COURSE OUTLINE: BS1005

Course Title

Biochemistry I

Course Code

BS1005

Offered Study Year 1, Semester 2
Course Coordinator Curtis Alexander Davey (Assoc Prof) Davey@ntu.edu.sg 6592 1549
Pre-requisites None
AU 3
Contact hours Lectures: 22, Laboratories: 12, Tutorials: 10
Approved for delivery from AY 2019/20 semester 2
Last revised 4 Oct 2019, 09:28

Course Aims

This course aims to introduce the structural, biophysical and chemical principles of key biological macromolecules found in living organisms. You will use your understanding of the underlying molecular bases and functions of the macromolecules involved in various biochemical reactions to solve problems related to nucleic acids, proteins, carbohydrates, lipids and vitamins. You will also develop the ability to conduct biochemical experiments in the lab and design new molecules based on knowledge of the protein data bank.

Intended Learning Outcomes

Upon successfully completing this course, you should be able to:

  1. Calculate dissociation constant (e.g. pKA and pH) and isoelectric point (pI)
  2. Determine the types and numbers of stereoisomers in nuclecic acids, proteins and carbhydrates
  3. Calculate torsion angles for macromolecules
  4. Design new primers for DNA sequencing and gene amplification
  5. Interpret the functional bases of major macromolecules towards the evolution of new activities
  6. Design experiments to purify nucleic acids and proteins
  7. Conduct experiments to detect and characterize proteins and sugars
  8. Design new macromolecules (e.g. peptides/proteins) via structural biology approaches
  9. Translate three-dimensional structures of proteins to aid in designing novel drug molecules
  10. Translate molecular bases of major lipid molecules to the development of diseases based on disregulated lipid metabolism
  11. Translate molecular bases of vitamin structure to diseases caused by vitamin deficiency

Course Content

Building blocks of macromolecules (covalent and non-covalent bonding, free energy, acids, bases, buffers)

Primary, secondary and tertiary structures of nucleic acids (DNA, RNA), proteins, polymers (carbohydrates, lipids)

Modifications of nucleic acid and proteins (e.g. spontaneous, chemical, genetic, post-translational)

Folding of proteins, quaternary structure of proteins (myoglobin, hemoglobin)

Carbohydrates (tautomers, stereochemistry, ring structures, saccharides)

Lipids (triglycerides, phospholipids, membrane transfer)

Vitamins (solubility, deficiency and disease, dietary issues)

How to use Pymol molecular visualization software

Accessing biological databases such as Protein Data Bank (PDB)

Assessment

Component Course ILOs tested SBS Graduate Attributes tested Weighting Team / Individual Assessment Rubrics
Continuous Assessment
Laboratories
Written Report 1, 2, 3, 5, 6, 7, 8, 9 1. a, b
2. a, b, e, g
3. a, b, e
5. a, b, c, d, e
6. c
7. a, b, c
50 individual See Appendix for rubric
Examination (2.5 hours)
Multiple Choice Questions 1, 2, 4, 5, 6, 8, 10, 11 1. a, b
2. a, e
3. a, b, e
5. a, c, d, e
6. c
7. c
50 individual
Total 100%

These are the relevant SBS Graduate Attributes.

1. Recognize the relationship and complexity between structure and function of all forms of life, resulting from an academically rigorous in-depth understanding of biological concepts

a. Possess a conceptual framework that identifies the relationships between the major domains in the field of biology.

b. Explain the relationship between structure and function of all forms of life at the molecular level

2. Critically evaluate and analyze biological information by applying the knowledge, scientific methods and technical skills associated with the discipline

a. Identify the assumptions behind scientific problems and issues

b. Create and evaluate hypotheses

e. Analyze the validity of qualitative and quantitative scientific data

g. Evaluate the results of their own experiments and decide on the next step

3. Develop and communicate biological ideas and concepts relevant in everyday life for the benefit of society

a. Simplify and explain scientific concepts and results of experiments to a non-biologist (avoiding jargon)

b. Display and explain scientific results clearly and persuasively to peers both verbally and in writing (includes the ability to graph data appropriately and accurately).

