Welcome!

Hello, and welcome to the IMD Biochemistry blog. This blog is intended as a tool to signal the availability of podcasts and vidcasts relevant to the Chemistry & Biochemistry course of the International MD program at the Università Vita-Salute San Raffaele (Milan, Italy).

You can subscribe to the RSS feed directly here (copy the link into your favorite RSS reader software), and you will be notified when new content is available. Then you can download the material, and view or listen to it using your favorite device. Please note that the files will be hosted on the UniSR server, and these should be downloaded manually.

Also, remember to sign up to the IMD Biochemistry group on Facebook in order to take part in discussions, and receive notifications on course events!

I hope you enjoy the course, and eventually come to appreciate how biochemistry represents one of the cornerstone disciplines for future physician scientists.

Sample questions, and how to approach the study of Biochemistry

The types of question you will find in the test are of three kinds:

1. Mnemonic. Some things you simply need to know, you cannot Google for them all the time. Take this as a training for Anatomy.
2. Clinical cases. A patient has certain symptoms. Based on your biochemical knowledge, you are required to make an educated guess to the most likely disease affecting the individual.
3. Biochemical scenarios. A certain situation in the cell is described, you must reason on the most likely consequence at the biochemical level. To answer these questions you must have a strong knowledge of the regulation of pathways, and their interplay.

Here are some sample questions, and a short discussion on how to get to the answer!

Q1. Which enzyme catalyzes the conversion of malate to oxaloacetate in the mitochondrion?

1. Fumarate hydratase
2. Malic enzyme
3. Malate dehydrogenase
4. Pyruvate carboxylase

Ok, this is a typical mnemonic question. If you know that malate and oxaloacetate are intermediates in Krebs’ cycle and remember the name of the enzyme, you mark quickly the correct answer. But, the adrenaline of the exam may be confusing you. So, let’s work it out. Fumarate hydratase, as the name says, uses fumarate as a substrate, so we can discard that as well (in Krebs’ cycle fumarate gets hydrated to malate and is derived from succinate). Pyruvate carboxylase synthesizes oxaloacetate, but starting from pyruvate.You remember that malate and oxaloacetate traffic to the cytosol, and the malic enzyme is involved in their interconversion. Yes, but the question says “in the mitochondrion”. So it’s not the malic enzyme. So, the correct answer is Malate Dehydrogenase.

Q2. Which of the following metabolites can be uptaken and used by the brain as an energy source?

1. Palmitic acid
2. Acetyl-CoA
3. beta-hydroxybutyrate
4. gamma-aminobutirate (GABA)

Here you must remember that there is a barrier between the brain and the blood, so certain molecules cannot cross it. Both palmitic acid and acetyl-CoA are unable to reach the brain. However, the trick used in our organism is the production of ketone bodies (acetoacetate and beta-hydroxybutyrate) that can cross the BBB and be converted back to acetyl-CoA for energy production. GABA is a neurotransmitter, and its function is to deliver signals in the central nervous system by binding to specific receptors. Not exactly an energy-producing molecule.

Q3. A 10-year old boy is admitted in the emergency room because of sudden fainting and dispnea a one hours after a meal. At the objective exam he is jaundiced and negative for ketone bodies. Blood tests show a decrease in red blood cells. Pending other laboratory tests, which of the following is the most likely condition?

1. Juvenile diabetes
2. Phenylketonuria
3. Haemolytic anemia
4. Pancreatic cancer

Let’s look at the symptoms: the dispnea means he is not getting enough oxygen. Jaundice indicates an overload of the heme breakdown system. Negative for ketone bodies means the brain functions are fueled by glucose. Also, the symptoms appearing after a meal indicates that it is not a hypoglycemic effect.

We can discard diabetes, as the patients should be positive for ketone bodies (acetone breath). Phenylketonuria does not have anything to do with the situation, here. Pancreatic cancer may affect metabolism, and the typical first sign is jaundice. However, the anemia is not directly associated with PC. Thus, hemolytic anemia is the most likely condition. Since the symptoms appeared after a meal, you may inquire whether the patient had some oxidants-containing foods, suspecting favism.

