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“How to Survive” Guide – Molecules to Cells 1
HOW TO SURVIVE
Molecules to Cells
Image taken from: http://www.sonoma.edu/users/t/thatcher/biol518/cell%20diagram.jpg
SPRING
2009
Co-Founders of SD Survival Guides: Samuel Anandan (Class of 2008), Akeem Marsh (Class of 2007)
TABLE OF CONTENTS Hello everyone! Congratulations on completing orgo, genetics, and biostat! This term promises to bring you into the world of medical school, as you begin your first medical courses, biochemistry and medical cell biology, which are conveniently packaged into one course called Molecules to Cells. You will also learn about community medicine and primary care through the HMS sequence of courses, which will also test your ability to write a 40+ page paper while maintaining your sanity. Good luck! Topic Pages How to Study for Molecules to Cells 2 Quizzes and Exams 5 Textbooks 6 Your Very First Miniboard! 7 Genetic Disease Presentations 8 Top Tips for Doing Well in M2C 8
Additional Advice from Upper Years 9 Specific Exam Advice
Spring Term, Exam 3 Advice Hormones on Nitrogen Metabolism Test
13
Useful Links 15
Top 3 Pieces of Advice for Getting Through 2nd Year, Spring Term 16
How to Survive: Molecules to Cells Akeem Marsh (Class of 2007) Samuel Anandan (Class 2009) Moury Sultana (Class 2010) Akia Caine (Class of 2011) Sebastian Rubino (Class of 2011) Christopher Bandera (Class of 2011) Jennifer Aquino (Class of 2010) Salina Lai (Class of 2010)
HOW TO STUDY FOR MOLECULES TO CELLS Now, you’re probably wondering how to study for Molecules to Cells. There’s a lot of information presented, and not as much time as you’d like to learn it. If we had to compare it to orgo, the material isn’t really harder per se, just that the time you have to master it makes it harder. And you’ll see, when you get to pathways, sometimes the info is so much that you really can’t learn all of it. Take, for instance, the third test you have in the fall semester, which covered signal transduction, amino acid metabolism, the urea cycle, all the rest of nitrogen metabolism, diabetes, hormones, nutrition, and twelve genetic disease presentations. That’s a lot of stuff, especially with Dr. Freedman, who puts the minutest detail in his handouts. That’s a whole lot of info to take in and digest, so we’ll tell you how we learned stuff for m2c, and maybe it’ll help you out. This is kind of specific for this class, so it may not work for other classes, and also, this may not work for everyone, so you have to try and see what your own study style is. First, try to form a study group. Study groups really help, even if you do them only right before a test or something, because someone’s bound to know something you don’t know, and vice versa. Just questioning each other back and forth is really helpful. Also, you don’t always have to read before lecture, although it helps. Even if you don’t, it’s really helpful to write notes on whatever’s mentioned in class, to look at later. And when you read the chapters, remember that the chapters often have overdetailed stuff that you don’t really need to know, especially that Smith textbook, if you all are using that this term. Lecture notes are the main focus of the exams. Use the textbook as a foundation and focus on what is presented in lectures. Definitely know what’s in the textbook, but in terms of what small little details to memorize, go right to the lecture notes. The lecture notes are all pictures, so definitely know all the details concerning that pictures. Remember, pictures are worth a thousand words (sorry for the cliché). Advice from Samuel Anandan: M2C was a learning experience in studying for me. I started out studying a lot first term, and it definitely paid off in the end because reviewing for the miniboard wasn’t so bad. But, depending on how easy this material comes to you, you may not have to spend hours on this class every day. It’s not about how much time you spend as much as how effectively you use the time. There are multiple techniques you can use while studying. If you’re not sure whether a method will work, try it out and see. Some people just read the book, and read it again later, and make the information stick.
