MCB63X: PRINCIPLES OF BIOCHEMISTRY
Course Instructors
Alain Viel, Rachelle Gaudet
Course Description
Principles of Biochemistry integrates an introduction to the structure of
macromolecules and a biochemical approach to cellular function. Topics addressing
protein function will include enzyme kinetics, the characterization of major metabolic
pathways and their interconnection into tightly regulated networks, and the
manipulation of enzymes and pathways with mutations or drugs. An exploration of
simple cells (red blood cells) to more complex tissues (muscle and liver) is used as a
framework to discuss the progression in metabolic complexity. Students will also
develop problem solving and analytical skills that are more generally applicable to the
life sciences.
In this updated version of the course, learners will also explore how alteration of these
metabolic pathways relates to the development and progression of some human
diseases.
Research
HarvardX pursues the science of learning. When you participate in this course, you
will also participate in research about learning. Read our research statement to learn
more.
Recommended Texts and Software
There is no required textbook. You may find the book Biochemistry by Berg,
Tymoczko, and Stryer to be a useful resource if you are able to obtain a physical or
PDF copy.
Course Structure
This is a self-paced course.
Grading
There are 2 different graded components of the course:
1. End of session (EOS) assessments. These occur after each topic and are
worth a total of 50% of your grade.
2. End of unit (EOU) assessments. These occur at the end of each unit are
worth a total of 50% of your grade.
Assessments are not timed. You may leave in the middle of an assessment and come
back later to complete it. All assessments are due by the close of the course run
(November 24, 2020).
All other components of the course (such as PyMOL exercises) are not for credit.
Certification
You must sign up for a Verified Certificate in order to be eligible to earn a
certificate.
If you achieve a cumulative score of 70% or greater (out of 100) and sign up for
a Verified Certificate before the deadline, you will receive a certificate for the
course. When you reach this point, you will see a "Request Certificate" option appear
on the Progress page!
COURSE OUTLINE
UNIT 0: PRELIMINARIES
UNIT 1: INTRODUCTION TO BIOCHEMISTRY
1.1: Introduction
Objectives: Students should be able to
Explain how the chemical properties of carbon explain the
structural diversity of organic molecules
Predict the evolution of a biochemical reaction
Determine the factors driving the equilibrium, directionality and
spontaneity of biochemical reactions
Understand how matter and energy flow between living systems
Learn the classification of living organisms based on their abilities
to extract and transform external sources of energy into usable
chemical energy
End of session assessment: Introduction
End of Unit 1 Assessment
UNIT 2: STRUCTURAL BIOCHEMISTRY
2.1: Protein Structure
2.2: Protein Folding
Objectives: Students should be able to
Draw the chemical structure of each of the 20 natural amino acids
Describe the three basic building blocks of protein structure (α-
helix, β-sheet and loop)
Describe the forces and interactions that promote protein folding
Evaluate, based on their knowledge of protein structure, whether a
given protein structure model is likely to represent a native
physiological protein structure.
Make predictions about the effect of mutations on protein
structure and folding
End of session assessment: Protein structure and folding
Learning PyMOL *optional and ungraded!*
Objectives: Students should be able to
Understand the purposes of different representations of protein
structures
Use PyMOL to navigate and illustrate protein structures
2.3: Enzyme Catalysis
2.4: Enzyme Kinetics
Objectives: Students should be able to
Explain how the interaction between enzyme and substrate affect
the velocity of a reaction
Apply the fundamental principles of Michaelis-Menten enzyme
kinetics
Predict the mode of action and the impact of different classes of
inhibitors on enzyme kinetics
Understand the kinetics of enzymes acting on several substrates
Design mutations hypothesized to affect different enzyme kinetic
parameters
End of session assessment: Enzymes
2.5: Lipid structure and membrane assembly
Objectives: Students should be able to
Explain the assembly of fatty acids into structural lipids
Describe the chemical and physical properties of lipids and how
they lead to the assembly of biological membranes
Make predictions about the impact of changes in lipid structure
and composition on properties of membranes
Describe the types of interactions between proteins and
membranes
Summarize the roles of membrane-associated proteins on
membrane properties
End of session assessment: Lipids
2.6: Carbohydrate structure
Objectives: Students should be able to
