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BIOSCI350

PROTEIN STRUCTURE AND FUNCTION

Course Breakdown

 

Mid-Semester Test: 15%
End-of-Semester Test: 15%
Laboratory Component: 20%
Exam: 50%

Course Information

 

Recommended textbooks:
Introduction to Protein Structure (2nd ed) - Branden & Tooze
Biochemistry (6th ed) - Berg, Tymoczko & Stryer
Principles of Biochemistry (2nd ed) - Lehninger
Biochemistry (3rd ed) - Matthews

Note that no one text book accurately covers the course content.

Official UoA Website: link.

Basic Information

In contrast to what you might have been expecting from previous biochemistry papers such as BIOSCI 106 and BIOSCI 203, BIOSCI 350: Protein Structure and Function will not be teaching you about how alpha-helices and beta-sheets are chemically arranged. Instead, this course is focused on delivering content based around how practical laboratory techniques are used to find out, manipulate and solve protein structures.

​This paper has 4 lecturers in total: Dr. Richard Kingston, Professor Tom Brittain, your course-coordinator Dr. Chris Squire, and Associate Professor Alok Mitra. Each lecturer takes a section that comprises of 9-10 lectures and there are a few topics that overlap between each. The mid-semester test has questions from the first half of lectures (Dr. Kingston and Professor Brittain) and the end-of-semester test tests the second half (Dr. Squire and Associate Professor Mitra), while the exam covers content taught during the entire semester. Each lecturer gave you two questions to choose from in the test and exam, with the exception of Associate Professor Mitra who wrote out three compulsory short-answer questions.

 

Laboratory Component

In 2015 the first three laboratories were taken by Dr. Richard Kingston, and are unlike the typical undergraduate laboratories you would have done up to this stage where you were given instructions to follow, perform an experiment and complete a lab worksheet to hand in. Instead, you were to carry out some authentic scientific research via basic experimentation to help characterize the the proteins involved in the replication of Wobbly Possum Disease Virus (WPDV) in which the outcomes were not completely known. Don't freak out - you will still be given very detailed instructions on how to go about performing the in-lab experiments but be wary that that post-lab questions will require you to think critically and show understanding about what you did during the lab - as always, make sure to ask lots of questions before you leave the lab to clear up any confusions as his questions can be tricky. Note, 2015 was the first year in which this sort of lab took place. For the lab reports, Kingston provided us with lab report outlines which contained all the questions which offered a bit more guidance.

In Dr. Chris Squire's lab - which in 2015 was a dry lab meaning you did not need a lab coat - you were to use a computer software to learn to visualize electron density, fit a mutant enzyme to an experimental electron density, build and fit a molecule of Tamiflu into the electron density map and finally discuss the mechanism of drug resistance. In one of his lectures he will actually briefly show you how to do this live, but don't be surprised if you find yourself struggling on the day - a lot of the time your progress may be stalled not because you don't know what to do but how to get the software to do it, so please ask the ever-helpful demonstrators for their expertise. The assignment sheet for this lab contains simple and straightforward questions, but make sure your Tamiflu molecule drawing contains the appropriate amount of detail required or you could lose easy marks here.

In the final laboratory with Associate Professor Mitra, he will spend most of it showing you diffraction patterns and explaining the relationship between images and their diffraction patterns - make sure you pay close attention to this as this knowledge is critical to the post-lab online quiz on CECIL, where you will match a set of images to their optical diffraction patterns jumbled in random order. There was a lot of confusion amongst my friends in regards to the correct answer, so if you are certain in your answers don't be afraid to do the quiz as you see fit. It goes without saying that playing with the computer program in class and asking the demonstrators will help you immensely for this task.

Overall, the laboratory component of BIOSCI 350 is not extremely difficult, but it is the little mistakes which can cost you so be careful, be diligent and ask lots and lots (and lots!!) of questions!! 

 

Lecture Content

Proteins: Purification & Analysis

Dr. Richard Kingston's lectures in 2015 were based around three broad topics:

  • Thermodynamic principles of protein structure and biological function

  • Protein Diffusion and its biological consequences

  • Protein purification and characterisation


​This module changed a bit from what was taught in 2014 in that there wasn't an emphasis placed on heterologous protein production and purification, which means previous exam questions may seem odd to you but of course Dr. Kingston will address this in his lectures. His module wasn't difficult and was not very heavy in content either, but you will need to rote learn for example different methods of protein purification, how they each work, and when to use them. He also introduced us to equations which we had to memorise and use to perform calculations, so it paid to have a calculator handy when he taught these topics. His last section focused on thermodynamic principles of protein structure and biological function was what I found the most conceptually challenging, but doing past exam papers helped me to put what I had learned into context and as usual don't be afraid to approach him for help as his material is examined in both the first in-course test and the final exam.

 

Protein actions and Interactions

Professor Tom Brittain was up next, and his lectures covered seven topics:

  • Protein interactions - theory

  • Protein interactions - experimental measurements

  • Absorption spectroscopy of proteins and its applications

  • Fluorescence-biological applications and green fluorescent protein (GFP).

  • Circular dichroism and protein secondary structure

  • Observation of molecular mechanisms

  • Nuclear Magnetic Resonance spectroscopy for protein structure determination


​Professor Brittain will specifically tell you which equations and details you DO NOT need to memorise for the second in-course test and exam, so make sure you do pay close attention during his lectures. I found his content to be conceptually easier to understand than Dr. Kingston's and although he introduces even more protein-studying techniques they were very well explained. I also found that his questions were quite predictable which helped in studying for his questions in the test and exam. There isn't much else to say here other than the fact that he is a very patient and kind lecturer who really does have your best interests at heart. 

 

Protein Structure Determination, Evolution and Drug Discovery

The very funny and entertaining Dr. Chris Squire kicked off the second half of the course - a note here that he does very hilarious demonstrations in class and cracks wicked jokes, so you do not want to miss his lectures. His module covered the following topics:

  • The impact of X-ray crystallography on modern biology

  • Hybrid methods for protein structure determination - the bacterial flagellum

  • Protein structure and evolution - the bacterial flagellum

In my opinion this is the module of BIOSCI 350 which is lightest on content - but that is not to say it is the easiest as to score high marks in his questions you are expected to weave together content from different lectures. He will also mention that sometimes he may set a question which you can answer from the content he taught you during his lectures (in which he will mark you more harshly for) OR content you have researched yourself from the sources he provides (in which he will mark you more easily for). Again, in my opinion if you take the time out at the beginning of the course to do your own research on your protein molecule(s) of interest then it can really pay off in the long run. In his review lecture, he also mentioned that should a question mention "you may draw diagrams to support your answer..." etc then always draw if you can to get bonus marks. Very interesting, entertaining and funny lectures from a very funny lecturer!!

 

Membrane Proteins

Finishing off the course is Associate Professor Alok Mitra, who covered the following eight topics:

  • Introduction to membrane structure and membrane proteins

  • Introduction to membrane transport

  • Conduction of electrical signals mediated by membrane proteins

  • (a) Topology of membrane proteins, (b) Biochemical handling of membrane proteins

  • Introduction to structural studies of membrane proteins

  • Electron crystallography and 2-dimensional crystals of membrane proteins

  • Three-dimensional structures of membrane proteins determined by electron crystallography

  • Details of membrane protein structures determined by electron crystallography - two examples


​While Associate Professor Mitra does not expect you to know any content outside of his lecture slides and what he teaches you during lectures, this also means he demands absolute mastery of what he has taught you in order to gain high marks in his test and exam questions, which is a feat the entire class struggled with in 2015. Do not underestimate his section! In 2015 his questions in the test and exam did not have an either/or option like the other three lecturers so we had to answer the entire question. Therefore, you need to be prepared to work very, very hard and know all his content thoroughly. In addition, he has said himself that to "stick to the main point of the question and avoid extraneous statements that do not pertain to the question. Furthermore, drawing properly and correctly annotated figures improve the quality of the answer."