Session 4.3b - Lecture 1 - Protein Structure Flashcards
Slides 12-23
Which amino acids have positively charged side chains?
Lysine
Arginine
Histidine (usually - although this is a little bit weird)
Which amino acids have negatively charged side chains?
Glutamate
Aspartate
What is different about histidine compared to the rest of its group? Name the other members of its group.
Histidine is an amino acid with a positively charged side chain, so is basic. However, it is weakly basic compared to lysine and arginine.
Glutamate and aspartate are part of which group?
Negatively charged side chains
Why are some amino acids positively or negatively charged?
This depends on the nature of the group - comes down to the pKa
What is the pKa?
The negative log (-log or p) of the acid dissociation constant (Ka)
What is Ka?
The acid dissociation constant
What is the acid dissociation constant?
Ka
What is the negative log of the acid dissociation constant named, and what does this determine?
pKa
(negative log [p] of acid dissociation constant [Ka])
Whether an amino acid is positively or negatively charged
What is pKR?
It is the pK specifically related to the pK value of the side chain of an amino acid, not thinking about the rest of the amino acid residue.
What do we denote the pK specific to an amino acid side chain?
pKR
What is the pKR value of lysine?
10.5
What are the pK values of Lysine, Arginine and Histidine?
Higher
Lysine 10.5
Arginine 12.5
Histidine 6.0
What does the pK value mean?
The pK value is the pH at which there’s no overall net charge on an acid or a base
OR
The point where there’s equal amounts of protonated and deprotonated forms (1:1 relationship)
The pH at which there’s no overall net charge on an acid or a base is called what?
pK
The point where there’s equal amounts of protonated and deprotonated forms (1:1 relationship) can be represented by what?
The pK value
Lysine has a pK value of 10.5. At what pH will lysine have no net charge?
10.5
Lysine has a pK value of 10.5. At what pH will there be equal protonated and deprotonated forms of lysine?
10.5
In what form does lysine appear at physiological pH?
Physiological pH is ~7.4.
Lysine has a pKa of 10.5.
This means it is always protonated at physiological pH (accepted a proton) and in positive charge form.
How do glutamate and aspartate appear at physiological pH?
These appear as anions, ionised forms of glutamic acid and aspartic acid
This means they have donated their protons and have become negatively charged.
What does it mean for their pK value if glutamate and aspartate are negatively charged at physiological pH?
They have low pK values.
What are the pK values of Glutamate and Aspartate?
Glutamate 4.3
Aspartate 2.8
(Lower)
Positively charged R groups have a _____ pKR value?
higher
Negatively charged R groups have a _____ pKR value?
lower