Download List of Possible Research Questions

List of Possible Research Questions
Biochemistry II CHE 4320
Spring 2012
Course Website: http://bonhamchemistry.com
Glycogen branching: Anderson’s disease is caused by a lack of or a defective glycogen branching enzyme
and leads to cirrhosis of the liver. Why does the absence of glycogen branching result in cirrhosis?
Muscle Contraction: Why does a muscle cramp when there is not enough ATP?
Glycogen: What is the complete make up of glycogen masses? Which molecules, enzymes, etc. are present?
Galactitol: Build up of Galactitol in the eye leads to the formation of cataracts. How does this occur?
Galactitol: an excess of galactitol an also lead to mental retardation, FTT, and death, How do these occur?
Sugar alcohols: How are sugar alcohols metabolized in humans? How much of them are absorbed and
metabolized?
Acetylcholine: Where are the acetylcholine-releasing nerves in the brain and what is(are) their primary
function(s)?
Acetylcholine: What are the details of acetylcholine receptor proteins?
Voltage-gated Channels: What is the mechanism by which voltage-gated channels go from inactivated to
closed?
Na+/K+: How do enzymes differentiate between Na+ and K+? What is the physiological reason that 3Na+
are transported across neural membranes and only 2K+ are transported?
Muscle cells: Ca2+ is required for muscle contraction. When the muscle contracts, Ca2+ rushes out of the
sarcoplasmic reticulum and into the muscle cell lumen. What are the concentrations of Ca2+ in the
sarcoplasmic reticulum and in the muscle cell lumen?
Blood-Brain Barrier: The blood-brain barrier only allows certain things to pass. What is the exact
mechanism of the blood-brain barrier? How does it selectively keep out certain things?
Glycogen Again: How is the size of glycogen molecules controlled?
Glycogen Metabolism: How many glycogen phosphorylase are in a cell?
Caffeine: In addition to stimulatory effects, caffeine can decrease inhibitions. How does it do this? What are
the details?
Hormone Receptors: What is the turnover number for hormone receptors?
Methylations: Many biochemical reactions/pathways include methylation of a substrate. What are the most
important methylations in biochemistry and why are they important?
Membrane Potentials: The equilibrium potentials for sodium and potassium are frequently given. Chloride
ion is also present. What is the equilibrium potential for Cl-?
Vitamin C: The enzyme necessary to synthesize vitamin C (gluconolactone oxidase) is not present in humans
and thus we cannot synthesize it on our own. What do/can humans use L-gluconolactone, L-gluconate, and/or
D-glucuronate for?
Vitamin C: Ascorbate is an antioxidant. It accepts a pair of electrons to become dehydroascorbic acid. Is
ascorbate capable of functioning via a free radical mechanism, i.e. accepting l electron at a time, or is it
required to accept both electrons at once? If it can accept one electron at a time, does it actually scavenge
free radicals in vivo?
Dopamine -hvdroxvlase: Is ascorbate a true cofactor for this enzyme?
Dopamine: If dopamine is hydroxylated, it becomes neurotoxic Dimethylate (3, 4-dimethoxy) dopamine and
it is hallucinogenic. Are these reactions related to behavior at all?
Mvelinated axons: How exactly does the next gap between myelin sheaths “feel” the previous membrane
depolarization?
Pacemaker: What exactly happens to make one necessary?
Hormones: At what speed and quantity are hormones released? How quickly do they get into a cell? How
fast do they degrade, and how long before they are gone? It may be easier to focus on one hormone (like
adrenalin) then a general study: different hormones have different values.
Chocolate: Chocolate contains a variety of compounds that have a variety of effects on the body and mind.
Explore Chocolate Food or Drug by T. Brunsman. What effects does chocolate have?
Nicotine: Nicotine itself is not what causes the damaging effects of smoking (it’s the carrier that contains
radioactive isotopes and toxic tar). Approximately 95% of schizophrenia patients are smokers, they use the
nicotine for self~medieation. What are the positive effects of nicotine?
Cardiac Health: New research has linked inflammation, not cholesterol, to poor cardiac health.
Also explore C-reactive protein.
Caffeine: In addition to affecting Cyclic AMP and keeping glycogen available longer, Caffeine affects mental
processes giving you a ‘lift’. It acts as an adenosine antagonist in the body and inhibits the inhibitors in the
brain. Caffeine is listed as an ingredient in many pain medications and is a vasoconstrictor(const1icts blood
vessels). Explore its stimulatory effects.
Protein: A high protein diet is a strain on the liver and kidneys. What is the reason for this, the mechanism
that is used? Is nitrogen important, after all your kidneys must process it, perhaps too much causes their
degradation. Does the amount of water you drink diminish this negative effect?
Insulin: Glucagon acts opposite to insulin, how? What role does insulin play in ‘respects to Inh l (inhibitor
one) in glycogen metabolism?
Sugar consumption: Is high sugar related to high blood pressure, thickening of capillary walls, and increased
blocked blood vessels?
Stress: How it affects the body.
Sleep: How the lack of it affects the body (is it similar to stress?) There is an increase in hormones that
control your appetite making you hungry. Some people have reported only sleeping 15 min a day since birth,
what is different in their system that allows this? How in the world did their parents manage?
Free Radicals: Is this how you age? Are antioxidants helpful?