Q4. The enzyme phosphofructokinase 1 (PFK1) catalyzes the committed step in ____ and (among other effectors) is activated by ____ and inhibited by _________.

1. glycolysis, fructose 2,6 bisphosphate, citrate
2. glycolysis, ATP, NADH
3. gluconeogenesis, ATP, glucose 6-phosphate
4. glycolysis, protein phosphatase 1, protein kinase A

The mnemonic aspect here is minimal. If you don’t remember that PFK1 works in glycolysis, you have hardly opened the book or read the material. Now, what activates and what inhibits? Since glycolysis is used to produce ATP, it makes no sense that ATP acts as an activator. PP1 and PKA have no established role in glycolysis. To be fair, the glucagon cascade leads to phosphorylation of PFK2, inactivating it and reducing the synthesis of F2,6-bP. But the question says “the enzyme PFK1”, and not “Glycolysis”. So, in case you did not know immediately, the answer is the first. Citrate signals a backlog in Krebs’ cycle, so you slow down glycolysis. F2,6-bP is an allosteric feedforward activator that also reduces the inhibition by ATP.

Q5. Which of the following organs can not use ketone bodies?

1. Brain
2. Liver
3. Skeletal muscle
4. Cardiac muscle

Ketone bodies are a soluble form of acetyl-CoA that can travel in the bloodstream. It is sensible that all organs may use them. Well, perhaps excluding the single organ that synthesizes them, otherwise they would not exit… Yes, it’s the liver, the site of synthesis.

Q6. The urea cycle is highly regulated to avoid ammonia toxicity. Under physiological conditions, the flux of metabolites in the cycle is strongly affected by_____.

1. Bicarbonate
2. Aspartate
3. N-acetyl glutamate
4. Glutamine

Bicarbonate and aspartate are reactants in the urea cycle. Under physiological conditions, these are not limiting, thus hardly affect the rate at wich the cycle proceeds. Glutamine is used to buffer the excess ammonia, and its concentrations do not affect directly the cycle. N-acetyl glutamate is synthesized when glutamate is abundant, and stimulates the oxidative deamination of glutamate by the NAD(P)+-dependent glutamate dehydrogenase. This enzyme provides the ammonium ion that enters the cycle, and determines the rate of the urea cycle.

Q7. How many ATP equivalents can be obtained from the complete aerobic oxidation of one butyric acid molecule?

1. 2
2. 10
3. 32
4. 128

Butyric acid is a C4:0 fatty acid. The question asks the maximum yield for its oxidation under aerobic conditions. Thus:

Butyric acid must first be linked to Coenzyme A. ATP is used in the process, yielding AMP + PPi, and PPi gets hydrolyzed to 2 inorganic phosphate molecules. So we use two ATP equivalents.

To completely oxidize C4 we need two rounds of mitochondiral beta oxidation. Each round of beta oxidation will yield 1 Acetyl-CoA, 1 NADH, and 1 FADH2. Thus, from beta oxidation 2 Ac-CoA, 2 NADH, 2 FADH2.

Each Acetyl-CoA will enter Krebs cycle, yielding 3 NADH, 1 FADH2, and 1 ATP (substrate level phosphorylation). Since we have 2 Acetyl-CoA molecules, we will get 6 NADH, 2 FADH2, and 2 ATP. So the total after beta oxidation and Krebs cycle is 8 NADH, 4 FADH2, and 2ATP. In oxidative phosphorylation, each NADH yields 3 ATP and each FADH2 2 ATP. So 8×3+4×2+2=34 ATP molecules. Note that the question explicitly asks for the ATP equivalents. We must subtract TWO ATPs, because we hydrolyzed two phosphoanhydridic bonds to promote the butyryl-CoA synthesis. So the answer is 32.

Q8. Which of the following best describes the process carried out by the aspartate-malate shuttle?

