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BioChem > Quiz 3 > Flashcards

Quiz 3 Flashcards

1
Q

What are the four major regulatory mechanisms that control enzyme activity?

A

Allosteric control, Isozymes, covalent modification, proteolytic activation

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2
Q

Describe allosteric control. Give an example.

A

enzyme regulation involving the binding of a non-substrate molecule at a regulatory site on the enzyme other than the active site. Exhibits cooperativity.
Example- ATCase

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3
Q

Define cooperativity.

A

Activity at one functional center affects the activity at others.

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4
Q

What ways can allosteric control affect enzymes?

A

Can either have a positive or negative effect on enzyme activity or cooperatitivity.

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5
Q

Describe isozymes. Give an example

A

Enzymes with identical function but different structure, which allows the to regulate the same reaction at different places, and with potentially different enzyme kinetics.
Example- lactate dehydrogenase

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6
Q

How many different isozymes and subunits does lactate dehydrogenase have?

A

five different isozymes using two different subunits, H (heart) and M (skeletal muscle)

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7
Q

Describe Covalent modification. Give an example

A

Addition or removal of chemical groups, can influence the properties of the target protein. Can be reversible or irreversible.
Examples- Phosphorylation and acetylation

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8
Q

Describe Proteolytic activation. Give an example.

A

Activation of an enzyme by peptide cleavage. Inactive precursor (proenzyme or zymogen) is irreversibly cut to yield the active form.
Examples- Digestive enzymes, Pepsinogen is cleaved to form pepsin.
Formation of trypsin
Blood clotting is mediated by a cascade of proteolytic activation.

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9
Q

Describe the reaction catalyzed by ATCase. How is ATCase regulated?

A

ATCase catalyzes the first step in the pyrimidine biosynthetic pathway, formation of carbamoyl aspartate. It is inhibited by CTP, the final product of the pyrimidine pathway. It is activated by ATP (signals that there is energy available for DNA synthesis)

(APT stabilizes R state, CTP stabilizes the T state)

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10
Q

Describe the subunit composition of ATCase.

A

ATCase has regulatory and catalytic subunits. Only the regulatory are responsible to ATP and CTP.

When treated with p-hydroxymercuribenzoate the subunits dissociate.

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11
Q

Describe the 3D subunit arrangement of ATCase

A

Catalytic subunits consists of 3 chains (c3) and regulatory subunits consists of 2 chains (r2). The active complex (c6r6) consists of two catalytic trimer subunits on “top” and “bottom” surrounded by three regulatory subunits.

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12
Q

Describe the evidence for an allosteric transition of ATCase

A

PALA resembles the reaction intermediate and is a competitive inhibitor of ATCase. It binds to the active site and facilitates a conformation from the T (tense) state to the R (relaxed) state by stabilizing the R state.

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13
Q

Define T state vs R state.

A

T state is compact, low substrate affinity, low catalytic activity.

R state is open conformation, high substrate affinity, high catalytic affinity.

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14
Q

What basic reaction is catalyzed by protein kinases?

A

Phosphorylation

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15
Q

What basic reaction is catalyzed by protein phosphatases

A

Dephosphorylation

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16
Q

Why is phosphorylation an effective control mechanism?

A
  • The reaction is very favorable
  • The addition of a phosphorylation group adds two negative charges, altering electrostatic interactions
  • A phosphorylation group can form three or more hydrogen bonds
  • The reaction can take place in less than a second or over a span of hours
  • Effects are often highly amplified (single kinase can phosphorylate very quickly)
  • Uses ATP as the currency, links energy status of the cell to the regulation of metabolism
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17
Q

How is PKA activated by cAMP?

A

Under normal conditions PKA consists of R2C2 (regulatory, catalytic) subunit with the R2 functioning as a pseudo subunit for both C subunits, blocking activity. In the presence of cAMP the R2 subunit no longer inhibits the C subunits, which dissociate off of the R2 subunit and become active

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18
Q

Define Zymogen/pro-protein

A

Inactive enzyme precursors that are activated by proteolytic cleavage

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19
Q

Give some examples of zymogens

A

Digestive or pancreatic enzymes such as pepsinogen, chymotrypsinogen, trypsinogen, or procarboxypeptidase.
Blood clotting has multiple zymogens.