Recall the classification and the structure of monosaccharides
Explain the structural reason behind the central role of glucose
Understand how the chemical structure of monosaccharide leads
to the formation of complex and branched carbohydrates
Describe structural and functional properties of extracellular
carbohydrates
End of session assessment: Carbohydrates
End of Unit 2 Assessment
UNIT 3: CELLULAR BIOENERGETICS
3.1: Glycolysis
3.2: Unique features of glycolysis in red blood cells
Objectives: Students should be able to
Recall the steps of ATP synthesis by glycolysis
Explain the contribution of fermentation to glycolysis
Describe how glycolytic intermediates impact oxygen binding,
and protect red blood cells against reactive oxygen species
End of session assessment: Glycolysis
3.3: Bacterial energetics
Objectives: Students should be able to
Predict the biochemical impact of linear and branched
fermentation pathways
Explain the metabolic switches in bacteria exposed to changes in
their environments
Contrast and compare aerobic and anaerobic respiration
Correlate the complexity of the human microbiota and human
health
End of session assessment: Bacterial energetics
3.4: The citric acid cycle
3.5: Electron transport
3.6: ATP synthesis
Objectives: Students should be able to
Describe the production of reduced electron carrier during the
citric acid cycle
Describe each steps of the production of ATP by oxidative
phosphorylation
Correlate the number of ATP molecules produced with the point
of entry of electrons in the electron transport chain
To compare the yield of ATP synthesis by substrate level
phosphorylation and oxidative phosphorylation
End of session assessment: Oxidative phosphorylation
3.7: Regulation of glycolysis in liver cells
3.8: Regulation of blood sugar by the liver
Objectives: Students should be able to
Explain the role of allosteric enzymes as valves controlling the
flux of intermediates in a pathway
Determine how transient covalent modification affects enzymes
controlling key steps in metabolic pathways
Explain the hormonal regulation of metabolic pathways
Predict how changes in blood glucose level affect the biochemical
and hormonal regulations of metabolic pathways including
glycolysis, gluconeogenesis, glycogen synthesis and, glycogen
degradation
End of session assessment: Regulation by the liver
End of Unit 3 Assessment
UNIT 4: TISSUE-SPECIFIC METABOLISM
4.1: Liver metabolism
Objectives: Students should be able to
Identify the major energetic pathways operating in human cells
Describe the response of the liver to metabolic perturbations
Recall the physiological changes that occur during fasting and
starvation
End of session assessment: Liver metabolism
4.2: Brain metabolism
Objectives: Students should be able to
Identify the primary metabolic regulatory hormones that operate
in humans, and their main functions
Describe why the brain is metabolically different from many other
tissue
Explain the response of the brain to hypoglycemia and hypoxia
End of session assessment: Brain metabolism
4.3: Muscle metabolism
Objectives: Students should be able to
Describe the metabolic adaptations of muscle that enable it to
rapidly generate ATP for mobility
Differentiate between metabolism in cardiac and skeletal muscle
Recall how the body and muscle adapt to physical challenges of
different durations
End of session assessment: Muscle metabolism
End of Unit 4 Assessment
UNIT 5: SYNTHESIS AND DEGRADATION OF BIOMOLECULES
5.1: Nucleic acid metabolism
Objectives: Students should be able to
Compare the synthesis of purines and pyrimidines
Compare the recycling and degradation pathway of nucleotides
Recall the different steps of the urea cycle
Describe the metabolic basis and treatment of gout
End of session assessment: Nucleic acid metabolism
5.2: Carbohydrate metabolism
Objectives: Students should be able to
Describe the processing of complex and simple dietary
carbohydrates
Compare the biochemical transformations of the simple sugars
feeding the glycolytic pathway
Recall the different steps of the pentose phosphate pathway and its
role
End of session assessment: Carbohydrate metabolism
5.3: Fatty acid metabolism
Objectives: Students should be able to
Demonstrate how fatty acid synthase catalysis leads to the
production of fatty acids with an even number of carbons
Predict the energy inputs and energy yield of fatty acid anabolism
and catabolism
Relate genetic deficiencies in fatty acid metabolism to human
diseases
End of session assessment: Fatty acid metabolism
5.4: Cancer and metabolism
Objectives: Students should be able to
Describe the relationships between metabolic and cell signaling
pathways in cancer pathogenesis
Describe the role of redox balance in cell proliferation
Describe how Positron Emission Tomography (PET) works
End of session assessment: Cancer and metabolism
End of Unit 5 Assessment
