Amino acid, peptide and proteins
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Transcript of Amino acid, peptide and proteins
Sunday, January 8,
2017Rajesh Chaudhary | Lecturer
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Department of Biochemistry, Nepalgunj Medical College, Nepal
Sunday, January 8,
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Amino acids
Asparagine: Asparagus
Glutamate: Wheat gluten
Tyrosine: Cheese
Glycine: Sweet in tasteSunday, January 8,
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Essential AA vs Non-essential AA
Phenylalanine
Valine
Tryptophan
Threonine
Isoleucine
Methionine
Histidine
Arginine
Leucine
Lysine
Rest of the amino acids of 20 common are non-
essential !
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Structural feature of AA
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Non-polar side chains
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1.Do not bind
2. Do not give off
protons
3. Do not participate in
hydrogen bond or ionic
bonds
4. Thought as oily or
lipid-like property that
promotes hydrophobic
interactions
Location of non-polar AAs in proteins
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AA with uncharged polar sidechain
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Albumin and Disulfide bond
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Structure of albumin
is stabilized by the
disulfide (-S-S) bond.
Amino acid with acidic side chain
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Amino acids with BASIC side chain
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Classification of AA
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Abbreviations and symbols
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Abbreviations and symbols
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Abbreviations and symbols
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Optical properties of AA
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Amino acids act as “acids” and “bases”
As ACID
As BASE
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Acidic and basic properties of AA
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Titration of AA
ALANINE
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Amino acids differ in their acid base property
Most of the AA with chiral center and non-ionizable R-
group behaves just like Glycine.
Difference in pKa values reflects on the effect of R-group.
AA with ionizable R-group have complex titration curve
compared to non-ionizable R-group AA.
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Titration of Glycine
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Absorption of UV by AA
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Uncommon amino acids
4-hydroxy proline
5-hydroxy lysine
Methyllysine: myosin, contractile protein
g-carboxylglutamate: prothrombin
Connective tissues
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Structure
Peptide and Protein
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Formation of peptide bond by condensation
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How long a peptide and protein can be, and what can be its molecular weight?
Biologically active peptide have vast
range of size and composition.
Oxytocin (9 AA): p. pitutiary
Thyrotropin-releasing hormone (TRH)
(3 residue): hypothalamus
Amanitin: poisonous mushroom
Can we calculate number of residues in a protein?
Ans.: YES! molecular weight/average molecular weight of a single
peptide. Sunday, January 8,
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Some protein contains groups other
than AADefinition of conjugated protein
Prosthetic group
Conjugated proteins are classified according to chemical
nature of prosthetic group
Glycoprotein
Lipoprotein
Metalloprotein
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Structures of Proteins
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Primary structure of PROTEIN
All covalent bond (mainly polypeptide and disulfide)
20 – 30% of protein in human is POLYMORPHIC.
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Primary structure of proteins
1. Peptide bond
1.1. Naming peptide
1.2. Charactersticks of peptide bond
1.3. Polarity of peptide bond
2. Determination of AA composition of polypeptide.
3. Sequencing of the peptide from its N-terminal end.
4. Cleavage of polypeptide into smaller fragments.
5. Determination of protein’s primary structure by DNA
sequencing.
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Peptide bond and its characteristics
1. Breaking a
peptide bond.
2. Naming peptide
3. Nature of
peptide bond
4. Polarity of
peptide bond
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NOTE: When polypeptides are named all AA have their residues suffixes (-ine, -
an, -ic, or –ate) changed to “-yl” with exception of C-terminal residue.
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Polarity is net zero charge with uneven distribution of that charges !
Secondary structure of PROTEIN
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Helical turns
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a-helical structure
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1.Hydrogen bond.
2.Amino acid per turn
3.Amino acids that that disrupts a-
helix
Stability of a-helix
Alanine shows greater propensity to
make a-helix.
AA in side chain affect: long chain of
Glutamate prevent a-helix formation.
+ve charge on Lys & Arg, repeals each other
prevents a-helix formation.
Glycine occurs frequently in a-helixes.
Reason: flexibility
Stability of a-helix
is affected by the
following factors:
1. Bulkiness of R-
group
2. Charge on side
chain
3. Presence of Proline
AA.
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Amino acids that disrupts a-helical
structure
Proline: inserts kink in the structure which is incompatible
with the smooth helical structure.
Large number of charged amino acids: Glutamate,
histidine, lysine, aspartate
Bulky side chain: tryptophan, valine, isoleucine.
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Why does a-helix form more readily
than any other possible conformation?
Because it makes use of internal hydrogen bond (except
those @ the end of helix)
Structure is stabilized by hydrogen bond formed by
hydrogen atom attached to electronegative nitrogen atom
of a peptide linkage and electronegative carbonyl oxygen
atom of the fourth AA on the amino-terminal side of that
peptide bond.
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Comparison between a-helix and b-pleated
a-helix b-pleated sheet
1. Hydrogen bonds are parallel
to imaginary axis.
1. Hydrogen bond are
perpendicular to axis.
2. Peptide chain: contains
single peptide chain.
2. Contains 2 or more
polypeptide chain.
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b-turn
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Tertiary structure of protein
Types of tertiary protein
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Fibrous Globular
Forces stabilizing tertiary structure of
protein
1. Disulfide bond
2. Hydrophobic interaction
3. Hydrogen bond
4. Ionic interactionSunday, January 8,
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Disulfide bond and Hydrophobic interaction
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Hydrogen bonds and hydrophobic interaction
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Common structural motif
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Steps in protein folding
Formation of secondary structure Formation of domains
Formation of final monomer
protein
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Protein misfolding
Amyloidoses
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Protein misfolding
Alzheimer’s disease
Refolding and misfolding of b-amyloid protein leading to self-aggregation of protein accumulation of protein in brain
Prion disease
Transmissible spongiform encephalopathies (TSEs)
Bovine Spongiform Encephalopathy (BSE)
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Protein degradation – proteasomal
degradation
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Proteins are stabilized by several forces
1. Hydrophobic effect has greatest influence in protein
stability.
2. Electrostatic interaction contribute to protein stability.
3. Disulfide bonds cross-link extracellular proteins.
4. Ionic interaction.
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References
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