Alternatively, what i used to do was write notes outlining each chapter in detail, and then I won’t look at the book again except maybe to look at the pictures. Then, before tests, I’d just read the notes I made. I only started doing this with m2c. It’s really time consuming but helpful. Another option, which was recommended by upper years and i used near the end, was making up questions based on the readings as you read. This really helps, since you can always just go back and test your knowledge of the material that way. Stuff sticks in your mind that way too. Also, it’s a lot quicker than writing notes. Some people used flashcards too. The important thing is that if something doesn’t work for the first exam, try something new. One thing, and this is really important.... make sure you go all out with studying this term. You definitely want a cushion for next term, so that even if you happen to do bad (but don’t slack off, lol) you won’t be in real danger of failing. There are a good number of people in my year in that position, who were borderline first term and are now in great danger of remediation. And with a class like this, you definitely don’t want that. Especially considering how packed everything becomes at the end of second term with papers, finals, workshops, etc. Go all out this term, and you won’t regret it. Plus, reviewing for the miniboard will be a whole bunch easier. For now, learn your amino acids, including the one-letter abbreviations. This way, you can come up with really easy mnemonics when you get to harder pathways. For example, the amino acids cleaved by chymotrypsin are methionine, phenylalanine, tryptophan, leucine, tyrosine. Just memorizing that is annoying, but if you come up with a mnemonic based on the one-letter abbreviations, it’s a lot easier. For example, when learning about what amino acids one enzyme cleaves, one of my classmates came up with My Freaking Women Lick Yams. Trust me, it’s really helpful to learn the amino acids and structure, three letter abbreviations, and definitely the one-letter abbreviations. I know this was covered in orgo, so just review the packets you got, or the amino acid chart in the textbook. When studying pathways, I found it super helpful to write my own pathway map, intergrating all of glucose metabolism on one map, and lipid metabolsim on the other. This was very helpful, because after writing it over and over, i had that mental picture in my head. Include in the map when ATP is formed, regulation, enzyme names, and names of the compounds. The key to pathways is understanding the relevance of it first, so you can at least find it tolerable. i actually liked them, because the big picture when all the pathways are together is pretty cool. But the names have a logical progression much of the time. For example, in glycolysis you have fructose-6-phosphate, which undergoes a reaction catalyzed by phosphofructokinase-1. Now you don’t have to totally memorize the next compound. A kinase phosphorylates, so the next compound’s gonna be fructose-1,6-bisphosphate. Minimize the amount of memorizing you have to do by structuring things in your head so you can figure out stuff based on what you memorized. Like, if you memorize that dehydrogenases make NADH or NADPH, then you don’t have to memorize when NADH and NADPH are made in a pathway. Go for the bigger picture and work your way down, and don’t do rote memorization, do structured memorization. Advice from Moury Sultana: Always review the quizzes after they are available and make sure you allot a good amount of time to review them. Hastily reviewing the quizzes would mean you might not understand the questions fully and because you can’t take them home or take notes on it you should make sure you understand what you did wrong and why the right answer is right. Usually Professor Piñol-Roma is around when you are going over the quizzes so you can always ask him your questions. Also review all the quizzes before every test, it’s a good refresher. Using BRS or Pretest (or both!) to do questions before an exam is a good idea. Sometimes the questions show up on the test! It’s a good idea to do these questions after you have finished studying. Try to group your wrong answers into general areas (i.e Fatty Acid metabolism) so that you can go back to those areas and review them. Always keep in mind the fed/fast cycle. That is the big picture you need to go back on. Everything you learn can tie together to these cycles. Make sure you understand first what happens during these cycles and then go into details. Many people get bogged down by details (which are on the tests) and forget how this plays a role in our bodies everyday and this main concept will help you understand questions that link different areas of metabolism together.
Don’t even bother using the textbooks for Professor Chan’s lectures on action potentials. They are useless in these areas. Instead pay extra attention in class and write down all the questions you have so that you can ask them during the review that Professor Chan hold before the exam. Use online resources or readings from other textbooks to help you with this topic. Professor Freedman takes his questions from the handouts he gives. They may not be the most visually appealing handouts but they have all the information you need to know. Don’t ignore anything on his handouts because everything on them is important. Lippincotts is awesome! Live it, breathe it, have dinner with it. Make it your study buddy but don’t rely on it solely. The flowcharts in the back are a great way of consolidating information.
