Anne Rosenwald
Georgetown University
Revision of Biochemistry (Biology 151)
Revision of Glycolysis and TCA Cycle Lectures
Framework
Sophomore level course, but may include juniors and seniors
One of two choices in “Molecules Bin” (other is Genetics)
Mixed backgrounds – students at a minimum have had the 2 semester Foundations
sequence
Mixed Biology majors (many of whom are premed), premed non-majors, and postbacs
60-90 students
Lecture hall with stadium seating – hard to do group work except for nearby
partners
This will eventually be a course that fulfills Writing-in-the-Discipline req (new req
for all entering students beginning in 2016(?))
Needs to be consonant with Departmental Learning Goals (see end of this doc*)
Learning Goals for Course as a Whole
Students will
1) increase their knowledge of chemical underpinnings of life processes
2) be able to solve problems from fundamental principles
3) enhance skills in reading scientific literature
4) enhance skills in communicating science to a variety of audiences
5) develop skills in metacognition
Learning Goals for Glycolysis and the TCA Cycle
Students will be able to
1) identify and characterize the types of reactions that occur in both pathways
(isomerases, kinases, etc.)
2) identify and characterize the products of reactions that occur in both
pathways (ATP, GTP, NADH, etc.)
3) describe how regulation of the pathways occurs in normal cells and cancer
cells
4) compare and contrast the differences between cancerous cells and normal
cells with respect to these two pathways
Formative Assessment - Glycolysis/TCA Cycle Basics (Pre-Monday Lecture FA)
Students read in preparation the two chapters from the book (“Glycolysis” and “TCA
Cycle”)
Point here is to see if they have basic knowledge so that we can go on and discuss
the more difficult stuff when we’re all in class together (the regulation). Students
will do this via BB. Gets at Specific LO’s 1 and 2.
1. Why do cells metabolize glucose?
2. Can cells metabolize other monosaccharides in addition to glucose?
3. What is at the “bottom” of the glycolytic pathway?
4. What are the three fates of this molecule? (In other words there are three
different molecules that are derived from this “bottom” molecule – what are they?
5. One of these molecules then is metabolized in the TCA Cycle – which one of the
three is it?
6. Do cells that grow anaerobically have a TCA cycle?
7. Why do aerobic cells have a TCA cycle?
8. What are two important products that come from the TCA cycle?
9. What does “anabolic” mean?
10. What does “anapleurotic” mean?
Could try to think of something more creative here, but I’m not the game playing
type....
Monday Lecture
Will give theme of the week – for this section, Cancer. Then move into basic
biochem facts and how they related to cancer. Hope is that students will get the
basics on their own (have weekend quiz to guide me here) – then I can focus on the
more difficult material in class - REGULATION
Formative Assessment – Muddiest Point (end of day on Monday)
After Monday lecture – what do I need to clarify for Wednesday lecture?
Students put this on BB – though Didem suggested making a GoogleDoc instead – so
student comments are kind of “self-arranged”.
Will need to generate directions here (not really a rubric b/c they get credit for
doing, not for content)
Wednesday Lecture
Clarify issues left over from Monday.
Practice problems alone, then in small groups, then all together (practice for exam)
Problems will be pulled from previous exams and problems book – rewritten to
correspond to the cancer theme. Gets to Specific LO3.
Pre-Friday Journal Club
Students read assigned journal article before class on Friday and post questions
they had, comments they want to make about the article, related info they found
from popular press, Youtube, etc.
Need directions for students here as well – what I’m looking for in terms of
“substantive comments”.
Potential Papers for Journal Club
Warburg Effect
http://www.nature.com/nature/journal/v452/n7184/full/nature06734.html
The M2 splice isoform of pyruvate kinase is important for cancer metabolism and tumour
growth
Heather R. Christofk1, Matthew G. Vander Heiden1,2, Marian H. Harris3, Arvind
Ramanathan4, Robert E. Gerszten4,5,6, Ru Wei4, Mark D. Fleming3, Stuart L. Schreiber4,7 &
Lewis C. Cantley1,8
Microarray data on up/down-regulation in pancreatic cancer
http://www.plosone.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjourn
al.pone.0032996&representation=PDF
Differential Expression of Metabolic Genes in Tumor and Stromal Components of Primary
and Metastatic Loci in Pancreatic Adenocarcinoma
Nina V. Chaika et al PLoS One
These papers might be tricky b/c we haven’t talked explicitly about reg of gene
expression (microarrays) or mutations here yet in this class (gets to problem of
mixed population of students). A couple of folks suggested posting YouTube videos,
etc. so they can get up to speed on their own.
Joan K. suggested investigating a new drug that inhibits PDH – might be easier to
assimilate this within the current framework. In any case, will do deeper
exploration to find a good paper to use.
Friday Journal Club – Jigsaw
Groups are assigned a figure or two – each discusses until all satisfied they can
explain, then regroup so new groups have entire paper covered by experts. Discuss
as a group, then reconvene as class group to pull threads together with reference to
Q’s posted by students night before. If all students seem completely befuddled, then
I’ll present entire thing myself – asking students to answer Q’s as we proceed. Gets
to specific LO’s 3 and 4.
