bio chem 4
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protein backbond is held twisted in what way in alpha helical?
right handed *clockwise helical held together by hydrogen bonds
how is the alpha helical arranged?
- every possible carbonyl oxygen is hydrogen bonded to the amino hydrogen of the fourth residue further along the sequence
- hydrogen bonds linear
- cooperativity between hydrogen bonds
how does polypeptide chains reverse direction?
by making B-turns, carbonyl oxygen is H bonded to NH group of residue 3. 3^10
what are the different types of alpha helices?
- 2^7, 3^10, 4^13, 5^16
- 4^13 is the most common
what are the purposes of domains?
- evolution's way to mix and match proteins
- -not changing amino acid but changing whole proteins around; enzymes usually cut at site where two domains meet (most exposed)
what is a prosthetic group?
a part of the protein other than the 20 naturally occurring amino acids (heme in hemoglobin)
what does crystallography provide?
electron density not positions of the atoms in the crystal
how do proteins break down to individual amino acids and prosthetic group?
- acid hydrolysis
- Gln and Asn are converted to Glu and Asp. trp is completely destroyed and Cys is partially destroyed
what does the heme group contain?
protopoephyrin IX with an iron atom bound; both are extremely hydrophobic
which oxidation state of iron binds oxygen?
ferrous (Fe2+) binds oxygen is unstable and spontaneously oxidizes to ferric (Fe3+) which can't bind oxygen
what must happen in hemoglobin and myoglobin in binding oxygen?
must bind reversibly, which only Fe2+ can; Fe2+ is stabilized by the highly hydrophobic environment around the heme
what is P50
partial pressure of oxygen when saturation (Y) is 0.5
how is the Kp and pO2 related at p50
at point when saturation is 0.5, the pO2 equals the Kp
what is the structure and function of myoglobin?
- all alpha helix with one prosthetic group used for oxygen storage in muscle
- polar residues on the surface while the non-polar side chains are internal
what do we do to lessen the affinity of binding of CO to free heme
the placement of His E7 distorts the binding of CO and dramatically reduces its affinity; therefore, trace amounts of CO do not completely destroy the function of myoglobin
what is the purpose of 2-mercaptoethanol?
break down disulfide in mercaptoethanol and disulfide in protein
what is the purpose of urea and guanidinium chloride?
breakdown protein structure by allowing alternate hydrogen bonding interactions; competition of hydrogen bonds
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