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With the sequencing of the human genome an understanding of how the one-dimensional information of the genome results in a healthy human has never been closer. Understanding these processes will lead to a better understanding of how they can go wrong, producing malformation and disease. This course introduces critical aspects of this process and the first of four modules describes what DNA is, how it replicates and how it is packaged into the genomes of bacteria and higher organisms. This first module will also describe how we can manipulate DNA in order to explore its secrets. The second module will describe the properties of amino acids, peptides and proteins, which contribute to the structure and function of our bodies. This module will also describe how we can analyse the structure and function of proteins. The third module will explore the processes that control the expression of genes in both bacteria and higher organisms. This critical aspect of gene function controls where, when and the extent to which genes are turned on; this is the key to multicellular complexity and environmental response. The fourth and final module will be devoted to the study of genes in families and populations. This final module will also discuss how genes can go wrong and lead to disease.
The aims of the course are to enable students:
(a) To establish an understanding of the structures and functions of nucleic acids and to examine their importance in packaging, replicating and maintaining genetic information;
(b) To understand the main principles of protein biochemistry, structure and function;
(c) To understand the basic mechanisms that control the expression of genes at the levels of transcription and translation in both prokaryotes and eukaryotes
(d) To understand the principles of how genetic processes can go wrong as a result of mutation and genome rearrangements, thus leading to disease.
The subject-specific learning outcomes are such that, at the end of the course, students should be able:
(a) To compare and contrast the structure of genomes in eukaryotes and prokaryotes and how they are replicated and packaged;
(b) To appreciate the role of protein chemistry and structure in function;
(c) To describe the molecular mechanisms involved in gene transcription and translation with specific examples;
(f) To describe how genetic mechanisms can go wrong to produce malformation and disease.
Practical skills advanced comprise:
(a) Ability to follow set protocols and develop competence in measuring volumes and calculating concentration; and the ability to obtain, record, collate and analyse information in the laboratory.
Numerical and Communication skills are encouraged by opportunities:
(a) To analyse laboratory-acquired information and approach some tutorial problems; and produce written laboratory reports and verbally address topics during tutorials.
Interpersonal and Teamwork skills are encouraged by opportunities:
(a) To work productively with others in the laboratory; and recognise and respect the views and opinions of others during tutorials.
Self-Management skills are needed in:
(a) Balancing the various demands of this and other courses you are studying.
(b) Achieving learning outcomes through a series of lectures, tutorials and practical classes. These three elements complement each other.
The function of the lectures is to enable information to be transmitted to a large group. Lectures provide an indication of the quality and quantity of knowledge and understanding expected to be gained by the end of the course. In the majority of cases attendance at lectures is directly linked to exam success. Lectures serve to introduce the student to the information required to pass the exam in a measured and easily digestible format. Failure to attend 25% or more of lectures, without good reason, will result in the student being reported to Registry as being “at risk” (C6).
Practical classes enable the class to use a few of the techniques mentioned in the lectures, and to gain experience in the acquisition, recording, evaluation, interpretation and presentation of experimental results. Subject-specific, intellectual and written communication skills are assessed in the written degree examination and in practical reports. Practical and numerical skills are assessed in practical reports. Communication, interpersonal and teamwork skills are encouraged in tutorials and practicals; these are not formally assessed. All practical sessions are compulsory and each practical report will contribute 5% of final mark.
The continuous assessment sessions that follow each of the course modules provide the opportunity for students to engage with the lecture material in a staged and structured manner. Each assessment will follow a relevant tutorial session that will provide the student with the opportunity to discuss lecture material in a small group setting. These 50 minute assessments can be attempted by the students on any computer at any time over a period of a week after the finish of the relevant block of lectures. Each assessment will contribute 5% of final marks
Learning to understand is an active process and we encourage you to check and organise (in ways best suited to your learning style) material presented in each set of lectures by referring you to the set text. In the notes on Assessment you will see that “Detailed and thorough answer showing both knowledge and comprehension” is the standard for 1st class marks. This means that a well organised and argued response that demonstrates knowledge and understanding will attract the highest marks.
Lecture 1
Title: Introduction to BI20M3 course
Lecturer: Dr. Alasdair MacKenzie
Content: A welcome and introduction to the course. This lecture will include a summary of course requirements and student responsibilities.
Module 1; Nucleic Acids
This module will provide an overview of nucleic acid biochemistry with emphasis on the dynamic structure of DNA and the way in which it is replicated and packaged into chromosomes. The basic principles of modern recombinant DNA technologies will also be introduced. This module will be followed by a 50 minute in-course assessment.
