CIS Biology Team – Gene Expression and Mutations
Mutations and Gene Expression
A mutation is a change in the DNA of a cell. It can happen in individual genes or
entire chromosomes.
A gene is a length of DNA that codes for a single protein.
Gene Mutations
Gene mutations usually occur during DNA replication. So before we learn about gene
mutation, we have to understand DNA replication.
DNA Replication (Detailed)
There are three main stages in DNA replication: initiation, elongation and
termination.
1) Initiation
In DNA replication, the double helix unwinds. Helicase is an enzyme that is used to
make the DNA wind, break the hydrogen bonds between the bases, and hold the
strands apart during replication. The separated strands of the DNA then act as
templates for the formation of new adjacent strands.
After helicase unwinds a replication fork is formed. Multiple replication forks along
the DNA molecule create replication bubbles.
2) Elongation
RNA primase, an enzyme, then adds a complementary RNA primer to the template
strand as a starting point for replication. An enzyme called DNA polymerase III then
reads this template strand in the 3’ to 5’ direction, whilst adding new nucleotides
opposite the strand in the 5’ to 3’ direction. This is because DNA polymerase III can
ONLY work in the 5’ to 3’ direction. The strand that is being synthesized in the
direction of the replication fork is known as the leading strand. The leading strand is
synthesized continuously as the DNA continues to unwind and the leading strand is
extended by DNA polymerase III.
Due to the structure of DNA, the new nucleotide strands can only fit the ‘unzipped’
or ‘unwound’ strands if they are anti-parallel to them (i.e. going in the opposite
direction).
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CIS Biology Team – Gene Expression and Mutations
This anti-parallel nature of DNA thereby allows replication to occur in TWO directions.
RNA polymerase adds another complementary RNA primer to the other template
strand, and allows the strand to replicate in the 5’ to 3’ direction AWAY from the
replication fork. This strand is called the lagging strand, and it consists of fragments
of DNA that are produced – Okazaki fragments. Because of these Okazaki fragments,
the lagging strand is said to be synthesized discontinuously.
3) Termination
DNA polymerase I (not III) first removes the RNA primers between the Okazaki
fragments and replaces them with DNA. Then an enzyme known as ligase joins the
segments together through phosphodiester bonds.
Each pair of new double strands winds up into a double helix. After the new DNA
helixes are formed, DNA polymerase III proofreads them. This enzyme also
condenses the sugar and phosphate groups of the new nucleotides.
To conclude, DNA replication is referred to as semi-conservative replication because
half the original molecule is kept the same.
Gene Mutations
Gene mutations occur when the wrong nucleotide is used while the DNA is
replicating, and this alters the entire sequence of bases in a gene. This means that
the gene could code for the wrong protein, and there are several ways in which this
can occur:
1. Duplication
In duplication, the nucleotide is inserted twice instead of once. The codons are
changed entirely and now code for a different protein
2. Deletion
A nucleotide is missed out, altering the entire base sequence.
3. Substitution/Missense Mutation
A different nucleotide is used. The codon in which the mutation occurs is
changed and it may code for a different amino acid. If it does, the structure of the
protein molecule will be different. However, as there are only 20 amino acids and
some amino acids have degenerate codes, (i.e. having more than one codon to
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CIS Biology Team – Gene Expression and Mutations
code for them), substitution may not always result in a gene mutation.
4. Nonsense Mutation
In this type of mutation the altered DNA sequence prematurely signals the cell to
stop building a protein. This type of mutation results in a shortened protein that
may or may not function.
5. Inversion
The sequence of bases in a codon is reversed. Inversion’s effects are similar to
substitution, because only one codon is affected and not necessarily the entire
protein structure.
6. Repeat expansion
Nucleotide repeats are short DNA sequences that are repeated a number of
times in a row. For example, a trinucleotide repeat is made up of 3-base-pair
sequences. A repeat expansion is a mutation that increases the number of times
that the short DNA sequence is repeated. This type of mutation can cause the
resulting protein to function improperly.
7. Frameshift Mutation
This type of mutation occurs when the addition or loss of DNA bases changes a
gene’s reading frame. Reading frames will be discussed later; however, the
reading frames of a gene are very important as a reading base basically dictates
the sequence of amino acids and thus the protein structure that the amino acids
code for.
Mutagens
External factors, or agents, that can cause gene mutations to occur are called
mutagens. These include:
1) Ionizing radiation (UV light, X-rays or gamma rays);
2) Chemicals e.g. mustard gas and nitrous oxide etc.
Benefits of Gene Mutations
Gene mutations can be advantageous to individual organisms; bacteria, for example,
can develop antibiotic resistance because of mutations. As a result of natural
selection, which will be covered later, their offspring will also become resistant as
well.
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CIS Biology Team – Gene Expression and Mutations
Adverse Gene Mutations
Most gene mutations are adverse and either cause the cell they develop in to die, or
divide in an uncontrolled way, thereby causing the development of tumors. This is
what happens when people get cancer; an initially cancerous cell formed by a gene
mutation is allowed to divide rapidly, eventually spreading to other organisms.
Chromosome Mutations
Chromosome mutations occur during cell division. To understand chromosome
mutations, we must understand cell division as well. However, to simplify the
processes for now, just bear in mind that cell division occurs in two ways. One way is
mitosis (in which two homologous pairs of chromosomes copy themselves, the cell
divides into two, and each new cell has a copy of each of the chromosomes). The
other method is meiosis (which occurs for gametes, the sex cells).
Chromosome mutations occur however when bits of chromosomes break off one
chromosome and attach to another, and usually result in the death of the cells
formed.
