Questions

…What is the airspeed velocity of an unladen swallow?

So many questions abound in this world. How old is the universe? Will we ever find the beginning of Life? Did i mention the $3 off coupon on my XL pizza? The mind boggles… Thankfully, some answers are known, and I happen to know some of them. So, type your questions here in the comment section (If I can find something to make a chat room without having you guys sign up for anything, I’ll add that). If you see a question that you can answer, try to answer it! It is perhaps the most useful way to expertly know a subject: teach it. As Einstein once said,

“If you can’t explain it simply, you don’t understand it well enough.”

  1. Hey!
    I’m just starting out studying the first chapter and lecture, and I am wondering how much memorizing I should expect to/should do? What specifically would you recommend spending the most time memorizing at what should I just become familiar with?
    Thanks 🙂

    • Hi Ellen, thanks for the question! Well, let me answer your question in regards to the first chapter/ lecture. A good rule of thumb for this class is that Dr. Burns in general asks questions about the things on her lecture slides, not the book. If it’s on her slides, it’s something she wants you to know. That being said, some things are more important than others. For example, What defines Life, the levels of Biological Organization (Molecules to Biosphere), Feedback Systems, Biological Classification, and the Basics of Evolution are vital to know not only for the test but because they form the foundations of what you will learn. You should know the scientific method, but as a rule, this isn’t your first science class. By the way, a good way to remember Biological classification (taxonomy) is the pneumonic “Do Kings Play Chess On Fine Green Silk?”. The stuff in the book will give you a more complete picture, and I recommend reading it, but for time reasons, focus on the lecture slides and notes from class. The memorization will be easy at first, but during the course of this class (and others in the series if you take them), you will need to memorize many different parts, much more than now. To this end many students report success with flash cards (never worked for me, but one must learn how they learn best). Come Biological Molecules, you will need more emphasis on memorizing, since this is the first true Bio chapter you get. Read ahead, if you have time, but if you don’t (which tends to be the case with us college students) studying the Important Concepts at the end of her lectures go a long way to understanding the material. Ask me again if you need more assistance or details as time goes on, and thanks for the question!

      • What about definitions from the textbook? Do those need to be memorized?

        • Well, the textbook has some vocabulary words which Dr. Burns does not use in her lectures. However, familiarizing yourself with them can only increase your understanding. Generally, there aren’t too many terms that she excludes, so learning the chapter vocabulary is a safe bet, but again, her online lecture slides and in-class lectures define the words she wants you to know. That being said, it sounds like you’re off to a great start. This proactive approach should serve you well in the coming chapters!

  2. Whats up man, I have a quick question. So far I’ve been keeping up with the important concepts at the end of Dr. Burns lecture handouts. Do you think this is enough or is there anything else in particular you could or would recommend?

    Thanks.

    • It’s always a good habit to keep up with the important concepts. They do cover most vital things. The best study model is to read the chapter and review the important concepts, but for this time in the class (which should be review), I think that’s just fine IF you’re very comfortable with chemistry. Also, I hope you take notes from what she says in class. You probably do, but in the odd case you don’t, occasionally she’ll mention something not found in the book, yet still something you’ll need to know (it may be in the slide if this is the case). It’s not often, especially now, but it does occur throughout the semester. Just a heads up. However, it seems that you’re quite proactive with studying, and for now you’re probably doing fine. The Important Concepts are great study guide tools, but you may wish to read the chapter as well once we hit biological molecules (this is because this is the first true “Biology” section the class presents that’s not review). Study Groups also help, and from what students tell me, flash cards work well for them (again, once we hit biology or if you are iffy with the current subject matter). Thank you for asking and keep up the good work!

      -The SI

  3. Hi, Aaron! Would it be possible for you to post the answers for her previous final exam?

  4. How do eukaryotes regulate gene transcription?

    • Well, they have a host of transcription factors, some near the TATA BOX and some far away upstream. There is not much to say about them because she kinda skimmed over eukaryotes, saying she didn’t want you guys to know about specific names of Transcription factors. She DID, however, want you to know the 3 main motif in their structure: Helix-turn-Helix, Zinc Fingers, and Leucine Zipper Proteins. Also, know Differential Gene Expression (the fact that cells with the same genome will express different genes). That’s about it.

  5. What part of the ribosome is the catalytic region?

  6. One of the important concepts for Protein Synthesis is “Be able to ‘read’ the mRNA to make a protein given the table of codons.” Can you explain how to do this?

    • Certainly. You “read” mRNA in the 5′ to 3′ direction. Every 3 bases is a codon. The letters of the codon correspond to a certain amino acid. Say, you read the codon ACG. You look at the chart you are given and find that ACG codes for the amino acid Threonine. So, now you look at the next codon in the chain on the mRNA, and it reads AAA. You look at your chart and it say “Lysine”. So, the polypeptide chain is now Threonine-Lysine. Keep doing this until you reach a stop codon. Bam. You have a Polypeptide.