Post-Friday Assignment
Students write a crafted response to the week’s events (esp. the JC article). Gets to
WID practice and will help me figure out what needs to be reviewed – good advice
from Patrice here about coming full circle and responding back to the students.
Prompts could include:
 what did you learn?
 what did you find challenging that was resolved by the end of the week?
 what did you find challenging that was not resolved by the end of the week?
Summative Assessment
Note – need to better consider Bloom’s levels here. These particular questions are
on the low end.
Also need to perhaps frame these relative to theme (Cancer in this case)
Old Question 3 from 2010 Exam 2 (black text)
In Harry Potter and the Prisoner of Azkaban, Harry encounters a man, Sirius Black,
with unusual abilities. Avid readers of Harry’s adventures will know that Sirius is an
animagus and has the ability to turn himself into a dog (i.e. a mammal).
A. (2 points) We talked about 3 fates for pyruvate. What is the usual fate of
pyruvate in the muscles of dogs? Why?
Correct answer: Under normal circumstances, the oxidative fate of pyruvate is the
one that occurs in muscle – in other words – pyruvate is converted into acetyl CoA
Rewrite as multiple choice:
The fates of pyruvate are listed below. Which one is the fate that occurs in sleeping
dogs?
A. lactate
B. ethanol
C. acetyl-CoA
D. none of the above
E. all of the above
Rewrite as matching (this encompasses part D too):
Match the following (each letter should have only 1 number associated with it)
A. lactate
1. muscles of sleeping dogs
B. ethanol
2. muscles of dogs running really fast for a long time
C. acetyl CoA
3. Baker’s yeast
B. (2 points) What is the committed step for glycolysis in dogs? (You can
either name the enzyme or give the reaction this important enzyme catalyzes). Why
is this step the crucial control point?
Correct answer: Same as in other organisms: PFK-1 – this is the crucial place b/c
this is the first step that is unique to glycolysis (remember than glucose 6-P has
other fates in addition to entering glycolysis so the hexokinase step, although
regulated is not the most important point).
Rewrite as multiple choice:
What enzyme catalyzes the committed step for glycolysis in dogs?
A. phosphofructokinase-1
B. enolase
C. aldolase
D. triosephosphate isomerase
E. there is no committed step
Give them the pathway and ask them to mark the committed step and the two other
regulated steps
C. (2 points) Allosteric modulators control the activity of the enzyme
catalyzing the committed step. For the enzyme you mentioned above in 3 B, name a
single
Positive modulator: AMP, ADP, or Fr 2,6 bisP
Negative modulator: ATP or citrate
D. (2 points) If Sirius the dog has been running flat out for awhile, what
alternate fate of pyruvate occurs in his muscles? Briefly explain why this happens.
Correct Answer: Oxygen would be limiting – therefore the only other fate available
is conversion of pyruvate to lactate (lactate is the thing that makes your muscles
sore). This needs to happen to regenerate NAD+ so that glycolysis can continue.
(Conversion to ethanol is not a possibility here – this is done by microorganisms, not
mammals.)
Old Question 4 from 2010 Exam 2
4. (8 points) Harry and the Sphinx
In the Harry Potter and the Goblet of Fire, Harry meets a Sphinx in the maze, who
asks him a riddle. In order for him to get past the Sphinx, he must answer the riddle
correctly. Here is a riddle for you:
Here are two reactions that occur in the TCA cycle
Malate + NAD+ <------------> oxaloacetate + NADH + H+ G’o = 29.7 kJ/mol
Oxaloacetate + acetyl-CoA + H2O <---------> citrate + CoSH G’o = -32.2 kJ/mol
A. (2 points) Calculate the G’o of the combined reaction. What does the G’o
value tell you about the rate of the combined reaction in cells (one word answer,
please)?
Add the two together: 29.7 + -32.2 = -2.5 kJ/mol; tells you NOTHING about the rate.
Many people said “spontaneous” here, which is true, but that didn’t answer the
question.
Rewrite first part as multiple choice:
Calculate the G’o of the combined reaction.
A. -2.5 kJ/mol
B. 2.5 kJ/mol
C. -61.9 kJ/mol
D. 61.9 kJ/mol
E. -0.92 kJ/mol
B. (2 points) Given that the first reaction is endergonic (non-spontaneous, +
G), how does it ever occur in cells?
Correct answer: Because it is part of a pathway – as for instance it is coupled
to the 2nd reaction which does have a – G’o. Another way to say this is that the
direction depends on the real concentrations of substrates and products in cells.
