How does the cell manufacture these magnificent machines? Proteins, that is…

1. How does the cell manufacture these magnificent machines? Proteins, that is…

2. Proteins • Long polymers of amino acids, joined by peptide (amide) bonds are called polypeptides • Polypeptides fold into stable three- dimensional shapes and are called proteins • Shape determines the function of proteins (active sites are on the surface)

3. Proteins - classified by functions Enzymes-catalytic activity and function Transport Proteins- bind & carry ligands Storage Proteins-ovalbumin, gluten, casein, ferretin Contractile  (Motor):can contract, change shape, elements of  cytoskeleton  (actin, myosin, tubulin) Structural  (Support):collagen of  tendons & cartilage, elastin of ligaments (tropoelastin),   keratin of hair, feathers, & nails, fibroin of silk & webs Defensive  (Protect):antibodies (IgG),  fibrinogen & thrombin, snake venoms,  bacterial toxins Regulatory  (Signal): regulate metabolic processes, hormones, transcription factors & enhancers,                            growth factor proteins Receptors (detect stimuli): light & rhodopsin, membrane receptor proteins and acetylcholine or insulin.

5. Structure of Proteins the Variety of Protein Structures may be INFINITE... average protein has 300-400 amino acid's  &  has a MW of 30kD to 45kD           a PROTEIN of 300 amino acids made with 20 different kinds            of amino acids can have 20300different linear arrays of aa's  [10390 different proteins] 1st protein sequenced was BeefInsulin           by Fred Sanger - 1958 Nobel Prize winner           to date about 100,000 protein have been sequenced only about 10,000structures known  [2K/yr]                E. coli make about 3,000 proteins,                     humans make about 100,000 proteins. 

6. 4 levels of protein structure are recognized primary      - linear sequence of aa's secondary  - regular, recurring orientation of aa in a peptide chain due to H-bond tertiary      - complete 3-D shape of a peptide quaternary - spatial relationships between different polypeptides or subunits Start with the building blocks: amino acids (aa’s)

7. Two views of an amino acid

8. There are three types of side chains…. • Nonpolar (hydrophobic) • Polar uncharged (hydrophilic) • Polar charged (hydrophilic)

13. Single-letter code: M D L Y

15. Primary sequence… Linear sequence of amino acids in a polypeptide           repeated peptide bonds form the back bone of the polypeptide chain           R side groups project outward on alternate side Chain... one end of polypeptide chain has a free (unlinked) amine group:  N-terminus                   other end has a free (unlinked) carboxyl group: C-terminus N-C-C-N-C-C-N-C-C-N-C-C-N-C-C-N-C-C          Size… protein size is specified by mass (MW in daltons = 1 amu)                     average MW of a single amino acid ≈ 113 Da           thus if a protein is determined to have a mass of 5,763 Da  ≈  51 amino acids           average yeast protein  =  52,728 Da  [52.7 kDa] with about 466 amino acids    Protein Primary Sequence today is determined by reading the GENOME Sequence          Function is derived from the 3D structure (conformation) specified by          the primary amino acid sequence and the local environs interactions.

17. Four levels of protein structure

18. -helix = Pitch 3.6 aa per turn

19. In a Beta sheet, R-groups of alternating amino acids protrude above and below the sheet

20. Proteins are 3-dimensional molecules Primary structure = Amino acid sequence -sheet Secondary structure = Alpha helix Beta sheet Tertiary structure = 3-D shape Quaternary structure = ?? -helix

21. Tertiary level level most responsible for3-D orientationof proteins in space         is the thermodynamically most stable conformation of a protein... and is due to                          – weak non-covalent interactions                           - hydrophobic interior & hydrophilic exterior -via H-bonds                          - & S-S bridges      results in Protein Foldingintospecific 3D shapes &unique binding sites    

22. Disulfide bridge formation stabilizes protein structure Cys - S - S - Cys Cys - S - H + H - S - Cys

24. denaturation

36. An antibody (right) binding with the globular HA2 domain of Hemagglutinin (space-filled model)