Download MOLECULAR BIOLOGY and GENETICS

University of Sydney
MBLG 1001 and MBLG 1901
SEMESTER 2, 2009
MOLECULAR BIOLOGY and GENETICS
MBLG1001 is designed to give you an introduction to Molecular Biology. It is a 6
credit point junior level course offered in 2nd semester. This course is essential
for all students wishing to study either Biochemistry or Molecular Biology and
Genetics at intermediate or senior levels, and is highly recommended for all
students planning to study Biology at higher levels.
The theory component of the course is presented in 25 lectures (2 per week). It covers the
physical and chemical properties of the information containing biopolymers; nucleic acid and protein,
and the flow of genetic information from DNA to RNA to Protein. The basic principles of molecular
genetics are also introduced and some of the current techniques used in molecular biology research are
presented.
The practical course (6 five hour sessions; one every fortnight) gives you hands-on experience in
the methodology behind many of the modern techniques in molecular biology. It is hoped that at the
end of this laboratory course you will have gained the strategies to design an assay to measure enzyme
activity, to isolate macromolecules such as DNA, to perform and to analyse restriction digestions and
to use spectrophotometry to identify compounds and measure their concentrations in a wide variety of
experimental situations. These experiments have been chosen to give you a solid foundation from
which you can later develop the more sophisticated techniques of molecular biology. A strong
emphasis is placed in the acquisition of generic skills (such as writing, communication, computing,
problem solving and experimental design) in the laboratory sessions.
The advanced component is designed for students interested in continuing in molecular
biology. It consists of 7 advanced lectures (replacing 7 regular lectures) and 3 advanced laboratory
sessions (replacing 3 regular practical classes). The advanced lectures will focus on the experiments
which led to key discoveries in molecular biology. The advanced practical sessions will give students
the opportunity to explore alternative molecular biology experimental techniques. Attendance at
MBLG1999 seminars is strongly encouraged.
MBLG1001 & MBLG1901 Handout
page 1
THE LECTURE COURSE
Lecture
Day
Time
Location
MBLG1901 (Adv) 1st
Monday
12 noon
Chemistry Lecture Theatre 4
MBLG1901 (Adv) 2nd
Wednesday
8 am
Eastern Avenue Lecture Theatre
1st
Monday
9 am
Eastern Avenue Auditorium
1st lecture repeated
Tuesday
9 am
Eastern Avenue Auditorium
2nd
Thursday
9 am
Eastern Avenue Auditorium
2nd lecture repeated
Friday
12 noon
Eastern Avenue Auditorium
Lecturers
Your lecturers for this course are:
Dr Dale Hancock Room 377, Biochemistry & Microbiology Building, Ph. 9351 4024,
Email: [email protected]
Assoc. Prof. Gareth Denyer, School of Molecular & Microbial Biosciences
Email: [email protected]
Professor Mitchell Gus, School of Molecular & Microbial Biosciences
Email: [email protected]
Professor Merlin Crossley, School of Molecular & Microbial Biosciences
Email: [email protected]
Dr. Bruce Lyon, School of Biological Sciences,
Email: [email protected]
TEXTBOOK:
A custom publication entitled “An introduction to Molecular Biology” by Horton et al; Klug
and Cummings is available from the Co-Op bookshop.
Biology by Knox et al, your first semester Biology textbook is also recommended as an
additional reference.
MBLG1001 & MBLG1901 Handout
page 2
LECTURE OUTLINE MBLG1001
Week
1
Starting Lecture
Mon Number
th
27 July
1
2
2
Introduction to
Molecular
Biology
Administrative details then introduces the scope of Molecular
Biology, the concepts involved in the flow of genetic
information. Why is life carbon based?
2
Molecules of
Life:
Biopolymers
Introduces the general properties of biopolymers, briefly
describing the four classes of biopolymers. The distinction
between sequence dependent, hence template directed
versus non-sequence dependent is discussed.
3
Amino Acids:
the building
blocks of
proteins
The diversity of amino acid side chains is introduced by
functional group, charges on amino acid side chains at
physiological pH and phosphorylation and acetylation
modifications are discussed.
