Amino Acids, Peptides,

and Proteins
Introduction to Amino Acids

• Ami no acids form polymers through a nucleophilic attack by the ami no group of an ami no acid at the electrophilic
carbonyl carbon of the carboxyl group of another ami no acid.
• The carboxyl group of the ami no acid must first be activated to provide a better leaving group than OH-.
• The resulting link between the amino acids is an amide link which is called a peptide bond. In this reaction, water is
released. In a reverse reaction, the peptide bond can be separated by water (hydrolysis).
• When two ami no acids link together to form an amide link, the resulting structure is called a dipeptide. Likewise, we can
have tripeptides, tetrapeptides, and other polypeptides. At some point, when the structure is long enough, it is called a
protein. There are many different ways to represent the structure of a polypeptide or protein, each showing differing
amounts of information.
• Proteins are polymers of twenty naturally occurring ami no acids. In contrast, nucleic acids are polymers of just 4 different
monomeric nucleotides.
• Both the sequence of a purotein and its total length differentiate one purotein from another. Just for an octapeptide, there
are over 25 billion different possible arrangements of amino acids. Compare this to just 65536 different oligonucleotides
of 8 monomeric units. Hence the diversity of possible proteins is enormous.
Biopolymer: the monomeric ami no acids are
linked through an
amide bond (the carboxylic acids of one AA with
the -amino
group of a second)

peptide (< 50 amino acids)

protein (> 50 amino acids)
 Structural Features of Amino Acids
Common structure: By properties of their side chains:

By location of ami no group:

Acid-Base Behavior of Amino Acids
Amino acids exist as a zwitterion: a dipolar ion having both a formal positive and
formal negative charge (overall charge neutral).

pKa ~ 5 pKa ~ 9
Amino acids are amphoteric: they can react as either an acid or a
base. Ammonium ion acts as an acid, the carboxylate as a base.

Isoelectric point (pI): The pH at which the amino acid exists

largely in a neutral, zwitterionic form (influenced by the nature
of the sidechain)
Synthesis of Amino
Ami noAcids
Acids

Strecker Synthesis (reductive amination and cyanohydrin formation :

Amydomalonate Synthesis :
 Reactions of Amino Acids
Amino acids will undergo reactions characteristic of the amino (amide formation) and
carboxylic acid (ester formation) groups.

Biochemical Reactions of Amino Acids. Many enzymes involved in amino acid biosynthesis,
metabolism and catabolism are pyridoxal phosphate (vitamin B6) dependent.
Peptides
• Peptides are amino acid polymers containing 2–50 individual units
• Peptides with >50 units are called proteins
• By convention, peptide structures are written with the N-terminal
amino acid on the left and the C-terminal amino acid on the right.
O
H3N CH2 C NH CH CO2
CH3
A dipeptide glycylalanine = gly-ala
Peptides
glycylalanine = gly-ala
O
H3N CH2 C NH CH CO2
CH3
glycine
amino-terminal amino acid
Peptides
glycylalanine = gly-ala
O
H3N CH2 C NH CH CO2
CH3

peptide bond
Peptides
A tetrapeptide:
O O O
H3N CH2 C NH CH C NH CH C NH CH2 CO2
N-terminus CH2OH CH2C6H5 C-terminus

glycylserylphenylalanylglycine
gly-ser-phe-gly
Peptides
• The Peptide (Amide) Bond
• The amide nitrogen is sp2 hybridized and the lone pair is conjugated with the
carbonyl group

• There is considerable C–N double-bond character

• Rotation about the C–N bond is difficult

O O
C C
N N
H H
Peptides
• The Peptide (Amide) Bond
• The amide groups are planar.

gly-ser-phe-gly
Peptides
• The Peptide (Amide) Bond
• The amide groups are planar.
• The R-groups are on opposite sides of the plane.

gly-ser-phe-gly
Peptides
• The only other type of covalent bond between amino acids in proteins and
peptides is the disulfide linkage between two cysteine units:

NH HN
O C C O
CH CH2 S S CH2 CH
HN NH
Peptides
• Note:
• Thiols are readily oxidized to disulfides.
• Disulfides are readily reduced to thiols.

[O]
R SH + HS R R S S R
[H]
Peptides
• Disulfide links serve to connect polypeptide chains:





S S 



 

  
Peptides
• … or can form a macrocycle:
Cys.Tyr.Ile.Glu.Arg.Cys.Pro.Leu.Gly.NH2

S S
bovine oxytocin
Peptides
-Conotoxin G I
S S

Glu-Cys-Cys-Asn-Pro-Ala-Cys-Gly-Arg-His-Tyr-Cys-NH2

S S
• A peptide neurotoxin isolated from the venom of the fish-hunting cone snail Conus
geographicus.

• It is a paralytic toxin that blocks nicotinic cholinoreceptors.

