MCB 150 Frequently Asked Questions

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• Are we required to memorize the the structures of all 20 amino acids? Or is there an easier way?
  No, please don't spend your time memorizing amino acid side chains. You will be given a table of amino acid structures as part of your ...
• Are all the prokaryotes unicellular, or can they be multicellular? Are all the eukaryotes multicellular, or can they be unicellular also?
  Your second question is easier to answer than your first. There are lots of unicellular eukaryotes, including amoebas, paramecium, yeast, and so on. As to ...
• Are the nuclear envelope and RER/SER the same? I heard that we say nuclear envelope because they are made of two parts. Does two parts mean rough ER+smooth ER?
  If you look closely at what separates the nucleus from the cytoplasm (and we will, in time) you'll see that what we call the nuclear ...
• Archaea and eukarya are most similar biochemically? What is exactly meant by 'biochemically'?
  What that means is in their metabolic process, like protein synthesis for example, the way the archaea carry out their reactions, and the molecules themselves, ...
• Are ribosomes considered organelles since they are part of the rough endoplasmic reticulum (RER), or are they not, because the subunits are synthesized in the cell?
  Ribosomes are not organelles and this is very important so it is a good thing that you asked. They are not membrane-enclosed, instead they are ...
• Are alpha glucose and beta glucose isomers?
  No, to be isomers they would have to differ in their straight chain forms, but glucose is glucose, whichever way it circularizes. ...
• Are we required to memorize the the structures of all 20 amino acids? Or is there an easier way?
  No, please don't spend your time memorizing amino acid side chains. You will be given a table of amino acid structures as part of your ...
• Are there covalent bonds in the secondary strucutre of proteins? or only hydrogen bonds?
  Just hydrogen bonds. Secondary structure is a very specific type of protein interaction. Not only is it just hydrogen bonds, it's just among atoms that ...
• Are amino acids with oxygen in the R-group always polar?
  They're always hydrophilic, but not necessarily polar. Glutamic acid and aspartic acid have oxygens in their side chains too, but they are fully negative under ...
• Among the forces that contribute to the tertiary structure of proteins, which one of the following is least frequently used? The choices were: Glycosidic Linkages, ionic bonds, hydrogen bonds, covalent bonds (Disulfide bridges) or Van der waals forces. I know that Disulfide bridges are covalent bonds that are involved in determining tertiary structures...but I'm not sure if there are a lot of specific cysteine side chains in them...my guess is that there are not a of specific cysteine side chains so they (disulfide bridges) are less likely used. Am I correct?
  Yes, disulfide bridges are part of tertiary structure. And since they are dependent on cysteine amino acids, which is only 1 of 20, they aren't ...
• Are there covalent bonds in the secondary strucutre of proteins? or only hydrogen bonds?
  Just hydrogen bonds. Secondary structure is a very specific type of protein interaction. Not only is it just hydrogen bonds, it's just among atoms that ...
• Are alpha helices considered polar and beta sheets considered polar? I am trying to understand why there are holes/plaques in tissues diagnosed with spongiform encephalopathies.
  Alpha helices and beta sheets are both created by hydrogen bonding of main chain atoms. These hydrogen bonds develop from dipole moments in the N-H ...
• Are there Van Der Waals interaction in both 3rd and fourth structure of protein folding? Is primary structure influenced by its side chain?
  Van Der Waals interactions occur because as two atoms come near each other, they generally have a peripheral contact with each other. The contact in ...
• Aren't hydrophobic interactions the same as van der waals forces?
  Hydrophobic interactions and Van der Waal's forces are caused by different interactions. Hydrophobic interactions occur when nonpolar (hydrophobic) amino acids associate with each other and ...
• Are Glycolipids considered membrane proteins?
  No. They contain serine as the 3 carbon backbone, but are otherwise composed of sugar (glyco) and lipids.  ...
• Apart from dNTP, are there dUTP,dCTP,dTTP,dATP and dGTP? Why? Similarly, apart from NTP, are there TTP,CTP, UTP, ATP and GTP. Why?
  Think about what we mean by "dNTP." We are referring to a nucleoside tri-phosphate with deoxyribose as its sugar. So dGTP would refer to a ...
• Are phosphodiester linkages covalent bonds?
  Yes, absolutely! ...
• Are there two phosphodiester linkages between each sugar in a nucleic acid? One connecting each sugar to a side of the phosphate? Or is that only considered a single phosphodiester linkage?
  A phosphodiester linkage forms between two different nucleotide monomers. A bond forms between the 3'OH group the sugar of one monomer and the 5' ...
