This is a list of medical mnemonics, side-notes, and generalizations I wrote down while going through my 2010 First Aid book while supplementing with 2012 Falcon, Kaplan, and a bit of Goljan. I stopped at around three-quarters of the text because I got tired and felt like not many people would be interested, but if you want me to post the rest some day, feel free to ask me.
P.S. If you want to find a topic fast, I suggest Ctrl+F
Anonymous asked: compre between prokaryotic and euokaryotic dna polymerse
Um, happy winter vacation to you, too. lol
I’m sorry, but other than eukaryotes having a more proficient DNA repair system, as far as I know, both prokaryotic and eukaryotic DNA polymerases act the same way.
However, since I don’t want to leave you empty handed, I’ll list the S-phase equivalents and their functions in order below:
Hey thank you so much for replying!…for micro i’m fine with the viruses and bacteria but i have a weak understanding about all of mini 1. i’ve looked through it and im fine with Rh factor and blood types (who isn’t though lol), but things like recombination, heavy chain light chain, binding to mhc 1, cd4, b7/cd28, b and t cells, etc i just can’t seem to put it together. if you have any help with that that would be great. —A
Okay, I’ll try to make this simple, but let me know if this explanation requires clarification.
Let’s start with B cell maturation. Our location: the bone marrow.
You are a stem-cell who has a choice in becoming a B or T cell. As in elections, since you’re for becoming a B cell, you’re pro-B, however, to become pre-B, you need a heavy chain to whip away your political opponents (jk, but you do need a heavy chain). Just like how you need a strong base when building a house, you’ll need a heavy (as opposed to light) chain to start building a receptor/antibody/immunoglobulin(Ig). To do this, you have to go through somatic recombination of VDJ segments.
What are VDJ segments? On a chromosome, there are multiple V (V1, V2, V3…), D (D1, D2, D3…), and J genes (J1, J2, J3…). It’s important to know that the heavy chain can be considered “heavy” because it expresses three (V, D, and J) genes while the future light chain only expresses two (V and J) genes. The heavy chain likes to think of itself as a cool “Puff daddy” or “Big daddy” or the like, so it gets its “DJ” genes rearranged before recombining with the V gene. How does it do that?
Think of the (V)DJ gene sequence as a long piece of tape. The RAG enzymes randomly choose two spots (one random D gene and J gene) on the piece of tape to stick together and makes a loop. Artemis comes along and cuts out the loop and there’s a repeat of this loop-snipping upstream with the V-segment. Then you end up with a unique VDJ recombination (e.g., V3-D7-J5 gene combination) attached to a full sequence of constant regions (mu, delta, gamma...). Then TdT comes along, thinking that the VDJ combination isn’t random enough, and vomits random nucleotides all over its ends until it’s satisfied. Ligase just wants to get work over with, so it glues everything together, and voila! You have the DNA blueprint for the heavy chain.
Okay, that’s all and well. Now that you have a heavy chain, you are now officially pre-B! But, wait!! Rather than just being pre-B cell, wouldn’t it be better if you were actually a B cell?! So, let’s do it. All, you’ll need is a light chain.
Uh-oh. If you’re like me, you have a difficult time making choices. Your mom and your dad both have lamda and kappa chains. Each different chain has a VJ segment that you can rearrange. This means you have four choices (and consequently, four chances) to recombine a great light chain. Okay, once you finally make your decision, you undergo somatic recombination again with the RAG, TdT, and ligase enzymes to create your very own “VJ + nucleotide vomit” light chain blueprint.
Now, before we go any further, why did you need both light and heavy chains and what does idiotype and isotype mean?
To simplify things, the constant region of the heavy chain determines the isotype of the receptor/antibody/immunoglobulin (I think the the “S” in isotype occurs later in the alphabet than the “D” in idiotype and so the S occurs in the chain with more letters (V, D, and J)) and the variable regions on the light chain determines the idiotype. You can think of the heavy chain/isotype as being a car and the light chain/idiotype being an undercover officer. Now the undercover officer has been given a case to catch a very specific criminal. In fact, this undercover officer is actually a Terminator and was built solely for catching this one person (antigen). It’s in his robotic DNA, which cannot be reprogrammed. Meanwhile, he owns a Transformer disguised as a default police car (IgM). Once he spies the criminal, if occasion calls for a faster or more bad-ass vehicle, then he can isotype switch his Transformer to a boat (i.e., IgA which is secreted with mucus, etc) or submarine (i.e., IgG which can cross the placenta).
I think I may have lost you, so let me reexplain here.
