All users may post questions about MCAT, DAT, OAT, or PCAT cell/molecular biology, genetics, and biochemistry here. Anatomy, physiology, development, embryology, and evolution questions should be posted in the other biology thread. We will answer the questions as soon as we reasonably can. If you would like to know what biology topics appear on the MCAT, you should check the MCAT Student Manual (http://www.aamc.org/students/mcat/s...anual/start.htm)

Acceptable topics:
-general, MCAT-level biology.
-particular MCAT-level biology problems, whether your own or from study material
-what you need to know about biology for the MCAT
-how best to approach to MCAT biology passages
-how best to study MCAT biology
-how best to tackle the MCAT biological sciences section

Unacceptable topics:
-actual MCAT questions or passages, or close paraphrasings thereof
-anything you know to be beyond the scope of the MCAT

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If you really know your cell/molecular biology, I can use your help. If you are willing to help answer questions on this thread, please let me know. Here are the current members of the Cell/Molecular Biology Team:

-Nutmeg (thread moderator): My background is in neurobiology. Please note that I am nocturnal, and generally only post between the hours of 10pm and 8am PST.

I'm going to make this thread a bit different than the others, because the material covered in the BS section is a bit different. With o-chem, gen-chem, and physics, there are a number of core concepts to understand. While there is also a lot of that in the BS, there is also a great deal of specific knowledge involved in this section (relative to the others). Test questions often introduce an experimental set-up, asking for either expected results or the interpretation of results. As such, passages might relate to advanced concepts that you are not expected to know coming into the test, and that they will explain in the passages. Any familiarity that you have with these concepts will make the test easier.

While in general this forum is designed for people studying for the MCAT, I welcome any questions relating to molecular biology, even though they might be beyond the scope of the MCAT. I know some people also like to use these threads to get help on homework questions, and I welcome that, too.

-LT2: LT2 is finishing her MS in microbiology.

The cell is considered to be haploid after the first round of division (i.e., after meiosis I). This is true even though there are still two copies of each chromosome from the sister chromatids in the daughter cells. However, the two homologues have been separated at this point, and it is because of this that we consider each of the daughter cells from meiosis I to be haploid, not diploid any more.

What do our taste receptors actually detect?

I mean chemically, i.e.:

sweet = OH groups?
salt = ions, but which ones?
sour = protons?
bitter = ?
umami (meatiness; whatever MSG adds) (assuming this "taste" exists) = ?

How much do I really need to know about the cellular-level energy cycles?

What do I really need to know about organelles? Which organelles?

How much do I really need to know about the cellular-level energy cycles?

For all of the pre-health tests (MCAT, PCAT, DAT, and OAT), you should be able to follow the generation of ATP in each step, and also the energy carrier reduction (NAD and FAD) in each stage. You do NOT need to memorize any enzymes or pathway intermediates; they will make you do that in your professional school biochem class. You should also know that oxygen is the final electron acceptor of the electron transport chain, and that anaerobic respiration is insufficient to sustain human life. In addition, fermentation produces lactic acid as a byproduct in humans, and ethanol in yeast. Finally, you should know where in the cell each stage of respiration occurs. Here is a list of the energy conversions for each stage and where in the cell they take place:

Glycolysis: (anaerobic, occurs in the cytoplasm)
2 net ATP (4 total made, but 2 needed to complete this stage)2 NADH produced (making 4 ATP in ETC for eukaryotes and 6 ATP for prokaryotes)

Fermentation: (anaerobic, occurs in the cytoplasm)
0 ATP; its main purpose is to reoxidize the NADH produced in glycolysis

Pyruvate Decarboxylation: (aerobic, occurs in the cytoplasm for prokaryotes, mitochondrial matrix for eukaryotes)
0 ATP produced2 NADH produced (making 6 ATP in ETC)

TCA Cycle: (aerobic, occurs in the cytoplasm for prokaryotes, mitochondrial matrix for eukaryotes)2 ATP produced 6 NADH produced (making 18 ATP in ETC) 2 FADH2 produced (making 4 ATP in ETC)

Electron Transport Chain (ETC): aerobic, occurs across the inner cell membrane for prokaryotes, inner mitochondrial membrane for eukaryotesNADH oxidation back to NAD and FADH2 oxidation back to FAD occur along with ATP production, allowing the earlier stages to continue

Summary: 36 net ATP produced in eukaryotes, 38 net ATP produced in prokaryotes (because the electrons from the NADH produced from pyruvate decarboxylation do not have to be transported across the mitochondrial membrane in prokaryotes; doing this causes a net loss of two ATP in eukaryotes)

QofQ Thank you for your clear, well organized answer. I was wondering about your thoughts on texts, including TPR materials, that assume: that each NADH yields only 2.5 ATP and FADH2 yields only 1.5 ATP. The total would therefore, yield 30 ATP in euk. & 32 in prok. . Is this a significant discrepancy?
Also how significant is prok. anaoerbic respiration (as opposed to fermentation). My understanding is that in anaoerbic respiration, there is e- transport leading to the phosphorylation of ADP, but that some chemical other than O (often S) is the final electron acceptor.
Thanks

What do our taste receptors actually detect?

I mean chemically, i.e.:

sweet = OH groups?
salt = ions, but which ones?
sour = protons?
bitter = ?
umami (meatiness; whatever MSG adds) (assuming this "taste" exists) = ?(This is mostly pretty recent, and there are a few details that remain to be hammered out, and some of this may not be correct, but here's what I learned last year).

Sweet reception is more than just a detection of -OH groups. THere is a family of transmembrane g-protein coupled receptors called the T1Rs. The various tastes are sensed by various cells, differentiated by the type of receptors expressed in the cell.

The sense of sweetness is detected by cells that express a combination of the T1R2 and T1R3 receptors. There is a quality about the sugars that trigger the perception of sweetness such that they bind to one of each of these receptors, creating a heterodimer and trigger the cascade that makes the cell fire. The umami sense is triggered likewise by a coupling of the T1R1 and T1R3 receptors. Some cells are known to express either only T1R2 or only T1R3, and these have a low affinity detection of sugars (or perhaps there is a yet unrecognized ligand for these cells).

Sour is detected in sour-sensing cells by H+ ion blocking of the K+ channels, slowing K+ efflux and ultimately depolarizing the cell. Saltiness is detected by Na+ entering the Na+ channels and depolarize the cell.

Bitterness is mediated by several distinct receptors that bind to various types of alkaline (often amine) molecules, in the T2R family. Bitterness is usually associated with potential toxins, so many receptors detect many things.

QofQ Thank you for your clear, well organized answer. I was wondering about your thoughts on texts, including TPR materials, that assume: that each NADH yields only 2.5 ATP and FADH2 yields only 1.5 ATP. The total would therefore, yield 30 ATP in euk. & 32 in prok. . Is this a significant discrepancy?
Also how significant is prok. anaoerbic respiration (as opposed to fermentation). My understanding is that in anaoerbic respiration, there is e- transport leading to the phosphorylation of ADP, but that some chemical other than O (often S) is the final electron acceptor.
Thanks

I am not familiar with the TPR materials, so I am not sure how they came up with those numbers that each NADH yields 2.5 ATP instead of 3. Maybe Shrike or another TPR instructor can chime in on this one? But in the whole scheme of things, I would say it is less important to know how many ATP each NADH yields than it is to know how many NADH are formed at each stage. It is entirely plausible that both numbers are not perfectly accurate, because there are probably other factors that affect the efficiency of the entire respiration process. (Biological processes are always more complex than an introductory level textbook makes them out to be. :p ) But of course we are way over the level of knowledge you are expected to have for the MCAT here.

For your second question, I think you are asking about sulfur-reducing bacteria? (They make H2S rather than H2O.) If so, you do not need to know about this at all for the MCAT; if they asked you any questions about it, it would be explained to you in a passage.

What do I really need to know about organelles? Which organelles?

I will post further details about them at a later time, but for MCAT, DAT, OAT, and PCAT biology, you should know the structure and function of the following organelles:


nucleus
cell membrane
cytosol (cytoplasm)
cytoskeleton (microtubules, microfilaments, and intermediate filaments)
endoplasmic reticulum
Golgi apparatus
vesicles
vacuoles
ribosomes
lysosomes
microbodies
mitochondria
chloroplasts
cell wall
centrioles


You should also know that prokaryotes do NOT have any membrane-bound organelles, such as a nucleus, mitochondria, or Golgi apparatus.

