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 = O = H = 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 Exploit Van der Waals contacts
Based on the Gecko
Adhesion depends on close contact between surfaces “StickyBot”
Video link

7. H2O Can form 4 hydrogen bonds Highly polarized
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 Why are reactions so pH sensitive?
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
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 Metabolic intermediates
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 plastid “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 RNA DNA 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
Guanosine triphosphate (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 Gln Trp Glu Arg Thr 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
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