Textbook Questions - DNA & Proteins

• Describe why not all DNA in chromatin is easily expressed

  In the DNA that can be expressed, the DNA is more exposed and not wound up tightly by histone proteins. By contrast genes or DNA that are switched off tend to be wound up tightly and are inaccessible to RNA polymerase and are therefore unavailable for transcription.
• Some genes are expressed 'continuously'

  Describe what it means

  Give examples of such genes and state why it is necessary for them to be expressed in this way.

  • They are active genes and are frequently being transcribed to produce polypeptides and protein molecules
  • Such genes are often termed 'housekeeping genes' and may be involved in energy supply for the cell
• Nerve and muscle cells have exactly the same genetic makeup. Explain how it is possible for these cells to have the same DNA but very different structures and functions.

  This is the process of cell differentiation where cells become specialised for particular role in the organisms. The cells end up with these special structures and functions as the same genes are not expressed in each cell. Gene expression is regulated differently in different cells
• Once cells in an organism have fully differentiated, they are almost 'locked in' permanently to that cell type and the inactive DNA tends to remain permanently switched off. Explain how this is possible.

  The epigenetic tags that define a cells specialisation are passed on to the daughter cells. This results in all cells arising from the cell having the same specialisation and starts of the formation of a tissue. The methylation of cytosines and deacetylation of histones can permanently cause chromatin to pack tightly and RNA polymerase cannot access certain genes, switching them off.
• Explain why stem cells are unlike specialised cells and retain their genetic potential.

  This is because these stem cells do not have gene sequences or genes are are permanently switched off. As such, they retain their genetic potential and can theoretically transcribe into any of the approximate 21,000 genes (in humans)
• Describe how baldness in males illustrates the effect of gender on gene expression.

  Baldness is more common in men and not generally found in women. Males have higher levels of hormones like testosterone and this is involved in regulating or influencing the genes linked to baldness.
• Describe two instances where complementary binding of molecules to surface receptors is involved in directing the outcome of cell differentiation.

  Cells may interact with others in the near vicinity as they possess surface cell receptors that are complementary.

  Cells may release hormones that bind to other cells with complementary receptors. In both instances they may stimulate genes and direct cell specialisation.
• In an experiment, cold packs were attached to the back of a young developing Himalayan rabbit. It was noticed sometime later that the fur that grew was black in colour compared to white fur when a cold pack had not been attached. This colouration was noted as a permanent change.

  Predict the likely reasons for the change in fur colour.

  • It would appear likely that temperature has influenced the activity of the gene that produces the black coloured protein in the fur.
• In an experiment, cold packs were attached to the back of a young developing Himalayan rabbit. It was noticed sometime later that the fur that grew was black in colour compared to white fur when a cold pack had not been attached. This colouration was noted as a permanent change.

  Explain how this supports the idea that environmental factors can influence gene expression.

  • A change in environmental conditions (external temperature) has affected which gene i.e. white of black colour is expressed
• The process of DNA methylation has been implicated in cancer

  Compare the likely differences between methylation in a normal cell compared to a cell that is cancerous.

  • Cancer cells tend to have abnormal methylation i.e. too little or too much depending on the gene. Genes involved in cancer include suppressor genes and oncogenes.
• The process of DNA methylation has been implicated in cancer

  Predict the likely reasons that these changes in DNA methylation might lead to cancer

  • An example could be a gene involved in DNA repair. If this gene was supressed (over-methylated) then DNA repair would be slowed and some abnormal DNA may lead to cancerous cells.
• Transcription factors are molecules that can affect the rate of transcription and hence, gene expression

  Describe how an activator protein influences gene expression

  • An activator will often bind in a promoter region (or another region) prior to the gene and trigger transcription, possibly by triggering RNA polymerase to release from the promotor region and start transcription

  Describe how repressor factors influence transcription of a specific gene

  • The repressor is likely to bind to the DNA and prevent the action of RNA polymerase from transcribing a specific gene
• Specialised cells have not arisen from differential expression of different sets of genes but varying levels of expression of the same group of genes'. Evaluate the above statement.

