hafiz m waseem university of education lahore msc zoology basically iam from mailsi vehari studied in multan then in lahore

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