There has been recent debate as to whether or not NADH produces 3ATP and FADH2 yields 2 ATP. The recent texts seems to say that the actual ATP produced is slightly less then the previously accepted values. However, I was told that for the MCAT we should use the old numbers of 3 and 2.

QofQ Thank you for your clear, well organized answer. I was wondering about your thoughts on texts, including TPR materials, that assume: that each NADH yields only 2.5 ATP and FADH2 yields only 1.5 ATP. The total would therefore, yield 30 ATP in euk. & 32 in prok. . Is this a significant discrepancy?
Also how significant is prok. anaoerbic respiration (as opposed to fermentation). My understanding is that in anaoerbic respiration, there is e- transport leading to the phosphorylation of ADP, but that some chemical other than O (often S) is the final electron acceptor.
Thanks
This really is not required for the MCAT, but if you are interested in knowing, the debate is still going on.

It all boils down to the P/O ratio. The P/O ratio refers to the number of molecules of ATP formed in oxidative phosphorylation for every two electrons flowing through a defined segment of the electron transport chain. There is still some debate regarding this value.

10H+ are transported out of the matrix for every two electrons that pass from NADH to O2

4 H+ are transported into the matrix for every ATP synthesized
P/O = (1 ATP/4H+)*(10H+/NADH)*(1 NADH/2e') = 2.5 ATP/2e'

This is more or less close to the 3 ATP's for each NADH that enters oxidative phosphorylation quoted previously

For all of the pre-health tests (MCAT, PCAT, DAT, and OAT), you should be able to follow the generation of ATP in each step, and also the energy carrier reduction (NAD and FAD) in each stage. You do NOT need to memorize any enzymes or pathway intermediates; they will make you do that in your professional school biochem class. You should also know that oxygen is the final electron acceptor of the electron transport chain, and that anaerobic respiration is insufficient to sustain human life. In addition, fermentation produces lactic acid as a byproduct in humans, and ethanol in yeast. Finally, you should know where in the cell each stage of respiration occurs. Here is a list of the energy conversions for each stage and where in the cell they take place:

Glycolysis: (anaerobic, occurs in the cytoplasm)
2 net ATP (4 total made, but 2 needed to complete this stage)2 NADH produced (making 4 ATP in ETC for eukaryotes and 6 ATP for prokaryotes)

Fermentation: (anaerobic, occurs in the cytoplasm)
0 ATP; its main purpose is to reoxidize the NADH produced in glycolysis

Pyruvate Decarboxylation: (aerobic, occurs in the cytoplasm for prokaryotes, mitochondrial matrix for eukaryotes)
0 ATP produced2 NADH produced (making 6 ATP in ETC)

TCA Cycle: (aerobic, occurs in the cytoplasm for prokaryotes, mitochondrial matrix for eukaryotes)2 ATP produced 6 NADH produced (making 18 ATP in ETC) 2 FADH2 produced (making 4 ATP in ETC)

Electron Transport Chain (ETC): aerobic, occurs across the inner cell membrane for prokaryotes, inner mitochondrial membrane for eukaryotesNADH oxidation back to NAD and FADH2 oxidation back to FAD occur along with ATP production, allowing the earlier stages to continue

Summary: 36 net ATP produced in eukaryotes, 38 net ATP produced in prokaryotes (because the electrons from the NADH produced from pyruvate decarboxylation do not have to be transported across the mitochondrial membrane in prokaryotes; doing this causes a net loss of two ATP in eukaryotes)


I was thinking about making index cards to memorize. Should I just study as to what goes in and what it ends up making. Ex: Krebs starts with Pyruvate---> ATP, etc... or should I put more detail. I'm still struggling as to how to best tackle memorize these.

I often see stated as a fact that triaclglycerol is the body energy storage and that it supplies the most ATP per carbon. TPR has a straight forward question reinforcing this "fact". When I do the math, I can't make it add up.

Using the simple conversion of 3 ATP per mitoch. NADH & 2 ATP per FADH2. Each glucose molecule yields 36 ATP or 6 ATP per C.
For every 2 Cs in the fatty acid chain we get 1 turn of the Krebs cycle. Each turn of the Krebs cycle yield 3 NADH, 1 GTP, 1 FADH2 for a total of 12 ATP. Or 6 ATP per C. The glycerol will also be converted to PGAL and enter pathway at a point that seems to also generate 6 ATP.

I can see that the C of triaclglycerol with many bonds to H and few to O is more reduced than the C of glucose, But why doesn't my math confirm this by yielding more ATP per C? Can ATP possibly be generated by the beta- oxidation of fatty acids to acetyl-CoA?

I often see stated as a fact that triaclglycerol is the body energy storage and that it supplies the most ATP per carbon. TPR has a straight forward question reinforcing this "fact". When I do the math, I can't make it add up.

Using the simple conversion of 3 ATP per mitoch. NADH & 2 ATP per FADH2. Each glucose molecule yields 36 ATP or 6 ATP per C.
For every 2 Cs in the fatty acid chain we get 1 turn of the Krebs cycle. Each turn of the Krebs cycle yield 3 NADH, 1 GTP, 1 FADH2 for a total of 12 ATP. Or 6 ATP per C. The glycerol will also be converted to PGAL and enter pathway at a point that seems to also generate 6 ATP.

I can see that the C of triaclglycerol with many bonds to H and few to O is more reduced than the C of glucose, But why doesn't my math confirm this by yielding more ATP per C? Can ATP possibly be generated by the beta- oxidation of fatty acids to acetyl-CoA?
Yes, it can and is, and for exactly the reason you state. Before the fat is metabolized in the Citric Acid Cycle, it must be converted to Acetyl CoA. This is done by beta oxidation, which produces FADH2 and NADH while consuming one ATP per pair, which gives another 4 ATP per pair of carbon molecules. The total then is 4 from beta oxidation plus 12 from Krebs cycle for a net of 16 ATP per two carbons, or about 8 ATP per carbon.

in response to lindyhoppers question regarding anaerobic respiration in prokaryotes, many bacteria create energy which works somewhat similarily to aerobic respiration. you seem to have the correct idea. in aerobic respiration, bacteria utilize oxygen as a terminal electron acceptor. in anerobic respiration, they use things like nitrate, sulfate, etc. it is not as efficient as aerobic respiration, however it is far more energy efficient than fermentation. just know that aerobic respiration, anaerobic respiration and fermentation are all separate things (and very basically, why). hope this helps a bit.

Hi Q of Q, can you please go over the repressible and inducible operons and can you also please go over the fungi stuff we need to know? Thank you

Hi-

I can try to answer your question regarding operons, but the fungi would best be left to someone else.

operons in prokaryotes consist of groups of genes that typically work together and are all controlled by one promoter, which is in turn controlled by an operator region. this means that all of the genes in the operon are turned on and off together.

(i wish i had the means to draw pictures, if you'd like pictures, let me know and i'll try to make some with powerpoint)

As far as inducible operons go, the first example that comes to mind is the lac operon. the genes in the operon, lac Z, Y, and A, code for proteins that DEGRADE/utilize lactose. these genes are preceeded by an operator region. the operator region is the "control region" of the operon. with the lac operon, in the absence of lactose, an inhibitor (protein) binds to the operator region DNA, and the operon is effectively turned off because the inhibitor interferes with RNA polymerase binding. when lactose is around, it binds the inhibitor and releases it from the operator DNA. once the repressing inhibitor is removed, RNA polymerase can bind and transcribe the operon (the Z,Y and A genes), and the operator is considered "induced" or turned on. if you look at this from the standpoint of the cell, it makes sense. the cell only needs the proteins that utilize lactose when lactose is around, right? so it's set up that the genes that utilize lactose are only "turned on" when there is sufficient lactose in the cell (ie. the cell doesn't waste energy making proteins it doesn't need).

For "repressible" operons, the tryptophan operon comes to mind. in this operon, the genes for tryptophan (trp) SYNTHESIS are grouped together. these genes are also preceeded by an operator region that controls expression of the operon. however, in this operon, there is a repressor that is only active (ie it will only bind the operator) when it is also bound to trp. this means that there has to be a relatively high level of trp in the cell to bind the repressor which will then turn off the genes for trp production. this also makes sense from the standpoint of the cell... if you need more trp, the genes will be turned on until there is enough trp in the cell. when there is enough trp in the cell, the genes will be turned off.

i hope this makes sense, it really helps if you have a picture to look at, but let me know if you have any other questions... :o

Could somebody clarify what the P, A, E sites are in the translation.
I got the P site is when the methione codon(initialtion codon) hooks up with the ribosome(rRNA and proteins) in the mRNA. A site is the same for the tRNA(anticodon) which pairs with the mRNA and the E site is the next codon after the start codon, when the actual elongation starts and the actual sequence begins. :confused:

I PMed one of the thread moderators of this sub-forum, and when this mod didn't know the answer I was told to post this in the biochem thread. I saw the disclaimer at the top saying not to post embryology questions here, so I hope this isn't in the wrong place.

