Chapter 7
The cell types in a multicellular organism become different from one another because they synthesize
and accumulate different sets of RNA and protein molecules, this is done without altering the sequence
of their DNA.
External signals can cause a change in gene expression. Different cell types respond very differently to
the same extracellular signal.
A cell can control the proteins it makes by:
1. Controlling when and how often a given gene is transcribed (transcriptional control).
2. Controlling the splicing and processing of RNA transcripts (RNA processing control).
3. Selecting which completed mRNAs are exported from the nucleus to the cytosol and
determining where in the cytosol they are localized (RNA transport and localization control).
4. Selecting which mRNAs in the cytoplasm are translated by ribosomes (translational control).
5. Selectively destabilizing certain mRNA molecules in the cytoplasm (mRNA degradation
control).
6. Selectively activating, inactivating, degrading or localizing specific protein molecules after they
have been made (protein activity control).
1. Transcriptional control
Sequence-specific DNA-binding proteins
• Transcriptional control is based on a group of proteins called transcription regulators. These
proteins recognize specific sequences of DNA that are often called cis-regulatory sequences
(→ They must be on the same chromosome, in cis, to the genes they control).
• Transcription regulators bind to cis-regulatory sequences, this binding puts a series of
reactions into motion that ultimately specify which genes are to be transcribed and at what
rate.
Sequence of nucleotides in the DNA double helix
Transcription regulators must recognize short, specific cis-
regulatory sequences within the double helix. The edge of each
base pair presents a distinctive pattern of hydrogen-bond donors,
hydrogen-bond acceptors and hydrophobic patches in both the
major and minor grooves. The major groove is mainly used by
transcription regulators since it’s wider and displays more
molecular features than the minor groove.
Each transcription regulator makes a series of contacts with the
DNA, involving hydrogen bonds, ionic bonds, and hydrophobic
interactions. Each individual contact is weak, but the 20 or so
contacts that ar formed at the protien-DNA interface add together
so that the interaction is both highly specific and very strong.
Each example of protein-DNA recognition is unique in detail, however there are some similarities.
Many transcription regulators contain one or another of a small set of DNA-binding structural motifs.
These motifs generally use either alpha helices or beta sheets to bind to the major groove of DNA. The
amino acid side chains that extend from these protein motifs make the specific contacts with DNA.
1
,Common structural motifs in transcription regulators
Helix-turn-helix proteins
→ Constructed from two alpha helices connected by a short extended chain of amino acids, which
constitutes the ‘turn’. The two helices are held at a fixed angle, primarily through interactions between
the two helices. One of the helices is more C-terminal and is called the recognition helix because it fits
into the major groove of DNA.
Leucine zipper proteins
→ Two alpha helices, one from each monomer, are joined together to form a short
coiled-coil. These proteins bind DNA as dimers where the two long alpha helices are held
together by interactions between hydrophobic side chains (often on leucines) that extend
from one side of each helix. Just beyond the dimerization interface, the two alpha helices
separate from each other to form a Y-shaped structure, which allows their side chains to
contact the major groove of DNA.
Homeodomain proteins
→ In the image two different views of the structure are seen: (A) The
homeodomain is folded into three alpha helices, which are packed
tightly together by hydrophobic interactions. The part contain helices 2
and 3 closely resembles the helix-turn-helix motif. (B) The recognition
helix (helix 3, red) forms important contacts with the major groove of
DNA. The asparagine (Asn) of helix 3, for example, contacts an adenine.
A flexible arm attached to helix 1 forms contacts with nucleotide pairs
in the minor groove.
Beta sheet DNA recognition proteins
→ A two-stranded beta sheet, with amino acid side chains extending from
the sheet toward the DNA, reads the information on the surface of the
major groove. This beta sheet motif can be used to recognize many
different DNA sequences; the exact DNA sequence recognized depends on
the sequence of amino acids that make up the beta sheet.
Zinc finger proteins
→ Includes one or more zinc atoms as structural
components. The zinc atom holds an alpha helix and
a beta sheet together. The alpha helix of each finger
contacts the major groove of DNA, forming a nearly
continuous stretch of alpha helices along the groove.
The repetition of this basic structural unit creates a
strong and specific DNA-protein interaction. The
image on the most right shows three zinc fingers.
2
,Helix-loop-helix proteins
→ Consists of a short alpha helix connected by a loop to a second,
longer alpha helix. One helix folds back and parks against the other,
forming the dimerization surface. The two-helix structure binds to
both DNA and to the two-helix structure of a second protein to
create either a homodimer or heterodimer. Two alpha helices that
extend from the dimerization interface make specific contacts with
the major groove of DNA.
The affinity of a transcription regulator for DNA depends on how closely the DNA matches the optimal
sequence.
