Learning objectives
At the end of this lecture a student should be able to :• Classify the amino acids based on polarity, nutritional requirements, side
chains and chemical side chains
• Describe the pathways of Protein turnover. Explain Ubiquitin proteosome
pathway
• State the four levels of protein structure and explain how the sequence of
amino acids leads to the final three dimensional configuration of the
protein
• Explain Protein misfolding and its clinical implications
• Analyse the Concept of zwitter ions and its clinical applications
L-Form Amino Acid Structure
Carboxylic group
Amino group
+
H3 N
R group
COO
a
-
H
H = Glycine
CH3 = Alanine
Compounds having same structural formula , but differ in spatial
configuration are known as stereoisomerism.
Penultimate Carbon
Mirror Images of Amino Acid
a
Mirror
image
Enantiomers
a
Amino Acids Classification
•
•
•
•
Based on polarity
Based on side chain
Based on metabolic function
Based on nutritional requirement
Based on Side chain
Classes Side chain
Polarity
Example
I
Aliphatic
Apolar
Gly, Ala, Val, Leu, and Ileu.
II
Sulphur
Apolar
Cys* and Met
III
Aromatic
Apolar
Phe, Tyr & Trp
IV
Hydroxyl
Polar
Ser, Thr and (Tyr)
V
Acidic
Polar
Asp , Asn and Glu, Gln
VI
Basic
Polar
Lys , Arg and His
VII
Imino
Apolar
Pro
USMLE !
Aliphatic side chains
(non-polar)
Imino acid ( Non-polar)
•
1.
2.
3.
Glycine :
Smallest amino acid
Inhibitory neurotransmitter
Most common amino acid of collagen
• Valine, Leucine and isoleucine :
1. Leucine – ketogenic amino acid
2. Maple syrup urine disease
•
Proline – imino acid , disrupts amino acid
structure
Aromatic amino acids
Indole ring
•
1.
2.
Phenyl Alanine :
Essential amino acid : forms tyrosine
Def : phenyl ketonuria ( phenyl alanine hydroxylase deficiency)
•
1.
2.
3.
4.
Tyrosine :
Precursor of melanin
Catecholamines – dopamine, norepinephrine and epinephrine which act
as neurotransmitters
Parkinson disease : def of dopamine
synthesis of thyroxine .
•
1.
2.
3.
Tryptophan : (indole ring)
Melatonin - circadian rhytm
Serotonin – mood alterations
Source of Niacin – def causes hartnup’s disease
Sulphur containing amino acids
• Cysteine :
1. Used to make disulfide bonds – secondary structure of
proteins
2. Glutathione – detoxifying agent and free radical scavenger.
•
•
•
•
Pharmacology : N –acetyl cysteine
Paracetamol toxicity
Cystic fibrosis
Cyclophosphamide toxicity – treatment
• Methionine :
1. S-adenosyl Methionine : methyl donor
2. Homocysteine – derived from methionine
Side chains with Basic groups
(polar )
Guanidino group
Imidazole group
• Lysine and arginine – due to positive charges , main
components of histone proteins.
•
1.
2.
3.
Arginine :
Synthesis of nitric oxide
Release of urea
Semi-essential amino acid – positive nitrogen balance
• Histidine :
1. Histamine – major inflammatory mediator .
Acidic groups and their amides
(polar)
Side chains with –OH groups
21st and 22nd aminoacid
• Selenocysteine
• Pyrrolysine
Based on Nutritional requirement
Essential Amino Acids
• Not synthesized in the body
• Essential in diet
Non - Essential Amino Acids
• Synthesized in the body
Nutritionally essential mnemonic – MATTVILPHLY
OR
PVT TIM HaLL
USMLE !
Classification based on essentiality
PVT TIM HaLL
Arginine also.
Based on Metabolic function
Classification of Amino Acids by Polarity
POLAR
Acidic
Asp
NONPOLAR
Glu
Ala
Val
Neutral
Asn
Cys *
Gln
Ser
Tyr
Thr
Basic
Arg
His
Lys
Ile Gly Phe Trp
Leu Met Pro
Non-polar substances likely to be inside the cell membrane , polar things OUTSIDE !
•Cysteine is polar because of its thiol group but free cysteine residues are
found to associate with hydrophobic regions of proteins
USMLE !
Zwitter ion
• An amino acid acts as a
zwitterion, i.e., it can be
either:
1) Positively charged in an
acid solution
2) Negatively charged in an
alkaline solution
3) Neutral at the isoelectric
point.
Formation of Peptide Bond
Formation of Peptide Bonds by Dehydration
Amino acids are connected head to tail
NH2
1
COOH
2
NH2
COOH
Dehydration
Carbodiimide
-H2O
O
NH2
1
C N
H
2
COOH
Amino acids are joined by peptide
bonds
• Characteristics of PEPTIDE BOND
– Partial double bond(The distance is 1.32 A which is midway b/w single
bond (1.49 A)and double bond(1.27A))
– Rigid and Planar
– The partial double bond renders the amide group planar, occurring in
either the cis or trans isomers.