When a zygote divides in the early stages to produce identical twins, is it possible for the split to be uneven? Also, I've read that often the splitting is caused by problems with the genes, and the zygote is trying to dispense of the bad genes to produce a more viable embryo. If one twin dies in-utero, and then has a lot of health problems later in life, could this be because of the split of the zygote? Because there were problems with the embryo to begin with, and nature tried to remedy that, but it didn't work out all the way and the embryo actually survived and was born?

I realize this isn't really MCAT related, and it's impossible to identify the cause of different health problems. I know someone who has been told he has bad genes by his doctor, while his siblings have no health problems at all. I was just curious if someone could point me towards some research in this area, or answer my question.

Thanks!

The ribosome sites are as follows:

A site is the "acceptance" site where incoming tRNA's go before their amino acid gets tacked onto the growing chain (it's like the on deck circle at a baseball game)

the P site is the "peptide" site where the amino acid gets tacked onto the chain. the growing amino acid chain elongates and stays here.

the E site is the last site, the "empty" site where the empty tRNA's are released from the ribosome.

make sense??

The ribosome sites are as follows:

A site is the "acceptance" site where incoming tRNA's go before their amino acid gets tacked onto the growing chain (it's like the on deck circle at a baseball game)

the P site is the "peptide" site where the amino acid gets tacked onto the chain. the growing amino acid chain elongates and stays here.

the E site is the last site, the "empty" site where the empty tRNA's are released from the ribosome.

make sense??

Thanks a lot :thumbup:
I didn't find the EK to be very clear on this.
empty tRNA's are the portion of the tRNA that is done or "use up" right? after that portion is translated.

yes, "empty" tRNA's are tRNA's that have no amino acids attached to them, so i suppose they could be considered "used up".

i'll try to do a blurb on transcription and translation sometime soon...

yes, "empty" tRNA's are tRNA's that have no amino acids attached to them, so i suppose they could be considered "used up".

i'll try to do a blurb on transcription and translation sometime soon...

Thanks.
If somebody could do the same for the cellular respiration, because it doesn't seem like we have to know that much about the krebs cycle with the exception of Acetyl CoA, pyruvate, and NADH. Also the electron transport chain with the ATP synthase with the proton motive force.

LT2, thanks for that nice summary on "operators" control of the operon. I know it is hard to say ALWAYS in biology (Just too much damn diversity) but is it generally true that:
Activation of an inducible operon, like the lac operon, is induced by the release of the repressor from its OPERATOR, while activation of a repressible operon, like trp, is repressed by the binding of a repressor to its operator.

RE the lac operon, I would like to point out, that there is also an activator that binds, not at the operator site, but just upstream of the promoter at the CAP binding site. CAP the "catabolite activator protein" is activated by cAMP.
low glucose levels leading to high cAMP levels, and therefore, the activation & binding of CAP.
Therefore, if glu levels are high, & lac are low, the CAP activator does not bing and the repressor stays bound to the operator resulting in no transcription.
If Glu & lactose levels are both high, the CAP activator does not bind, but the repressor is freed from the operator resulting in low levels of transcription.
If Glu level are low but Lac is high - The low Glu levels result in high levels of cAMP resulting in the activation of CAP. The lactose will induce the release of the repressor from the OPERATOR resulting in high levels of transcription.

Can I get some help with the immune system? T cell mediated vs. B-cell mediated methods of fighting off pathogens. Primary vs. secondary action, and to what extent we have to know this stuff for the MCAT. It seems that T-cell is for extracellular pathogens, while B is for intracellular, while their methods are very similar. Just need some boning up on my immunology.

B cells make antibodies, not T cells!!

For Humoral Immunity:
Antibodies (also known as Immunoglobulins) neutralize toxins, bacteria, etc (in a matter of speaking). They have two heavy chains and two light chains. within these chains are constant regions and a variable regions. the constant region defines the "type" of antibody (IgM, IgA, IgD, IgG, and IgE), and the variable region is specific for epitopes of the toxin, bacteria, etc. B cells are derived from bone marrow and they produce antibodies when they encounter an antigen. this is the primary response (and is relatively slow 7-10 days). The original proliferation of B cells in response to the antigen become memory cells. when the body encounters the antigen again, these memory cells activate and produce antibodies quickly. this is the secondary response.

Cell-mediated Immunity:
This type of immunity is regulated by T cells (which also come from bone marrow). Cell mediated immunity is typically used in response to viral infections. There are a couple of types of T cells, cytotoxic T cells, suppressor T cells and helper T cells (these help activate the B cells mentioned above). T cells secrete interferons and cytokines that help deal with infection. T cells are also responsible for inflammatory response.

Hope this helps...

B cells make antibodies, not T cells!!

For Humoral Immunity:
Antibodies (also known as Immunoglobulins) neutralize toxins, bacteria, etc (in a matter of speaking). They have two heavy chains and two light chains. within these chains are constant regions and a variable regions. the constant region defines the "type" of antibody (IgM, IgA, IgD, IgG, and IgE), and the variable region is specific for epitopes of the toxin, bacteria, etc. B cells are derived from bone marrow and they produce antibodies when they encounter an antigen. this is the primary response (and is relatively slow 7-10 days). The original proliferation of B cells in response to the antigen become memory cells. when the body encounters the antigen again, these memory cells activate and produce antibodies quickly. this is the secondary response.

Cell-mediated Immunity:
This type of immunity is regulated by T cells (which also come from bone marrow). Cell mediated immunity is typically used in response to viral infections. There are a couple of types of T cells, cytotoxic T cells, suppressor T cells and helper T cells (these help activate the B cells mentioned above). T cells secrete interferons and cytokines that help deal with infection. T cells are also responsible for inflammatory response.

Hope this helps...

Is cell mediated immunity specific in its action? I know that humoral immunity is highly specific due to antibodies but it's confusing me if this level of specificity is involved with T cells.

Cell mediated immunity is non-specific in that the products secreted (interferons, etc) will kill what ever is in the vicinity. They are also somewhat involved with humoral immunity in that they activate B cells to start making antibodies. so they are technically non-specific, but they dabble in both modes of immunity.

hope that helps...

Cell mediated immunity is non-specific in that the products secreted (interferons, etc) will kill what ever is in the vicinity. They are also somewhat involved with humoral immunity in that they activate B cells to start making antibodies. so they are technically non-specific, but they dabble in both modes of immunity.

hope that helps...

But they have proteins on their membranes that have to match to the antigen don't they?

yes, the t cells recognize antigens (specifically) but the response (ie IFN's etc) are not specific.

I am confused as to how I should understand the ribosomes.These are the two ways that I am thinking of them just tell me which is correct.

1. The major components(large, small subunits and the rRNA) are made in the nucleolus which get "activated" in the cytosol by the substances contained in the cytosol and do their stuff eventually "depositing" the synthesized protein into the rough ER.

2. The rRNA are made within the nucleolus and move to the cytosol which combines with the subunits and get activated in the cytosol, and do the same as above. The rRNA acts as a key "turning on" the ribosome.

Which one is the closest representation of the Ribosomes?

BTW I am beginning to understand why membranes are key in Eukaryotes aside from being the distinguishing feature from Prokaryotes. :thumbup:

Just wondering if anyone had advice on who best covers molecular biology --Kaplan, TPR, EK -- because I know the MCAT is increasingly slanted that way and I didn't know if the courses had changed their material accordingly.

Thanks.

I am confused as to how I should understand the ribosomes.These are the two ways that I am thinking of them just tell me which is correct.

1. The major components(large, small subunits and the rRNA) are made in the nucleolus which get "activated" in the cytosol by the substances contained in the cytosol and do their stuff eventually "depositing" the synthesized protein into the rough ER.

2. The rRNA are made within the nucleolus and move to the cytosol which combines with the subunits and get activated in the cytosol, and do the same as above. The rRNA acts as a key "turning on" the ribosome.

Which one is the closest representation of the Ribosomes?

