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Structure varies with pH
•
•
•
pH<pKa
At low pH all ionizable groups are protonated – cationic form H+ on
At mid pH range the zwitterionic form dominates No net charge
a
At high pH the ionizable groups are deprotonated – anionic form pH>pK
+
H off
His, pKa 6 – positively charged side chain
H+ on
–NH3+
–COOH &
R-group+
H+ on
–NH3+
R-group+
H+ off
-COO-
H+ on
–NH3+
H+ off
-COO-R-group
H+ off
-COO-NH2
-R-group
For a.a. :
+1 → -1 for no charge on R-group
+2 → -1 for + charged R-group (ie: His, Arg, Lys)
+1 → -2 for – charged R-group (ie: Asp, Glu)
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Isoelectric Point
The pH at which the
molecule carries no net
charge is known as the
isoelectric point or pI
It is important to know
the pI because
compounds are the least
soluble when they have
no net charge
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Easy way to Calculate pI
• List all the pKa values in ascending order
• Calculate net charge for a pH range that includes
each pKa value of all ionizable groups
• Identify the two pKa values that when titrated
result in the net charge changing from :
pKi
pKj
+1 → 0 → -1
• Use these two pKa’s to calculate pI
• pI = ½ (pKi + pKj)
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Titration curve for Ala
No net charge
pI = ½ (pK1 + pK2)
pI = ½ (2 + 9)
pI = 5.5
What about amino acids with Rgroups that contain ionizable groups?
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Histidine Titration
No net charge, so:
pI for His is calculated,
pI = ½ (pK2 + pK3)
pK2
pK1
Net Charge
+2
+1
pK3
0
-1
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pI of His
Example His – 3 pKa values: 2.2 (-COOH) , 6.0 (R-group) & 9.5 (-NH2)
pH <
Net Charge
+2
2.2
< pH <
6.0
+1
< pH <
9.5
0
< pH
-1
pKa1
pKa2
pKa3
pH < 2.2 < pH < 6 < pH < 9 < pH
pI = ½ (pKa2 + pKa3) = ½ (6 + 9) = 7.5
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20 Amino Acids
• Need to know
–
–
–
–
–
Names
3 Letter Abbreviations
1 Letter Abbreviations
Structures
Classification based on side chain
• Non-polar, polar (+/- charged, uncharged)
– pKa values associated with each amino acid
– How to calculate isoelectric point (pI) 30
Tips for Learning Amino Acids
• Amino acid ABC’s
– 26 letters in alphabet, 20
amino acids with a single
letter designation
• ie: A – Alanine, Ala, nonpolar, R group is CH3- a
methyl, hydrophobic,
contains two ionizable
groups – carboxylic acid
and amino groups, pKas of
2 and 9
– Notecards/Flashcards
• Draw amino acid on one
side, put facts on the
back
– Dry Erase boards
• Draw structures and
write out facts
• Must know you amino acids
• Determine your effective
learning style as memorizing
structures and understanding
how they function is a big
part of biochemistry
• Are you visual, audio, tactile?
• Learn to study using an
effective method that fits
your learning type:
– Classifications:
1.Listening learners
2.Seeing learners
3.Touch / experience learners
Remember it isn’t the time you spend studying that counts, but
rather the learning that takes place as a result of the studying
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Suggested Reading and Ch Problems
• Chapter 4
– pp 77-88
• Practice Problem Set will be available
online
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