Transcription regulators bind cooperatively to DNA, so once a protein binds, more proteins start
binding. Whereas when no protein binds, then the chance of any protein binding is rare. So this means:
the cis-regulatory sequence is either nearly empty or nearly fully occupied and rarely something in
between.
Transcription regulators bind to DNA in nucleosomes with lower affinity than they do to naked DNA.
There are two reasons for this difference:
1. The surface of the cis-regulatory sequence recognized by the transcription regulator may be facing
inward on the nucleosome, toward the histone core, and therefore not be readily available to the
regulatory protein.
2. Even if the face of the cis-regulatory sequence is exposed on the outside of the nucleosome, many
transcription regulators subtly alter the conformation of the DNA when they bind, and these
changes are generally opposed by the tight wrapping of the DNA around the histone core. For
example, many transcription regulators induce a bend or kink in the DNA when they bind.
Transcription regulators can switch genes on and off (prokaryotes)
In bacteria, five genes can code for enzymes that manufacture the amino acid tryptophan. These genes
are arranged in a cluster on the chromosome and are transcribed from a single promotor as one long
mRNA molecule (= operons). These operons are rare in eukaryotes, in eukaryotes genes are typically
transcribed and regulated individually. The working of the operon depends on the surroundings:
Low tryptophan levels → operon is transcribed → mRNA translated to produce a full set of biosynthetic
enzymes → synthetization of tryptophan from much simpler molecules. However, when the tryptophan
levels are high, then the enzymes get shut down.
This mechanism works as follows: Within the operon’s promotor is a tryptophan operator (=the cis-
regulatory sequence) that is recognized by a tryptophan repressor (=the transcription regulator) that
can only bind to DNA if it has also bound
several molecules of tryptophan, since the
binding of tryptophan causes a subtle
change in its 3D structure. When this
regulator binds to the sequence, the access
of RNA polymerase to the promotor gets
blocked, which prevents transcription of
the operon and thus production of the
tryptophan-producing enzymes. If the
tryptophan levels drop, then the
tryptophan dissociate from the repressor,
so: Low tryptophan levels → Tryptophan dissociates from the repressor → Repressor no longer able to
bind to DNA → The tryptophan operon is transcribed.
3
, A small amount of the repressor protein is always being made so that the bacterium can respond
rapidly to a rise or fall in tryptophan concentration.
Some bacteria contain transcriptional activator proteins that
activate genes instead of repressing them like transcriptional
repressor proteins, such as tryptophan repressors, do. The
transcriptional activator proteins work on promotors that are
only marginally able to bind and position RNA polymerase on
their own, however an activator protein can bind to nearby cis-
regulatory sequences and help attract the RNA polymerase to
the promotor to help it initiate transcription, making the
promotor fully functional. Activator proteins often have to
interact with a second molecule to be able to bind DNA (e.g.
activator protein CAP has to bind cAMP before it can bind to
DNA).
Sometimes more regulators are needed to control one operon.
The Lac operon is controlled by both the Lac repressor and the
CAP activator. The Lac operon encodes proteins required to
import and digest the disaccharide lactose. In the absence of
glucose, the bacterium makes cAMP, which activates CAP to switch on genes
that allow the cell to utilize alternative sources of carbon, including lactose.
If the lactose levels are also low, then inducing expression of the Lac operon
would be a waste. So in absence of lactose, the lactose repressor shuts down
the Lac operon.
The cis-regulatory sequences that control the transcription of a gene can be
located hundreds and even thousands nucleotide pairs from the bacterial
genes control. DNA looping allows a protein bound at a distant site along the
DNA to contact RNA polymerase.
Complex switches control gene transcription (eukaryotes)
In eukaryotes, transcription regulation involves many more proteins and much longer stretches of
DNA. Eukaryotes also contain activators and repressors, just like prokaryotes. However, there are some
differences. (1) The interactions between DNA-bound transcription regulators and RNA polymerase is
indirect, many intermediate proteins, including the histones, act between the DNA-bound
transcription regulator and RNA polymerase. (2) It is common in multicellular organisms to have
dozens of transcription regulators control a single gene, with cis-regulatory sequences spread over
tens of thousands of nucleotide pairs (DNA looping required). (3) Transcription initiation must have
extra levels of control as nearly all DNA in eukaryotes is compacted by nucleosomes and higher-order
structures.
Gene control region
= The whole expanse of DNA involved in regulating and initiating transcription of a eukaryotic gene.
This includes the promotor, where the general transcription factors and the polymerase assemble and
all of the cis-regulatory sequences to which transcription regulators bind to control the rate of the
assembly processes at the promotor. Most of the DNA in gene control region is packaged into
nucleosomes and higher-order forms of chromatin, thereby compacting its overall length and altering
its properties.
As opposed to prokaryotes, eukaryotes rarely have operons and instead, each gene is regulated
individually.