BTW I am beginning to understand why membranes are key in Eukaryotes aside from being the distinguishing feature from Prokaryotes. :thumbup:

The ribosomal subunits are synthesized in nucleolous and assembled when they attach to mRNA. They can be found both in cytosol and ER. The ribosomes in the cytosol make proteins to be used in the cell and the other to be exported. Hope that helped.

Not to be a thread Nazi, but perhaps issues of blood vessels would be more appropriate for the organismal biology thread...

I agree. I'm moving those posts to the organismal bio thread: http://forums.studentdoctor.net/showthread.php?t=207484 Posters, please post about systemic level biology in that thread, and only post about cellular/molecular level biology here.

The ribosomal subunits are synthesized in nucleolous and assembled when they attach to mRNA. They can be found both in cytosol and ER. The ribosomes in the cytosol make proteins to be used in the cell and the other to be exported. . .

I wanted to elaborate on "myfavred" nice concise statement. Translation begins on a free floating ribosome in the cytosol. If the nascent polypetide expresses a hydrophobic SIGNAL SEQUENCE in the first 16-30 amino acids, a signal recognition particle (SRP) will carry the entire complex to the ER. The growing protein will either be inserted into the ER lumen or threaded through the membrane of the ER.
What peptides have the SIGNAL SEQUENCE, & thus will be translated at the ER?
Proteins destined to be secreted, or end up in the "secretory pathway" will have the SIGNAL SEQUENCE. These include polypeptides that will eventually be in the lumen, or membranes of the ER, Golgi, lysomes, plasma membrane, as well as all secreted proteins.

What polypeptides will be translated in the cytosol because they lack the hydrophobic signal sequence?
Pretty much all the rest, including, proteins that will "live" in the nucleus, cytolsol, & mitochondria.

. . . I don't think you're responsible for the intricate details regarding the signal sequence and polypeptide recognition.
I'm not sure just what level will ultimately be tested, but, this level of detail is taught by TPR & a similiar level is presented in EK's book.
I think understanding the start of the secretory pathway is a pretty fundamental step in cell bio.

. . . They can be either found free in the cytoplasm or attached to the ER which is then called the RER. . .

A good point to keep clear is that translation begins on ribosomes in the cytoplasm. It is only if the nascent polypeptide is destined to enter the secretory pathway will the ribosome/mRNA complex be taken to and become attached to the ER.
Your summary was simple & good, but at TPR (where I teach MCAT bio) we stress the above point.

Please excuse me if the material is slightly long or beyond the scope of MCAT. But, I think, this should summarize most of eukaryotic transcription. For the purposes of this post, I'm only going to summarize RNA pol II (mRNA synthesis) mediated transcription. RNA pol I regulates rRNA synthesis and Pol III regulates 5s RNA and tRNA synthesis.

The mechanism of gene transcription by RNA pol II follows 3 general steps, initiation, elongation and termination. These 3 steps are followed by RNA processing.
Initiation
In eukaryotes initiation is regulated by the presence of regulatory regions, promoters and enhancers. Common promoter elements are the TATA and CCAAT boxes, found upstream of the transcription start site. Enhancers can be found upstream, downstream, or within the coding region
Promoters are recognized by basal transcription factors and are necessary for initiating transcription, while enhancers, as the name suggests are necessary for enhancing transcription and also for regulating and mediating cell and tissue specific transcription.
The basal transcription factors (TFs) such as TFIID, along with other TFs, recruit RNA pol II to the promoter element and initiate basal transcription.
Other enhancer elements and TFs mediate higher levels of transcription.
Elongation
During elongation, RNA pol II moves along the DNA, close to the bubble that represents separation of the two strands of DNA. As the enzyme moves forward along the bubble, RNA is synthesized in the 5’ to 3’ direction. DNA ahead of the bubble is unwound and behind it is rewound. Elontation continues until the enzyme reaches a termination point.
Termination
If I may, termination in eukaryotic genes is not very specific. Pol II continues to transcribe RNA for a few thousand (1000-2000) bases past the end of the mature mRNA. The exact end is determined during RNA processing.
Processing
RNA processing is characterized by capping at the 5’ end, polyadenylation at the 3’ end and intron splicing.
5' Capping
A methylated guanine nucleotide is added to the 5’ end of the mRNA in a 5’ to 5’ phosphodiester linkage. This capping is essential for mRNA recognition by ribosomes during translation.
3' Polyadenylation
A polyadenylation signal (AUAAA) is present in most of the mRNA transcripts and this signal is reconized by an enzyme that cleaves the transcript about 20 nucleotides downstream and adds a series of As (~200) to the 3’ end. These As are added without the need for a template and prevent the mRNA from degradation.
Splicing
Removal of the introns from the pre-mRNA to yield mature mRNA is called splicing. Splicing is carried out by spliceosomes that contain at least 5 known small nucleotide ribonucleoproteins (snRNPs). These snRNPs contain small nuclear RNAs (snRNAs) and together they detect intron/exon boundaries and cleave the RNA at those specific junctions. The spliced RNA is then joined together to form the mature mRNA transcript.

Salient points of eukaryotic mRNA transcription:
1) occurs in 5’ to 3’ direction
2) mRNA synthesis regulated by RNA pol II
3) mRNA synthesis involves initiation, elongation and termination followed by processing to make the mature transcript.
4) Initiation is mediated by promoters and enhancers, and elongation by the RNA pol II. Termination in eukaryotes occurs way downstream and is not very specific, unlike in prokaryotes.
5) mRNA processing to produce the mature trancript involves 5’ capping, 3’ polyadenylation and intron splicing.

Travelbug that's definately the post of the week!
I've always been a little cloudy on enhancers. I assume that enhancers are sequences of DNA. To enhance or lessen transcription, must a protein bind to the enhancer? Are these proteins called "enhancer elements"?
In the case of enhancers thousands of bp from the promoter what possible mechanism can enhance the binding of TFs? Does the chromatin bend to put the enhancer elements in physical contact with the basal TFs?
In the case of enhancers within the promoter- How are they different from sequence specific TFs?

Any guidance would be welcome.

Reply to Lindyhopper

I assume that enhancers are sequences of DNA. To enhance or lessen transcription, must a protein bind to the enhancer? Are these proteins called "enhancer elements"?

Yes, enhancers are sequences of DNA that enhancer binding proteins or enhancer elements bind to. In addition, it is possible (and more often the case) that these enhancer binding proteins also bind to TFs present in the promoter region, thereby creating a loop, like you said.

In the case of enhancers thousands of bp from the promoter what possible mechanism can enhance the binding of TFs? Does the chromatin bend to put the enhancer elements in physical contact with the basal TFs?

Look above

In the case of enhancers within the promoter- How are they different from sequence specific TFs?

Enhancers within or outside of promoter region are not TFs per se but require the binding of TFs. The role of enhancers is to stimulate transcription, often in differentiated cell or tissue types, thereby making it cell or tissue specific transcription.

I hope I have answered your questions, if not, please feel free to ask.

Thank you

Please feel free to add if I may have missed anything or correct if I'm even partially wrong.

tRNA molecule
• Single chain, contains 73-93 ribonucleotides
• Contains many unusual bases such as inosine, pseudouridine
• tRNA is L shaped
• 5’ end is phosphorylated
• 3’ end ends in CCA and contains the amino acid attachment, it is at one end of the L
• The other end of the L, far from the amino acid end, is the anticodon loop


The process of translation, like transcription, is also divided into three phases:
initiation, elongation and termination. These three phases are regulated by initiation, elongation and termination factors respectively.

Initiation

Initiator tRNA (tRNAi) that carries methionine is the only tRNA capable of initiating translation. An initiation complex called 43S, comprising methionine tRNAi, the small 40S ribosomal subunit, and initiation factors such as eIF2. The 43S complex is recruited to the 5’ end of the mRNA by eIF4E. This complex now scans the mRNA in the 5’ to 3’ direction to find the first 5’-AUG-3’. Scanning is an ATP dependent process. As soon as the met-tRNAi finds the first AUG, the larger ribosomal subunit is recruited and this recruitment is mediated by eIF5. Assembly of the large ribosomal subunit completes the initiation step. The large subunit has 3 binding sites, E, P and A and the first codon (AUG) is aligned at the P site.

