Ch. 5 Protein Function Flashcards

1
Q

How is genomic information regulated (2)?

A

RNA and proteins, but this section focuses on proteins.

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2
Q

What are the three types of genomic regulatory protiens?

A
  1. Reversible binding proteins (RNA does this too)
  2. Catalytic proteins (RNA does this too)
  3. Motor proteins
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3
Q

What are reversible binding proteins?

A

Proteins that reversibly bind to nucleic acids.

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4
Q

What are the six principles of reversible binding proteins?

A
  1. The DNA bound by a protein is the ligand, which is NOT chemically modified
  2. Ligand binds to a binding site of a protein through various non-covalent interactions
  3. Proteins have conformational flexibility: they have different shapes when bound and unbound by ligand
  4. Protein/ligand interactions often require induced fit: the protein conformation changes to better fit a ligand
  5. Cooperativity: conformation change of a subunit may lead to altered conformation of a different protein subunit
  6. The activity of proteins can be altered through interactions with one or more ligands
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5
Q

How many binding sites do proteins have?

A

A single protein may have multiple binding sites for different ligands.

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6
Q

What are DNA binding proteins?

A

Proteins that can bind DNA and can modify genome structure or function WITHOUT covalently modifying the DNA.

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7
Q

What are nonspecific DNA binding proteins?

A

Proteins that bind to DNA WITHOUT a strong preference for base sequence.

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8
Q

What are specific DNA binding proteins?

A

Proteins that bind to DNA WITH a stronger preference for base sequence based on DNA surface features.

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9
Q

How do DNA binding proteins that bind both specifically and nonspecifically work?

A

The attach at the major groove of DNA and search for their target sequence.

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10
Q

What are some examples of nonspecific DNA binding proteins (3)?

A

chromosome packaging proteins
DNA replication proteins
histones, etc.

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11
Q

How do nonspecific DNA binding proteins interact?

A

noncovalently

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12
Q

How do many specific DNA binding proteins bind to DNA?

A

Often bind nonspecifically to the major groove of DNA and move along the major groove until they interact with the target sequence.

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13
Q

Why do specific DNA binding proteins often bind at the major groove?

A

It is likely due to greater base exposure and opportunity for interactions between bases and amino acids.

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14
Q

What is an example of a DNA binding protein that is specific and nonspecific?

A

LacI

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15
Q

What is LacI and how does it work?

A

LacI is a regulatory protein for the lac operon.
1. It nonspecifically bids DNA and moves until recognizing a specific inverted repeat
2. It binds the repeat more strongly and causes a structural change in the DNA

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16
Q

What is the binding region of LacI?

A

A helix-turn-helix motif, which is common in bacterial and some eukaryotic proteins.

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17
Q

What is a DNA motif?

A

A pattern of bases (i.e. inverted repeat)

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18
Q

What are reaction catalysts (catalytic proteins)?

A

Proteins that speed up the rate of a reaction by decreasing the activation energy.

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19
Q

What does catalytic activity depend on for catalytic proteins?

A

Catalytic activity depends on conformation. Activity could be denaturing, slightly altering structure, etc.

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20
Q

What are the two things some enzymes require?

A

cofactors and coenzymes

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21
Q

What is a cofactor?

A

An inorganic metal ion like Mg²⁺.

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22
Q

What is a coenzyme?

A

A metallo-organic compound like a vitimin.

23
Q

What is a holoenzyme?

A

A complete, catalytically active enzyme containing the necessary cofactor and/or coenzyme.

24
Q

What are the four key principles of catalysis?

A
  1. An enzyme binds a substrate, which IS chemically altered during the reaction
  2. The substrate specifically interacts with the active site of an enzyme
  3. Catalysis requires conformational flexibility, induced fit, and cooperativity
  4. Activity of many enzymes is REGULATED
25
What does the interaction between enzyme and substrate provide the reaction?
Interactions between enzyme and substrate provide binding energy, which can offset the activation energy.
26
How is binding energy obtained?
Via noncovalent interaction between the substrate and enzyme.
27
Why might a favorable reaction still occur slowly?
It may still happen slowly because of the activation energy required to reach the transition state.
28
How do enzymes speed up a reaction?
Enzymes lower the activation energy required to reach a transition state making it easier to reach.
29
How do non-living/non-biological things overcome activation energy?
Activation energy can be overcome with heat, lightning, etc. NOT ENZYMES!
30
No enzyme = ______________
No enzyme = slow reaction
31
How can an enzyme impede a reaction?
If the enzyme has a shape complementary to the substrate, it may stabilize the substrate and impede.
32
How can an enzyme encourage a reaction?
If the enzyme has a shape complementary to the transition state, the binding energy provides the activation energy for the reaction to proceed.
33
What are motor proteins?
Proteins that move.
34
What do movements of cells or structures require?
Movement of cells or structures within a cell require motor proteins that are fueled by ATP (usually).
35
How does movement of a motor protein happen?
Movement occurs through noncovalent interactions between motor proteins and other proteins.
36
What are the motor proteins most related to molecular biology (4)?
helicases polymerases (catalytic too!) topoisomerases (i.e. gyrase) and more that move along DNA...
37
How to motor proteins work (broadly)?
They work by combining ligand (DNA) binding to ATP hydrolysis.
38
What do helicases do generally?
Various helicases bind to and move along DNA and RNA.
39
What is DNA helicase?
DNA helicase separates dsDNA to ssDNA during replication.
40
What is RuvB?
A helicase involved in migration of Holiday junctions during homologous recombination.
41
What is Rho?
A helicase involved in terminating bacterial transcription.
42
What do all types of helicases have in common (3)?
They have similar protein domains, exhibit directionality, and utilize ATP hydrolysis to cause conformation changes that allow them to "step" along DNA.
43
What effect can the movement of helicases have (4)?
Movement may disrupt H-bonds, displace other proteins, change conformation of nucleic acids, or remodel chromatin.
44
What are allosteric enzymes?
Enzymes that have two or more binding sites. One binds the substrate and another binds a modulator.
45
What is a modulator?
A chemical that either increases or decreases enzyme activity.
46
What is autoinhibition?
When a portion of an enzyme blocks its own active site, inhibiting activity.
47
How is autoinhibition removed?
Binding of other ligands causes a conformational change that repositions the inhibitory portion, allowing substrate to bind to the enzyme.
48
What is reversible covalent modification?
A protein regulation method that adds a small chemical group to the enzyme causing conformational change.
49
What is phosphorylation?
A common mechanism of reversible covalent modification.
50
What adds phosphate groups?
Protein kinases
51
What remove phosphate groups?
phosphotases
52
What effect can phosphorylation have on a protein/enzyme?
The negative charges on the phosphate may repel neighboring "﹣" charges and may H-bond to neighboring amino acids.
53
What is proteolytic cleavage?
A method of protein regulation where an inactive precursor protein called a proenzyme is cleaved to form an active enzyme.