10/16/24, 11:41 BCH 224-Introductory to Molecular
AM Biology
LECTURE MATERIALS
BCH 224: INTRODUCTORY MOLECULAR BIOLOGY (3 UNITS)
Gene Structure
Genes contain the information necessary for living cells to survive and
reproduce.
In most organisms, genes are made of DNA, where the particular DNA
sequence determines the function of the gene. A gene is transcribed (copied)
from DNA into RNA, which can either be non-coding (ncRNA) with a direct
function, or an intermediate messenger (mRNA) that is then translated into
protein. Each of these steps is controlled by specific sequence elements, or
regions, within the gene. Every gene, therefore, requires multiple sequence
elements to be functional. This includes the sequence that actually encodes
the functional protein or ncRNA, as well as multiple regulatory sequence
regions. These regions may be as short as a few base pairs, up to many
thousands of base pairs long. Much of gene structure is broadly similar
between eukaryotes and prokaryotes. These common elements largely result
from the shared ancestry of cellular life in organisms over 2 billion years
ago. Key differences in gene structure between eukaryotes and
prokaryotes reflect their divergent transcription and translation
machinery. Understanding gene structure is the foundation of
understanding gene annotation, expression, and function.
Common gene structure features
The structures of both eukaryotic and prokaryotic genes involve several
nested sequence elements. Each element has a specific function in the multi-
step process of gene expression. The sequences and lengths of these
elements vary, but the same general functions are present in most genes.
Although DNA is a double stranded molecule, typically only one of the
strands encodes information that the RNA polymerase reads to produce
protein-coding mRNA or non-coding RNA.
1
about:blan 1/
k 33
,10/16/24, 11:41 BCH 224-Introductory to Molecular
AM Biology
This 'sense' or 'coding' strand, runs in the 5' to 3' direction where the
numbers refer to the carbon atoms of the backbone's ribose sugar. The open
reading frame (ORF) of a gene is therefore usually represented as an arrow
indicating the direction in which the sense strand is read.
Regulatory sequences are located at the extremities of genes. These
sequence regions can either be next to the transcribed region (the promoter)
or separated by many kilobases (enhancers and silencers). The promoter is
located at the 5' end of the gene and is composed of a core promoter
sequence and a proximal promoter sequence. The core promoter marks the
start site for transcription by binding RNA polymerase and other proteins
necessary for copying DNA to RNA. The proximal promoter region binds
transcription factors that modify the affinity of the core promoter for RNA
polymerase.
Genes may be regulated by multiple enhancer and silencer sequences
that further modify the activity of promoters by binding activator or
repressor proteins. Enhancers
and silencers may be distantly located from the gene, many thousands of
base pairs away. The binding of different transcription factors, therefore,
regulates the rate of transcription initiation at different times and in
different cells.
Although all organisms use both transcriptional activators and
repressors, eukaryotic genes are said to be 'default off', whereas prokaryotic
genes are 'default on'. The core promoter of eukaryotic genes typically
requires additional activation by promoter elements for expression to occur.
The core promoter of prokaryotic genes, conversely, is sufficient for strong
expression and is regulated by repressors.
An additional layer of regulation occurs for protein coding genes after
the mRNA has been processed to prepare it for translation to protein. Only
the region between the start and stop codons encodes the final protein
product. The flanking untranslated regions (UTRs) contain further regulatory
sequences. The 3' UTR contains a terminator sequence, which marks the
endpoint for transcription and releases the RNA polymerase. The 5’ UTR
binds the ribosome, which translates the protein-coding region into a string
2
about:blan 2/
k 33
,10/16/24, 11:41 BCH 224-Introductory to Molecular
AM Biology
of amino acids that fold to form the final protein product. In the case of genes
for non- coding RNAs the RNA is not translated but instead folds to be
directly functional.
Eukaryotes
The structure of eukaryotic genes includes features not found in
prokaryotes (Figure 1). Most of these relate to post-transcriptional
modification of pre-mRNAs to produce mature mRNA ready for translation
into protein. Eukaryotic genes typically have more regulatory elements to
control gene expression compared to prokaryotes. This is particularly true in
multicellular eukaryotes, humans for example, where gene expression varies
widely among different tissues.
