Intro to Cell & Molecular Biology

1. Intro to Cell & Molecular Biology • How do we study cell biology? • Reductionist view • Cells as tiny complex machines • Sum of parts = whole • Your goal: • be able to explain the roles various molecular parts play in cell biological processes • With the same clarity as with macroscopic items (bicycles, stoves, trains, etc…)

2. Intro to Cell & Molecular Biology • How do we study cell biology? • Parsimony • the simplest explanation for all relevant data is preferred over more complex explanations • The most parsimonious answer is not necessarily perfectly correct • More data could make us revise it

3. Chemical basis: Bonding • Covalent Bonds: sharing of e- • One pair shared = single bond C C • Two pairs = double bond C C • Three pairs = triple bond C C • Electronegativity (EN) is the ability of an atom to attract electrons to itself • C = 2.5 N = 3.0 O = 3.5 H = 2.1 S = 2.6 • Sharing is unequal between different atoms in a molecule • Polar molecules have significant EN differences • H2O, CH3COOH • Nonpolar molecules have little EN differences • CH3(CH2)nCH3 • Amphipathic molecules have different EN characteristics at different positions • CH3(CH2)nCOOH

4. Chemical basis: Bonding • Noncovalent Bonds: attractive forces between atoms of opposite charge • Ionic: fully charged Na+ Cl- • Strength dependent on environment (salt crystal vs aqueous) • Hydrogen: partial charge (polar molecules)

5. Noncovalent bonding • Noncovalent Bonds: continued… • Van der Waals: transient dipole interactions • Hydrophobic: water fearing • Hydrophilic: water loving

6. Robot Lizards ExploitVan der Waals contacts • Based on the Gecko • Adhesion depends on close contact between surfaces “StickyBot” • Video link

7. H2O • Can form 4 hydrogen bonds • High energy barrier to liquid --> gas phase transition • Highly polarized • Asymmetric structure - both H atoms on one side • Can dissolve many compounds

8. H2O • Can dissolve many compounds • Acids: can release H+ • Bases: can accept H+ pH = - log [H+] • Pure H2O pH = 7 , [H+] = [OH-] = 10-7 M • Why are reactions so pH sensitive? • Amino acid functional groups can change state based on pH

9. Carbon Central to the chemistry of life. Can form four covalent bonds, with itself or other atoms. Carbon-containing molecules produced by living organisms are called biochemicals.

10. Chirality and Stereoisomerism Chirality and Stereoisomerism: Asymmetric carbons bond to four different groups. Two mirror-image configurations: Enantiomers, (aka) Stereoisomers Can be either D- or L-isomers Natural amino acids = almost all L-isomers Natural carbohydrates = almost all D-isomers

11. Classes of molecules • Miscellaneous co-factors • Vitamins, ATP, NADPH, etc • Metabolic intermediates • Glycolysis, TCA cycle, etc • Monomers • Amino acids • rNTPs = A, G, C, U • dNTPs = A, G, C, T • Sugars • Macromolecules

12. Classes of molecules • Macromolecules • Lipids • Fats = glycerol esterified with 3 fatty acids • Saturated, unsaturated, cis, trans • Phospholipids = glycerol + 2 fatty acids + 1 phosphate • Steroids = cholesterol and derivatives

13. Classes of molecules • Macromolecules • Lipids • Fats = glycerol esterified with 3 fatty acids • Saturated, unsaturated, cis, trans • Phospholipids = glycerol + 2 fatty acids + 1 phosphate • Steroids = cholesterol and derivatives

14. Classes of molecules • Macromolecules • Lipids • Fats = glycerol esterified with 3 fatty acids • Saturated, unsaturated, cis, trans • Phospholipids = glycerol + 2 fatty acids + 1 phosphate • Steroids = cholesterol and derivatives

15. Classes of molecules • Macromolecules • Lipids • Fats = glycerol esterified with 3 fatty acids • Saturated, unsaturated, cis, trans • Phospholipids = glycerol + 2 fatty acids + 1 phosphate • Steroids = cholesterol and derivatives

16. Monomers and polymers

17. Classes of molecules • Macromolecules • Carbohydrates • ( CH2O )n • At n ≥ 5 self-reaction to form rings • C5 = ribose monomer • C6 = glucose monomer

18. Classes of molecules • Macromolecules • “Nutritional” sugars: • Glycogen = branched alpha 1-4 linkage, dense granules in cell cytoplasm in animals • Starch = helical and branched alpha 1-4 linkage, within membrane bound plastids in plants plastid

19. Classes of molecules • Macromolecules • “Structural” sugars: • Cellulose = long and unbranched, beta 1-4 linkage, resist tensile (pulling) forces, plants • Chitin = unbranched, N-acetylglucosamine, invertebrates • Glycosaminoglycans = components of extracellular matrix for cartilage and bone, repeating (A-B)n structure