• Are free-floating phospholipids equal to purified phospholipids?
  Yes ...
• Are the fatty acids in cholesterol categorized by saturated and unsaturated?
  Please refer to one of the slides from lecture 8 showing the chemical formula of cholesterol. As you can see, the short hydrocarbon chain is ...
• Are Glycolipids considered membrane proteins?
  No. They contain serine as the 3 carbon backbone, but are otherwise composed of sugar (glyco) and lipids.  ...
• Are the first three steps of glycolysis endergonic or exergonic? I think the first and third steps are endergonic...but isn't the second one is just an isomerization?
  Yes, that's correct. The first three steps collectively are called the Investment Phase, since overall they require an input of energy from the cell's available ...
• ATP is not a tremendously high energy molecule, thus less energy is lost as heat when ATP is hydrolyzed. Why is this correct?
  If ATP was a very high energy molecule, there would be two problems. One, much more energy would be released than what the coupled endergonic ...
• Are telomeres on both the leading and lagging strand, or just important to Okazaki fragments? The book confused me a little.
  To be honest, thinking about telomeres in the context of DNA replication goes beyond what we're going to do in our class. So you can ...
• At the end of one of our lectures, we talked about how certain factors affect the melting temperature that denatures DNA. We said that if there are more GC pairs then it's more stable and harder to disrupt so you would need a higher melting temperature. Then another point is the salt concentration, however I did not catch how that affects the melting temperature. I don't quite understand how the presence of salts would change the melting temperature.
  Anything you do to stabilize a double helix means it will take more energy to separate the strands. Since DNA has negative charges lining its ...
• Are histones basic and negatively charged? If they are, why are histones attracted to DNA, if DNA contains negatively charged phosphates?
  Remember from way back at the beginning of the semester, basic amino acids carry a positive charge. So yes, they're basic, but no, they're not ...
• Are topoisomerases responsible for the both the forward and the backward reactions?
  Yes, but different members of the topoisomerase family. ...
• A diagram in handout shows nucleus of a cell that has just entered mitosis still has more euchromatin than heterochromatin. Does this mean that the cell continues to condense its chromatin even after it enters mitosis, or is it unnecessary for all of the chromatin to be in the most condensed form (the X-shaped chromosomes) during mitosis?
  This is a "snapshot" in time as the chromatin is being condensed. The chromatin from a given pair of sister chromatids will continue to be ...
• Aren't histones basic? Therefore don't they carry a negative charge.
  They are basic, however, basic amino acids carry a positive charge. At the pH of the cell, the basic amino acids have already accepted their protons ...
• Are the leading and lagging strand eventually connected by DNA ligase?
  The only place where there would be a connection between leading and lagging strand would be at the ori, where the one leading strand is ...
• Are Okazaki fragments unique to eukaryotes? Or is it universal, so it's present in bacterial DNA replication as well?
  Yes, since DNA replication in prokaryotes and eukaryotes is bidirectional, there will be leading and lagging strand synthesis in both types of organisms. Okazaki fragments ...
• After listening to your lecture on Chromatin structure I came across you making a point of, "the beads are positively charged to give the negatively charged DNA so give the DNA a 'happy place' to be rung around." This concept makes perfect sense to me, but I am confused on how these basic proteins can be positively charged. If you're basic, aren't you given a negative charge? I just need some help understanding that concept, thanks.
  The charge of a histone protein is positive because histone proteins are made up of many basic amino acids. It may be helpful to look ...
• Are topoisomerase and helicase in the same group of enzymes or do they counteract each other's function?
  Topoisomerases and helicases are not in the same group or family of enzymes. I wouldn't say that they necessarily counteract each other's functions as a ...
• Are splicesomes and snRNPs the same thing?? I thought snRNPs removed the introns and connected exons...but that's what splicesomes do too!
  The spliceosome is the entire complex of material that's taking part in splicing. So that includes the precursor mRNA that's being spliced, and all of ...
• Among the functions of the Poly(A) tail, I don't understand how it aids in allowing multiple proteins to be efficiently made from a single eukarytotic mRNA.
  There are proteins that bind to a poly-A tail. These proteins will in turn bind to the assembly of proteins that gathers at the 5' ...
• Are the introns being spliced made up of DNA or RNA? i know that they are initially regions of DNA which do not code for RNA..but what happens after transcription?
  The introns are in the genes themselves, so they're part of the DNA, but since RNA polymerase II doesn't "know" intron DNA from exon DNA, ...
