BCM3521
PROTEIN BIOCHEMISTRY
SCHOOL OF MATHEMATICAL AND NATURAL SCIENCES
DEPARTMENT OF BIOCHEMISTRY
STUDY GUIDE
2020
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BIOCHEMISTRY COURSE OUTLINE
FOREWORD
Welcome to the Biochemistry Department. The aim of this module is to help you gain an understanding
of the roles of proteins in cellular processes. The module seeks to address the structural organization
of proteins, the concept of protein folding, the structure-function features of proteins, protein
domains, intracellular signal transduction pathways including neurotransmission biochemistry, and
the role of proteins in transport. Practical classes are presented every week during the semester where
students are trained to develop experimental skills in analytical determination of biochemical
molecules and other metabolites as well as the use of apparatus in the Biochemistry Laboratory.
Students are expected to attend ALL lectures and in particular, practical sessions for this module are
compulsory. NEVER ATTEMPT TO ABSCOND FROM PRACTICAL SESSIONS AS YOU WOULD NOT BE
CREDITED FOR WRITING UP PRACTICAL REPORTS WITHOUT ATTENDING THE PRACTICAL SESSIONS.
COURSE LECTURER
Dr. A. Burger
New Life Sciences Building
Office SF013, 2nd Floor
Consultation hours: Open door policy
TEXT BOOKS
Prescribed: Essential Biochemistry, Third Edition
Charlotte W. Pratt, Kathleen Cornely
Free download: [Link]
[Link]
How Proteins Work
Mike Williamson
Note that reading supplementary sources such as other Biochemistry text books and current research
articles addressing relevant subject matter is highly recommended to enhance understanding.
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MODULE GENERAL INFORMATION
Module: Protein Biochemistry
Code: BCM3521
NQF Credits: 16
VENUES AND CONTACT SESSION SCHEDULE:
There will be two scheduled contact hours per week for lectures as well as one practical session per
week
DAY VENUE TIME
Tuesday A1 13:00 – 13:50
LECTURES
Wednesday A1 11:00 – 11:50
Wednesday 2nd Year Laboratory 13:00 - 17:00
PRACTICALS
Friday 2nd Year Laboratory 13:00 – 17:00
INTENDED OUTCOMES FOR THE COURSE
✓ To identify various forms of protein conformations in relation to their roles
✓ To collect, analyze and interpret information related to the module
✓ To demonstrate an understanding of the role of proteins in normal and disease states
✓ To use technology such as computer programs to study protein structure and predict their
function
ASSESSMENTS
In order to qualify to sit for examinations, the student must have:
✓ Attended lectures, tutorials and practicals
✓ Written and completed all tests and assignments
✓ Attended, written-up, and handed in all practicals and tutorials
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Students absent from any practical, tutorial or test must hand in a written explanation indicating the
reason for their absence (with medical certificates and/or appropriate documents) to the lecturer
involved within five working days of the date of absence.
FORMATIVE ASSESSMENT
Grading Scheme
Assessment tasks may include:
✓ Class Tests and Tutorials 10 %
✓ Practical Reports & Exam 30 %
✓ Semester Test 1 20 % 3 March 2020
✓ Semester Test 2 20 % 31 March 2020
✓ Semester Test 3 20 % 5 May 2020
SUMMATIVE ASSESSMENT
A three hour examination paper out of 100 marks is written at the end of the semester.
Pass Requirements:
The final pass mark is 50 %.
Final mark compilation:
Semester mark (60 %) + exam mark (40 %)
A student must get a subminimum mark of 40 % in the exam.
APPLICATION FOR DEFERRED (AEGROTAT) TESTS/EXAMINATIONS
Rules and procedures regarding deferred assessment opportunities:
✓ A make-up assessment may take any format (practical, assignment, essay, oral)
✓ A student may be granted a special assessment opportunity if he/she applied in writing
within 5 working days subsequent to the original date of assessment missed
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Reasons for absence Documentation as proof
Illness Valid medical certificate completed by the
medical practitioner with official stamp
Compassionate reasons (immediate family only) Relevant documents such as death certificate,
or a letter from the community leader
Legitimate reasons An affidavit signed and stamped by a
commissioner of oaths, accompanied by a letter
detailing the circumstances and student details
The discretion of the department will make the final determination on all cases.
