Cellular Control
Mutations and their Effects
Protein Synthesis Recap
Transcription
The DNA is too large to exit the nuclear pore.
The double helix untwists, revealing a coding and a template strand
The enzyme helicase breaks the hydrogen bonds between complementary bases which ‘unzips’ the DNA.
Complementary bases are exposed.
Activated free nucleotides pair up with the exposed template strand.
RNA polymerase forms phosphodiester bonds between adjacent nucleotides to seal the backbone (working 3’ to 5’), allowing hydrogen bonds to form between complementary bases.
This continues until an exact replica is formed. mRNA then exits the nucleus by the nuclear pore and the DNA helix reforms.
Translation
mRNA enters the groove between the two subunits of a ribosome.
The ribosome is large enough for two mRNA codons to be side by side.
A tRNA molecule with an anticodon complementary to the mRNA codon lines up with the mRNA strand
Hydrogen bonds form between the mRNA strand and the anticodon of the tRNA
A second tRNA bonds to the next codon on the mRNA. rRNA catalyses the formation of a peptide bond between the two neighbouring amino acids.
The ribosome moves along one codon at a time along the mRNA molecule, to allow the next tRNA to bind until it reaches the stop codon
Defintions
Mutation
A random change in the sequence of, or arrangement of, the genetic material in a cell.
Chromosomal mutation
A random change to parts of, or whole, chromosomes.
DNA nucleotide mutation
A random change to genes due to changes in nucleotide base sequences
Types of Mutations
Point Mutation
Where one nucleotide base is replaced by another.
Insertion Mutation
Where one or more nucleotide bases are inserted causing a frame shift.
Deletion Mutation
Where on or more nucleotide bases are deleted causing a frame shift.
Mutation Generalised
Silent Mutation
No effect on the phenotype.
Nonsense Mutation
Truncated polypeptide as a stop codon is formed.
Missense Mutation
A different polypeptide is formed.
Effects of Mutations
No effect
As a normal functioning protein is synthesised. This may be due to coding for the SAME amino acid, or for an amino acid with an R group with similar properties.
Damaging
Due to a change of the primary structure, the normal functioning of the protein is affected eg cystic fibrosis; non-functioning ion channel, sickle cell anaemia, Huntington’s disease
Beneficial
Due to a change in the primary structure, the normal functioning of the protein is affected in a beneficial way eg changes to a human plasma membrane protein that prevents binding of the HIV virus and subsequent infection.
Chromosal Mutuation
Translocation
A section of one chromosome breaks off and joins another non-homologous chromosome.
Inversion
A section of a chromosome breaks off, is reversed, and then joins back on the same chromosome.
A section of chromosome breaks off and is lost within the cell.
Mutation Causes
Mutations can occur spontaneously during DNA replication, but the rate of mutation is increased by ‘mutagens’; chemical, physical or biological agents that cause mutations.
Regulation of Gene Expression
Why do genes need to be regulated?
Some proteins are needed all of the time and are produced at a fairly constant rate by housekeeping genes.
Some proteins are only needed by certain cells, under certain environmental conditions, and are not produced at a constant rate
What the Stages?
Gene Regulation
(Pre-) transcriptional regulation - genes made inaccessible.
Transcriptional regulation - genes turned on or off.
Post-transcriptional regulation - mRNA modified.
Translational regulation - translation stopped or started.
Post-translational regulation - protein modification.
Pre Transcription
For the vast majority of genes, gene expression should only take place during a proportion of interphase. The cell therefore must ensure that genes cannot be accessed at other times.
DNA is organised into a chromatin complex made up of DNA tightly wound around histone proteins.
DNA supercoils during prophase leading to viable chromosome structures. This change is called chromatin remodelling. The production of heterochromatin during supercoiling prevents gene expression as the tight structure prevents access of RNA polymerase
The proteins that DNA is coiled around are called histones. This coiling occurs because DNA is negatively charged and histones are positively charged. Histone modification is the addition of molecules to the histone that results in a charge shift (eg acetyl group make histone more negative). Histone modification can lead to tighter or looser coiling which affects the accessibility of the genes
Transcriptional
Directly before a gene on the DNA, there is a region called the promoter; RNA polymerase binds to the promoter to start transcription.
Transcription factors are proteins that either help RNA polymerase to bind (‘activators’), or stop RNA polymerase from binding (‘repressors’); thereby switching gene expression on/off.
Post Transcription
In order to survive the journey through the cytoplasm to the ribosome (and prevent being broken down) the mRNA must first be processed.
The introns (non-coding sections of mRNA) are spliced out of the primary mRNA and the exons are joined together. Different exons may be joined together to form different proteins (‘alternative splicing’).
In order to survive the journey through the cytoplasm to the ribosome (and prevent being broken down) the mRNA must first be processed.