QUIZZES AND EXAMS Quizzes are 1% of your grade, so although each one is worth around 1 point, it adds up, so do take them seriously. Study for the quizzes by reading your assigned readings and knowing your lectures slides really well. Something else really important is how to take the test itself. If you know a lot of you’re stuff, you’ll be able to answer most, if not all, of the questions. However, you may see stuff you don’t know, and that’s when you have to do what i call systematic guessing. It’s definitely possible to guess correctly on these tests if you know enough. Here’s an example. Try to do it right now, even though you may not know anything about it. Which of the following is true of the electron transport chain?
a) Cytochrome oxidase reduces oxygen to water. b) Oxygen is required for ATP generation.
c) Cyanide can inhibit cytochrome oxidase. d) b and c e) all of the above
Questions like this have appeared on our test, where you may have no idea what they were talking about. So let’s walk through this step by step. Choice A says that you need cytochrome oxidase to reduce oxygen to water. Sounds like it could work. Choice B says oxygen is needed to ATP generation. Seems like a feasible choice. Cyanide can inhibit cytochrome oxidase. Also sounds fine. So now, everything sounds good, and you’re stuck, right? Not exactly. The first step, and this is the risk, is taking once choice to be definitely true, and work from there. Let’s take A to be true, because it has the word oxidase in it, so maybe that has something to do with oxygen. If A is true, that means oxygen is used, and you may recall from high school or Bio 207 had the electron transport chain makes energy. So, if you reduce oxygen, maybe oxygen is needed to make ATP, making B true. Now A and B are true, because A was a really good indication that B was true. D is now out, and since you know A and B are both true, the answer must be E. And you would turn out to be correct. Note that this isn’t a surefire way to get questions right, but it’s a technique of guessing that can be used to help answer questions like this on the test. We hope the above explanation made sense to some extent, but if not, feel free to email SDSG and we will try to better help.
TEXTBOOKS Now, the question of textbooks. Here are the books we used for this course and would recommend. Different books appeal to different types of learning types. If you learn well from pictures, Lehninger’s is great for a textbook and Lippincott’s is an awesome review book. If words are more your thing, go with the required Marks book, and BRS .One thing though. If you decide to use Lippincott’s, read it along with the course readings, because it’ll clear up a lot of stuff. Honestly, some of us didn’t even seriously read the textbook for our nitrogen metabolism test and just used Lippincott’s, and almost everything we needed to know was in there! But don’t follow that example. Read all your assigned readings along with Lippincott’s, don’t substitute Lippincott’s, BRS, or any other review book for the text. These textbooks can be expensive. If you want to get Lehninger’s, you don’t need the 4th edition, the 3rd edition was fine. You can find a lot of these books used, or from upper years. If you want to check them used, check out eBay or half.com. Alternatively, you can get books from the bookstore, or regular online places like Barnes and Noble or Amazon.com. Textbook Name Description ISBN Mark’s Basic Medical Biochemistry
required- be sure to do the readings in here. This book can be annoyingly written sometimes, with silly examples and stuff, so do your best with this book.
0781721458
The Cell required- this book is better written than Marks, but sometimes the readings are like 40 pages long. But if you’re having trouble with a concept in Marks and it’s covered in The Cell, it’s easier to learn from The Cell.
0878932143
Eckert’s Animal Physiology
This was your Bio of Organisms book. This comes in really handy during Dr. Chan’s lectures on action potential, because that stuff is not in any biochem or cell bio book. Definitely use this to grasp
0716738635
the concepts for action potentials, electrical potentials across membranes, ion channels, etc. If you don’t have it, make a copy from someone who does, because this is really helpful.
Lippincott’s Illustrated Reivews: Biochemistry
This book is like gold for this class, because it’s written in a really clear way with excellent pictures. i didn’t use this much during first term, but i should’ve. For second term, i didn’t read the Marks book much for nitrogen metabolism but read Lippincott’s well and it had all you need to know. Definitely get this, and make sure to get the 3rd Edition and not the cheaper 2nd edition, because there are big differences between the two, as the 2nd edition is 14 years older or so.
0781722659
BRS Biochemistry Good questions, and great concise review for the Miniboard. Also a good read before a test, to reinforce key facts.
0683304917
BRS Biochemistry and Molecular Biology
Excellent review for class exams and the miniboard, and good questions as well.
078178624X
Pre-Test: Biochemistry and Genetics
Definitely the best review source for the miniboard. If you use this with BRS and Lippincott’s, you should be good for the miniboard, because Pre-Test gives you really good questions that are clinically oriented like they are on the Miniboard.
0071437479
Lehninger’s Principles of Biochemistry
This book is more detailed than Marks, but if you’re looking for a much clearer alternative with better pictures (and in color, not green and black like Marks) this is definitely a great book. You can get the older 3rd edition because that’s what i used and it had all you need to know in there.
