MCB63X

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
 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!*

 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
 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
 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
 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
UNIT 3: CELLULAR BIOENERGETICS
3.1: Glycolysis
3.2: Unique features of glycolysis in red blood cells
 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
 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
 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
 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
UNIT 4: TISSUE-SPECIFIC METABOLISM
4.1: Liver metabolism
 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

 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
 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
UNIT 5: SYNTHESIS AND DEGRADATION OF BIOMOLECULES
5.1: Nucleic acid metabolism
 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
 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
 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
 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

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MCB63X: PRINCIPLES OF BIOCHEMISTRY

Recommended Texts and Software

Objectives: Students should be able to

 Explain how the chemical properties of carbon explain the

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

End of session assessment: Protein structure and folding

Learning PyMOL *optional and ungraded!*

Objectives: Students should be able to

2.3: Enzyme Catalysis

2.4: Enzyme Kinetics

Objectives: Students should be able to

 Explain how the interaction between enzyme and substrate affect

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

End of session assessment: Lipids

2.6: Carbohydrate structure

Objectives: Students should be able to

 Recall the classification and the structure of monosaccharides

End of session assessment: Carbohydrates

End of Unit 2 Assessment

UNIT 3: CELLULAR BIOENERGETICS

3.2: Unique features of glycolysis in red blood cells

Objectives: Students should be able to

 Recall the steps of ATP synthesis by glycolysis

End of session assessment: Glycolysis

Objectives: Students should be able to

 Predict the biochemical impact of linear and branched

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

End of session assessment: Oxidative phosphorylation

3.7: Regulation of glycolysis in liver cells

Objectives: Students should be able to

 Explain the role of allosteric enzymes as valves controlling the

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

End of session assessment: Liver metabolism

4.2: Brain metabolism

Objectives: Students should be able to

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

End of session assessment: Muscle metabolism

End of Unit 4 Assessment

Learning PyMOL optional and ungraded!