Other Information Exam 2 Flashcards
Cofactor
help a protein / enzyme catalyze a reaction
can be inorganic, organic, or permanently attached
What do we call permanently attached cofactors?
Prosthetic groups
What are types of inorganic cofactors?
metals, ions
What do we call organic cofactors?
coenzyme
What is alpha keratin’s quaternary structure determined by?
disulfide bonds
What does alpha keratin’s structure include?
apart from alpha helix secondary structure, lots of hydrophobic regions to promote packing
What is proline’s structure made of?
Gly-X-Y repeats to facilitate the left-handed helix
Why does proline use Gly and Pro?
Glycine gives flexibility and proline introduces a kink that can form a turn
How does proline’s structure come together?
there is a coiled coiled which is linked through covalent bonds
what is silk’s protein name?
fibroin
What amino acids do Beta sheets include? Why?
alacine and glycine
R-groups are small and can be stacked closely on top of each other
What two molecules regulate ATCase?
ATP and CTP
How does CTP regulate ATCase?
CTP is a product of ATCase, so it negatively regulates through feedback inhibition when concentrations are high enough
How does ATP regulate ATCase?
large concentrations of ATP indicate that metabolism is pumping and the cell might need to grow and need more products
so ATP positively regulates
Does ATCase show homotropic or hetereotropic inhibition?
It exihibits both!
How do ATP and CTP both regulate ATCase?
heterotropic regulation
How is ATCase regulated homotropically?
through a separate aspartate substrate binding?
is the Vmax of ATCase affected?
no
alpha+beta
easy to pick out regions of alpha and beta secondary structure
alpha/beta
hard to pick out regions of alpha and beta secondary structure
What are the highly hydrophobic side chains?
methionine, leucine, phenylalanine, and isoleucine
How do the H+ protons in a lower pH stabilize the T-state?
The H+ protons bind at histidine and make it positively charged
Histidine interacts with a negatively charged aspartate to stabilize the T-state
Additionally, H+ causes lots of histidines to be positively charged which creates large repulsion which triggers a conformational change into the T-state
How does CO2 stabilize the t-state?
besides lowering the pH, it also interacts with the amino terminus of the hemoglobin and forms a carbonyl group
How does BPG stabilize the t-state?
BPG is negatively charged and interacts with postively charged amino acids in the central portion of hemoglobin
this allows the subunits to be held in the T-state
How does O2 stabilize the r-state?
cooperativity
How does CO stabilize the R-state?
at non-saturating concentrations, it increases the affinity for O2 through cooperativty
Does an enzyme lower the activation energy?
yes
Does an enzyme speed up the forward and reverse reactions?
yes
How do tropomyosin, troponin, and Ca++ work in muscle contraction?
Tropomyosin is a fibruous protein that lays across actin and prevents myosin from binding to actin
When Ca++ is released from the sarcoplasmic reticulum, it will interact with troponin and cause a conformational change
This conformational change pulls tropomysosin off of actin and exposes the actin myosin-binding sites
How many rings do pyrimidines and purines have?
Pyrimidines have 1 ring
Purines have 2 rings
How many nitrogens do pyrimidines and purines have?
Both have 2 nitrogrens
What is the difference between uracil and thymine?
Uracil lacks a methyl group compared to thymine
What does “deoxy” imply?
the 2’ -OH group was removed
pAGCG has what on its 3’ end?
A 3’ -OH group
pAGCG has what on its 5’ end?
a phosphate on it’s 5’ hydroxyl
Are nucleic acids planar?
yes, roughly
In Watson and Crick model, is the distance between the two glysodic (base-sugar) bonds roughly the same?
yes
Chargoff’s rule
A+G = C+T
What allows bases to lie perpendicular to the helical axis?
the absence of 2’-OH group
What is the distance between two bases in DNA?
3.4 Angstroms
What is the diameter of B form DNA?
20 Angstroms
What stabilizes the B form of DNA?
nonspecific Van der Waals base stacking interaction between two adjacent bases in the same strand
Difference between RNA and DNA double strands?
RNA double strands are normally the A form
Does the glycosidic bond of DNA break when heated?
no
What is the most important to living cells for the chemical modification of DNA?
oxygen and UV light
Nucleoside versus nucelotide
Nucleoside does not have a phosphate group
What is the covalent backbone of DNA made out of?
phosphate groups and pentose sugars
Is base stacking hydrophillic?
no
we are in the hydrophobic interior
Duplexes in turns of stability
RNA-RNA > RNA-DNA > DNA-DNA
What contributes to the pKa of histidine raising in chymotrpsin?
having the aspartate adds electron density and makes it more likely for histidine to be protonated
histidine is less likely to loss that proton and the pKa increases
How many steps is HIV protease mechanism? What is the nucleophile?
just one step
water is the nucleophile which aspartate residue makes a good nucleophile through base catalysis
What are the steps of transpeptidase mechanism?
First is acylation with serine as the nucleophile
Then is deacylation with another amino acid as the nucleophile (not water)
has two steps
What are the steps of B-lactamase?
First is acylation with serine as the nucleophile
Then is deacylation with water as the nucleophile
since water is the second nucleophile, penicillin does not remain as acyl intermediate with serine. Unbinds penicillin
