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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
What does protein folding do to distant amino acids
It brings them into proximity
26
What are the steps in the catalytic mechanism involving 3 amino acid side chains in Trypsin
Step 1: cleavage of peptide bond with formation of a covalent substrate-enzyme complex Step 2: hydrolysis of acyl enzyme complex
27
Enzymes exhibit pH optima which can reflect;
1. Active site acid-base chemistry 2. Sensitivity of overall protein conformation to charge distribution
28
Why does a chymotrypsin reaction not occur below a pH of 7
Chymotrypsin has little activity below pH 7 because it depends on an acid-base reaction between two key active site residues
29
Why is the conformation of chemotrypsin disrupted above a pH of 9
Structurally important amino groups become unprotonated and uncharged
30
How are enzymes in a pathway often physically associated with one another
By direct binding interactions or by binding to a common scaffold protein
31
What is the relationship between proximity of amino acids and the ability to receive products
The closer amino acids are to each other, the more efficient it is to pass on products
32
What conformation has the best efficiency in product delivery
Scaffold protein conformation
33
What can the binding of a ligand at one site lead to
Conformational changes that affect the binding of another ligand molecule at a different site
34
What is a major manifestation of allosteric effects
Conrformational switches in regulatory proteins in response to ligand or post-translational modification
35
What is used as allosteric switches to control protein activity
Noncovalent binding of Ca2+ and GTP
36
What does ca++ binding to cal modules do and what does it allow it to do
Changes its conformation and allows it to bind to target peptides on other proteins thus regulating their structure and activity
37
How is switching from on to off done on G proteins
On = GTP bound Off = GDP bound
38
How is Switching from on to off facilitated on G-proteins
GAPs
39
How is switching from off to on facilitated on G-proteins
GEFs
40
What are the characteristics of modification of protein conformation and activity through phosphorylation
Phosphorylation of amino acid side chains is a rapidly reversible covalent modification of protein structure, a post-translational modification
41
What is phosphorylation
Addition of phosphate by kinases using ATP
42
When a protein undergoes conformational change, is its active site still available
Yes
43
What is the target of a kinase or a phosphates
Another kinase or phosphates creating a cascade effect
44
Hat do kinase cascades permit
Amplification of a signal and many levels of fine tuning
45
What makes a stable binding/complex ?
3D structures that match, series of molecular characters on protein complementary to the other protein
46
What are the two sites on an enzyme and what do they do
1. Substrate binding site: selects substrate 2. Catalytic site: does the reaction
47
What does Km depend on vs not depend on
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
What does trypsin hydrolyze peptide bonds adjacent to
Arginine and Lysine (large basic side chains)
49
What happens when the peptide bond in the catalytic site to be cleaved is cleaved
The protein has an N terminal fragment and a C terminal fragment
50
Depending on the enzyme, what characteristics have to be adjusted in order for it to interact with the side chain
If they are bulky or not (size) charge, anything that is complementary to the binding site
51
How does catalysis between Asp-102, His-57 and Ser-195 happen if they are so apart
When they are folded they just so happen to be close together which allows catalysis
52
What do both subreactions with Asp-102, His-57 and Ser-195 depend on and when does this reaction happen best
His-57’s ability to bind and to release a proton readily and happens when pH is near pK for His-57
53
What is the first step of the catalytic mechanism involving 3 amino acid side chains Asp, His and Ser
Cleavage of peptide bond with formation of a covalent substrate complex
54
What is the second step of the catalytic mechanism involving 3 amino acid side chains Asp, His and Ser
Hydrolysis of acyl enzyme complex
55
What is the conformation of His 57 side chain when it’s inactive vs active
Inactive with a charge, extra H (low pH) Active with no charge
56
Why can two enzymes have different optimal pH?
They have different catalytic site chemistry
57
What are three ways for proteins to turn reactants into products
1. Separated 2. Joined either close together or in a scaffold 3. As a polypeptide
58
What is the structure of calmodulin without calcium
4 EF hands motif
59
What is the conformation/interaction between calcium and calmodulin bound to target peptide
Target peptide regulated by calmodulin, stable and throng interaction between calcium bound calmodulin and target protein through side chains
60
What does GAP do in G protein activation
Turns system off (inactive) aka releases Pi
61
What does GEF do in G protein activation
Turns systems on by helping GDP fall out
62
How does modification of protein conformation and activity through phosphorylation and dephosphorylation work
Phosphorylation = active state (by protein kinase) Not phosphorylation = inactive state (by protein phosphates)

BIOL 200 (13 decks)

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