amino acid,peptide and protein.

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• SEMINAR REPORT
• ON
• AMINO ACID,PEPTIDEPROTEIN.
• 
  SUBMMITED BY
• 
  ATTUL NAJI

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Amino Acid Structure
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• REACTIONS
• As amino acids have both a primary amine group
  and a primary carboxyl group, these chemical can
  undergo most of the reactions associated with
  these functional groups.
• These include nucleophilic addition, amine bond
  formation and amines formation for the amine
  group and esterification, amide bond formation
  and decarboxylation for the carboxylic acid
  group.
• The combination of these functional groups allow
  amino acids to be effective polydented ligands
  for metal-amino acid chelates.
• The multiple side chain of amino acid can also
  undergo chemical reaction.

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• O NH2
  NH2 O
• KCN H
  
• C C
  C C
• / \ NH4CL / \\\ /
  
• R H R N
  R OH
• The strecker amino acid synthesis

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Essential and Non- Essential amino acid

• Amino acids which are essential for maintenance
  of proper nitrogen balance in the body, but all
  amino acids can not be synthesised within living
  organisms.
• Out of 22 amino acids that make up proteins, 13
  amino acids are synthesised by our bodies which
  is known as non- essential amino acid. And n 9
  are called essential amino acid because the human
  can not synthesised from other compounds at the
  level needed for normal growth. So, they must be
  obtain from food.

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• 22 amino acids are naturally incorporated into
  polypeptides and are called proteinogenic or
  natural amino acids, of these 20 are encoded by
  the universal genetic code. The remaining 2
  selenocysteine and pynolysine are incorporated in
  proteins by unique synthethic mechanisms.
• Selenocysteine is incorporated when the mRNA
  being translated includes a SECIS element, which
  causes the UGA codon to encode selenocysteine
  instead of a stop codon.

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• Pyrolysine is used by some methanogenic Achaea in
  enzymes that they used to produce methane. It is
  coded far with the codon UAG, which is normally
  a stop codon in other organism.
• H se
• \
• C
• C OH
• / \ /
• H2N C
• O
• The amino acid selenocysteine

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THE NAMING OF ESSENTIAL AND NON-ESSENTIAL AMINO
ACID

• ESSENTIAL AMINO ACID
• Histidine
• Isoleucine
• Leucine
• Methionine
• Phenylalanine
• Threonine
• Tryptophan
• Valine

• NON-ESSENTIAL AMINO ACID
• Alanine
• Arginine
• Asparagine
• Aspartic acid
• Cysteine
• Glutamic acid
• Glutamine
• Glycine
• Arnithine
• Proline

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Structure of all amino acids
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• Zwitter ion
• It is an amino acid molecule containing both a
  positive and a negative charge i.e they are
  neutral and have no net charge.
• O
  O
• 
  
• R- CH- C- O- H
  R- CH- C- O-
• 
  
• NH2
  NH3
• 
  Zwitter ion

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REACTION OF ZWITTER ION
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ISOELECTRIC POINT
It is point at which pH of
amino acid exist as a zwitter ion.

• Anion
• H2N CH COO-
• 
  (BASIC)
• R
• 
  H3N - CH COO-
• 
  
• 
  R Zwitter ion
• 
  ( neutral solution)
• 
  (ACID)
• Cation
• H3N CH COOH
• R

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PEPTIDES

• Peptides are the amides formed by the
  condensation of amino group of one alpha amino
  acid with carboxyl group of another molecules of
  the same or different alpha amino acids with the
  elimination of a molecule of water.
• O H
  O
• 
  -H2O
• H2N CH C OH H N CH C OH
• 
  
• R
  R (Alpha amino acid)
• O H O
• H2N CH C - N CH C OH
• R R
  ( A Depeptide)
• The shortest peptide are depeptide.

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Polypeptides

• Amino acid chains are called polypeptides

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• POLYPEPTIDE
• If a large number of amino acids are joined by
  peptide bonds, the polyamide thus formed is
  called a polypeptide.
• H2N- CH- COOH n H2N- CH- COOH H2N- C-
  COOH
• 
  
• R
  R R
  
  
  
• H2N- CH- CO(NH- CH- CO)n NH- CH- COOH
  (n1) H2O
• 
  
• R R
  R
• Here R, R and R may be H or same or
  different alkyl or aryl group.

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Formation of a Peptide
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• It is clear from the polypeptide that each
  polypeptide chain has a free amino group at one
  end and the free carboxylic group at the other
  end. The amino acid unit having free NH2 group
  is called the N- terminal end, whereas the amino
  acid unit having the free COOH group is called
  the C- terminal end.

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Examples of Oligopeptides
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Planarity of Peptide (Amide) Bond
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PEPTIDE CLASSES

• 1) Milk peptide
• 2) Ribosomal peptides
• 3) Non- Ribosomal peptides

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PROTEIN

• Protein are complex nitrogeneous compounds
  essential for the growth and maintenance of life.
  Chemically proteins are linear unbranched
  polymers of alpha amino acids. Actually proteins
  are polypeptides having molecular mass grater
  than 10000. In human beings they are the main
  ingredients of muscles, skin, hair, nails, etc.

