Biochemistry

Chapter 2:
Amino Acids, Peptides
 CHAPTER 2
Amino Acids, Peptides,
Proteins

Learning goals:
• Structure and naming of amino acids

• Structure and properties of peptides

• Ionization behavior of amino acids and peptides

 Proteins:
Main Agents of Biological Function
• Catalysis
– enolase (in the glycolytic pathway)
– DNA polymerase (in DNA replication)

• Transport
– hemoglobin (transports O2 in the blood)
– lactose permease (transports lactose across the cell membrane)

• Structure
– collagen (connective tissue)
– keratin (hair, nails, feathers, horns)

• Motion
– myosin (muscle tissue)
– actin (muscle tissue, cell motility)
 Amino Acids:
Building Blocks of Protein
• Proteins are linear heteropolymers of -amino acids

• Amino acids have properties that are well-suited to carry

out a variety of biological functions
– Capacity to polymerize
– Useful acid-base properties
– Varied physical properties
– Varied chemical functionality
Amino acids share many features,
differing only at the R substituent
 Most -amino acids are chiral
• The -carbon always has four substituents and is
tetrahedral
• All (except proline) have:
– an acidic carboxyl group
– a basic amino group
– an -hydrogen connected to the -carbon
• The fourth substituent (R) is unique
– In glycine, the fourth substituent is also hydrogen
 Amino Acids: Atom Naming
• Organic nomenclature: start from one end
• Biochemical designation:
– start from -carbon and go down the R-group
 All amino acids are chiral (except glycine)

Proteins only
contain L amino
acids

L- and D-alanine, are nonsuperposable mirror images of each other (enantiomers)

 Amino Acids: Classification

Common amino acids can be placed in five basic

groups depending on their R substituents:
• Nonpolar, aliphatic (7)
• Aromatic (3)
• Polar, uncharged (5)
• Positively charged (3)
• Negatively charged (2)
 Polarity

The presence of –NH2 and –COOH is common in all alpha amino

acids, only the side chain vary from molecule to molecule.

The side chain effects the polarity of a molecule because –NH2

group and –COOH on an alpha carbon atom can neutralise each
other. On the basis of polarity, amino acids can be classified as polar
and non-polar amino acids. 

Polar amino acids can again classify as positively charged and

negatively charged amino acids.
 Amino Acids: Classification

Non Polar Amino Acids have equal number of amino and carboxyl groups and are
neutral. These amino acids are hydrophobic and have no charge on the 'R' group.
 Amino Acids: Classification

These amino acid side chains absorb UV light at 270–280 nm

 Amino Acids: Classification

These amino acids side

chains can form
hydrogen bonds as
proton donors or
acceptors.
Cysteine can form
disulfide bonds.

These amino acids do not have any charge on the 'R' group. These amino acids
participate in hydrogen bonding of protein structure.
 Amino Acids: Classification

+
H

Polar amino acids with positive charge have more amino groups as compared to
carboxyl groups. The amino acids, which have positive charge on the 'R' group are
placed in this category.
 Amino Acids: Classification

Polar amino acids with negative charge have more carboxyl groups than amino
groups. The amino acids, which have negative charge on the 'R' group are placed in
this category.
 Amino Acids: Codes

Alanine Ala A Histidine His H

Arginine ArgR Isoleucine Ile I
Asparagine Asn N Leucine LeuL
Aspartic acid Asp D Lysine Lys K
Cysteine Cys C Methionine MetM
Glutamic acid Glu E Phenylalanine Phe F
Glutamine Gln Q Threonine Thr T
Glycine Gly G Tryptophan Trp W
Proline Pro P Valine Val V
Serine Ser S
Tyrosine Tyr Y
 Ionization of Amino Acids
• At acidic pH, the carboxyl group is protonated and the amino
acid is in the cationic form.
• At neutral pH, the carboxyl group is deprotonated but the
amino group is protonated. The net charge is zero; such ions
are called Zwitterions.
• At alkaline pH, the amino group is neutral –NH2 and the amino
acid is in the anionic form.
 Ionization of Amino Acids

