THE UNIVERSITY OF THE WEST INDIES
ST. AUGUSTINE
FACULTY OF SCIENCE AND TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
Title: BIOC2061 Bioenergetics
Credits: 3
Level: Undergraduate Level II
Semester I
Pre-requisites: BIOL1362 Biochemistry I or BIOL1061 Cell Biology and Genetics and either
CHEM1066 Introduction to Chemistry I and CHEM1067 Introduction to Chemistry II or
CHEM1060 Introductory Chemistry.
Anti-requisites: BIOL2361 Biomolecules and Energy Metabolism
Offering Department: Department of Life Sciences, Faculty of Science and Technology, The
University of the West Indies
Course Description
This course provides an overview of how living organisms derive energy from their environment
and how they use it to drive unfavourable biological reactions. The course will cover the
fundamentals of thermodynamics and its application to biological systems, membrane transport
oxidative phosphorylation and photosynthesis. The differences and similarities of plant, fungal and
mammalian systems will be explored. Students are expected to have a basic foundation in
biochemistry and chemistry before taking this course. Teaching will be conducted using lectures
and tutorials supported by myelearning Assessment is designed to encourage students to work
continuously with the course materials, explore and critically analyse topics in this field.. Tutorial
participation and the worksheets for these sessions will form part of the overall assessment of the
course, alongside tutorial quizzes, two incourse examinations and a final examination.
Instructor information
Dr. Adrian M. Lennon
Room 323 old wing Natural Science Building Phone ex 83216
Email [email protected]
Purpose of the Course
This course will provide the student with a fundamental understanding of bioenergetics and
biological energy transduction. Living organisms require an input of free energy and as such an
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understanding of how organisms derive energy and how it can be used to drive metabolic
pathways is one of the foundation stones of biochemistry.
COURSE CONTENT
TOPIC 1 - pH and Buffers (2 lectures)
The polar nature and solvent properties of water. Definition of pH. Calculations involving
conversion of hydrogen ion concentration to pH and vice versa. Review of ionic equilibria - the
conjugate acid/conjugate base pair. The Henderson-Hasselbalch equation. Buffer solutions mechanism of buffering. Control of physiological pH. Preparation of buffers for research. Ionic
strength.
TOPIC 2 - Bioenergetics (2 lectures)
Review of free energy change and standard free energy change in chemical reactions. Criterion
for predicting spontaneity of a process - G0. Standard states and the standard free energy change
- G0 . The modified standard state for biochemical applications, pH of 7 - G0. Use of
equilibrium constants to determine standard free energy change. Structure, properties and free
energies of ATP, ADP, AMP. Metabolic roles of ATP. Other "high energy" compounds.
Phosphoryl group transfer potential. Nucleotidyl-group transfer. Conservation of energy from
biological oxidations as reduced coenzymes. Oxidation/reduction reactions - the Nernst equation.
Proton motive force (membrane potential and pH gradients)
TOPIC 3 - Lipids and Membranes (5 lectures)
Structures of the lipids of biological membranes - phosphoglycerides, sphigomyelin, cerebroside,
ganglioside, cholesterol. Membrane proteins - peripheral vs integral. The fluid mosaic model
structure of biological membranes. Factors that determine membrane fluidity. Introduction to
membrane transport.
TOPIC 4 - Tricarboxylic Acid Cycle (3 lectures)
Overview of the TCA cycle as the final common pathway for the oxidation of fuel molecules. The
amphibolic nature of the TCA cycle. Details of the pyruvate dehydrogenase reaction for
conversion of pyruvate to acetyl CoA. Reactions of the cycle and the production of reduced
coenzymes. The TCA cycle as a multistep catalyst. Entry and exit of metabolites to and from the
cycle. Regulation of the TCA cycle. The glyoxylate cycle - a modification of the TCA cycle.
TOPIC 5 - Electron Transport and Oxidative Phosphorylation (4 lectures)
The organization of the respiratory electron-transport chain with reference to the ultrastructure of
the mitochondrion. Characteristics of the carriers - enzyme complexes - involved in the transfer
of electrons from reduced coenzymes to the terminal acceptor, molecular oxygen. Ubiquinone,
cytochromes, iron-sulphur clusters, copper ions etc. Coupling of electron transport to
phosphorylation of ADP. Mechanism of ATP synthesis - chemiosmotic theory conformational
coupling. The mitochondrial ATP synthase, F0F1. P/O ratios. Aerobic oxidation of cytosolic
NADH. Transporters of the mitochondrial inner membrane. Regulation of oxidative
phosphorylation. Plant and fungal respiratory chains,
TOPIC 6 – Photosynthesis (5 lectures)
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Discussion of the overall process of photosynthesis and the two distinct phases of chemical events.
