L2 - Acids, Bases & Buffers

osmolarity and ionic strength: - are necessary when working with cells and macromolecules

salts

cells exert osmotic pressure, preventing -

animal cells, lacking cell walls, need to be maintained in - solutions to avoid osmotic shock

hypotonic shock

isotonic

why is water and counter ions near open circles?

open circles = polar or charged aa residues, located near surface of folded proteins

which amino acids are typically protonated at neutral pH?

basic aa are protonated

which amino acids are de-protonated at neutral pH?

phosphodiester bonds of both DNA and RNA will - in acid

hydrolyze

strong acids at high temperatures are capable of breaking a - into its components

polynucleotide chain

weak acid can cause - of DNA

RNA is - (less/more) susceptible to de-purination

de-purination

less

at alkaline pH, dsDNA is denatured into - but the polynucleotide chains are stable

2 single strands

at alkaline pH, RNA is -

hydrolyzed

what is this?

what bases are this?

purine

adenine and guanine

what is this?

what bases are this?

pyrimidine

cytosine and thymine

what is this

5’ ribonucleotide

what is this

3’ deoxynucleotide

water can donate or accept H+ ions in solutions, acting as either - or -

acid, base

proton jumping via H bonds is much - (slower/faster) than hydrolysis of H₂O into H⁺ and OH^-

which explains - (slow/rapid) rate of acid-base catalyzed reactions in aqueous solutions

faster

rapid

acid is a substance that can - a proton

base is a substance that can - a proton

donate

accept

acid reacts with base to form - and -

conjugate acid, conjugate base of acid

henderson-hasselbach equation?

at equilibrium, [H⁺] = -

pH = -

K_a

pK_a

minor additions of OH- or H+ to weak acids or bases at equilibrium/close to pKa - (do/don’t) shift pH value

this is why weak acids/bases are used in biological buffers

don’t

buffering acids are typically provided as -, they serve s counter ions for the acid/base but don’t contribute to its buffering properties

- = ionic strength of buffer

salts

salt concentration

polyprotic acids can donate - proton during acid-base reactions

more than one

glycine is a key component of the discontinuous buffer system in SDS-PAGE because of its - properties

zwitterionic

at low pH, both carboxyl and amino groups of glycine are - and glycine is a -

at neutral pH, carboxyl group is -, amino group is - and glycine is both anionic and cationic but net neutral and glycine is a -

at high pH, both carboxyl and amino group - and glycine is -

protonated, cation

de-protonated, protonated, zwitterion

de-protonated, anionic

for SDS-PAGE, the stacking gel has pH 6.8, and the glycine - stack nicely

zwitterions

for SDS-PAGE, the separating gel has pH 8.8, once glycine enters the gel, anionic glycine predominates and migrates - of proteins, allowing proteins to freely separate according to their -

ahead, MW