Download Freeman 1e: How we got there

CHAPTER 8
Metabolic Respiration
Overview of Regulation
• Most genes encode proteins, and most
proteins are enzymes. The expression of
such a gene can be regulated by controlling
the activity of the enzyme or controlling the
amount of enzyme produced.
An Overview of Gene Regulation
Regulation of Enzyme Activity
Noncovalent Enzyme Inhibition
• Many metabolic reactions can be regulated
through control of the activities of the
enzymes that catalyze them.
• An important type of regulation of enzyme
activity is feedback inhibition (Figure 8.2),
in which the final product of a biosynthetic
pathway inhibits the first enzyme unique to
that pathway.
Feedback
Inhibition
• An allosteric enzyme has two binding sites,
the active site, where the substrate binds, and
the allosteric site, where the inhibitor (called
an effector) binds reversibly (Figure 8.3).
• Some biosynthetic pathways under feedback
inhibition employ isoenzymes, different
proteins that catalyze the same reaction but
are subject to different regulatory controls
(Figure 8.5).
Isoenzyme and feedback inhibition
3-deoxy-D-arabinoheptulosonate 7phosphate
Covalent Modification of
Enzymes
• Covalent modification is a regulatory
mechanism for changing the activity of an
enzyme. Enzymes regulated in this way can
be reversibly modified. One type of
modification is adenylylation (the addition of
AMP) (Figure 8.6).
•Others are phosphorylation and methylations
Regulation of glutamine synthetase by adenylation
1. GS inhibition by several a. a. and compounds involved in nucleotide metabolism
2. GS (12 identical subunits) is also inhibited by covalent modification adenylation
Nitrogen rich medium
Nitrogen poor medium
(Lot of glutamine available)
• Protein splicing (Figure 8.7) is a form of
posttranslational modification.
Topoisomerase II (GyrA)
in Mycobacterium leprae
(Lyprosae disease)
DNA-Binding Proteins and
Regulation of Transcription by
Negative And Positive Control
• Certain proteins can bind to DNA because of
interactions between specific domains of the
proteins and specific regions of the DNA
molecule (Figure 8.8).
DNA Binding Proteins
homodimers
• In most cases, the interactions are sequencespecific. Proteins that bind to nucleic acid
may be enzymes that use nucleic acid as
substrates, or they may be regulatory proteins
that affect gene expression.
• Several classes of protein domains are
critical for proper binding of these proteins to
DNA. One of these is called the helix-turnhelix motif (Figure 8.9).
Lac and trp repressors and lambda repressor (>250)
Cysteine (C) and histidine (H)
• Another domain is the zinc finger, a protein
that binds a zinc ion (eukaryotes).
Negative Control of
Transcription: Repression and
Induction
• The amount of an enzyme in the cell can be
controlled by decreasing (repression, Figures
8.11, 8.13) or increasing (induction, Figure
8.12) the amount of mRNA that encodes the
enzyme.
Expression of arginine biosynthetic pathway (Operon)
(Arginine)
• This transcriptional regulation involves
allosteric regulatory proteins that bind to
DNA. For negative control of transcription,
the regulatory molecule is called a repressor
protein and it functions by inhibiting mRNA
synthesis.
Positive Control of Transcription
• Positive control of transcription is
implemented by regulators called activator
proteins. They bind to activator-binding sites
on the DNA and stimulate transcription. As in
repressors, activator protein activity is
modified by effectors.
• For positive control of enzyme induction,
the effector promotes the binding of the
activator protein and thus stimulates
transcription (Figures 8.14, 8.15).
Induction of lac operon (negative regulation)
(beta galactosidase)
Maltose operon regulation (positive)
(Absence of inducer - maltose)
(maltose)
Global Regulatory
Mechanisms
Global Control and the lac
Operon
• Global control systems regulate the
expression of many genes simultaneously.
Catabolite repression is a global control
system, and it helps cells make the most
efficient use of carbon sources.
• The lac operon is under the control of
catabolite repression as well as its own
specific negative regulatory system (Figure
8.20).
cAMP and CAP(catabolite activator protein)
The Stringent Response
• The stringent response (Figure 8.21) is a
global control mechanism triggered by amino
acid starvation.
•The alarmones ppGpp and pppGpp are
produced by RelA, a protein that monitors
ribosome activity.
ppGpp
• The stringent response achieves balance
within the cell between protein production and
protein requirements.
Other Global Control
Networks
• Cells can control several regulons by
employing alternative sigma factors.
Alternative signal factors in Escherichia coli
are shown in Table 8.2.
• These recognize only certain promoters and
thus allow transcription of a select category of
genes. Other global signals include cold and
heat shock proteins that function to help the
cell overcome temperature stress.
• Table 8.1 shows examples of global control
systems known in Escherichia coli.
Quorum Sensing
• Quorum sensing (Figure 8.22) allows cells
to survey their environment for cells of their
own kind and involves the sharing of specific
small molecules. Once a sufficient
concentration of the signaling molecule is
present, specific gene expression is triggered.
Other Mechanisms of
Regulation
Attenuation
• Attenuation is a mechanism whereby gene
expression (typically at the level of
transcription) is controlled after initiation of
RNA synthesis (Figure 8.25).
• Attenuation mechanisms involve a coupling
of transcription and translation and can
therefore occur only in prokaryotes.
Signal Transduction and TwoComponent Regulatory
Systems
• Signal transduction systems transmit
environmental signals to the cell.
• In prokaryotes, signal transduction typically
involves two-component regulatory systems
(Figure 8.26), which include a membraneintegrated sensor kinase protein and a
cytoplasmic response regulator protein.
•The activity of the response regulator
depends on its state of phosphorylation.
• Table 8.3 shows examples of twocomponent regulatory systems that regulate
transcription in Escherichia coli.
Regulation of Chemotaxis
• Chemotaxis is under complex regulation
involving signal transduction in which
regulation occurs in the activity of the
proteins involved rather than in their
synthesis (Figure 8.27).
MCP= methyl accepting chemotaxis proteins
• Adaptation by methylation allows the system
to reset itself to the continued presence of a
signal.
RNA Regulation and
Riboswitches
• RNA regulation is a rapidly expanding area
in both prokaryotic and eukaryotic molecular
biology.
• In Escherichia coli, for example, a number
of small RNAs (sRNAs) have been found to
regulate various aspects of cell physiology by
binding to other RNAs or even to small
molecules.
• One mechanisms for sRNA activity is found
in the signal recognition particle. A second
mechanism is the binding of the sRNA to an
mRNA by complementary base pairing
(Figure 8.28a).
• A unique form of small RNAs are the
riboswitches. These are mRNAs that contain
sequences upstream of the coding sequences
that can bind small molecules (Figure 8.28b).
Metabolite binding effects secondary
structure of RNA