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BIOL 200 > KH5 > Flashcards

KH5 Flashcards

1
Q

What is a ligand

A

The molecule to which a protein binds

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2
Q

What are the diverse functions of proteins dependant on

A

Protein binding

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3
Q

What are the two properties of primary importance in ligand-binding

A

Specificity and affinity

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4
Q

What is specificity

A

The ability of a protein to bind only one particular ligand, even in the presence of a vast excess of irrelevant molecules

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5
Q

What is affinity

A

The tightness or strength of binding, expressed as dissociation constant (Kd) The stronger the interaction the lower the Kd

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6
Q

Binding is an interaction between what kind of surfaces

A

Complementary molecular surfaces

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7
Q

What does protein specificity arise from

A

Numerous interactions which are individually weak but if numerous, collectively strong

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8
Q

How do antibodies generally bind their antigens

A

With high specificity and high affinity

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9
Q

What is the structure of antibodies

A

Two identical heavy chains and light chains

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10
Q

What is the structure of the antigen binding surface or CDR

A

Multiple protein loops from both the heavy and the light chains

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11
Q

What are the characteristics of the multiple protein loops in antibodies

A

Highly variable in amino acid sequence among antibody encoding genes so the total repertoire of possible CDR’s in the antibody is large

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12
Q

What are enzymes

A

An extremely diverse class of catalytically active proteins whose ligands include the substrates of the reactions they catalyze

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13
Q

What occurs at the enzyme’s active site

A

Substrate binding and reaction catalysis

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14
Q

Where does substrate specificity arise from

A

The substrate binding site (complementary molecular surfaces)

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15
Q

What are the possible contributions of some amino acids in the enzyme polypeptides

A

Contribute to substrate biding site or the catalytic site

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16
Q

What is Vmax

A

The maximal rate of catalysis given saturating amounts of substrate

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17
Q

What does Vmax depend on

A

Amount of enzyme and how fast in can work

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18
Q

What is Km

A

Substrate concentration that supports a rate of catalysis equal to half of the Vmax

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19
Q

What does Km depend on

A

Depends on and is a measure of the affinity of enzyme-substrate binding

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20
Q

What is an example of enzyme substrate binding and catalytic site details

A

Serine protease trypsin

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21
Q

What does trypsin do

A

Hydrolyzes peptide bonds adjacent to arginine and lysine (large basic side chains)**

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22
Q

When does proper substrate binding occur

A

When the substrate amino acid side chain fits into a negatively charged pocket within the substrate binding site

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23
Q

What defines enzymes different specificities

A

Differences in substrate recognition pocket in the related enzymes

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24
Q

Why does elastase cleave adjacent to amino acids with small side chains (alanine and glycine)

A

The pocket in elastase is obstructed by bulky valine side chains

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25
Q

What does protein folding do to distant amino acids

A

It brings them into proximity

26
Q

What are the steps in the catalytic mechanism involving 3 amino acid side chains in Trypsin

A

Step 1: cleavage of peptide bond with formation of a covalent substrate-enzyme complex
Step 2: hydrolysis of acyl enzyme complex

27
Q

Enzymes exhibit pH optima which can reflect;

A
  1. Active site acid-base chemistry
  2. Sensitivity of overall protein conformation to charge distribution
28
Q

Why does a chymotrypsin reaction not occur below a pH of 7

A

Chymotrypsin has little activity below pH 7 because it depends on an acid-base reaction between two key active site residues

29
Q

Why is the conformation of chemotrypsin disrupted above a pH of 9

A

Structurally important amino groups become unprotonated and uncharged

30
Q

How are enzymes in a pathway often physically associated with one another

A

By direct binding interactions or by binding to a common scaffold protein

31
Q

What is the relationship between proximity of amino acids and the ability to receive products

A

The closer amino acids are to each other, the more efficient it is to pass on products

32
Q

What conformation has the best efficiency in product delivery

A

Scaffold protein conformation

33
Q

What can the binding of a ligand at one site lead to

A

Conformational changes that affect the binding of another ligand molecule at a different site

