2b

Question 1

aa are normally in what form

Answer 1

dipolar ions

aka zwitterions

Question 2

do aa like to have their amine and carboxylyc groups neutral or charged

Answer 2

they prefer them to be charged

but for the overal charge to be 0.

Question 3

how do diff phs change aa

Answer 3

the amine and cooh groups have diff charges at diff phs

Question 4

aa physical properties are influenced by the ionic states of what groups

Answer 4

• ionic alpha coo-
• ionic alpha nh3+
• ionic groups in the R side chain

Question 5

why does the ph and therefore the ionic states of the FG important and what do they influence

Answer 5

ph is important bc the fg have diff ionic states at diff phs

diff ionic states can influence the 3d protein structure and the function of the protein aka if its an enzyme u can change the acrive site and change its function etc.

Question 6

HA + H2O equation

Answer 6

HA + H2O <–> H3O+. + A-

Question 7

ka equation

Answer 7

ka = (H3O+)(A-) / (HA)

Question 8

the larger the ka the what

Answer 8

the larger the ka = the more acidic the thing ,, bc u get more of the A- and H3O+ stuff bc those are the numerators which HA aka the non dissociated state is the denominator.

more dissociation = more acidic

Question 9

pka in terms of ka

Answer 9

pka = -log (ka)

Question 10

pka and ph ,, what does what mean

Answer 10

low pka = more acidic !!!

bc more ka = more aicdic

and pka = -log(ka)

so the larger the ka for being more acidic ,, the lower the pka value.

Question 11

what does pX mean

Answer 11

the -log of X

Question 12

2H2O equation

Answer 12

2H2O <–> H3O+ + OH-

Question 13

kw = what

Answer 13

(H3O+)(OH-) = 10^-14

Question 14

pkw = what

Answer 14

pka + pkb = 14

Question 15

ph in terms of H3O+

Answer 15

ph = -log(H3O+)

so (H3O+) = 10^-ph

Question 16

when does (A-) = (HA)

Answer 16

when half of it is dissociated

Question 17

if (A-) = (HA) how does this effect ph = pka + log( (A-)/(HA))

Answer 17

it makes the fraction = 1,, and the log of 1 =0

so u can avoid that part so the pH = Pka when the conc of A- and HA is the same!! aka when its half deionised

Question 18

when is pH > PKA

Answer 18

when (A-) > (HA)

aka at high PH’s

bc at high phs,, the NH3 becomes NH2 meaning u just have the coo- giving it a - sign

the conc of the conjugate base is larger

Question 19

when is pka > ph

Answer 19

more acidic ph
lower ph

when (HA) > (A-)
the conc of the acid is larger

Question 20

(A-) / (HA) = what

Answer 20

10^4

ph is 4 units greater than pka. the major component is the conc of A-

Question 21

normal cooh pka is

Answer 21

4.6

Question 22

amino acid alpha cooh is what pka

Answer 22

2.19

Question 23

alpha cooh pka range is what

Answer 23

2.2 - 2.3

Question 24

why is the pka of alpha cooh less than a normal cooh

Answer 24

in alpha cooh,, u have the NH3+ near it,, aka attached to the same carbon,, meaning it attracts some of the e- via inductive effect,, stabilising the negative charge and therefore making it more acidic.

whereas in a normal cooh,, theres no inductive stabilisation from NH3+

and the NH3+ is the way it is bc its in an acidic env,, so obvs its gonna be the NH3+ form

Question 25

what happens when theres an extra COOH in the R side chain,, whats the pka of these

Answer 25

it depends on how far away it is from the NH3+ and therefore the chiral carbon. the further away it is,, the closer th epka to a normal COOH at 4.76. the closer it is,, the smaller pka and more acidic it is,, bc its getting more inductive effect stabilisation