• Are the conserved sequences at the ends of mRNA that denote splicing sites considered non-translated RNA?
  Introns can fall anywhere in a primary transcript, not just at the ends. But more to your question -- the conserved regions that tell a ...
• Are ATP and GTP ever used in transcription?
  Yes, anywhere there is a thymine or a cytosine in the template. ...
• As this exam is not going to be about memorization, but more about understanding concepts, what is a good way to remember the difference between CONSERVED and CONSENSUS sequences in promoter recognition? I tend to get those two confused.
  The terms do overlap in what they are describing. A conserved sequence is remarkably consistent among species. Examples include the primary sequence of histones or ...
• Are the 5' cap and 3' poly-A tail attached to the mature mRNA after splicing of the non-coding sequences taken place? or are they put at the pre-mRNA?
  The 5' cap, poly-A tail and splicing of introns all occur "post-transcriptionally," which only means after RNAP II has transcribed. (Transcription does not need to ...
• Are the conserved sequences at the ends of mRNA that denote splicing sites considered non-translated RNA?
  Introns can fall anywhere in a primary transcript, not just at the ends. But more to your question -- the conserved regions that tell a ...
• Are UTR's only in prokaryotes? And am I correct in saying they are not similar to introns becayse introns are edited out before translation, but UTR's are not?
  No, actually you can find UTR's in any mRNA. UTR is just a fairly generic term that means untranslated region, which in turn just means ...
• A homework problem asked: "Which one of the following steps in elongation is directly dependent on ATP or GTP hydrolysis?" I picked polypeptide bond formation but the correct answer is "attachment of charged tRNA to A site." I am confused, doesn't attaching tRNA's just involve hydrogen bonding? Why is peptide bond formation not the correct answer?
  The tRNA is bound to an elongation factor (EF-Tu) which is bound to GTP. If the anticodon matches the codon, then the ribosome deems it a "good ...
• Are we required to memorize the entire Standard Codon Table of Amino Acids as seen in lecture 18? I understand we must have a basic understanding of how to use the table but do we have to know it in and out?
  I have good news- you do not need to memorize the codon table. A copy of the codon table will be attached to the exam. ...
• Are transposons a part of plasmids?
  Transposons can be found on some plasmids, yes, but they are not required to be on a plasmid, and in fact if you're talking about ...
• Are localization signals necessary to move a protein through the normal course of action, from the ER to the Golgi to the vesicles, or do you only need them to get to specialized places like lysosomes, the nucleus, mitochondria, etc.?
  It was initially thought, and still possible, that once you get to the ER, the default behavior is to continue on through the secretory pathway. ...
• Aside from ribosomal proteins, Which molecules have an NLS and an NES? I see that a nuclear transport receptor also has both a NES and a NLS. But I am a bit confused as to what the mRNA binds to in order to be exported out of the nucleus. I tried to phrase it like this: "In order for a processed mRNA molecule to be transported out of the nucleus, it is coated by proteins, which have a NES, and the proteins are then bound to exportin. One of these proteins is a nuclear transport receptor, which has both an NLS and an NES because it needs to get returned to the nucleus." Is this correct?
  A variety of proteins have NLS or NES as signals- it really depends on a protein's function or where they need to work. The "nuclear ...
• Are the chaperones added to the protein in the matrix while the mitochondrial hsp70 acts as a ratchet? Also, the last slide of lecture 25 then shows the final protein going to a chaperonin. what's the point of it going to chaperonin if it already has chaperones on it? also, what is the atp used for along the arrow to the chaperonin and out of the chaperonin?
  Yes, the chaperones are likely being added to the protein in the matrix as it is being ratcheted through Tim (if it needs additional folding ...
• Are GPI anchors always added to the C-terminus of transmembrane proteins (like the picture in the book and in lecture 27)? I would imagine that they could be added to whatever terminus is in the lumen of the ER. Also, I'm guessing that they are only attached to single-pass transmembrane proteins. It's hard to tell if what Professor Mehrtens said in lecture and the picture in the book is just an example, or if that's the way GPI anchors always work.
  The lecture and text are showing you the way GPI anchors work. GPI anchors are added on proteins where there is a C-terminal GPI anchoring ...
• Are both sphingomyelin and glycolipids considered membrane lipids? Also, I know you mentioned something unique about sphingomyelin in lecture, could you reiterate that for me please?
  Yes, they're both membrane lipids. What's unique about sphingomyelin is that it's the only commonly encountered membrane phospholipid that isn't based on glycerol as its ...
