LESSON PLAN FACULTY OF CHEMICAL ENGINEERING

UNIVERSITI TEKNOLOGI MARA

CBE 647/ BIOINFORMATICS
PAGE 1/3

1.0 COURSE INFORMATION

Course name : BIOINFORMATICS
Code : CBE 647
Programme : EH 222
Part : 7
Credit Unit : 3
Contact Hours : 5
Course Status : Non Core
Prerequisite : NIL

2.0 SYNOPSIS
The course is designed to introduce the basic concepts, methods, and tools used in
Bioinformatics for beginners. Topics include bioinformatics databases, sequence
alignment, molecular dynamics simulation and protein structure visualisation.
Emphasis will be put on the understanding and utilisation of these concepts and
techniques in bio-chemical engineering.

3.0 OBJECTIVES
Upon completion of this course students should be able to:
1. Understand basic concepts in bioinformatics and computational techniques.
2. Perform simple data mining of biological databases.
3. Visualize protein structures by using visualization tools.

4.0 METHODS OF INSTRUCTION

Lectures and computer laboratory
Lectures: 2 hours/week
Labs : 3 hours/week

5.0 LESSON PLAN

WEEK CHAPTER / CONTENT ACTIVITIES

1 PART I: BIOINFORMATICS BASICS Introduce and explain lesson
plan and course outline.
1. Introduction Introduce Bioinformatics and
1.1 What is bioinformatics other major players: DNA,
protein sequences and
1.2 Fundamentals in genes and genomes
structures.
1.3 Principles of protein structure
Hands-on introduction to
Pre-lab 1: Introduction bioinformatics.

23 2. Bioinformatics Databases Introduce genomes and

2.1 Introduction proteomes, databases and
2.2 Database search information retrieval, the World
2.2.1 Nucleotide sequence databases Wide web and computer
programming.
2.2.2 Protein sequence databases
Read Chap. 1 and 3 of
2.2.3 Protein structure databases Introduction to Bioinformatics,
2.3 Data retrieval systems Lesk, A. M.
LESSON PLAN FACULTY OF CHEMICAL ENGINEERING
UNIVERSITI TEKNOLOGI MARA
CBE 647/ BIOINFORMATICS
PAGE 2/3

Lab 1: Using the NCBI and Biology Workbench Group discussions

Sites
Assignment 1 (W4)
Lab work 1 (W5)
46 3. Alignment Introduction to the alignment
3.1 Similarity and Homology as a tool in finding similarity
3.2 Conserved regions and homology in the
3.3 Methodological principles relationship analysis.
Principles of methods and
3.4 Statistical significance
statistical significance are also
3.5 Simple pairwise alignment introduced.
3.6 BLAST searching
Lab work 2 (W6)
Lab 2: Protein Structure and Homology

7
TEST 1

8 - 10 PART II: Introduce the basic concepts

BIOMOLECULAR SIMULATIONS of biomolecular simulations
such as its units and
4. Molecular Dynamics Simulation derivaties, force field options,
and non-bonded interactions.
4.1 Introduction
4.2 Force field and energy landscape Describe the importance of
4.3 Simple MD algorithms utilising periodic boundary
4.4 Periodic boundary condition condition, Ewald summation,
4.5 Truncation of non-bonded interactions Implicit solvent model and
4.6 Implicit solvent model and continuum continuum electrostatics in MD
electrostatics calculations.

Lab 3: MD Lab work 3 (W11)

11 - 12 5. Protein structure Prediction Introduce protein structure and

5.1 Introduction methods in predicting protein
5.2 Defining a secondary structure and higher level secondary structure.
structure element
Describe and discuss treating
5.3 Methods for predicting secondary structure
protein structure.

Read Chap. 5 of Introduction

to Bioinformatics, Lesk, A. M.

Group discussions

13
TEST 2

14 5. Protein structure Prediction Discuss different softwares

5.4 Visualisation and demonstration on three-
dimensional protein structure
and folding.
LESSON PLAN FACULTY OF CHEMICAL ENGINEERING
UNIVERSITI TEKNOLOGI MARA
CBE 647/ BIOINFORMATICS
PAGE 3/3

6.0 ASSESSMENTS
Tests : 50 %
Lab Reports and Assignments : 50 %

7.0 GRADING SCALE

A+ 90 - 100 C 50 - 54
A 80 - 89 C- 47 - 49
A- 75 - 79 D+ 44 - 46
B+ 70 - 74 D 40 - 43
B 65 - 69 E 30 -39
B- 60 - 64 F 0 - 29
C+ 55 - 59

8.0 TEXTBOOK USED

1. Choudhuri S (2014), Bioinformatics for Beginners: Genes, Genomes, Molecular
Evolution, Databases and Analytical Tools, Elsevier Science Publishing Co Inc.

9.0 REFERENCES
1. Lesk, A (2002), Introduction to Bioinformatics, Oxford University Press, USA

10.0 ADDITIONAL INFORMATION

Please make appointments for consultancy.
Attendance is compulsory.
No make up test will be given unless with medical reasons with legal documents
presented.
No cheating and plagiarism in any aspect. Non-compliance will be met with severest
disciplinary actions.

PREPARED BY: APPROVED BY:

SIGNATURE: SIGNATURE:

NAME: DR. FAZLENA HAMZAH

NAME: DR. TAN HUEY LING POSITION: KPP Chemical Engineering
POSITION: SENIOR LECTURER (BIOPROCESS)

DATE: 1 SEPTEMBER 2017 DATE: