Download Seminar compendium 2016/2017

Dept of Medical Biochemistry and Biophysics
Bachelor´s programme in Biomedicine
Medical Biochemistry
2016/2017
Seminars
in
Medical Biochemistry
Seminar 1: Introduction to Medical Biochemistry:
Carbohydrates, Lipids, Proteins and Energy
Through the diet we obtain several types of carbohydrates, mainly starch and
sucrose, that during the passage through the mouth and further down the
gastrointestinal channel are broken down into monosaccharides for absorption.
Common sugar, sucrose, is composed of D-glucose and D-fructose. Draw Fischer-projections of
these monosaccharides and show how they are cyclized and form anomers! What is happening
chemically during the ring closure? Draw Haworth-projections of the cyclized molecules!
Describe the glycosidic bond using the disaccharide lactose as an example!
What are epimers? Explain by using glucose and galactose as an example!
Lipids are a storage form of fuel and serve as structural components in
membrane barriers of cells and organelles.
Study the structure of triacylglycerols (depot fat) and phospholipids (membrane components). Draw
schematic structures and identify asymmetric carbon atoms!
Describe the bonds keeping a cell membrane together and what is the importane of having fatty acid
components with cis double bonds?
In addition to phospholipids, what other components are common in membranes?
Proteins are the most versatile biomolecules with a particularly prominent role as
enzymes.
Describe the bonds maintaining structural integrity of proteins. Use different amino acid side-chains
as examples!
Many hormones such as glucagon and adrenalin (epinephrine) bind to membrane protein receptors of
7TM-type. Describe the structure and function of such a receptor!
Enzymes need to have different activity in different cells and at different times. The regulation can
be carried out by various modes. Two important mechanisms are covalent modification and allosteric
regulation. Discuss the principles for these modes!
Many enzymatic reactions are energy-requiring and ATP is commonly employed to provide the
necessary input of energy. Discuss the structure of ATP, why the molecule is energy-rich, and how
the energy is released for chemical work!
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Seminar 2: Glycolysis and gluconeogenesis
In a race such as Vasaloppet or Stockholm Marathon, large amounts of ATP is needed to maintain
muscle contraction over an extended time period. How do the muscles get the ATP energy in the
beginning of such a race? Which compounds are already present in the muscle and which come via
the blood?
Training increases the blood supply to the muscles. How can this fact explain the numbness that
frequently occurs in the legs when you are not well trained? Which compound is responsible for this
and how is it formed from glucose? Go through all steps from glucose to this compound in detail
(with formulas). Give the names of all intermediates, enzymes, coenzymes and cosubstrates. Also
describe what happens chemically in each step and how the enzymes participate. How are the ratelimiting steps regulated?
By which process do the muscles and the brain get their energy during fasting? How is this process
different from glycolysis and how is it regulated? Go through the details of the steps that differs from
glycolysis.
What is the net production and consumption of ATP (ATP-equivalents) in the two processes
discussed in this seminar?
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Seminar 3: Citric acid cycle and oxidative phosphorylation
After training for some time, the blood circulation in the legs improves and the oxygen-uptake in the
lungs is more efficient, leading to a better oxygen supply in the cells. How is glucose metabolized in
the muscle when the cells get the oxygen they need? Where in the cell do the participating processes
take place, and how are substances transported between compartments? How is the aerobic product
of glycolysis transformed to a substrate for the citric acid cycle?
Describe the citric acid cycle in detail with names and formulas of all intermediates. Give all
enzymes, coenzymes and cosubstrates. Why does citrate have to be isomerized before being
oxidized? What happens chemically in the individual steps and in the cycle as a whole? Look at the
role of the enzymes. How is the decarboxylation of oxalosuccinate (a β-keto acid) explained? How is
the citric acid cycle regulated?
An important role of the citric acid cycle is to produce reduced coenzymes that can be oxidized in the
respiratory chain. Where is this located, how is it organized and how does it work? Explain how the
oxidation of coenzymes causes the formation of ATP. How much ATP is obtained? How is the
process regulated?
NADH formed outside the mitochondrion, i.e. in the cytosol, can also be oxidized in spite of the
impermeability of the mitochondrial membrane to NADH. Explain how this is possible!
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Seminar 4: Glycogen metabolism
In order to prepare for a longer physical effort such as Vasaloppet it is important to train regularly
several times a week. During heavy physical exercise, large amounts of carbohydrates are oxidized
to provide the energy for muscle contraction. Therefore it is common practice to consume a lot of
carbohydrate-rich food in the form of e.g. spaghetti and rice the days before.
Between periods of training, glucose is converted to glycogen, the main storage form of glucose in
humans and animals. How is the glycogen structure built up? Describe the steps and enzymes in the
synthesis of glycogen!
