Chapter 8

Question 1

Overview of Regulation

Answer 1

Cells metabolically complex.
Cells need to change metabolic activities to adjust:
-phase of cell cycle
-environmental conditions
-presence of organisms
Metabolism requires enzymes that must be present and functional.

Question 2

Major modes of regulation

Answer 2

Gene expression- transcription followed by translation.
Most proteins are enzymes that carry out biochemical reactions.
Constitutive proteins needed at same level.
Microbial genomes encode many proteins not needed always.

Question 3

Two major levels of regulation in cells

Answer 3

Control activity of preexisting enzymes:
-post translational regulation
-very rapid 
Control amount of enzyme:
-regulate level of transcription
-regulate translation
-slow

Question 4

Constitutive enzymes

Answer 4

Catalyze metabolic reactions that constantly occur:
-independent of growth conditions
-independent of cell cycle
Ex. pyruvate decarboxylase (Kreb’s)

Question 5

Regulating an enzyme that already exists

Answer 5

Post translational regulation, happens after protein is made.
2 major strategies for post translational regulation:
-feedback inhibition
-covalent modification

Question 6

Feedback inhibition

Answer 6

Molecules in cell bind to enzyme and inactivate it.
Binding reversible when conditions change.
Used in biosynthetic pathways. (amino acid synthesis).
Often first enzyme is inhibited by end product.

Question 7

Feedback Inhibition: Allostery

Answer 7

Allosteric enzymes have 2 binding sites:

• Active site which binds substrate and catalyzes metabolic reaction.
• Allosteric site which binds inhibitor.

Question 8

Allostery: Inhibitor binds allosteric site:

Answer 8

• shape of enzyme changes, including active site.
• Substrate no longer fits in active site.
• Binding reversible.

Question 9

Covalent modification

Answer 9

Adds or removes small molecule. 
Frequent examples involve:
-phosphate groups 
-methyl groups
Molecule is covalently bound to enzyme.

Question 10

Enzyme production method: DNA binding proteins

Answer 10

mRNA has short half life:
-prevents production of unneeded proteins.
Regulation of transcription often requires proteins that bind DNA.
Small molecules influence binding of regulatory proteins to DNA:
-proteins regulate transcription.

Question 11

DNA binding proteins

Answer 11

DNA binding proteins interact with DNA in sequence specific manner
-phosphate backbone of DNA
Major groove of DNA main site of protein binding
Inverted repeats frequently binding site for regulatory proteins.

Question 12

DNA binding protein structures

Answer 12

Homodimeric proteins: proteins composed of two identical polypeptides.
Protein dimers interact with inverted repeats on DNA.
-Each polypeptide binds to one inverted repeat.

Question 13

DNA binding protein structures: helix turn helix

Answer 13

First helix recognition helix.
Second helix stabilizing helix.
Many different DNA-binding proteins from bacteria contain helix turn helix.

Question 14

DNA binding protein structures: Zinc finger

Answer 14

Protein structure that binds zinc ion.

Typically two or three zinc fingers on proteins that use them for DNA binding.

Question 15

DNA binding protein structures: Leucine zipper

Answer 15

Leucine residues spaced every seven amino acids.

Does not interact directly with DNA .

Question 16

DNA binding proteins: End result

Answer 16

1. Binding protein may catalyze specific reaction on DNA molecule.
2. Binding event can block transcription (negative regulation).
3. Binding event can activate transcription (positive regulation).

Question 17

Negative control of transcription: repression

Answer 17

Negative control: a regulatory mechanism that stops transcription.

• Repression: preventing synthesis of an enzyme in response to a signal.
• enzymes affected by repression make up small fraction of total proteins
• typically affects anabolic enzymes

Question 18

Negative control: Induction

Answer 18

Induction: production of an enzyme in response to a signal.

• typically affects catabolic enzymes.
• enzymes synthesized only when needed.

Question 19

Negative control: Terms

Answer 19

Inducer: induces enzyme synthesis.
Corepressor: represses enzyme synthesis.
Effectors: term for inducers and repressors
-effectors affect transcription indirectly by binding specific DNA binding molecules

Question 20

Negative control: Operon

Answer 20

Operon: cluster of genes arranged in a linear fashion whose expression is under control of a single operator.
-located downstream of promoter
-transcription physically blocked when repressor binds to operator
Addition of inducer inactivates repressor and transcription can proceed.
Repressor’s role: negative control.