1. - Genetic control of protein structure and function - Control of gene expression

2. DNA DNA is made of nucleotides which contain a deoxyribose sugar, a phosphate and a base. DNA nucleotides join together to form polynucleotide strands. Two polynucleotide strands join together by hydrogen bonds between the bases and coil to form the DNA double-helix. DNA contains genes which code for proteins (polypeptides). Genes are sequences of bases which are arranged in a particular order, coding for amino acids which make up proteins. codon 1 amino acid is coded for by 3 bases, called a codon The genetic code* is: Non-overlapping: each codon is only ‘read’ once Degenerate: amino acids have more than one codon Universal: the same codons code for the same amino acids in all organisms! *the genetic code is the sequence of base triplets (codons) in mRNA that code for specific amino acids and hence code for a polypeptide. The genetic code therefore contains instructions to make a protein

3. RNA single- stranded Sections of DNA (genes) are transcribed onto a single- stranded molecule called RNA. RNA is similar to DNA, but has a ribose sugar (not deoxyribose), is single stranded and has the base Uracil instead of thymine. mRNAtRNA mRNA is a long strand arranged in a single helix. It forms a mirror copy of base sequences to DNA (except uracil). It is therefore complementary to the bases on the single strand of DNA (template strand) it was made from. It is made during transcription It carries the genetic code from the nucleus into the cytoplasm where it acts as a template upon which proteins are built tRNA is a single strand folded into a clover shape tRNA has an amino acid binding site at one end and a specific sequences of bases called the anticodon at the other end. This anticodon consists of 3 bases that are complementary to a codon on the mRNA. It is found in the cytoplasm where it is involved in translation (protein synthesis)

4. Transcription and splicing Transcription Transcription is the process of making pre-mRNA and occurs as follows : DNA helicase DNA helicase acts on a specific region of DNA (the site of a particular gene) and breaks the hydrogen bonds between bases, causing the two strands in DNA to separate, exposing the bases. RNA polymerase RNA polymerase attaches to the template strand of DNA at the beginning of a gene. This enzyme moves along the template strand causing nucleotides on the strand to join with complementary ones that are present in the nucleus. (N.B. adenine joins with uracil) When the RNA polymerase reaches a triplet code called a ‘stop code’, it detaches and the production of pre-mRNA is complete Splicing Non-coding DNA called introns interfere with the synthesis of a polypeptide so they are therefore removed from the pre-mRNA by a process called splicing. exons The remaining exons can now rejoin in a variety of different ways, meaning one gene can code for many different proteins, depending on the order of the exons. Once splicing has occurred the mRNA leave the nucleus via nuclear pores

5. Translation Translation is the process by which a polypeptide is synthesised A ribosome attaches to the starting codon of mRNA A tRNA molecule with a complementary anticodon pairs up with the codon of the mRNA molecule (in the presence of the ribosome) Another tRNA molecule has a complementary anticodon to the next codon on the mRNA molecule and therefore attaches The amino acids attached to the tRNA molecule are therefore adjacent to each other and by the means of an enzyme they become joined by a peptide bond. The first tRNA molecule detaches as the ribosome moves along the strand of mRNA to the next codon. This process continues until a polypeptide is made. Once the ribosome reaches a stop codon the ribosome moves away an translation stops. Many ribosomes can pass immediately behind the first, meaning identical polypeptides can be made simultaneously

6. Quick summary and questions The DNA triplets that make up a gene determine the codons on mRNA The codons on the mRNA determine the order in which tRNA molecules line up This determines the sequence of amino acids in the polypeptide and hence the overall shape of the protein. What are the two stages of protein synthesis? Transcription(+splicing) and translation Where does the first stage of protein synthesis occur? In the nucleus Where does the second stage of protein synthesis occur? In the cytoplasm What is a polypeptide? A sequence of amino acids joined by peptide bonds What is a codon? A sequence of 3 bases on a mRNA molecule that codes for an amino acid What is an anticodon? A sequence of 3 bases on a tRNA molecule that is complementary to the codon on mRNA What two enzymes are involved in transcription and what are their functions? DNA helicase (splitting double strands of DNA into two by breaking the hydrogen bonds) RNA polymerase (causes complementary nucleotides to join to the DNA template strand)

7. Gene mutation Any change to the base sequence of DNA is called a gene mutation Types of gene mutation include: Substitution Deletion Substitution mutations A nonsense mutation: when the substituted base results in the formation of a stop codon e.g. UAG. The production of a polypeptide will be stopped prematurely therefore resulting protein will not function properly A mis-sense mutation: when the substituted base results in a different amino acid being coded for. The polypeptide produced will differ by just one amino acid. The significance of this difference will therefore depend on the role of the amino acid. If this amino acid is important in forming bonds that determine the tertiary structure, the final shape of the protein will be different. A silent mutation: when the substituted base results in a different codon BUT still codes for the same amino acid, due to the degenerate nature of the genetic code. This will result in no change in the polypeptide. Deletion mutations When a base is lost from the sequence of DNA ‘frame-shift’ occurs. This means that all the codons that occur after the base that was deleted will now be read in the wrong triplet order as the bases will have ‘shifted’. This may result in a completely different polypeptide if the deletion happens near the start of the sequence *frame shift also occurs when a base is added to a sequence.