How long time, on the average, do the glycogen deposits last during a race such as Vasaloppet? In
which organs/tissues is glycogen stored and what is the main function for the glycogen in the
respective tissue? Describe the steps and enzymes that are needed for glycogen breakdown. How is
the glycogen metabolism regulated (glycogenesis and glycogenolysis) and how are these processes
coordinated? Describe the overall effects of insulin and glucagon/epinephrine on the glycogen
metabolism. Describe the hormonal signal transduction mechanisms (from the receptor protein to the
target enzyme).
The central metabolite glucose-6-phosphate in both glycogen synthesis and degradation is also the
starting point for the HMP shunt. What is the HMP shunt and why is it important for the supply of
NADPH and nucleotides? Explain!
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Seminar 5: Biosynthesis of lipids
Describe the conversion of pyruvate to fatty acids. Where in the body does it take place, and what is
the subcellular localization of the steps? Which steps are regulated and rate-limiting, and what is the
mechanism behind the regulation?
Fatty acids are not stored as such (why?) but instead as triacylglycerols. How are these formed?
The fatty acids we get in the diet are not always those that we need in the body. How are fatty
acids modified? An example is the conversion of linoleic acid to arachidonic acid. Describe the
principles of this conversion!
The body needs fatty acids for several purposes, e.g. in cellular membranes. Phospholipids are
important membrane components. Describe the structure and synthesis of phosphatidylcholine,
phosphatidylethanolamine and phosphatidylserine, and how these phospholipids can be
interconverted. Show how phosphatidylinositol is formed and used in signal transduction and to
anchor proteins to the cell surface.
Cholesterol is also an important membrane component and the starting point for the synthesis of the
steroid hormones. We get cholesterol from the diet but it is also formed in the body. Where and how
does this take place? Describe the steps to mevalonate in detail and thereafter briefly the main
intermediates and principles.
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Seminar 6: Lipolysis, ketone bodies
When in a long race the muscle glycogen stores are going down and eventually finish, fatty acids
gradually phase in to supply the required energy. Which hormones activate and which inhibit
lipolysis and the generation of fatty acids, and what is the mechanism? How are the triacylglycerols
in adipose tissue degraded and how and where are the products transported?
How is energy derived from the fatty acids in muscle cells? Describe the steps from fatty acid to
acetyl CoA that can enter the citric acid cycle. Briefly, how does oxidation of unsaturated fatty acids
and odd numbered fatty acids take place? How much energy (ATP) is obtained in complete oxidation
of palmitic acid and linoleic acid? Which cells cannot use fatty acids as an energy source?
During fasting the fatty acids are transported to the liver and are converted to ketone bodies. How is
this regulated? Describe the synthesis of ketone bodies, which they are, and the effects they have.
How are ketone bodies utilized in tissues? Which cells cannot use ketone bodies?
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Seminar 7: Amino acid metabolism
During fasting there is still a need for glucose, in particular to the brain, and therefore muscle
proteins are degraded. How is this regulated hormonally? Where do the released amino acids go, and
how are they converted into glucose? Which amino acids leave the muscle and which are
metabolized locally?
Characteristic for the amino acids is the nitrogen. How is nitrogen handled when the amino acids
form glucose? Describe the initial enzymatic reactions in detail. How is the nitrogen excreted from
the body?
Serotonin is a substance with multiple physiological roles, e.g. regulation of sleep, blood pressure,
temperature, pain perception and mood. Describe the synthesis of serotonin!
What are the catecholamines and from which amino acid are they formed? Briefly review the steps in
their formation! How does S-adenosylmethionine (SAM) apply to this synthetic route?
Both liver and muscle damage cause leakage to the blood of enzymes involved in amino acid
metabolism – which ones, and what is their function? Liver damage can also cause icterus due to
increased levels of bilirubin in the blood. Bilirubin is formed from heme. Briefly describe the
formation of heme and the formation and excretion of bilirubin! Why is the level of bilirubin
elevated in liver disease?
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Seminar 8: Nucleotides
Gout is a disease causing severe pain in small joints, e.g. in the toes. Explain these symptoms by
discussing the metabolism of nucleotides. Consider the de novo synthesis of purine- and pyrimidine
nucleotides. The ”salvage pathway” is very important to maintain the concentrations of purine
nucleotides. How is the carbohydrate part in the nucleotides formed from glucose? How are purine
and pyrimidine nucleotides catabolized? What is the mechanism behind the effect of allopurinol?
Nucleotides are building blocks for RNA and DNA. Which are the most important steps in the de
novo synthesis of AMP and GMP? How are ATP and GTP formed, and how are the corresponding
deoxyribonucleotides formed? Which are the most important steps in the de novo synthesis of UMP?