Elongation

Elongation begins with the delivery of an amino-acyl tRNA (corresponding to the appropriate codon on the mRNA) to the A site on the ribosome by EF-Tu and this is followed by GTP hydrolysis. A peptide bond, catalyzed by peptidyl transferase, is formed between methionine and the aminoacyl tRNA by the transfer of methionine to the A site, leaving the deacylated tRNA at the P site. The next step of elongation is translocation, where, the deacylated tRNA moves to the E site, the dipeptidyl-tRNA (met + aminoacyl tRNA) moves to the P site and the mRNA moves forward by 3 bases, thereby aligning the next codon for the appropriate aminoacyl tRNA. Translocation is mediated by elongation factor G. A and E sites cannot be occupied at the same time, therefore, as soon as the A site is occupied, the E site containing the deacylated tRNA is emptied. Elongation proceeds in this fashion until a stop codon is encountered.

Termination

Normally, tRNAs do not have anticodons corresponding to the stop codons (UAA, UAG or UGA. At termination the polypeptide chain is at the P site and the stop codon is at the A site. Stop codons are recognized by proteins called release factors (RFs) or termination factors. Peptidyl transferase is activated when an RF binds to a termination codon at the A site. The activated peptidyl transferase hydrolyzes the bonds between the polypeptide and the tRNA at the P site. The released polypeptide chain, tRNA and mRNA leave the ribosome in that order. The ribosome dissociates into its subunits ready for another round of protein synthesis.

Summarizing eukaryotic protein translation

• mRNA is always translated in the 5’ to 3’ direction
• proteins are synthesized in the amino to carboxyl direction
• several ribosomes can simultaneously translate an mRNA molecule and such an mRNA molecule (with many ribosomes attached) is called a polysome or a polyribosome
• amino acids are added sequentially to the carboxyl end of a polypeptide chain
• aminoacyl tRNAs are the activated precursors in which the carboxyl group of an amino acid is attached to the 3’ hydroxyl group of a tRNA
• the above step is catalyzed by an aminoacyl tRNA synthetase and is driven by ATP
• initiator tRNA, met-tRNAi, occupies peptidyl (P) site, the next aminoacyl tRNA, added during elongation, occupies the aminoacyl (A) site
• peptide bond is formed between carboxyl group of met and aminoacyl tRNA
• dipeptidyl tRNA moves from A to P site
• deacylated tRNAi moves to E (exit) site and leaves ribosome
• a new aminoacyl tRNA occupies A site
• elongation proceeds until stop codon is encountered
• stop codon (UGA, UAA, or UAG) recognized by release factors that facilitate release of the completed polypeptide from the ribosome

Nondisjunction the failure of homologous chromsomes to successfully seperate results in diseases such as trisomy 21 (Down's Syndrome) & Turner Syndrome (XO).
When does this failure take place? There would seem to be two possible candidates. In Anaphase I it seems quite possible that the homologous chromosomes could get tangled, resulting in the imperfect seperation.
In Anaphase II when the sister chromatid are seperated, it seems possible that an inappropriate split at the centromere could result in both sister chromatids going to same gamete.

For the MCAT, is it necessary to know what intermediates the carbhohydrates, fats and proteins are converted into and where they enter the Krebs cycle?

Nondisjunction the failure of homologous chromsomes to successfully seperate results in diseases such as trisomy 21 (Down's Syndrome) & Turner Syndrome (XO).
When does this failure take place? There would seem to be two possible candidates. In Anaphase I it seems quite possible that the homologous chromosomes could get tangled, resulting in the imperfect seperation.
In Anaphase II when the sister chromatid are seperated, it seems possible that an inappropriate split at the centromere could result in both sister chromatids going to same gamete.

Nondisjunction could occur during mitosis, meiosis I or meiosis II. However, monosomies and trisomies are more common because of nondisjunction during meiosis than mitosis and more so during meiosis I than meiosis II.

Hi,
In incomplete dominance, the dominant allele is only partially expressed. The classic example is the red rose being incompletely dominant over the white rose resulting in pink offspring.
In codominant alleles both alleles are expressed. One common example is the ABO blood types.
The other common example of codominance, fur color, is less clearly different than incomplete dominance. If one expresses both co-dominant allele for say brown & red fur the result is sort of a "blend". Does anyone know how on a physical level this "co-dominant" expression is different from the incomplete dominance seen in the "blended" pink rose. In the co-dominant fur, are alternate hairs brown & red? Or perhaps, are both pigments translated in each hair but our eyes see a blend? Or something else?

Hi, Could someone explain reciprocal cross? :o Also, explanations & tips with reading pedigrees would be really helpful! Thanks!

Hi, maybe someone can clarify this.
-A mountain climber living at sea level ascends to a very high altitude during the course of a day long climb. By the end of the day all of the following acclimazations will occur EXCEPT:

A- increased tidal volume
B- increased respiration rate
C- right shift of hemoglobin dissociation curve
D- increased concentration of erythropoietin in the blood.

The answer they give is C

However I picked D. At the end of the climb 2,3 DPG should be increased thus shifting the curve to the right. The purpose of 2,3 DPG is to allow for a better deliver of oxygen to the muscles until erythropoeitin can increase which takes a few days. It has been a while since i delt with biochem so if someone can help out this would be appreciated.

(Im hoping that Kaplan made a mistake so I get a 12 instead of an 11 haha)

Thank you for responding but it says EXCEPT lol. Therefore a one day climb ISNT enough time to make D true... which is my reasoning.

A- increased tidal volume- (Will occur)
B- increased respiration rate (Will occur)
C- right shift of hemoglobin dissociation curve (Will occur due to 2,3 DPG)
D- increased concentration of erythropoietin in the blood. (Not enough time to occur)

So I thought D should be the correct answer for the question....

Hmm, yea i dont like this question. It appears that it may take 2-3 days for 2,3 DPG to kick in but it takes even longer for erythropoietin to increase. So there are two bad answers. Ehh i dont know, Im not going to let kaplan win that easy, time to google some more information lol.

Yay! I get one extra point lol. If anyone cares to look at this question its # 211 on kaplan FL3

For the MCAT, is it necessary to know what intermediates the carbhohydrates, fats and proteins are converted into and where they enter the Krebs cycle?

I am quite new to this and still have not figured out how to post a topic under this thread. I know we have to know transcription and translation for eukaryotic organisms, but do we need to know them for prokaryotic organisms in depth? And are the eukaryotic gene expression regulations such as the TATA box important, and if not, what are some that we should definitely know?

Is cell mediated immunity specific in its action? I know that humoral immunity is highly specific due to antibodies but it's confusing me if this level of specificity is involved with T cells.

If a postmenopausal woman is given progesterone and estrogen supplaments, what side effect will they see?

the answer was periodic menstration

I thought that when woman were impregnanted the corpus luteum produced progesterone and estrogen to maintain the endomentrium to not allow menstration. In turn inhibiting GnRH which inhibits LH and FSH? any thoughts?

Could someone please explain the Michaelis M constant and enzyme enhibition related to Km, Vmax, etc. I can't seem to find any text that explains it well.

Exactly how much genetics are we supposed to know? Over on the MCAT disucssion board, people are saying that in recent years, the MCAT has focused more on genetics. The only genetics I've really covered is dominance, linked genes, punnet squares. What else is there? Hardy-Weinberg?

Could someone please explain the Michaelis M constant and enzyme enhibition related to Km, Vmax, etc. I can't seem to find any text that explains it well.

Some of it just takes some pondering, but I'll see what I can do. I'll assume you copy of a standard velocity vs. concentration graph and a copy of a Lineweaver-Burke plot to look at while you read this.

When you look at an enzyme reaction, you're really looking at two reactions:

E+S <--> ES --> E + P

So in those rxns, E is the enzyme, S is the substrate, and P is the product. You'll notice that substrate binding is reversible, so you could say that we're looking at three possible reactions. Call the first forward reaction R1. Call the reverse of that reaction R2. Call the release of product from the enzyme R3.

So what happens with the Michaelis constant, Km, is that you make a ratio out of the rates of those three reactions to come up with a ratio for the overall reaction. That ratio is (R2+R3)/R1. So take a look at that ratio, and think about this: R2 and R3 are the two reactions that remove the substrate from the enzyme, and R1 is the reaction that binds the substrate to the enzyme. This means that Km is a ratio of separation:binding. So Km is related to the affinity of the enzyme for the substrate.