Lectures 1 and 2
Title: Chemistry and structure of DNA and RNA
Lecturer: Dr. John Barrow
Content: The genetic code is held within a complex biological polymer, DNA. Moreover, to convert this genetic information into molecules that do work (proteins), a second nucleic acid, RNA, is needed. This lecture describes the structure of DNA and RNA, how their structures were elucidated and the relationship between structure and function in nucleic acids. The concept of chemical instabilities within DNA giving rise to mutations is also introduced.
Lecture 3
Title: Chromosome structure
Lecturer: Dr. John Barrow
Content: Chromosomes must not only contain genes but must also encode sequences that regulate gene transcription and the replication and segregation of chromosomes. Thus these huge DNA molecules, especially when considered in relation to the size of a cell, must be packaged into a more compact form. This is a particular problem for eukaryotes with their multiple very large chromosomes. DNA supercoiling is essential to compact DNA but is not sufficient on its own. Histones and other proteins bound to the DNA are needed to pack the DNA into highly ordered structures. The same principles apply to the compaction of prokaryotic chromosomes but these nucleoprotein structures are less ordered in prokaryotes.
Lecture 4
Title: DNA replication
Lecturer: Dr. John Barrow
Content: The complex structure of DNA requires complex systems to replicate it. This lecture will describe the fundamental rules of DNA replication and experiments which helped to uncover these rules. The basic reaction of DNA replication will be described followed by a detailed description of how this reaction is catalysed in E. coli. The essential requirements of accuracy and processivity will be related to the structure and function of the E. coli replication machinery.
Lecture 5
Title: DNA repair and genome evolution
Lecturer: Dr. John Barrow
Content: The consequences of the chemical instability of DNA (mentioned in the first two lectures) will be described in relation to the generation of mutations. How cells try and minimise the chances of alterations in the genetic code occurring will be described. No biological process is 100% accurate and some of these changes to the DNA sequence arise as a result of errors made by DNA polymerases. How these errors are corrected by mismatch repair will be discussed. Other changes to the genetic code arising from non-enzymatic transformations (DNA damage) must also be minimised and the many repair options that exist to deal with the different types of DNA damage will be described. The effects of DNA damage on DNA replication and genome evolution will also be introduced.
Lectures 6 and 7
Title: DNA technologies
Lecturer: Dr. John Barrow
Content: The late 20th century explosion in molecular biological techniques has facilitated major leaps in our understanding of fundamental biological processes. It has also allowed the genetic engineering of organisms. This lecture will describe the basic techniques of DNA cloning. It will also describe how the chemical properties of DNA can be exploited to analyse recombinant DNA molecules by hybridisation, by DNA sequencing, and by the polymerase chain reaction. The use of DNA microarrays to analyse not just single genes but whole genomes will also be discussed.
Lecture 8
Title: Genome alterations – genetically modified organisms
Lecturer: Dr. John Barrow
Content: The technologies of molecular biology discussed in lectures six and seven can be exploited to alter the genomes of a wide range of organisms. This lecture will describe how recombination can be harnessed to introduce stretches of engineered DNA into the genomes of bacteria, plants and animals.
Module 2; Gene expression and regulation
One of the most important questions within modern biology centres on how one- dimensional information held within the DNA is turned into healthy living 3-dimensional organisms that are able to interact with their environments. This module will describe how this information is decoded by transcription and translation to form proteins and how organisms control these processes to ensure that the correct proteins are produced in the correct cells at the correct times and in the correct amounts. Textbook references, Lehninger Principles of Biochemistry (4th ed), Chapter 26, 27 and 28. This module will include a small group tutorial session that will afford students the opportunity to address the course content with a member of staff. The module will be followed by a 50 minute course assessment.
Lecture 1
Title: Transcription in prokaryotes
Lecturer: Dr. Alasdair MacKenzie
Content: The first lecture in this series will deal with basal transcription in prokaryotes and will describe how the RNA polymerase enzyme "transcribes" the genetic information in DNA to the messenger RNA that will encode a protein. We will also describe how rates of prokaryotic transcription are controlled using specific examples of metabolic enzymes whose activity is controlled at the level of transcription (e.g. β-galactosidase).
Key words: Transcription, mRNA, tRNA, rRNA, DNA-directed RNA polymerase, -factor, Template strand, termination, Operator, Operon, lac operon
Lecture 2
Title: Transcription in Eukaryotes
Lecturer: Dr. Alasdair MacKenzie
Content: This lecture will describe the major differences between prokaryotic and eukaryotic transcription. Although the basic principles are the same, eukaryotic transcription is a much more complex process than prokaryotic transcription and allows for the greater degrees of control required to produce complex multicellular organisms. This lecture will introduce basic concepts in eukaryotic transcription such as the assembly of the basal transcriptional machinery to form the preinitiation complex (PIC).