1. It is essentially irreversible
2. It transports NADH from the cytosol to the matrix
3. During gluconeogenesis, malate moves to the cytosol
4. It sustains glyceraldehyde 3-phosphate dehydrogenase activity during glycolysis

The shuttle is used to provide oxaloacetate during gluconeogenesis. Shuttles are by no means irreversible. NADH is not transported. GAPDH activity primarily relies on NAD+ regeneration through lactic acid fermentation.

Q10. Medium-chain acyl-CoA dehydrogenase (MCAD) is a mitochondrial enzyme that is essential for the beta oxidation of fatty acids. A patient with MCAD deficiency displays hypoglycemia because____

1. The conversion of acetyl-CoA to pyruvate is inhibited
2. MCAD activity is essential for the activity of fructose 1,6 bisphosphatase
3. Medium chain fatty acids inhbit glycogen phosphorylase
4. Beta oxidation cannot release acetyl-CoA to activate pyruvate carboxylase

When glucose levels drop, the liver attempts to provide the glucose via a) glycogen breakdown; b) gluconeogenesis. Hypoglycemia derives from the inability to perform such functions efficiently. Glycogen phosphorylase is not influenced by fatty acids, just by AMP, ATP, and glucose. Fructose 1,6 bisphosphatase is also not regulated by fatty acids. In humans, acetyl-CoA cannot be converted to pyruvate. Acetyl-CoA instead is a crucial activator of pyruvate carboxylase to its active form, the initial step of gluconeogenesis. So, a reduced MCAD activity limits the amounts of mitochondrial Acetyl-CoA, that in turn slows down gluconeogenesis and hence leads to hypoglycemia.

Q11. You are purifying a protein in the native state to perform structural and functional studies. At the present, your sample is contaminated by a second protein that has the same molecular weight, but differs in the isolectric point.  Which chromatographic technique will give you the best chance of separating the two species?

1. Affinity chromatography with the Ni-NTA resin 
2. Size-exclusion (gel filtration) chromatography
3. Ion exchange
4. SDS-PAGE

Affinity chromatography with Ni-NTA requires the protein of interest to have a polyhistidine tag, and this is not specified in the test. Size exclusion separates proteins based on size, and the two proteins have the same molecular weight, hence very similar sizes. SDS-PAGE denatures the proteins, so it is not a correct technique to purify proteins in the native state. Ion exchange (either cation or anion, depending on the pI of the two proteins) gives you the best chance for separation: you load the proteins onto the resin at a certain pH, and elute them with a salt gradient. The difference in pI will cause different affinities towards the resin, and they will detach from it at different elution volumes

Q12. How many base pairs are present in one complete turn of DNA double helix of the B form?

1. 3.6
2. 4.4
3. 10
4. 20

Ten bases, of course. Don’t be confused by 3.6, the number of residues in one turn of alpha helix in proteins, or 4.4 (pi helix, for those who went the extra length to read the table in the book). It is even correct in the hovering DNA…

Frequently Asked Questions

Ok, here are some questions I am typically asked.

First of all, a little exam etiquette:

• Wait outside the class until you are asked to enter. Take this opportunity to switch off and store in your bag your cell phone.
• Leave your personal belongings on the side or the back of the room.
• Bring only pens/pencils, eraser, calculator (if you are taking Chemistry). You can bring some water, if needed. You must also have your badge with you.
• Sit where the sheets of paper are placed. Do not move them. Do not turn the paper until instructed to do so.
• Listen to the instructions, then start.
• Once finished, hand in all papers, get quietly your personal belongings, and leave the room. Please do engage in loud conversations outside the classroom, rather reach an appropriate area to vent your happiness on having finished the Biochemistry nightmare 😉

Q1. I passed Chemistry, what do I have to do?

A1. Study Biochemistry (from biological macromolecules to the end), sign up for the exam online, and show up at the right date and time. You will be handed a paper with 100 Biochemistry questions. Answer the questions. Hand in the paper. Wait for an email with the score. Show up at registration to register a positive mark.

Q2. I did not pass Chemistry…

A2. See A1. Chemistry and Biochemistry tests are offered on the same day. The only difference is that you will be handed also a 20 questions Chemistry test, that you need to pass. You may bring a calculator, since some Chemistry questions require simple calculations.