Rewrite first part as multiple choice: Characterize the first reaction. Is it:
A. non-spontaneous, + G?
B. non-spontaneous, - G?
C. spontaneous, +G?
D. spontaneous, -G?
E. none of the above?
C. (2 points) Calculate the K’eq for the second reaction. Assume 25oC.
- RT ln Keq => -32200 J/mol = 8.315 J/mol K * (25 + 273 K) ln Keq =
ln Keq = 13 => Keq = 4.4 x 105
Many people had problems here because you didn’t pay attention to units! Note R
was given as J/mol K, but G’o was given as kJ/mol
G’o =
Rewrite as a multiple choice:
A. 4.4 x 105
B. 2.2 x 105
C. 4.4 x 10-5
D. 4.4 x 102
D. (2 points) Note that the first reaction shown above is a redox reaction.
What substrate is getting oxidized?
Malate is oxidized to oxaloacetate
What substrate is getting reduced?
NAD+ is reduced to NADH
Need to dig out the Q’s written for Cancer exam (final exam??) from 2008 (?) as well –
remember there was one on there about Warburg effect in particular ....
[Random insertion that I don’t want to forget: Possibility for protein structure
section from Joan Kiely – this might be great for lab: Toobers – foam covered wires
to make protein structures
Start with PDB – molecule of the month
Students have to build a protein, read a paper to go along with – model in context
Choose a theme that links the different proteins so students can talk to each other
Could investigate Protopedia? OR model with Jmol rather than Toobers (but I kind
of like the manipulatives)]
* Department of Biology Learning Goals – Summer 2007
Insight into the Process and Product of Science
We begin our learning goals with a focus on process to emphasize our belief that the
goal of a biology education is to enable students to make creative and careful use of
their knowledge. Only then will they be scientists.
1. Integration of New Knowledge into Existing Intellectual Frameworks
• Ability to interpret, evaluate and critique texts, primary literature and
presentations
• Ability to structure and contextualize understanding with proper reference
to literature
• Ability to speculate on meanings of scientific data and on possible future
directions
• Intersection with other natural sciences and intersecting fields
2. Engagement with Scientific Inquiry
• Ability to evaluate the significance and context of the area of investigation
•
•
•
Ability to use and evaluate texts, primary literature, presentations and
construct mathematical models to stimulate questioning and develop
scientific hypotheses
Ability to appropriately design and perform experiments and construct
mathematical models in order to test scientific hypotheses
Ability to interpret data to evaluate hypotheses and place findings into an
intellectual framework to plan further experiments
3. Representing and Interpreting Data in Quantitative and Statistically Meaningful
Forms
• Recognition of the critical importance of quantitative data and the facility
to work with it in biological inquiry and understanding
• Ability to distinguish between and work rigorously with both qualitative
and quantitative data
• Ability to construct and interpret visual representations of quantitative
data
• Ability to use probability and statistical analyses to evaluate and interpret
data
4. Communicating Scientific Understanding in Oral and Written Forms
• Ability to communicate scientific understanding to both scientific and
general audiences
• Ability to present scientific ideas arguing from evidence
• Ability to write and speak precisely
• Ability to stimulate interest of the audience
5. Appreciating the Epistemology of Science
• Ability to understand how the history of scientific thought shapes the
development of scientific principles and hypothses
• Ability to apply scientific principles to interpret new data
• Ability to recognize the limitations of methodologies as they affect the
interpretation of data
• Ability to understand the biological basis of scientific debate and the role
of probability and uncertainty in science
• Ability to appreciate and participate in a scientific community as a forum
for scientific thinking, research, debate and progress
• Recognition of the gap between society’s perception of science and the
true nature of science
Fundamental Biological Concepts
Two themes rise above the five categories of fundamental biological concepts that we
describe below and we highlight them here:
• All of biology operates under constraints defined by our understanding of math,
physics, and chemistry. It is therefore essential that Biology students have a
strong foundational understanding of these fields – of both their concepts and
their “ways of knowing”.
• All of biology operates under the constraints of the mechanisms of evolution. It is
therefore essential that Biology students have a strong foundational
understanding of the theories, evidence, and mechanism of evolution.
6. Organization of Molecular, Cellular, Organismal and Ecological Systems
• Building blocks of biological systems
• Structure/Function relationships
• Hierarchy of biological organizations (individual, population; community,
ecosystem; atoms, molecules, cell, tissue, organ, systems)
7. Evolution as a framework for understanding biological systems
• Theories of and evidence for evolution
• Variational evolution and Darwinian natural selection
• Particulate inheritance
• Phylogenetic concepts used to formulate and test hypotheses
• Mechanisms of evolution and their action at the molecular, developmental
and phenotypic level and their interrelationships
8. The Flow of Biological Information
• Central dogma of information flow
• Genetic exchange between cells
• Epigenetic modulation of information systems
• Cellular signaling pathways
9. Flow of Energy and Matter in Biological Systems
• Metabolic pathways
• Mechanisms of harvesting energy from organic and inorganic sources
• Food webs and biogeochemical cycles
10. Interdependence and Interactions within Biological Systems and their Emergent
Properties
• Interactions between genetic and environmental factors leading to
emergent properties of phenotypes
• Plasticity, integrity and homeostasis of biological systems
• Intracellular, intercellular and interorganismal communication, interactions
and behavior
• Understanding of population and species interactions leading to the
organization of ecological communities
• Immunological responses