The chemical structures and roles of chlorophylls and accessory pigments. Photosystems I and II.
The Z-scheme of the electron transport in chloroplasts. Cyclic electron transport. Carbon dioxide
fixation-the dark reactions. The Hatch-Slack C4 pathway. Photorespiration. Crassulacean acid
metabolism; Photorespiration and GOGAT, Chlororespiration
TOPIC 7 – Plastid- Mitochondrial Interactions (1 lecture)
Redox communication and exchange of metabolites between mitochondria and chloroplasts.
Supply of ATP during the day and night
TOIPIC 8 – Mitochondrial Dysfunction (1 lecture)
Role of mitochondria in disease states; Cytoplasmic male sterility
LEARNING OUTCOMES
pH AND BUFFERS (2 lectures)
At the end of this topic students will be able to:
1.
2.
3.
4.
5.
6.
7.
describe the structure and molecular nature of the water molecule
explain why certain molecules are able to dissolve in water
calculate Kw from first principles
calculate the pH of solutions contain strong acids and bases
compare weak and strong acids
derive the Henderson- Hasselbalch equation from first principles
use the HH equation to calculate the pH of solutions containing weak acids/bases and
buffers
8. experimentally determine pKa values
9. explain the concept of a buffer and to use the HH equation to calculate buffer
components
BIOENERGETICS (2 LECTURES)
At the end of this topic students will be able to:
1. define the first and second laws of thermodynamics
2. explain how free energy can be used to predict spontaneity of a reaction
3. explain how displacement from equilibrium effects free energy
4. derive equations relating G to displacement from equilibrium
5. relate G to Go
6. explain why ATP can perform useful work in the cell
7. explain the structural basis for the high group transfer potential of ATP
8. derive redox couples from redox reactions
9. describe how redox potentials are determined experimentally
10. explain how standard potential can be related to actual redox potentials and to free energy
11. calculate the energy in ion electrochemical potential
12. derive the proton motive force equation
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LIPIDS AND MEMBRANES
Lecture 1
At the end of this topic students will be able to:
1. relate structures of lipids to their physical properties
2. identify the different classes of lipids from their chemical formulae
Lecture 2
At the end of this topic students will be able to:
1. describe the components and structure of a biological membrane
2. explain the fluid properties of membranes and the role of cholesterol
3. describe the dynamic nature of the membrane and explain the experimental evidence for
fluidity
4. describe the three classes of membrane proteins and their nature of interaction with the
membrane
5. describe the hydropathy modelling technique and explain its limitations
6. describe the structure and functions of lipid rafts
Lectures 3, 4 and 5 - Membrane Transport
At the end of this topic students will be able to:
1. relate the characteristics of a molecule to its ability to diffuse across a biological
membrane
2. use Fick’s law to calculate the rate of diffusion
3. explain the differences between diffusion and protein mediated transport
4. describe the three major classes of protein transporters
5. relate the kinetics of passive transporters to their mode of action
6. explain the differences between the two classes of active transporters
7. describe the structure, function and mechanism of the 4 classes of ATPases
8. describe some of the medical conditions related to primary active transporters
9. explain the roles of ion channels and compare to other transporters in their kinetics and
mechanism
10. describe the nature of membrane pores
TCA CYCLE
Lecture 1
At the end of this topic students will be able to:
1. describe the nature of the 3 enzymes making up the PDH complex and their cofactors
2. describe the organization of the complex derived from various species
3. explain the series of chemical reactions that constitute the overall oxidative
decarboxylation reaction
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4. define the concept of substrate channelling and list its advantages
5. describe how and why the complex is regulated
6. compare the role of Ca2+ in mammalian skeletal muscle to other regulators of the
complex.
Lecture 2
At the end of this topic students will be able to:
1. describe the series of reactions that constitute the TCA cycle showing chemical structures
and reaction mechanisms
o/
2. summarize reasons behind and the interplay between the highly –
of the citrate
o/
of the malate dehydrogenase reaction
3. list the points at which the cycle is regulated and explain how this regulation is related to
the energy charge of the cell
4. compare the energy yield per glucose from that derived by anaerobic to aerobic
respiration
Lecture 3
At the end of this topic students will be able to:
1. compare the anabolic to the catabolic roles of the Krebs cycle
2. describe which metabolites can leave the Krebs cycle and the biosynthetic products they
can lead to
3. explain the role of the anaplerotic reactions
4. describe the Anaplerotic reactions and the nature of their regulation
5. explain why mammals cannot have a net synthesis of sugars from acetyl Co A
6. explain why certain bacteria can use the glyoxylate cycle to grow on acetate
7. describe how the regulation of the Krebs and glyoxylate cycle are regulated at the level of
isocitrate
8. describe the glyoxylate cycle and draw the structure of the intermediates in both bacterial
and plant cycle
RESPIRATORY CHAINS
Lecture 1
At the end of this topic students will be able to:
1. describe the redox centres found in the respiratory chain their structures and the nature of
the redox chemistry they undergo
2. compare the role of one and two electron carriers in the respiratory chain
3. describe the structure of complex I and the series of redox reactions it undergoes and the
nature of energy conservation
4. describe the structure and organization of complex II, the nature of the redox chemistry it
undergoes and explain the role of the b heme
5. describe the alternative mechanisms that lead to the reduction of ubiquinone
Lecture 2
5
At the end of this topic students will be able to:
1.
