| CHEM 431
Exam I Study Guide
Final 2008 Version
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?
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?
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.).
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.
Residue. Peptide bond (= amide bond); stability in
aqueous solution; planar nature of bond (resonance). Calpha, rotation angles - many
are forbidden. Periodic peptide structures: & (be able to describe these structures). What are some properties of & 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 structures. -turn. Are these the only periodic structures found in proteins? The only extensive ones? The only extensive ones in 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).
- Hydrophobic forces
- Hydrogen bonds
- Ion pairs = salt linkages
- Van der Waal's bonds
- Which are the most important bonds/forces at each level?
- Cooperativity effects in bonding.
- The effect of the aqueous environment on bond strength.
- Periodic peptide structures: & (be able to describe these structures).
- What are some properties of & structures?
- Why are they so common? (ease of nucleation, peptide H-bonds are satisfied). What aa(s) disrupt them?
- Remember there are two structures.
- Are these the only periodic structures found in proteins?
- The only extensive ones?
- The only extensive ones in globular proteins?
Supersecondary Structure/ Motifs.
- What is the relationship between folds and motifs?
- What are some common motifs we've looked at/are in your text?
- What are some common folds we've looked at/are in your text?
Domains. Give examples to illustrate these concepts:
- Hinges and domains.
- Binding site/active sites are often split between domains.
- Domain types (e.g. all , /, + , random)
- What's the difference between a domain type and a motif?
Or is there one? Do the definitions overlap?
Domains, split active sites, genes and adaptation - example of antibodies:
- What is IgG?
- How many chains does it have?
- Does it represent a tertiary or quaternary structure? Defend
- How many domains ?
- How are the domains related?
- How do we believe the domains arose?
- Where are the active sites?
- Assume your genome codes for 100 light chains and 100 heavy
chains. How many different IgG molecules can you make (without
mutations in the hypervariable region)?
- IgG has been touted as a model for the evolution of advanced
proteins in eukaryotes. Explain.
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.
- What are the two structural "families" of fibrous
- 1 - made up of fibers much like a rope, e.g. collagen, keratin, silk fibroin.
- What are the special properties of keratin and silk fibroin?
- What's special about collagen:
- The collagen triple helix
- Sequence (periodicity of primary structure)
- Why so many gly?
- Why pro?
- 2 - made up of globules much like a string of 'snap beads'
(or analogous to a chain).
- e.g. microtubules, microfibrilles (actin fibers).
- Why quaternary structure?
- List and explain advantages.
- How does it occur?
- why do proteins often aggregate/precipitate with heat?
- Chemical agents
- Be able to discuss urea as a denaturant.
- Why/How does it work (mechanisms)?
- When is a disulfide reducing reagent needed? Why only for
- Generally the lowest global G
is not attained in folding proteins.
- What is argument for this statement?
- What is meant by a local G minima?
- How do we envision a protein finding a stable structure?
- Folding pathways and nucleation.
- -Helices, -strands
- -helix - -strand
associations (super-2°/motif formation) and stabilization.
- Folding vs. rate of translation. Is there a temporal effect
in folding large proteins? Explain.
- Why domains in folding?
- What is a "heat shock" protein?
- What is a "chaperonin"?
- What is it used for?
- How do we think chaperonins work?
- Why do we think ATP is necessary (how is it used)?
- How do we rationalyze the need for ATP with the statement that protein folding is determined by primary structure and that cahperonins (and chaperones generally) do NOT affect final folded form?
- Why are they (and other types of chaperones) needed?
- What are the other families of chaperones we discussed and how do we think they operate?
Myoglobin/Hemoglobin and Binding
- Be able to discuss these proteins as oxygen storage/carrier
- Be able to discuss these proteins as examples of the topics
we have discussed under the general rubric of protein structure
- Describe the 1°, 2°, motif, domain, 3°, and 4°
structures. (Note, not all levels may be represented, or separately
- Note the heme group, how it is held, and by which subunits.
- Note the designation of the Hb tetratmer as an 2
- If a protein had 8 subunits, with 3 of one kind, duplicates
of two kinds, and a singlet, how would you disignate this structure?
- Why is Hb called a dimer of dimers?
- What are the dimers?
- How are the monomers held in the dimers? (In general terms,
- What kinds of bonding predominate?
- How are the dimers held together?
- What kinds of bonding predominate?
- Be able to discuss these proteins as examples of binding
phenomena and its interpretation in proteins.
- When do we see a rectangular hyperbolic curve?
- What kind of a shape is this (be able to sketch it)?
- What kind of binding does it signify?
- What kind of binding (mathematical) model underlies it?
- What is a sigmoidal curve?
- What do we mean by cooperativity?
- What is the meaning of n in cooperative proteins?
Allosterism and Allosteric Enzymes
- What do V vs. [S] plots look like?
- Explain why this shape should arise from cooperative behavior (think about concentrations and multiple collision frequency/probability).
- What is meant by cooperativity?
- Describe a 100% cooperative system vs. a partially cooperative system
- What can we say about a system that exhibits a cooperativity of 2.5 ?
- Negative effector
- Negative effector vs. inhibitor (can be considered a special case).
- How does a (-) effector affect a V vs. [S] plot for a allosteric system? Why?
- What effect does does a (-) effector have on cooperativity? Why?
- Positive effector
- How does a (+) effector affect a V vs. [S] plot for a allosteric system? Why?
- What effect does does a (+) effector have on cooperativity? Why?
- Concerted (symmetry) model for allosteric enzymes.
- Be able to explain model (shifting equil.) for substrates (homotropic ) and effectors - correlate to kinetics.
- Be able to explain model (shifting equil.) for effectors (heterotropic) - correlate to kinetics.
- Sequential Model for allosteric enzymes. - explain.
What is an enzyme? (define) Turnover number. velocity.
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).
Last modified 10 October 2008