• After the vesicle enters the Cis and passes through the Golgi Stack what happens as the vesicle goes through the stacks?
  After a vesicle fuses with the Golgi, its contents are mixed with the contents of the lumen of the stacks of the Golgi. The enzymes ...
• Are phagosomes and autophagosomes considered endosomes?
  No, they don't meet the requirements to call them endosomes, so they're given those special designations and fused with lysosomes to degrade the contents inside. ...
• Are there are two critical concentrations, one for the plus end and one for the minus end, and the Cc for the minus end is higher than the Cc for the plus end? So if the actual critical concentration for the minus end is above its Cc, then it will be polymerizing, and if it's below its Cc, then it will be depolymerizing, and if it's at its Cc, then there is no net growth. And the same is true for the plus end??
  Yes,there are two critical concentrations, one for the plus end and one for the minus end, and the Cc for the minus end is higher ...
• Are there any example of actin binding proteins which hide surplus G-actins to lower ATP-bound G-actin concentration?
  I mentioned the concept of "actin binding proteins" or ABP's, although I didn't mention any of them specifically by name. There are lots of examples ...
• Are the centriole MT's capped, and if not what prevents them from polymerizing or depolymerizing?
  Yes, both ends are occupied, otherwise the centrioles might in fact disappear! ...
• Are the axonemes capped at the plus end? Are the basal bodies inside the cilia, or are they part of the centrosome?
  Yes for the first question, none of the above for the second. The basal body is the "root" of a cilium or flagellum, but isn't ...
• Are the basal bodies transported to the cilia?
  No, they are the root of the cilium or flagellum. There are nine triplets of MTs in a basal body. Of each of these triplets, ...
• Are the microtubules just extended and then somehow a basal body created (like a knot?) at the basal body point in the cilia?
  You're on the right track, but it's actually just the opposite. Cilia don't grow into basal bodies, basal bodies grow into cilia (or flagella). ...
• After the dyneins moving along cilia or flagella and reaching the end of the (-) end, where will they go next?
  They will only move as far toward the minus end as allowed by the dynein which is closest to the basal body. After that, they just ...
• Are the NPC proteins in the Nuclear Membrane Vesicles, so during Telophase, they just reassemble the Nuclear Pore complex?
  I don't know for sure, but my guess would be that some of the NPC proteins stay associated with the nuclear membrane vesicles, while others ...
• Are the centrosomes replicated during interphase or prophase?
  This is one of the last things that happens during interphase. ...
• Are spindle fibers and kinetocore microtubules the same thing?
  Actually, all three types of Mitotic microtubules are collectively called spindle fibers. ...
• Are cytokinesis and mitosis two separate parts of the cell cycle along with interphase, or is cytokinesis a step in mitosis? I know it's the separation of cytoplasm and mitosis is separation of chromosomes, but sometimes we talk about it as if it's the last step of mitosis.
  Cytokinesis is not the last step of mitosis, but it is the last thing that finishes in M-phase. Remember that M-phase consists of both mitosis ...
• Are spindle fibers and spindle microtubules synonymous, at least in the context in which we are using the two terms?
  Yes, the "fibers" to which we refer are in fact microtubules. ...
• A homework problem says that the statement "An example of positive regulation is lactose binding to lac repressor" is false. Why is that?
  Because lifting negative regulation is not the same thing as positive regulation. ...
• Are plasmids already in prokaryotes, or do they get in through conjugation, or attachment and injection like in the case for virus?
  Where the first plasmid came from is a matter of conjecture, but once established, they can be transferred to other cells via conjugation. That's the ...
• Are linear genomes limited to eukaryotes and circular genomes limited to prokaryotes as far as viral DNA is concerned? Why or why not?
  No, there may be a lot of circular genomes in phage and a lot of linear genomes in eukaryotic viruses, but there are plenty of ...
• Are replicase and reverse transcriptase two choices that the RNA virus can use, or do they use both?
  No, it's one or the other based on your need. If you go from RNA to RNA, replicase is the tool of choice. If you ...
• Are both copies of the ss RNA in the HIV genome changed into ds DNA and inserted into the genome of the host cell? If yes, does this mean that the virus must have two copies of integrase in its capsid, or does integrase also have an NES?
  It's still not absolutely clear what the reason is for the duplicate copies of retroviral genomes, but it probably has more to do with the ...
• Aren't restriction enzymes also used to cut viruses that enter? What is that nucleic acid then used for?
  Yes, this is the job of restriction enzymes in the "real world" outside the laboratory. Those bases are just recycled by the bacterium. ...