Chapter 18: Control of Gene Expression
1. Gene Regulation
a. “Turning on or off” gene transcription in response to environmental changes, i.e.
to maintain HOMEOSTASIS
b. In unicellular or prokaryotic organisms, for metabolic efficiency “waste not
want not”
c. In multicellular organisms
i. Efficiency of metabolism in cell AND body as a whole
ii. Directs development, specialization
2. Levels of Gene Regulation
a. Transcriptional Control
i. Most common, in proakryotes and eukaryotes
ii. Most efficient – mRNA not synthesize if not needed
iii. Regulating promoter access to RNA polymerase
1. Regulates initiation of transcription
2. Building sites on DNA for regulatory proteins that either block
RNA polymerase (repressors) or stimulate RNA polymerase
binding (activators)
b. Post Transcriptional Control
i. Less common
ii. Occurs after mRNA is synthesized
iii. May involve translation or enzyme regulation
3. Role of Regulatory Proteins in Transcriptional Control
a. Special proteins that bind to outside double helix without unwinding it
b. Recognize specific sequences by inserting DNA-binding motifs intro the major
groove where the edges of the bases protrude
c. 4 Motifs
i. Helix-turn-helix motif
1. Keeping the shape bound; cannot unzip
ii. Homeodomain
iii. Zinc finger
iv. Leucine zipper
4. Prokaryotic Gene Regulation: Jacob Monod Operon Hypothesis
a. Based on studies of E. coli bacteria
b. Operon
i. Group of adjacent genes coding for a series of proteins (enzymes) with a
related function (biochemical pathway) in prokaryotes
ii. Genes are regulated and transcribed together
c. Two types of operons
i. Repressible operons
1. Control transcription of genes for enzymes needed in anabolic
reactions (synthesis of molecules)
2. Genes usually “on,” producing enzymes to synthesize end produce
(metabolite)
3. When enough end product, the genes turn “off” – transcription is
repressed
ii. Inducible operons
1. Control transcription of genes for enzymes needed in catabolic
reactions (breaking down molecules)
2. Genes usually “off” if no substrate available to breakdown
3. If substrate is available & needed, genes are turned “on” –
transcription is induced
d. Components of the Operon (DNA)
i. Structural genes – series of related genes, coding for proteins/enzymes
ii. Promoter site – binding site for RNA polymerase
iii. Operator site – binding site for regulatory protein = repressor
1. Usually within promoter site to block RNA polymerase
2. Repressor proteins mediate both repression and induction of
operons
3. Repressors are allosteric proteins with 2 binding sites
a. Binding site for operator site on DNA
b. Binding site for effector molecules/metabolites/signals that
change repressors configuration to bind or not to bind to
operator
4. Regulatory genes either produce active or inactive repressors
a. Active repressors bind to the operator and stop
transcription
b. Inactive repressors cannot bind to operator so
transcription occurs
e. Repressible Operon – trp* operon (example) – see handout #349
i. Regulator gene produces inactive repressor – cannot bind to operator
because of its configuration
ii. Genes for enzymes needed to synthesize trp are “on” – transcribed
iii. Repressible operons used for anabolic (synthesis) reactions
iv. Tryptophan* (amino acid) is synthesized for the cell
v. When enough tryptophan is synthesized it, it binds to inactive repressor,
changes its configuration, makes it “active”