Key words: RNA polymerase II, TATA binding protein, Pre-initiation complex (PIC), Initiator sequence, promoter sequence, Transcription factors. Initiation complex, elongation, termination
Lectures 3 and 4
Title: Gene regulation in Eukaryotes
Lecturer: Dr. Alasdair MacKenzie
Content: In order for complex processes such as embryonic development and human health to occur the activity of a large number of genes within the genome must be coordinated with an enormous degree of precision. This precision is controlled by a class of DNA binding proteins called DNA-binding transactivators that, when activated by the cellular machinery, displace histones to bind DNA sequences called enhancers to form enhancesome complexes. Enhancesome complexes may form at some distance from the gene being activated and it is now known that they interact with the pre-initiation complex through long distance looping of intervening DNA. This lecture will introduce these processes many of which have only recently been discovered.
Key Words: Enhancer, promoter, DNA-binding transactivators, Histones, co-activators, TFIID.
Lecture 5
Title: RNA processing
Lecturer: Dr. Alasdair MacKenzie
Content: This lecture will introduce the concepts of post transcriptional processing of eukaryotic mRNA and will describe how the primary transcript is spliced, "capped" and "tailed" before being transported from the nucleus to the cytoplasm to take part in the next stage of gene expression; translation.
Key words: Intron, Exon, 5’ cap, Poly(A) tail, Splicing, alternative splicing
Lecture 6
Title: The genetic code
Lecturer: Dr Alasdair MacKenzie
Content: This set of lectures deals with the way in which genetic information carried in the structure of DNA is translated into the structure of proteins encoded by DNA. Three bases read in sequence along a DNA template form a ‘triplet’ code-word. Sequences of triplets are transcribed into sequences of complementary three-base ‘codons’ in messenger RNA (mRNA). Codon sequences are translated into sequences of amino-acid residues in polypeptides. Each of the twenty coded amino-acids has at least one codon. The genetic code (that is, which 3-base code-words specify which amino-acids) was solved using synthetic RNA molecules as mRNAs in a test-tube protein-synthesising system. The code turns out to be degenerate (several amino-acids are specified by more than one code-word), non-overlapping (individual code-words are discrete), comma-less (individual code-words are not separated by non-coding bases) and near-universal (with few exceptions, the same code-words are assigned to the same amino-acids throughout nature). Code-words that are similar to one another tend to be assigned to the same amino-acid or to amino-acids with similar structures. This non-random assignment and degeneracy in general minimise deleterious effects of mutation.
Key Words: Translation, Messenger RNA (mRNA), Central Dogma of Molecular Biology, Genetic Code, Triplet, Codon, Degeneracy, Non-overlapping, comma-less, near-universal nature of code, Frame-shift mutation, Point (single-base) mutation, Silent mutation, Conservative mutation, Open reading frame, Overlapping genes
Lecture 7
Title: Transcription
Lecturer: Dr Alasdair MacKenzie
Content: The genetic code contained within the mRNA must be “translated” into proteins. This lecture will describe the fascinating choreography of the ribosome subunits, tRNA, mRNA and Amino-acyl tRNA synthetases required for the production of a complete polypeptide.
Key Words: Transfer RNA (tRNA), Adaptor function, Clover-leaf structure, Anticodon, Amino-acyl tRNA synthetase, Wobble hypothesis, Proof-reading during translation
Lecture 8
Title: Post transcriptional modification and degradation.
Lecturer: Dr Alasdair MacKenzie.
Content: Once translated many proteins in eukaryotes need to be further altered by a number of processes that include proteolytic cleavage, the formation of disulfide bonds, glycosylation and phosphorylation. Collectively these processes are called post-translational modifications and they are essential for the normal functioning of most human proteins. In eukaryotes any of these processes occur in a part of the cell called the endoplasmic reticulum (ER). Once translated and modified proteins are then sorted and distributed by another cellular structure called the Golgi apparatus. Another critical aspect of protein metabolism is protein degradation where proteins are “tagged” for destruction. This avoids the build up of excessive un-needed protein in the cell.
Key words: Post-translational modification, disulfide bonds, glycosylation, phosphorylation endoplasmic reticulum, Golgi apparatus, protein degradation.