4
Forming the
Protein
The formation of the peptide bond and its properties. The
weak forces which maintain protein 3-D structure. Why
proteins have secondary structures (alpha helix, beta sheet).
Folded proteins and their function.
5
Protein
Structure
The importance of protein structure for function. Tertiary
structures, subunits and quaternary structures. Examples of
proteins that interact with nucleic acids, in a non-sequence
specific and sequence specific manner.
6
Enzymes as
Biological
Catalysts
What are enzymes? How do they work? Kinetics versus
thermodynamics. How do we measure enzyme activity? plus
a brief introduction to kinetics, identifying Km, Kcat and
Vmax.
7
Introduction to
nucleic acids
Presents the historical context to introduce DNA structure,
the key experiments; Avery, McLeod et al, Waring blender,
Chargaff, Watson and Crick. How the structure was solved.
Properties of genetic material.
Nucleic acid
structure
The chemistry of nucleic acids starting with
ribose/deoxyribose, bases, base pairing and tautomers, the
formation of phosphodiester bonds, the major and minor
grooves. How proteins interact in a base specific manner
through the major groove.
th
3
10
August
3
th
4
4
17
August
Description
1
rd
3
August
Title
8
MBLG1001 & MBLG1901 Handout
page 3
LECTURE OUTLINE MBLG1001 cont
Week
Starting
Monday
Lecture
Number
24
August
5
9
10
Enzymology of
Replication
Enzymes involved in the of unwinding the strands,
Supercoiled DNA and topoisomerases, polymerisation and
processing the Okazaki fragments, putting it all together.
11
Introduction to
Transcription
Transcription initiation, elongation and termination in
prokaryotes. The structure and properties of E.coli RNA
polymerase, a multi-subunit enzyme, sigma subunit and
initiation, Rho dependent and independent termination,
polycistronic mRNA.
12
Regulation of
Gene
Expression
Importance of regulating gene expression, transcriptional
initiation as the major site, different sigma factors, proteins
which control transcription.
13
The genetic
code
The triplet code, elucidation of the genetic code,
degeneracy-synonyms, start codons, nonsense codons,
frameshift mutations, role of tRNA, initiator RNA, formyl
methionine in prokaryotes
14
Translation
Review of the three different RNA types, mRNA, tRNA,
rRNA , modified bases in tRNA. Amino acyl tRNA
synthetase (details of its activity), structure and assembly
of ribosomes, the catalytic role of RNA, translation by the
E.coli ribosome, initiation, elongation and release factors,
15
Eukaryotic
Gene
Expression
Eukaryotic transcription, types of RNA polymerases,
introns and exons, RNA splicing & processing, role of
transcription factors, enhancers, eukaryotic translation,
mitochondria.
16
DNA isolation
Key Laboratory
Restriction endonuclease digestion
Techniques in
Agarose gel electrophoresis
Molecular
DNA-DNA hybridization
Genetics
DNA amplification with the PCR
17
Genetic
Mapping of
Genomes
st
6
31
August
6
th
7
7
September
7
th
8
14
September
8
st
9
21
September
Description
Semi-conservative replication, Meselson-Stahl experiment,
Evidence for bidirectional replication in E. coli and the
Introduction to
problems it presents. Initiation.The search DNA
DNA Replication
polymerases and the discovery of DNA polI and Klenow.
