BIOCHEMISTRY - BCHM 321

syllabus
Interactive Web Programs
Worried results; Survey Results
Chemical Logic; simple molecules make complex polymers

• find all relevant course information on the course web sites
• understand general expectations for the class

Chapt 1A - Lipid Struct.

Chapt 1B - Lip in Water

• draw line structures of fatty acids given their trivial and symbolic names and the reverse
• draw line structures of common phospholipids
• draw graphs/diagrams to explain the similarities in behavior when salts, organic solvents, and lipids are added to water
• state the differences between single and double chain amphiphiles, the structures they form in water (micelles and bilayers), and the intermolecular forces involved in their interactions with self and water
• explain the changes in amphiphiles with water and self in the formation of liposomes

Chapt 1C; Dynamics of membrane lipids;

Chapt 1D - Lipids in Water: Thermodynamics (to red line)
(Review Thermodynamics );Quiz PC

• state the different kinds of dynamical motions of double chain amphiphiles in lipid bilayers, differentiating between motion of entire molecules and motion within a molecule

• describe experiments that could be used to study lateral and flip-flop diffusion in vitro and in vivo

• explain the use of exogenous labels (fluorescent, radioactive, electron spin resonance) that allow laboratory determination of lipid location and movement

• explain similarities and differences in  measurement and explanations of phase transitions in water and in lipid vesicle

• explain the biological effects and necessities of membrane dynamics

• guess relative enthalpic and entropic contributions to formation of micelles from single chain amphiphiles based on their understanding from earlier chem classes.

 Chapt 1D - Lip Water: Thermodynamics

Chapt 1E - Why Micelles, Bilayers?

Chapt 1F - What's New?

• explain the uses  and advantages disadvantages of gel filtration and dialysis
• describe and differentiate the thermondynamic parameters ΔG, ΔH, ΔS, Δμ, and the standard counterparts, ΔG⁰, ΔH⁰, ΔS⁰, Δμ⁰
• describe the contributions of ΔH⁰ and ΔS⁰ to Δμ⁰ for transfer of nonpolar molecules from water to more nonpolar enviroments.
• define the hydrophobic effect based on experiments studying the transfer of nonpolar molecules from water to more nonpolar environments.
• in nonmathematical language explain why single chain amphiphiles generally form micelles while double chain amphiphiles form bilayers.
• describe how lipid bilayers participate in signal transduction.

• integrate the factual knowledge and understanding gained in the study of lipids to analyze and explain experimental observations and data from the literature,;
• to draw conclusions consistent with the literature data
• learn how to draw relevant "cartoons" that help visualize biochemical processes
• gain experience in reading biochemistry literature

Chapt 2A - Prot/A. Acids

• state the charge on amino acid side chains using the Henderson Hasselbach equation and the approximate charge by inspection at any given pH
• draw mechanisms and identify products for the reaction of nucleophilic side chains Lys and Cys with common chemical modification agents and extend this understanding to reactions of His.
• draw mechanisms for disulfide exchange reactions for sulfhyrls using them and oxidation numbers to explain redox reactions of cysteine/cystine. 

Chapt 2B - Prot: Compo, Sequence, Conform.

PS1 Due

• molecular weight
• presence of certain specific amino acids
• amino acid composition
• N and C terminal amino acid
• specific amino acid necessary for binding and activity
• amino acid sequence
• secondary structure
• 3D structure

Chapt 2C - Prot: Conformation

• describe the differences between primary, secondary, supersecondary, tertiary and quaternary protein structure
• explain the basis of CD measurements for secondary structure
• describe the similarities between torsion angles and an energy vs torsion angle plot for the rotation of the C2-C3 torison angle with phi/psi angles of peptide bonds and the 2D plots off allowed conformations around a given amino acid in a protein (Ramachandran plot).
• (from reading give explanation for observed propensities of amino acids for different secondary structure)

Chapt 2D: Protein Folding/Stability

• Review:  draw typical excitation and emission spectra for fluorophores;  differentiate between emission wavelength maximum and emission intensity; describe solvent effects on fluorescence from fluorophores that are generally nonpolar but have regions with dipoles due to heteroatoms
• Differentiate between thermodynamic (equilibrium) and kinetic (timed) approaches to the study of protein folding reactions
• Describe techniques to study transient (kinetic) and long-lived (thermodynamic) intermediates in protein folding
• describe the following intermediates in protein folding:  molten globule, X-Pro isomers; Disulfide bond
• interpret spectral and chromatographic data from protein folding studies.
• explain the difference between the environments for protein folding when performed in vitro and in vivo
• state the role of molecular chaperones in in vivo protein folding