  This can be seen as a brief summary of the process involved in differentiation. All human cells have the same 21,000 genes but a liver cell; e.g. has different genes that are expressed compared to a nerve cell.
• Explain why identical twins can exhibit many physical and behavioural differences as they age.

  This is indicative of the effect of environmental factors e.g. temperature, diet, and lifestyle on DNA methylation and other epigenetic changes. As the twins age, they are exposed to more different environmental factors and their epigenomes become increasingly different. These differences are then expressed physically and behaviourally.
• Describe how some epigenetic tags could negatively impact the identical twins.

  An individual may develop disease associated with changes to DNA expression OR offspring may inherit epigenetic changes that may predispose them to a particular disease.
• Name two types of genes where hyper-methylation could possible lead to tumour formation.

  • Such genes include oncogenes that are genes that cause abnormal cell division and DNA repair genes and repair DNA before cells divide
• Suggestion how hyper-methylation might serve as a biomarker for colon cancer, allowing for easily detection of the disease.


  If hyper-methylation could be detected in genes known to be associated with the disease, prior to the onset of the disease, this could alert the patient and health professionals and more screening tests could be undertaken. This would provide a greater prognosis for individuals. Additionally, a genetic test of intestinal cells could be made routine for over 50 year olds who are at higher risk of developing this disease.
• Provide another name for post-transcriptional factors

  Translation factors
• Describe how miRNA influences gene expression

  miRNA is a short segment of RNA that is complementary to a section of a specific mRNA molecule. When present, it can bind to the mRNA to prevent any further transcription as it blocks the ribosome from accessing the full code of the mRNA strand.
• Describe how IncRNAs can affect the role miRNA plays in gene expression

  Specific IncRNAs can bind to specific miRNAs in a complementary fashion. Therefore, the miRNA cannot bind to the mRNA strand to stop its translation. As a result, gene expression will continue or be promoted.
• Explain one possible way that synthetic siRNA could be used to treat some types of cancers.

  Some cancers are caused by the overexpression of genes that stimulate cell division, for example proto-oncogene. Researches could synthesise siRNA that is complementary to a section of the mRNA transcribed from proto-onco genes being overexpressed. This could result in the mRNA of proto-oncogenes being degraded and not being expressed slowing down cell division and the spread of cancer.
• Using your knowledge of the interaction between science and society, discuss how research on possible cancer treatments like synthetic siRNAs is influenced by society.

  Many members in society have lost someone close to them from cancer. It is a horrible disease, and it is hard for people to watch their loved one's battle through the treatments, which can often fail. As such, it is a very emotive topic in society, and this influences many people to fundraise for cures, donate to cancer research and put pressure on governments to increase funding, to hopefully find a cure.
• Explain why scientists only change on variable when they are conducting their research.

  If multiple variables are changed, the results collected from an experiment would be invalid. A fair experiment only changes one variable called the independent variable. If other factors are not controlled, the cause of the change in the dependent variable cannot be determined.
• Discuss one possible unexpected consequence to society of the researchers being successful at developing a drug to induce weight loss through epigenetic changes to white fat cells.

  If successful in developing a drug that works, increasing numbers in society could turn to this medication to control their weight instead of exercising. This could have the unexpected consequence of decreased gym memberships, putting gym owners under financial stress and personal trainers lose their jobs due to less demand.
• Discuss one possible biological side effect that the researchers would have to determine prior to applying for their new medication to be approved for sale to treat obesity.

  The researchers will have to determine if the drug they have created causes any additional changes to the epigenome and the physiological effect of any resultant changes. They will also have to determine if the desired change only occurs in the target white fat cells and not other specialised cell types before applying for approval.
• Describe some examples of normal cellular processes that control and regular gene expression.