GENERAL RULES
✓ The University of Venda code of conduct is to be respected and will be strictly enforced,
especially regarding academic dishonesty, misconduct and class attendance
✓ ALL lectures and practicals are compulsory
✓ Noise or any form of disturbance will not be tolerated during lecture and practicals; disciplinary
actions will be taken against such students displaying misconduct (students will be asked to
leave)
✓ NO LATE coming
✓ Cell phones must be switched off before entering the lecture hall
✓ Due dates for the tasks must be respected
✓ Test dates and venues will be confirmed during lectures
✓ Students who copy or allow others to copy (test, assignment, reports) will automatically be
awarded zero for a particular task/assessment exercise
PLAGIARISM
Plagiarism is defined as using or closely imitating the work of others without approval or referencing.
It involves presenting another person’s work as your own. Plagiarism is considered as academic theft
and fraud and is taken very seriously by the university. Plagiarism offences are dealt with according to
the university policy and can result in exclusion from the university.
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MODULE CONTENT SUMMARY
Structural organization of proteins, the concept of protein folding, protein structure and function,
protein domains, intracellular signal transduction pathways, role of proteins in transport.
MODULE SEQUENCE
MATERIAL LECTURE NO. LECTURE CONTENT
1 Introductory lecture
Chapter 4: 2, 3, 4 Protein structure
Protein Proteins are chains of amino acids;
Structure secondary structure – the conformation of
the peptide group; tertiary structure and
protein stability; quaternary structure;
analyzing protein structure
Handouts: 5, 6, 7 Protein folding
1. “Protein Protein folding landscape; protein folding
folding” versus aggregation; molecular chaperones;
2. “Morimoto Heat shock response; Hsp70; GroEL
2012 Heat
shock
response”
Chapter 5: 8, 9, Protein function
Protein Myoglobin and hemoglobin: oxygen-
Function binding proteins; structural proteins; motor
proteins
Handouts: 9, 10 Protein domains and oligomers
Protein
domains and
oligomers
Chapter 9: 10, 11, 12 Membrane transport
Membrane The thermodynamics of membrane
Transport transport; passive transport; active
transport; membrane fusion
Chapter 10: 12 Signaling
Signaling General features of signaling pathways;
protein signaling pathways; receptor
tyrosine kinases; lipid hormone signaling
Handouts: 13 Techniques for studying proteins
Techniques for Protein expression; PCR; lac operon based
studying plasmids ; nickel affinity chromatography;
proteins SDS-PAGE and Western blot analysis; co-
immunoprecipitation; bioinformatics
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Students must be able to address all the problems provided at the end of each chapter of
the prescribed textbook.
Module Objectives
Students need to adequately address the following broad objectives from each chapter in order to
successfully complete the module. In addition, students must be able to address all the problems
provided at the end of each chapter of the prescribed textbook.
Protein Structure:
✓ To describe concepts pertaining to the “central dogma”
✓ To know the structures, properties and classification of all 20 amino acids
✓ To name and draw four uncommon and four non-protein amino acids
✓ To describe, calculate and analyze the acid/base properties of amino acids ie. pI; zwitterion,
pKa
✓ To draw, calculate and analyze titration of amino acids at high and low pH
✓ To draw, name and identify peptides
✓ To fully define and describe each level of protein structure including the type of bonds and
interactions involved
✓ To fully describe features of protein secondary structure including α-helices, ß sheets and
turns/loops
✓ To describe the principles defined by Ramachandran, and analyze the Ramachandran plot
✓ To describe properties of the peptide bond, and explain “resonance of the peptide unit” with
aid of a diagram
✓ To describe with the aid of diagrams the different conformations around a peptide bond
✓ To list the consequences of the amide plane, and explain the steric constraints on torsion
angles phi and psi
✓ Histidine has three pKa values (pK1 = 1,82; pK2 = 6; pK3 = 9,17). Draw the titration curve for
glutamate, and calculate the pI.