vi. Active repressor binds to operator site
vii. RNA polymerase is blocked
viii. Operon genes are “off” – no transcription, no enzymes synthesized, no
tryptophan produced
ix. Presence of repressor on the operator is Negative Control
x. Also illustrates Negative Feedback Mechanism
1. What turns trp operon back on?
a. The lack of tryptophan in the cell
b. Cell removes tryptophan from binding site on repressor,
converting it back to its inactive form
f. Inducible Operon: lac* Operon (example) – see handout #351 and #353
i. Inducible operons control the synthesis of enzymes needed for catabolic
reactions
ii. Genes are transcribed “off” until there is a substrate
iii. lac operon controls the metabolism of *lactose into glucose and galactose
for energy BUT only if glucose not available & lactose is present
iv. Regulatory gene produces active repressor, binds to operator, “off”
v. When lactose is present, allolactose, metabolite of lactose, binds to
repressor as effector, changing its shape, releases it from operator, “on”
vi. Presence of repressor – Negative Control
vii. BUT, there is also a Positive Control
viii. To insure glucose is used when present & not lactose, another regulatory
protein is used, CAP = Catabolite Activator Protein
ix. CAP stimulates transcription in presence of cAMP, when glucose is not
available or low
x. cAMP increases when glucose is low because less ATP is made by
respiration
xi. cAMP-CAP complex binds to CAP site and allows RNA polymerase to
bind to transcribe enzymes needed to breakdown lactose
xii. If glucose is present, then no cAMP present, therefore, no cAMP-CAP
complex binds to CAP site and RNa polymerase does not bind to
promoter. If lactose is also present, no repressor BUT since no RNA
polymerase binds, OPERON is OFF, no transcription, no lactose
metabolism. This insures that ONLY glucose is used for energy, not
lactose! Efficiency!
5. Transcriptional Control in Eukaryotes
a. More complex than prokaryotes because genes are not grouped by function
within cell (No Operons!)
b. Gene regulation based on chromosome structure/condensation
i. Heterochromatin – highly condensed areas
ii. Additional histones block promoter sites from RNA polymerase
iii. Genes unexpressed in these area, ex: centromeres, Barr bodies, in
specialized cells certain genes
iv. Permanent
c. Use of methylation
i. Methyl groups (-CH3) added to cytosine during replication
ii. Stops transcription of genes permanently
d. “Control at a Distance” – Transcription Complex Mechanism
i. Many genes interact with one another requiring many more interacting
elements around promoter site
ii. Binding sites for regulatory proteins may not be adjacent to genes, ie
“distant sites” exerting control on transcription
iii. Transcription factors and formation of initiation complex – see
handout #356
1. Basal Transcription Factors
a. Necessary for binding of RNA pol II to promoter
b. Do not increase rate of transcription
c. TFIID – binds pol II to TATA box
2. Transcription associated factors, TAF, also needed for initiation
3. Each factor is a protein transcribed from other genes
iv. Activators and Enhancers
1. Activators – transcription factors/regulatory proteins that enhance
transcription
2. Enhancers – binding sites for activators “distant” from gene
3. DNA loops to bring activators to promoter site
v. Co-activators – transcription factors that mediate between activators and
basal factors – see handout #359
vi. Purpose: Greater regulation and control of gene expression
6. Post-Transcriptional Control in Eukaryotes – see handout #365
a. mRNA processing or alternate splicing (Chapter 15)
i. Different exons can be spliced together yielding different proteins from
same primary transcript*/gene in nucleus
ii. Antibodies and hormones
b. Transport of mRNA through nuclear membrane
i. Receptors on nuclear membrane pores detect if splicing is completed by
absence of spliceosomes
ii. If Poly-A tails not added, signals processing incomplete and mRNA not
permitted to pass
c. Selection of mRNA to be translated
i. Translation factors allow mRNA to attach to ribosome
ii. Repressor proteins prevent mRNA to attach to ribosome
d. Selectively Degrading mRNA Transcript
i. Endonucleases break down mRNA
ii. Specific sequence near poly-A tail signals how long the mRNA will last in
cell before poly-A tail is removed and mRNA degraded
e. Post-translational control
i. Phosphorylation of proteins – activates enzymes/proteins when
needed
f. Small RNA’s (sRNAs) – see handout #364
i. Short segments of RNA (21-28 nucleotides)
ii. Play major role in regulating gene expression by interacting directly with
primary gene transcripts. RECENT! RNA interference (RNAi)
iii. “Double stranded” RNA forms from areas of RNA which may not need to
be translated.
iv. Enzyme “dicer” recognizes double stranded RNA on the mRNA transcript
and cuts them making small RNA (sRNA)
v. sRNA’s regulated gene translation in three ways (see fig. 18.21, handout
#364)
1. miRNA – micro RNA, formed by dicer, binds to any mRNA
containing complementary sequences, blocking translation
2. siRNA – small interfering RNA, picked up by enzyme complex,
RISC (RNA-Induced Silencing Complex)
a. Used to degrade particular mRNA complementary to
siRNA
b. RNA interference
3. siRNA also influences how DNA is packaged into nucleosomes
and blocked from transcription – epigenetic change/regulation