Module 3; Proteins
This module will provide a comprehensive introduction to protein biochemistry, building on the basic chemistry of amino acids and peptides. The properties of proteins will be described, using a number of specific examples. The final lectures in the module will consider the methods used to study proteins. These provide the information that underlies our current understanding of protein structure and function. This module will include a small group tutorial session that will afford students the opportunity to address the course content with a member of staff. The module will be followed by a 50 minute in-course assessment.
Lecture 1
Title: Amino acid biochemistry; amino acids as buffers; amino acid diversity
Lecturer: Dr John Barrow
Content: Proteins fulfil a diversity of functions, for example as enzymes, as structural elements of cells and tissues, as carriers of gases and nutrients, as contractile elements in muscle, as antibodies, and as hormones. All this diversity comes from relatively simple building-blocks, L-amino-acid residues. Amino-acids act as zwitterions, and may therefore be used as buffers for biological studies. Buffering ability is an important property of proteins, the charge of which alters as the pH changes. The pH at which a particular protein has no net charge is called its isoelectric point.
Keywords: Amino acid, buffering
Lecture 2
Title: Protein structure
Lecturer: Dr John Barrow
Content: Four levels of structure in a protein molecule may be distinguished. The primary structure is the sequence of amino-acid residues, which is always written with the N-terminus on the left and the C-terminus on the right. The terms secondary and tertiary structure describe features of the three-dimensional folding of the polypeptide chain; they determine the final shape of the molecule and the juxtaposition of individual amino-acid residues within the folded structure. Secondary structural features such as the -helix and the -sheet occur in varying proportions in different proteins. Tertiary structure relies on a number of different types of force, including hydrogen bonds, ionic bonds, hydrophobic interactions and disulphide bonds. Quaternary structure describes the aggregation of several polypeptide chains, with specific interactions between the polypeptide sub-units (also called monomers); the sub-units are held together mainly by hydrophobic interactions.
Keywords: three-dimensional structure, -helix, -sheet
Lectures 3 and 4
Title: Globular proteins (1 and 2)
Lecturer: Dr John Barrow
Content: Different types of protein structure are required for different functions. All proteins fall into two broad classes: globular and fibrous proteins. Globular proteins include insulin, which is important in glucose homeostasis, and immunoglobulins, which are one of the body’s responses to infection. Other globular proteins include myoglobin, which acts as an oxygen carrier and contains a haem prosthetic group. Haemoglobin is a member of the same family, but is more complex in its structure. It contains four subunits, held together by hydrophobic forces. It shows co-operative binding of oxygen and allosteric regulation by carbon dioxide and protons. The mode of action of transcription factor proteins is reliant on their modular structure. We will examine how transcription factors can generally be divided into 2 components; a DNA binding domain and an RNA polymerase activation domain. This lecture will describe the different DNA binding domains or "motifs" and how these allow DNA binding. In addition, the modes of action of various activation domains will be described.
Keywords: globular protein, insulin, immunoglobulin, myoglobin, haemoglobin, transcription factors
Lecture 5
Title: Fibrous proteins – keratin, elastin and collagen
Lecturer: Dr John Barrow
Content: In contrast to most enzymes, circulating and intracellular proteins, which are globular, fibrous proteins have structural roles. An example is keratin, which is made up of -helices. Collagens contain an unusual triple helix that is quite distinct from the -helix. These helices form only when there are repeat structures in the polymer, in which glycine occurs at every third monomer position. Collagen is also rich in proline and lysine residues, both of which may be hydroxylated; this is an example of a post-translational modification. Elastin achieves the necessary flexibility by means of unique cross-links between lysine residues.
Keywords: fibrous protein, -keratin, collagen, elastin
Lecture 6
Title: Membrane protein, transmembrane proteins
Lecturer: Dr John Barrow
Content: Membranes represent a barrier but also contain important activities, reflecting their protein components. The structures of important membrane proteins will be explained, with emphasis on how an α-helix can form the transmembrane part of a protein. Proteins are a major component of cells and are present in all cellular compartments.
Key words: Membrane, phospholipid, GPI-anchor, hydrophobic, hydrophilic, cell-cell interactions, membrane fusion, membrane transport, receptors
Lecture 7
Title: How we study proteins (1)
Lecturer: Dr John Barrow
Content: Proteins are analysed by techniques like electrophoresis, which can give information on size and charge. The important technique of SDS-PAGE will be described in detail, as will the analysis of data to allow us to estimate the molecular mass of proteins and their component chains.