Q3. Can I take the Chemistry test only?

A3. Yes

Q4. I did not pass Chemistry. Can I take Biochemistry only? Or, what happens if I pass Biochemistry but fail Chemistry?

A4. You cannot take the Biochemistry exam without either having already passed Chemistry, or without taking Chemistry as well. If you fail Chemistry but perform well in Biochemistry, the positive vote in Biochemistry will stand until you pass Chemistry on another exam date.

Q5. What happens if I fail the exam? Can I sit on the next available date?

A5. Absolutely. However, if you get a score that is extremely low,you should seriously consider the option of devoting more study time to the subject, rather than hoping for an easier set of questions on the next date.

Q6. What subjects will be covered by the questions?

A6. The overall subjects are the ones that professor Corti and myself mentioned at the lectures. So, if I did not cover something that is in the syllabus due to time constraints, you will not be tested on those parts. Also, the parts or details that I explicitly excluded from the lectures will also be absent in the exam. Amino acid biosyntesis, as an example.

Q7. Will the test include questions with “open” answers, such as “Describe the glcolytic pathway”?

A7. No

Q8. Will the test include questions that require drawing of chemical structures?

A8. No

Q9. Will the test include questions that require to identify a chemical compound (picture of a structure, tell me what it is)?

A9. Yes

Q10. Can I bring external sources of information at the exam? Ask a colleague about an answer I am unsure of? Use whatever method to gain unfair advantage?

A10. I take any violations of the honor code very seriously. The first consequence is immediate disqualification from the exam. Then, you will be forbidden to sit on the next exam date. You will also receive a reprimand letter from the director of studies that will be permanently part of your official documentation (meaning that it will be passed to future possible employers).

Q11. I have a doubt concerning a specific question in the test. Can I get clarifications?

A11. Certainly. Raise your hand and I will be available for clarifications. The goal is to allow you to show your level of knowledge, not to trick you into a wrong answer.

Q12. What material can I bring to the exam?

A12. Only writing tools (pens/pencils), eraser, your badge, a bottle of water. A calculator may be used by those who takes the chemistry test. Positively NO CELL PHONES or devices that can store/access information. NO SHEETS OF PAPER.

Q13. I passed Chemistry and had a positive mark in Biochemistry. However, the overall mark is not as high as I hoped based on my knowledge. Can I think about it before signing? Does the mark have an expiration date?

A13. The mark does not have an expiration date, and you can sign at ANY official exam date.

Example: you have a final mark of 24/30, and you are unsure whether to sign for it or not. You simply tell me/drop me a line and decide what to do. Let’s say you feel it’s not worth studying more, and wish to sign it. You sign up for the next exam, send me an email reminding me that you already passed the exam and only wish to register your positive mark. Then, show up at the exam, sign the papers, and you’ll be done.

If you decide to study more, sign up for the exam and take the new test. It could be that during the exam you feel that you are unsure about many answers, and perhaps you are doing worse than the previous exam. Then, hand in your papers before time is up and tell me you do not wish the paper to be graded. Then you can either sign the “stored” mark, or re-take the exam. If instead you hand in the paper for grading, your “stored” mark will be replaced by the new one. So, you may get a better mark (that is usually the case) but let it be clear that you could get a worse score, or even fail. If your performance is worse, there is no going back to the old mark, as your current knowledge of biochemistry is what you displayed in the last test.

Getting ready for the exam

Ok, we covered a good portion of the biochemistry that pertains basic life functions. Keep in mind that every single process in living organism has an underlying biochemical event, may it be a series of chemical reactions catalyzed by specific enzymes (e.g. the blood clotting cascade, where proteases are involved; signal transduction, where kinases and phosphorylases act in concert to ultimate modulate gene expression) or the interaction between macromolecules to form active complexes (e.g. the recognition of antigens by the immune system; the formation of a transcriptional complex onto DNA stretches). As your career as a medical student progresses you will run into such examples, and the foundation of those events will be the same as the examples we had in the study of metabolism. This post and the following ones are meant as a guide for the preparation of the exam.