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20
Q

What is the pathway for secretion of pancreatic zymogens?

A

Pancreatic zymogens are synthesized in exocrine acinar cells of the pancreas and release upon stimulation.
They are modified in the ER.
RER->Golgi->Granule->Lumen

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21
Q

What is chymotrypsin?

A

A digestive enzyme (breaks down proteins)

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22
Q

How is chymotrypsinogen converted to chymotrypsin?

A

Trypsin cleaves a single peptide bond between Arg15 and Ile16. The newly freed alpha-amino group of Ile16 is electrostatically attracted to the carboxylate group of Asp 194. This interaction triggers multiple conformational changes, which result in the formation of the substrate-specificity site.

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23
Q

The substrate specificity site of chymotrypsin codes for which amino acids?

A

Aromatics (Tyr, Phe, Trp)

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24
Q

How is trypsinogen converted to trypsin?

A

Enteropetidase activates trypsinogen.

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25
Q

What is the master activation step for the pancreatic zymogens?

A

Formation of trypsin, the common activator of all pancreatic zymogens.

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26
Q

What inhibits Trypsin formation, and why does it need an inhibitor?

A

Trypsin has a positive feedback loop, it is inhibited by pancreatic trypsin inhibitor and alpha-1 antitrypsin.

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27
Q

How is pepsinogen converted to pepsin?

A

At normal pH the active site is blocked. After eating, acid is released by stomach cells, protonating Asp and breaking the salt link between it and Lys.

28
Q

What are the general steps of the blood clotting response?

A
  1. Vasoconstriction, diverting and decreasing blood flow
  2. Platelet aggregation, platelets adhere and aggregate to the damaged vessel, forming a clump that can plug and stop minor bleeding.
  3. Clotting occurs through cascade of zymogen activations
  4. Conversion of soft fibrin clots to hard clots by thrombin
29
Q

What occurs during platelet aggregation?

A

the platelets adhere to the damaged blood vessel and then to each other, forming a clump that can plug and stop minor bleeding. They release chemicals that further potentiate coagulation. As they adhere they change shape and are called “activated”. They finally initiate blood clotting by activating a number of clotting proteins.

30
Q

Most clotting factors are what?

A

zymogenic serine proteases

31
Q

What are the two pathways to blood clotting?

A

The intrinsic pathway of blood clotting- activated by exposure of anionic surfaces on rupture of endothelial lining
The extrinsic pathway - trauma exposes tissue factor

32
Q

Differentiate the structure and properties of fibrinogen from fibrin

A

Fibrinogen is a large molecule made up of three globular units. It is soluble and contains many highly anionic/repelling residues.

Fibrin is fibrinogen after the release of the anionic residues, it can now bind to other fibrin monomers

33
Q

Describe the conversion of fibrinogen to fibrin

A

Thrombin converts fibrinogen to fibrin through the releasing of the four highly anionic/repelling residues called fibrinopeptides (lots of Arg and Lys)

34
Q

Describe how fibrin monomers bind to each other

A

The ends of the fibrin chains bind to the binding holes of the central globular domains

35
Q

Describe the activity of Factor XIIIa

A

Fibrin-stabilizing factor Factor XIIIa joins the C-terminus segments of gamma chains of fibrin monomers by forming is-peptide bonds between Gln on one gamma unit and a Lys on the other

36
Q

Describe prothrombin

A

The three-domained zymogen of thrombin that circulates in the plasma. It is cleaved twice to yield thrombin, a dimer of A and B chains

37
Q

What is the function of calcium for blood clotting?

A

The binding of calcium by prothrombin anchors it to the phospholipid membranes derived from blood platelets after injury. It brings prothrombin in close proximity to 2 clotting proteins that convert it into thrombin.

38
Q

How does vitamin K and calcium help create blood clots?