Now look at the velocity vs. concentration curve. Km is the substrate concentration at 1/2 of Vmax. Remember that Vmax is the mechanical limit of the enzyme -- it's churning out the product as fast as it possibly can. So look at a pair of enzymes, one with a high Km, and one with a low Km. An enzyme with a low Km reaches 1/2 Vmax at very low concentrations, because the enzyme has a high affinity for the substrate. An enzyme with a high Km, though, doesn't have a strong affinity for the substrate, so it takes a lot more of the substrate to get the enzyme up to 1/2 Vmax.

Now look at the Lineweaver-Burke plot of 1/Vo vs. 1/[substrate], aka the double reciprocal plot. The important things to remember about Lineweaver-Burke plots are the x and y intercepts. The x-intercept = -1/Km, and the y-intercept = 1/Vmax. Just learn these, and I'll help you make sense of them by discussing inhibition.

InhibitionThe best way to understand these graphs is to look at what happens with different types of inhibition.

First, think about competitive inhibition. You've got another substrate competing for the same enzyme. So what changes? Well, the enzyme suddenly has something else it can bind to, so its affinity for the substrate is reduced. At the same time, if you cram in enough substrate to overwhelm the competition, you can eventually reach Vmax. So in competitive inhibition, Km increases while Vmax remains the same. Look at your V/[S] graph, and the curve will stretch, because it takes a lot more substrate to get that Km at 1/2 Vmax. Look at your Lineweaver-Burke plot. The y-intercept stays the same because Vmax doesn't change. But Km has gone up, which means that -1/Km has gotten closer to zero, increasing the slope of the line and rotating it on the y-axis.

Now look at noncompetitive inhibition. In noncompetitive inhibition, you have something binding to another site on the enzyme, changing the structure of the binding site, and thus affecting the amount of enzyme that is able to bind substrate. This means that Vmax is reduced. Km, the affinity of the functional enzyme, remains the same, though. Looking at the V/[S] curve, you simply squish the maximum down. Looking at Lineweaver-Burke, Km is the same, so your x-intercept doesn't move. Vmax is smaller, so 1/Vmax is larger. This means that your line will have a higher slope and rotate on the x axis.

There are other conditions possible, but that covers the basics. If you comprehend those, you can figure out the rest on your own. Oh, and notice I didn't actually mention the Michaelis-Menten equation or the Lineweaver-Burke equation. Questions involving those are memorization w/plug&chug calculation. Understanding what happens on the graphs is much more intuitive.

Well, that's what they look like to me at least...

What I'm referring to are the parallel chromosomes
with lettered genes that appear in genetics passage.

My bio classes didn't cover any MCB or genetics --
so I haven't a clue what the diagram conveys or
or how to work through the passages.

Any input is appreciated. Thanks!

Hi again, I went through the list of MCAT topics and found skimpy information in my review books or old textbooks for these. If someone could write up a quick summary on each of these topics, that'll be extremely helpful. Thanks!

Specifc coupling of free nucleic acids
Cancer as a failure of normal cellular controls
Oncogenes
Post-transcriptional control (GEC)
Genes: recombination, single and double crossovers
Prokaryotic Cell: Plasmids and extragenomic DNA
Hardy Weinberg Principle



:)

Hi-

i don't know if you have any particular questions regarding prokayrotic plasmids and extragenomic DNA, i'd be happy to answer them.

plasmids are non-essential, circular pieces of DNA found in prokaryotes. they are commonly used in biotech in order to move genes around, for cloning, and for protein expression. they are also seen in nature and sometimes carry toxins or virulence factors. i don't know if you need to know about f' plasmids or not but they are fertility plasmids that are passed via conjugation between bugs.

if you need specifics, feel free to ask...

Hello,
I have a couple of quick questions pertaining to biochemistry and cell bio.

1. What is the first committed/irreversible step in the glycolytic pathway?
Is it fructose-6-phosphate to fructose-1,6-bisphosphate? What is the reasoning behind the answer? Does it have anything to do with a step being strongly exothermic?

2. In what stage of interphase are centrioles replicated?
On p.54 of my Kaplan MCAT notes it says during G1, but on p. 593 of my Cell & Molec. Bio textbook (Gerald Karp) it says at the beginning of the S phase, along with chromosome replication. I have also heard that it occurs during G2, and so I am looking for clarification on this question.

Thank you, any help is greatly appreciated.

Hi again, I went through the list of MCAT topics and found skimpy information in my review books or old textbooks for these. If someone could write up a quick summary on each of these topics, that'll be extremely helpful. Thanks!

Specifc coupling of free nucleic acids
Cancer as a failure of normal cellular controls
Oncogenes
Post-transcriptional control (GEC)
Genes: recombination, single and double crossovers
Prokaryotic Cell: Plasmids and extragenomic DNA
Hardy Weinberg Principle



:)



If these questions are not answered before the end of next week (my summer II finals are next week), I can try answering some.

I do not follow what you mean by specific coupling of free nucleic acids, also can you please expand GEC?

Thank you

I had trouble figuring this question out. It was found in the AAMC 7R Q. 166, part of the independent section (non-passage based)
It reads:

Embryonic mouse cells divide every 10 hours at 37 C. How many cells would be produced from an egg after three days?

A) Fewer than 50
B) Between 50 and 500
C) Between 500 and 5000
D) More than 5000

To solve this problem I first determined the numbers of hours in 3 days. So, 3 x 24 hours = 72 hours. Since the mouse cells divided every 10 hours, this meant the 72 / 10 = 7 complete cell divisions occured. I then calculated that 2 ^7 = 128 and circled answer choice (B). To my surprise, the correct answer is (D), not (B). How is this possible?

Hello,
I have a couple of quick questions pertaining to biochemistry and cell bio.

1. What is the first committed/irreversible step in the glyoclytic pathway?
Is it fructose-6-phosphate to fructose-1,6-bisphosphate? What is the reasoning behind the answer? Does it have anything to do with a step being strongly exothermic?



Hitman, the production of F 1,6, Bisphosphate from F-6-P is the first irreversible step in glycolysis, according to my BioChem textbook. It has the do with the fact that the reaction happens spontaneously due the large negative delta G (free energy) ...-14.2 kJ/mol to be exact. For clarification, this reaction is spontaneous, which may or may not be "exothermic", depending on reaction conditions. Remember that G = H - TS. "H" represents the exothemic part. It quite possible to have an endothermic reaction (positive H) and still be spontaneous (negative G). Hope this helps.

Hitman, the production of F 1,6, Bisphosphate from F-6-P is the first irreversible step in glycolysis, according to my BioChem textbook. It has the do with the fact that the reaction happens spontaneously due the large negative delta G (free energy) ...-14.2 kJ/mol to be exact. For clarification, this reaction is spontaneous, which may or may not be "exothermic", depending on reaction conditions. Remember that G = H - TS. "H" represents the exothemic part. It quite possible to have an endothermic reaction (positive H) and still be spontaneous (negative G). Hope this helps.

Nnguyen72, thank you for your help. I also tried to answer your question, and got the exact same answer by the same reasoning. Pehaps there is an error in the answer key?

I had trouble figuring this question out. It was found in the AAMC 7R Q. 166, part of the independent section (non-passage based)
It reads:

Embryonic mouse cells divide every 10 hours at 37 C. How many cells would be produced from an egg after three days?

A) Fewer than 50
B) Between 50 and 500
C) Between 500 and 5000
D) More than 5000

To solve this problem I first determined the numbers of hours in 3 days. So, 3 x 24 hours = 72 hours. Since the mouse cells divided every 10 hours, this meant the 72 / 10 = 7 complete cell divisions occured. I then calculated that 2 ^7 = 128 and circled answer choice (B). To my surprise, the correct answer is (D), not (B). How is this possible?

the answer key and explanation I have say the correct answer is B

Hey dtreese.

Thanks for such a thorough answer!

Hello,

I have a few questions on the polypeptide structure.
The translation of polypeptide takes place on a ribosome (or polysomes) that is attached to a rough endoplasmic reticulum. When polypeptide enters the cisternae, what structure does it have? It’s definitely primary. Where does it have modifications that result in the secondary, tertiary structures? Where do 2 or more polypeptides combine to become a protein?

Thank you

specific coupling of free nucleic acids, also can you please expand GEC?

Thank you

It's in the AAMC list. I'm wondering the same too -- but at this point, I'll just ignore that.

I got stumped in one of those pedigree-type Qs where the answer was male X-link. However, not all the men were affected, so I thought it was autosomal. What am I missing?

How are cancer/oncogenes structurally different than normal genes? How is DNA replication activated? By steroids or peptides or just pure mutation? I recall reading that they have extra-long telomeres, which enable repeated replication. So they spend more time in the S phase? I really don't know anything in this area -- not sure what I need to know.