DNA pol I mutants
th
5
Title
MBLG1001 & MBLG1901 Handout
Cystic Fibrosis: mapping the gene for an inherited disease
Markers for genetic maps & linkage
Restriction fragment length polymorphisms (RFLPs)
Gene mapping by human pedigree analysis,
page 4
LECTURE OUTLINE MBLG1001 cont
week
Starting
Monday
9
Lecture
Number
18
Title
Description
Physical Mapping
of Genomes
FISH (Fluorescent In Situ Hybridisation)
Physical mapping by restriction digestion
Chromosome walking
Physical mapping & cloning of the CF mutant
gene,
Mid semester break
th
10
5
October
10
Monday holiday
19
Whole Genome
Analysis
20
Bacteria as model organisms
Escherichia coli as
Growing
bacteria on solid & liquid media
a Model Genetic
Transposons,
plasmids & bacteriophage
System
Mapping genes in bacteria,
21
Gene Cloning
Fundamentals
Plasmid cloning vectors
Restriction, ligation & transformation
Antibiotic selection
Clone screening (insertional inactivation),
22
Gene Cloning
Strategies
Cloning genes or whole genomes
Plasmid gene libraries
cDNA & expression libraries
Screening of gene libraries,
23
Disease diagnosis (RFLPs)
Pre-natal Diagnosis
DNA fingerprinting (VNTRs & microsatellites)
& Genetic Testing
Genetic testing (social & ethical issues),
24
Genetic transformation (somatic or germ-line)
Mammals made-to-order (pharming & knockGene Therapy &
outs)
Pharmacogenomics
Human gene therapy (CF mutant gene)
Genetic medicine (DNA chips),
25
Sequence analysis of CF mutant gene alleles
How do different alleles arise?
Genes, Populations
Changing frequencies of alleles in
& Evolution
populations lead to evolution
Why are deleterious alleles maintained?
th
11
12
October
11
th
12
19
October
12
th
13
13
26
October
The Human Genome Project
Structural, comparative & functional
genomics
Bioinformatics
Proteomics,
MBLG1001 & MBLG1901 Handout
page 5
LECTURE OUTLINE MBLG1901
Week
1
Starting Lecture
Mon Number
th
27 July
1
2
3rd
August
2
10
August
3
4
17th
August
4
Introduction to
Molecular
Biology
Administrative details then introduces the scope of
Molecular Biology, the concepts involved in the flow of
genetic information. Why is life carbon based?
2
Molecules of
Life:
Biopolymers
Introduces the general properties of biopolymers, briefly
describing the four classes of biopolymers. The distinction
between sequence dependent, hence template directed
versus non-sequence dependent is discussed.
3
Amino Acids:
the building
blocks of
proteins
The diversity of amino acid side chains is introduced by
functional group, charges on amino acid side chains at
physiological pH and phosphorylation and acetylation
modifications are discussed.
4
Forming the
Protein
The formation of the peptide bond and its properties. The
weak forces which maintain protein 3-D structure. Why
proteins have secondary structures (alpha helix, beta
sheet). Folded proteins and their function.
5
Enzymes as
Biological
Catalysts
What are enzymes? How do they work? Kinetics versus
thermodynamics. How do we measure enzyme activity?
6
Measuring
Enzyme Action
How do enzymes work? Quantitating enzyme activity – rate
of the reaction, speed vs efficiency, Km, Kcat, Vmax
7
Introduction to
Nucleic Acids
How similar techniques were used to elucidate the structure
of DNA. The experiments of McLeod, Avery & McCartney
and Hershey & Chase, Chargaff, Watson and Crick
8
Nucleic acid
structure (adv)
Stability of DNA, UV absorbance, Negative charge,
Detection by fluorescence, manipulating the weak forces,
proteins that interact with DNA.
9
Semi-conservative replication, Meselson-Stahl experiment,
Evidence for bidirectional replication in E. coli and the
Introduction to
problems it presents. Initiation.The search DNA
DNA Replication
polymerases and the discovery of DNA polI and Klenow.
DNA pol I mutants
10
Enzymology of
Replication
th
5
5
24
August
Description
1
th
3
Title
MBLG1001 & MBLG1901 Handout
Enzymes involved in the of unwinding the strands,
Supercoiled DNA and topoisomerases, polymerisation and
processing the Okazaki fragments, putting it all together.
page 6
LECTURE OUTLINE MBLG1901 cont
Starting
Monday
week
6
st
31 August
6
7
th
7 September
7
8
th
14 September
8
9
st
21 September
Lecture
Title
Number
Description
11
Introduction to
Transcription
Transcription initiation, elongation and termination in
prokaryotes. The structure and properties of E.coli RNA
polymerase, a multi-subunit enzyme, sigma subunit and
initiation, Rho dependent and independent termination,
polycistronic mRNA.