A

Thrombin has many Glu residues on its N terminus. Vitamin K carboxylates those into Gla. Those function with Ca+ ions to anchor thrombin to the injury site

39
Q

What is common to all serine proteases (clotting factors and digestive factors)

A

They break ester and peptide bonds using His-activated serine in a catalytic triad.
They contain a specificity pocket for particular AAs and oxyanion hole that stabilizes the negatively charged Oxygen

40
Q

Where does Vitamin K function?

A

post translational modification of prothrombin in the ER

41
Q

Describe the genetic defect in hemophilia

A

Defective factor VIII (8), a clotting protein. Also known as anti hemophilic factor (AHF)

42
Q

What is the general pathway for clotting to occur?

A

Intrinsic/Extrinsic → Common Pathway → Prothrombin to Thrombin → Fibrinogen to Fibrin → Crosslinking

43
Q

What is the function of plasmin?

A

Splits fibrin clots into peptides

44
Q

What is the function of TPA?

A

Tissue Plasminogen Actor, converts plasminogen to plasmin

45
Q

What are the most common acceptor residues for phosphorylation?

A

Serine, Threonine, Tyrosine (-OH)

46
Q

What is the physiological role of myoglobin?

A

Binds oxygen in muscle cells, functions for storage

47
Q

What is the physiological role of hemoglobin?

A

Transports oxygen from the lungs to the tissues.

48
Q

Which displays cooperativity, myoglobin or hemoglobin?

A

hemoglobin

49
Q

Describe the heme group

A

Center of myoglobin and the four subunits of hemoglobin. An organic molecule protoporphyrin and a central iron ion.

50
Q

What state must the iron of the heme group be in to bind oxygen?

A

In its ferrous Fe2+ form.

51
Q

Where can the iron form additional bonds? What bonds at these sites?

A

Iron can form additional bonds at the fifth and sixth coordination sites. Fifth site binds proximal histidine, sixth site binds oxygen

52
Q

Where does the distal histodine bind?

A

To the oxygen on the sixth site of the iron

53
Q

When heme is not a part of globin, what is it missing?

A

Its distal histidine

54
Q

What is the function of the distal histidine?

A

Prevents release of superoxide ion. Also lowers affinity towards carbon monoxide by forcing it to bind at an angle

55
Q

Differentiate between the composition of adult and fetal hemoglobin

A

Adult hemoglobin is an alpha dimer and beta dimer.

Fetal hemoglobin is an alpha dimer and a gamma dimer

56
Q

What is the functional difference between adult and fetal hemoglobin?

A

Adult hemoglobin does not bind oxygen as well. Allows the fetus to gain oxygen at an O2 concentration that the mother is releasing oxygen

57
Q

Compare oxygen binding in myoglobin to hemoglobin

A

Myoglobin binds oxygen more tightly than hemoglobin

58
Q

Describe the two oxygen dissociation curves for myoglobin and hemoglobin

A

Myoglobin has a hyperbolic curve, hemoglobin has a sigmoidal curve

59
Q

Summarize how the cooperative binding of oxygen by hemoglobin makes it a better oxygen transporter

A

Allows for 98% oxygen saturation in blood compared to 32% in tissue, which means 66% loading and unloading capacity. This is compared to 38% unloading capacity with no cooperativity, or 7% for myoglobin.

60
Q

Explain CO poisoning

A

CO binds to heme with 200x the affinity of oxygen, and prevents oxygen from binding

61
Q

What is the mutation that causes sickle cell anemia?

A

Mutation in hemoglobin replaces beta subunit with S

62
Q

In cysteine proteases what is in the active site? What is the carbonyl attacked by?

A

Thiol in active site. Carbonyl is attacked by his-activated cysteine

63
Q

In aspartyl proteases what is in the active site? What is the carbonyl attacked by?

A

Carboxyl in active site. Carbonyl is attacked by aspartate-activated water

64
Q

Which protease is the HIV protease?

A

Aspartyl protease. Cleaves viral proteins into active forms

65
Q

What is the carbonyl attacked by in metalloproteases?

A

Attacked by metal-activated water

66
Q

What is the carbonyl attacked by in Serine Proteases

A

Attacked by His-activated serine

67
Q

What does chymotrypsin rely on?

A

Serien 195

BioChem (6 decks)

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