Chapter 11

Question 1

What are the four phases of metabolism?

Answer 1

Fueling: ATP, Reducing Power, Precursor Metabolites (entry, feeder pathways, central pathways).

Biosynthesis: Use products of fueling to generate building blocks.

Polymerization: DNA-RNA-Protein

Assembly: Cell Envelope.

Question 2

What is the rationale for coordination?

Answer 2

• Bacterial cells exposed to constantly changing conditions (many methods of regulation are required to adapt to this variation).
• Regulation is important for efficient use of energy (making RNA and protein very energetically expensive).

Question 3

What evidence shows that metabolic reactions are coordinated?

Answer 3

1. Coordination in Biosynthesis
2. Coordination in Fueling
3. Coordination in Marcromolecular Composition

Question 4

Coordination in Biosynthesis:

Experimental Media:

Answer 4

Radiolabeled glycerol as carbon source, unlabeled histidine. (no histidine in cell labeled)

Question 5

What does the presence of any one compound in the medium do?

Answer 5

The presence of any one compound in the medium stops endogenous synthesis of that compound

Question 6

Coordination of Fueling:

Answer 6

Cells adjust ratios of products of fueling to satisfy the needs of the cell. Therefore, cells must sense growth potential, respond.

Question 7

Coordination in marcromolecular composition:

Answer 7

At the same growth rate, cells have the same macromolecular composition (proteins, DNA, lipids, carbohydrates).
Richness of medium affects growth rate.

Question 8

How does richness of medium affect growth rate?

Answer 8

1. Faster growth rate, richer in certain components, like RNA.
2. Control rate of synthesis of each macromolecule to reflect richness of media and potential growth rate.

Question 9

What are the three ways regulations refers to the regulation of enzymes?

Answer 9

1. Changing enzyme activity.
2. Changing amount of enzyme.
3. Changing amount of substrate.
   (text- not much focus—changing the first 2 results
   in changes in substrates through biochemical
   pathways)

Question 10

Why is controlling enzyme amounts more common in prokaryotes than in plant and animal cells?

Answer 10

Substrate limited
Coupled transcription and translation (adjust quickly)
mRNAs are short lived
Operons

Question 11

Controlling enzyme activity:

Answer 11

Less common
Rates of metabolic reactions and to coordinate some cellular processes
Covalent modification (like phosphorylation)
Allostery (more common)

Question 12

Covalent modification:

Answer 12

Examples: phosphorylation, adenylation

Not as common; important in some pathways, like chemotaxis.

Question 13

Allosteric Interactions:

Answer 13

More common
Can be positive or negative, effect rate or substrate affinity
Binding of an effector to enzyme allosteric site
Not the same as competitive inhibition

Examples:
Biosynthesis- feedback common
Fueling- inhibition or activation dependent on allosteric effectors
Regulating RNAs

Question 14

Feedback inhibition:

Answer 14

Nearly all building blocks control their own synthesis
by acting as negative allosteric effectors of the first
enzyme in their biosynthetic pathway

Question 15

Regulatory sRNAs:

Answer 15

Question 16

Regulatory Mechanisms of Protein Synthesis Diagram:

Answer 16

Question 17

Regulatory Mechanisms:
1. DNA topology

Answer 17

Prevent or promote Sigma/RNAP binding the promoter
Supercoiling or packaging

Question 18

Regulatory Mechanisms:
2. Promoter Recognition

Answer 18

Interfere with promoter recognition.
Alternative sigma factors that direct RNAP to certain genes in the chromosome
Different Sigma factors expressed under different conditions.

Question 19

Regulatory Mechanisms:
3, 4, and 5: Transcriptional repression, activation, and enhancement

Answer 19

DNA control regions (like operators) are in, near, or far away from promoters.
Regulatory proteins bind control regions.

Question 20

Enhancers:

Answer 20

Long distance control DNA sequence, bending of DNA- enhancer-binding proteins.

Question 21

Activators:

Answer 21

Positive regulator (protein)- increase reaction.

Question 22

Repressors:

Answer 22

negative regulator (protein), decrease reaction.

Question 23

Where are most protein coding genes?

Answer 23

In operons.

Question 24

Most protein regulation is based on what?

Answer 24

Operon regulation.

Question 25

What is an operon?

Answer 25

Group of co-localized genes (cistronic), same promoter, same transcript (mRNA). -Polycistronic

Question 26

What are the five parts of the Lac operon?

Answer 26

1. Promoter 2. Genes 3. Transcription terminator 4. Operator 5. Regulatory gene

Question 27

What are the three things the lac operon has taught us?

Answer 27

1. Initiation of transcription from the promoter of an operon can be a site of regulation 2. Initiation of transcription can be controlled by allosteric proteins 3. Increase in the expression of an operon can be triggered by relief of a negative control

Question 28

Transcription termination: Attenuation

Answer 28

Transcription prevented, because translation can occur. Prevents cell from making tryptophan if trp is present. High trp in cell, ribosome translation moves through trp codons in leader sequence (stem loop transcription terminator) Low trp in cell, ribosome stalls on trp codons- different stem-loop, allows reaction.

Question 29

sRNAs: Some RNAs are regulatory, what do they do?

Answer 29

* Mimic Open Complex and bind RNAP-Sigma70 holoenzyme * Binds to Promoter DNA * Termination loop formation on mRNA that stops RNAP elongation

Question 30

mRNA stability:

Answer 30

Some mRNAs have a shorter or longer life span.

Question 31

What does sRNA bind to and do?

Answer 31

Bind and trigger degradation of target mRNA molecules

Question 32

Translational control:

Answer 32

Regulation of initiation of translation. Too much protein present in cell- will not be translated. Binding to mRNA- sRNA, metabolites, or r-proteins.

Question 33

Proteolysis:

Answer 33

Degradation of protein following translation. -regulated often for regulatory proteins (like Sigma factors)

Question 34

Regulons:

Answer 34

Frequently; multiple operons, simultaneously regulated by same proteins

Question 35

Modulons:

Answer 35

Group of regulons.

Question 36

What are the two system types of modulons?

Answer 36

* Catabolite Repression System * Stringent Response System

Question 37

When is glucose used in catabolite repression?

Answer 37

First, it's a better energy source.

Question 38

When glucose is gone, what happens?

Answer 38

When gone: increases frequency of transcription initiation for operons that control expression of genes involved in catabolism of other substrates

Question 39

What is the stringent response system a response to?

Answer 39

Starvation.

Question 40

Why regulate both protein activity and amounts?

Answer 40

* Save energy * Fast response * Metabolic coordination