Keywords: Electrophoresis, SDS-PAGE
Lecture 8
Title: How we study proteins (2)
Lecturer: Dr John Barrow
Content: Proteins may be identified by determining their amino-acid composition and, especially, their N-terminal sequence. Many analyses of proteins require them to be cut into smaller pieces by specific proteases.
Keywords: amino-acid composition, amino-acid sequence, proteases
Lecture 9
Title: How we study proteins (3)
Lecturer: Dr John Barrow
Content: The specificity of antibodies is used to provide fast and sensitive assays in many different applications. Among these are enzyme-linked immunosorbent assays (ELISA) and immunoblotting (or western blotting).
Keywords: antibodies, enzyme-linked immunosorbent assay (ELISA), immunoblotting
Textbook Reference: Lehninger Principles of Biochemistry, Chapters 5, 6, 7 and 12
Module 4; Genetic disease
This module will explain how genomes can be compromised by mutation and chromosomal rearrangements leading to disorders such as Downs syndrome, cystic fibrosis, fragile-X syndrome and cancer. Recommended text Human Molecular Genetics by Strachan and Read (3rd edition) and Emery's Elements of medical genetics (any edition). This module will be followed by a one hour in-course assessment.
Lecture 1
Title: Genetic disease
Lecturer: Dr Martin Collinson
Content: This first lecture will revise and extend 1st year lectures on genetic inheritance, covering the basic types of Mendelian inheritance (autosomal recessive, autosomal dominant and X-linked), with particular reference to human genetic disease families, and will outline the different types of genetic disease – simple (Mendelian) and complex.
Keywords: Mendelian, inheritance, pedigree, autosomal, X-linked, dominant, recessive
Lecture 2
Title: Cystic fibrosis and autosomal recessive inheritance
Lecturer: Dr Martin Collinson
Content: The autosomal recessive condition, cystic fibrosis, is carried by around 1 in 25 of the Caucasian population. The gene for the condition, the CFTR gene, produces a protein which forms a chloride iron channel. Mutations within the gene can have different effects on the production of the protein and on its function within the cell. The spectrum of different mutations that give rise to the disease will be described.
Keywords: Cystic fibrosis, autosomal, recessive, mutation, ion channel
Lecture 3
Title: Cancer and autosomal dominant inheritance
Lecturer: Dr Martin Collinson
Content: Cancer affects 1 in 3 individuals in their lifetime but only a very small percentage of them are associated with the genetic predisposition. Most cancer is multifactorial but there are several types that show autosomal dominant inheritance. In this lecture we will consider one of these, colorectal cancer, which can be associated with several genetic conditions for which the genes and their mutations have been identified. As a result of this individuals found to be predisposed may be offered appropriate screening to decrease their risk.
Keywords: Cancer, autosomal, dominant, multifactorial
Lecture 4
Title: Genome rearrangements and disease
Lecturer: Dr Martin Collinson
Content: Triplet repeat diseases – Huntington’s disease, fragile X mental retardation, myotonic dystrophy and others – are caused by expansions of unstable trinucleotide sequences such as (CTG)n. Mechanisms of DNA instability and triplet repeat expansion will be described. We will also look at chromosomal deletions and translocations, their effects on gene expression, and their importance in genetic disease and cancer.
Keywords: Huntington, myotonic dystrophy, fragile X, trinucleotide repeat, DNA instability, deletion, translocation, cancer
Lecture 5
Title: The Human genome and genome projects
Lecturer: Dr Martin Collinson
Content: Humans and other species, such as experimental animals and agriculturally important animals and plants, are having their genomes sequenced. This lecture gives an overview of technology – the factory-scale application of molecular genetics with computers and automation; the basic dideoxy sequencing method and its automation; top-down and bottom-up strategies, and contigs. We will look at web-based databases of genome project information, and how these can help scientists quickly find genome information. Most human genes have homologues in other species – we have a common evolutionary origin. Large regions of mammalian genomes are “syntenic”, i.e. the genes and their arrangement are conserved between species.
Keywords: Genome, human, homologue, DNA sequence, contig
Lecture 6
Title: Genetic diagnosis and gene therapy
Lecturer: Dr Martin Collinson
Content: The implications of genetics research for prenatal diagnosis, predictive testing and surveillance will be discussed and put in context. Methods for diagnosis based on DNA testing of samples obtained by amniocentesis and chorionic villus sampling will be described. The role of the genetic counsellor and other professionals, and the ethical and practical issues that arise, will be discussed. Recent advances in gene therapy will also be covered.
Keywords: Diagnosis, prenatal, gene therapy, genetic counselling
This course includes Practical sessions.