The format

The course covered Chemistry and Biochemistry. If you passed the mid-term exam with professor Freccero, at the exam you will receive a paper with only Biochemistry question. Just to be clear, with Biochemistry it is meant everything covered by professor Corti and myself. If you did not pass the chemistry mid-term, you will be handed a chemistry AND a biochemistry paper. If you received partial credits for the course, you will receive a tailored test (please remember to send me an email at least one week in advance when you plan to sit for the exam).

• Each test will be multiple choice answers only. Each question will have four possible answers, only one is correct.
• A correct answer gives you one point, no answer 0 points, wrong answer -0.25 points. The sum of the points and deductions will give the score of your exam.
• The Biochemistry test will contain 100 questions.
• The Chemistry test (ONLY for those who did not pass the mid-term) will contain 20 questions.
• The time allocated will be 1h 40min for Biochemistry, 2h for Chemistry + Biochemistry
• The Chemistry paper is graded with pass or fail. In order to pass you must answer correctly at least 11 questions.
• In order to obtain the minimum mark to pass the Biochemistry exam (18/30), you must achieve at least a score of 48/100. In order to achieve the top score 30/30 you need to score 90/100.
• Thus, if you need to take both Chemistry and Biochemistry, you must obtain a “pass” mark for the Chemistry part AND at least 48/100 in the Biochemistry test.

Registration

Typically 1-5 days after the exam we will meet for the registration of the marks. Thus, if you need to make travel arrangements, be aware of this.

You will be notified the marks by email as soon as all papers are checked.

If you obtain a mark that is less than 18/30, you will need to sign up for another test. The same format will apply. You do not need to be present at registration, although you may benefit from a review of the wrong answers.

If you obtain a mark that is greater than 18/30 you have two choices

1. You are happy with the result, and register the mark
2. You think you can do better, and decide to re-take the exam
3. You are unable to decide at the moment (most frequent situation)

In the latter case, be informed that your positive mark will stand until you either a) register it, or b) HAND IN a different paper to be corrected at another exam date. Once a new paper is scored, that score replaces the previous. For better or worse.

The pentose phosphate pathway and gluconeogenesis

The journey of glucose (fructose, mannose, and galactose) through glycolysis under anaerobic conditions is the process by which we transform some of the free energy present in hexoses into ATP molecules. However, the free energy can be transformed into something different that our organism needs in the anabolic (synthetic) pathways, and that is reducing power.

In biological systems, the electrons required for reductions in biosynthesis are stored in NADPH molecules. When a reduction is needed (e.g., a ketone to an alcohol) NADPH is used as a cofactor by a dehydrogenase (reductase) enzyme as an electron pair donor, reducing the substrate and oxidizing the cofactor to NADP+. NADPH is also important as part of our organism official Cleaning System, as it reduces the peptide glutathione after is oxidation by exogenous agents. And without a functional cleaning system, bad things can happen.

The pentose phosphate pathway is a series of reactions that, starting from glucose 6-phosphate, lead to the synthesis of NADPH. Moreover, the pathway can generate the pentose ribose 5-phosphate (now, where did we encounter that before…). According to the needs of the organism, glucose 6-phosphate can thus be used to generate ATP or these metabolites,.

Gluconeogenesis (new synthesis of glucose) is the first anabolic process we encounter in this course: starting from pyruvate we can synthesize glucose. Why do we want to do this? Well, because in times of plenty you, o cell, may want to act generously and release excess energy so that the rest of the organism may thank you later. It you are an hepatocyte (liver cell), it is your duty, too! We will see how gluconeogenesis cannot be simply the inverse of glycolysis. First, you need to overcome the three irreversible steps of glycolysis. Second, you want to be able to regulate independently glycolysis and gluconeogenesis so that only one at the time is active in a cell. The best way to achieve both goals is to separate part of the pathways, and regulate these in opposite ways.