8. Causes of mutation Can arise spontaneously during DNA replication Mutation rate is increased by mutagenic agents/mutagens which include: - high energy radiation e.g. UV rays - chemicals that alter DNA structure/interfere with transcription - viruses can disrupt DNA Mutagens increase the mutation rate by acting as a base, therefore changing the base sequence of DNA. By altering or deleting bases which again will change the sequence of DNA. By changing the structure of DNA. Mutations produce genetic diversity necessary for natural selection & speciation Mutations can cause cancer- uncontrolled cell division Mutations can cause genetic disorders – cystic fibrosis Hereditary mutation: mutations that occur in gametes and are passed onto offspring Acquired mutation: mutation that occurs in individual cells after fertilisation

9. Genes that control cell division In normal cells, the division rate is controlled by two genes: tumour suppressor genes and proto-oncogenes. During cell division growth factors attach to receptor proteins on the cell- surface membrane, activating a relay protein in the cytoplasm which ‘turns on’ the genes necessary for DNA replication If a mutation occurs in these genes the rate of cell division will not be controlled, which can lead to cancer Proto-oncogenesTumour suppressor genes  Proto-oncogenes stimulate cell division  A mutation can cause a proto-oncogene to mutate into an oncogene.  Oncogenes can cause receptor proteins to become permanently activated so cell division is switched on in the absence of growth factors  Oncogene may code for a growth factor which is produced in large amounts, over- stimulating cell division Tumour suppressor genes inhibit cell division and prevent the formation of tumours If a tumour suppressor gene is mutated, it will become inactivated Cell division therefore increases beyond normal the rate Mutant cells formed are structurally and functionally different from normal cells. Harmful tumours=malignant Harmless tumours-benign

10. Quick summary and questions A gene mutation is a change in the base sequence of DNA Mutations occur spontaneously Mutation rate is increased by mutagens Proto-oncogenes stimulate cell division Tumour suppressor genes inhibit cells division What is a substitution mutation and give three examples? A genetic mutation that results in one base being substituted for a different one. Nonsense, mis-sense and silent mutations are examples. What is a deletion mutation? A genetic mutation that results in the deletion of a base, causing frame shit How do mutagenic agents cause mutations? By acting as a base (therefore can cause a substitution mutation), by altering bases (e.g. by deleting them) or by changing the structure of DNA How is cell division normally controlled? By proto-oncogenes and tumour suppressor genes. Growth factors attach to protein receptors, activating a relay protein which stimulates DNA replication How does a mutation to a proto-oncogene cause cancer? Mutated proto-oncogene is called an oncogene. Oncogenes can cause protein receptors for growth factors to become permanently activated. They also code for growth factors which are produced in excessive amounts due to the mutation. This leads to uncontrollable cell division = cancer How does a mutation to a tumour suppressor gene cause cancer? Mutation causes tumour suppressor gene to become inactive therefore cell division is not inhibited, which therefore increases uncontrollably. This can result in a tumour and hence cancer.

11. Regulation of transcription and translation All cells in an organism contain the same DNA and therefore the same genes. However the structure and function of different cells varies. Not all genes in a cell are expressed. When different genes are expressed, different proteins will be made which therefore modify the cell’s structure. Gene expression causes cells to become specialised. Transcription of genes is controlled in the following way: Transcriptional factors have a site that binds to a specific region of DNA in the nucleus. Transcriptional factors control gene expression by controlling the rate of transcription. Some transcriptional factors are activators and increase the rate of transcription Some transcriptional factors are suppressors and decrease the rate of transcription When a gene is not being expressed, the site on the transcriptional factor (activator) that binds to DNA is blocked by an inhibitor molecule, therefore the transcriptional factor is prevented from binding to DNA and transcription is prevented.

12. The effect of oestrogen on gene transcription Hormones like oestrogen can switch on a gene therefore activating transcription and translation which results in the production of a protein/enzyme that produces the required response. Oestrogen activates transcription in the following way: Oestrogen easily diffuses through the phospholipid layer of the cell- surface membrane of target cells, due to being lipid soluble. Oestrogen then binds to a receptor molecule that is attached to the transcriptional factor. By combining with this receptor, oestrogen changes the tertiary structure of the molecule which releases the inhibitor from the binding site of the transcriptional factor. The transcriptional factor is now able to bind with the region of DNA that contains a certain gene, therefore it moves into the nucleus via nuclear pores and combines with DNA. Once the transcriptional factor binds to DNA it stimulations transcription of a certain gene (‘target gene’). This in turn results in the production of a particular protein.

