COURSE CODE BIO3110

COURSE TITLE BIOCHEMISTRY II- INTERMEDIARY METABOLISM

CREDITS 3

Level 3

Semester 1

Exemptions Equivalent training/course

Pre-requisites BIO2205 Biochemistry I

Follow-on Courses BIO4112 Molecular Biology and Biotechnology,

BIO4213 Genomics and Informatics BIO4205
Internship; BIO4200 Capstone Research Project

Course Description
Metabolism refers to the sum of all chemical reactions that occur in living organisms including
digestion and the elimination of nitrogenous wastes, but also the transport of substances into and
between cells. It is the latter set of reactions, within the cells, that is referred to as intermediary
metabolism. Hence, intermediary metabolism may be de-fined as the intracellular processes by
which nutritive material is converted into cellular components - either energy for vital processes or
the production of other substances necessary for life. Intermediary metabolism is a vast subject
within biochemistry hence; there is only enough time in this course to present a few fundamental
pathways whereby students may gain a preliminary understanding of intermediary biochemistry.
This course emphasizes how the pathways are regulated by specific molecules and hormones in living
systems. Further, students will consider how several human diseases arise from defects in metabolic
pathways, and will review papers in the current scientific literature on new techniques by which
metabolites are characterized in the laboratory. This course offers a foundation for students seeking
careers as biochemists, pharmacologists, secondary level educators, etc.

Student Learning Outcomes

On successful completion of the course, students should be able to:
1. Explain clearly what is intermediary metabolism and the concept of metabolic pathways.
2. Differentiate accurately between anabolism and catabolism.
3. Explain why metabolic pathways are not considered as closed systems.
4. Deduce the existence of common metabolic pools in cells using relevant examples.
5. Discuss how several human diseases arise from defects in metabolic pathways.

Course Content
WEEK 1
● Carbohydrates and Glycobiology

1
 ● Principles of bioenergetics
WEEK 2
● Carbohydrate biosynthesis
● Regulation and disease associated
● Link to Citric acid cycle
WEEK 3
● Glycolysis & gluconeogenesis
● Regulation of glucose and glycogen
● Glycogen storage diseases
● Why fructose is different
TEST 1
WEEK 4-5
● Citric acid cycle
● Regulation and disease associated
● Amphibolic nature of Citric acid cycle
● Alternative TCA cycles
● Involvement of Citric acid cycle in transamination and gluconeogenesis
WEEK 6
● Fatty acid catabolism
● Fatty acid synthesis and protein synthesis with carbohydrates (and their de-rived
substrates)
● Regulation and disease associated
WEEK 7-8
● Amino acid oxidation
● Urea cycle
● Urea cycle disorders
● Oxidative and photophosphorylation
■ Oxidative damage and disease
TEST 2
WEEK 9
● Lipid biosynthesis
● Protein and lipid metabolic pathways
WEEK 10
● Synthesis of nucleotide and amino acids
WEEK 10-13
● Cancer cell metabolism
● Human starvation
● Metabolic limits of human performance
TEST 3

Revision
Final Examination

2
Laboratory practical work
Practical classes will be selected from the following:
● Activity of salivary amylase and to show enzymes are proteins
● Effect of varying substrate concentration on enzyme activity
● Effect of varying temperature on enzyme activity
● Effect of varying enzyme concentration on enzyme activity
● Regulatory enzymes - allosteric enzymes, regulation by feedback inhibition
● Substrate specificity of enzymes
● Immobilization of enzymes
● Competitive inhibition of succinate dehydrogenase by malonate
● Demonstration of stimulation and inhibition of allosteric enzymes
● Demonstration of release of heat energy in chemical reactions
● Demonstration of enzymes involved in biological oxidation and reductions - dehy-drogenase
and catalase activity
● Determination of respiratory quotients
● Extraction of enzymes
● Enzymes in diagnosis

Methods of Teaching

● Presentational and Interactive Approaches

● Interactive classes involving taught sessions
● Problem-Based Learning and Collaborative Learning Approaches
● Small-group sessions (problem-based learning and critical thinking tutorials)
● Discovery, Experiential and Observational Learning Approaches
● Practical sessions (laboratory experiments/instrumentation/data analysis)
● Review of scientific paper
● Twenty First Century Technologies Engagement Approaches/Technology-Enhanced Teaching
● Learning Management Systems
● Computer animations,
● Multimedia Presentations, etc.