4
The cell types in a multicellular organism become different from one another because they synthesize
and accumulate different sets of RNA and protein molecules, this is done without altering the sequence
of their DNA.
External signals can cause a change in gene expression. Different cell types respond very differently to
the same extracellular signal.
A cell can control the proteins it makes by:
1. Controlling when and how often a given gene is transcribed (transcriptional control).
2. Controlling the splicing and processing of RNA transcripts (RNA processing control).
3. Selecting which completed mRNAs are exported from the nucleus to the cytosol and
determining where in the cytosol they are localized (RNA transport and localization control).
4. Selecting which mRNAs in the cytoplasm are translated by ribosomes (translational control).
5. Selectively destabilizing certain mRNA molecules in the cytoplasm (mRNA degradation
control).
6. Selectively activating, inactivating, degrading or localizing specific protein molecules after they
have been made (protein activity control).
1. Transcriptional control
Sequence-specific DNA-binding proteins
• Transcriptional control is based on a group of proteins called transcription regulators. These
proteins recognize specific sequences of DNA that are often called cis-regulatory sequences
(→ They must be on the same chromosome, in cis, to the genes they control).
• Transcription regulators bind to cis-regulatory sequences, this binding puts a series of
reactions into motion that ultimately specify which genes are to be transcribed and at what
rate.
Sequence of nucleotides in the DNA double helix
Transcription regulators must recognize short, specific cis-
regulatory sequences within the double helix. The edge of each
base pair presents a distinctive pattern of hydrogen-bond donors,
hydrogen-bond acceptors and hydrophobic patches in both the
major and minor grooves. The major groove is mainly used by
transcription regulators since it’s wider and displays more
molecular features than the minor groove.
Each transcription regulator makes a series of contacts with the
DNA, involving hydrogen bonds, ionic bonds, and hydrophobic
interactions. Each individual contact is weak, but the 20 or so
contacts that ar formed at the protien-DNA interface add together
so that the interaction is both highly specific and very strong.
Each example of protein-DNA recognition is unique in detail, however there are some similarities.
Many transcription regulators contain one or another of a small set of DNA-binding structural motifs.
These motifs generally use either alpha helices or beta sheets to bind to the major groove of DNA. The
amino acid side chains that extend from these protein motifs make the specific contacts with DNA.
1
,Common structural motifs in transcription regulators
Helix-turn-helix proteins
→ Constructed from two alpha helices connected by a short extended chain of amino acids, which
constitutes the ‘turn’. The two helices are held at a fixed angle, primarily through interactions between
the two helices. One of the helices is more C-terminal and is called the recognition helix because it fits
into the major groove of DNA.
Leucine zipper proteins
→ Two alpha helices, one from each monomer, are joined together to form a short
coiled-coil. These proteins bind DNA as dimers where the two long alpha helices are held
together by interactions between hydrophobic side chains (often on leucines) that extend
from one side of each helix. Just beyond the dimerization interface, the two alpha helices
separate from each other to form a Y-shaped structure, which allows their side chains to
contact the major groove of DNA.
Homeodomain proteins
→ In the image two different views of the structure are seen: (A) The
homeodomain is folded into three alpha helices, which are packed
tightly together by hydrophobic interactions. The part contain helices 2
and 3 closely resembles the helix-turn-helix motif. (B) The recognition
helix (helix 3, red) forms important contacts with the major groove of
DNA. The asparagine (Asn) of helix 3, for example, contacts an adenine.
A flexible arm attached to helix 1 forms contacts with nucleotide pairs
in the minor groove.
Beta sheet DNA recognition proteins
→ A two-stranded beta sheet, with amino acid side chains extending from
the sheet toward the DNA, reads the information on the surface of the
major groove. This beta sheet motif can be used to recognize many
different DNA sequences; the exact DNA sequence recognized depends on
the sequence of amino acids that make up the beta sheet.
Zinc finger proteins
→ Includes one or more zinc atoms as structural
components. The zinc atom holds an alpha helix and
a beta sheet together. The alpha helix of each finger
contacts the major groove of DNA, forming a nearly
continuous stretch of alpha helices along the groove.
The repetition of this basic structural unit creates a
strong and specific DNA-protein interaction. The
image on the most right shows three zinc fingers.
2
,Helix-loop-helix proteins
→ Consists of a short alpha helix connected by a loop to a second,
longer alpha helix. One helix folds back and parks against the other,
forming the dimerization surface. The two-helix structure binds to
both DNA and to the two-helix structure of a second protein to
create either a homodimer or heterodimer. Two alpha helices that
extend from the dimerization interface make specific contacts with
the major groove of DNA.
The affinity of a transcription regulator for DNA depends on how closely the DNA matches the optimal
sequence.
