Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chemistry 438 - Spring 2013

 Exam I Study Guide

Spring 2013

Introduction

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? Weak Bonds: What is a weak bond? What are the different types? (van der Waal's and Hydrogen bonds). Compare the relative strengths and stabilities of covalent, ionic, van der Waal's, and H-bonds. Be able to discuss these different bond types.

Cells

How are prokaryotes and eukaryotes distinguished? What are the various organelles we discussed and what happens in each? (basic biochemically important pathways, etc.)

Energy & Thermodynamics

What is thermodynamics? What can it tell you about a process? Pathway independent.

Energy capture in catabolism: ATP is the common energy "currency" of metabolism.

Proteins

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's happening? Memorize structures for: gly, ala, asp, lys, cys, ser, leu, met, glu, phe.

Peptides

Residue. Peptide bond (= amide bond); stability in aqueous solution; planar nature of bond (resonance). Calpha, rotation angles - many are forbidden.

Globular Proteins

What is a globular protein?

Levels of description (Primary - Quaternary)

Periodicity, clustering, patterns. "Random" structure. "Random" folding regions.

What are the characteristics of each level (residue relations, bonding types, steric relations).

Weak "bonds"

Secondary Structure.

Supersecondary Structure/ Motifs

Domains

Give examples to illustrate these concepts:

Tertiary structure

Describes the overall folding of a single covalent structure.

Disulfide bonds - when are they formed, what are they good for, do they help in folding (as process - no), extra - vs. intracellular proteins.

Be able to discuss a protein's structure in terms of hierachical levels and functional units/segments.

Fibrous Proteins

Quaternary/Supramolecular Structures

Protein Folding

Chaperon Proteins (see also Discussion, below)

Myoglobin/Hemoglobin and Binding

Allosterism and Allosteric Enzymes

Enzymes

What is an enzyme? (define) Turnover number. velocity.

Specificity

Lock and Key model and its failure. Induced fit model - explain. How do substrates bind? Chemical specificity. Why are enzymes big (<5% of surface is active site)?

Zymogens: What are they? Why do they exist? (What enzymes commonly occur as zymogens?)

Enzyme Kinetics

What are main assumptions in steady-state derivation of the Michaelis-Menten eqn?

Note the consequences of the M-M eqn at:

Be able to interpret the Michaelis-Menten (vi vs. [S]) and Lineweaver-Burke (double-reciprocal) plots for both uninhibited and inhibited reactions. Be able to find and/or show on/with both plots:

Know the three type of classical, reversible Inhibition

Be able to draw and interpret plots of:

Allosteric Enzymes (see Hb above)

Catalysis

Know major types we discussed

What is meant by a "concerted" mechanism?

Be able to explain an enzyme mechanism in terms of the catalytic types we have discussed.

Be familiar with the mechanisms of lysozyme and the catalytic triad of the Serine proteases as we saw in class.

Vitamins and Cofactors

What are vitamins?

Discussion Topics

There will be one or two questions from discussion on the exam (10-20%)

Prions

Chaperons and Protein Folding

HIV and AIDS

Thermodynamic Bumble Bees

 

You may bring a data/information sheet to the exam, however you must not exceed one side of a single sheet of 5.5" x 8.5" paper (half of a standard sheet of paper) for this sheet! GOOD LUCK!


Syllabus

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Schedule

Last modified 1 March 2013