A key feature of the structure of eukaryotic genes is that their
transcripts are typically subdivided into exon and intron regions. Exon
regions are retained in the final mature mRNA molecule, while intron
regions are spliced out (excised) during post- transcriptional processing.
Indeed, the intron regions of a gene can be considerably longer than the
exon regions. Once spliced together, the exons form a single continuous
protein-coding regions, and the splice boundaries are not detectable.
Eukaryotic post- transcriptional processing also adds a 5' cap to the
start of the mRNA and a poly- adenosine tail to the end of the mRNA.
These additions stabilise the mRNA and direct its transport from the
nucleus to the cytoplasm, although neither of these features are directly
encoded in the structure of a gene.
3
about:blan 3/
k 33
, 10/16/24, 11:41 BCH 224-Introductory to Molecular
AM Biology
Figure 1: The structure of a eukaryotic protein-coding gene. Regulatory sequence controls
when and where expression occurs for the protein coding region (red). Promoter and
enhancer regions (yellow) regulate the transcription of the gene into a pre-mRNA which is
modified to remove introns (light grey) and add a 5' cap and poly-A tail (dark grey). The
mRNA 5' and 3' untranslated regions (blue) regulate translation into the final protein
product.
Prokaryotes
The overall organization of prokaryotic genes is markedly different from that
of the eukaryotes (Figure 2). The most obvious difference is that prokaryotic
ORFs are often
grouped into a polycistronic operon under the control of a shared set of
regulatory sequences. These ORFs are all transcribed onto the same mRNA
and so are co-regulated and often serve related functions. Each ORF
typically has its own ribosome binding site (RBS) so that ribosomes
simultaneously translate ORFs on the same mRNA. Some operons also
display translational coupling, where the translation rates of multiple ORFs
within an operon are linked. This can occur when the ribosome remains
attached at the end of an ORF and simply translocates along to the next
without the need for a new RBS. Translational coupling is also observed
when translation of an ORF affects the accessibility of the next RBS through
changes in RNA secondary structure. Having multiple ORFs on a single
mRNA is only possible in prokaryotes because their
4
about:blan 4/
k 33
AM Biology
LECTURE MATERIALS
BCH 224: INTRODUCTORY MOLECULAR BIOLOGY (3 UNITS)
Gene Structure
Genes contain the information necessary for living cells to survive and
reproduce.
In most organisms, genes are made of DNA, where the particular DNA
sequence determines the function of the gene. A gene is transcribed (copied)
from DNA into RNA, which can either be non-coding (ncRNA) with a direct
function, or an intermediate messenger (mRNA) that is then translated into
protein. Each of these steps is controlled by specific sequence elements, or
regions, within the gene. Every gene, therefore, requires multiple sequence
elements to be functional. This includes the sequence that actually encodes
the functional protein or ncRNA, as well as multiple regulatory sequence
regions. These regions may be as short as a few base pairs, up to many
thousands of base pairs long. Much of gene structure is broadly similar
between eukaryotes and prokaryotes. These common elements largely result
from the shared ancestry of cellular life in organisms over 2 billion years
ago. Key differences in gene structure between eukaryotes and
prokaryotes reflect their divergent transcription and translation
machinery. Understanding gene structure is the foundation of
understanding gene annotation, expression, and function.
Common gene structure features
The structures of both eukaryotic and prokaryotic genes involve several
nested sequence elements. Each element has a specific function in the multi-
step process of gene expression. The sequences and lengths of these
elements vary, but the same general functions are present in most genes.
Although DNA is a double stranded molecule, typically only one of the
strands encodes information that the RNA polymerase reads to produce
protein-coding mRNA or non-coding RNA.
1
about:blan 1/
k 33
,10/16/24, 11:41 BCH 224-Introductory to Molecular
AM Biology
This 'sense' or 'coding' strand, runs in the 5' to 3' direction where the
numbers refer to the carbon atoms of the backbone's ribose sugar. The open
reading frame (ORF) of a gene is therefore usually represented as an arrow
indicating the direction in which the sense strand is read.