When chromosome mutations occur in the sex cells, however, this can result in the
new cells having more chromosomes than normal. One relatively common
chromosome mutation in ova (female sex cells) is when it contains two copies of
chromosome 21. The zygote that is produced after fertilization will contain three
copies of chromosome 21, and this results in Down’s syndrome.
Types of Chromosome Mutations
1. Deletion of Genes
During cell division genes that aren’t attached to the centromere become lost
forever.
2. Duplication of Genes
During cell division, genes from the homologous chromosome are copied and
inserted into the genetic sequence.
Gene Expression & Protein Synthesis
Before getting into gene expression and protein synthesis, we need to understand an
essential element of both processes: RNA.
Characteristics of RNA
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CIS Biology Team – Gene Expression and Mutations
1) Messenger RNA – mRNA
 Encodes amino acid sequence of a polypeptide.
2) Transfer RNA – tRNA
 Brings amino acids to ribosomes during translation.
 Translates three-base sequence (codon) into an amino acid
sequence.
 Has a cloverleaf shape.
 On one side, contains an ANTICODON, which is
complementary to the codon of mRNA.
 On the other side, contains a site where a particular amino
acid out of 20 can be joined.
3) Ribosomal RNA
 Makes ribosomes by working with proteins.
4) Small nuclear RNA – snRNA

With proteins, form complexes that are used in RNA
processing in eukaryotes.
Gene Expression
Gene expression is the process by which genes are used to produce functional RNA
and protein molecules in a cell. Gene expression includes a process called protein
synthesis, and protein synthesis occurs in two stages: transcription and translation.
Transcription
Transcription occurs in the nucleus. In this process, the gene is copied to produce an
RNA molecule with essentially the same sequence as the gene. Most human genes
are divided into exons and introns. Exons and introns refer to specific nucleotide base
sequences in the genetic code that are involved in producing proteins. Exons are
the DNA bases that are transcribed into mRNA and eventually code for amino
acids in the proteins. Introns are DNA bases, which are found between exons, but are
not transcribed because they are non-coding.
To take a slight detour from exons and introns, we must also examine the structure of
a gene itself. As you already know, a gene is a length of DNA coding for a single
protein. Besides having regions inside the gene where the gene codes for this single
protein, the gene also has regular regions known as promoters or promoter sites.
These promoters provide a position for about 50 different protein transcription
factors, to form a complex. The promoter region is also a binding site for RNA
polymerase, an enzyme which is required for forming the new mRNA strand.
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CIS Biology Team – Gene Expression and Mutations
RNA polymerase then works with the transcription factors to unwind the DNA helix.
The unwound DNA strands act as a template for the formation of a complementary
mRNA strand. As the RNA polymerase travels along the DNA strand, it
assembles ribonucleotides into a strand of RNA.
Each ribonucleotide is inserted into the growing RNA strand following the rules
of base pairing. Thus for each C encountered on the DNA strand, a G is inserted in
the RNA; for each G, a C; and for each T, an A. However, each A on the DNA guides
the insertion of uracil (U). There is no T in RNA.
Going all the way back to exons and introns, as only exons carry information required
for protein synthesis, the gene is processed by a process called RNA splicing to
remove intron sequences and generate a messenger RNA that only contains exons.
This ‘mature’ mRNA is then ready for translation.
Amino Acid Activation
The second step of protein synthesis is amino acid translation. This essentially means
that (the 20) amino acids available for protein synthesis are joined to the tRNA
through an enzyme. Amino acid activation occurs in the cytoplasm.
Translation
Translation is the final step of protein synthesis. In this step, the mRNA is read by the
ribosomes, which move along the mRNA’s nucleotides, reading one codon (a
three-base sequence) at a time.
At the same time, the codons of the mRNA are joined to the anti-codons of the tRNA
by temporary hydrogen bonds. The anti-codon of a tRNA is a sequence of 3 unpaired
nucleotides which can bind, following the rules of base pairing, to the
complementary triplet of nucleotides — the codon — in a messenger RNA (mRNA)
molecule. A reading frame is a way of breaking a sequence
of nucleotides in DNA or RNA into three letter codons which can be translated in
amino acids. A reading frame starts with a start codon and ends with one or
more stop codons. These start and stop codons exist in the RNA, and the start codon
is usually AUG is found at the beginning of all reading frames concerning proteins.
The stop codon basically signals the end of gene transcribing or the translation of
nucleotides into amino acids. There are several types of stop codons in RNA: UAG,
UAA and UGA, and for DNA: TAG, TAA and TGA.
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CIS Biology Team – Gene Expression and Mutations
The amino acids on the other end of the tRNA then form peptide linkages with the
other tRNA-amino acid complexes that have lined up opposite the mRNA. This results
in the formation of a polypeptide (a chain of amino acid residues), which are
essentially proteins!
Gene expression occurs differently for all human genes. Some are expressed in cells
all the time, or only in specific cell conditions, or at varying stages of development.
As genes are surrounded by DNA sequences that control their expression, these DNA
sequences allow proteins called transcription factors to bind to them. These
transcription factors, their availability and specific activities are what differentiate
one type of gene expression from another.
Bibliography
http://ghr.nlm.nih.gov/handbook/mutationsanddisorders/possiblemutations
http://genome.wellcome.ac.uk/doc_wtd020757.html
http://genome.wellcome.ac.uk/doc_wtd020755.html
http://www.mansfield.ohio-state.edu/~sabedon/biol1065.htm#start_codon
http://www.news-medical.net/health/What-is-Gene-Expression.aspx
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Translation.html
Gene Expression Control
http://staff.jccc.net/pdecell/expression/control.html#dna
Codons for RNA
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Translation.html
RNA splicing
http://en.wikipedia.org/wiki/RNA_splicing
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