Section 8: The control of gene expression Flashcards
Mutations are changes in the sequence of nucleotides in DNA molecules. Name the four types of mutations:
- Insertion/Deletion
- Duplication
- Inversion
- Translocation
Translocation is a type of mutation, describe how it occurs?
A group of bases become separated from the DNA sequence on one chromosome and are inserted into the DNA sequence on another chromosome.
Describe how inversion ( a type of mutation ) occurs?
A group of bases become separating from the DNA sequence and then re-join at the same position but in the reverse order.
What two type of mutations cause a frameshift
Insertion/deletion
Duplication
Gene mutations can be cause by mutagenic agents that affect DNA, name 3 potential causes of gene mutations:
- Chemical mutagens - alcohol, benzene, tar
- Ionising radiation - UV and Xray
- Spontaneous errors in DNA replication
Define Stem Cell
Undifferentiated cells which can keep dividing to give rise to other cell types
What does pluripotent mean?
can form any cell type in the body, excluding placental cells. often used in replacing damaged tissues in human disorders
What does totipotent mean?
A type of stem cell that can give rise to all types of specialised cells
What does multipotent mean?
Can differentiate into other cells types but are more limited e.g. the cells in the bone marrow and umbilical cords
What does unipotent mean?
Cells can only differentiate into one type of cell
Name the four different types of stem cells.
- Totipotent
- Pluripotent
- Multipotent
- Unipotent
Where do stem cells originate from in mammals?
- Embryonic stem cells
- Umbilical cord blood stem cells
- Placental stem cells
- Adult stem cells (some are in body tissues to maintain and repair tissues)
What does iPS stand for?
induced pluripotent stem cells
Describe how induced pluripotent stem (iPS) cells are generated.
(4 marks)
Somatic cells (e.g., skin cells) are collected from an individual.
Four specific genes (Oct4, Sox2, Klf4, and c-Myc) are introduced into these somatic cells.
These genes reprogram the somatic cells, turning them into pluripotent cells (iPS cells).
iPS cells are capable of developing into a wide variety of cell types, similar to embryonic stem cells.
Explain two potential medical applications of iPS cells.
(4 marks)
Cell therapy: iPS cells can be used to generate tissues or organs for transplant, reducing the risk of rejection.
Disease modelling: iPS cells can be used to create models of diseases (e.g., Alzheimer’s, Parkinson’s) for drug testing and research.
What are the advantages of using induced pluripotent stem (iPS) cells?
Lower ethical concerns: iPS cells are derived from adult somatic cells (e.g., skin cells), avoiding the destruction of embryos.
No embryo destruction: There is no involvement of embryos, avoiding debates about the moral status of embryos.
Reduced risk of rejection: Since the cells are genetically similar to the donor, there are fewer concerns about immune rejection and tumour formation.
What are the ethical concerns associated with the use of embryonic stem cells?
Higher ethical concerns: Embryonic stem cells are derived from human embryos, involving the destruction of the embryo.
Moral status of embryos: The use of embryos raises debates about when human life begins and whether embryos should be considered for research.
Exploitation risks: The process may involve the exploitation of women for egg donation and potential commodification of human life.
Describe the action of oestrogen in controlling transcription in 3 points.
- Oestrogen diffuses across membrane binds to receptor molecule of transcription factor
- Alters shape of DNA binding site on transcription factor
- Transcription factor therefore enters nucleus via nuclear pore and binds to DNA
What effect foes oestrogen have on transcription?
Stimulates transcription of the gene that makes up DNA (does this by altering DNA binding site on transcription factor so it can bind to DNA)
How does oestrogen enter a cell?
Oestrogen is lipid soluble so it can diffuse freely across the phospholipid bilayer
What is the role of transcriptional factors in gene expression?
Transcriptional factors are proteins that bind to specific DNA sequences to regulate the transcription of genes.
They can either activate or repress gene expression by promoting or inhibiting the binding of RNA polymerase to the DNA.
Activators increase transcription by helping RNA polymerase bind, while repressors decrease transcription by blocking RNA polymerase or altering the chromatin structure.
What is the role of siRNA in gene silencing?
siRNA binds to a complementary sequence of mRNA.
siRNA is usually single stranded and the cell therefore detects the double stranded from on mRNA and view it as abnormal.