  7. What are the steps of transcription and translation? I was looking through the handouts but I couldn’t find specific steps… Also, the direction of mRNA are both built and read in the 5′ to 3′ direction, right?

    • The steps are difficult to describe.Transcription could go something like this:
      1. Transcription factors bind to the promoter region (and TATA Box for Eukaryotes).
      2. RNA Polymerase attaches to the promoter region and begins to unwind DNA.
      3. As DNA unwinds, RNA is made from the DNA template.
      4. As the RNA Polymerase passes, the mRNA detaches from the DNA and the DNA helix binds back together.
      5. RNA Polymerase stops when it reaches a sequence (In Eukaryotes it’s a poly-A tail attachment sequence).

      Yeah, that’s an extended version of “RNA Polymerase does everything”. Easier than DNA replication, that’s for damned sure. Don’t forget about the post-trancrtiptional changes, like the 5′ Guanine cap and Exon/Intron Spicing. As for Translation, I found these steps on page 17 of the protein synthesis packet:
      Initiation
      1. The mRNA binds with the small subunit of the ribosome
      2. The beginning of the coding region of mRNA is AUG
      3. The tRNA with the anticodon UAC has methionine attached to it.
      4. The tRNA with met attached binds to the P site of the ribosomes.
      5. This requires energy in the form of GTP
      Elongation
      6. Large subunit joins the small subunit
       This is the stage where amino acids are added to the growing polypeptide chain
      7. A tRNA with the next amino acid comes into the A site, requires GTP for energy
      8. The amino acids are bound by a peptide bond
      9. The bond is between the carboxyl end of the P site amino acid and the amino side of the A amino acid
      10. The now ribosome moves so the free tRNA is at the E site and the tRNA with the polypeptide chain moves is at the P site = translocation
      11. This requires GTP
      12. The free tRNA exits the ribosome
      Termination
      13. The end of the coding region will have a stop codon that signals the end of the polypeptide chain
      14. No tRNA binds to this codon, instead a release factor binds, requires GTP for energy
      15. The polypeptide chain is released

      As for the RNA questions, yes, they are both created and read in the 5′ to 3′ direction.

  8. For Protein Synthesis, what monomers are bound together to make a protein and what kind of bonds hold them together?

  9. Prior to the beginning of Mitosis, the DNA was replicated in the S phase. So does this mean that prior to the beginning of Mitosis the chromosome count is doubled? For example, if a cell usually containing 10 chromosomes is about to begin Mitosis it has 20 chromosomes? Or, is it because they join with sister chromatids the count remains at 10?

    • Hi Gaby, my apologies for not responding sooner. This was something that confused me for years, although I figured out. Something I wish they did was add one more label to mitosis and meiosis. Your last statement is the correct one, because the count is based on Distinct (genetically different) chromosomes. In this hypothetical cell, 5 distinct chromosomes come from the mother, and 5 distinct chromosomes come from the father, so the total is 10 genotypically distinct chromosomes (2n). In S phase, they are all copied and attach to their respective homologous partners. There are still only 10 distinct chromosomes (as the others that were just created are clones of already existing ones), therefore the chromosome count is still 10, but now they are duplicated. Before S phase, it is 10 unduplicated. So in a sense the fact that they pair up is why we count 10 in mitosis, but also because you can say that the number is based off of distinct chromosomes. I went through this lengthy explanation because the most common question I’m asked is about the similar processes in Meiosis, and counting distinct chromosomes instead of all chromosomes, whether they be paired or not, helps to avoid the confusion of having 2 sister chromatids be called 1 chromosome, and then is turned into two chromosomes. People start counting the sister chromatids and doubling the number of distinct chromosomes, and all hell breaks loose. Calling them “distinct” or “clones” I found helps in keeping the count straight in both meiosis and mitosis. Thanks for the question!

  10. a protein manufactured to function in RER, will that protein still travel to Golgi for further modification and then be shipped back to RER? or after the polypeptide enters the RER and is folded will it just remain there?

    • Interesting question. I have never once heard of a situation where a protein heads to the Golgi to be modified and then heads back to the RER, nor have I ever heard of a receiving end of the RER. But, just to be safe, I found this study about the protein dsl1 which researchers found to be critical in ER to Golgi transport in yeast cells. The introductory paragraphs confirm the existence of “backwards”, or “Retrograde” as they say, vesicle pathways for almost every connection in the Endomembrane system. So, I believe that, if a protein is not already folded properly in the ER, it very well could go to the Golgi and return, although this would not be the case for ALL ER proteins. Thanks for your question! here is the paper I found:
      http://www.molbiolcell.org/content/12/12/3783.full.pdf

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