12
Regulation of
Gene
Expression
Importance of regulating gene expression, transcriptional
initiation as the major site, different sigma factors, proteins
which control transcription.
The genetic
code (adv)
The triplet code, elucidation of the genetic code,
degeneracy-synonyms, start codons, nonsense codons,
frameshift mutations, role of tRNA, initiator RNA, formyl
methionine in prokaryotes Experiments on how the genetic
code and the wobble were predicted (Crick) and how they
were elucidated.
14
Translation
Review of the three different RNA types, mRNA, tRNA,
rRNA , modified bases in tRNA. Amino acyl tRNA
synthetase (details of its activity), structure and assembly
of ribosomes, the catalytic role of RNA, translation by the
E.coli ribosome, initiation, elongation and release factors,
15
Eukaryotic
Gene
Expression
Eukaryotic transcription, types of RNA polymerases,
introns and exons, RNA splicing & processing, role of
transcription factors, enhancers, eukaryotic translation,
mitochondria.
16
Key Laboratory
Techniques in
Molecular
Genetics
DNA isolation, Restriction endonuclease digestion
Agarose gel electrophoresis
DNA-DNA hybridization
DNA amplification with the PCR
17
Genetic
Mapping of
Genomes
Cystic Fibrosis: mapping the gene for an inherited disease,
Markers for genetic maps & linkage
Restriction fragment length polymorphisms (RFLPs)
Gene mapping by human pedigree analysis,
13
MBLG1001 & MBLG1901 Handout
page 7
LECTURE OUTLINE MBLG1901 cont
week
Starting
Monday
9
Lecture
Number
18
Title
Description
Physical Mapping
of Genomes
th
28 Sept
FISH (Fluorescent In Situ Hybridisation)
Physical mapping by restriction digestion
Chromosome walking
Physical mapping & cloning of the CF mutant
gene,
Mid semester break
th
10
5
October
10
19
20
Whole Genome
Analysis (adv)
21
Bacteria as model organisms
Escherichia coli as
Growing bacteria on solid & liquid media
a Model Genetic
Transposons, plasmids & bacteriophage
System
Mapping genes in bacteria,
21
Gene Cloning
Fundamentals
Plasmid cloning vectors
Restriction, ligation & transformation
Antibiotic selection
Clone screening (insertional inactivation),
22
Gene Cloning
Strategies
Cloning genes or whole genomes
Plasmid gene libraries
cDNA & expression libraries
Screening of gene libraries
23
Pre-natal Diagnosis
The power of the PCR in disease diagnosis &
& Genetic Testing
forensic identification
(adv)
24
Genetic transformation (somatic or germ-line)
Mammals made-to-order (pharming & knockGene Therapy &
outs)
Pharmacogenomics
Human gene therapy (CF mutant gene)
Genetic medicine (DNA chips),
25
Genes, Populations Molecular insights into the workings of
& Evolution (adv)
evolution.
th
11
12
October
11
th
12
19
October
12
th
13
13
26
October
Monday Holiday
MBLG1001 & MBLG1901 Handout
The science & politics behind the Human
Genome Project
page 8
LABORATORY OUTLINE MBLG1001 & 1901
Lab
Session
Title
Description
Introduction to Pipetting
This prac session is designed to familiarise students
with automatic pipettes, to introduce students to
biochemical calculations and the use of Excel in a
laboratory context. Assessment: lab calculations
assignment.
Introduction to Pipetting
The calibration of pipettes will be checked using 3
different methods of verification: weight,
spectrophotometry and radioactivity. Assessment
evaluation of validation methods, errors, accuracy and
reproducibility
Spectrophotometry
Introduces students to absorption spectra in the visible
range as a means of identification, extinction
coefficients, conversion factors and finding the
concentration of an unknown using a standard curve.
Measuring enzyme
Activity
Students set up an enzyme assay to measure the rate
of LDH activity in normal and abnormal sera. The rate
is calculated from spectrophotometric data and the
relationship between rate and [enzyme] is established.
The tissue origin of the LDH in the abnormal sera is
determined by zone electrophoresis. Assessment,
both Normal and Advanced: diagnostic reports.
DNA Isolation
DNA is isolated from bacterial cultures of E. coli. The
yield and purity are assessed by UV
spectrophotometry. Assessment: legend & protocol
corrections, spectrum and yield calculations.
DNA isolation
DNA is isolated from bacterial cultures of E. coli. The
yield and purity are assessed by UV spectrophotometry
and Sybr fluorimetric assay. Assessment: Evaluate
methods of quantifying RNA and DNA, differences in
RNA and DNA.
5
Restriction Digestion and
Electrophoresis
The quality of the DNA from last session is assessed
by agarose gel electrophoresis. Digestion of lambda
DNA by restriction enzymes and the separation of
fragments by agarose gel electrophoresis is
investigated.Assessment; Both normal and
advanced: Short report and separate Bioinformatics
exercises
6
Skills Test
Assess pipetting, spectrophotometry, basic lab
calculations and Excel; both normal & advanced.
1
1adv
2
3
4
4adv
MBLG1001 & MBLG1901 Handout
page 9
ASSESSMENT: MBLG1001 & MBL1901
The lecture component of the course is worth 50% of the final assessment and the material is
assessed in one 2.5 h exam held in the exam period. Two thirds of the marks in this exam are
awarded to questions relating to the lecture material.
The practical component contributes 50% to the final mark and is assessed both with insemester tasks (a calculations assignment, laboratory reports and a skills test) and in the end-ofsemester 2.5 h exam. For a more detailed assessment breakdown refer to the table below.
ASSESSMENT
Calculations Assignment (MBLG1001), 10 basic laboratory
calculations involving concentration, # moles, dilutions, pH
Pipette calibration report (MBLG1901) includes a
discussion of errors, accuracy and reproducibility and an
evaluation of the 3 methods for validating the pipette calibration
(weight, spectrophotometry and radioisotopes).
DNA isolation (MBLG1001) including legend & protocol
corrections, spectrum, yield and concentration calculations
DNA isolation (MBLG1901) includes an evaluation of the
various methods of quantifying nucleic acids and distinguishing
DNA from RNA
DNA electrophoresis (MBLG1001) includes identification of
unknown restriction enzyme and virtual digest.
DNA electrophoresis (MBLG1901) includes identification of
unknown restriction enzyme and bioinformatics exercises.
LDH diagnostic report (MBLG1001) includes the
experimental results and summary report.
LDH diagnostic report (MBLG1901) includes the
experimental results and proteomics.
Skills Test (MBLG1001 & 1901) includes Excel, pipetting,
spectrophotometry and calculations.
Lab Notebooks (MBLG1001 & 1901)
End of Semester Exam (MBLG1001), a 2.5 hour exam paper
held in the exam period. This paper includes BOTH theory and
theory of prac questions .
End of Semester Exam (MBLG1901), a 2.5 hour exam paper
held in the exam period. This paper includes BOTH theory and
theory of prac questions .
TOTAL
MBLG1001 & MBLG1901 Handout
MBLG1901
MARKS
MBLG1001
MARKS
20
20
10
10
10
10
10
10
40
40
10
10
200
200
300
300
page 10
However, a pass in both the theory and practical sections is essential.
The Schools of Molecular and Microbial Biosciences (MMB) and Biological Sciences adhere to the
Academic Board and Faculty of Science recommendations regarding the award of merit grades.
Therefore, ALL marks are PROVISIONAL until your final grade is ratified at the Examiners
meeting. In other words, marks for any component can be scaled up or down to meet academic
board guidelines.
SUBMISSION OF ASSESSMENTS
There is no group work in MBLG1001 or MBLG1901, beyond reports which may be handed in as a
pair. If reports are handed in as a pair both partners will receive the same mark. If you
want to hand in separate work you may. For separate submissions please ensure ONLY your name
appears on the report. THERE WILL BE NO REPORTS HANDED IN AS A GROUP OF
THREE OR MORE. If the experiment is carried out as a threesome (and this sometimes happens
with odd numbered practical groups) each member of the group must hand in an individual report.
