c430 final exam amino acids, proteins

1.



2. Amino terminus ---- carboxy terminus

1. Trans, planar, 40% double bond character due to resonance seen in C-N.

2. Trans (10 KJ more stable) because it's less likely to have steric hindrance.

3. No.

4. Only around a-carbons (think of a-carbons as hinge points), all four atoms in an amino acid travel together in a plane.

1. 3

2. N-aC and aC-C ( and ) or (torsiol & dihedral) bonds.



3. Sterics

4. Size and/or charge of the R group

5. C-N bond

• 1. Ramachandran plots
• 2. Unallowed b/c of sterics
• 3. A specific enantiomer of an amino acid (e.g., L-alanine)

4. No steric overlap and fully allowed

5. Medium blue? conformations allowed at extreme limits for unfavorable atomic contacts

Light blue - conformations that are permissible if a little flexibility is allowed in dihedral angles


6. Tan - disallowed combos b/c it is sterically unfavorable and thermodynamically impossible

7. A-helices

1. Steric interference

2. yes.

3. Synthetic AA aspartame or phenylalanine, b/c they're missing phenylhydroxylase which turns phenylalanine into tyrosine.

1. Linear sequence of AA, dictates protein function & determines folding of protein.

2. 3D path in space of amide backbone (doesn't consider contribution of R groups) - primary for stabilizing structure

3. 3D folding of protein w/ contributions of R groups included. R groups help bring in whole structure

4. Optional - composed of more than one polypeptide subunit (i.e., Hb)


2. same forces hold tertiary and quaternary structures together

• 1. Primary, sterics (ramachandran plot)
• 2. H bonding
• 3. Point out and away from backbone
• 4. Contiguous phi and psi angles that are identical lead to a-helix and b-sheet

5. 3.4 residues/turn

6. n and n+4

1. H-bonding between adjacent chains, but it's not contiguous

• 
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1. Disulfide bond (2 cysteine residues) - covalent bond sole strong force -S-S <---> -SH HS- via redox.

2. Ionic interactions via salt bridges

3. H-bonding

4. Hydrophobic interactions

5. Metallic ion interactions (i.e., Fe2+, Mg2+, Mn2+)

• 1. Almost folded protein
• 2. Hydrophilic exterior and hydrophobic interior thanks to dS
• 3. Stabilizing forces are the same as tertiary forces (disulfide bonds, ion interactions, H-bonding, hydrophobic, metallic ion)

1. Nonpolar R groups on the interior, Polar R groups on exterior, and nonrandom processes that drive organization from primary structure to tertiary (quaternary) structure.

2. Fodled state

3. Nonrandom, we know this b/c if we searched for every possible conformation, it would take a REALLY long time. However, it takes much less time, so we know its nonrandom.

1. More likely due to entropy than enthalpy


2. b/c huge exothermic rxn would denature the protein

3. ENTHALPY - b/c H2O molecules are released to the outside, away from hydrophobic molecules, there is a net increase in dS, despite new compactness of protein.

1. With the use of chaperones. Chaperones are folding catalysts that prevent formation misformed proteins.

2. Because high [protein] or incorrect folding can lead to aggregation or precipitation, which is bad.

3. Mechanism:  (1) when proteins fold, there is the exposure of hydrophobic R groups. 

(2) Chaperones will bind to exposed R groups to facilitate correct folding

4. Yes.

• 1. Heat, pH, chaeotropic salts
• 2. BME
• 3. Heat (think of freezing a fried egg)
• 4. Denatures by interacting with R groups, amide backbone interactions,hydrophobic interactions etc that put proteins together.

5. Urea allowed protein to be denatured but to stay in solution as well

1. He wanted to show that denaturation of some proteins was reversible.

2. Urea (broke up hydrophobic bonds) and reducing agent (broke disulfide bonds)

3. He removed the urea & reducing agent using dialysis and added in an oxidizing agent

4. The protein spontaneously refolded into its correct position and had full catalytic actvitiy

5. (1) protein folding isn't random (2) chaperones aren't rquired (3) as long as you have the prim seq, you can get correct folded structure

1. Disrupts weak forces. In a small temp range, protein collapses, meaning that dissolution of one area --> dissolution of another (domino effect). Irreversible!

2. pH interferes with net charge on protein, causing electrostatic repulsion & H-bond disruption.

Ex. Lys+| |Asp- salt bridge. IF pH decreases, Asp will be protonated losing salt bridge.

3. Urea - mainly for hydrophobic interactions - allows protein to be denatured but to stay soluble in solution.

Ammonium sulfate - allows protein to stay folded, but affects solubility

1. Unique characteristics due to unique primary sequence

2. Mechanical methods (blender/sonication (using high freq sound waves to open cell)

and Enzymatic methods (lysozyme - naturally occurring hydrolase found in tears that degrade bacterial cell wall).

3. Solubility - use chaeotropic salts, charge - ion exchange chromatography, size - gel filtration and natural binding affinity.

1. Each protein has its own isoelectric point. At that point, the solubility of the molecule is minimized.

2. Increasing [salt] decreases protein solubility. Add salt, centrifuge lysate to separate precipitate from solution, then continue to add salt, etc. Ammonium sulfate.

1. Ion exchange, size exclusion, and natural affinity

1. Intrinsic charge of protein (size AND magnitude of charge) - matrix = stationary phase that is a synthetic polymer containing bound charged groups

2. Cation exchangers are resins with bound anionic groups; anion exchangers have bound cationic groups

3. pH (which determines ionization state of the molecule) and the concentration of competing free salt ions in the surrounding solution

4. Add excess salt to disrupt electrostatic interactions

1. Separating proteins w/ very large difference in molecular weight. Otherwise use SDS page.

• 1. Large proteins
• 2. Excess salt/excess free ligand solution

3. Size, shape, and charge

4. Same shape (linear) & charge:mass ratio.

Shape - SDS breaks all noncovalent bonds, denaturing protein into its linear form.

Charge - SDS is highly negative, binds all around protein, making it super negative. Separates everything based on MW.

5. Coommassie blue

6. Smaller

7. Disulfide bonds (b/c they're covalent)