DNA and Biotechnology

DNA structure
Outline DNA nucleotide structure in terms of sugar (deoxyribose), base and phosphate.
Chemical formulas and the purine/pyrimidine subdivision are not required. Simple shapes can be used to represent the component parts. Only the spatial arrangement is required.
State the names of the four bases in DNA.
Outline how the DNA nucleotides are linked together by covalent bonds into a single strand.
Only the spatial arrangement is required.
Explain how a DNA double helix is formed using complementary base pairing and hydrogen bonds.
Describe the structure of DNA including the antiparallel strands, 3'-5' linkages and hydrogen bonding between purines and pyrimidines.
Major and minor grooves, direction of the 'twist', alternative B and Z forms, and details of the dimensions are not required.
Draw a simple diagram of the molecular structure of DNA.
An extension of the diagram in 2.4.3 is sufficient to show the complementary base pairs of A - T and G - C, held together by hydrogen bonds and the sugar-phosphate backbone. The number of hydrogen bonds between pairs and details of purine/pyrimidines are not required.
Outline the structure of nucleosomes.
Limited to the facts that a nucleosome consists of DNA wrapped around eight histone protein molecules and held together by another histone protein.
State that only a small proportion of the DNA in the nucleus constitutes genes and that the majority of DNA consists of repetitive sequences.
The function of the repetitive sequences is not required but students should know that the presence of such sequences is used in DNA profiling. (see 3.4.3).
DNA replication
State that DNA replication is semi-conservative.
Explain DNA replication in terms of unwinding the double helix and separation of the strands by helicase, followed by formation of the new complementary strands by DNA polymerase.
It is not necessary to mention the fact that there is more than one helicase and polymerase or that more enzymes are involved.
Explain the significance of complementary base pairing in the conservation of the base sequence of DNA.
State the DNA replication occurs in a 5' --> 3' direction.
The 5' end of the free DNA nucleotide is added to the 3' end of the chain of nucleotides which is already synthesized.
Explain the process of DNA replication in eukaryotes including the role of enzymes (helicase, DNA polymerase III, RNA primase, DNA polymerase I and DNA ligase), Okazaki fragments and deoxynucleoside triphosphates.
The function of the enzymes listed should be stated in general terms only. The explanation of Okazaki fragments in relation to the direction of DNA polymerase III action is required. DNA polymerase III adds ucleotides in the 5' --> 3' direction. DNA polymerase I excises the RNA primers and replaces them with DNA. Details of Meselson and Stahl's experiment are not required.
State that in eukaryotic chromosomes, replication is initiated at many points.
Transcription
Compare the structure of RNA and DNA.
Limit it to names of sugars, bases and number of strands.
Outline DNA transcription in terms of the formation of a RNA strand complementary to the DNA strands by RNA polymerase.
State that transcription is carried out in a 5' --> 3' direction.
The 5' end of the free RNA nucleotide is added to the 3' end of the RNA molecule which is already synthesized.
Explain the process of transcription in eukaryotes including the role of promoter region, RNA polymerase, nucleoside triphosphates and the terminator.
The following details are not required: there is more than one type of RNA polymerase, features of the promoter region, the need for transcription protein factors for RNA polymerase binding, TATA boxes (and other repetitive sequences), the exact sequence of the bases which act as terminators.
Gene regulation can be limited to the presence of other genes (often on other chromosomes) that affect binding RNA polymerase to the promoter region, and to the control of both the post-transcriptional modification of RNA and post-translational modification of proteins.
Distinguish between the sense and antisense strands of DNA.
The sense strand is the coding strand and has the same base sequence as mRNA (with uracil instead of thymine). The anitsense strand is transcribe and has the same base sequence as tRNA.
State the eukaryotic RNA needs the removal of introns to form mature mRNA.
Further details of the process of post-transcriptional modification of RNA are not required.
State that reverse transcriptase catalyses the production of DNA from RNA.
This is an opportunity to relate some aspects of the DNA viral life cycle with that of the AIDS virus (an RNA virus).
Explain how reverse transcriptase is used in molecular biology.
This enzyme can make DNA from mature mRNA (eg human insulin), which can then be spliced into host DNA (eg E. coli), without the introns.
Outline the lac operon model as an example of the control of gene expression in prokaryotes.
Operons are found only in prokaryotes. Mention only the idea of a regulator gene producing a protein that prevents RNA polymerase binding to the promoter region.
Translation
Explain the relationship between one gene and one polypeptide.
Describe the genetic code in terms of codons composed of triplets of bases.
Define the terms degenerate and universal as they relate to the genetic code.
Degenerate -- having more than one base triplet to code for one amino acid. Universal -- found in all living organisms.
