BIOCHEM – lecture What are the Structures and Properties of

AMINO ACIDS AND PEPTIDES Amino Acids?

Protein: Structure and Function
Types of proteins
 Structural - for support of structures and tissues; ex.
Collagen, elastin
 Catalytic - for hastening biochemical reactions; Ex.
Amylase
 Transport –for transport of other substances;
Ex. Hemoglobin, protein channels in cellular membranes
 Regulation –for regulation/coordination of bodily
activities; Ex. Insulin, glucagon
 Receptor –for response of cell to external stimuli;
Ex. Neuron receptors in nerve cells
 Contractile –for movement; Ex. Myosin, actin
 Defensive –for protection against disease; Ex. Antibodies
Amino Acid General Structure
 Contains the ff. chemical/functional groups attached to
α-carbon:
- Amino group
- Carboxyl group
- Side chain group (R) –helps classify the amino
acids and determines its properties
 Amino acids contain a central tetrahedral
carbon atom
•There are 20 common amino acids
•Amino acids can join via peptide bonds
•Rarely, several other amino acids occur in
proteins
•Some amino acids are not found in proteins
Anatomy of an amino acid. Except for proline
and its derivatives, all of the amino acids
commonly found in proteins possess this type
of structure.
Two amino acids can react with loss of a water
molecule to form a covalent bond. The bond
joining the two amino acids is called a peptide
bond.

Amino Acid: Stereochemistry

 All amino acids (except glycine) have at least one
The 20 Common Amino Acids
stereocenter(α-C) and are chiral.
You should know names, structures, 3-letter and
 Two stereoisomers:
1-letter codes
- L-and D-amino acid are mirror images
Classification :
(enantiomers)
•Nonpolar amino acids –cannot interact with
- α-amino acids occurring in nature are of the L-
water
configuration
•Polar, uncharged amino acids
•Acidic amino acids
•Basic amino acids

•According to Nutritional Requirements (based on

the ability to synthesize de novoby the organism)
–Non-essential –A, N, Q, D, C, E, G, P, S, Y
–Essential –H, I, L, K, M, F, T, W, V, R
Review – Stereochemistry
 Stereochemistry -involves the study of the
relative spatial arrangement of atoms; also
called 3D chemistry
 Chiral C –the carbon with 4 different
groups attached to it.
 Compounds with chiral Care capable of
forming enantiomers or mirror images.
Non-polar (hydrophobic) amino acids
Polar, uncharged amino acids

“relatives”

Basic amino acids

Acidic amino acids

 Remember: An amino acid contains
ionizablechemical groups (carboxyl and amino
groups)attached to α-carbon.
– Carboxyl group (-) and amino group
(+) are charged at neutral pH.

– Without charged groups on side

Several Amino Acids Occur Rarely in Proteins chain, amino acids exist in neutral
We'll see some of these in later chapters solution as zwitterions with no net
•Selenocysteine in many organisms charge
•Pyrrolysine in several archaeal species Titration of Amino Acids
•Hydroxylysine, hydroxyproline-collagen
•Carboxyglutamate - blood-clotting proteins
•Pyroglutamate– in bacteriorhodopsin
•Phosphorylated amino acids –a signaling device

When an amino acid is titrated, the titration curve

represents the reaction of each functional group
with the hydroxide ion
Ionization of Amino Acids

(b) Some amino acids are less common, but

nevertheless found in certain proteins. Hydroxylysine
and hydroxyproline are found in connective-tissue
proteins; carboxy-glutamate is found in blood-clotting
proteins; pyroglutamate is found in bacteriorhodopsin.

(c) Several amino acid derivatives that act as

neurotransmitters and hormones.

Acid- Base Properties of an Amino Acid Titration of histidine with NaOH

 •is usually found in the transconformation
•has partial (40%) double bond character
•N partially positive; O partially negative
Isoelectric pH •has a length of about 0.133 nm -shorter than a
typical single bond but longer than a double bond
 Isoelectric pH, pI: the pH at which the majority of Due to the double-bond character of the peptide
molecules of a compound in solution have no net bond, the six atoms of the peptide bond group
charge define a plane –the amide plane
𝑝𝐾𝑎1 + 𝑝𝐾𝑎2
𝑝𝐼 =
2

–the pI for glycine, for example, falls midway between

the pKa values for the carboxyl and amino groups
1
𝑝𝐼 = ( 𝑝𝐾𝑎 𝛼 − 𝐶𝑂𝑂𝐻 + 𝑝𝐾𝑎 𝛼 − 𝑁𝐻3 )
2
1
= (2.35 + 9.78) = 6.06
2
–Net charge of an amino acid:
•pH < pI negative
•pH = pI neutral
•pH > pI positive
^the trans conformation of the peptide bond
What is the Fundamental Structural Pattern in Proteins?
What is the Fundamental Structural Pattern in
•Proteins are unbranched polymers of amino acids Proteins?
•Amino acids join head-to-tail through formation of
covalent peptide bonds
•Peptide bond formation results in release of water
•The peptide backbone of a protein consists of the
repeated sequence –N-Cα-Co-
•“N”is the amide nitrogen of the amino acid
•“Cα”is the alpha-C of the amino acid
•“Co”is the carbonyl carbon of the amino acid
(a) The peptide bond has partial double bond
character. One of the postulated resonance forms
is shown here.
Peptide formation is the creation of an amide bond
between the carboxyl group of one amino acid and the
amino group of another amino acid.

The Peptide Bond

•The peptide bond has considerable C-N double bond

character; stabilized by resonance.
•Rotation about the peptide is restricted.

•Peptide bond structure is planar.

(b) The peptide bond has partial double bond character.
Another of the postulated resonance forms is shown here.

(c) The peptide bond is best described as a resonance
hybrid of the forms shown on the two previous slides.
The coplanar relationship of the atoms in the amide group
is highlighted here by the imaginary shaded plane lying
between adjacent α-carbons.
The Peptide Bond
•In contrast to the peptide bond, rotations are permitted
at the bonds between the amino group and the carbonyl
group with the α-carbon; allowing for two possible
conformations in respect to the α-carbons, trans (highly
favored) and cis conformations.
•N-terminal: residue that has free amino group
•C-terminal: residue that has free carboxyl
group
“Peptides”
•Short polymers of amino acids
•Each amino acid unit is called a residue
•2 residues -dipeptide
•3 residues -tripeptide
•12-20 residues -oligopeptide
•many –polypeptide
“Protein”
One or more polypeptide chains
•One polypeptide chain -a monomeric protein
•More than one -multimeric protein
•Homomultimer-one kind of chain
•Heteromultimer-two or more different chains
•Hemoglobin, for example, is a heterotetramer
•It has two alpha chains and two beta chains
Proteins – Large and Small
 Insulin –consists of an A chain of 21 residues,
and a B chain of 30 residues -total mol. wt. of
5,733
 Glutamine synthetase-12 subunits of 468
residues each -total mol. wt. of 600,000
 α-Connectin(a muscle protein) -MW 2.8 million
 β-Connectin-MW of 2.1 million, with a length of
1000 nm -it can stretch to 3000 nm
The Sequence of Amino Acids in a Protein

•Is a unique characteristic of every protein

•Is encoded by the nucleotide sequence of DNA
•Is thus a form of genetic information
•Is read from the amino terminus to the carboxyl
terminus