The light chain’s VJ—the somatic recombination that determined the antibody’s specificity for a certain antigen—has been set in stone (because it was a DNA recombination). Meanwhile, although the heavy chain’s VDJ has been set in stone, it still contained the full sequence of constant regions (mu, delta, gamma…). You know that DNA is just a blueprint. It’s the RNA that determines what proteins will be made. So, when the initial mRNA was made from the heavy chain blueprint, only the mu and delta regions were expressed as IgM/IgD. When certain conditions are met, it can go back to the DNA blueprint, and using “switch regions”, selectively splice out the constant regions it no longer wants to express (i.e., police car mode). In doing so, it can now be a boat (IgA) or sub (IgG), etc. However, now that we’re rearranging DNA, once the antibody becomes IgA, it can no longer become an IgM. That part of the blueprint for it is gone forever.
Okay, so right now we have this highly specific Terminator currently driving a Transformer in its default IgM police car mode. He then gets a call from officer TH1 from the lymph node germinal center, and there, the officer presents to him the finger he shot off the criminal/antigen. The Terminator alarmingly eats the finger and then begins to divide. Let’s briefly switch back to medical terminology here.
After the B-cell comes in contact with the antigen, it can do multiple things.
If triggered by TH1’s CD40L, it can undergo isotype switching (we’ll address TH1 later). This is what I said earlier about the Transformer changing shapes. This means that the heavy chain undergoes DNA splicing of the constant regions and expresses gamma or alpha or other constant regions such as IgG or IgA, etc instead of IgM and IgD. Now it can chase after the antigen wherever it goes (as opposed to being a huge, chunky IgM pentamer that’s stuck in one spot).
The B cell can undergo somatic hypermutation. HYPERMUTATION, NOT RECOMBINATION. Remember, somatic recombination occurs in the bone marrow, where V(D)J’s recombined. This hypermutation is also exactly what it sounds like. The variable regions (the regions that are selective for the antigen) are randomly mutated to try become more adept (“sticky”) at catching the antigen. Of course this could fail and the antibody could become less selective for the antigen, but those are quickly discarded. It’s survival of the fittest, and the B-cell that has the mutation that produces the immunoglobulin that’s best at catching the antigen, can further become:
Plasma cells: these B-cells produce antibodies/immunoglobulins to secrete all over the place (like those robotic spiders in Minority Report)
Memory cells: these B-cells are very long-lived and help defend against reinfection. They keep immunoglobulins on their surface as receptors (as opposed to antibodies which are released).
We’ll go more into the mechanism of B cell activation later. For now, we’ll say that Plasma-Terminator is on the move, secreting tons of antibodies. What do these antibodies do?
They swarm and bind to the antigen and prevent it from damaging or binding to cells.
They coat the antigen and alert macrophages and other proper immunological authorities to remove or destroy the antigen
They trigger the complement pathway to also remove or destroy the antigen
They’re pretty much a swarm of target-locked, heavy flags.
Now onto T cell maturation.
We shall start once again at the bone marrow. This time, you want to be a T-cell, so you’re pro-T cell. The requirements for being a pre-T cell are similar to being a pre-B cell: you need a heavy chain, except in this case, it’s called a β chain. I hope I explained somatic recombination well to you earlier, because that’s exactly what you do here with V, D, and J gene segments. It should be no surprise to you that to become an immature T-cell, you also need your light chain, in this case called an α chain, also achieved via somatic recombination of the V and J genes. α and β chains combine to form something known as the T-cell receptor (as opposed to a B-cell receptor/immunoglobulin/antibody). Along with the T-cell receptor, the CD3 (basic signaling), CD4, and CD8 receptors are attached to the immature T-cell. Now are where things get different. Let’s move over to the thymus.
In the thymus, starting from the cortex, our immature T-cell is confronted by multiple TEC cells bearing both MHC1 and MHC2’s. We’ll get to how MHC’s present antigens in a bit, but first let’s learn the rule of 8’s:
CD8 binds to antigens presented on MHC1 (which is found on all nucleated cells) because 8*1=8
CD4 binds to antigens presented on MHC2 (which is found only on antigen presenting cells) because 4*2=8
Now, whichever receptor, CD4 or CD8, binds first to a TEC cell, basically decides what kind of T cell it will become. Unsurprisingly, if CD4 binds first, the T cell will become a CD4 cell (and CD8, then CD8 T cell) and the unbound receptor will “fall off.” However, if the T cell fails to bind to a TEC, it’s destroyed. This is called positive selection (because it had to bind to an MHC to live).
The survived T cell migrates down to the cortico-medullary junction inside the thymus and is confronted by dendritic cells which present our own antigens (self-antigens) to the T cell. Our body doesn’t want T cells that attack our own cells, so if these T cells bind too strongly to these dendritic cells, then these T cells are also destroyed. This is called negative selection (because it had to not bind too strongly to live).
