Proteins I

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Proteins I

• Amandeep S. Sidhu
• Data Mining in Bioinformatics (Week 7)

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Outline

• Proteins
• Types of Proteins
• Amino Acids
• Types of Amino Acids
• Essential Amino Acids
• Peptide Bond
• Peptides
• Protein Synthesis
• Primary Structure of Proteins
• Secondary Structure of Proteins
• Tertiary Structure of Proteins
• Exercises
• Summary
• Proteins II

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Proteins

• A protein (in Greek p??te??? first thread) is a
  complex, high molecular weight organic compound
  that consists of amino acids joined by peptide
  bonds. Proteins are essential to the structure
  and function of all living cells and viruses.
• They are amongst the most actively studied
  molecules in biochemistry and were discovered by
  Jöns Jakob Berzelius, in 1838.
• Almost all natural proteins are encoded by DNA.
  DNA is transcribed to yield RNA, which serves as
  a template for translation by ribosomes.

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Types of Proteins

• Type Examples
• Structural tendons, cartilage, hair, nails
• Contractile muscles
• Transport hemoglobin
• Storage milk
• Hormonal insulin, growth hormone
• Enzyme catalyzes reactions in cells
• Protection immune response

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Amino Acids

• Building blocks of proteins
• Carboxylic acid group
• Amino group
• Side group R gives unique characteristics
• R side chain
• I
• H2NC COOH
• I
• H

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Examples of Amino Acids

• H
• I
• H2NC COOH
• I
• H glycine
• CH3
• I
• H2NC COOH
• I
• H alanine

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Types of Amino Acids

• Non-Polar R H, CH3, alkyl groups, aromatic
• O
• Polar ll
• R CH2OH, CH2SH, CH2CNH2,
• (polar groups with O-, -SH, -N-)
• Polar/Acidic
• R CH2COOH, or -COOH
• Polar/ Basic
• R CH2CH2NH2

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Non-Polar Groups
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Polar Groups
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Polar Groups
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Essential Amino Acids

• 10 amino acids not synthesized by the body
• arg, his, ile, leu, lys, met, phe, thr, trp, val
• Must obtain from the diet
• All in diary products
• 1 or more missing in grains and
  vegetables

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Peptide Bond

• Amide bond formed by the COOH of an amino acid
  and the NH2 of the next amino acid
• O CH3
• NH3CH2CO H3NCHCOO
• O CH3
• NH3CH2C NCHCOO
• peptide bond
• H

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Peptides

• Amino acids linked by amide (peptide) bonds
• Gly Lys Phe Arg
  Ser
• H2N- -COOH
• end Peptide bonds end
• Glycyllysylphenylalanylarginylserine

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Protein Synthesis

• Biochemists refer to four distinct aspects of a
  protein's structure
• Primary structure the amino acid sequence
• Secondary structure highly patterned
  sub-structuresalpha helix and beta sheetor
  segments of chain that assume no stable shape.
  Secondary structures are locally defined, meaning
  that there can be many different secondary motifs
  present in one single protein molecule.
• Tertiary structure the overall shape of a single
  protein molecule the spatial relationship of the
  secondary structural motifs to one another

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Protein Synthesis

• Quaternary structure the shape or structure that
  results from the union of more than one protein
  molecule, usually called subunit proteins
  subunits in this context, which function as part
  of the larger assembly or protein complex.
• In addition to these levels of structure,
  proteins may shift between several similar
  structures in performing their biological
  function. In the context of these functional
  rearrangements, these tertiary or quaternary
  structures are usually referred to as
  "conformations," and transitions between them are
  called conformational changes.

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Primary Structure of Proteins

• The particular sequence of amino acids that is
  the backbone of a peptide chain or protein

Ala-Leu-Cys-Met
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Secondary Structure of Proteins

• Three-dimensional arrangement of amino acids with
  the polypeptide chain in a corkscrew shape
• Held by H bonds between the H of N-H group and
  the O of CO of the fourth amino acid along the
  chain
• Looks like a coiled telephone cord

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Secondary Structure of Proteins

• Polypeptide chains are arranged side by side
• Hydrogen bonds form between chains
• R groups of extend above and below the sheet
• Typical of fibrous proteins such as silk

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Secondary Structure of Proteins

• Three polypeptide chains woven together
• Glycine, proline, hydroxy proline and
  hydroxylysine
• H bonding between OH groups gives a strong
  structure
• Typical of collagen, connective tissue, skin,
  tendons, and cartilage

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Collagen and pleated sheet
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Tertiary Structure of Proteins

• Specific overall shape of a protein
• Cross links between R groups of amino acids in
  chain
• disulfide SS
• ionic COO H3N
• H bonds CO HO
• hydrophobic CH3 H3C

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Exercises

• Information Retrieval
• RASMOL
• http//www.umass.edu/microbio/rasmol/index2.htm
• http//www.openrasmol.org/

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Summary

• Amino Acids
• Peptides
• Protein Structure
• Visualization Rasmol

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Proteins II

• Protein Functions
• Genetic Defects
• Protein Structure Prediction