  • There are a range of factors involved in regulating gene expression such as transcription factors, translation factors, and epigenetic factors.
  • RNA splicing can regulate what sections of mRNA are translated
  • Promoters are regions of the DNA that can be either activated or repressed by factors binding to them, again either switching genes of or on
  • miRNA, siRNA, and IncRNA can all influence gene expression post-transcription
• Explain how factors such as the diet and exposure to environmental chemical may alter the way that genes are expressed. Link your understanding here to the higher incidence of asthma in New York City children.

  • The environment can influence gene activity. Diet and lifestyle, temperature, and a range of chemicals are a few examples that can influence change in epigenetic markers.
  • Histone proteins are packed with the DNA and in regions where they are tightly packed, genes are usually switched off; therefore, RNA polymerase cannot access the DNA
• Name one chemical, physical, and biological factor that can act as a mutagen

  Biological: Viruses

  Physical: UV radiation, gamma radiation, x-rays

  Chemical: cigarette smoke, benzene, asbestos
• Name four types of large scale chromosome mutations that occur and lead to an alteration in chromosomes number or structure

  The four main types of chromosome mutation are deletion, duplication, translocation, and aneuploidy
• Point mutations occur when...

  During DNA replication where bases are exposed and single base substitutions, insertions, and deletions can occur
• Large scale chromosomes mutations occur...

  Often occurs during meiosis where chromosomes pair together providing the opportunity to occur. The homologous pairs then separate to form gametes with these new large scale mutations.
• Describe how ionising radiation is likely to increase the rate of mutation.

  Interfering with normal base pairing and creating bonds that would not normally occur or breaking DNA links or bonds.
• Using your knowledge of the complementary base pairing of DNA, suggest likely ways that chemical mutagens might alter the normal sequence of DNA

  The chemical mutagens may mimic the shape (or be similar to the shape) of a normal base, and hence bonds with its complementary base instead of a nucleotide base. The chemical may alter or damage normal bases interfering with their normal base pairing.
• With reference to the table above, explain the effect this type of mutation will have on the polypeptide chain/protein that forms from this altered sequence.

  As a single base was deleted, the codes are all different after the deletion and the 'reading frame' has been moved. This will have a significant effect on the structure and function of the protein and could also result in a stop codon being introduced earlier and result in a shorter polypeptide.
• Compare and contrast mutation sand epigenetic changes in DNA

  Both mutations and epigenetic changes can alter gene expression and both can be inherited if the changes appear in gametes. Mutations, through, are permanent changes to the base sequence and can give risk to altered or fault proteins. Epigenetic changes are usually expressed by methylation and can be changed as an organism's environment and experiences change. This means gene expression is dynamic and can range from being switched on to being completely switched off.
• Explain this effect of this type of mutation on the haemoglobin protein and its role in an organism

  Protein structure is a determining factor for its function. Changing one amino acid in a critical position may alter the 3D structure and hence affect the function of haemoglobin. This will affect its role of transporting oxygen to the body's cells as it may not be able to bind to oxygen as efficiently.
• Explain how benzopyrene could contribute to lung cancer associated with cigarette smoking

  If benzopyrene causes a mutation that alters a particular gene's function, that controls cell division it may alter the normal function of the associated protein and lead to uncontrolled cell division
• Explain why lung cancer associated with cigarette smoking would not be an inheritable disease

  The mutation is in a somatic or tissue cell. Only mutations in germ-line cells giving rise to gametes can be passed on to the next generation
• Explain how an accumulation of mutation in DNA over millions of years has contributed to the variety of species on Earth today

  If all life evolved from a common ancestor, then as mutations are the only source of new genes, it is the mutations in DNA which made new species possible as new characteristics rose from changes to the DNA
• Use examples, explain the different effects of mutations to these two types of cells and the individual

  Somatic or tissue mutations could give rise to cancer, but it would only affect the individual. Germ-line mutations could be passed on to the next generation and affect the descendant but not the individual