So in short, positive and negative selection are used to select for T cells that are able to recognize antigens (positive), but not attack its host (negative).
There are two types of T cells now, CD8 and CD4. CD8 cells (aka “cytotoxic T cells”) kill infected cells in order to destroy the pathogens within (like viruses or intracellular organisms). CD4 cells (aka “helper cells”) help infected cells destroy the cells they ingested (inside phagosomes) and also help B cells isotype switch and produce more antibodies.
Let’s start with CD8 T cells.
CD8 T cells currently have a T-cell receptor, CD3 (for signaling), and CD8 receptor (among others unnamed). They go through the medulla, through the HEV, and to the lymph nodes. In the lymph node’s medulla, they meet with an antigen presenting cell (APC) that, well, present antigens to them. What happens next?
The immature CD8’s T-cell receptor and CD8 receptor bind the APC’s MHC1 just like it did with the TEC in the thymus. However, the CD8 matures when its CD28 receptor binds the APC’s B7 receptor (aka CD80/86). This second signal stimulates CD8’s maturation and allows CD8 to kick ass. The T cell then secretes a whole bunch of IL2 to replicate itself, then its clone army leaves the lymph nodes and travels to the site of the infection. There, they bind infected cells and release perforins and granzymes to aid in cellular destruction. No cell = no home for the intracellular pathogen.
Now for CD4 T cells.
Likewise in the medulla of the lymph nodes, the immature CD4 cells encounter an APC presenting an antigen on their MHC2. Like with CD8, the CD4 matures when both the CD4 receptor and the CD28 receptors bind the APC’s MHC2 and B7 receptors, respectively. The T cell then can secrete IL2 to form another clone army. Here, the APC decides which of two types of CD4’s the T cell will become:
If the APC secretes IL12, the CD4 will become a TH1 cell.
TH1’s go to the site of infection and latch onto an infected cell’s MHC2. By releasing interferon-γ, the target (infected) phagocytes release toxins to destroy bacteria trapped inside their vesicles.
TH1’s CD40ligand (CD40L) can also attach to a B-cell’s CD40 receptor inducing B cell isotype switch!!
They can also upregulate the B cell’s B7 (CD80/86) receptors. Remember that when B7 binds an immature B or T cell’s CD28 receptor, the B or T cell matures!
If the APC secretes IL4, the CD4 will become a TH2 cell.
TH2’s secrete IL5 and IL6, which stimulate B cell antibody secretion. TH2’s can also make more of itself by secreting IL4. Since TH2 stimulates antibody production, it’s the best T cell to prevent future reinfections. It should also be noted that the secretion of IL4 decreases the secretion of IL12 and consequently decreases the production of TH1’s; likewise, the secretion of IL12 suppresses the secretion of IL4 and decreases the production of TH2’s.
Okay, now for MHC’s.
I already mentioned this before, but:
MHC1 is found on all nucleated cells and presents antigens to CD8. CD8 T cells kill infected cells and intracellular, cytosolic pathogens (i.e., viruses).
MHC2 is found on APC’s and presents antigens to CD4. CD4 T cells help infected cells kill ingested, vesicle-contained pathogens (i.e., bacteria).
Let’s start with MHC1. MHC1 is expressed via HLA-A, HLA-B, and HLA-C. Here is how it presents an antigen.
Say a virus injects itself into a cell and gets broken down into pieces by proteases.
The viral peptides enter the cell’s endoplasmic reticulum (ER) through a TAP channel.
MHC1 stored inside the ER bind the peptides.
The bound MHC1 moves from the ER to the Golgi and is packaged in a vesicle.
The vesicle floats to the cell-surface like a balloon, where the receptor is released and presents the bound viral peptide for CD8’s to see.
Now for MHC2. MHC2 is expressed via HLA-DP, HLA-DQ, and HLA-DR. See how it has an extra letter? Well, consider that extra letter an extra component of the MHC2, because unlike MHC1, MHC2 has a clip. Here is how MHC2 presents an antigen:
Say a bacterium gets engulfed by a phagocyte and is trapped inside a vesicle.
A lysosome comes along and fuses with that vesicle and chews up the bacterium.
MHC2 gets notice of entry and is moved from the ER to the Golgi, where it’s packaged into a vesicle.
The MHC2 floats up with its clip and its vesicle fuses with the phago-lysosome.
The clip is acidified off and MHC2 binds the chewed up bacteria.
The MHC2 floats up to the surface and presents its antigen to CD4’s.
Okay, I think that’s enough for both you and me. I hope this helps you and if you have any questions, just ask. :-) phew!
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