Cascading Reaction: How fast are they Example: blood clots, what other systems use them? Explore
feedbacks and inhibitors.
DNA: How did the DNA code become standardized? Why/ how do mammals read code differently then
plants?
Vitamin C: Why do humans lack the enzyme necessary (Gluconolactone oxidase) to synthesis it when cats,
dogs, and primates can?
Insecticides: How do they work on bugs, and why do the chemicals affect them and not people? How are
they deleterious to people? What works the best? How do I keep wasps out of my yard?
Calcium: Is everywhere, bones and signal transmission. Antifreeze kills you by binding the free the Ca2+ ions
in your system. What makes Ca special? (Similar to Westhiemer’s article except about why nature chose
calcium not phosphates)
Homocvsteine: Increased amount is correlated with stress, inflammation, vessel plasticity, plaque build-up,
and heart disease. It may be a better indicator then cholesterol. What is the effect on free radicals? What is a
normal level and what can I do about high levels?
Antibuse: Antibuse if taken every day will cause a person to have a very violent reaction to alcohol. How
does this work, why would you take it, and is it currently in use?
Mutagen/ Carcinogens: When your liver digests the blackened char from a barbeque it turns it into a
mutagen / carcinogen. Why/ how does your liver do this, and in what other ways does you liver shorten you
life?
Vitamin E: Is it good or bad for you? How much you need? Can too much be bad for you?
Fibrillar substance: A iibrillar substance is present in the synaptic cleft between neurons. Why is it there?
What exactly is its function?
Ninhvdrin: What is its mechanism when reacting with amino acids?
DNA methylation: Restriction endonucleases modiiy DNA by methylating it at particular sites. They also cut
foreign DNA at the same sites if it is not methylated. When does the methylation occur? How is this
controlled so that foreign DNA is only cut and not methylated?
PCR History: What is the research leading to knowing which primers to use to get the desired piece of DNA?
Polvacrvlamide gel: Polyacrylamide gel is a polymer used for gel elecrophoresis.
How is it made and what is the mechanism of its polymerization?
True or False: if one could take all the bacteria on/in the Earth and pack it on the surface, they would cover
the entire Earth to a depth of Sft.
Genetic Code: Why are there deviations from the universal genetic code in mitochondrial DNA? \Vhat other
organisms have deviations in their genetic code? How did this come around evolutionarily?
Gout: Gout is caused by the formation of sodium urate crystals in the joints (typically in the big toe). What is
the Ksp for soditun urate? Does it explain why it crystallizes so easily?
Nucleotide Salvage: Purines are salvaged by means of a salvage pathway. Do pyrimidines have a salvage
pathway? Why or why not? If they do, what is it?
More Nucleotide Salvage: What detail necessitates the salvage pathway for purines? (build up of uric acid?
Conservation of energy? Etc?)
Alloxanthine: Allopurinol is a drug which is used to prevent the buildup of uric acid in the treatment of gout. lt
inhibits the enzyme xanthine oxidase and remains tightly bound to the enzyme. What is the mechanism of this
reaction and why does alloxanthine remain so tightly bound to the enxyme?
Lesch-Nyhan Syndrome: Lesch-Nyhan Syndrom is caused by the lack of hypoxanthine-guanine phosphoribosyl
transferase. What is known about this disease? What are the details? Vfhat can be done?
Pvrimidine Catabolism: What is the fate of 2-deoxyribose-l-phosphate?
Glutamine Synthetase Regulation: Elaborate on the regulative pathways. Does it make sense that there is such
a fine-tooth control on the less active form of the enzyme? Why is this? Why/how do alanine and glycine
inhibit the enzyme?
Phosphofructo kinase: How is this enzyme controlled?
Carcinogen Testing: It used to take ~2 years and $200,000 to test Whether a chemical was a carcinogen.
What is the current price and duration of testing?
How many different testing systems are available now?
Chicken Soup: Chicken soup contains n-acetyl cysteine. Does this promote glutathione synthesis? Does this
have anything to do With why it is allegedly so ‘good for you’?
Ribonucleotide reductase: The proposed mechanism involves a very curious radical. How is the
carbocation/radical stabilized?
Cy_tosine: What is the rate constant for cytosine -9 Thymine?
Fatty Acids: Double bonds in fatty acids are necessarily not conjugated. Why is this?
Vitamin E: Does the daily recommended requirement conform with the fact that one molecule of vitamin E
can protect ~l 000 membrane lipids? Take into consideration how fast is it metabolized, how much is
absorbed, etc.
Selenium: Selenium is required for the enzyme glutathione peroxidase. What else (if anything) is it
needed/used for? What are the consequences of selenium overdose? How is it incorporated into a protein?
Glutathione peroxidase: ls it present in anaerobes? ls oxygen toxicity in anaerobes strictly due to the lack of
enzymes only?
Radiation: What is the accepted definition for g rays and x rays? ls one strictly from the nucleus or from an
electronic state transition?
Electron Capture: ln electron capture, an electron from the innermost shell combines with a proton from the
nucleus. Presumably, the electron must be in the nucleus for this to occur. Is this accurate? What is the
probability of a K-electron being in the nucleus?
Electron Capture: Electrons from outer shells must transition to lower energy shells When electron capture
occurs. The first transition emits an x-ray. What is/are the wavelength(s) of photons emitted due to the
transitions of outer electrons?
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