Peptides
• Conotoxin G I
S S

Glu-Cys-Cys-Asn-Pro-Ala-Cys-Gly-Arg-His-Tyr-Cys-NH2

S S
Structure Determination of Peptides
• Amino Acid Analysis. Find out which amino acids and how many make up the
peptide

• Terminal Residue Analysis. Find out what’s on the ends

• N-Terminal Analysis
• Edman degradation

• C-Terminal Analysis
• Carboxypeptidase
Structure Determination of Peptides
• Partial Hydrolysis (enzymatic)
• Hydrolyze the peptide into smaller fragments.
• Trypsin - Cleaves at lys and arg

• Chymotrypsin - Cleaves at phe, tyr, and trp

• Pepsin - Cleaves at phe, tyr, trp, leu, asp, glu

• Cyanogen bromide (not enzymatic) - Cleaves at met

• Determine the sequence of the fragments.

• Successive Edman degradations.
Sample Problem
Give the sequence for a 20 amino acid polypeptide
with amino acid analysis:
gly2ala4leu4phe3trp1lys2met2ser1arg1

• Step 1: Terminal residue analysis:

• N-terminus = ala
• C-terminus = phe
Sample Problem
Step 2: Trypsin hydrolysis (cleaves at lys and arg) gave four fragments:
I. trpphearg
II. alaleuglymetlys
III. leuglyleuleuphe
IV. alaalasermetalaphelys
Sample Problem
Step 2: Trypsin hydrolysis (cleaves at lys and arg) gave four fragments:
I. trpphearg
II. alaleuglymetlys Fragment III represents
III. leuglyleuleuphe the last five amino acids
IV. alaalasermetalaphelys (trypsin does not cleave
at phenylalanine).
Sample Problem
Step 2: Trypsin hydrolysis (cleaves at lys and arg) gave four fragments:
I. trpphearg
II. alaleuglymetlys Either fragment II or IV
III. leuglyleuleuphe must be N-terminus
IV. alaalasermetalaphelys (cannot know which).
Sample Problem
Step 3: Cyanogen bromide cleavage gave three fragments:
1. alaleuglymet
2. alaphelysleuglyleuleuphe
3. lystrppheargalaalasermet
Sample Problem
Step 3: Cyanogen bromide cleavage gave three fragments:
1. alaleuglymet Fragment 2 must be
2. alaphelysleuglyleuleuphe the C-terminus.
3. lystrppheargalaalasermet
Sample Problem
Step 3: Cyanogen bromide cleavage gave three fragments:
1. alaleuglymet
Fragment 1 must be
2. alaphelysleuglyleuleuphe the N-terminus.
3. lystrppheargalaalasermet
Sample Problem
Step 4: We can now assemble the peptide:

BrCN
trypsin trypsin
ala-leu-gly-met-lys-trp-phe-arg-ala-ala

ser-met-ala-phe-lys-leu-gly-leu-leu-phe
BrCN trypsin
Sample Problem
Step 4: We can now assemble the peptide:

BrCN
trypsin trypsin
ala-leu-gly-met-lys-trp-phe-arg-ala-ala

ser-met-ala-phe-lys-leu-gly-leu-leu-phe
BrCN trypsin
Proteins
• biopolymers consisting of many amino acid units connected by
peptide bonds.
• some proteins are the main components in tissue structures
(muscles, hair, nails, skin)
• Protein function depends on structure.
• Depends on various amino acids.
• Primary Structure
• Secondary Structure
• Tertiary Structure
• Quaternary Structure
Proteins

• Primary Structure: The amino acid sequence.

H R O H R O H R O H R O

N C C N C C N C C N C C
H H H H
Peptide chains connected by amide bonds (peptides)
Proteins
• Secondary Structure: The “local” hydrogen-bonding scheme.
• -Helix
H H
C
C
O N
R
H
N R
Hydrogen C
C
bonds O H
R H
C
N
H C
O
Proteins
• Secondary Structure: The “local” hydrogen-bonding scheme.
• -Helix
Proteins
• Secondary Structure: The “local” hydrogen-bonding scheme.
• b-Sheet

O R H O
C CH N C
CH N C CH N
R H O R H

O H R O
C N CH C
N CH C N
H R O H

Interchain hydrogen bonds

Proteins
• Tertiary Structure: How the protein, with all of its regions of secondary structure
(-helix, b-sheet) has folded over upon itself

• Interaction between R-groups is important

• All intermolecular forces we have studied are at play

Proteins
• Tertiary Structure: Chemical bonds between cysteines

CH2 SH + HS CH2

CH2 S S CH2

Disulfide bonds
Proteins
• Tertiary Structure: Interaction between R-groups
CH2 CH3
CH2 CH CH2
O H N NH CH3
CH2
Hydrophobic
Hydrogen bonding interactions

O H
O H
CH2 CH2 C H3N CH2 CH2 CH2 CH2 H
O
C O H O H
Ionic bonding H
H
H Hydrophilic
(“salt bridge”)
O interactions
H
Proteins
• Tertiary Structure: How the protein, with all of its regions of secondary structure
(-helix, b-sheet) has folded over upon itself.
Proteins
• Tertiary Structure: How the protein, with all of its regions of secondary structure
(-helix, b-sheet) has folded over upon itself.

-Helix regions
Proteins
• Tertiary Structure: How the protein, with all of its regions of secondary structure
(-helix, b-sheet) has folded over upon itself.

b-Sheet regions
Proteins
• Quaternary Structure: How protein subunits aggregate into a larger
functional unit.

Hemoglobin has two  and two b

subunits that fit together to form
the whole hemoglobin molecule
with four hemes and their
associated iron atoms to
transport O2 and CO2