0716743396
First Aid for the USMLE Step 1
Good tips and mnemonics, very useful before the miniboard. It really helps on other miniboards too. Definitely check eBay, because you don’t need a new edition, and older editions are like $4 including shipping and stuff. Or better yet, download the PDF 2006 edition from the Sophie Treasure Chest!
0071461159
If you want to know which books are really necessary, we would say get the required books, plus BRS, Lippincott’s, and Pre-Test. And First Aid, definitely be sure to read that before exams and the miniboard, it is an essential resource for success!
YOUR VERY FIRST MINIBOARD! Next up, the miniboard. The best strategy is to start reviewing for the miniboard around a month before, starting with pathways. Pathways are the hardest part to recall, so definitely start with that. The best book for the miniboard is Pre-Test. At least, that’s what many of us found, and it helped us immensely. Maybe three days before the miniboard, do all the biochem question in there, and read all the answers, even the ones you got right. Be warned that Pre-test has some wrong answers, so if you really really think you’re right on a question you just might be. For review, it depends on how good your memory is. If your memory sucks, you can use Lippincott’s as a general refresher, and then use BRS for a quick and concise review. If you used Lippincott’s throughout the term as we recommend, it’ll be much easier for you to go through it. For BRS, definitely read the last two chapters, on molecular endocrinology and tissue metabolism . Molecular endocrinology definitely appeared on the miniboard and is not taught in detail in the course, at least not when we took it. The tissue metabolism chapter is a nice summary of all the pathways and stuff you learned.
GENETIC DISEASE PRESENTATIONS Genetic disease presentations come in the second term, where you have to research a disease Dr. Piñol-Roma gives you, and make a presentation with two other people (he assigns the groups) and write a paper. You also have to make a handout. It’s in your best interest to make a short handout because anything on the handout is fair game for the test. We had some people do a size 10 font, wide margined front and back info-filled sheet. Now, chances are stuff on the test will be basic, but still, why take a chance? Your handout can be very short, and it will not affect your presentation or your grade. When studying the diseases, try to remember a main point, because the questions may be very clinical and mention a few characteristic symptoms, or ask a main feature of the disease. For instance, they may ask what builds up in Tay-Sachs disease (GM2 gangliosides), or they may ask what disease is characterized by dark colored urine and madness (acute intermittent porphyria). Don’t stress on learning every aspect of every disease, it will probably be only like 4 or 5 questions on the exam at most, and probably only 2 or 3. The paper is pretty straightforward, don’t stress out on that one. Just make sure to include everything he says, he will send out a format for it during the fall term.
TOP TIPS FOR DOING WELL IN m2c
1.) Read all assigned readings 2.) Memorize things in a structured way rather than by rote, to help you remember everything 3.) Use guessing to your advantage on multiple choice questions you have no idea on. 4.) Try different techniques; if one doesn’t work, try another till you find what works for you. 5.) Form a study group as early as possible, and definitely try to study in a group before the exams. 6.) Use Pre-Test for the miniboard 7.) Try to enjoy what you’re learning!
Lastly, try to enjoy the course! You’re learning interesting stuff, from how DNA is translated into proteins which form enzymes that control the vital metabolic reactions of your life. Try to remember that important big picture when studying the small details. And please, don’t get caught up with small details, just try your very best and we’re sure all of you will succeed! Best of luck, and feel free to email [email protected] with any questions and we’ll try our best to answer them. Good luck!
ADDITIONAL ADVICE FROM UPPER YEARS Advice from Akia Caine (M2C, Semester 1) I thought this term was going to be simple and pleasant. I thought I would just learn some biochemistry and write a paper. I figured that I was good at biology, and good at chemistry, so biochemistry wouldn’t be so bad. As a result, I got lazy. I hope you have developed discipline and self control, and effective study habits. If not, this is your last chance to do so.
