The role of pH and pKa Flashcards
What is the henderson-hasselbalch equation and why is it useful for protein structure?
pH=pKa + log( conj. base/conj. acid)
This is useful as we use it to determine the ionization of the amino acids in the protein at cytosolic pH which can influence the role these amino acids play in the formation of the proteins secondary and tertiary structure as it will control their availability for salt bridges
What general relationships can be made about pH and pKa to determine amino acid ionization?
pH=pKa then the amino acid is 50% ionized
pH>pKa then amino acid will mostly in its basic form (acidic groups are negative, basic are neutral)
pH<pKa then amino acid will be mostly in its acidic form (acidic groups are neutral, basic are positive)
What is the pKa of both aspartic and glutamic acid?
4.1
What is the pKa of histidine?
6.0
What is the pKa of cysteine?
8.3
What is the pKa of tyrosine?
10.9
What is the pKa of Lysine?
10.8
What is the pKa of arginine?
12.5
Why are extreme pHs denaturing to proteins?
The like charges repel each other resulting in loss of organized structure
What are Imidazole groups?
Histidine sidechains which act as pH buffers in biological systems
What is the pI of a protein?
The iso-electric or iso-ionic point where proteins have a net zero charge and are at their least soluble , away from this point proteins have a distinctive charge and can determined through gel electrophoresis or ion exchange chromatography
How does pKa play a role in enzyme catalysis?
Enzymatic reactions often involve the donation or acceptance of a proton however in order for this reaction to occur the amino acid must have a native conformation which is in the state where it is ready to either accept or donate a proton, this results in the pKa providing a limit for the range of pH in which the protein can function
How is the pKa of amino acid side chains able to be changed within the protein?
Charge-Charge interactions where there are two charges in close proximity, these have a greater impact if they occur in a hydrophobic region
Charge-Dipole interactions interaction with dipole via H-Bonding, Interaction alpha helix dipole
Burying charge within hydrophobic envrionment
How do charge-charge interactions affect side chain pKa?
Two -ves= increased pKa of one negative charge to decrease repulsion
Conversely, two +ves=decreased pKa of one group
If two opposite charges are brought together -ve has pKa increase, +ve has pKa decrease to promote favourable charged interactions
Why is the effect of charge-charge interactions stronger in a hydrophobic environment?
Coulumbs Law is states that if there is a lower dielectric constant then there will be a greater electric force as the hydrophobic interior of the protein has a much lower dielectric than the aqueous cytosol charge-charge interactions are more powerful within in the protein core
