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

3. 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)

4. 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.

6. 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 20 300 different linear arrays of aa's [10 390 different proteins] 1st protein sequenced was Beef Insulin by Fred Sanger - 1958 Nobel Prize winner to date about 100,000 protein have been sequenced only about 10,000 structures known [2K/yr] E. coli make about 3,000 proteins, humans make about 100,000 proteins.

7. 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)

8. Two views of an amino acid

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

14. Single-letter code: M D L Y

16. 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.

18. Four levels of protein structure

19. = Pitch 3.6 aa per turn  -helix

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

21. Proteins are 3-dimensional molecules Primary structure = Amino acid sequence Secondary structure = 1.Alpha helix 2.Beta sheet Tertiary structure = 3-D shape Quaternary structure = ??  -helix  -sheet

22. Tertiary level level most responsible for 3-D orientation of 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 Folding into specific 3D shapes & unique binding sites

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

25. denaturation

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