Nucleic acids and proteins

A.S.	Obj.	6.1 DNA structure (1h)
6.1.1	2	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.
6.1.2	1	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).
6.1.3	2	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.

		6.2 DNA replication (1h)
6.2.1	1	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.
6.2.2	3	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.
6.2.3	1	State that in eukaryotic chromosomes, replication is initiated at many points.
		6.3 Transcription (2h)
6.3.1	1	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.
6.3.2	2	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.
6.3.3	3	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.
6.3.4	2	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.
6.3.5	1	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.
6.3.6	1	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).
6.3.7	3	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.
		6.4 Translation (2h)
6.4.1	3	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.
6.4.2	2	Outline the structure of ribosomes including protein and RNA composition, large and small subunits, two tRNA binding sites and mRNA binding sites.
6.4.3	1	State that translation consists of initiation, elongation and termination.
6.4.4	1	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.
6.4.5	3	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.
6.4.6	1	State that free ribosomes synthsize proteins for use primarily within the cell and that bound ribosome synthesize proteins primarily for secretion and lysosomes. Cross reference with 1.4.7.
		6.5 Proteins (1h)
8.5.1	3	Explain the four levels of structure of proteins, indicating each level's significance. Quanternary structure may involve the binding of a prosthetic group to form a conjugated protein.
8.5.2	2	Outline the difference between fibrous and globular proteins, with reference to two examples of each protein type.
8.5.3	3	Explain the significance of polar and non-polar amino acids. Limited this to controlling the position of proteins in membranes, creating hydrophilic channels through membranes and the specificity of active sites in enzymes. Cross reference with 1.4.
8.5.4	1	State six functions of proteins, giving a named example of each. Membrane proteins should not be included.
		6.6 Enzymes (2h)
6.6.1	1	State that metabolic pathways consist of chains and cycles of enzyme catalyzed reactions.
6.6.2	2	Describe the "induced fit" model. This is an extension of the 'lock-and-key' model. Its importance in accounting for the broad specificity of some enzymes (the ability to bind several substrates) should be mentioned.
6.6.3	3	Explain that enzymes lower the activation energy of the chemical reactions that they catalyze. Graphical representation of both exergonic and endergonic reactions should be covered, but no specific energy values need be recalled.
6.6.4	3	Explain the difference between competitive and non-competitive inhibition, with reference to one example of each. Competitive: an inhibiting molecule structually similar to the substrate molecule binds to the active site preventing the substrate binding. Examples: inhibition of butanedioic acid (succinate) dehydrogenase by propanedioic acid (malonate) in the Krebs cycle and inhibition of folic acid synthesis in bacteria by the sulfonamide Prontosil™ (an antibiotic). Non-competitive: limited to an inhibitor molecule binding to an enzyme (not to its active site) that causes a conformational change in its active site, resulting in a decrease in activity. Examples include Hg²⁺, Ag⁺, Cu²⁺, and CN^- inhibition of many enzymes (eg cytochrome oxidase) by binding to -SH groups, thereby breaking -S-S- linkages; nerve gases like Sarin and DFP (diisopropyl fluorophosphate) inhibiting ethanoyl (acetyl) cholinesterase. Reversible inhibition, as compared to irreversible inhibition is not required.
6.6.5	3	Explain the role of allostery in the control of metabolic pathways by end-product inhibition.. Allostery as a form of non-competitive inhibition. Mention that the shape of allosteric enzymes can be altered by the binding of end products to an allosteric site, therby decreasing its activity. Metabolites can act as allosteric inhibitors of enzymes earlier in a metabolic pathway and regulate metabolism according to the requirements of organisms; a form of negative feedback. Examples include ATP inhibition of phosphofructokinase in glycolysis and inhibition of aspartate carbamoyltransferase (ATCase) which catalyzes the first step in pyrimidine synthesis.