This class requires studying and reading, and lots of it. You should read the textbook before class, and the lecture slides if they are available. You should read the textbook and the lecture slides and notes after class as well. You have to make sure that you know everything on the lecture slides. The exams are not impossible. It is entirely multiple choice, so just make sure that you skip whatever you don’t immediately know on the first pass, then answer those questions later. Make sure you answer every question, even if it’s a guess. Use other questions on the exam to help you answer other questions. You should not miss any lectures, nor should you sleep during class. You need to take good notes, and also compare your notes with your classmates. You may think that your notes are complete, but there is always something that you missed but someone else wrote down, and visa versa. This course promotes self directed learning. Some lecturers are great, some are good, some not so good, so it is up to you to fill in the gaps in teaching ability. You must purchase the textbook and read it. I also purchased “The Cell” and have not used it at all. I think that the Lippincott’s Review book for biochemistry is too vague to be useful. So stick with the normal textbook and the lecture slides. I like that the BRS book is small but has all the diagrams needed, so that you can study on the train and whatnot. Advice from Sebastian Rubino (M2C, Semester 1) Molecules to Cells is an awesome course. It is different from the chemistry courses you have just completed because it is not taught by one person. Dr. Pinol-Roma is the course director and aside from teaching, he also arranges for different expert lecturers to teach a series of lectures on their particular subject. Many students find the BRS, Pretest, and/or Lippincotts review books very helpful. As far as the required texts, the Marks’ book is an extremely comprehensive book. Often times it includes minute details upon which you will not be tested; you will quickly learn how to decipher what you may skim and what you really need to read. The Cooper and Hausman book is more of a traditional text and is slightly easier to read. The best advice I can give for this course is to ALWAYS TRY TO KEEP UP WITH THE SYLLABUS AND THE ASSIGNED READING. The reason for this is because, often times, lectures move swiftly. There is a limited amount of time to cover a certain amount of material and lecturers need to keep a steady pace when covering the material. As you can see there is a plethora of material out there; two textbooks, three review books, and any other references you may find. You can easily become overwhelmed with all that learning material in a fairly short amount of time. You should try to find a combination of learning material that works best for you. Additionally, another reason to keep up with the syllabus and assigned reading is because quizzes are given after a certain amount of material is covered. The quizzes are not surprises BUT they are announced with approximately a week’s notice (sometimes more, sometimes less) and it is hard to catch up on reading assignments once you are behind. Each quiz is worth 1% of your final grade. If you do the required reading for the quiz, you will be fine. After the quizzes are graded, you have the ability to go over them. THIS IS A GREAT WAY TO REVIEW AND TEST YOUR KNOWLEDGE. Try to do your best on these quizzes but also remember that they are to serve as learning tools. Do not get upset if you do not perform as expected on any particular quiz; see where you made your mistake and correct it for the exam. Many students form study groups as way of learning and reviewing the material. This is helpful because something you know may help a fellow student and visa versa. However, this method of studying may not be productive for everyone. Different people learn differently. One last thing you should try to do is KEEP THE BIG PICTURE IN MIND. The fed/fasting states are very complex and involve many different pathways. It may be easy to exclusively focus on particular pathways when initially learning them, but you should also try to remember how they affect other pathways and the general purpose of the state overall. Lastly, as previously stated, everyone does things differently. This is to serve as a guide and is not absolute. When you take the class, you will be able to assess within the first few weeks what you personally need to do in order to be successful. Good Luck! Advice from Chris Bandera (M2C, Semester 1)
This course offers you a glimpse of future medical school courses, and lays a foundation upon which most of your future education will be based. The material in this course is not harder than that of your previous Organic Chemistry course. However, you will learn more in a shorter amount of time. Therefore, you especially have to know how to manage your time efficiently in order to succeed in this course. It is important to complete the assigned readings prior to the lecture, so you have a better understanding of what is being taught. It is easy to get lost during lecture if you do not understand a particular point. There are two required textbooks for this course – Marks’ Basic Medical Biochemistry (Smith, Marks, and Lieberman, 2nd