Therefore the mRNA is broken down by enzymes preventing translation
What are two applications of siRNA in research and medicine?
Gene function analysis:
siRNA is used to silence specific genes in research to study their function by knocking them down at the mRNA level.
Therapeutic use: siRNA can be designed to target and silence disease-causing genes, such as in viral infections or cancer, offering potential treatments by reducing harmful gene expression
What is epigenetics?
Epigenetics is the study of changes in gene expression or phenotype that do not involve changes to the DNA sequence itself.
How does DNA methylation affect gene expression?
DNA methylation involves adding a methyl group (-CH3) to the DNA, typically at cytosine bases.
Methylation of genes silences their expression by preventing the binding of transcription factors or RNA polymerase.
This often leads to a decrease in gene activity and can be inherited through cell divisions, affecting gene expression over generations.
How does DNA acetylation affect gene expression?
DNA acetylation involves the addition of an acetyl group (-COCH3) to histone proteins.
Acetylation of histones reduces the positive charge on the histones, causing them to loosen their grip on DNA.
This relaxation of DNA packaging allows transcription factors and RNA polymerase to bind more easily, promoting gene expression
How do histone modifications influence gene expression?
Histones are proteins that DNA wraps around, and their modification can influence gene expression.
Acetylation of histones (addition of an acetyl group) loosens DNA packaging, allowing genes to be more easily transcribed.
Methylation of histones can either activate or repress gene expression depending on the specific site of modification.
What is the effect of decreased DNA acetylation?
Decreased acetylation of histones increases there positive charge, so they bind to DNA more tightly. When this happens transcription factors can no longer access the DNA, so the gene is switched off.
Why do histones associate with DNA?
Histones are positively charged proteins that interact with the negatively charged DNA molecules.
This electrostatic attraction between the positive charge of histones and the negative charge of the phosphate groups in DNA helps DNA to coil tightly around the histones, forming nucleosomes.
Define cancer.
Cancer is the uncontrolled cell division caused by mutations in genes that regulate the cell cycle.
This leads to the formation of tumours and, in some cases, the spread of cancer cells to other parts of the body (metastasis)
What is metastasis?
Metastasis is the spread of cancer cells from the original (primary) tumor to other parts of the body, forming secondary tumors.
Cancer cells break away, travel through the blood or lymphatic system, and invade other tissues.
What are the differences between benign and malignant tumours?
Benign tumours consist of specialised cells and are usually encapsulated, meaning they do not invade surrounding tissues. They grow slowly and do not spread.
Malignant tumours contain unspecialised cells, are not encapsulated, and invade surrounding tissues. They can spread to other parts of the body through metastasis and often evade the body’s defensive tissues
What are the two main types of genes that play a role in cancer?
Tumour suppressor genes and oncogenes
What role does proto-oncogenes play in cancer?
Proto-oncogenes stimulate cells divide by producing proteins that stimulate cell division, allow the checkpoints of the cell cycle to be passed, and can cause cancer if mutated.
How are oncogenes formed?
They are formed from mutated proto-oncogenes.
What is the result of the formation of an oncogene? How does it do this?
Result in uncontrolled cell division.
It does this by permanently activating a cell surface receptor or coding for a growth factor
How do tumour suppressor genes control cell division?
cause the cell cycle to stop when damage is detected.
Also play important role in the programming of apoptosis (cell death). When switched off the cell cycle becomes unregulate.
What is apoptosis?
Cell death
How does abnormal methylation of tumour suppressor genes and oncogenes contribute to cancer?
Abnormal methylation of tumor suppressor genes (e.g., hypermethylation) can silence these genes, preventing them from inhibiting cell division and allowing cells to divide uncontrollably.
Abnormal methylation of oncogenes (e.g., hypomethylation) can activate these genes, leading to overexpression and excessive cell growth.
Both processes disrupt the normal regulation of the cell cycle and contribute to the development of cancer.
Why can increased oestrogen concentrations be linked to breast cancer?
Because they bind to transcription factors which activate genes promoting cell division, potentially leading to tumour formations. Elevated levels are usually found in fatty tissues call adipose tissue.
What is in vivo cloning?
In vivo cloning is a method of gene cloning that involves inserting a gene into a living organism (such as a bacterium) where it is replicated as the organism divides
What does In vitro mean?