– In the unfolded state of proteins, the peptide groups are free to
isomerize and adopt both isomers; however, in the folded state, only a
single isomer is adopted at each position (with rare exceptions).
Numbering of amino acids in Peptides
and Proteins
• Free alpha amino group at one end – AMINO
TERMINAL( N –TERMINAL )
• The amino acid contributing the alpha amino group is
called as first amino acid.
• Biosynthesis of protein starts from this terminal end
only.
• Free carboxy group on other end – CARBOXY
TERMINAL(C –TERMNAL ) –> LAST AMINO ACID
Amino acid sequences
• Greek Proteios meaning PRIMARY
• BUILDING BLOCKS OF THE BODY
• 3/4TH DRY BODY WEIGHT = PROTEINS
• CONTAIN C, H , O, N as major components, while
S and P are minor constituents.
• N content of ordinary proteins is 16% by weight.
PEPTIDES
• Proteins are made by polymerisation of amino acids
through peptide bonds.
• 2 AA joined to form a DIPEPTIDE
• 3 AA -> TRIPEPTIDE
• 4 AA-> TERTAPEPTIDE
• 5- 10 AA -> OLIGOPEPTIDE
• 10- 50 POLYPEPTIDE
• >50 PROTEIN
3 AA means 20 3 COMBINATIONS = 8000 possible types of peptides.
An ordinary protein with 100 amino acid = 20100 possible
combinations !!!
Primary
Assembly
Secondary
Folding
Tertiary
Packing
Quaternary
Interaction
PROCESS
STRUCTURE
Biology/Chemistry of Protein Structure
PRIMARY STRUCTURE OF PROTEINS
The sequence of the amino acids in a polypeptide
chain denotes its primary structure.
•
•
•
•
•
linear
ordered
1 dimensional
sequence of amino acid polymer
by convention, written from amino end to
carboxyl end
• a perfectly linear amino acid polymer is neither
functional nor energetically favorable  folding!
primary structure of human insulin
CHAIN 1: GIVEQ CCTSI CSLYQ LENYC N
CHAIN 2: FVNQH LCGSH LVEAL YLVCG ERGFF YTPKT
Secondary structure
• The term secondary structure denotes the
configurational relationships between
residues which are about 3-4 amino acids
apart in linear structure.
• It is stabilized by non-covalent bonding
Secondary Structure
• non-linear
• 3 dimensional
• localized to regions of an
amino acid chain
• formed and stabilized by
hydrogen bonding,
electrostatic and van der
Waals interactions
(Pauley and Corey 1951)
•
Spiral structure
•
Polypeptides form the back bone and the
side chains of amino acids extend b/w NH
& C=O groups
•
Distance b/w adjacent a.a is 1.5 A
•
3.6 aa per turn
•
RIGHT HANDED
•
IT IS THE MOST COMMON AND STABLE
CONFORMATION OF S POLYPEPTIDE
CHAIN
•
Abundant in hemoglobin and myoglobin
and and absent in chymotrypsin. Proline
and hydroxy proline will not allow the
formation of alpha –helix.
The spirals look like they are going
down clockwise.
H
N
C
C
O
H
N
R
C
C
O
H
C
C
N
O
C H
C
O N C
O
C
H
C
C
N
O
C
O
H
N
R
R
R
R
R
R
H
N
R
R
R
R
R
R
R
Secondary
structure
a -helix
(Pauling and Cory
1951)
•
the polypeptide in beta-pleated sheet is
almost fully extended.
• The distance b/w adjacent a.a. is 3.5 A.
• It is stabilized by hydrogen bonds
between NH and C=O groups of
neighbouring polypeptide segments.
• Adjacent strands can run in same
direction(parallel) or opposite
direction(anti-parallel) with regard to
amino and carboxy terminal.
• Abundant in Silk (anti-parallel),
Flavodoxin (parallel), Carbonic –
anhydrase (both).
Secondary structure
beta pleated sheet
O
C
C
H
C N
C
O
N
H
O
C
N
H
C
O
C
H
C N
C
C
N
H
C
C
O
N
H
O
H
N
C
O
C
C
O
H
C N
C
O
N
H
O
H
N
C
O
C
C
C
N
H
C
C
H
N
C
O
C
O
C
H
C N
N
H
C
O
O
H
N
C
N
H
C
C
O
C
Protein Folding
• Occurs in the cytosol
• Involves localized spatial
interaction among primary • ADVANTAGES :structure elements, i.e. the
amino acids
Tumbles towards
conformations that
• May or may not involve
reduce E (this process is
chaperone proteins
thermo-dynamically
favorable)
Yields higher structures of
proteins.