ed.) and The Cell: A Molecular Approach (Cooper and Hausman, 4th ed.). Marks’ is a bit dense, but completely presents the material with helpful clinical applications, and has great chapter summaries and review questions. The Cell, however, is more simplified. As a rule of thumb, consult Mark’s first, then read The Cell to simplify anything that confused you. Also, it is helpful to obtain review books to further supplement the required readings. BRS: Biochemistry and Molecular Biology (Swanson, Kim, and Glucksman, 4th ed.) provides concise outlines of key concepts, and is perfect to review right before a test. Lippincott’s Illustrated Reviews: Biochemistry (Champe, Harvey, and Ferrier, 3rd ed.) provides helpful illustrations of metabolic pathways. Finally, PreTest: Biochemistry and Genetics (Wilson, 3rd ed.) provides clinically-oriented practice questions (This is also available through the Sophie Davis Treasure Chest). It is important, however, to do the assigned readings before consulting these books. You will take four exams in the spring semester of this course. Each exam consists entirely of multiple choice questions. The timing is paced to prepare you for your first Mini-Board, which you will take following the second semester of this course. In preparation for tests, the lecture handouts and your class notes are your best sources of information. Every question will have been covered at some point, either in a lecture or in a small group discussion, where you clinically apply lecture concepts. Also, review your quizzes to understand broad concepts. While the material may not reappear on tests, the format foreshadows the test. When taking the tests, use basic multiple-choice methods to eliminate incorrect answer choices. You will almost always be able to limit possible answers to two or three choices. Furthermore, many students suggest forming study groups. While this may help some people, you need to know how you study best. If you study best alone, do not join a group because other people suggest it. Only join if you know you work well in a group. Also, Dr. Piñol-Roma is readily available to answer any questions you may have. It is extremely important to know broad concepts in this class, and then apply them to particular situations. If you stress over every detail, you will have entirely too much to learn in a short amount of time. Instead, a thorough understanding of general concepts allows you to answer more questions correctly through application than minute details will. For example, when you get into pathways, not every enzyme or intermediary step is important. Only major rate-limiting enzymes and intermediates are important enough to warrant your full understanding. This method will make you more efficient when studying. Finally, know that you receive one grade for this two semester course. It would be smart to work hard this semester, so that you have a cushion for the fall semester – just in case. Advice from Salina Lai (M2C, Semester 2) Read all assigned readings. I recommend going through, at the very least, the diagrams in Marks and Lippincott’s the night before a lecture, then subsequently rereading afterwards to fill in on anything you’ve missed. Quizzes count! 2nd years, make sure you study all your slides and notes before one. If there are pathways involved, make sure you know those, too, including rate-limiting enzymes, several drugs that inhibit specific parts of the pathway, and how pathways interact. 3rd years, you should know your fed/starving/diabetic states by now. Use this semester to integrate what you’ve learned this past year to the fullest extent.
Don’t leave PreTest until miniboard time. Go through it before every exam. As for BRS, use the newer version (BRS Biochemistry and Molecular Biology, 4th edition by Swanson): I think the diagrams are better illustrated, there are fewer errors, and its emphasis on cell biology and genetics is much better than the older version’s. Come miniboard time, I highly recommend taping huge sheets of paper on the wall, writing out and linking all the pathways together (color-coding works!), and just study from it for several weeks. Advice from Jennifer Aquino (M2C, Semester 2) This semester, keep pathways in mind. You’ll learn about amino acids, and how they feed into the cycles you’ve already gone through. It’s smart to use the new material to review the old material for the miniboard. This semester, you’ll also be getting lectures from Dr. Kirzenbaum (Histology). The material on cell adhesion, mitosis and meiosis takes him about 2 weeks to cover in M2C but only 1-2 hours in histology. So, I suggest learning it well this time around so it’s just a review later on. If you take notes as you read then you might want to photocopy an upper year’s histology book, take notes now, and save them for histology. Also, you get lectures from Dr. Gresik on cancer and the cell cycle. Again, this stuff comes back and there are some questions on the miniboard on Dr. Gresik’s material. Oh the miniboard! Okay! For this miniboard, I went all out because I was so nervous and paranoid. Anyway, I used pretest (learn from the questions you get wrong), I READ BRS THOROUGHLY (I started Thanksgiving break by the way), I read KAPLAN after going through BRS. Also, I am the kind of person that has to have a quick review before an exam. So a couple of days before the miniboard I looked at the biochemistry section in FIRST AID. The morning of the miniboard I also looked at it. It’s a nice, quick summary with cool mnemonics. Lastly, presentations! The diseases are interesting and some will come back in other courses. Work together, split the work, and learn! Plus, you get to dress up. That’s always fun J