How is this compound converted into UTP, CTP, dTTP and dCTP?
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Seminar 9: Articles
Answer the following general questions for each article:
What is the study about? What was known before, and where can one find information about
this? What has been carried out, and how can we get more information about the techniques
employed? What is new knowledge? How are the results explained? How can they be put into a
wider context?
Answer the following specific questions for the article:
Ron S. Ronimus and Hugh W. Morgan (2004): Cloning and biochemical characterization of a
novel mouse ADP-dependent glukokinase. Biochem Biophys Res Commun, 315, 652-658.
1.
2.
3.
Briefly describe the purpose of the study and tell from where the idea arose that the enzyme might exist?
How was the enzyme activity determined? Give the full reaction sequence and explain
When Km was determined in Fig. 3, the authors have quite arbitrarily included data where the glucose
concentration has been below or equal to 0.35 mM only. Which would the effect be on the Km-value if
all data points would have been included? Explain!
4. How was the molecular mass of the enzyme determined and if the enzyme was a monomer or an
oligomer? Explain the principles for the methods used!
5. Derive and write the net reaction for anaerobic glycolysis with the assumption that all glucose
phosphorylation is carried out by ADP-GK, and that fast equilibrium is attained in the adenylate kinase
reaction!
Discuss the conclusion in the discussion section that the process ”saves” ATP.
Michel A. Sciotti, Steven Tam, Bendicht Wermuth, Michael E. Baker (2006): Differences in
catalytic activity between rat testicular and ovarian carbonyl reductases are due to two amino
acids. FEBS Letters, 580, 67-71.
1.
2.
3.
4.
5.
Which endogenous substances can be substrate for the carbonyl reductases studied?
CR was purified using chromatography. Explain the background to the method used, how it is carried out
and why a separation is achieved.
How was it determined that the enzyme preparation was homogeneous? Explain the background to the
method used!
Which carbonyl reductase or mutant should give the fastest conversion of menadion at high
concentrations, and which one should give the slowest conversion at very low concentrations? Explain!
Which amino acid is located in position 235 in CR1 and CR2, respectively, and which effect does the
difference have? Explain on the basis of the structure of the amino acid!
J. Gloerich, J.P.N. Ruiter, D.M. van den Brink, R. Ofman, S. Ferdinandusse, R.J.A. Wanders
(2006): Peroxisomal trans-2-enoyl-CoA reductase is involved in phytol degradation. FEBS
Letters, 580, 2092-2096. ONLY IF TIME ALLOWS!
1.
2.
3.
4.
5.
In what type of food can we find phytol, and in which organ is phytol metabolized in humans?
Recombinant human trans-2-enoyl-CoA-reductase is generated as a fusion protein with maltose binding
protein. Why did the authors prepare this fusion protein? Explain!
How was the fusion protein MBP-TER characterized? Which method was used, how is the analysis
carried out and what is the physico-chemical background to the separation?
From Fig. 2A, the authors calculated Km for NADPH to 106 μM. Roughly, what was Vmax
(the specific activity) under these circumstances? How do you get the value from the figure?
Draw a scheme for the transformation of phytol to acetyl-CoA and a citric acid cycle intermediate. Which
reactions take place in the peroxisome and which in the mitochondrion?
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Seminar 10: Integration of intermediary metabolism (based on
diabetes)
There are several types of diabetes, e.g. diabetes insipidus and mellitus. Diabetes mellitus exists in
two types. Diabetes type-1 often shows up in early life. The first symptoms of diabetes are large
amounts of urine, increased thirst and reduction of weight. Frequent drinking and many visits to the
toilette (also during the night) are typical. Additional symptoms are fatigue, indolence and
convulsion in the legs also after minor physical effort. Diabetes type-1 always requires insulin.
Obesity is the common releasing factor for diabetes type-2. Very often acceptable blood values are
obtained after changing the diet, exercise and the usage of specific drugs.
What is analyzed in order to establish the diagnose diabetes mellitus?
Specify the concentration for normal blood glucose (what unit is commonly used in Sweden and
Europe?) and what concentration levels can be measured in diabetes. How does normal blood
glucose fluctuate during twenty-four hours?
Explain the first symptoms of untreated diabetes type-1 (see above).
Which metabolic disturbances originate from shortage of insulin? Explain how they arise. The acidbase balance is also disturbed in untreated diabetes type-1. Why? What similarities and
dissimilarities are observed between fasting/starvation and untreated diabetes type-1?
Discuss the cellular mechanisms that cause the late complications in diabetes. How can the
formation of sorbitol be influenced? Which organs are most affected?
How can the blood glucose level for a diabetic patient be monitored during an extended period?
How is the metabolism changed in a diabetic patient when insulin treatment has been initiated?
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