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Primary Structure of Bovine Insulin
First protein to be fully sequenced (by Fred
Sanger in 1953). For this, he won his first Nobel
Prize (his second was for the Sanger dideoxy
method of DNA sequencing).
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TYPES OF PROTEIN

• 1) Fibrous protein
• 2) Globular protein

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• 1) Fibrous Protein
• These protein consist of linear thread like
  molecules which lie side by side.
• There is extensive formation of hydrogen bonding
  between neighbouring chains.
• They are insoluble in water.
• They serve as the chief structural material of
  the animal tissue.
• e.g.- collagen, fibroin, myosin, keratin of
  hair.

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• 2) Globular protein
• These protein consist of molecules which are
  extensively folded into compact units approaching
  almost spherical shapes.
• Hydrogen bonding and Vander walls interaction
  exist between different parts of polypeptide
  chain.
• They function as enzymes, regulate metabolic
  processes and act as antibodies.
• E.g.- Insulin, haemoglobin, albumin.

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STRUCTURE OF PROTEIN

• 1) Primary Structure
• 2) Secondary Structure
• a) Alpha- Helix structure
• b) Beta- Helix structure
• c) Flat sheet structure
  
• 3) Tertiary Structure
• 4) Quaternary Structure

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PRIMARY STRUCTURE

• The numbers of amino acids vary (e.g. insulin
  51, lysozyme 129, haemoglobin 574, gamma globulin
  1250)
• The primary structure determines the folding of
  the polypeptide to give a functional protein
• Polar amino acids (acidic, basic and neutral) are
  hydrophilic and tend to be placed on the outside
  of the protein.
• Non-polar (hydrophobic) amino acids tend to be
  placed on the inside of the protein

2007 Paul Billiet ODWS
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Primary, secondary, tertiary quaternary
structure of protein
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The secondary structure is primarily composed of
alpha helices and beta-pleated sheets.
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Flat sheet or beta helix

• This produces the alpha helix and beta pleating
• The length of the helix or pleat is determined by
  certain amino acids that will not participate in
  these structures (e.g. proline)

Text2007 Paul Billiet ODWS
Dr Gary Kaiser
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SECONDARY STRUCTURE

• The folding of the N-C-C backbone of the
  polypeptide chain using weak hydrogen bonds

Text 2007 Paul Billiet ODWS
Science Student
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TERTIARY STRUCTURE

• This folding is sometimes held together by strong
  covalent bonds (e.g. cysteine-cysteine
  disulphide bridge)
• Bending of the chain takes place at certain amino
  acids (e.g. proline)
• Hydrophobic amino acids tend to arrange
  themselves inside the molecule
• Hydrophilic amino acids arrange themselves on the
  outside

2007 Paul Billiet ODWS
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TERTIARY STRUCTURE

• The folding of the polypeptide into domains whose
  chemical properties are determined by the amino
  acids in the chain

MIL1 protein
2007 Paul Billiet ODWS
Anne-Marie Ternes
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The tertiary structure is the proteins 3D shape.
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QUATERNARY STRUCTURE

• Some proteins are made of several polypeptide
  subunits (e.g. haemoglobin has four)

Protein Kinase C
Max Planck Institute for Molecular Genetics
Text 2007 Paul Billiet ODWS
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The quaternary structure is the assembly of
folded subunits.
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QUATERNARY STRUCTURE

• These subunits fit together to form the
  functional protein
• Therefore, the sequence of the amino acids in the
  primary structure will influence the protein's
  structure at two, three or more levels

2007 Paul Billiet ODWS
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Result

• Protein structure depends upon the amino acid
  sequence
• This, in turn, depends upon the sequence of bases
  in the gene

2007 Paul Billiet ODWS
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CLASSIFICATION OF PROTEIN

• 1) Simple Protein
• 2) Conjugated Protein
• 3) Derived Protein

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DENATURATION OF THE PROTEIN

• When native protein (i.e, protein occuring in the
  biological system) are subjected to heat acids or
  alkalis, they are coagulated or precipitated.
  This process is called denaturation. As a
  consequence of denaturation, protein loss their
  biological activity.

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CHEMICAL SYNTHESIS

• Short protein can also be synthesized chemically
  by a family of methods known as peptide synthesis
  which rely on organic synthesis techniques such
  as chemical ligation to produce to produce
  peptides in high yield.
• Chemical synthesis allows for the introduction of
  non-natural amino acids into polypeptide chains
  such as attachment of fluorescent probes to
  probes to amino acid side chain. This method are
  useful in laboratory biochemistry and cell
  biology.

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Protein Synthesis

• The production or synthesis of polypeptide
  chains (proteins)
• Two phases Transcription Translation
• mRNA must be processed before it leaves the
  nucleus of eukaryotic cells

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A ribosome produces a protein using mRNA as a
template.
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DNA RNA Protein
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Processing of mRNA
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Proteins can be functionally classified.
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Summary

• Proteins are biological workhorses that carry out
  most of the functions within the cell.
• Proteins are large biological molecules that
  serve diverse functional and structural roles
  within cells.
• Proteins are synthesized during the translation
  process.

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Summary contd

• Proteins are composed of amino acids that are
  covalently linked by peptide bonds.
• Proteins have four basic levels of structure.
  However, proteins must fold correctly in order to
  function properly.

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• THANK YOU