Proteins are polymers of amino acids joined by peptide bonds. There are 20 common amino acids that make up proteins. Amino acids contain an amino group, a carboxyl group, and a side chain that differs between each amino acid. Proteins can range in size from small peptides of a few amino acids to large polymers of thousands of amino acids. Proteins have primary, secondary, tertiary, and quaternary levels of structure that determine their shape and function in the body.

2. Amino acids,Peptides& Proteins
PrinciplesofBiochemistryBy Albert-Leningher Chap:03
Introduction
• Proteins are the most abundant biological macromolecules, occurring in all cells and all
parts of cells
• Great variety;
– Thousands of different kinds
– Ranging in size from relatively small peptides to huge polymers
• Enormous diversity of biological functions
• The most important final products of the information pathways

3. Amino Acids
• Proteins are polymers of amino acids each residue joined to its neighbor by covalent bond
• Twenty different amino acids are commonly found in proteins
• The first to be discovered was asparagine, in 1806
• The last of the 20 to be found, threonine, in 1938
• All the amino acids have trivial or common names, derived from the source from which
they were first isolated
– Asparagine was first found in asparagus
– Glutamate in wheat gluten
– Tyrosine was first isolated from cheese
• In addition to 20 amino acids there are many less common ones, present in living
organisms but not as constituents of proteins
Structural Features of A.A
• A.A have a carboxyl groupand an aminogroup bondedtothe same carbon atom
• They differ from each other in their side chains, or R groups, which vary in:
– Structure
– Size
– Electric charge
– Solubility of the amino acids in water
• All Amino acids are essentially α-amino acids:
alpha carbon (IUPAC #2 position)
H2N – C – COOH
|
R
• When R is not H, the alpha carbon is asymetric, giving rise to isomers

4. • Only L-amino acids are constituents of proteins
Classification of A.A
(Based on R group) These aminoacidscontaina varietyof differentfunctional groups:
• Alcohols (R-OH)
• Phenols (Ph-OH)
• Carboxylic acids (R-COOH)
• Thiols (R-SH)
• Amines (R-NH2)
• And others….

5. Classification of A.A
(Based on R group)

7. Classification of A.A
(Based on functions )
• Essential Amino Acids:
– Isoleucine
– Leucine
– Lysine
– Methionine
– Phenylalanine
– Threonine
– Tryptophan
– Valine
– Arginine
– Histidine
• Non-essential A.A
– ??????
Classification of A.A
(Uncommon amino acids )
• Some 300 additional amino acids have been found in cells with a variety of functions but are not
constituents of proteins
• Ornithine and citrulline,which are not found in proteins, are intermediates in the biosynthesis
of arginine and in the urea cycl
• Selenocysteine is a constituent of just a few known proteins

8. • Another important uncommon amino acid is -carboxyglutamate, found in the bloodclotting
protein prothrombin and in certain other proteins that bind Ca+2 as part of their biological
function
Properties of A.A
• Carboxylic acids are donating a proton in aqueous solution while Amino groups function
as bases, accepting a proton
• At low pH, proton concentration [H+]is high, both amines and carboxylic acids are
protonated (-NH3
+ & -COOH)
• At high pH, proton concentration is low, both amines and carboxylic acids are
deprotonated (-NH2 &-COO-)
• At neutral pH, amines are protonated (-NH3
+) and carboxylates are deprotonated (-COO-)
• Zwitter Ions:Ions bearing two charges were named zwitter ions by German scientists; the
name still applies today, especially for amino acids at neutral pH:
+H3N – CH2 – COO-
• Acid-Base Properties of Amino Acids
pH=1: +H3N – CH2 - COOH
pH=7: +H3N – CH2 – COO-
pH=12: H2N – CH2 – COO-
What are peptides??
• Chains of Amino Acids polymerized via amide or “peptide” bonds
• Peptide bond formation is an example of a condensation reaction by removal of the
elements of water (dehydration) from the -carboxyl group of one amino acid and the –
amino group of another
• Biologically occurring peptides range in size from small to very large, consisting of two
or three to thousands of linked amino acid residues
– Dipeptide (two AA residues e:g, aspartame )
– Oligopeptide ( a few AA residues e:g, oxytocin- a nonapeptide)
– Polypeptide (many AA residues e:g, Insuline)

9. Peptide Bond Formation
Ionization Behavior of Peptides
• Peptides contain only one free -amino group and one free -carboxyl group, at opposite
ends of the chain
• These groups ionize as they do in free amino acids
• The -amino and -carboxyl groups of all nonterminal amino acids are covalently joined in
the peptide bonds, which do not ionize and contribute to the total acid-base behavior of
peptides
• R groups of some amino acids can ionize, contribute to the overall acid-base properties of
the molecule
• Thus the acid-base behavior of a peptide can be predicted from its free -amino and -
carboxyl groups as well as the nature and number of its ionizable R groups

10. AA composition of Peptides
• Hydrolysisof peptidesor proteinswith acid yieldsa mixture of free -aminoacids
• The 20 common amino acids almost neveroccur inequal amounts in a protein
• Some amino acids may occur only once or not at all ina giventype of protein;othersmay
occur inlarge numbers
• Complete hydrolysisalone isnot sufficientfor an exact analysisof amino acid composition,
some additional proceduresare usedto resolve the ambiguities
What are proteins??
• Proteins can be very long polypeptide chains of 100 to several thousand amino acid
residues
• The sequence of amino acids in a protein is characteristic of that protein
• Some proteins are composed of several noncovalently associated polypeptide chains,
called subunits
• Simple proteins yield only amino acids on hydrolysis; conjugated proteins contain in
addition some other component, such as a metal or organic prosthetic group
Size of Polypeptides
• Naturally occurring peptides range in length from two to many thousands of amino acid
residues
• The smallest peptides can have biologically important effects as the artificial sweetener
aspartame
• Many small peptides exert their effects at very low concentrations as oxytocin (nine
amino acid residues), secreted by the posterior pituitary and stimulates uterine
contractions

11. • Corticotropin is a 39-residue hormone (slightly larger) of the anterior pituitary gland that
stimulates the adrenal cortex
Monomeric proteins
• Consistof single polypeptide chain(humancytochrome c has 104 AA residueslinkedin
a single chain)
Multimeric proteins
• Have two or more polypeptide chainsassociatednoncovalently(haemoglobinhasfour
polypeptide subunits,twoidentical alpha chains and two identical beta chains
How long a Polypetide canbe??

12. AA Composition of Proteins

13. Conjugated Proteins
Protein Structural Organization
• Primary(1°) ProteinStructure
– linearsequence of aminoacids
• Secondary(2°) ProteinStructure
– localizedregional structures
• Teritary(3°) ProteinStructure
– overal shape of proteins
• Quaternary(4°) ProteinStructure
– interactionsbetweenproteins

14. Levels of protein structure