“In glass”
DNA (containing gene) is copied many times over by Polymerase Chain Reaction using PCR machine
What is a vector?
A length of DNA that carries the gene of interest into the host cell.
It has to be big enough to contain the gene
Explain the role of a vector during in vivo gene cloning.
A vector is used to transfer the desired gene (DNA fragment) into a host cell
The vector ensures the foreign DNA is replicated when the host cell divides
It may also carry marker genes to allow identification of successfully transformed cells
What could be used as a vector?
Plasmids
Bacteriophages (viruses that infect bacteria)
What is a plasmid? Why is it commonly used as a vector?
A plasmid is a small, circular DNA molecule found in bacteria. It’s used as a vector because it can replicate independently and carry foreign genes.
Name the group of enzymes that cut DNA
Restriction enzymes ( also known as restriction endonucleases)
Name the enzyme that joint nucleotides in a DNA strand.
DNA ligase
What are sticky ends?
• Sticky ends are exposed, unpaired bases at the ends of a DNA fragment.
• They are produced when DNA is cut by restriction enzymes in a staggered manner. • Sticky ends are complementary to other sticky ends cut by the same enzyme, allowing DNA fragments to join.
Why is a promoter region added to the DNA fragment?
• The promoter region allows RNA polymerase to bind.
• This ensures the target gene is transcribed and expressed in the host cell.
Why is a terminator region added to the DNA fragment?
• The terminator region signals RNA polymerase to stop transcription.
• This ensures the correct length of mRNA is produced.
Give two ways a gene can be isolated from a piece of DNA. Name the enzymes involved
• Using restriction enzymes to cut the desired gene from the DNA at specific recognition sites.
• Using reverse transcriptase to produce complementary DNA (cDNA) from mRNA.
What does palindromic sequence mean?
• A palindromic sequence is a sequence of DNA bases that reads the same in both directions on complementary strands.
• For example:
• 5’ — GAATTC — 3’
• 3’ — CTTAAG — 5’
What is the name of the type of DNA formed from vector DNA and inserted DNA fragment?
Recombinant DNA
What is meant by the process ‘transformation’?
Transformation is the process of introducing recombinant DNA (such as a plasmid) into a host cell.
What is a genetic marker?
• A genetic marker is a gene that produces an observable characteristic, allowing scientists to identify cells that have successfully taken up the recombinant DNA.
• Examples include antibiotic resistance genes or fluorescent protein genes.
How can bacteriophages act as vectors?
Bacteriophages are viruses that infect bacteria; they can inject foreign DNA directly into bacterial cells.
What role do restriction enzymes play in vector preparation?
Restriction enzymes cut DNA at specific sequences, creating sticky or blunt ends that allow foreign genes to be inserted into the vector.
What is a recombinant plasmid?
A recombinant plasmid is a plasmid that has had a foreign gene inserted into it.
Describe the steps involved in inserting a gene into a plasmid vector.
The plasmid and target gene are cut with the same restriction enzyme to create complementary sticky ends. DNA ligase then joins the gene to the plasmid, forming a recombinant plasmid.
How are sticky ends important in forming recombinant DNA?
Sticky ends are complementary overhanging sequences that allow DNA fragments to anneal and form stable recombinant molecules.
How is a vector introduced into a host cell?
Through transformation, often by heat shock or electroporation.
What is transformation in the context of genetic engineering?
Transformation is the process of introducing a recombinant vector into a host cell.
Describe the process of identifying cells that have successfully taken up the vector.
Cells are grown on agar plates containing antibiotics or other selective agents. Only transformed cells with resistance genes (from the vector) will survive.
Why are marker genes important in vector-based genetic engineering?
Marker genes help identify cells that have successfully taken up the vector.
What types of marker genes are commonly used in recombinant DNA technology?
Antibiotic resistance genes or genes that produce fluorescent proteins.
How are antibiotic resistance genes used in vector identification?
Cells that have taken up the vector will survive on agar containing the corresponding antibiotic.
Explain how fluorescent markers can indicate successful gene insertion.
Fluorescent marker genes cause transformed cells to glow under UV light, indicating successful gene uptake.
What is the purpose of inserting a promoter sequence into a vector?
