1-amino acids

Question 1

which C is C1

Answer 1

the C=O one

Question 2

which C is C2

Answer 2

alpha carbon

Question 3

do all amino acids have beta carbon

Answer 3

all but glycine

Question 4

which aa have branced beta carbons

Answer 4

valine and isoleucine

Question 5

which aa have branched gamma (4) carbons

Answer 5

leucine

Question 6

what is the weight of free aa (average)

Answer 6

128Da

Question 7

what is the weight of aa residue (average)

Answer 7

110Da

Question 8

what makes the difference in average weight of free aa and residue

Answer 8

the mass of water from peptide bond formation

Question 9

how many H bonds can histidine donate

Answer 9

2 when protonated

Question 10

how many H bonds can histidine accept

Answer 10

none when protonated

1 if non protonated

Question 11

how many H bonds can amides donate

Answer 11

2 (from NH2)

Question 12

how many H bonds can amides accept

Answer 12

2 (2 lone pairs on C=)

Question 13

how many H bonds can arginine donate (just the R group)

Answer 13

5

Question 14

rate
Phe, Tyr, His, Trp
in order of decreasing polarity

Answer 14

His, tyr, Trp, Phe

Question 15

where do tyrosine and tryptophan absorb strongly in ultraviolet

Answer 15

280nm

Question 16

when does cysteine become cystine

Answer 16

oxidizing environments - extracellular/lumen

Question 17

what is lost in the reaction to make cystine

Answer 17

2H+ and 2e-

Question 18

is cysteine polar or non polar

Answer 18

polar

Question 19

is cystine polar or non polar

Answer 19

non-polar

Question 20

how are some uncommon amino acids made

Answer 20

modification of amino acids after incorporation into a polypeptide chain (PTM)

Question 21

is L or D more common

Answer 21

L

Question 22

what is the pKa of a functional group at the pH

Answer 22

when base and acid forms are equal

Question 23

does the acid or base form predominate below the pKa

Answer 23

acid

Question 24

does the acid or base form predominate above the pKa

Answer 24

base

Question 25

what is a zwitterion

Answer 25

net charge at zero, has x amount of negative and x amount of positive

Question 26

what does diprotic mean

Answer 26

there are two titratable groups (COOH and HN3+)

Question 27

is it generally negative or positive above the pI

Answer 27

negative

Question 28

is it generally negative or positive below the pI

Answer 28

positive

Question 29

how do you find the net average charge on the moledule

Answer 29

add the net average charge on each potentially charged functional group

Question 30

what is the isoelectric point of a moledule

Answer 30

pH at which the overall/net charge on a molecule is zero (equivalent negative and positive)

Question 31

how do you calculate pI for diprotic amino acids

Answer 31

average of pK1 and pK2

Question 32

how do you calculate pI for triprotic amino acids

Answer 32

average pK values bounding species with net 0 charge

Question 33

how many buffering regions in triprotic amino acids

Answer 33

3

Question 34

what can change the pKa for functional groups

Answer 34

presence of electron withdrawing groups or other charged groups

Question 35

what does a +ve charge generally do to pKa

Answer 35

lower

(pulls e from groups that may be deprotonated, makes it easier)

Question 36

what does a -ve charge generally do to pKa

Answer 36

raise

charges not as cancelled out so not as strong acid so higher pKa

Question 37

if pKR of Sec is 5.43 and Cys has pKR of 8

what is pI of Sec compared to Cys

Answer 37

lower (pH7 cys=0 and Sec=-1, pI lower

also the average in the calculation will be lower)