All assessment tasks must be handed in at the beginning of the following laboratory session
to your assigned demonstrator. Any assignment handed in later than 15 mins after the beginning of
the lab session will incur a late penalty (see page 14 of this handout).
Any reports which are handed in late, with or without an application for special consideration,
must be submitted to Dr. Hancock or Dr. Kant (in room 377). A coversheet (located in a tray just
outside the door and WebCT) must be filled in and attached to each late report. PHARMACY
students should hand late reports to Dr. Katie Jakes in Carslaw Room 513
ASSESSMENT TASK
COURSE
MODE
Calculations Assignment
MBLG1001
Individually, handwritten
Pipetting Report
MBLG1901
Individually, typed (Word)
DNA Isolation Report
MBLG1001
Pairs, typed (Word)
DNA Isolation Report
MBLG1901
Pairs, typed (Word)
DNA Electrophoresis Report
MBLG1001
Pairs, typed (Word)
DNA Electrophoresis Report
MBLG1901
Pairs, typed (Word)
LDH Diagnostic Report
MBLG1001
Pairs, typed (Word)
LDH Diagnostic Report
MBLG1901
Pairs, typed (Word)
Lab Notebooks
MBLG1001 & 1901
Individually, handwritten (see
Skills Test
MBLG1001 & 1901
Individually
Record keeping section of lab manual)
MBLG1001 & MBLG1901 Handout
page 11
Plagiarism
A Plagiarism Compliance Statement (see introduction section in your lab manual) covering all
assessment tasks for the semester MUST be signed and submitted with your first assignment (the
calculations assignment, MBLG1001 or the Pipetting Report, MBLG1901). Submitted reports, which
appear to be copied or otherwise plagiarized may be seen as evidence of academic misconduct and
may be subject to an investigation by the University Registrar. The University policy on plagiarism
may be viewed at:
http://www.usyd.edu.au/senate/policies/Plagiarism.pdf
Plagiarism detection strategies are employed both for in-semester assessments and in the final
examination.
THE PRACTICAL CLASSES
General Arrangements
Each student will do a 5 h practical session once every fortnight. These laboratory classes are not
only designed to complement and augment the material taught in lectures but also to teach you a
wide range of scientific and generic skills (i.e. the sorts of skills much loved by employers).
Practical classes commence in the FIRST week of the Semester.
Practical classes will be held in laboratory Room 380 (located on the right-hand side of Level 3 as
you enter the Biochemistry building from Wentworth). Classes run from 1 to 6 pm Monday to
Friday. Pharmacy students will do their laboratories in Carslaw 301. Classes run from 1 to 6 pm
Tuesday – Thursday.
Depending on the other subjects you are studying, you will be allocated to a practical class on one of
these days, on either odd or even weeks. In each practical class you will be placed in a
particular group (usually 16 - 18 students) and supervised by a designated demonstrator. It is
particularly important that you do not miss the first hour of each practical class when the
introductory talk is given. Failure to attend will disadvantage you for the successful completion and
understanding of the experiment.
Your allocated Practical Group will have a name such as: 2TueA. The 2 denotes you will do your
labs on even weeks (weeks 2, 4, 6, 8, 10 and 12), the TueA means you will have practical classes on
Tuesday in group A.
If you are unable to attend on your allocated practical day:
You must contact Dr. Hancock or Dr. Kant BEFORE your first practical session. You may be
allowed to switch days but you must provide reasons for needing to change IN WRITING.
PHARMACY students should follow the same procedures but see Dr. Katie Jakes in Carslaw Room
513
MBLG1001 & MBLG1901 Handout
page 12
YOU MUST NOT TAKE IT UPON YOURSELF TO CHANGE PRACTICAL GROUPS.
Group change requests must be channeled through Dr. Hancock or Dr. Kant. All requests must be
made in writing.
For Science students: MMB Class Computer Facilities
There are +20 Macintosh computers in the laboratory. You may use the computer facility on any day
from 9.30 am - 4.30 pm. Computers may ONLY be used for MBLG specific work. In particular, the
printers must NOT be used to print out any material that is not directly connected
with your practical class. During lab classes, priority will be given to those students who are
involved in the lab class at the time.