This course comprises 26 hours of taught classes, 2-3 hours of laboratory-based work per week over
a 13-week period. The learning environment is enhanced with the use of 21 st century teaching and
learning technologies comprising interactive lectures, low-stakes testing, multimedia presentations
e.g. computer-based animations and small-group tutorials incorporating problem-solving sessions
and critical thinking. Scientific interpretative skills will be assessed through review a selected
scientific paper in a topical area of intermediary metabolism. Laboratory-based sessions will expose
students to analysis of basic intermediary metabolic processes. Presentation outlines and other
support materials are available on the Moodle learning platform.

Methods of Assessment
In course tests (e.g. SRQ, MCQ, etc.) (3 @ 8%) 24%
Written assignment (1 @ 10 %) 10%
Laboratory reports 16%
Final written examination 50%

3
Required Reading

Baquer, N. Z. (2007). Intermediary metabolism. Interrelationships of Metabolic Path-ways. School

of Life Sciences Jawaharlal Nehru University New Delhi – 110 067. Retrieved July 2016 from
http://nsdl.niscair.res.in/jspui/bitstream/123456789/109/1/MetabolicPathways.pdf

Recommended reading

Morowitz, H. J., Kostelnik, J. D., Yang, J. & Cody, G. D. (2000). The origin of intermediary
metabolism. Proceedings of the National Academy of Sciences of the United States
of America 97 (14): 7704–7708. doi: 10.1073/pnas.110153997. Available at
http://www.pnas.org/content/97/14/7704.full.pdf

Recommended Resources: Useful Websites

WormBook: Intermediary metabolism. Retrieved July 2016 from

http://www.wormbook.org/chapters/www_intermetabolism/intermetabolism.html

The Interconversion of Fuels and why we get fat from eating too many sweets! Retrieved July 2016
from
www.biology-pages.info/I/IntermediaryMetabolism.html

Examples of homework and problem-based learning questions

http://www1.udel.edu/chem/white/CHEM643F12.html

Whole Enzyme Catalog database on enzymes

Joyce Diwan's Biochemistry of Metabolism website at RPI

The Medical Biochemistry Page

Kyoto Encyclopedia of Genes and Genomes (KEGG) Database

The Main Metabolic Pathways on Internet

Other Resources

3D Glucose cyclization animation - an animated representation of glucose folding from

the linear to the cyclical conformation.
http://www.pitt.edu/~jbrodsky/biosc1820/documents/studyguide/glucanim.htm

Follow the Carbon - Glycolysis - Reference - a representation of the glycolysis pathway which allows
you to trance any of the carbons in the original glucose molecule throughout
the pathway. http://www.pitt.edu/~jbrodsky/biosc1820/documents/studyguide/pw_glyc.htm

Follow the Carbon - Glycolysis - Quiz - this quiz tests student’s ability to follow a labeled carbon
atom throughout the glycolysis pathway. (Student must know the names of the
glycolysis-intermediates to complete this quiz).
http://www.pitt.edu/~jbrodsky/biosc1820/documents/studyguide/glyc_quiz.htm

4
Citric Acid Cycle - Self Quiz - allows students to test knowledge of the intermediate-names
and the names of the enzymes that catalyze them. (Write out the pathway a few
times before working with the applet).
http://www.pitt.edu/~jbrodsky/biosc1820/documents/studyguide/tca.htm

Cofactor-Matching Game - This game will provide practice for the "matching" sections on
your exams. This edition contains cofactors that you are responsible for knowing on the
midterm.
http://www.pitt.edu/~jbrodsky/biosc1820/documents/studyguide/cof_quiz2.htm

ExPASy Biochemical Pathways - This site allows you to view ALL the pathways of interme-diary
metabolism, and by "clicking" on any segment of this road-map you can get a close-up view
of the chosen reactions. http://web.expasy.org/pathways/