Protein folding:
✓ To define terms including “class”, “motif”, “fold”, “architecture”, “domains”, “topology”, and
but not limited to “fold/superfamily”
✓ To identify and name secondary structural motifs
✓ To exhaustively describe principles involved in protein folding
✓ To describe the “Anfinsen Experiment” in protein folding and the conclusions that were
drawn
✓ To elaborate on protein folding versus protein aggregation
✓ To explain how in vivo protein folding differs to in vitro protein folding
✓ To understand the energetics of folding and general principles of thermodynamics
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✓ To describe the protein folding/folding landscape using Ken Dill’s folding funnel as an
example
✓ To define and describe the effects of macromolecular crowding
✓ To exhaustively discuss molecular chaperones
✓ To describe and illustrate the “heat shock response”
✓ To correctly classify heat shock protein families, and the general roles of each family
✓ To describe and illustrate the structure, function, mechanism of action and protein partners
of Hsp70; and GroEL
✓ To name and describe common functional experimental assays used to study molecular
chaperones
✓ To analyse an aggregation suppression assay
✓ To name and describe chemical chaperones
✓ To name diseases linked to protein misfolding, and the affected proteins and mechanism of
action
✓ Fully describe the Hsp70 functional cycle, and include the names and roles of nucleotides,
and partner proteins
Protein Function:
✓ To classify proteins by structural characterization and by function
✓ To fully describe the hydrophobic effect and its role in stabilizing protein structure
✓ To name and describe non-covalent interactions; protein-solvent interactions
✓ To name examples of and describe fibrous proteins, and globular proteins
✓ How do the structural elements of alpha keratin differ from that of collagen?
Protein Domains and Oligomers:
✓ To differentiate between homologues, paralogues and orthologues with the aid of a diagram
✓ To describe the domain organization of the lysozyme and ankyrin proteins
✓ To explain the structure and specific functioning of the Rossmann Fold, the TIM barrel, the
HTH domain
✓ To explain how protein domains serve as an inconvenient cost to the cell and as
advantageous cellular tools
✓ To explain how protein domains assist in autoregulation of functions of some proteins
✓ To distinguish between a protein domain and scaffold proteins
✓ To describe various forms of post-translational modification to proteins and how they affect
protein function
✓ To describe how intramolecular domain-peptide binding facilitates autoinhibition
✓ To define protein oligomerization
✓ To distinguish between hetero- and homo-oligomers
✓ To identify amino acids that occur mostly at inter-domain interfaces
✓ To explain how oligomers influence/regulate protein function
✓ To describe how oligomers influence function of proteins such as haemoglobin, transcription
factors, restrictions enzymes etc.
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Membrane Transport:
✓ To describe how the ratchet mechanism works in unidirectional movement of myosin driven
muscle contraction
✓ To explain how proteins in the membrane facilitate movement of molecules across cells
✓ To identify and describe and illustrate processes that are facilitated by symporters and
antiporters
Signaling
✓ To describe the challenges that signaling pathways have to overcome
✓ To describe lipophilic signals that can cross membrane barriers
✓ To describe how receptor dimerization facilitates signaling across membrane barriers
✓ To describe and illustrate the mechanism of action of the insulin receptor
Techniques for studying proteins
✓ To explain the role and mechanism of action of a PCR reaction
✓ To explain how genes are cloned into plasmids tpwards their expression as recombinant
protein in E. coli
✓ To describe how E. coli cells transformed fro recombinant protein production are induced
based on the concept of the lac operon
✓ To explain how to purify His-tagged proteins expressed in E. coli cells
✓ To describe and distinguish between SDS-PAGE and Western blot as protein resolving tools
✓ To explain why size and not charge influence movement of proteins resolved by SDS-PAGE
✓ To explain the application of immunoprecipitation
✓ To align multiple protein sequences