Regulatory sequences are located at the extremities of genes. These
sequence regions can either be next to the transcribed region (the promoter)
or separated by many kilobases (enhancers and silencers). The promoter is
located at the 5' end of the gene and is composed of a core promoter
sequence and a proximal promoter sequence. The core promoter marks the
start site for transcription by binding RNA polymerase and other proteins
necessary for copying DNA to RNA. The proximal promoter region binds
transcription factors that modify the affinity of the core promoter for RNA
polymerase.
Genes may be regulated by multiple enhancer and silencer sequences
that further modify the activity of promoters by binding activator or
repressor proteins. Enhancers
and silencers may be distantly located from the gene, many thousands of
base pairs away. The binding of different transcription factors, therefore,
regulates the rate of transcription initiation at different times and in
different cells.
Although all organisms use both transcriptional activators and
repressors, eukaryotic genes are said to be 'default off', whereas prokaryotic
genes are 'default on'. The core promoter of eukaryotic genes typically
requires additional activation by promoter elements for expression to occur.
The core promoter of prokaryotic genes, conversely, is sufficient for strong
expression and is regulated by repressors.
An additional layer of regulation occurs for protein coding genes after
the mRNA has been processed to prepare it for translation to protein. Only
the region between the start and stop codons encodes the final protein
product. The flanking untranslated regions (UTRs) contain further regulatory
sequences. The 3' UTR contains a terminator sequence, which marks the
endpoint for transcription and releases the RNA polymerase. The 5’ UTR
binds the ribosome, which translates the protein-coding region into a string
2
about:blan 2/
k 33
,10/16/24, 11:41 BCH 224-Introductory to Molecular
AM Biology
of amino acids that fold to form the final protein product. In the case of genes
for non- coding RNAs the RNA is not translated but instead folds to be
directly functional.
Eukaryotes
The structure of eukaryotic genes includes features not found in
prokaryotes (Figure 1). Most of these relate to post-transcriptional
modification of pre-mRNAs to produce mature mRNA ready for translation
into protein. Eukaryotic genes typically have more regulatory elements to
control gene expression compared to prokaryotes. This is particularly true in
multicellular eukaryotes, humans for example, where gene expression varies
widely among different tissues.
A key feature of the structure of eukaryotic genes is that their
transcripts are typically subdivided into exon and intron regions. Exon
regions are retained in the final mature mRNA molecule, while intron
regions are spliced out (excised) during post- transcriptional processing.
Indeed, the intron regions of a gene can be considerably longer than the
exon regions. Once spliced together, the exons form a single continuous
protein-coding regions, and the splice boundaries are not detectable.
Eukaryotic post- transcriptional processing also adds a 5' cap to the
start of the mRNA and a poly- adenosine tail to the end of the mRNA.
These additions stabilise the mRNA and direct its transport from the
nucleus to the cytoplasm, although neither of these features are directly
encoded in the structure of a gene.
3
about:blan 3/
k 33
, 10/16/24, 11:41 BCH 224-Introductory to Molecular
AM Biology
Figure 1: The structure of a eukaryotic protein-coding gene. Regulatory sequence controls
when and where expression occurs for the protein coding region (red). Promoter and
enhancer regions (yellow) regulate the transcription of the gene into a pre-mRNA which is
modified to remove introns (light grey) and add a 5' cap and poly-A tail (dark grey). The
mRNA 5' and 3' untranslated regions (blue) regulate translation into the final protein
product.
Prokaryotes
The overall organization of prokaryotic genes is markedly different from that
of the eukaryotes (Figure 2). The most obvious difference is that prokaryotic
ORFs are often
grouped into a polycistronic operon under the control of a shared set of
regulatory sequences. These ORFs are all transcribed onto the same mRNA
and so are co-regulated and often serve related functions. Each ORF
typically has its own ribosome binding site (RBS) so that ribosomes
simultaneously translate ORFs on the same mRNA. Some operons also
display translational coupling, where the translation rates of multiple ORFs
within an operon are linked. This can occur when the ribosome remains
attached at the end of an ORF and simply translocates along to the next
without the need for a new RBS. Translational coupling is also observed
when translation of an ORF affects the accessibility of the next RBS through
changes in RNA secondary structure. Having multiple ORFs on a single
mRNA is only possible in prokaryotes because their
4
about:blan 4/
k 33