Transcription regulators bind cooperatively to DNA, so once a protein binds, more proteins start
binding. Whereas when no protein binds, then the chance of any protein binding is rare. So this means:
the cis-regulatory sequence is either nearly empty or nearly fully occupied and rarely something in
between.
Transcription regulators bind to DNA in nucleosomes with lower affinity than they do to naked DNA.
There are two reasons for this difference:
1. The surface of the cis-regulatory sequence recognized by the transcription regulator may be facing
inward on the nucleosome, toward the histone core, and therefore not be readily available to the
regulatory protein.
2. Even if the face of the cis-regulatory sequence is exposed on the outside of the nucleosome, many
transcription regulators subtly alter the conformation of the DNA when they bind, and these
changes are generally opposed by the tight wrapping of the DNA around the histone core. For
example, many transcription regulators induce a bend or kink in the DNA when they bind.
Transcription regulators can switch genes on and off (prokaryotes)
In bacteria, five genes can code for enzymes that manufacture the amino acid tryptophan. These genes
are arranged in a cluster on the chromosome and are transcribed from a single promotor as one long
mRNA molecule (= operons). These operons are rare in eukaryotes, in eukaryotes genes are typically
transcribed and regulated individually. The working of the operon depends on the surroundings:
Low tryptophan levels → operon is transcribed → mRNA translated to produce a full set of biosynthetic
enzymes → synthetization of tryptophan from much simpler molecules. However, when the tryptophan
levels are high, then the enzymes get shut down.
This mechanism works as follows: Within the operon’s promotor is a tryptophan operator (=the cis-
regulatory sequence) that is recognized by a tryptophan repressor (=the transcription regulator) that
can only bind to DNA if it has also bound
several molecules of tryptophan, since the
binding of tryptophan causes a subtle
change in its 3D structure. When this
regulator binds to the sequence, the access
of RNA polymerase to the promotor gets
blocked, which prevents transcription of
the operon and thus production of the
tryptophan-producing enzymes. If the
tryptophan levels drop, then the
tryptophan dissociate from the repressor,
so: Low tryptophan levels → Tryptophan dissociates from the repressor → Repressor no longer able to
bind to DNA → The tryptophan operon is transcribed.
3
, A small amount of the repressor protein is always being made so that the bacterium can respond
rapidly to a rise or fall in tryptophan concentration.
Some bacteria contain transcriptional activator proteins that
activate genes instead of repressing them like transcriptional
repressor proteins, such as tryptophan repressors, do. The
transcriptional activator proteins work on promotors that are
only marginally able to bind and position RNA polymerase on
their own, however an activator protein can bind to nearby cis-
regulatory sequences and help attract the RNA polymerase to
the promotor to help it initiate transcription, making the
promotor fully functional. Activator proteins often have to
interact with a second molecule to be able to bind DNA (e.g.
activator protein CAP has to bind cAMP before it can bind to
DNA).
Sometimes more regulators are needed to control one operon.
The Lac operon is controlled by both the Lac repressor and the
CAP activator. The Lac operon encodes proteins required to
import and digest the disaccharide lactose. In the absence of
glucose, the bacterium makes cAMP, which activates CAP to switch on genes
that allow the cell to utilize alternative sources of carbon, including lactose.
If the lactose levels are also low, then inducing expression of the Lac operon
would be a waste. So in absence of lactose, the lactose repressor shuts down
the Lac operon.
The cis-regulatory sequences that control the transcription of a gene can be
located hundreds and even thousands nucleotide pairs from the bacterial
genes control. DNA looping allows a protein bound at a distant site along the
DNA to contact RNA polymerase.
Complex switches control gene transcription (eukaryotes)
In eukaryotes, transcription regulation involves many more proteins and much longer stretches of
DNA. Eukaryotes also contain activators and repressors, just like prokaryotes. However, there are some
differences. (1) The interactions between DNA-bound transcription regulators and RNA polymerase is
indirect, many intermediate proteins, including the histones, act between the DNA-bound
transcription regulator and RNA polymerase. (2) It is common in multicellular organisms to have
dozens of transcription regulators control a single gene, with cis-regulatory sequences spread over
tens of thousands of nucleotide pairs (DNA looping required). (3) Transcription initiation must have
extra levels of control as nearly all DNA in eukaryotes is compacted by nucleosomes and higher-order
structures.
Gene control region
= The whole expanse of DNA involved in regulating and initiating transcription of a eukaryotic gene.
This includes the promotor, where the general transcription factors and the polymerase assemble and
all of the cis-regulatory sequences to which transcription regulators bind to control the rate of the
assembly processes at the promotor. Most of the DNA in gene control region is packaged into
nucleosomes and higher-order forms of chromatin, thereby compacting its overall length and altering
its properties.
As opposed to prokaryotes, eukaryotes rarely have operons and instead, each gene is regulated
individually.
4