We will also mention one more use of sugars, in the synthesis of glycoproteins. Extracellular proteins, either soluble or membrane-associated, can undergo glycosylation in the endoplasmic reticulum and the Golgi complex. This is to enhance their solubility (sugars are hydrophilic) and to shield them from the attack by immune system molecules, such as antibodies. We will see how this very important process is carried out.

Energy from sugars: glycolysis

The first catabolic pathway we will analyze will clarify how we can extract energy from glucose and other sugars through an oxidative process. Glycolysis is a series of enzyme-catalyzed reactions that ultimately convert one molecule of glucose into two molecules of pyruvate (pyruvic acid). In the process, energy is released and used to synthesize two ATP molecules. Also, NAD+ is reduced to two NADH molecules.

The study of glycolysis will put all the general concepts discussed in the introductory lecture into real-life examples. You will see how group-transfer reactions are used to trap glucose in the cell and to destabilize the molecule. Then a series of rearrangements and cleavage of C-C bonds will lead to the formation of two three-carbon atom molecules. Finally, these molecules will be used to transfer phosphate groups to ADP, yielding ATP. The final metabolite, pyruvate, may have different fates according to the cell type and needs. Yeast, for instance, will use it to produce ethanol!

Deficiency in the glycolytic enzymes will cause disease. No surprise, since glucose is the major fuel for most types of cells in our body. However, some cells are more sensitive than others to glycolytic deficiency, and this is because they cannot extract energy from other nutrients, such as fat. One example are the red blood cells (RBCs, erythrocytes), that can obtain energy only from glycolysis. When one glycolytic enzyme is deficient, the most typical clinical manifestation is anemia: RBCs die of exhaustion. However, some glycolytic enzyme deficiencies can also affect muscles, the nervous system, or the immune system.

Note that cancer cells have normally an elevated glycolytic metabolism, since they require energy to synthesize nucleotides and DNA for cell proliferation. Hmmm, could inhibition of glycolysis be a target for cancer chemotherapy, I wonder…? Well, while you ponder this possibility let me break you the news that arsenic poisoning acts also through inhibition of a glycolytic enzyme.

An introduction to metabolism

After the description of the cell membrane and the traffic of solutes across membranes, we shall deal with the cell metabolism. With metabolism we mean an extensive, intricate, and highly regulated array of chemical reactions taking place in the cell. Each reaction is catalyzed by specific enzyme(s), in order to provide the adequate rates of conversion between metabolites. In this complex network, we can distinguish a series of consecutive reactions that form a metabolic pathway. For instance, we define as glycolytic pathway (or glycolysis) a collection of enzyme-catalyzed reactions that convert a molecule of glucose into two molecules of pyruvate, producing two ATP and one NADH molecules in the process.

Metabolic pathways vary in length, complexity, and scope. We have catabolic pathways, that break down a specific metabolite in an oxidative series of reaction, and release energy in the process. Anabolic pathways are instead reductive, and lead to the synthesis of complex compound that either store energy or are used by the cell for its physiological function.

A crucial aspect of metabolic pathway is their regulation: we need to be able to have an active pathway only when substrate is available, and when we have effective need of the product, may it be energy or a specific molecule. How can we regulate the flux of metabolites along the pathways? Several strategies are possible:

1. Transcriptional control: if you do not transcribe the gene coding for enzymes along the pathway, the reactions cannot take place.
2. Enzyme inhibition: molecules that are the product of the pathway may bind to a previous enzyme along the pathway, inhibiting its action through either a competitive or non competitive mechanism.
3. …hey, you do not want all the fun to be spoilt right here!

So, it’s probably a good idea before the lecture to review the concepts of free energy in enzymatic reactions once more, and the different types of enzyme inhibition. See you in class!

Transport across membranes

We spent quite some time looking at the role of the phospholipid bilayer as a barrier to polar solutes. Indeed, a cell faces several issues of communication with the extracellular space:

1. The cell requires several polar molecules to stay alive. For instance, glucose for energy production, and ions for enzyme function. These solutes cross a bilayer very slowly, way too slow for the timescale of cellular life
2. The cell produces metabolites that need to stay inside the cell, and not diffuse outside
3. The cell must keep appropriate concentrations of substances such as ions, expelling the excess in the extracellular space. Such is the case for sodium ions. However, the extracellular concentration of Na+ is higher than the intracellular one, thus the process is not spontaneous.

