Understanding Proteins: The Building Blocks of Life

1. Proteins Dinosaur Protein

2. Proteins - classified by functions  Enzymes Transport Proteins Storage Proteins Contractile (Motor)   Structural (Support) Defensive (Protect) Receptors (detect stimuli) Regulatory (Signal)

3. Protein Structure • Proteins are unbranched polymers • Monomers are Amino Acids • Standard Amino Acids (20/700) Classified according to side-chain polarity • Non-Polar • Polar Neutral • Polar Acidic • W/ 2nd carboxyl group • Polar Basic • W/ 2nd amine group • Essential vs.Non-essential • PVT. TIM HALL

4. Amino acids central carbon = the -Carbon Covalently bonded to the alpha carbon is: 1) a Hydrogen atom, H 2) a carboxyl functional group, (COOH) 3) an amine functional group, (NH2) 4) a side chain (R). Each side chain distinguishes one kind of amino acid from another.

5. Protein Chirality Most a-amino acids in living creatures are Levo-oriented, not Dextro-oriented (opposite of chirality in monosaccharides) “Handedness” (L or D) in standard amino acids: Line up the C chain vertically and look at the position of the horizontally aligned -NH2 group.

6. Acid-Base Properties • Amino Acids can participate in “internal” acid-base reactions. There is an internal donation of a H+ ion from the COOH group to the NH2 group. The result is a double ion, both positive and negative, whose charges cancel each other out. Isolated amino acids (neutral solution) are zwitterions

7. Equilibrium of Amino Acids • Depending on the pH of the solution the equilibrium position is “pushed” in a particular direction. • Remember to consider the source of extra ions!

8. Isoelectric Points & Electrophoresis • Isoelectric point: the pH at which the amino acid has no net charge (zwitterion) • This point is measured in an electric field • The movement of charged molecules in an electric field is the basis for electrophoresis.

9. Peptide Bonds • Peptide bonds = covalent bonds between the carboxyl group on one amino acid and the amino group on an adjacent amino acid • This is a Condensation Reaction • A polypetide chain has an “N” terminal and a “C” terminal

10. Biochemically Important Small Peptides • Hormones • Ex.: Oxytocin, Vasopressin • Both have 9 amino acids • Neurotransmitters • Ex.: Enkaphalins • Morphine & Codeine bind to the same sites • Antioxidants • Ex.: Glutathione

11. Protein Structure • Proteins have at least 50 amino acids • Monomeric vs. Multimeric • Simple vs.Conjugated 4 levels of protein structure: primary      -linear sequence of a.a.'s (held together by peptide bonds)  secondary  - arrangement in space of the backbone portion (caused by hydrogen bonds between carbonyl oxygen and amino hydrogen at different locations on the chain) tertiary      - complete 3-D shape of a peptide (caused by hydrogen bonds, disulfide bonds, electrostatic attractions & hydrophobic attractions  quaternary - spatial relationships between different polypeptides or subunits

12. Primary (1o) structure: the amino acid sequence Like letters forming words: Same letters used over, but sequence changes. Misplaced letters may still be readable. Missing letters may ruin the “word” Human myoglobin.

13. Insulin

14. Results of changing the Primary sequence: • Polymorphism: proteins vary in primary sequence but have the same function. • Between species [different  a.a. sequences]  • Within a species [liver vs. kidney] • Site Specificity: unique sequences determine intra-cellular location of transmembrane signals, binding sites, etc…  • Families of Proteins: different but related functions evolved from a single ancestral protein  e.g. trypsin, chymotrypsin, and elastase  (protein choppers) • Homologous Proteins: structurally similar; may perform the same cellular function, but in different species    • e.g.: cytochrome-C • in duck & chickens = 2 variants  • in yeast & horses = 48 variants   • Mutation - change in primary amino acid sequence = a defective protein • e.g. sickle cell

15. Secondary structure : • Highly patterned sub-structures: •  helix or •  pleated sheet or • unstructured “random” chain segments. • Spatial arrangement of protein backbone. • There can be many different secondary structures • present in one single protein molecule

16. Secondary Structure The hydrogen bonding between the carbonyl oxygen atom of one peptide linkage and the amide hydrogen atom of another peptide linkage.

17. Helix • H-bonds between every 4th amino acid • Most are right-handed spirals • R-groups point outward & toward N-terminal Extensible structure – springy!

18. 4 views of the a helix protein structure: (a) Arrangement of protein backbone. (b) Backbone with hydrogen-bonding shown. (c) Backbone atomic detail shown. R groups point away from the long axis of the helix

19.  pleated sheet • Two types: parallel and anti-parallel • R-groups point outward on sides • NOT extensible – NOT springy • Short segments (5-8 residues) that fold & H-bond into ZIG-ZAG pleated sheets. • Localized shapes.   • Resist pulling (tensile) forces = strengthof silk

20.  pleated sheet protein structure: (a) emphasizing the H bonds (---) between chains. (b) emphasizing pleats and location of R groups.