Chapt 2E: Lab Det ΔG^o;

Chapt 2F: Thermo and IMF in Protein Fold/Stab.
Read up to RED LINE

• from a graph of an observable vs [denaturant], determine the ΔG⁰ in the absence of denaturant for the N to D transition
• from a graph of an observable vs T, determine the ΔG⁰, ΔH⁰, and ΔS⁰ at a given temperature for the N to D transition

2F (up to red line)

• Differentiate between general charge and specific ion-ion pairs and summarize their role in protein stability
• Draw the structure of N-methylacetamide  (NMA) and explain why it is a useful small molecule model to study the role of H bond in protein stability
• Draw  thermodynamics cycles for the transfer of a hydrogen bonded dimer of  NMA from water to a nonpolar environment.  From the ΔG⁰ for steps in the cycle, and extending this model to protein, predict if  buried H bond formation drives protein folding
• Explain if studied of low temperature protein denaturation, high temperature protein, and ΔG^o transfer of nonpolar side chains from water support the hydrophobic effect in protein stability
• summarize the relationship between the empirical Hofmeister series and preferential binding of reagents into the hydration sphere of protein to explain the effects of denaturants (urea, guanidine salts) and stabilizers (glycerol, ammonium sulfate) of proteins

Chapt 2F: Thermo and IMF in Protein Fold/Stab. Finish

2F: past red line:

• Using benzene solubility in water as a model to study the role of hydrophobic effect in protein unfolding and by inference in protein stability, interpret graphs of ΔG⁰, ΔH⁰, ΔS⁰ and ΔC_p for the transfer of benzene to water, as a function of temperature.

• from the above graph, explain if trends in the thermodynamic parameters for benzene transfer into water predict the observed protein unfolding/stability behavior of proteins as a function of temperature?

• Give a molecular interpretation of the observed ΔC_p for the transfer of nonpolar molecules into water.

• Describe chain conformational entropy, relate it to conformational changes in acyl side chains in single and double chain amphiphiles with temperatures, and describe it role in protein stability.

• state which of several given explanations for the observed destabilizing effects of Asn to Ala mutations in protein account for those observation

• summarize graphically the magnitude and direction of the major contributors (inter- and intramolecular forces and effects) to protein stability

Chapt 2G: Predict 2⁰ and 3^o struct;

Chapt 2 H: Prot. Aggregates

• find web based proteomics protein to analyze protein sequences and structures
• describe the basis for methods used to predict the secondary structure and hydrophobic structures of proteins
• analyze secondary structure and hydropathy plots from web-based proteomics programs.
• describe differences between intergral and peripheral membranes proteins, and how each could be purified.
• explain how hydropathy and secondary structure plots can be used to predict membrane spanning sequences of proteins
• describe in general the theoretical and empirically based methods to predict protein tertiary structure from a primary sequence
• describe possible early intermediates in protein folding as determined by theoretical methods

2H:

• describe experimental evidence to show that protein misfolding and aggregation depends on the amino acid sequence and the environment in which folding occurs.
• describe conditions in vitro that may promote aggregation and how these might be minimized in vivo
• describe alternative conformations of prion proteins and relate them to a energy topology landscape
• explain how prion diseases may be transmitted in the absence of genetic material

Literature Learning Module:  Proteins

Chapt 3A: Mono/Disacch.

Chapt 3B: Complex Oligos
Intro to Carbohydrates:  Carbohydrate Jeopardy

Chapt 3C: Glycoproteins
Literature Learning Module:  CHO

Chapt 5C: Mb, Hb and O2 to red line

Chapt 5D: binding and gene expression

Chapt 5D: binding and gene expression;

Chapt 5E: Drug Dev.

Chapt 6A: Diffusion

Chapt 6B: Rap. Eq/SS Enz. Kinetics

Chapt 6C: Models of Inhib.
Chapt 6D: More Complicated Models of Enz. Catalysis;

Literature Learning Module:  Binding

Chapt 7A: Catalysis

Chapt 7B: Mech. Enz. Catalyzed Rxs

Chapt 7C: Cofactors and Electron Pushing

Chapt 7D: Enz. Cat. Rxs in Organic Solvent;

Chapt 7E:  Ribozymes

4/11 F D3

Literature Learning Module:  Catalysis

Chapt 8C: ATP and OxPhos

Chapt 8C: ATP/Oxphos;

Chapt 8D: Photosynth.

Chapt 9A: Nrg - ATP

Chapt 9B: Neurochem

Chapt 9C: Kinases, Phosphatases
Web Survey