20. Classes of molecules • Macromolecules • Nucleic Acids • Nucleotide monomers (rNTPs, dNTPs) • Storage and transmission of genetic information • Phosphate + 5C ribose sugar + nitrogenous base RNA DNA H

21. Classes of molecules • DNA is usually double stranded • RNA is usually single stranded • RNA may fold back on itself to form complex 3D structures, as in ribosomes. • RNA may have catalytic activity; such RNA enzymes are called ribozymes. • Adenosine triphosphate (ATP) is a nucleotide that plays a key role in cellular metabolism • Guanosinetriphosphate (GTP) serves as a switch to turn on some proteins.

24. DNA is a useful reference-frame for sizes

25. Classes of molecules • Macromolecules • Proteins • Amino acid monomers • Peptide bond formation • N-terminus versus C-terminus • Backbone is common, side chains (R) differ

26. Classes of molecules • Macromolecules • Proteins • Backbone is common, side chains differ • 4 categories of amino acid side chains • Polar charged D, E, K, R, H • Polar uncharged • Nonpolar • Unique

27. Classes of molecules • Macromolecules • Proteins • Backbone is common, side chains differ • 4 categories of amino acid side chains • Polar charged D, E, K, R, H • Polar uncharged S, T, Q, N, Y • Nonpolar • Unique Post-translational modifications: Phosphorylation of –OH groups

28. Classes of molecules • Macromolecules • Proteins • Backbone is common, side chains differ • 4 categories of amino acid side chains • Polar charged D, E, K, R, H • Polar uncharged S, T, Q, N, Y • Nonpolar A, V, L, I, M, F, W • Unique

29. Classes of molecules • Macromolecules • Proteins • Backbone is common, side chains differ • 4 categories of amino acid side chains • Polar charged D, E, K, R, H • Polar uncharged S, T, Q, N, Y • Nonpolar A, V, L, I, M, F, W • Unique G, C, P

30. Hydrophobic and hydrophilic amino acid residues in the protein cytochrome c

31. Levels of protein structure • Primary • Sequence of the polypeptide chain H3N-MQWERTYIHAHAPKLCVN-COOH H3N-Met GlnTrpGluArgThr Tyr Ile… H3N-Methionine Glutamine Tryptophan…

32. Levels of protein structure • Secondary • Alpha-helix (collagen) • Beta-sheet (spider silk) • Side-chain dependence to which form is adopted but stabilization comes from backbone - backbone hydrogen bonding interactions

33. Levels of protein structure • Tertiary • Side-chain dependent and mediated packing of the secondary elements • Fibrous proteins = elongated, often structural roles • Globular = compact, often enzymes

34. Protein domains can be modular • Protein Domains • Domains occur when proteins are composed of two or more distinct regions. • Each domain is a functional region

35. Protein structures can be dynamic • Dynamic Changes within Proteins • May occur with protein activity. • Conformational changes are non-random movements triggered by various events (e.g. binding, chemical mods…)

36. Levels of protein structure • Quaternary • Interactions between 2 or more distinct polypeptide chains

37. Protein-Protein Interactions • Results from large-scale studies can be presented in the form of a network. • A list of potential interactions can elucidate unknown processes.

38. Disease • Sickle-Cell Anemia (SCA) • Painful • Life-threatening periods of crisis • e.g. vaso-occlusive crisis • block blood flow in capillaries

39. Disease • Sickle-Cell Anemia (SCA) • Hemoglobin is composed of four polypeptide chains • Two alpha-globin subunits + two beta-globin subunits • SCA is caused by a single amino acid substitution in beta-globin • E6V

40. Protein structure and folding • Anfinsen RNase A experiment • Denature (unfold) protein in urea • Observed loss of activity • Dialyze the urea away • Observed refolding • Regain of activity • Demonstrated structural information is inherent to protein sequence • Follow a folding pathway • Fold to the lowest energy state

41. Two alternate pathways for protein folding

42. Chaperones prevent mis-folding • Molecular Chaperones • HSP70 during translation of nascent peptide • Binds exposed hydrophobic regions • Hydrolyzes ATP in a bind-release cycle Hartl, et al (2011)

43. Chaperones prevent mis-folding • Molecular Chaperones • HSP70 during translation of nascent peptide • Binds exposed hydrophobic regions • Hydrolyzes ATP in a bind-release cycle • Chaperonins assist post-translation

44. Protein folding and Disease • CJD (Mad Cow) & Alzheimers Disease • PrPC --> PrPSc --> plaque • APP --> Ab42 --> plaque