Biochem

In order to create a buffer system, you must have at most what ratio of acid to conjugate base?

([A-]/[HA])< 10, or pKa-1 <pH< pKa+1 Must choose a WEAK acid with pKa close to desired pH

Which amino acids have negatively charged polar side chains? What are their pKa's?

- Aspartic acid (D) and glutamic acid (E) (normally in aspartate and glutamate forms) - Aspartic acid pKa= 3.9 - Glutamic acid pKa= 4.2

What can prevent the unfolded protein from getting to the native state?

- The unfolded or partially/mis-folded protein can form Amorphous aggregates due to exposed non-polar groups. These can be very stable and in experiments this is why you may see higher concentrations of protein that expected - partially unfolded structures can lead to the formation of stable Amyloid Fibers; associated with diseases due to mis-folding (e.g. scrapie, Alzheimers)

Describe what chaperone proteins do

1) bind to unfolded proteins, preventing aggregation 2) Actively break apart aggregates 3) Bind unfolded protein, sequester (prevent aggregation by separation), allow protein to fold properly 4) Binds to a mis-folded (stable) protein--> unfolds the protein to allow it to fold again in the proper way

How far apart must two charged side groups be in order to create a salt bridge?

4-5 A

How far apart are is one turn of an alpha-helix? How many amino acids per turn? Which amino acids are commonly found in alpha-helices and which are uncommon?

5.4 A per turn 3.6 amino acids per turn (i+4) e.g.- if an alpha helix has 10 turns then it has ~36 amino acids and is ~54 A long Alanine is commonly found, as well as glutamate and lys (which both help create stability in the helix due to their negative and positive charges, respectively) Proline is uncommon because it's rigid and bc of steric clash that results Glycine disfavors forming the helix because of its high flexibility

What are the ideal phi and psi angles for alpha-helices and beta-sheets?

Alpha-helices - phi= -60 - psi= -50 Beta - phi= -150 to -100 - psi= +120 to +160

Why is it that protein folding is favorable if the unfolded protein has a higher, positive, entropy?

Because when the protein folds, the hydrophobic side groups fold to the inside and this results in the H2O that was initially surrounding the unfolded protein to break away, thus increasing the entropy of the surroundings S(overall)= S(conformational) + S(hydrophobic effect)

Describe disulfide bonds and their existence inside and outside of the cell

Disulfide bonds exist outside of the cell They DO NOT exist inside of the cell because that environment is highly reductive due to high concentrations of glutathione (reducing agent)

Which are the nonpolar aliphatic amino acids? (which are most hydrophobic?) Which appear on surfaces/turns?

From least hydrophobic to most hydrophobic (last three are very hydrophobic): glycine, proline, alanine, methionine, valine, leucine, isoleucine Glycine and proline (less hydrophobic) are usually found on suraces of proteins due to glycine's ability to form tight turns (achiral), and proline's rigid ring.

Which amino acids have positively charged polar side chains? What are their pKa's? Which amino acid is special and why?

Lysine (K), Arginine (R), Histidine (H) - Lysine pKa=10; conjugate base acts as nucleophile - Arginine pKa=12.5; weak acid - Histidine pKa= 6.0 -Histidine is special because it can act as an acid or base/nucleophile since it exists in a protonated and deprotonated form.

Which amino acid side chains absorb UV light (~280nm)?

Nonpolar side chains with aromatic rings (tryptophan has higher absorptivity than tyrosine, ignore Phe)

Which amino acids have uncharged polar side chains? What are their features (i.e. what can they do)? Where are they found? Which one can ionize, what is its pKa, what is so special about this amino acid?

Serine, Threonine, Cysteine, Asparagine (N), Glutamine (Q) - These side chains can form hydrogen bonds with water and/or other good H-bond donors and acceptors - found on surfaces of proteins and can contact other cells in the outside environment Cysteine (a thiol) can ionize at high pH; pKa=8.3. When deprotonated it can act as a nucleophile (S-). Is able to form disulfide bonds, can be involved in oxidation-reduction (redox) reactions - Asparagine and glutamine are amides

Which are the nonpolar aromatic side chains? (which can ionize/what is the pka?) Which is the most hydrophobic?

Tyrosine, tryptophan, phenylalanine Tyrosine ionizes at high (basic) pH levels; has a pKa=10.1; weak acid Phenylalanine is most hydrophobic (with val, leu, ile; thus has low solubility)

What are some chemical denaturants that cause proteins to unfold

Urea- very polar, interfere with hydrophobic effect preventing it from occurring Detergents have similar effect as urea beta-mercaptoethanol works as a reducing agent to break disulfide bonds