A promoter ensures the inserted gene is transcribed and expressed in the host cell.
Why might some cells fail to take up a recombinant plasmid during transformation?
Factors include inefficient heat shock conditions, damaged plasmids, or natural resistance of cells to transformation.
How can gene expression be controlled once a vector is introduced into a host?
By using inducible promoters that activate gene expression in response to specific environmental factors.
What are the ethical concerns surrounding the use of vectors in genetic modification?
Concerns include potential environmental impacts, gene escape, and the modification of human genes.
What are the 5 overview steps of gene cloning?
- Isolation (of DNA fragments)
- Insertion
- Transformation
- Selection
- Culturing
Name the three methods to create fragments of DNA.
- Reverse transcription
- Restriction endonucleases
- Gene machine
Describe the process of using reverse transcriptase to produce DNA fragments.
- Enzyme makes DNA copies from mRNA
- Naturally occurs in viruses, such as HIV
- A cell that naturally produces the protein of interst is selected
- These cells should have large amounts of mRNA for the protein
- The reverse transcriptase enzyme joins the DNA nucleotides with complementary bases to the mRNA sequence
- Single stranded DNA is made (cDNA)
- To make this DNA fragment double stranded, the enzyme DNA polymerase is used
What is the advantage of using reverse transcription to produce DNA fragments?
The cDNA is intron free because it is based on mRNA template.
Prokaryotic cells do not have the ability to remove introns so very useful if using those
Describe how restriction endonucleases produce DNA fragments?
• Restriction endonucleases are enzymes that cut DNA at specific sequences called recognition sites.
• These recognition sites are palindromic sequences, meaning they read the same in opposite directions on complementary strands.
• The enzyme cuts the sugar-phosphate backbone of the DNA at these sites.
• This cut can produce either:
• Sticky ends — staggered cuts that leave exposed, unpaired bases at each end. These are useful for joining DNA fragments with complementary sticky ends.
• Blunt ends — straight cuts that leave no exposed bases.
What are sticky ends?
staggered cuts that leave exposed, unpaired bases at each end. These are useful for joining DNA fragments with complementary sticky ends.
What are blunt ends?
straight cuts that leave no exposed bases.
What is the gene machine?
The gene machine is a method of synthesising DNA fragments without the need for a pre-existing DNA template.
What is the starting point for synthesising a gene using the gene machine?
The desired gene sequence is designed on a computer.
How does the gene machine assemble the DNA fragment?
The computer designs small, overlapping sections of DNA called oligonucleotides, which are chemically assembled and joined together to form the complete DNA sequence.
What happens after the oligonucleotides are assembled?
The assembled DNA sequence is checked for errors and replicated using the polymerase chain reaction (PCR).
What is added to the synthetic DNA to allow it to be inserted into a vector?
Sticky ends are often added to enable the DNA fragment to be inserted into a plasmid or other vector.
Name an advantage and disadvantage of using the gene machine to produce DNA fragments.
Advantage: Can desing exact DNA fragment you want, with sticky ends, labels and preferential codons
Disadvantage: Need to know the sequence of amino-acids or bases
Why is the removal of introns important in gene machine synthesis?
Prokaryotic cells cannot splice out introns, so producing intron-free DNA ensures successful gene expression.
What are some applications of the gene machine?
• Producing genes for medical research.
• Creating genes for genetically modified organisms (GMOs).
• Developing synthetic biology solutions.
Name an advantage and disadvantage of using reverse transcriptase to produce DNA fragments.
Advantage: mRNA present in cell is from actively transcribed genes, so lots of the mRNA of interest available to make cDNA
Disadvantage: More steps so more time consuming and technically more difficult
Name an advantage and disadvantage of using Restriction endonuclease to produce DNA fragments.
Advantage: Sticky ends on DNA fragment make it easier to insert to make recombinant DNA
Disadvantage: Still contains introns
Give two epigenetic mechanisms used to prevent transcription
Increased methylation of DNA
Decreased acetylation of histones
What name is used for the non-coding sections of a gene?
Introns
Name one type of gene that can prevent tumour growth
Tumour suppressor gene
During which part of the cell cycle are gene mutations most likely to occur? Suggest why.
Interphase and S phase
Interphase is when DNA replication happens most chance of spontaneous mutation
