Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chemistry 438 - Spring 2013

 Exam I Study Guide

Spring 2013

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.

• G What is G (in words)?
  • G° (definition)
  • G° ' (definition)
  • G = H- T S.
    • What does it indicate about energy availability?
    • What does G tell you about a system?
  • G = G° '+ RT lnQ.
  • G° ' = -RT lnK_eq.
• Know how to solve simple problems using thermo relationships.
  • How do you find G for a series of reactions? K_eq?
  • Driving reactions by coupling:
    • sequentially,
    • in parallel. (Note special function of enzymes in this case.)

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

• Why ATP?
  • Phosphoric acid anhydride bond is unstable to hydrolysis (thermodynamically unstable)
  • However, Phosphoric acid anhydride bond is not readily hydrolyzed (kinetically stable)
• Shifting Equilibria (G) with ATP.
• "Hi Energy".
  • What do we mean by "hi energy?" (The compound has a large negative G° ' of hydrolysis, where 'large' means greater than or equal to G° ' of ATP.)

Amino Acids

Know general acid/base properties, appearance of titration curve, approximate values of pK_a'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). C_alpha, 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.

• Primary
• Secondary
• Tertiary
• Quaternary

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 bonds/forces at each level?
  • Cooperativity effects in bonding.
  • The effect of the aqueous environment on bond strength.

Secondary Structure.

• Periodic peptide structures: alpha helix & beta strand (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, peptide H-bonds are satisfied). What aa(s) disrupt them?
• Remember there are two basic ways of arranging beta strands to give beta sheets (are sheets secondary or supersecondary structures? defend your answer).
• beta-turn.
• 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 difference between a fold and a motif?
  • 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 alpha, alpha/beta, alpha+ beta, 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 your answer!
• 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.

Fibrous Proteins

• What are the two structural "families" of fibrous proteins?
  • 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).

Quaternary/Supramolecular Structures

• Why quaternary structure?
• List and explain advantages.

Protein Folding

• Denaturation/renaturation.
  • Define
• How does it occur?
  • Heat
    • why do proteins often agregate/precipitate with heat?
  • Chemical agents
    • Be able to discuss urea as a denaturant.
      • Why does it work (mechanisms)?
    • When is a disulfide reducing reagent needed? Why only for these proteins?
• Generally the lowest global DG is not attained in folding proteins.
  • What is argument for this statement?
  • What is meant by a local DG minima?
  • How do we envision a protein finding a stable structure?
    • Folding pathways and nucleation.
    • -Helices, -strands and nucleation.
    • -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?
  • Kinetics.
  • Genetics.

Chaperon Proteins (see also Discussion, below)

• 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.
• Be able to discuss these proteins as examples of the topics we have discussed under the general rubric of protein structure and function.
  • Describe the 1°, 2°, motif, domain, 3°, and 4° structures. (Note, not all levels may be represented, or separately represented.)
    • Note the heme group, how it is held, and by which subunits.
  • Note the designation of the Hb tetratmer as an ₂₂ or protein.
    • 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, via ₁₁ contacts.)
      • 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).
  • Homotropic.
    • 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 ?
  • Heterotropic.
    • 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.

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:

• [S] >> K_m,
• [S] << K_m,
• [S] = K_m.
• Be able to identify/explain reaction order at various [S].

Be able to interpret the Michaelis-Menten (v_i 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:

• V_max and apparent V_max
• K_m and apparent K_m.

Know the three type of classical, reversible Inhibition

• competitive: model mechanism, kinetics, plots;

• non-competitive: model (mechanism), kinetics, plots;

• un-competitive: model (mechanism).

Be able to draw and interpret plots of:

• rate vs. temperature

• rate vs. pH.

Allosteric Enzymes (see Hb above)

• Define
• What do v_i vs. [S] plots look like?
• Cooperativity,
  • Heterotropic.
  • Homotropic.
• Concerted (symmetry) model for homotropic allosteric enzymes.
  • Be able to explain model (shifting equil.) for substrates and effectors - correlate to kinetics.
• Sequential Model - explain.

Catalysis

Know major types we discussed

• general acid/base (as opposed to specific),
• covalent,
• proximity/orientation,
• distortion/transition state binding,
• transition state charge stabilization,
• metal ion.

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.

• Given the substrates and catalysts,
  • be able to explain them in catalytic terms,
  • be able to show reasonable electron (electron pushing) and atom movements for bond making/breaking

Vitamins and Cofactors

What are vitamins?

• Why are they vitamins?
• Know relationship between vitamins and cofactors we have discussed.
• Niacin vs. NAD⁺ and NADP⁺
  • NAD⁺ = most common oxidation cofactor (catabolism)
  • NADP⁺ = most common reduction cofactor (anabolism)
• Riboflavin vs. FAD and FMN
  • stronger oxidizer then NAD⁺
• Pantothenate vs. Coenzyme A
  • carrier of acyl groups (activated)
• lipoate
  • linked to lysine to give lipoamide "arm."
• biotin
  • linked to lysine to give biotinamide "arm."
• 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 is the function of the "ADP" portion of NAD⁺, NADP⁺, and FAD?
  • What common theme connects NAD⁺, FAD, and Coenzyme A?
• What are the specific major metabolic functions of Coenzyme A, lipoic acid, and biotin?
  • What common themes connect these three cofactors?
  • How long is the acyl (pentanoate) plus lysine "arm" for lipoate and biotin (measure in "atoms")?
  • How does this compare to the "arm" in coenzyme A?
• What are the fat soluble vitamins and their major functions?
  • A (source of retinoate for rodopsin pigment in vision)
  • D (calcium uptake homone)
  • E (anti-oxidant).

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

Prions

1. Be able to argue for or against the prion proposal.
   1. Why has the concept of Prions been so controversial?
2. The prion diseases most closely resemble viruses. One way to conceive of viral infections is as an introduction of foreign (and disruptive) information into the host system (thus the use of the term "virus" for invasive information in computer systems).
   1. What "kind" of information does the author postulate the prion transmits?
   2. How is this information transmitted/inherited?
      1. What evidence is there that only proteins are involved?
      2. What is thought to happen to the prion protein during transmission of the disease?
3. There seem to be genetically transmitted prion diseases (or predilections to prion diseases). How do these diseases fit within the Prusiner model?

Chaperons and Protein Folding

1. What is the function of the chaperons? Is their existence and necessity in many cases consistent with the idea that ALL of the folding information for proteins is in the primary sequence?
2. Why might protein aggregation be a major problem for cells without chaperons? How do Chaperones prevent aggregation?
3. What are the different types of chaperones (describe) and how do their functions differ?
4. Reconcile (or refute) the fact that chaperonins require ATP energy for their activity with the statement that proteins "self-assemble."
5. Is the suggestion of co-translational domain folding consistent with a requirement for chaperons? Explain.

HIV and AIDS

1. Consider the actions of the various drugs-what they are doing. Be able to describe in terms of enzyme inhibition.
2. Consider the viral responses (types of mutations, enzymes involved) to the drugs..
3. Consider the conclusions from this research, and the supplemental (evolutionary) articles regarding:
   1. how HIV responds to challenges
   2. why HIV always "wins".

Thermodynamic Bumble Bees

1. Be able to solve a simple problem involving thermodynamics as in this example (same basic question, different numbers).
2. Understand and note the various approximations made.
3. Defend your approximations.

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

C438 Home

Schedule

Last modified 1 March 2013