What is a double crossover? What triggers it and what are its effects? I'm assuming genetic variability.

I got stumped in one of those pedigree-type Qs where the answer was male X-link. However, not all the men were affected, so I thought it was autosomal. What am I missing?


All males do not have to be affected for a disorder to be X-linked recessive. But of the affected persons, the vast majority have to be male because they can not have a corresponding dominant gene on the X chromosome (as females do). Keep in mind that the presence of one or two affected females (who are homozygous recessive on their X chromosomes) does NOT mean that the disease does not follow X-linked recessive inheritance patterns. As long as the large majority of affected individuals are male, it is a very good indication X-linked recessiveness is the answer, but again, ALL of the males do not have to be affected (they may simply receive X chromosome from their mother that has the dominant allele). Hope this clarifies a bit.

[QUOTE=medworm]How are cancer/oncogenes structurally different than normal genes? How is DNA replication activated? By steroids or peptides or just pure mutation? I recall reading that they have extra-long telomeres, which enable repeated replication. So they spend more time in the S phase? I really don't know anything in this area -- not sure what I need to know.QUOTE]

I don't know if this is what you're looking for, or how much this will help, and i'm a bit rusty, but i'll give it a try. there are genes called oncogenes (or c-onc for cellular oncogenes) that are players in regulating the cell cycle. certain viruses (ie retroviruses like the rous sarcoma virus) can modify these genes to create v-onc genes (viral oncogenes) that throw the cell cycle off. in v-onc genes, many times only a portion of the cellular oncogene is present. in v-onc there can be a loss of cellular control elements like promoters or repressors. also, deletions or rearrangements can be present that may affect the structure of the protein itself.

hope that made a bit of sense...

How are cancer/oncogenes structurally different than normal genes? How is DNA replication activated? By steroids or peptides or just pure mutation? I recall reading that they have extra-long telomeres, which enable repeated replication. So they spend more time in the S phase? I really don't know anything in this area -- not sure what I need to know.

What is a double crossover? What triggers it and what are its effects? I'm assuming genetic variability.

I don't think we really need to know much about this for the MCAT...maybe just know that the cell cycle is controlled by proteins called cyclin dependent kinases (CDKs))...and that they will spend much more time in S phase relative to the other normal stages - G1, G2, and mitosis.

...but if you're interested in more than the MCAT...(if you're not, don't read ahead! no need to waste precious brain cells remembering this stuff)

Oncogenes are simply modified "normal" genes (called proto-oncogenes). They could result from a base pair substitution, a deletion, or an insertion. Usually the product of an oncogene will create a hyper-functional protein - a protein that cannot be inactivated by the normal process. (the RAS protein is an example of this. when bound to GTP, it is in the "on" position and heavily promotes cell growth. when the proto-oncogene ras becomes an oncogene ras, oftentimes the modification results in a protein which cannot have the GTP removed. the RAS is stuck in the "on" position".)

Proto-oncogenes are akin to a the gas pedal on a car. Cancer keeps the pedal to the metal and doesn't let the gas pedal up.

DNA replication is activated by a complex pathway, but the main protein involved is the RB protein, which acts as a checkpoint before entry to S phase. Normally, RB is not phosphorylated and is bound to and inhibits a protein called E2F, which is a transcription factor for many S phase specific genes. CDKs (4 and 6) phosphorylate RB, releasing its inhibition of E2F, and thereby allow entry into S and DNA replication to occur. Many if not most cancers have some aberration in this RB pathway.

RB is called a "tumor suppressor", because it delays cell growth & replication normally. It's like the brake pedal on a car. Cancers cut the wire to the brake pedal, making it useless.

Cell Immunity

can someone explain when the body does Humoral Mediated Immunity and when it does Cell Mediated Immunity? never really understood the difference even though i know how each one works....thanks

Thank you! That was a nice summary. :)

Cell Immunity
can someone explain when the body does Humoral Mediated Immunity and when it does Cell Mediated Immunity? never really understood the difference even though i know how each one works....thanks

I'll let someone else do the detailed explaining, 'cuz frankly not my forte. But if you get confused as to which one matches up with T-cells and which is for B-cells, I have a mnemonic:

T-Cell as in T-Mobile is cellular.
B-Humor as in B-rated Comedy.

Your body activates both types, often at the same time, and their actions are coordinated. For example, T-helpers solicit B-cells to bind to antigens when foreign bodies (namely viruses) are present.

I hope it's safe to say that for the MCAT, CELLULAR responds to antigenic viruses that have taken up residence in a host cell and HUMORAL responds to pathogens in the blood, lymph and tissue fluids.

And lastly, nonspecific includes complement system, interferons, natural killer cells and histamines/inflammation.

I'll let someone else do the detailed explaining, 'cuz frankly not my forte. But if you get confused as to which one matches up with T-cells and which is for B-cells, I have a mnemonic:

T-Cell as in T-Mobile is cellular.
B-Humor as in B-rated Comedy.

Your body activates both types, often at the same time, and their actions are coordinated. For example, T-helpers solicit B-cells to bind to antigens when foreign bodies (namely viruses) are present.

I hope it's safe to say that for the MCAT, CELLULAR responds to antigenic viruses that have taken up residence in a host cell and HUMORAL responds to pathogens in the blood, lymph and tissue fluids.

And lastly, nonspecific includes complement system, interferons, natural killer cells and histamines/inflammation.

Hey, so Cellular responds to infected human cells (virus/bacteria inside the human cell), and humoral responds to extracellular pathogens like plain bacteria?

Also, I just wanted to make clear that in this sentence...

I don't think we really need to know much about this for the MCAT...maybe just know that the cell cycle is controlled by proteins called cyclin dependent kinases (CDKs))...and that they will spend much more time in S phase relative to the other normal stages - G1, G2, and mitosis.

...Cancer cells spend more time in S relative to other cell cycle stages, but most normal cells will spend more time in G1 (or really G0) than other cell cycle stages.

Cells of the Immune System: derived from the hematopoietic stem cell

1. Lymphoid Lineage

T lymphocytes (T cells, made in the thymus)

B lymphocytes (B cells, made directly from the bone marrow)

Natural Killer cells (NK cells)

2. Myeloid lineage

Monocytes that give rise to macrophages

Langerhans cells and Dendritic cells

Megakaryocytes that give rise to Platelets

Granulocytes (eosinophils, basophils and neutrophils)


Primary lymphoid tissues: bone marrow and thymus

Secondary lymphoid tissues: spleen, lymph nodes


Leukocyte migration: T and B cells leave the thymus and bone marrow respectively as naïve lymphocytes, migrate into the blood and then into the secondary lymphoid tissue. Antigen presenting cells (APCs), such as dendritic cells, also derived from the bone marrow, migrate into tissues, take up antigen and bring it back to the secondary lymphoid tissues to present the antigen to the T and B cells. The T and B cells are now primed or activated and they migrate to the sites of infection and inflammation to mount an attack.

Immune Response

Pathogens usually have two locations: Extracellular and Intracellular

Extracellular Pathogens are targeted by antibodies by at least one of three processes: Neutralization, Opsonization and Complement Activation

Neutralization: antibody may bind to bacterial toxin and neutralize, thereby preventing the pathogen from interacting with host cells. These antibody tagged toxins are later degraded

Opsonization: Antigens are coated with antibodies and are targeted for phagocytosis.

Complement Activation: Antibodies coat bacterial cells and these antibodies act as receptors for the first protein of the complement system, eventually forming a protein complex leading usually to phagocytosis.

Antibodies in each class have different sites of action and therefore vary in their effectiveness in neutralization, opsonization and complement activation.

Intracellular Pathogens are targeted by a T-cell mediated response. There are two intracellular locations:

Cytosol (continuous with nucleus via nuclear pore): site of all viruses and some bacteria

Vesicular System (ER, Golgi, endosomes, lysosomes etc): site of some bacteria and some parasites

There are also two T cells and the intracellular location determines the type of T cell.

Cytotoxic T cells (Tc or CTL): Express CD8 and kill pathogens in cytosol

Helper T cells (Th): Express CD4 and are again of two kinds

Inflammatory Th1 that kill vesicular pathogens

Th2 (True helper cells) are involved in antibody production by B cells against T-dependent antigens on extracellular pathogens.


Both antibody (humoral) and cell-mediated responses contribute to eliminating the pathogen.

