| Schedule |
 |
| Chem431 |
|
F 2001 |
|
|
Cells: How are prokaryotes and eukaryotes distinguished? What are the various organelles we discussed and what happens in each? (nucleus, mitochondrion, golgi complex, smooth and rough endoplasmic reticulum, lysosome, chloroplast; basic biochemically important pathways, etc.). Which of the organelles we discussed are unique to plants?
Biomolecules: What are the main elements used by living organisms? What are the rationales for life depending on H, O, N, & C? Why add S & P? And how about the elements occurring mainly as ions (Na, K, Ca, Cl, etc., & Fe, Zn, Cu etc.)? Why should life be mainly a phenomena of the 2nd and 3rd electron shells? (Think about this but don't spend too much time on it on my account!) What are the main families of biomolecules and what are their characteristic functional groups and functions?
Water: Ionization; ion product; hydrophilicity - what
does this mean? Hydrophobicity - what does this mean? acid/base
properties of water. How can H+ move through water
apparently faster than the rate of diffusion? Structure of liquid
water. How does water structure affect solubility of other molecules?
hydrophobicity?
Amino Acids: Know general acid/base properties, appearance of titration curve, approximate values of pKa's and ionic forms predominating at any pH. Know general formula for aa's. Know which amino acid side chains are: hydrophobic, hydrophilic, neutral, charged, polar.What's special about proline? Chirality of aa's. Why is this significant? D & L. How many aa's are used to synthesize proteins? Others are found in proteins - what'shappening? Memorize structures for: gly, ala, asp, lys, cys, ser, leu, met, glu, phe.
Peptides: Peptide bond (= amide bond); stability in aqueous solution; planar nature of bond (resonance). Residue, Ca, rotation angles - many are forbidden. Periodic peptide structures: alpha & beta (be able to describe these structures). What are some properties of alpha & beta structures? How are they stabilized? Why are they so common? (ease of nucleation). What aa's or strings of aa's may disrupt them? Remember there are two b structures. b-turn. Are these the only periodic structures found in proteins? The only extensive ones? The only extensive ones in globular proteins?
Globular Proteins: What is a globular protein? Levels of description - periodicity, clustering, patterns. "Random" structure. "Random" folding regions. Primary, secondary, tertiary and quaternary levels of structures: what are the characteristics of each level (residue relations, bonding types, steric relations). Weak "bonds" (hydrophobic forces, hydrogen bonds, ion pairs = salt linkages, van der Waal's bonds): which are the most important at each level? Cooperativity effects in bonding. The effect of the aqueous environment on bond strength. Super secondary structures. Domains. Give examples to illustrate these concepts. Hinges and domains. Domain types: all a, a/b, a+ b, random. Be able to discuss a protein's structure in terms of these various concepts. Disulfide bonds - when are they formed, what are they good for, do they help in folding (as process - no), extra - vs. intracellular proteins. Domains, split active sites, genes and adaptation - example of antibodies.
Structural Proteins: What's special about collagen: sequence (periodicity of primary structure) the collagen triple helix (why so many gly? Why pro?)
Protein Folding: Denaturation/renaturation. Lowest global DG not attained (What is argument for this statement?). Local DG minimum. Folding pathways and nucleation. a-Helices and nucleation - choosingthe DG minima. Folding vs. rate of translation. Is there a temporal effect in folding large proteins? Explain. Why domains in folding?(Kinetics, genetics.) What is a "heat shock" protein? What is it used for? What is a "chaperonin"? What is it used for? How do we think chaperonins work? Why are they needed?
Myoglobin/Hemoglobin and Binding: Be able to discuss these proteins as oxygen storage/carrier molecules and as examples of the topics we have discussed under the general rubric of protein structure and function, as well as examples of binding phenomena and its interpretation in proteins. What is a sigmoidal curve? What do we mean by cooperativity? What is the meaning of n in cooperative proteins? What is a Hill plot? What information does it provide? Be able to interpret one of these plots.
Supramolecular Structures: Why quaternary structure?
List and explain advantages.
What is a nucleotide? nucleoside? free base? What is the structure of ATP. Know (be able to draw) the basic purine and pyrimidine ring structures. In what portion (specifically) does the chemistry take place in each of these cofactors? What are the major metabolic functions of NAD+ and FAD? What distinguishes NAP+ from NADP+? What is the metabolic consequence of this difference? What do we mean by metabolic compartmentation? What distinguishes FAD from FMN? What is the function of the "ADP" portion of NAD+, NADP+, and FAD? What common theme connects NAD+, FAD, and Coenzyme A?
Fatty acids. Triacylglycerols (triglycerides). Phospholipids. What is th chirality of triglycerides and phospholipids? Micelle. Bilayer. Memorize structures for: glycerol, choline, ethanolamine, stearic acid, oleic acid, palmitic acid. Be able to draw phospholipids and/or triacylglycerols composed of any of the components above. What are some membrane functions? Chain length and saturation of fatty acid residues vs. membrane fluidity- explain. Cholesterol and membrane fluidity. Lipid bilayers as barriers. Fluid Mosaic Model. Lipid functions in membranes. Protein functions in membranes. Membrane flow and membrane biogenesis. How do proteins get into membranes? What are lipoproteins? What do they do?
What distinguihs the CHO's? What is the chirality of the CHO's in nature? What are the major functions for these molecules? What is the most common and important sugar? What are the other common hexoses? pentose? trioses? Aldose. Ketose. Why are ring forms of pentoses and hexoses stable? Note teh new chiral center in the rings. What bond stablizes these rings? How are sugar residues joined together in polysaccharides? Are there any patterns distinguishing fuel and structural forms of CHO's? Why? What are the common forms of fuel storage? How do they differ? What are advantages/disadvantages for each? How do animals and plants differ? Why? Be able to describe how structural forms are able to accomplish their jobs and special properties they have. What is a glycosamine? Give an example and its function. What are glycoproteins? Give an example and its function.
