molecules, medicines and drugs

Question 1
This question carries 40% of the marks for this assignment. It will be assessed according to how well you demonstrate the following learning outcomes in your answer:
Kn3 Demonstrate general knowledge and understanding of some of the basic facts, language, concepts and principles relating to either polar science or the development of drugs and medicines.
C1 Describe, analyse, interpret and evaluate scientific information including textual, numerical, graphical and multimedia material.
This question is about chemical structures. You will need to include drawn structures in some of your answers. Such drawings must be of your own construction (and not cut and pasted from any resource). You may choose to draw these by hand and then either scan or photograph them for inclusion. Alternatively you can draw them electronically using any software of your choice.

(a) Describe the precautions that are taken when designing the third clinical phase of a drug trial, to make sure the conclusions drawn from the results of the trial arise only from genuine biological effects of the drug being tested. Explain the reasons for the precautions you have described. (Advisory word limit: 75-100 words)

(b)
(i) Draw a pair of geometrical isomers that have the structural formula shown in compound A below. Explain why this isomerism arises. (Advisory word limit: 75-100 words)
Br-CH=CH-CH3
I
Br

Compound A

(ii) Draw the structure of another isomer of compound A that retains a double bond and that does not give rise to a pair of geometrical isomers.

(c)

(i) Using structural formulae, write a chemical equation to show one molecule of valine reacting with one molecule of serine to form water and a molecule of a product that contains an amide (peptide) bond. Label the amide bond on the structural formula of your product.

(ii) Identify and explain the features of your product molecule that would enable it to undergo further reactions with amino acids and hence to take part in the formation of the primary structure of a protein. (Advisory word limit: 100words)

(iii) Why do all molecules of a specific protein that is also an enzyme always have exactly the same amino acids in exactly the same order? (Advisory word limit: 100words)

(d)
By using a diagram of your own construction, make a copy of the structure of
Salmeterolasgiven in eChapter 6, Section 6.6 (‘Asthma drugs’), of the topic text.
Your structure may be hand drawn and then scanned or photographed into your TMA answers or may be drawn using any software of your choice.Label your structure to identify the appropriate features that make salmeterol:
(i) longer lasting in treating asthma than salbutamol
(ii) resistantto deactivation by enzymes
(iii) non-addictive.
Explain how the features that you identified achieve the outcomes in (i), (ii) and (iii).
(Advisory word limit: 100–130 words in total for part (d))
Question 2
This question carries 32% of the marks for this assignment (approximately 11% of your overall continuous assessment score). It will be assessed according to how well you demonstrate the following learning outcomes in your answer:
C2 Apply knowledge and understanding of scientific concepts to address familiar and unfamiliar situations.
Ky1 Make sense of and use information presented in different ways, including textual, numerical, graphical and multimedia material.

(a) The generalised structure of a penicillin molecule is given in
eChapter 8, Section 8.6.1 (‘The Penicillins’), together with some R groups that determine to which specific penicillin the structure refers. Draw the structure of penicillin G and label it to identify:
(i) one of the chiral carbon atoms
(ii) a carboxylic acid group
(iii) an amide group.
The drawing should be of your own construction. Your structure may be hand drawn and then scanned or photographed and inserted in your TMA answers or may be drawn using any software of your choice.

(b) The reaction between penicillin and an –NH2 group on the protein chain of the enzyme that catalyses the production of the new cell wall during bacterial replication is well established and is described in the Molecules, medicines and drugs ebook.
However, this cannot be the complete story, as the side chain (R) was found to be necessary for activity against bacteria. It therefore seems likely that the R group must bind in some way to the enzyme to hold the penicillin molecule in the correct place.
State and explain the type of intermolecular attraction that you would expect the R group of penicillin G to form with the side chain of a leucine residue in a protein chain.
Why would this attraction be more likely to form to a leucine residue rather than a serine residue? (Advisory word limit: 75 words)

(c) A recording of Alexander Fleming speaking in 1945 about the dangers of penicillin on the audio sequence ‘Frontiers: The new antibiotics’, refers to ‘educated microbes’becoming a problem. What did he mean by ‘educated microbes’ and have his fears been justified by subsequent events? (Advisory word limit: 90 words)

Question 3
This question carries 28% of the marks for this assignment (approximately 9% of your overall continuous assessment score). It will be assessed according to how well you demonstrate the following learning outcomes in your answer:
Kn3 Demonstrate general knowledge and understanding of some of the basic facts, language, concepts and principles relating to either polar science or the development of drugs and medicines.
Ky2 Communicate scientific topics clearly and concisely, using methods and scientific language appropriate to your purpose and audience.
Each of the following question parts has a mandatory word limit and you should give a word count at the end of each answer.
You should provide references at the end of your answers (a, b and c) to the online topic text of ‘Molecules, medicines and drugs’. Full details on how to style references can befound in the S142 Referencing Guide in the Assessment resources area. Forexample, to refer to eChapter 9.1 online, you would include (The Open University, 2015) at the end of your answer. The full reference would be: The Open University (2015) ‘eChapter 9:
Antiviral drugs’, S142 Molecules, medicines and drugs [Online].
Available at
https://learn2.open.ac.uk/mod/oucontent/view.php?id=617403 (Accessed 07 April 2015).

(a) Why is it much more difficult to develop drugs to act against viruses than it has been to develop drugs to act against bacteria? What ability do bacteria and viruses have in common that can lead to a drug that may act against them only providing temporary benefit? (no more than 180 words)

(b) The surface of an influenza virus has two types of protein spike attached to it, both of which can bind to sialic acid but they do so at different stages of the replication of the virus. Name the protein spikes and describe how each type is involved at the appropriate stage of virus replication. (no more than 90 words)

(c) At which stages of viral replication mentioned in (b) was the drug zanamivir designed to be effective and how does it achieve its action? (no more than 50 words)