e. Discuss current critical questions in the field of biology

5. Develop communication, creative and critical thinking skills for life-long learning

a. Learn independently and then share that knowledge with others

b. Learn collaboratively and be willing to share expertise with peers

c. Demonstrate critical thinking skills such as analysis, discrimination, logical reasoning, prediction and transforming knowledge

d. Question the assumptions, sources, and contexts of scientific investigation

e. Demonstrate good observation skills and a curiosity about the world

6. Develop codes of social responsibility and scientific ethics, particularly in relation to biological advancement and applications

c. Respect regulations involving plagiarism and copyright

7. Demonstrate information literacy and technological fluency

a. Locate and evaluate information needed to make decisions, solve problems, design experiments, and understand scientific data

b. Work effectively with common technologies in biology

c. Evaluate and use biological databases (literature and public datasets)

Formative Feedback

Formative feedback: Lecturers and TAs will be closely working with you to monitor your learning progress. They will provide you with timely feedback to improve your technical skills and also provide you with suggestions for the experiments and data analysis. Furthermore, you will be given opportunities to express your ideas and discuss them with lecturers and TAs as course progresses. This will help you to achieve intended learning outcomes 1, 2, 3, 4, 5, 6, 7, 8 and 9.

Summative Feedback: Summative feedback on reports will be given. For written reports, an examiner report will be provided with comments on mistakes, areas of improvement and examples of good practice in scientific writing etc at the end of semester. This will help you to achieve intended learning outcomes 2, 3, 7, 8 and 9

Learning and Teaching Approach

Lectures
(22 hours)

You will be spending time to learn detailed biochemical principles of biological small molecules and macromolecules (water molecules, DNA/RNA, proteins, carbohydrates, lipids, vitamins) and related research skills and technological advances, which will help you to engage in molecular design initiatives (such as for biotechnology or drug development) and to conceive of ideas for designing new experiments and contemplating modern problems in biochemistry. To better engage you in class, we will make use of macromolecular graphics display and a mixture of modern and old school humour. In addition, you will be encouraged to ask questions or have discussions after the lecture.

Laboratories
(12 hours)

You will have four lab sessions-- two of which are computer based and two of which are wet laboratory. You will acquire hands-on skills in analyzing biological macromolecules and also gain further insights into underlying molecular and chemical principles of proteins and carbohydrates. After each lab, you will be required to submit a written report to evaluate your scientific data analysis skills, writing skills, and level of understanding on molecular principles.

Tutorials
(10 hours)

TAs will provide materials containing concepts taught in classes and cover related applications derived from corresponding lectures. You will be assigned to a small group for interactive discussions, which will help you to develop your own critical thinking capability and problem solving skills.

Reading and References

Recommended textbook: Biochemistry, 4th Ed (2013), Mathews / Van Holde / Appling /Anthony-Cahill; ISBN-13: 978-0138004644

Recommended reference textbook: Lehninger Principles of Biochemistry, 5th Ed (2008), Nelson / Cox; ISBN: 9780716771081, W. H. Freeman, 2008

Course Policies and Student Responsibilities

1. You are expected to read the lecture/tutorial/lab materials prior to the lecture/tutorial/lab session in question. This will help you to learn much more efficiently as you will already have an impression on the topics to be covered. You should also read through both of the two textbooks as outlined in the Weekly Schedule.

2. There are four laboratory sessions. You will be required to submit the lab reports within two weeks of each lab. The four lab reports will be part of your continuous assessment.

Academic Integrity

Good academic work depends on honesty and ethical behaviour. The quality of your work as a student relies on adhering to the principles of academic integrity and to the NTU Honour Code, a set of values shared by the whole university community. Truth, Trust and Justice are at the core of NTU’s shared values.

As a student, it is important that you recognize your responsibilities in understanding and applying the principles of academic integrity in all the work you do at NTU. Not knowing what is involved in maintaining academic integrity does not excuse academic dishonesty. You need to actively equip yourself with strategies to avoid all forms of academic dishonesty, including plagiarism, academic fraud, collusion and cheating. If you are uncertain of the definitions of any of these terms, you should go to the Academic Integrity website for more information. Consult your instructor(s) if you need any clarification about the requirements of academic integrity in the course.