2.
3.
4.
5.
6.
7.
8.
describe the structure and organization of complex II
describe the series of redox reactions that make up the Q-cycle
explain why the Q-cycle is required
list the inhibitors of complex II and the sites of action
describe the structure and organization of complex IV.
describe the series of electron transfers that occur in complex IV
describe the mechanism for the reduction of water
explain why this series of reactions are required and the importance of avoiding ROS
production
9. explain how chemiosmosis links ATP synthesis to electron transport
10. List Mitchell’s postulates
11. describe and explain the experimental evidence that confirms the chemiosmotic
hypothesis
Lecture 3
At the end of this topic students will be able to:
1.
2.
3.
4.
5.
6.
7.
8.
describe the structure of the ATP synthase
explain how pr
explain Boyer’s conformation change model of ATP synthesis
explain the concepts of respiratory control and the P/O ratio and why the P/O ratio does
not need to be an integer.
compare the P/O ratios of succinate and NADH
contrast the differences between mammalian, plant and fungal mitochondria
describe the molecular nature of the alternative oxidase and explain how it can compete
for electrons with the cytochrome pathway
List the major roles of the alternative pathway
Lecture 4
At the end of this topic students will be able to:
1. explain how brown fat cells can produce heat rather than synthesize ATP
2. describe the two mechanisms by which cytosolic NADH can be utilized by the
mammalian mitochondria
3. analyze the interactions between the ATP synthase, phosphate carrier and adenine
nucleotide carrier
4. explain how mitochondria accumulate Ca2+
5. list the effects of raised Ca2+ on mitochondrial metabolism
6. analyze the mitochondrial permeability transition
7. describe the ammonium swelling technique
8. describe the structure and explain the function of mitochondrial anion transporters
PHOTOSYNTHESIS
Lecture 1
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At the end of this topic students will be able to:
1. calculate how much energy can be derived from light
2. describe the structures of the photosynthetic pigments and explain how they can capture
light energy
3. explain why plants use many different pigments during light capture
4. describe the structures and localization of the photosystems and the b6f complex
5. state the roles of the LHC’s
6. describe the structure of the antenna complexes and explain why such complexes are
required
7. describe the three mechanisms by which energy may be transferred between
photosynthetic pigments
Lecture 2
At the end of this topic students will be able to:
1.
2.
3.
4.
5.
6.
explain how the Z scheme relates to the energetics of electron transfer
describe the series of redox reactions that make up the Z scheme
describe the process of water splitting and explain why such reactions are required
list the mechanisms by which energy is conserved during the Z scheme
compare the various models of cyclic photophosphorylation
describe the two classes of herbicides that interact with the z scheme and explain how
these interactions lead the death of the plant
Lecture 3
At the end of this topic students will be able to:
1.
2.
3.
4.
5.
discuss the structure and organization of Rubisco
describe the carboxylation reaction performed by the Rubisco complex
describe the reactions leading to the production of sugars
describe how a five carbon sugar is regenerated from a three carbon compound
explain how the light reactions regulate the light independent reactions
Lecture 4
At the end of this topic students will be able to:
1.
2.
3.
4.
describe the oxygenase reaction performed by Rubisco
explain why natural selection has been unable to remove the oxygenase activity
describe the series of reactions that constitute the photorespiratory pathway
explain the energetics of the photorespiratory pathway and why it is used by plants in
temperate regions
5. Explain the role of GS-GOGAT in C3 metabolism and the experimental evidence for this
role.