Further details will be provided within the accompanying Practical & Tutorial manual.
Please read these notes carefully. They are designed to help you. They are not, however, comprehensive, since rules and notices cannot in themselves ensure safety. You have an important part to play in ensuring your own safety. Think carefully about all you do in the laboratory, and, if you are in doubt, ask the supervisory staff for advice.
Protective Clothing:
You must possess and wear a laboratory coat during laboratory classes, and will not be allowed to carry out practical work without one. Make sure that your footwear is non-slip, and able to protect your feet from falling glassware, etc. Safety spectacles are available in the laboratory, and, for certain procedures, must be worn.
Fire and Accident Precautions:
During the first practical class of the session, the supervisory staff will tell you where the fire-extinguishers and first-aid equipment are located in the rooms in which you will be working. If you enter any other room during the class, note where these facilities are before starting work.
If you should have an accident in the laboratory – even a minor one – notify the supervisory staff immediately.
Details will be provided within the accompanying Practical & Tutorial manual.
For students intending to study Biochemistry and or Molecular Biology as a final degree option the following is advised. Also note that this is the textbook for the BI25M7 Energy for Life course that runs next term –
Lehninger Principles of Biochemistry by D.L. Nelson & M.M. Cox (2005) Fifth Edition, Worth Publishers Inc., New York. ISBN 0-7167-4339-6. Price £41.99. Queen Mother Library Heavy Demand Section Reference Number 574.192 Leh 4.
For Dr Collinson’s Lectures; Recommended texts include Human Molecular Genetics by Strachan and Read (3rd edition) and Emery's Elements of Medical Genetics (any edition).
Students who are studying other degrees may prefer the following instead:
Instant Notes in Molecular Biology by Turner, P.C., McLennan, A.G., Bates A.D. & White M.R.M. (2000) Second Edition, Bios, Oxford. ISBN 1859961525 [574.88 Tur]. Price £17.99. Queen Mother Library, Heavy Demand Section.
Reference number 574.192 (Ham).
The University has strict regulations on plagiarism. Make sure that you understand what constitutes plagiarism by reading the University guide on plagiarism at:
http://www.abdn.ac.uk/writing
Copying or plagiarising another person’s work, either from other students or published material in books or papers and submitted as your own for assessment is considered a form of cheating. This is considered by the University to be a serious offence and will be penalised according to the extent involved and whether it is decided there was an attempt at deliberate deception, or whether bad practice was involved. If you do use information or ideas obtained from textbooks or other published material you must give a precise reference to the source both at the appropriate point in your narrative and in a list of references at the end of your work. Direct quotations from published material should be indicated by quotation marks and referenced in the text as above.
TurnitinUK
TurnitinUK is an online service which compares student assignments with online sources including web pages, database of reference material, and content previously submitted by other users across the UK. The software makes no decision as to whether plagiarism has occurred; it is simply a tool which highlights sections of text that have been found in other sources thereby helping academic staff decide whether plagiarism has occurred.
As of Academic Year 2011/12, TurnitinUK will be accessed directly through MyAberdeen. Advice about avoiding plagiarism, the University’s Definition of Plagiarism, a Checklist for Students, Referencing and Citing guidance, and instructions for TurnitinUK, can be found in the following area of the Student Learning Service website: www.abdn.ac.uk/sls/plagiarism
Assessment in BI20M3 consists of:
(i) Four fifty minute in-course test to be carried out after each teaching module (20% of final mark).
(ii) Assessment of practical reports (20% of final mark);
(iii) A 2 hour written examination (60% of final mark).
(a) Computer based continuous tests ~ online computer based tests will be available online for one week after the last lectures on each module. Thus tests 1, 2, 3 and 4 can be attempted during the whole of weeks 15, 18, 21 and 23 respectively. These tests will not be invigilated and only 50 minutes will be allowed to complete the test once the session is started by the students so it is advisable that the students know their lecture material before the start of the test to make best use of their time. Only one attempt will be allowed so it is advisable to prepare well before the test. These tests will contribute 20% of the students final marks. For further enquiries, please contact the course co-ordinator Dr MacKenzie or Lyndsay McEwan.
(b) The Examination paper in January will take the form of four essay type questions to be answered over a two hour period of time. The exam paper is divided into four sections (A -D) that reflect the contents of each course module. There are two questions in each section and you may answer a maximum of one question in each section. All questions carry equal marks. The Course Co-ordinator will give more information about material examined in the different sections of the paper during the course.