SPECIFIC EXAM ADVICE
SPRING TERM, EXAM 3 ADVICE So, it’s about time for m2c Exam 3. All those darn pathways, fructose that and galactose this and enoyl-CoA and NADH, etc. It’s a lot at first, especially after you learn all the carbohydrate stuff, and then have to go and learn all the lipid stuff. But it’s not that bad, if you pace yourself from the start. But this may definitely be the hardest test so far from Term 1. Here’s what we think you should do. First, read Lehninger’s Principles of Biochemistry. The book is available from eBay, but you can also get it from the LRC. It has EXCELLENT diagrams, so if you learn through pictures, this is definitely the book for you. For this section, basically read through the relevant Lehninger material first, looks at your lecture notes and handouts, and then go to the textbook and review books. Second, come up with mnemonics. If you’re having problems memorizing the names, which can be a lot, try to come up mnemonics. This is one i heard for the TCA Cycle, which was pretty helpful: Oh Cindy Is Kinky So She Fornicates More Often (Oxaloacetate, Citrate, Isocitrate, α-Ketoglutarate, Succinyl-Coa, Succinate, Fumarate, Malate). If there’s no existing mnemonic that you know of, come up with your own. For example, for oxidation of odd numbered fatty acids, you can come up with this nifty Star Wars mnemonic: Palpatine Does Magic Lightsaber Moves Superbly (Propionyl-Coa, D-Methylmalonyl-CoA, L-Methylmalonyl-Coa, Succinyl-Coa). Mnemonics really help, so try to come up with them from the start, especially with this lipid stuff. Third, use Lippincotts, especially for integration of pathways. This may not be for everyone, but for me, Lippincott’s was a very clear and concise review of the pathways. Especially read the sections on the integration of metabolic pathways in the well fed and fasting states. These put everything together, so you can see the big picture. That was the big plus of Lippincott’s, it allows you to see the big picture of what you’re learning, which makes learning the smaller details a bit easier. Fourth, draw maps. There are maps available already that you can look at, but drawing them out really helps. You can pretty much put all the carbohydrate cycles (glycogen synthesis, glycogenolysis, glycolysis, pentose phosphate pathway, gluconeogenesis, TCA cycle, electron transport chain, galactose and fructose metabolism, glucuronide formation) on one page. Lipid metabolism isn’t easy to fit on one page, but as many as it takes, it’s easier if you draw out maps over and over till you master these pathways. When you’re trying to learn which reaction produces NADH, FADH2, etc. keep this in mind. If an enzyme is named reductase, most likely it produces NADH or FADH2. A kinase produces ATP or an equivalent (like GTP), and this is also an example of substrate level phosphorylation, which basically is creating ATP (or equivalent) during a pathway rather than through the electron transport chain. So, the reaction of succinyl-CoA to succinate is an example of substrate level phosphorylation, while the reaction of isocitrate to α-ketoglutarate is not an example of substrate level phosphorylation. And most carboxylases (not sure if all of them) have biotin as a cofactor. And remember that glutathione (gly-cys-glu) is important in detoxification of hydrogen peroxide. This is accomplished by NADPH, which is made by Glucose-6-Phosphate Dehydrogenase. A definicy in this, for most cells, doesn’t impace detoxification a lot because malic enzyme, which converts malate to pyruvate, also produces NADPH. However, in red blood cells, which don’t have malic enzyme, glucose-6-phospate dehydrogenase deficiency can be really bad news. Just remember, pace yourself, get sleep and eat well, and you’ll get through all these pathways. Good luck!
HORMONES ON NITROGEN METABOLISM TEST
For an upcoming test, there are a few questions on hormones that may not have been emphasized enough in lecture. On our test (fall 2005), there were like four questions just dealing with cortisol. Here's a basic overview of the cortisol secretion pathway-
There's a region of your brain called the hypothalamus, which starts off the pathways for secretion of many
hormones. In the case of cortisol, the hypothalamus secretes CRH (corticotropin releasing hormone), which travels to the anterior pituitary (don't worry too much about what this is yet, you'll see it next term). Once it gets there, it causes the anterior pituitary to release ACTH (adrenocorticotropin releasing hormone), which travels to the zona fasciculata region of the adrenal glands (right above your kidneys) to make cortisol. You don't need to know all those details, but basically remember that CRH --> ACTH --> cortisol. Also, keep in mind that high cortisol levels have a negative feedback effect on CRH - cortisol goes back to the hypothalamus to inhibit CRH release.