In order to survive the journey through the cytoplasm to the ribosome (and prevent being broken down) the mRNA must first be processed.
he spliced mRNA has a cap and a tail added to it, to stabilize it and prevent it from being broken down, making mature mRNA.
During RNA processing, RNA editing can occur in which base additions, deletions or substitutions can be made.
RNA editing has a similar effect to a mutation in that the resulting protein will be different, however it is not called a mutation as it is not random (important distinction)!
Translational
An inhibitory protein may bind to the mRNA preventing it from binding to the ribosome; preventing translation.
The production of initiation factors may aid the binding of the mRNA to the ribosome. Initiation factors can be important in regulating when the mRNA is translated.
Protein kinases are enzymes that catalyse the addition of a phosphate group to the protein. Phosphorylation of the protein change the bonding and thus the tertiary structure of the protein. This process is often used to activate the protein; eg many enzymes are phosphorylated to activate them.
Post Translational
Addition of non-protein groups (e.g. carbohydrates or lipids) Modification of amino acids and therefore bonds within the protein eg adding disulphide bridges. Folding or shortening of the protein Activation of the protein eg an enzyme, by cyclic AMP (cAMP) by altering the protein’s tertiary structure. All of these processes lead to shape changes in the protein thus changing the protein's function.
Body Plans and the Homeobox
Transcriptional Level Control
Lac Operon
Development of Organisms
Living organisms come in a variety of shape and sizes. In any multicellular organism, growth and development is controlled and coordinated so that cells, tissues and organs end up where they are meant to be. In order for a zygote to develop into a multicellular organism several processes are required include; cell division (mitosis) cell differentiation morphogenesis (the process that causes an organism to develop its shape).
Morphogenesis is the regulation of the pattern of development and follows a strict body plan. This is also controlled by regulating gene expression, so that specific genes are expressed at specific times.
Genes involved with development can be activated by other genes.
Directly before a gene on the DNA, there is a region called the promoter; RNA polymerase binds to the promoter to start transcription.
Transcription factors are proteins that either help RNA polymerase to bind (‘activators’), or stop RNA polymerase from binding (‘repressors’); thereby switching gene expression on/off.
In eukaryotic organisms the expression of certain genes can have consequence on the expression of other gene.
These genes are called homeobox/ Hox genes (in animals) and they can effectively switch other genes on and off.
Homeobox
The genes which control the body plan are called homeobox genes. Homeobox (Hox) genes are 180 base pairs long. They code for small protein transcription factors (60 amino acids long). Transcription factors bind to DNA allowing it to be transcribed and ‘switch on or off’ many genes in a cascade effect.
Homebox and Development
Homeobox genes code for transcription factors; that are involved with development of a body plan
A fly has a head section, thorax (three segments T1, T2 and T3) and abdomen.
Each of the thorax sections has a pair of legs; there is a pair of wings on T2; and a pair of balance organs on T3. Homeobox genes ensure that everything is in the correct place by controlling- 1)polarity of the body (front and back)
2)polarity of the segments (left and right)
3)development of individual segments (legs/ no legs)
Thalidomide
Explained
The situation is similar in humans where Hox A11 and Hox D11 switch on the genes for development of the forelimb.
It has been suggested that thalidomide may have switched off the homeobox genes for limb development.
This caused the birth defects typical of thalidomide use.
Thalidomide can certainly insert itself into DNA and inhibits production of new blood vessels in limb buds.
Defintions
Transcription factor
Proteins that affect the rate of transcription.
Homeobox Genes
Highly conserved genes responsible for the development of body plans.
Hox genes
Highly conserved genes responsible for the development of body plans
. Homeobox sequence
The part of the homeobox gene that codes for the homeodomain.
Homeodomain
Highly conserved sequence of amino acids found in all homeobox proteins; it binds to DNA to regulate transcription of developmental genes.
Developmental genes
Genes that control the growth and development of an organism.
Body Plans and Apoptosis
Low Power vs High power
Biological Drawings
Low power magnification :Shows the distribution of main tissues within an organ but does not show individual cells.
High power magnification:Show as much detail as the microscope will allow.
Necrosis Vs Apoptosis
Apoptosis
Necrosis
Programmed cell- meditated death that occurs after a multiple (50) mitotic divisions; “cell suicide”
Traumatic cell death due to invasion or damage from pathogens which releases hydrolytic enzymes; “cell murder”
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Process
Enzymes break down cell cytoskeleton
Cytoplasm becomes dense, with organelles tightly packed
Chromatin condenses and nuclear envelope breaks.
DNA and organelles breaks down
Blebs form in cell membrane
Cell breaks into vesicles which are phagocytosed
Why does this process need to occur?
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Allows digits to form (removing ‘webbing’).
Removes ineffective or harmful T lymphocytes as the immune system develops.
Tadpoles lose their tails by apoptosis when they turn into frogs.
Occurs when cells get too old (ageing).