Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chemistry 431 - Fall 2008

 CHEM 431

 Exam I Study Guide

 R. Paselk

 

Final 2008 Version

Introduction

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? 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.

Origin and Early Evolution of Life

How old is the Earth? How long ago did the Precambrian end? What are some of the major occurances important to life in the Precambrian? (origin, procaryotes, eucaryotes, multicellularity, etc.).

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. 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 beta structures. beta-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 (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:

    Domains, split active sites, genes and adaptation - example of antibodies:

    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.

    Be able to classify a protein or Explain/discuss the Protein classification system discussed in your text.

    Fibrous Proteins:

    Quaternary/Supramolecular Structures

    Protein Folding

    Chaperon Proteins

    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).


    Syllabus

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    Last modified 10 October 2008