unit 1 exam Flashcards
what is the hydrophobic effect
the favorable increase in entropy of water when it is released from nonpolar molecules
characteristics of peptide bonds
partial double bond character between carbonyl carbon and amide nitrogen
specific activity formula
activity/total protein (units/mg)
number of H-bonds in alpha helix
(# amino acids)-4
uses for gel electrophoresis
separate molecules by size; unfold protein but maintain primary structure
does lower Kd correspond to ligand binding more or less tightly
more tightly
myoglobin properties
oxygen storage protein
binds to heme (porphyrin ring and iron atom)
iron atom in +2 ox state
monomer
bad transporter
tertiary
hyperbolic O2 binding curve
hemoglobin properties
oxygen transporter
tetramer
T state: binds less strongly to O2
R state: binds most strongly to O2
more BPG
more T state
less BPG
more R state
high affinity state conditions
more R state, less BPG, higher pH, less O2 released
(fetal hemoglobin has less BPG)
low affinity state conditions
more T state, more BPG, lower pH, more O2 released
Michaelis-Menten assumptions
k-2 is negligible
[ES] is constant
oxyanion hole purpose (chymotrypsin)
stabilizes transition state (2x in peptide breaking)
hydrophobic pocket purpose (chymotrypsin)
substrate binding specificity
histidine purpose (chymotrypsin)
gen acid/base
take H+ from ser, protonate amide, take H from H2O, protonate ser
serine purpose (chymotrypsin)
covalently bonds to carbonyl carbon
asparagine purpose (chymotrypsin)
H-bonds to stabilize the positive charge on histidine
allosteric enzyme characteristics
feedback inhibition
reversible
binding to enzyme makes it more active for substrate
product will shut down production
non michaelis-menten behavior
competitive inhibition m-m graph
constant vmax
Km increases
uncompetitive inhibition m-m graph
vmax and Km decrease at same rate
mixed inhibition m-m graph
vmax decreases
Km increases
sphingolipid purpose
important immunogenic determinant in blood
glycerophospholipid purpose
prostaglandins derived from them
sterol purpose
membrane structural lipid
Ramachondran plot purpose
gives possible rotations of functional groups
Glycine has most possible rotations because double H group
what is a post-translational modification?
covalently attaching functional groups after protein translation from ribosome
ex: hydroxyproline for collagen
how are peptides (peptide bonds) formed?
condensation reaction
what kind of amino acids are on the interior of a protein
nonpolar hydrophobic
Alfinsen RNase folding experiment
unfolded proteins, proved they were inactive, refolded, proved they were active
experiment proved that the primary sequence of a polypeptide is sufficient for proper protein folding activity
Beta-sheet characteristics
contain relatively few amino acid residues
H bonds form between strands
have a tendency to twist and are pleated
what are the 3 main catalytic strategies
acid/base catalysis, covalent catalysis, metal ion catalysis
Do larger Mr values belong to larger or smaller molecules
larger
how do you count ionizable groups
count number of -ate, -ine, -SH, and OH groups and add 2 for the terminal NH3 and COO-
do bacteria produce a higher ratio of saturated/unsaturated fatty acids at higher or lower temps
higher temps
COVID characteristics
surrounded by lipid membrane that can be destroyed with soap and simple hand washing
to infect another cell the virus fuses its lipid bilayer with the host cell bilayer and that process depends on viral spike protein binding to receptors on cell surface
what is the Bohr effect?
binding affinity for O2 decreases at lower pH
- more BPG - more T-state
what is the most abundant protein in humans?
collagen
what is keratin?
a fibrous protein found in hair and skin
what is a fibrous protein?
highly extended protein with repeating helical or beta sheet structure
