Biochem- Proteins And Enzymes

Front 1

What is the optimum pH for pepsin, trypsin, and chymotrypsin?

Back 1

Pepsin: low pH (acidic)
Trypsin and chymotrypsin: high pH (basic).

Front 2

Where does chymotrypsin cleave a protein?

What activates chymotrypsin?

Back 2

C terminal end of any aromatic amino acid (WYF i.e. Trp, Tyr, Phe).

Trypsin activates chymotrypsin in the small intestines.
Chymotrypsine is a serine protease.

Front 3

Where does trypsin cleave a protein?

Back 3

C terminal side of any positive residue, i.e. Lys and Arg (KR).

Front 4

Where does elastase cleave a protein?

Back 4

C terminal side chain of amino acids with small or no side chains, such as Gly and Ala (GA)

Front 5

What does a high Km mean?

Back 5

weak substrate binding.

Front 6

What does a high Vmax mean?

Back 6

High turnover of substrate molecule.

Front 7

Irreversible enzymes.

Where do they bind? Give examples.

Back 7

Usually bind at the active site. Called suicide inhibitor.

Examples:
Penicillin (binds transpeptidase)
Acetylsalicylic acid: acetylates cyclooxygenase so arachidonate cannot bind.
Disulfiram: binds aldehyde dehydrogenase (ADH) which normally converts alcohol to acetic acid.

Front 8

Competitive reversible inhibitor

Where do they bind?

Back 8

Inhibitor binds the active site.
Inhibitor is similar to substrate.
INCREASES Km (decreases affinity of substrate to enzyme).
Does not change Vmax.

Front 9

What does a low Ki mean?

Back 9

If enzyme inhibition constant is low, the enzyme has high inhibition efficiency.

Front 10

Uncompetitive inhibitors.

Where do they bind? What is the effect on Vmax and Km?

Back 10

Uncompetitive inhibitors bind the ES complex to form ESI complex.

DECREASES BOTH Vmax and Km.

Front 11

Noncompetitive inhibitors.

Where do they bind? What is the effect on Vmax and Km?

Back 11

Noncompetitive inhibitor binds the allosteric site at the E, ES. Also, S can bind E or EI.

Vmax is decreased, but Km is unchanged.

Front 12

Give an example of a transition state inhibitor. Describe the mechanism.

Back 12

Penicillin is a transition state inhibitor.

The beta lactam ring mimics the transition state of the normal substrate.

Bacterial cell wall cross-linking rxn is catalyzed by glycopeptide transpeptidase, that attaches a D-Ala to it. Eventually forming an acyl-enzyme intermediate.

Front 13

What does aspartate transcarbamylase (ATCase) catalyze? What is the structure of the enzyme?

Back 13

ATCase catalyzes the first step in pyrimidine biosynthesis.

The enzyme is two trimers, linked by three dimers of regulatory chains.

Front 14

How is the activity of ATCase regulated?

Back 14

Through allosteric interaction which alters the quaternary structure.

Front 15

How many active sites does ATCase have?

Back 15

ATCase has six active sites.

Front 16

What is the effect of PALA on ATCase?

Back 16

PALA binds at the substrate binding site, and stabilizes the R state (becomes more active). So PALA is a substrate analog.

But the effect depends on the concentration of PALA! At low concentration, the enzyme is more active (because the R state is stabilized). In high [PALA], PALA competes against the substrate so it decreases the enzyme activity.

Front 17

What are the two types of heterotropic allosteric enzyme regulation of ATCase?

Back 17

Negative regulator: CTP (final product) binds an allosteric site on ATCase rendering it inactive (stabilizes T state).

Positive regulator: ATP stabilizes the R state.

Front 18

What is the Hill coefficient for positive and negative homotrophic allosteric cooperativity?

Back 18

Negative: <1
Positive: >1

Front 19

Co-translational N-terminal acetylation.

What is the effect on protein stability? What enzyme facilitates this?

Back 19

Acetylation stabilizes the protein.

The enzyme N-terminal acetyltransferase (NAT) catalyzes this rxn. Not amino acid specific.

Front 20

What does alcohol dehydrogenase do? What activates ADH?

Back 20

ADH converts alcohol to acetylaldehyde.

ADH is activated by removal of the acetyl group from its N-terminus.

This is the only Co-translational modification. Everything else is post-translational modification.

Front 21

What enzyme hydroxylates proline?

What cofactor is required for proline hydroxylation?

Back 21

Prolyl hydroxylase.

Collagen contains 21% proline and hydroxyproline!

Vit C is required for proline hydroxylation.

Front 22

What enzyme methylates histidine side chains?

Back 22

N-methyl transferase.

Front 23

Does His73 have to be methylated or nonmethylated for proper muscle contraction?

Back 23

His73 mus be methylated for proper contraction (so that ADP can be released).

Front 24

What is the cofactor for Glu carboxylation?

What coagulation factor uses this?

Back 24

Vit K.

Prothrombin glutamate carboxylation makes prothrombin a much stronger chelator of calcium. The calcium anchors the prothrombin at the membrane, which is important for blood clotting.

Front 25

What is the effect of phosphorylation on glycogen phosphorylase?

Back 25

Phosphorylation of glycogen phosphorylase locks it in an active form.

Front 26

What is the Gag polyprotein in HIV?

Back 26

It's a protein that is in the budding HIV. After budding, it's cleaved (activated)by HIV protease to 6 protein products that play an essential role in the virus.

Inhibition of the proteolysis will prevent the spread of virions.

Front 27

What is the drug Crixivan used for? How does it work?

Back 27

Crixivan is used for controlling AIDS.

Crixivan is a protease inhibitor which inhibits HIV protease.

Front 28

What is N-linkage?

In which organelle does it take place?

Back 28

N-linkage is the glycosylation of the amide nitrogen atom on Asn.

Takes place in the sER.

Front 29

What is O-linkage?

In which organelle does it take place?

Back 29

O-linked glycosylation is the glycosylation of the oxygen atom on Ser or Thr.

Takes place in Golgi apparatus.

Front 30

I-cell disease.

What is it?

Back 30

Rare condition in which lysozomal enzymes lack the glycolyl markers that target them to the lysozome. (glycosylation disease)

Front 31

Glutathione.

Structure. What is the reduced form? Function. In which blood cells are they important?

Back 31

Structure: tripeptide.

Reduced form is GSH.

Function: maintain reduced state of cell, and fight oxidative stress.

Especially important in RBC's since they lack Mt. RBC's which lack GSH are susceptible to hemolysis.

Front 32

Thioredoxin.

Function. What processes is it involved in?

Back 32

Function: activation or inhibition of enzymes containing disulfide bridges.

It's involved in diverse pathways including glucose production, regulating CO2 conc., and photosynthesis in plants.