amino acids/proteins

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amino acids/proteins
2009-12-05 14:01:32
chemistry Amino Acids & Proteins

chemistry test 4
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  1. Amino Acids & Proteins
    • • Proteins are long chains of repeating amino acids linked via peptide bonds
    • • The amino acid sequence determines the identity of the protein.
    • • Proteins have many functions within an organism
    • – structural components
    • – regulation of biochemical reactions (hormones and enzymes)
    • – transport of essential substances (hemoglobin)
    • – nutrient storage
  2. Amino function
    • zwitterion
    • The zwitterion form of the amino acid has a large dipole
    • However, the net charge on the molecule is zero.
    • R group denotes 'any
    • C – bonded group'
  3. Classification
    • • Non-polar
    • – R group consists of hydrocarbon chain or other
    • non-polar group (alkyl sulfide or indole)
    • • Polar
    • – R group contains polar groups such as OH, SH, C=O
    • • Acidic
    • – R group contains a COOH (COO-) group
    • • Basic
    • – R-group contains a NH2 (NH3
    • +) group
  4. Amino Acid Key Points
    • •Amino acids exist in zwitterion form.
    • •All amino acids contained in proteins have the acid function (COOH) and NH2 function attached to the same carbon atom. (a amino acids)
    • • All the amino acids found in proteins are chiral except for glycine
    • •Arginine, Histidine, Isoleucine, Leucine, Lysine,meththionine ,Phenylalanine, Threonine, Tryptophan, and Valine cannot be synthesized by humans and must be obtained in the diet. (essential amino acids)
    • • Amino acids can link to one another via peptide bonds to form peptides and proteins.
    • •The protein amino acids all have the L-configuration
  5. In the Fischer Projection format, the amino group is on the left of the chain. Amino acids in proteins have the ‘L’ configuration
  6. Proteins
    • • Proteins are long chains (~50 to > 500) of amino acids linked by peptide bonds.
    • • Primary structure is determine by the sequence of amino acids
    • – Often written as "alphabetical abbreviation" of individual amino acid
    • – Thr-Leu-Phe-Gly-Gly-Phe-etc.
  7. Three Dimensional Structure of Proteins
    • There are Four Levels of Structure:
    • 1. Primary- the order of amino acids in the protein chain
    • 2. Secondary – results from hydrogen bonding between NH2 and CO groups on 'neighboring' amino acids.
    • 3. Tertiary- results from attraction or repulsive forces between R groups on the amino acids. Often 'long range' forces.
    • 4. Quarternary- applies to proteins containing more than one protein subunits.
  8. Proteins
    • • Secondary structure describes how the atoms are arranged in space.
    • – Influenced mainly by hydrogen bonding between N-H and O=C groups
    • • Three major secondary structures of proteins.
    • – a helix (alpha helix)
    • – beta pleated sheet
    • – triple helix
  9. Alpha Helix
    • Hydrogen bonds form between amino acids located 4 amino acids apart in the primary structure.
  10. Beta-Pleated Sheet
    • Chains are held 'side by side' by H- bonds. Amino acids tend to be those
    • having small R groups. (glycine, alanine, serine) This allows close stacking and strong interaction between chains Most common example is silk.
  11. Triple Helix
    • Three polypeptide chains are woven together A small amount of hydroxy proline and hydroxylysine are present, which result in increased H bonds. Long fibers having exceptional strength result Collagen is a protein having triple helix form. Found in connective tissue.
  12. Tertiary Structures
    • • Interactions among the R groups of the polypeptide chains are responsible for the tertiary structures
    • • These structures result in 'folds' and 'bends' in the chains, giving them a three dimensional structure
  13. Quarternary Structures
    • • Quarternary Structures describe the configuration of proteins which are composed of two or more protein units.
    • • Hemoglobin is an example
    • – 4 separate protein chains
    • – chains held together by intermolecular forces
    • (same forces as tertiary structures)
  14. Denaturing Proteins
    • • The forces responsible for the secondary, tertiary and quaternary structures are significantly weaker than the covalent bonds responsible for the primary structure.
    • • Heat, changes in pH, and mechanical agitation disrupt these forces
    • – protein loses shape and biological function
    • – "frying an egg"
  15. Enzymes
    • • Enzymes are biological catalysts
    • – protein structures
    • – provide low energy pathway for reactions to occur.
    • • Active site
    • – enzyme binds to "substrate". Binding site in the enzyme is called the 'active site'
    • – shape often determines what substrates may bind to the enzyme
  16. Enzyme Mechanisms
    • • Lock and Key
    • – substrate has proper shape and polarity to fit the active site
    • • Induced Fit
    • – Several related molecules may interact with the enzyme
    • – Approach of the substrate can change the geometry of the active site
  17. Inhibition Mechanisms
    • • Competitive inhibition
    • – inhibitor has similar shape and polarity
    • – occupies active site and prevents substrate from complexing
    • – addition of more substrate can reverse inhibition
    • • Non competitive inhibition
    • – inhibitor binds to site other than active site
    • – binding causes active site to change geometry
    • – Additional substrate will not reverse inhibition
  18. Inhibition Mechanisms
    • • Regulatory enzymes
    • – Reaction sequence in which the product of the last reaction inhibits the enzyme of the first reaction.
    • – Feedback system to control the production of the end product.