34
Q

What is a major manifestation of allosteric effects

A

Conrformational switches in regulatory proteins in response to ligand or post-translational modification

35
Q

What is used as allosteric switches to control protein activity

A

Noncovalent binding of Ca2+ and GTP

36
Q

What does ca++ binding to cal modules do and what does it allow it to do

A

Changes its conformation and allows it to bind to target peptides on other proteins thus regulating their structure and activity

37
Q

How is switching from on to off done on G proteins

A

On = GTP bound
Off = GDP bound

38
Q

How is Switching from on to off facilitated on G-proteins

A

GAPs

39
Q

How is switching from off to on facilitated on G-proteins

A

GEFs

40
Q

What are the characteristics of modification of protein conformation and activity through phosphorylation

A

Phosphorylation of amino acid side chains is a rapidly reversible covalent modification of protein structure, a post-translational modification

41
Q

What is phosphorylation

A

Addition of phosphate by kinases using ATP

42
Q

When a protein undergoes conformational change, is its active site still available

A

Yes

43
Q

What is the target of a kinase or a phosphates

A

Another kinase or phosphates creating a cascade effect

44
Q

Hat do kinase cascades permit

A

Amplification of a signal and many levels of fine tuning

45
Q

What makes a stable binding/complex ?

A

3D structures that match, series of molecular characters on protein complementary to the other protein

46
Q

What are the two sites on an enzyme and what do they do

A
  1. Substrate binding site: selects substrate
  2. Catalytic site: does the reaction
47
Q

What does Km depend on vs not depend on

A

Doesn’t depend on the amount of enzyme in the tube

Depends in the character of the interaction between the enzyme and the substrate and the ease of chemical binding

48
Q

What does trypsin hydrolyze peptide bonds adjacent to

A

Arginine and Lysine (large basic side chains)

49
Q

What happens when the peptide bond in the catalytic site to be cleaved is cleaved

A

The protein has an N terminal fragment and a C terminal fragment

50
Q

Depending on the enzyme, what characteristics have to be adjusted in order for it to interact with the side chain

A

If they are bulky or not (size) charge, anything that is complementary to the binding site

51
Q

How does catalysis between Asp-102, His-57 and Ser-195 happen if they are so apart

A

When they are folded they just so happen to be close together which allows catalysis

52
Q

What do both subreactions with Asp-102, His-57 and Ser-195 depend on and when does this reaction happen best

A

His-57’s ability to bind and to release a proton readily and happens when pH is near pK for His-57

53
Q

What is the first step of the catalytic mechanism involving 3 amino acid side chains Asp, His and Ser

A

Cleavage of peptide bond with formation of a covalent substrate complex

54
Q

What is the second step of the catalytic mechanism involving 3 amino acid side chains Asp, His and Ser

A

Hydrolysis of acyl enzyme complex

55
Q

What is the conformation of His 57 side chain when it’s inactive vs active

A

Inactive with a charge, extra H (low pH)
Active with no charge

56
Q

Why can two enzymes have different optimal pH?

A

They have different catalytic site chemistry

57
Q

What are three ways for proteins to turn reactants into products

A
  1. Separated
  2. Joined either close together or in a scaffold
  3. As a polypeptide
58
Q

What is the structure of calmodulin without calcium

A

4 EF hands motif

59
Q

What is the conformation/interaction between calcium and calmodulin bound to target peptide

A

Target peptide regulated by calmodulin, stable and throng interaction between calcium bound calmodulin and target protein through side chains

60
Q

What does GAP do in G protein activation

A

Turns system off (inactive) aka releases Pi

61
Q

What does GEF do in G protein activation

A

Turns systems on by helping GDP fall out

62
Q

How does modification of protein conformation and activity through phosphorylation and dephosphorylation work

A

Phosphorylation = active state (by protein kinase)
Not phosphorylation = inactive state (by protein phosphates)

BIOL 200 (13 decks)

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