(c) Criteria used in assessing Practical Reports and in marking Examination answers are set out in a table which is included in the Course Guide, and which gives details of the University Common Assessment Scale (CAS) used by the School.
(d) Oral Examinations may be arranged for students who, although failing, have marks that fall close to the pass/fail borderline. These examinations normally last for 15-20 minutes. In the examination, any aspect of the course may be examined. Students invited for an Oral Examination will be e-mailed as soon as possible after the Written Examination.
Important Notes
Students are responsible for checking whether they will he required for an oral examination by regularly monitoring their University email in the days following the written examination.
Students should also note that candidates asked to attend for oral examination, but failing to do so, will be assigned their pre-oral (failing) CAS assessment. It is important, therefore, that you do not plan to take a holiday in the three weeks or so after the exam unless you can be certain that you will not be required to attend an oral examination. Following the exam therefore, if you intend to be absent from Aberdeen, please check with the School of Medical Sciences office to see if you are to be called for a viva exam. This advice also applies to the August re-sit examinations.
(e) Re-sit Written Examination papers follow the same format as those used in the first diet of examination. For re-sit candidates, marks for Practical Reports and Continuous Assessments still count for a resit examination in the same academic year. Re-sit candidates may be invited to attend an Oral Examination, according to the criteria and arrangements set out in Section (d) above.
(f) Examination results will be posted on the student portals as soon as they are available (approx 3 weeks), after the examination.
(g) The External Examiner in Biochemistry is an overall arbiter in all matters connected with the assessment of students in this course.
Dr John Barrow
Prof Nuala Booth
Dr Alasdair MacKenzie
Prof Peter McGlynn
Prof Peer Wulff
Attendance is required at all lectures and practical classes and attendance is recorded.
Practical Reports must be handed in by the deadlines set out in the timetable. Failure to attend classes, irregular attendance at lectures and/or failure to submit Practical Reports by the specified deadlines may lead to the School reporting you to the Senate Office by recording a ‘C6’ on your student record. In addition the course organiser has the capacity to record a student as a “C7” with Registry for poor attendance at lectures, practical’s and tutorial that may result in the withdrawal of class certificates.
Practical Reports which are not submitted by the dead-line specified in the timetable will not be marked. Do not ask the Course Organiser, other lecturers, the Teaching Laboratory technicians, your demonstrator, or your tutor to accept late work. If you are unable to meet the dead-line for handing in a Practical Report, or if you are absent from a tutorial, practical or any other course work, must complete a “Missing Work and Absence from Classes” form (obtainable from the Teaching Labs) and leave it in the box provided. Forms must be submitted within 7 days of return after illness or 7 days from the hand-in date if the excuse is to be considered. A properly completed form containing a valid medical or other excuse will ensure that you are not penalised. Incomplete forms will not be accepted.
We value students’ opinions in regard to enhancing the quality of teaching and its delivery; therefore in conjunction with the Students’ Association we support the operation of a Class Representative system.
The students within each course, year, or programme elect representatives by the end of the fourth week of teaching within each half-session. In this course/school/programme we operate a system of course/year/programme representatives. Any student registered within a course/year or programme that wishes to represent a given group of students can stand for election as a class representative. You will be informed when the elections for class representative will take place.
What will it involve?
It will involve speaking to your fellow students about the course/year/programme you represent. This can include any comments that they may have. You will attend a Staff-Student Liaison Committee and you should represent the views and concerns of the students’ within this meeting. As a representative you will also be able to contribute to the agenda. You will then feedback to the students after this meeting with any actions that are being taken.
Training
Training for class representatives will be run by the Students Association. Training will take place in the fourth or fifth week of teaching each half-session. For more information about the Class representative system visit www.ausa.org.uk or email the VP Education & Employability vped@abdn.ac.uk . Class Representatives are also eligible to undertake the STAR (Students Taking Active Roles) Award; further information about the co-curricular award is available at: www.abdn.ac.uk/careers .
The University operates a system for monitoring students' progress to identify students who may be experiencing difficulties in a particular course and who may be at risk of losing their class certificate. If the Course Co-ordinator has concerns about your attendance and/or performance, the Registry will be informed. The Registry will then write to you (by e-mail in term-time) to ask you to contact their office in the first instance. Depending on your reason for absence, the Registry will either deal directly with your case or will refer you to your Adviser of Studies or a relevant Support Service. This system is operated to provide support for students who may be experiencing difficulties with their studies. Students are required to attend such meetings with their Adviser of Studies in accordance with General Regulation 8.