For Pharmacy students: BIOLOGY Class Computer Facilities
There are 15 Macintosh computers in the laboratory available for use during practical sessions, and
10 Macintosh computers in the Lizard Lounge (Carslaw Room 507) available for use Mon-Thu
between 9:00 am and 5:00 pm and Fri between 9:00 am and 12:30 pm. Please only use computers for
MBLG specific work. Printers must not be used to print out material not directly related to your
practical class.
If you miss a laboratory session:
It is a faculty rule that you MUST attend >90% of practical classes, even with medical certification.
This means that if you miss more than one class, you cannot expect to pass the practical course. In
special circumstances, however, it is possible to make up classes and this can be arranged with either
Dr. Hancock or Dr. Kant. DO NOT TAKE IT UPON YOURSELF TO OMIT AND/OR ENTER
SPECIFIC SESSIONS.
The Laboratory Manual:
The resource manual for the course is available from the University Co-op Bookshop (near the Noel
Martin Recreation Centre) at a cost of $15. Make sure you buy the current FIRST year manual (not a
second or third year one). The first year manual is green!
What else do I need to bring to Laboratory Classes?
•
A hard covered bound notebook. ALL original data (including gel pictures, calculations,
etc) must be recorded in this book. This book should serve you as a life-long resource of tips,
tricks and notes. Section 3 on record keeping will provide some hints.
•
A marker pen for writing on glassware; use the type in which the ink is insoluble in water.
•
A pair of safety glasses.
•
A calculator, preferably not your mobile phone.
•
Filled-in shoes, no thongs or sandals!
•
A laboratory coat.
MBLG1001 & MBLG1901 Handout
page 13
Before coming to lab classes…….
BE VERY SURE TO READ THE SECTION IN YOUR RESOURCE MANUAL ON
LABORATORY SAFETY.
THE SKILLS TEST
General Arrangements
As part of the assessment of MBLG1001 and MBLG1901 ALL students must sit a practical skills
test. This test will assess your competence at certain laboratory skills: automatic pipetting,
spetrophotometry and spreadsheet skills, as well as data manipulation and interpretation and written
communication.
The skills tests will be run in weeks 11 – 13. If you are unable to sit your skills test on the
designated day, arrangements must be made with Dr. Hancock or Dr. Kant to do the test on
another day.
ALL students must attempt the skills test to pass MBLG1001 or MBLG1901.
If you have been unable to sit the test throughout the skills test period, a make-up skills test will
be organized for you in StuVac, subject to the approval of your special consideration
application.
Students are allowed (indeed encouraged) to use their laboratory notebooks (BUT not
their laboratory resource manuals) in the skills test. There are, however, certain rules
governing acceptable material in the lab notebook. These rules are designed to encourage you to
keep your notebook throughout the semester and to include in this notebook all the tips, strategies,
hints and calculations that you have learned along the way. You will always learn something better if
it is handwritten (by you) rather than simply photocopied the night before the test. With this in mind:
Laboratory notebooks must be handwritten. The only photocopied items from the
laboratory resource manual acceptable in the notebook are the dye spectra from the
spectrophotometry practical, the safety rules and the pipette tables from the introductory section.
Typed reports, printed spreadsheets and gel scans are all acceptable.
Printed out answers to the calculations assignments are NOT acceptable, however, handwritten
model answers are acceptable and, again, are encouraged.
Printed out Powerpoint tutorials are NOT allowed, although handwritten notes from these
tutorials are acceptable.
Demonstrated Competence in the Use of automatic Pipettes.
One of the skills tested in the skills test is the correct use of automatic pipettes. This skill is
considered so essential to the study of molecular biology that ALL students MUST demonstrate
competence in the use of these pipettes before they can pass MBLG1001/1901 or be allowed to
progress to any intermediate courses in molecular biology, biochemistry, genetics or microbiology. If
a student does not demonstrate a sufficient level of competence in the pipetting exercise in the skills
MBLG1001 & MBLG1901 Handout
page 14
test, he or she will be required to come back at an agreed time in StuVac and review the use of these
pipettes before being signed off.