13. Inhibition of gene expression Small interfering RNA (siRNA) is double stranded RNA that prevents gene expression by interfering with translation. It does this by breaking down mRNA before it undergoes translation. siRNA is made when large double stranded RNA is cut into smaller sections by the means of an enzyme The effect of siRNA on gene expression: One of the two strands of siRNA combines with an enzyme. The bases on siRNA will attach to complementary bases on the mRNA molecule, therefore guiding the enzyme to the mRNA molecule. The enzyme then cuts mRNA into smaller sections, therefore preventing it from being translated into a polypeptide. The gene is therefore not expressed This mechanism by which siRNA works is called RNA interference. siRNA could be used to prevent diseases. As some diseases are caused by certain genes, siRNA could be used to block these genes and therefore prevent the disease e.g. cystic fibrosis is caused by a faulty gene. siRNA could be used to prevent the mRNA produced by this gene being translated.

14. Cell specialisation Although all cells contain the same genes, only certain genes are expressed. Differentiated cells are different from one other due to the production of different proteins which is a result of different genes being expressed. A fertilised egg has the ability to develop into all types of cells. Cells such as fertilised eggs which can mature into any type of body cell, are known as totipotent cells and there are not specialised. Some genes in specialised cells are not synthesised into proteins, as these proteins are not needed. The ways in which genes are prevented from expressing themselves include preventing transcription or translation (previous slides) Only a few totipotent cells exist in mature organisms and these are called adult stem cells (can be found in the bone marrow which produces white and red blood cells). Stem cells that occur in the earliest ages of development of an embryo are called embryonic stem cells

15. Use of stem cells Stem cells can come from adult tissue or embryos. Adult stem cellsEmbryonic stem cells  Obtained from the bone marrow  Can be obtained by a simple operation with very little risk involved, however does cause a lot of discomfort  Adult stem cells are not as flexible as embryonic stem cells as they can only specialise into a limited range of cells  Obtained from an embryo during the early stages of development  Embryos are created in the laboratory using in vitro fertilisation  Stem cells are removed from the embryo at approx. 4-5 days during development.  The embryo is then destroyed  Embryonic stem cells can develop into any type of cell, therefore have more flexibility than adult stem cells. Obtaining stem cells from embryos raises many ethical issues as the embryo could potentially become a fetus if it were to be placed in the womb. People argue whether an embryo less than 14 days old should be afforded the same respect as a fetus or an adult.

16. Use of stem cells part 2 Stem cell therapy Stem cells can be used to replace damaged cells due to illness of injury. Bone marrow transplants already exist and are used to replace faulty bone marrow (treatment for leukaemia, a cancer of the blood/bone marrow) Stem cell therapy can be used to treat severe combined immunodeficiency (SCID) which is a genetic disorder that effects the immune system. People with this disorder have defective white blood cells therefore have an impaired immune system so are susceptible to infections. Treatment with bone marrow transplants allows the production of stem cells without the faulty genes that cause SCID. Other treatments involving stem cells Stem cells can be grown in vitro and altered (using differentiation factors that affect gene expression) so they specialise into different types of cells, which can be used to treat disease Stem cells could be used to replace damaged heart tissue caused by heart disease Stem cells could be used to grow entire organs for transplants Stem cells could be used to grow into B-cells of the pancreas, treating diabetes Could be used to differentiate into skin cells, treating burns and wounds Stem cells can improve the quality of life for many people, and can even save lives.

17. Use of stem cells part 3 Plants contain totipotent cells which are found in parts of the plant which are growing such as the roots and shoots. Stem cells can be used to grow whole new plants in vitro. Growing plant tissue artificially is called tissue culture Growth of plants in vitro: 1.A single totipotent stem cells is taken from the root or shoot of a plant 2.The stem cell is placed in a growth medium that contains nutrients and growth factors (such as IAA) 3.The plant stem cell will divide into a mass of unspecialised cells 4.Depending on what growth factors are provided, the plant stem cells will mature into specialised cells 5.To cells then grow to form a plant organ, or even an entire plant again, depending on what growth factors are used

18. Quick summary and questions Cells that are unspecialised are called totipotent cells Totipotent cells differentiate into different cells by controlling which genes are expressed. Gene expression is controlled by regulating transcription and translation Transcription is regulated by transcriptional factors (activators or suppressors) Translation can be interfered by siRNA, which cuts mRNA into smaller sections, preventing translation Stem cells can be used in medicine to treat diseases and can also be used to grow plants What effect does oestrogen have on transcription? Oestrogen binds to a receptor molecule on the transcriptional factor, changing its shape therefore releasing an inhibitor molecule. This means the transcriptional factor can bind to the specific region of DNA and activate transcription. What are stem cells? Stem cells are undifferentiated cells that can specialise into any type of body cell Name the two types of stem cell Adult stem cell and embryonic stem cell Where are plant stem cells found? In growing parts of the plant such as the root or shoot