Explain the process of translation leading to peptide linkage formation.
Include the roles of messenger RNA (mRNA), transfer RNA (tRNA), codons, anticodons and ribosomes.
Explain in detail the process of translation including ribosomes, polysomes, start codon and stop codons.
Mention of the P and A sites, initiating methionine, details of the T factor and recall of actual stop codons are not required.
Outline the structure of ribosomes including protein and RNA composition, large and small subunits, two tRNA binding sites and mRNA binding sites.
State that translation consists of initiation, elongation and termination.
State that translation occurs in a 5' --> 3' direction.
During translation, the ribosome moves along the mRNA towards the 3' end. The start codon is nearer to the 5' end than the stop codon.
Explain how the structure of a tRNA allows recognition by a tRNA-activating enzyme that binds a specific amino acid to tRNA, using ATP for energy.
Each amino acid as a specific tRNA activating enzyme (the name aminoacyl-tRNA synthetase is not required). The shape of tRNA and CCA at the 3' end should be included. Degeneracy (some amino acids having more than one tRNA) should also be included.
State that free ribosomes synthesize proteins for use primarily within the cell and that bound ribosome synthesize proteins primarily for secretion and lysosomes.
Cross reference with 1.4.7.
Genetic Engineering and other aspects of biotechnology
State that PCR (polymerase chain reaction) copies and amplifies minute quantities of nucleic acid.
Details of methods are not required.
State that gel electrophoresis involves the separation of fragmented pieces of DNA according to their charge and size.
State that gel electrophoresis of DNA is used in DNA profiling.
Describe two applications of DNA profiling.
Applications could include paternity suits or criminal investigations (murder or rape) or the identification of people who died a long time ago (eg the dead tsars of Russia and some Egyptian mummies). The problems caused by contamination of sample should be mentioned.
Define genetic screening.
Genetic screening--testing an individual for the presence or absence of a gene.
Discuss three advantages and/or disadvantages of genetic screening.
Discuss three advantages, three disadvantages or any combination of the two. These may include ethical issues, pre-natal diagnosis of genetic diseases, immigration disputes and confirmation of animal pedigrees.
State that the Human Genome Project is an international cooperative venture established to sequence the complete human genome.
Describe two possible advantageous outcomes of this project.
It should lead to an understanding of many genetic diseases, the development of genome libraries and the production of gene probes to detect sufferers and carriers of genetic diseases (eg Duchenne muscular dystrophy). It may also lead to production of pharmaceuticals based on DNA sequences.
State that genetic material can be transferred between species because the genetic code is universal.
Cross reference with 2.6.5.
Outline a basic technique used for gene transfer involving plasmids, a host cell (bacterium, yeast or other cell), restriction enzymes (endonuclease) and DNA ligase.
The use of E. coli in gene technology is well documented. Most of its DNA is in one circular chromosome but it also has plasmids (smaller circles fo DNA heliz). These plasmids can be removed and cleaved by restriction enzymes at target sequences. DNA fragments from another organism can also be cleaved by the same restriction enzyme and these pieces can be added to the open plasmid and spliced together by ligase. The recombinant plasmids formed can be inserted into new host cells and cloned.
State two examples of the current uses of genetically modified crops or animals.
Examples include salt tolerance in tomato plants, delayed ripening in tomatoes, herbicide resistance in crop plants, factor IX (human blood clotting) in sheep milk.
Discuss the potential benefits and possible harmful effects of one example of genetic modification.
Some gene transfers are regarded as potentially harmful. A possible problem exists with the release of genetically engineered organisms in the environment. These can spread and complete with the naturally occurring varieties. Some of the engineered genes could also cross species barriers. Benefits include more specific (less random) breeding than with traditional methods.
Outline the process of gene therapy using a named example.
This involves replacement of defective genes. One method involves the removal of white blood cells or bone marrow cells and, by means of a vector, the introduction and insertion of the normal gene into the chromosome. The cells are replaced in the patient so that the normal gene can be expressed. Examples are the use in cystic fibrosis and SCID (a condition of immune deficiency, where the replaced gene allows for the production of the enzyme ADA--adenosine deaminase). A cure for thalassemia is also possible.
Define clone.
Clone--a group of genetically identical organisms or a group of cells artificially derived from a single parent cell.
Outline a technique for cloning using differentiated cells.
The method used to clone Dolly the sheep is a good example.
Discuss the ethical issues of cloning in humans.
Cloning happens naturally, for example monozygotic twins. Some may regard the in vitro production of two embryos from one to be acceptable. Others would see this as leading to the selection of those "fit to be cloned" and visions of "eugenics and a super-race".