amino acids

Nonpolar

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Polar uncharged

NYC QTS

Acidic polar

ascidic

• negative charge R grp

Basic

His Lys Arg basic

• Positive charge

Aromatic

WTY smells good

Proline is?

Rigid

Histidine is?

Can act as acid and base, imidazole ring

Which are involved in post translational modifications

OH: serine, thr ,tyr —> can accept phosphate group

NH3: asn and OH: ser, thr —> attachment sites of sugars

Which has SH?

Cys has SH — can disulfide bond.

Essential amino acids

PVT TIM HALL

• pneumonic not based on codes

pk1? pk2? pkr?

pk2--> amino grp

pk1--> carboxyl grp

pkr--> r grp

zwitterionic form?

all grps neutral in amino acid

pk=pH -->?

pk> pH -->?

pk<ph —>?

1. equal- no change

2. acidic environment (grp is protonated)

3. basic environment (grp is deprotonated)

what do labels and plateaus mean?Isoelectric Point?

• y axis: pH increases, x acis: OH- increases (solution getting more alkaline)

• starting low? (low pH), the amino acid is fully protonated

• buffering regions: plateaus horizontal-looking sections where adding base causes very little change in pH. Centers around pka value.

  • At pka= Half-equivalence point: The concentration of the protonated form equals the concentration of the deprotonated form

• Isoelectric Point: What it is: The pH at which the amino acid carries a net charge of zero (the zwitterion form).

  • for simple amino acids: pI= pka1+pka2/2

  • sits at the inflection point or halfway between the pka

• 
  

how to determine amino acids looking at Isoelectric Point?

henderson hasselbalch equation

calculates the pH of a buffer solution or estimates the ionization ratio of a weak acid and its conjugate base

PTMs - reactive side chains

Phosphorylation,

Acetylation methylation ubiquitination

Glycosylation

Oxidation and disulfide bond

Hydroxylation

1. Ser Thr Tyr

2. Lys Arg

3. Asn Ser Thr

4. Cys Met

5. Pro Lys

charge at ph 7

COO-

NH3+

• this is at ph 7. No need to apply changes

Ph <pka

Group protonated

NH3+

Or neutral COOH

ph > pka

group deprotonated

neutral NH2

Or COO-