exam 1

example of hydrophobic amino acids

tryptophan and leucine

example of positively charged amino acids

arginine and lysine

example of negatively charged amino acids

aspartate and glutamate

example of polar amino acids

cysteine and histidine

what is unique about histidine?

it can accept or donate protons because of its pKa near 6 (close to physiological pH)

when looking at a globular protein, where are the hydrophobic and hydrophilic regions?

it has a hydrophobic interior and hydrophilic exterior

when looking at a membrane-embedded protein through the lipid bilayer, where are the hydrophobic and hydrophilic regions?

the interior is a water-filled hydrophilic channel and the exterior is hydrophobic

what is myoglobin?

a compact globular alpha helical protein with heme

what are the characteristics of globular proteins

highly compact, asymmetrical, and soluble in water

what is an important feature about the quaternary structure of proteins?

the subunits can disassemble for reversible reactions

examples of fibrous proteins

alpha-keratin and collagen

what is the structure of collagen and why is it important?

3 helical polypeptide strands that form a super helical cable, hydrogen bonds between the strands, the interior is crowded so only glycine can fit

what is ribonuclease?

a single polypeptide chain with 124 amino acids and 4 disulfide bonds

what does BME do?

reduce disulfide bonds

what does urea do?

disrupts hydrogen bonds and electrostatic interactions

what are amyloidoses?

normally soluble proteins converted into insoluble fibrils rich in beta-sheets, prone to aggregate

what are the characteristics of prion diseases?

the transmission agent is a protein and PrPc is converted to PrPsc (now has beta-sheets)

what is L1/2

the ligand concentration at which half the receptor is bound to L and half free

match estrogen and tamoxifen to agonist or antagonist

estrogen = agonist
tamoxifen = antagonist

what type of group is heme?

a protein prosthetic group

what is fractional saturation (Y)?

the fraction of possible binding sites that contain O2

how does myoglobin differentiate oxygen from CO2?

heme iron favors CO2 but the myoglobin binding pocket favors O2

how does CO2 stimulate oxygen release?

by stabilizing the T state, reacts with water to form carbonic acid which dissociates to bicarbonate and H+, reacts with terminal amino groups to form - carbamates for ionic reactions

what is 2,3-Bisphosphoglycerate (2,3-BPG)?

an allosteric effector that binds to hemoglobin in the T state to decrease hemoglobin’s affinity for O2 and release oxygen to tissues

examples of proteases

papain, trypsin, thrombin, chymotrypsin, cysteine, aspartyl, and metalloproteases

where does trypsin cleave?

the C terminal to lysine or arginine

where does thrombin cleave?

within only certain arginine-glycine bonds within a particular sequence

how do enzymes accelerate reactions?

by facilitating the formation of the transition state

examples of suicide inhibitors

penicillin and FdUMP

how does competitive inhibition affect Km and Vmax?

increases Km and Vmax stays the same

how does non-competitive inhibition affect Km and Vmax?

Km stays the same and decreases Vmax

examples of protease inhibitors

DIPF, captopril, and indinavir (Crixivan)

what does CTP do to ATCase?

allosterically inhibits ATCase (committed step), stabilizes the T state

examples of acetylation

acetylating lysine removes its positive charge to increase gene expression, deacetylating lysine does the opposite