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Biochem > Other Information Exam 2 > Flashcards

Other Information Exam 2 Flashcards

1
Q

Cofactor

A

help a protein / enzyme catalyze a reaction

can be inorganic, organic, or permanently attached

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2
Q

What do we call permanently attached cofactors?

A

Prosthetic groups

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3
Q

What are types of inorganic cofactors?

A

metals, ions

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4
Q

What do we call organic cofactors?

A

coenzyme

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5
Q

What is alpha keratin’s quaternary structure determined by?

A

disulfide bonds

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6
Q

What does alpha keratin’s structure include?

A

apart from alpha helix secondary structure, lots of hydrophobic regions to promote packing

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7
Q

What is proline’s structure made of?

A

Gly-X-Y repeats to facilitate the left-handed helix

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8
Q

Why does proline use Gly and Pro?

A

Glycine gives flexibility and proline introduces a kink that can form a turn

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9
Q

How does proline’s structure come together?

A

there is a coiled coiled which is linked through covalent bonds

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10
Q

what is silk’s protein name?

A

fibroin

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11
Q

What amino acids do Beta sheets include? Why?

A

alacine and glycine

R-groups are small and can be stacked closely on top of each other

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12
Q

What two molecules regulate ATCase?

A

ATP and CTP

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13
Q

How does CTP regulate ATCase?

A

CTP is a product of ATCase, so it negatively regulates through feedback inhibition when concentrations are high enough

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14
Q

How does ATP regulate ATCase?

A

large concentrations of ATP indicate that metabolism is pumping and the cell might need to grow and need more products

so ATP positively regulates

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15
Q

Does ATCase show homotropic or hetereotropic inhibition?

A

It exihibits both!

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16
Q

How do ATP and CTP both regulate ATCase?

A

heterotropic regulation

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17
Q

How is ATCase regulated homotropically?

A

through a separate aspartate substrate binding?

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18
Q

is the Vmax of ATCase affected?

A

no

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19
Q

alpha+beta

A

easy to pick out regions of alpha and beta secondary structure

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20
Q

alpha/beta

A

hard to pick out regions of alpha and beta secondary structure

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21
Q

What are the highly hydrophobic side chains?

A

methionine, leucine, phenylalanine, and isoleucine

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22
Q

How do the H+ protons in a lower pH stabilize the T-state?

A

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

23
Q

How does CO2 stabilize the t-state?

A

besides lowering the pH, it also interacts with the amino terminus of the hemoglobin and forms a carbonyl group

24
Q

How does BPG stabilize the t-state?

A

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

25
Q

How does O2 stabilize the r-state?

A

cooperativity

26
Q

How does CO stabilize the R-state?

A

at non-saturating concentrations, it increases the affinity for O2 through cooperativty

27
Q

Does an enzyme lower the activation energy?

A

yes

28
Q

Does an enzyme speed up the forward and reverse reactions?

A

yes

29
Q

How do tropomyosin, troponin, and Ca++ work in muscle contraction?

A

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

30
Q

How many rings do pyrimidines and purines have?

A

Pyrimidines have 1 ring

Purines have 2 rings

31
Q

How many nitrogens do pyrimidines and purines have?

A

Both have 2 nitrogrens

32
Q

What is the difference between uracil and thymine?

A

Uracil lacks a methyl group compared to thymine

33
Q

What does “deoxy” imply?

A

the 2’ -OH group was removed

34
Q

pAGCG has what on its 3’ end?

A

A 3’ -OH group

35
Q

pAGCG has what on its 5’ end?

A

a phosphate on it’s 5’ hydroxyl

36
Q

Are nucleic acids planar?

A

yes, roughly

37
Q

In Watson and Crick model, is the distance between the two glysodic (base-sugar) bonds roughly the same?

A

yes

38
Q

Chargoff’s rule

A

A+G = C+T

39
Q

What allows bases to lie perpendicular to the helical axis?

A

the absence of 2’-OH group

40
Q

What is the distance between two bases in DNA?

A

3.4 Angstroms

41
Q

What is the diameter of B form DNA?

A

20 Angstroms

42
Q

What stabilizes the B form of DNA?

A

nonspecific Van der Waals base stacking interaction between two adjacent bases in the same strand

43
Q

Difference between RNA and DNA double strands?

A

RNA double strands are normally the A form

44
Q

Does the glycosidic bond of DNA break when heated?

A

no

45
Q

What is the most important to living cells for the chemical modification of DNA?

A

oxygen and UV light

46
Q

Nucleoside versus nucelotide

A

Nucleoside does not have a phosphate group

47
Q

What is the covalent backbone of DNA made out of?

A

phosphate groups and pentose sugars

48
Q

Is base stacking hydrophillic?

A

no

we are in the hydrophobic interior

49
Q

Duplexes in turns of stability

A

RNA-RNA > RNA-DNA > DNA-DNA

50
Q

What contributes to the pKa of histidine raising in chymotrpsin?

A

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

51
Q

How many steps is HIV protease mechanism? What is the nucleophile?

A

just one step

water is the nucleophile which aspartate residue makes a good nucleophile through base catalysis

52
Q

What are the steps of transpeptidase mechanism?

A

First is acylation with serine as the nucleophile

Then is deacylation with another amino acid as the nucleophile (not water)

has two steps

53
Q

What are the steps of B-lactamase?

A

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

Biochem (20 decks)

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