Active sites open up!!!
• Non-linear
Tertiary Structure
• 3 DIMENSIONAL STRUCTURE OF A
PROTEIN
• Global but restricted to the amino
acid polymer
• Formed and stabilized by hydrogen
bonding, non-covalent interactions
like hydrophobic packing toward core
and hydrophilic exposure to solvents.
• A globular amino acid polymer folded
and compacted is somewhat
functional (catalytic) and energetically
favorable  interaction!
• It represents the three 3D structure of the protein.
• It defines the steric relationships of a.a which are
far apart from each other in the linear sequence ,
but are opposed each other by non-covalent
interactions.
• Thermodynamically , the most stable structure .
• DOMAIN :- It is a term used to denote a compact
globular functional unit of a protein.A domain is a
relatively independent region of the protein , and
may represent a functional unit.
Quaternary Structure of a Protein
• Certain polypeptides aggregate to
form one functional unit. This is
called as Quaternary Structure .
• non-linear
• 3 dimensional
• global, and across distinct amino
acid polymers
• formed by hydrogen bonding,
covalent bonding, hydrophobic
packing and hydrophilic exposure
• favorable, functional structures
occur frequently and have been
categorized .
Structure of Hemoglobin
• Stabilized by H-bonding, electrostatic bonds ,
hydrophobic interactions and Van Der Walls
forces.
• Each polypeptide chain is termed as a subunit
or monomer.
• Eg. Hemoglobin :- 2 α, 2 β chains
– Creatine Kinase is a dimer
– LDH is a tetramer
– Aaspartate transcarbamoylase has 6 subunits.
• ENZYMES :– Enzyme catalysis needs precise binding of
the substrate to the active site of the
enzymes.
– This depends on structural conformation of
the active sides so that it is precisely
oriented for substrate binding.
• TRANSPORT PROTEINS
– Hb has a quaternary str with 2 α and 2β subunits.Binding
of O2 to one heme subunit facilitates oxygen binding by
other subunits.
– Binding of H+ and CO2 promotes release of O2 from
hemoglobin. This is called as BOHR effect.
• In Primary structure any amino acid change /deletion/
replacement of any one acid by another can cause
abnormalities in its function.
– Eg. Sickle cell anaemia :- In 6nd position of β-chain of
Hemoglobin if there is Valine instead of Glutamic acid .
Classification based on Functions :1. Catalytic proteins e.g.enzymes
2. Structural proteins e.g. collagen , elastin, keratin
3. Contractile proteins e.g. myosin, actin, flagellar proteins
4. Transport proteins , e.g. haemoglobin, albumin
5. Regulatory proteins e.g. ACTH , insulin , GH
6.Genetic proteins , e.g. Histones
7. Protective proteins e.g. Immunoglobulins
• Classification based on Nutritive Value
1)Nutritionally rich proteins or Complete
proteins or First class proteins: They contain all essential a.a. in required
proportion for ideal body growth and
development.
E.g egg albumin , milk casein
• 2.Incomplete proteins :- They lack one
essential amino acid. They cannot sustain
body growth in young individuals even if they
are able to maintain growth in adults. Eg
Pulses are deficient in methionine and cereals
are deficient in lysine .If both are combined in
diet , good growth can be obtained.
• 3.Poor proteins :-They lack in many essential
a.a. and a diet based on them cannot sustain
the original body weight e.g. Zein of corn lacks
Trp and Lys.
• Classification based on shape
.
1.Globular proteins :-They are spherical or
oval in shape.(l/b <10) eg albumin, globulin
2.Fibrous proteins :- They are elongated or
needle shaped and resist digestion .e.g.
collagen, elastin, keratin etc.
NITROGEN BALANCE
Nitrogen balance = Nitrogen ingested - Nitrogen excreted
(primarily as protein) (primarily as urea)
Nitrogen balance = 0 (nitrogen equilibrium)
protein synthesis = protein degradation
Positive nitrogen balance
protein synthesis > protein degradation
Negative nitrogen balance
protein synthesis < protein degradation
Negative nitrogen balance
•
•
•
•
•
•
Starvation
PEM
Uncontrolled Diabetes Mellites
Def of any essential aminoacid
Infection
Surgery, Burns
MCQ1)A mixture of ala,arg,his,gly,glu
is subjected to electrophoresis at pH 7.
-ve
• Identify this
amino
– A.Glycine
– B. Arginine
– C.Glutamate
– D.Valine
– E.ALANINE
+ve
MCQ2
• Several complexes in the mitochondrial ETC
contain non-heme iron tightly bound to a thiol
group of which amino acid?
– A. Glutamine
– B.Methionine
– C.Tyrosine
– D.Cysteine
– E.Serine
• Thank you