POLICY ON SPECIAL CONSIDERATION
It is Faculty of Science policy that there are no Supplementary Examinations for courses which
are only studied for one semester. However, we recognise that sickness or other misadventures can
have an adverse effect on your performance. Therefore, we have set up the following procedures to
ensure that you are not disadvantaged because of illness or other problems. The MMB Special
Consideration policy can be viewed at: http://www.mmb.usyd.edu.au/current_students/
For in-Semester work:
For late lab reports, calculations assignments etc.; lateness attracts a penalty of 10% (of the
original mark) per day. After 10 days, therefore, a mark of zero is returned. However, ALL
work must be handed in for you to complete the course.
• In cases of illness or misadventure, where an extension is requested you MUST apply for
special consideration with the science faculty. The process and the relevant forms can be found at
the following website:
http://www.science.usyd.edu.au/current/ug/special_consideration_application_pack.pdf
•
Applying for Special Consideration:
The student obtains an Application for Special Consideration form from the Student
Information Office or the Faculty website above.
Please note that any requests for a unit of study taught by another Faculty must be submitted
at that Faculty Office, and not at the Faculty of Science.
The student lodges the original of the application form and originals of any supporting
documentation at the Student Information Office. Where it is not possible to obtain original
documentation (e.g. death certificate, police report), submission of a certified copy will be
permitted. All other forms submitted must be originals, including the Professional
Practitioners Certificate (PPC).
Please note that it is also necessary to provide a copy of the application and all documentation
for each unit of study in which consideration is being sought, to be certified by the Faculty
and forwarded by the student to the School for assessment (i.e. if you are applying for
consideration for three units of study, you must submit the original documentation plus three
copies).
For consideration due to serious illness a student must have a registered medical
practitioner or counsellor complete the Professional Practitioners Certificate, which is
attached to the application form.
MBLG1001 & MBLG1901 Handout
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For consideration due to misadventure, a Professional Practitioners Certificate or other
form of appropriate documentation is required which indicates the likely duration and effect
of the misadventure on the student’s performance.
Please note that only the supporting documents provided at the time of initial application for
Special Consideration will be used to assess the request. It will not be possible to submit
further documentation relating to an initial application once an application has been lodged
with the Student Information Office. Only those circumstances brought to the attention of
staff at the time of lodgment will be taken into consideration when formulating an academic
judgment. Special Consideration applications must be lodged with the Student Information
Centre within seven (7) days of the missed class.
The Student Information Office checks the application at time of lodgment to ensure that a
student’s documentation is adequate and if so, will sign/stamp both the original application
form as well as the student’s copies to confirm lodgement of the application at the office. The
Student Information Office will enter the details contained on the application form into the
Special Consideration database, which will be used to monitor the progress of the application.
The student takes the stamped and dated application form and documentation to the relevant
Unit of Study Coordinator or School Administration Office for assessment. Please note that
this must be done for each Unit of Study for which consideration is being sought.
When an academic judgment has been entered into the Special Consideration database, the
Faculty will communicate the decision to the student via an e-mail to the student’s University
e-mail address. It is expected that a response will be received by the student within seven (7)
days of initial application.
What you should do if you miss an exam because of sickness or misadventure.
If you are unable to sit an end-of-semester exam, you must apply for Special Consideration
following the procedure outlined above, including submission of appropriate supporting
documentation, within seven (7) days from the date of the exam. If a student does not sit an
examination and is not granted Special Consideration, a grade of AF (Absent Fail) will
result for that UoS.
All messages and Special Consideration Forms MUST be left with the Student
Support Office (level 4, Biochem building G08).
As a result of the above, you may be permitted to sit for a deferred examination. It
will be held on Friday, 27th November. This will be a different paper. This exam will
cover the same material as the original exam, but will contain new questions and
may be in a different format. There will be no further testing. SIDs of those students
eligible to sit this deferred exam will be posted on the WebCT. IT IS YOUR
RESPONSIBILITY TO FIND OUT IF YOU ARE ELIGIBLE TO SIT THE DEFERRED
EXAM.
MBLG1001 & MBLG1901 Handout
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