You may also need to know a bit about thyroid hormones. The hypothalamus secretes TRH (thyrotropin releasing hormone), which goes to the anterior pituitary to secrete TSH (thyroid secreting hormone). TSH goes to the thyroid gland (in your neck region), which secretes the thyroid hormones, T3 and T4. T3 is the more active form of the hormone, but more T4 is initially produced because it's a faster reaction or something. But before you even make T3 and T4, you first need iodine, which reacts with thryoglobulin to make MIT and DIT (monoiodotyrosine and diiodotyrosine, respectively). Then, two DITs combine to make T4, or one MIT and one DIT combine to make T3. So basically, what you really need to know from this is that 2 DIT = T4, and MIT + DIT = T3, and that TRH --> TSH --> T3/T4. Also, T3 has a negative feedback effect on TSH synthesis and release.
Definitely know cortisol for sure, because those questions caught a lot of us by surprise on the test. Also, if you haven't done so already, definitely look at Lippincott's for the nitrogen metabolism, it's like gold for the test.
USEFUL LINKS Here are some useful sites for Molecules to Cells, courtesy of Akeem Marsh, Class of 2007: http://bob.usuf2.usuhs.mil/biochem/exams/exams.html (good questions! Maybe kashfi uses this site for some questions I think) http://web.indstate.edu/thcme/mwking/home.html (no questions, but really good lecture notes on there, for further explanation and clarification) http://www.kumc.edu/research/medicine/biochemistry/bioc800/exams.html (some more questions) http://www.ttuhsc.edu/som/courses/biochem/examdir.htm (more questions) http://www.fellinahole.com/med/ (website set up and run by former sophie ppl) http://www.med.uc.edu/medware2/uci_links.htm (general medical school website with links to other school’s websites with possible useful things) http://biochem.med.ufl.edu/images/examsandquizzes_fall2003.html (really similar to the style of questions that you would see on an exam in terms of difficulty, in my opinion) http://www.pnb.sunysb.edu/hby531/exams.asp (physiology website for action potential, Dr. Chan’s lecture) http://www.sumanasinc.com/webcontent/anisamples/molecularbiology/molecularbiology.html (site has a few but really good animations to help understanding)
http://carbon.cudenver.edu/~bstith/cellbio.htm (some more animations but im not sure of how good they are because it never worked on my computer lol) http://ocw.mit.edu/OcwWeb/Biology/7-88JProtein-Folding-ProblemFall2003/LectureNotes/index.htm (explains one of the topics covered in m2c, protein folding) http://greenberg.srhs.net/Practice_Exams___Helpful_Links/practice_exams___helpful_links.html#linksunit11 (nice general website with different things covered)
TOP 3 PIECES OF ADVICE FOR GETTING THROUGH 2 nd Yr., SPRING TERM
1.) Study M2C HARD right from the START. It may seem like a lot of information, you may be tired after Bio-Organic Chemistry, whatever the reason may be. Study HARD from the start. Do well on the first two tests. By the time your third test rolls around, a CHA draft will be due here, a Medical Anthopology draft here, probably an essay for a scholarship or fellowship’s in the works, and you have to learn all those darned pathways. It’s a lot safer to go all out at the start, when there’s barely any HMS2 or HMS1 work relatively. By the end, near the final, it’s even harder to time manage, at least for me. The CHA is due, the Medical Anthopology Portfolio is due, perhaps two response papers like we had, plus study DNA stuff and review the old stuff. Sometimes it’s too much, so if you study hard from the start and can build up a good average, you have a buffer zone to help you for the final. If you don’t do as well, it’s ok, you’re average will drop, but you can try and make that up in M2C part 2. But if you fail from the start, you’re in a hole, and even if you want to try really hard to come back up and, it gets harder and harder because of the other classes. So please, study HARD FROM THE START. 2.) Do CHA drafts correctly from the start. It’s annoying, and it takes a good amount of work, unless you’re a master crammer or something. But if you do your drafts as correctly as possible from the get go, you won’t have as much editing to do at the end. The CHA really isn’t so hard in terms of length, because you’ll see when you start, there’s a lot to write about, and the pages fill up fast. So don’t be concerned about the length. The fact that there are drafts makes life a lot easier, so use that to your advantage. 3.) The readings for HMS1 aren’t really necessary. They take away from time you can spend on the CHA, M2C, whatever. They’ll tell you time manage your stuff so you can do everything, but realistically, sometimes you have to choose and prioritize. This is of lowest priority, in my opinion. The HMS1 readings may or may not help you on exams, but you may have review sessions that give you a lot of the questions, plus Dr. Brandon has a review sheet that’s really helpful. For HMS2, you’ll look at the articles he gives you for parts of your CHA, so you can read them that way.
