pH-ing Around!
The pH at which a functional group is exactly 50% protonated and 50% deprotonated is equal to this value
What is the pKa?
These six letters of the alphabet are NOT used as one-letter amino acid codes
What are B, J, O, U, X and Z?
This is a neutral molecule that carries separate positively and negatively charged functional groups
What is a zwitterion?
This covalent bond cross-links two cysteine side chains, forming cystine
What is a disulfide bond?
This level of protein structure is the linear sequence of amino acids encoded by DNA
What is primary (1°) structure?
A buffer is most effective within this range around its pKa
What is ±1 pH unit?
K, W and Y
What are lysine, tryptophan and tyrosine?
When the solution pH is higher than a group’s pKa, the group is in this state
What is deprotonated?
This enzyme catalyzes disulfide bond formation as secreted proteins pass through the ER
What is protein disulfide isomerase (PDI)?
An α-helix has this many residues per 360° turn
What is 3.6?
This compound is the main buffer in human blood. The H⁺ it soaks up is ultimately exhaled as CO2
What is bicarbonate (HCO3⁻)?
Only this enantiomer of amino acids is the physiologically relevant form found in plant and animal proteins
What is the L form?
This number of the 20 standard amino acids exist as zwitterions as free amino acids at pH 7.4
What is 16?
This reducing agent is used in the lab, including in SDS-PAGE samples, to break disulfide bonds
What is β-mercaptoethanol (BME)?
This amino acid is called the “helix breaker”, yet it is common at position 2 of β-turns
What is proline?
At low pH, this amino acid at position 146 of hemoglobin gets protonated and forms a salt bridge with Asp94, making Hb release O2. The phenomenon is the Bohr effect
What is histidine (His146)?
Decarboxylation of histidine produces this derivative, known for its role in allergic responses
What is histamine?
Histidine has pKa values of 1.8, 6.0 and 9.2. Calculate its pI
What is 7.6?
Insulin contains this many disulfide bonds: two interchain and one intrachain
What is 3?
This is the primary driving force in protein folding
What is the hydrophobic effect?
A 10 mM HEPES buffer (pKa 7.48) is set to pH 8.5. Calculate [HA]
What is ≈ 0.87 mM? ([A⁻] ≈ 9.1 mM)
Asn (N) and Gln (Q) are non-essential because the body makes them by adding an amine to the side chains of these two amino acids
What are aspartate (Asp, D) and glutamate (Glu, E)?
The net charge of the tetrapeptide Asp–Ala–Arg–Lys at pH 7.4
What is +1?
Cytosolic proteins usually contain “free” cysteines rather than disulfides because of this property of the cytosol
What is its reducing environment?
In Anfinsen’s RNase experiment, letting disulfides re-form (removing BME) while urea is still present gives this result
What is scrambled, inactive RNase?