Set criteria are used to determine when a student should be reported in the monitoring system. You will be asked to meet your Adviser if any of the following criteria apply for this course:-
either (i) if you are absent for a continuous period of two weeks or 25% of the course (whichever is less) without good cause being reported;
or (ii) if you are absent from two small group teaching sessions (e.g. tutorial, laboratory class) without good cause;
or (iii) if you fail to submit a piece of summative or a substantial piece of formative in-course assessment by the stated deadline'
If you fail to respond within the prescribed timescale (as set out in the e-mail or letter), you will be deemed to have withdrawn from the course concerned and will accordingly be ineligible to take the end-of-course assessment or to enter for the resit. The Registry will write to you (by e-mail in term-time) to inform you of this decision. If you wish consideration to be given to reinstating you in the course you will require to meet with the Convener of the Students' Progress Committee.
ABSENCE FROM CLASSES ON MEDICAL GROUNDS
Candidates who wish to establish that their academic performance has been adversely affected by their health are required to secure medical certificates relating to the relevant periods of ill health (see General Regulation 17.3).
The University’s policy on requiring certification for absence on medical grounds or other good cause can be accessed at:
www.abdn.ac.uk/registry/quality/appendix7x5.pdf
You are strongly advised to make yourself fully aware of your responsibilities if you are absent due to illness or other good cause. In particular, you are asked to note that self-certification of absence for periods of absence up to and including eleven weekdays is permissible. However, where absence has prevented attendance at an examination or where it may have affected your performance in an element of assessment or where you have been unable to attend a specified teaching session, you are strongly advised to provide medical certification (see section 3 of the Policy on Certification of Absence for Medical Reasons or Other Good Cause).
A class certificate is defined as “a certificate confirming that a candidate has attended and duly performed the work prescribed for a course”. The period of validity for a class certificate is limited to the academic year in which it is awarded and the academic year immediately following. Hence, candidates have a maximum of four opportunities to take the end-of-course assessment without re-attendance i.e. the normal (January or May) diet and the August resit diet in the year in which the course is taken and the year immediately following.
Students who have been reported as ‘at risk’ through the system for monitoring students’ progress due to their failure to satisfy the minimum criteria (as outlined above) may be refused a class certificate. If you are refused a class certificate, you will receive a letter from the Registry (e-mail in term-time) notifying you of this decision. Students who are refused a class certificate are withdrawn from the course and cannot take the prescribed degree assessment in the current session, nor are eligible to be re-assessed next session, unless and until they qualify for the award of a class certificate by taking the course again in the next session.
If you wish to appeal against the decision to refuse a class certificate should do so in writing to the Head of School within fourteen days of the date of the letter/e-mail notifying you of the decision. If your appeal is unsuccessful, you have the right to lodge an appeal with the relevant Director of Undergraduate Programmes within fourteen days of the date you are informed of the Head of School’s decision.
You will receive a University e-mail account when you register with the University Computing Centre. The University will normally use e-mail to communicate with you during term-time. These e-mails will be sent to your University e-mail account, which you can access using the newly introduced Student mail network (http://www.abdn.ac.uk/studentmail/).
You should also access MyAberdeen as soon as you can and on a regular basis (at least once a day). In addition to providing learning resources, MyAberdeen will provide you with regular updates regarding the course including possible lecture cancellations, changes in room bookings and general discussions regarding the course. As far as possible this information will be posted at least a day before the event. Please take full advantage of this important resource.
It is your responsibility to check your e-mail on a regular (at least weekly) basis and to tidy the contents of your e-mail inbox to ensure that it does not go over quota (see http://www.abdn.ac.uk/diss/email/mailquota.hti for guidance on managing your e-mail quota). It is recommended that you use your University e-mail account to read and respond to University communications. If you already have a non-University e-mail account that you use for personal correspondence, it is possible to set up automatic forwarding of messages from your University e-mail account to your personal e-mail address (see http://www.abdn.ac.uk/local/mail.forward/) but, should you do so, it is your responsibility to ensure that this is done correctly. The University takes no responsibility for delivery of e-mails to non-University accounts.
You should note that failure to check your e-mail or failure to receive e-mail due to being over quota or due to non-delivery of an e-mail forwarded to a non-University e-mail account would not be accepted as a ground for appeal (for further information on appeals procedures, please refer to:
http://www.abdn.ac.uk/registry/quality/appendix5x18b.pdf)
Please note that the following items are provided in an accompanying hand-out:
1. Instructions for four Practical Classes, Practical Report templates and Laboratory Safety Notes
2. Instructions for 3 Tutorial Classes
3. Self-assessment questions and answers