Course Instructors

Instructor Office Location Phone Email
Curtis Alexander Davey (Assoc Prof) 04s-44 6592 1549 Davey@ntu.edu.sg

Planned Weekly Schedule

Week Topic Course ILO Readings/ Activities
1

Chemical Principles of Biochemistry

1, 2

MVAA Ch 1, 2, 3
Lehninger Ch 1, 2

2

DNA-1
•Structures and properties of nucleotides
•Nucleic acid chemistry
•Primary structures of nucleic acids
•DNA as genetic substance
•Secondary and tertiary structures of nucleic acids
•Watson-Crick DNA model
•Modifications of the double-stranded DNA model

2, 3, 4, 6

MVAA Ch 4
Lehninger Ch 8

3

DNA-2
•Unusual secondary structures of DNA
•Circular DNA and Supercoiling
•Stability of secondary and tertiary structure of DNA

2, 3, 4, 5, 6

MVAA Ch 4
Lehninger Ch 8, 9

4

RNA
•Primary structure of RNA
•Secondary structure of RNA
•Tertiary structure of RNA
•Prediction and determination of RNA structure
•RNA as self-catalytic enzyme

2, 5, 6, 8

MVAA Ch 4
Lehninger Ch 8, 26

5

Protein-I
•Amino acids as building blocks of polypeptides
•Chemistry and properties of amino acids

1, 2, 3, 5, 6

MVAA Ch 5
Lehninger Ch 3

6

Protein-II
•Primary structure of proteins
•Peptide backbone torsion angles
•Cleavage of peptides

1, 2, 3, 5

MVAA Ch 5
Lehninger Ch 3

7

Protein-III
•Folding of proteins
•Secondary structures of proteins
•Tertiary structures of proteins

5, 8, 9

MVAA Ch 6
Lehninger Ch 4

8

Protein-IV
•Quaternary structure of proteins
•Proteins in motions
•Structure and functional relationship: hemoglobin and myoglobin

5, 8, 9

MVAA Ch 7, 8
Lehninger Ch 5

9

Carbohydrates
•Tautomers
•Stereoisomers
•Ring structures
•Monosaccharides and their derivatives
•Oligosaccharides
•Polysaccharides

5, 7

MVAA Ch 9
Lehninger Ch 7

10

Lipids I
•Chemical properties of lipids
•Fatty acids
•Triglycerols
•phospholipids
•sterols
•other lipids

5, 10

MVAA Ch 10
Lehninger Ch 11

11

Lipids-II
•Lipid constituent of biological membranes
•Structure of membrane-bilayer
•Membrane transport

5, 10

MVAA Ch 10
Lehninger Ch 11

12

Vitamins
•Vitamins: a special class of biomolecules
•Fat-soluble and water-soluble vitamins
•Structure and chemical properties
•Vitamin deficiency and disease
•Dietary and other sources; unanswered questions.

5, 11

MVAA Ch 19
Lehninger Ch 11

Appendix 1: Assessment Rubrics

Rubric for Laboratories: Written Report (50%)

You will be required to conduct two experimental sessions using Pymol software to analyse biomacromolecules in particular scenarios and two experimental sessions to detect/characterize proteins and sugars (each lab session carries equal weight and the four lab sessions will be scaled to contribute to 50% of the course total). You will need to interpret and analyse your results.

Criteria Standards
Fail standard
(0-4 marks)
Pass standard
5-7 marks)
High standard
8-10 marks)
1. Experimetal data report

No correct data

Correct data

Correct answers

2. Data interpretation

No explanations about the data

Lack clear explanation of the data.

Clear explanations

3. Further discussion

No discussion or just superficial discussions

Lack deep discussions.

High quality further discussions

Appendix 2: Intended Affective Outcomes

As a result of this course, it is expected you will develop the following "big picture" attributes:

Appreciate the roles of biological macromolecules (DNA, RNA, proteins, vitamins) in the life sciences

Appreciate the role of scientific discovery in transforming people's lives