ORGANIC CHEMISTRY 3540

PROTEINS

CLASSIFICATION

STRUCTURE

DENATURATION

PROTEIN (POLYPEPTIDE) CLASSIFICATION

1. BY FUNCTION:

• ENZYMES
• HORMONES
• ANTIBODIES
• STRUCTURAL - SKIN, HOOVES
• TRANSPORT - HEMOGLOBIN
• CONTRACTILE - MUSCLE
• ETC.

2. BY SHAPE:

• FIBROUS - LONG, THREADLIKE, INSOLUBLE IN WATER
• GLOBULAR - COMPACT, SOLUBLE IN WATER

3. BY COMPLEXITY:

• SIMPLE - HYDROLYSIS GIVES ONLY AMINO ACIDS
• CONJUGATED - HYDROLYSIS GIVES AMINO ACIDS AND A PROSTHETIC GROUP (ORGANIC OR INORGANIC)

STRUCTURES OF PROTEINS

• PRIMARY
• SECONDARY
• TERTIARY
• QUATERNARY

1. PRIMARY STRUCTURE

• SEQUENCE OF AMINO ACIDS

2. SECONDARY STRUCTURE

• MANY OXYGENS
• MANY HYDROGENS ON NITROGEN
• POSSIBILITY OF HYDROGEN-BONDING
• DUE TO GEOMETRY OF PEPTIDE BOND, ONLY CERTAIN HYDROGEN BONDS ARE STABLE
  • BONDS TO ITSELF
    • HYDROGEN BONDS - TO AN AMINO ACID FOUR RESIDUES AWAY
    • GET AN ALPHA HELIX: INTERACTIVE, GIF1, GIF2
  • BONDS TO OTHER PEPTIDES
    • GET A SHEET STRUCTURE (BETA, PLEATED): INTERACTIVE, GIF

3. TERTIARY STRUCTURE

• FIBROUS PROTEINS
  • ALPHA-KERATINS - SKIN, NAILS, HAIR, FEATHERS - ALPHA-HELIXES COILED AROUND EACH OTHER TO GIVE A FIBER
  • COLLAGENS - CONNECTIVE TISSUES - A TRIPLE HELIX (INTERACTIVE) OF POLYPEPTIDES
  • BETA-KERATIN - FIBER CONSISTING MANY PLEATED SHEETS - SILK (INTERACTIVE)
• GLOBULAR PROTEINS
  • COMPLEX AND SPECIFIC FOLDING OF THE POLYPEPTIDE CHAIN
  • MAY CONTAIN PORTIONS WHICH ARE HELIXES OR PLEATED SHEETS
  • GET A UNIQUE CONFORMATION
    • PROTEIN G (INTERACTIVE)

    • LYSOZYME (INTERACTIVE)

• WHAT KEEPS PROTEIN IN ITS PARTICULAR CONFORMATION?
  1. SALT LINKAGE
  2. SALT BRIDGE
  3. HYDROPHOBIC INTERACTIONS
     • NONPOLAR GROUPS ASSOCIATE IN WATER SOLUTION
     • OFTEN IN INNER PORTION OF MOLECULAR CONFORMATION
  4. HYDROGEN BONDING
  5. DISULFIDE BRIDGE

4. QUATERNARY STRUCTURE

• COMBINATION OF SEVERAL PEPTIDE CHAINS
• COMBINATION WITH NONPEPTIDE GROUP(S) HEME HEME (INTERACTIVE)

• HEMOGLOBIN (INTERACTIVE)
  • IRON⁺² IS BONDED TO
    • FOUR NITROGENS OF HEME
    • HISTIDINE OF PROTEIN
    • OXYGEN (SOMETIMES)

  • FUNCTION OF PROTEIN
    • IF NO PROTEIN, IRON⁺² --> IRON⁺³ WHICH DOESN'T CARRY OXYGEN
    • PROTEIN KEEPS OXYGEN FROM GETTING TOO CLOSE TO IRON
    • HEME IS INSOLUBLE IN WATER
    • PROTEIN IS SOLUBLE IN WATER
    • HEME FITS INTO A "HYDROCARBON" POCKET
    • PROTEIN DESCREASES AFFINITY OF HEME TO CARBON MONOXIDE

DENATURATION OF PROTEINS, ETC.

• CHANGE CONFORMATION
• CHANGE ACTIVITY
• PROTEIN PRECIPITATES
  • HEAT - FRY EGGS
  • CHANGE pH - SOUR MILK
  • AGITATION - BEAT EGGS
  • ADD HEAVY METAL IONS - EGGS FOR METAL POISONING

• CHEMICALLY CHANGE PROTEIN
  • PERMANENT WAVE

• MUTATIONS
  • SUBSTITUTE AN AMINO ACID
  • CHANGE SHAPE
  • CHANGE PROPERTIES
  • REPLACE GLUTAMIC ACID WITH VALINE IN HEMOGLOBIN
    REPLACE IONIC GROUP WITH NONPOLAR GROUP
    OUTER NONPOLAR VALINE INTERACTS WITH NONPOLAR AREA ON ANOTHER HEMOGLOBIN FORMING A DIMER.
    SINCE IT HAPPENS ON TWO CHAINS, CAN "POLYMERIZE"
    • CHANGES SHAPE OF PROTEIN
    • SOLUBILITY GREATLY DECREACES
    • SHAPE OF CELL CHANGES
    • VISCOSITY OF BLOOD INCREASES
    • BLOOD FLOWS MORE SLOWLY
    • PRODUCES "SICKLE-CELL ANEMIA"