We will see how Nature beautifully addresses all these issues, by facilitating spontaneous diffusion in a highly selective manner. And how the energetic currency ATP comes into play when solutes must move in unfavorable energetic territory.

To fully enjoy the story about the cell Customs Officers please review the Gibbs’ free energy (what it is, how we calculate it, and which way is downhill), protein conformational changes, and the Michaelis-Menten equation (in particular, the meaning of the KM value).

Lipids and membranes

Welcome back after a loooong break. By now you are more proficient in chemistry than I am, so it is time to focus more on the aspects of chemistry that are important for the structure of living cells, as well as their life.

The fourth lecture will primarily focus on biological membranes. As you know, in living cells membranes act as boundaries between inside and outside, or different compartments. These boundaries are essential to regulate the flux of soluble molecules, and create compartments with defined functions. The biological membranes are primarily composed of lipids and proteins, with the role of providing both a hydrophobic barrier that limits free diffusion and a “gating” system for the controlled flow of metabolites.

We will see how certain lipids aggregate to form a water-tight barrier, and how proteins embedded in the membrane modulate its properties. Proteins can be associated with the lipid-rich membrane in several ways, according to their role and properties.

Finally, we will talk about another form of interplay between proteins and lipids, specifically how lipids are transported by proteins in the circulation. This a very important process, because both the lipids derived from the diet and the ones synthesized by our liver need to travel to the peripheral organs, tissues, and cells. And we will see how a dysfunction in this system leads to atherosclerosis, a common vascular syndrome with high social impact.

To fully appreciate this lecture, please review the structure of lipids (especially triacylglycerides, phospholipids, and cholesterol) and the reactivities of fatty acids. I suggest you also review the essential structural properties of proteins (yes, the amino acids, all twenty of them).

Nucleotides and nucleic acids: structure and function

Tomorrow will be an exciting day. It is the last lesson before the winter break (yay!) and, most importantly, we will talk about DNA and RNA! We cannot possibly condense decades of fervid research in one lecture, but we will describe some of the exciting actions that these molecules perform.

RNA and DNA are polymeric molecules (just like proteins) and their building blocks are nucleotides or deoxynucleotides, modular molecules composed of a sugar, a nitrogen-containing aromatic base, and phosphate. These molecules can form potentially infinite chains. The sequence of the nitrogenous bases along the polymer (the primary structure of the nucleic acid) is the crucial aspect of DNA, as it encodes the genetic information. RNA is more versatile, as it can perform diverse roles in living cells such as regulation of gene expression, transport of genetic information to the protein synthesis machinery, activation of amino acids for protein synthesis, and catalysis. In RNA, both the primary and tertiary structure are crucial for its function.

Nucleotides are not only building blocks for DNA and RNA. They are important metabolic products with astonishingly diverse functions, ranging from “energy currency” (I am sure you’ve heard the word ATP before, and that is a nucleotide) to hormones.

Knowing what these molecules look like is an important step towards the understanding of genetics, and all processes that keep a cell alive and able to generate a progeny. Finally, the intermolecular relationship between DNA, RNA, and proteins is described in the form of a central dogma of molecular biology.

So, do not miss the lecture, because at the very least it will make you look differently at the DNA model above the Ciborio…

Let’s be interactive: would you like to…?

 

Ok, this is your first chance to be interactive and express your opinion. This blog can be also used, through comments to posts, as a public discussion place. So we can use this space for communications, and discussion on specific topics. I will create posts on specific topics, and you will have the chance to ask questions of all sorts.

Some of you, including myself, are probably intensive Facebook users, and another possibility would be to use that social network instead. I can create a IMD Biochemistry group, and there we can discuss our topics of interest. The drawback of Facebook is that I cannot access it during working hours, so I can give my replies, comments, and feedback only at night or on weekends.

So, here is your chance to voice your preference:

Thanks for voting!