Question 26

pka of an alpha, beta and gamma cooh

Answer 26

alpha = 2.35 beta = 3.86 gamma = 4.07

Question 27

whats the acidicity of an alpha NH3+ in aa

Answer 27

9.47pka

Question 28

whats the acidity of a normal ammonium cation

Answer 28

10.76

Question 29

range of pka for an alpha nh3+

Answer 29

9-9.5

Question 30

whats cool about zwitterions

Answer 30

they can act as bases and as acids

Question 31

when things can act as an acid and a base,, what kind of behaviour do they have

Answer 31

they have amphoteric behaviour

Question 32

is nh3+ a strong or weak acid

Answer 32

its A WEAK ACID it gives a h to water its nh3+ form is preferred tho

Question 33

is coo- a strong or weak base

Answer 33

its a weak base it takes a h from water its coo- form is preferred tho

Question 34

describe an amino acid whenu have a neutral ph

Answer 34

u have the zwitterion form the nh3+ and the coo- form.

Question 35

describe an amino acid at acidic ph

Answer 35

u have the nh3+ but u have the cooh positive cation

Question 36

describe an amino acid in a basic environment

Answer 36

u have the NH2 but the coo- so u have the negative anion

Question 37

does ph affect both the nh3 and coo-

Answer 37

nope the ph normally just changes one of them ,, so think strategically about which one its gona be

Question 38

for non polar amino acids which a non ionisable side R chain,, the abundance of each form depends on what

Answer 38

depends o nthe pka and ph of the solution the pka depends on the pka of the ionisable nh3+ and coo-

Question 39

if u have the zwitterion // neutral form when u have a neutral ph,, when do u have the cationic and anionic form

Answer 39

anionic = u have the nh2 and coo- so this must be when the the ph> pka cationic = u have the NH3 and the cooH ,, so this must be in an acidic ph < pka

Question 40

at ph of 7 aka neutral ph,, how are the ionisable groups such as coohs or nh3s affected if theyre in the side R chain

Answer 40

they will be in their ionised form. if theres 2 nh type things in one r group,, the most basic one will change to the nh whilst the other one stays charged.

Question 41

aa normally exist as what specie

Answer 41

they normally exist as their charged specie

Question 42

write an equilirbium reaction for thr dissociation of leucine with a high aka basic ph.. what do we need to do

Answer 42

look at the diff pka values for the nh3 and coo-. obvs neutral: coo- and nh3+ giving a neutral species acidic ph where the ph < PKa u get cooh so u get a cationic specie when the ph> pka2,, u get NH2 and coo- meaning u have the anionic form!! u draw the diff forms with equilibrium arrows between the 3 species and then write low and high ph on the sides.

Question 43

what do we do when we want to calculate the ratio f the conc of leucine ionised species with a net charge 0 and with a ne charge of -1 for an aqueous solution at ph 8.2. the pka values of leucine are pka1 = 2.36 and pka2 = 9.60 which pka do we need to consider which of the two species will be present in the higher conc

Answer 43

okay so the ph of solution is 8.2 which is most similar to the pka2 of 9.60 meaning ur more basic than neutral ,, but not more than 9.60 which of the 2 soeies will be present at a higher conc : the neutral one,, bc the ph is higher than neutral but its not higher than pka2 just yet!!! so u have a higher conc of the neutral form . aka what pka is the ph more similar to ,, and then does the ph overtake it or not.

Question 44

calc the ratio of the conc of leucine ionised specie with a net charge of 0 and that with net charge = -1 for an aqueous solution at ph 7.4 pka 1 = 2.36 and pka2 = 9.60

Answer 44

ph = pka + log( [A-1]/[HA]) ph is most similar to pka2 ,, 9.60 so the equilirbium is between the neutral and anionic form . 7.4 = 9.60 + log( [AA-1]/[AA0]) -2.2 = log ([AA-1]/[AA0]) 2.2 = log ( [AA0]/[AA-1]) 10^2.2 = [AA0]/[AA-1]) so 158.5 = [AA0]/[AA-1]) so thats the ratio between the 2 species + the answer.