6. Explain how photorespiration may influence C3 plants responses to future climatic events
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Lecture 5
At the end of this topic students will be able to:
1. describe the C4 pathways and explain why these pathways evolved in some tropical
species
2. describe the CAM pathways and explain why certain plants evolved such pathways
3. analyze the energetic costs between the C3, C4 and CAM pathways
4. describe the molecular nature of the Ndh and PTOX complexes
5. explain the interaction of the chlororespiratory and photosynthetic ETCs
6. discuss the roles of chlororespiration
PLASTID-MITOCHONDRIAL INTERACTIONS
At the end of this topic students will be able to:
1. describe the exchange of reducing equivalents and carbon skeletons between organelles
2. analyze the ATP supply in the light: chloroplasts vs. Mitochondria
3. explain adenylate control of plant respiration in the light
4. explain how organelle interactions can be used to avoid over-reduction
5. describe how environmental factors can influence plastid-mitochondria interactions
6. describe the interaction between plastids and mitochondria in the dark
MITOCHONDRIAL DISFUNCTION
At the end of this topic students will be able to:
1. List the major mitochondrial genetic diseases
2. discuss the role of mitochondrial dysfunction in Parkinson’s, Huntington’s and
Alzheimer’s disease and Friedreich’s ataxia
3. Discuss the role of mitochondria in reperfusion injury
4. Describe the different mechanisms that result in cytoplasmic male sterility
5. Explain the economic importance of CMS
TEACHING STRATEGIES:
Contact hours (36 credit hours):
Lectures: Lectures will provide valuable synthesis and evaluation of the growing body of
available information, update current issues and events, and prioritize content relevant to course
assessment. For this course, the delivery strategy will be chalk-and-talk with continuous class
interaction and engagement. Posting lecture notes prior to class times will not be practiced as this
has resulted in a drop in attendance.
Tutorials: Tutorials will cover course topics in a problem-solving format to engage collaborative
and active learning techniques.
myeLearning: myeLearning will be used extensively during this course for official communication
among students and staff (email, discussions), official posting of important notices (coursework
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assessment notices, instructions, glossaries, and in-course marks/results), official posting of
syllabus, lecture notes, tutorials, posting of important web-related resource materials and links.
ASSESSMENT
Coursework
Consisting of:
2 incourse examinations covering weeks 1-4 and weeks 5-9
Tutorial participation and work sheets
4 tutorial quizzes (to be held in tutorial sessions as announced)
Final Theory Examination (2 hrs)
Consisting of 25 MCQ’s and 3 essay type questions
(50%)
(30%)
(10%)
(10%)
(50%)
REQUIRED READING
Essential Text
Lehninger: Principles of Biochemistry, 5th Edn., by Nelson & Cox
Recommended texts
Principles of Biochemistry 4th Edn., by Horton et al
Biochemistry 6th Edn (Int’l) by Berg, Tymoczko & Stryer
Molecular Biology of the Cell 5th Ed Alberts et al
Biochemistry and Molecular Biology of Plants Buchannan, Grisham and Jones (eds.) ASPB
Bioenergetics 3 - Nicholls and Ferguson Academic Press
EVALUATION: BIOL2XXX will be evaluated in two ways – (a) through the offices of the Class
Representative and the Life Sciences Student-Staff Liaison Committee, and (b) an end of semester
course evaluation survey. The class will elect two class representatives, whose role is to act as a
mediator between the Life Sciences academic staff and the students in the class. The
representatives will attend Liaison Committee meetings (held at least twice per semester), where
they will present feedback on the course to the Department for action. The UWI performs a course
evaluation survey at the end of every semester, and this information will also be used for overall
assessment of the course and guide possible actions for improvement in subsequent semesters.
Course Calendar
Week
Topic
Hours
1
Course Introduction
pH and Buffers
1
2
2
Bioenergetics
Tutorial
2
1
9
Week
3
Topic
Lipids and Membranes
Tutorial
Hours
2
1
4
Lipids and Membranes
3
5
Tutorial
Exam #1 weeks 1- 4
Exam Review
1
6
TCA Cycle
3
7
Tutorial
Electron Transport Chain
1
2
8
Electron Transport Chain
Tutorial
2
1
9
Photosynthesis
Tutorial
2
1
10
Incourse #2 weeks 5- 9
Exam Review
Photosynthesis
1
11
Photosynthesis
Tutorial
2
1
12
Plastid- Mito interactions
Mitochondrial dys.
Tutorial
1
1
1
13
Course Review/ Tutorials
3
1
ADDITIONAL INFORMATION:
Students must pay attention to the following important information concerning assessment,
attendance and plagiarism: The Life Sciences Undergraduate Handbook available from
http://sta.uwi.edu/fst/lifesciences/documents/handbook.pdf .
 The General Information and General Regulations in the Faculty Booklet available from
http://sta.uwi.edu/resources/documents/facultybooklets/ScienceTechUndergrad.pdf .
 As a general principle, medicals or other excuses may only excuse a student’s absence
from the original exam. Students must sit the makeup exam at the assigned date and time.
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
All course work submissions must be attached to a signed Coursework Accountability
Statement in order to be assessed. Refer to ‘University Regulations on Plagiarism’
available from http://sta.uwi.edu/resources/documents/Exam_Regulations_Plagiarism.pdf
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