Titration curves are obtained when the pH of

given volume of a sample solution varies after
successive addition of acid or base. The curves
are usually plots of pH against the volume of
titrant added or more correctly against the
number of equivalents added per mole of the
sample. This curve empirically defines several
characteristics:  
the pKa of the ionizing group(s), the buffer
region(s).
 Ionization of Amino Acids
Isoelectric point (pI) of amino acids
Isoelectric point is the pH of an amino acid at which it has no net electric charge.
For amino acids that have no ionizable side chain, the pI value is the average of its two pKa’s.
Consider glycine. Look at the equilibrium below; as we add hydroxide ions—in other words,
raise the pH—different charged forms of glycine exist. Form B has a net zero charge and is
called a zwitterion. Form A has a net charge of +1, and form C has a net charge of -1.
 Ionization of Amino Acids

Cation  Zwitterion  Anion

 Amino acids can act as buffers

Amino acids with uncharged side chains, such as glycine,

have two pKa values:
The pKa of the -carboxyl group is 2.34
The pKa of the -amino group is 9.6
It can act as a buffer in two pH regimes.
 Amino acids can act as buffers

Buffer
Regions
(zones)

In the middle part of the curve, it is flat because the addition of base or acid does
not affect the pH of the solution drastically - this is the buffer zone. However, once
the curve extends out of the buffer region, it will increase tremendously when a
small amount of acid or base added to the buffer system.
Amino acids carry a net charge of zero
at a specific pH (the pI)
• Zwitterions predominate at pH values between the pKa values of
the amino and carboxyl groups
• For amino acids without ionizable side chains, the Isoelectric Point
(equivalence point, pI) is

• At this point, the net charge is zero

– Amino acid is least soluble in water
– Amino acid does not migrate in electric field
Example:
Ionization of Amino Acids

When pH = pK: When the pH is equal

to pK1 (2.3), equal amounts of Forms
I and II of alanine exist in solution.
When the pH is equal to pK2 (9.1),
equal amounts of Forms II and III are
present in solution.
 Ionizable side chains can show up in
titration curves

• Ionizable side chains can be also titrated

• Titration curves are now more complex
Titration curve of Histidine
( Ionizable side chains)
 How to Calculate the pI When the
Side Chain is Ionizable
If the amino acid has an ionizable side chain, the pI value is the average of the
pKa’s of similarly ionizable groups.

What is the pI of histidine?

pI = 6 + 9.17 = 7.59
2
Peptides
 Formation of Peptides
• Peptides are small condensation products of amino acids
• They are “small” compared to proteins (Mw < 10 kDa)

In condensation, two amino acids approach each other, with the acid moiety of
one coming near the amino moiety of the other. One loses a hydrogen and oxygen
from its carboxyl group (COOH) and the other loses a hydrogen from its amino
group (NH2). This reaction produces a molecule of water (H2O) and two amino
acids joined by a peptide bond (-CO-NH-). The two joined amino acids are called a
dipeptide.
 Peptide ends are not the same
Numbering (and naming) starts from the amino terminus
AA1 AA2 AA3 AA4 AA5

The pentapeptide serylglycyltyrosylalanylleucine, Ser–Gly–Tyr–Ala–Leu, or SGYAL.

Peptides are named beginning with the amino-terminal residue, which by convention
is placed at the left. The peptide bonds are shaded in orange; the R groups are in pink.
 Naming peptides:
start at the N-terminus
• Using full amino acid names
– Serylglycyltyrosylalanylleucine
• Using the three-letter code abbreviation
– Ser-Gly-Tyr-Ala-Leu
• For longer peptides (like proteins) the one-
letter code can be used
– SGYAL
 Peptides: A Variety of Functions
• Hormones and pheromones
– insulin (think sugar)
– oxytocin (think childbirth)
– sex-peptide (think fruit fly mating)

• Neuropeptides
– substance P (pain mediator)

• Antibiotics
– polymyxin B (for Gram – bacteria)
– bacitracin (for Gram + bacteria)

• Protection, e.g., toxins

– amanitin (mushrooms)
 Proteins are:
• Polypeptides (covalently linked -amino acids) + possibly:
• cofactors:
 functional non-amino acid component (coenzymes)
 metal ions or organic molecules (prosthetic groups)
coenzymes
 organic cofactors (like vitamins); bind loosely
 NAD+ in lactate dehydrogenase
prosthetic groups
 covalently attached cofactors
 heme in myoglobin
• other modifications
Polypeptide size and number
varies greatly in proteins
Classes of Conjugated Proteins
 Chapter 2: Summary

In this chapter, we learned about:

• The many biological functions of peptides and proteins

• The structures and names of amino acids found in

proteins

• The ionization properties of amino acids and peptides