Travelbug-

Thanks for writing those great posts. :thumbup: If you are planning to write some more, you can post them directly into the Biochem Explanations Thread. You won't be able to edit the TOC, but I'll keep adding the new posts to the TOC as needed.

I'll let someone else do the detailed explaining, 'cuz frankly not my forte. But if you get confused as to which one matches up with T-cells and which is for B-cells, I have a mnemonic:

T-Cell as in T-Mobile is cellular.
B-Humor as in B-rated Comedy.

Your body activates both types, often at the same time, and their actions are coordinated. For example, T-helpers solicit B-cells to bind to antigens when foreign bodies (namely viruses) are present.

I hope it's safe to say that for the MCAT, CELLULAR responds to antigenic viruses that have taken up residence in a host cell and HUMORAL responds to pathogens in the blood, lymph and tissue fluids.

And lastly, nonspecific includes complement system, interferons, natural killer cells and histamines/inflammation.

I like your mnemonic; you should add it to the mnemonic thread on the main MCAT forum page. :)

Are skeletal muscles only activated by acetylcholine and not norepinephrine/epinephrine?

Does the phrenic nerve use acetylcholine to mkae the diaphragm contract?

Thanks!

bumping this thread

CELL CYCLE (Mitosis and Meiosis will follow in later posts)

There are two main phases to eukaryotic cell division: DNA doubling in S (synthetic) phase and halving of that genome in M (mitotic) phase. The S and M phase are interspersed with G1 (between M and S) and G2 (between S and M) phases. Therefore, it is G1, S, G2 and M.

So, what happens at each of these phases?

G1: growth and preparation of chromosomes for replication

S: DNA synthesis

G2: preparation for mitosis

M: Mitosis

Any stage other than mitosis is usually called the interphase.

What are some of the key players in cell cycle regulation?

Cyclins:
Cyclin D (G1 cyclin)
Cyclins E and A (S-phase cyclins)
Cyclins B and A (Mitotic cyclins)

The levels of these cyclins change depending on the stage of the cell cycle.

Cyclin-dependent kinases (Cdks)

Cdk4 is a G1 dependent Cdk
Cdk2 is an S-phase Cdk
Cdk1 is an M-phase Cdk

Cdks must bind to the appropriate cyclin to be activated. Their levels remain fairly constant throughout the cell cycle. However, the rise and fall of the cyclins determines Cdks’ activation. For example, Cdk4 is only activated when the level of G1 cyclins rises and thus prepares the cell for chromosome replication.


We all know that every cell has to encounter various check points to progress through each of these phases, so what are some examples of such check points?

DNA damage checkpoints: present at G1 (p53), S phase, G2 and at mitosis (MAD)
Spindle checkpoints (proteins such as kinesin):
arrest cells in metaphase if spindle fibers not properly attached to kinetochore
block cytokinesis by detecting improper spindle alignment
induce apoptosis if damage irreparable

What is G0?
When a cell exits the cell cycle at G1, either temporarily or permanently, it is said to be in G0. Many times cells in G0 are terminally differentiated and will not enter cell cycle, while other cells such as lymphocytes will reenter cell cycle upon stimulation (presence of antigen). During G0, genes needed for mitotic division are repressed. Most cancer cells cannot enter G0 and therefore replicate indefinitely.

Thanks for writing that cell cycle post, travelbug. :thumbup: I am going to copy it to the permanent cell bio thread so that it doesn't get buried in here.

Edit: Ok, you got it covered. Thanks again. :)

I've posted this on the Sticky (Biochem Explanations Thread) as well. I don't mean to double post but if somebody is not aware of the sticky, I don't want them to not have access to the post.

Interphase precedes both mitosis and meiosis and is the period between cell divisions during which time the chromosomes replicate and the chromosomes are not visible (loosely packed). During interphase, two pairs of centrioles lie next to each other, just outside the nucleus.

Mitosis is a process where in, one parent cell gives rise to two identical daughter cells. Mitosis can be divided into four stages: Prophase, Metaphase, Anaphase and Telophase.

Prophase: Chromosomes (two identical copies) condense, each chromosome has two arms and each copy of chromosome is called Chromatid. Spindle fibers form at centriole and centriole begin to separate. In addition, nuclear membrane disappears.

A short period just before metaphase, called prometaphase, comprises movement of centrioles to opposite ends of the cell and attachment of spindle fibers to each of the chromatids.

Metaphase: Chromosomes line up along an imaginary line, called the metaphase plate that divides the cell into two. The spindle fibers begin to pull the chromosomes to the opposite ends of the cell.

Anaphase: Spindle fibers separate sister chromatids to opposite ends of the cell.

Telophase: Chromatids, now called chromosomes move to each pole and new nuclear membranes form.

Once mitosis is complete, the rest of the cell divides, by a process called cytokinesis (division of the cytoplasm) and cell division is complete.


Meiosis is a type of cell division that is specific to reproduction and results in 4 daughter cells that have half the number of unidentical chromosomes (genetic information is contained from both parents). Meiosis is divided into two phases: Meiosis I and Meiosis II.

Meiosis I: comprises Prophase I, Metaphase I, Anaphase I and Telophase I

Prophase I: Chromosomes attach to nuclear membrane and pair up with corresponding chromosome (to from a tetrad) from the other parent. Homologous recombination occurs between chromosome pairs and genetic material exchange takes place.

Prometaphase I: Similar to prometaphase I in mitosis except, one chromosome (instead of chromatid) from the homologous pair is attached to each centriole. Therefore, 23 chromosomes (in humans) attach to fibers from one centriole and remaining 23 attach to the fibers from the other centriole.

Metaphase I: Chromosome pairs line up along the metaphase plate on either side.

Anaphase I: Chromosome pairs separate. One half of the chromosomes goes to one pole and the other half to the other pole.

Telophase I: Chromosomes reach opposite ends of the cell and a nuclear membrane forms marking the end of Meiosis I.

There is a major distinction between sperm and egg cells at this stage. While in sperm cells the cytoplasm is equally divided between the two emerging daughter cells, in oocytes, the cytoplasm is concentrated in one of the emerging daughter cells resulting in a large and a small daughter cell called the polar body.

Telophase I is followed by cytokinesis resulting in two daughter cells in case of sperms and one large cell and one small cell (polar body) in the case of the egg (primary oocyte to be precise).


Meiosis II follows a very short Interphase II but chromosome replication does not take place unlike in Mitosis and Meiosis I.

Meiosis II can also be divided into four phases: Prophase II, Metaphase II, Anaphase II and Telophase II. Meiosis II is very similar to Mitosis

Prophase II: Chromosomes condense, spindles form centrioles begin to separate and the nuclear membrane disappears. There is no homologous recombination.

Prometaphase II: Spindle fibers attach to chromatids and centrioles move to opposite ends of cell.

Metaphase II: Chromosomes align along the metaphase plate and fibers begin to pull at the chromosomes.

Anaphase II: Sister chromatids are pulled apart toward opposite ends of the cells.

Telophase II: Chromatids arrive at opposite poles, nuclear membranes form. Again, as in Telophase I, in the female cell, the emerging daughter cells will have unequal distribution of the cytoplasm resulting in one large and another small cell. The resulting large cell becomes the egg or ovum and the smaller cell is called the polar body. The first polar body formed at the end of Meiosis I also divides to form two polar bodies. Therefore, in females, at the end of Meiosis, there is one egg cell and three polar bodies.

Cytokinesis follows Telophase II to mark the completion of cell division.

Main differences between Mitosis and Meiosis I:

Prophase

Mitosis: Chromatids of chromosome begin to separate. There is no exchange of any genetic material
Meiosis I: Pairing of homologous chromosomes, tetrad formation and homologous recombination (exchange of genetic material) take place

Metaphase

Mitosis: Chromosomes line up along metaphase plate
Meiosis I: Chromosome pairs line up along metaphase plate

Anaphase

Mitosis: Sister chromatids pulled to opposite ends of cell
Meiosis I: Separation of chromosome pairs to opposite ends of cell

Telophase and Cytokinesis

Mitosis: Two daughter cells with identical chromosomes and exact number of chromosomes as parent cells
Meiosis I: Two daughter cells with chromosomes from both parents and half the number as parent cells and this is followed by Meiosis II

PS: Opposite ends of cell and opposite poles have been used interchangeably

In the PR sample Bio passages, there is a passage that deals with enzyme substrate interaction. Experiment 1 has no inhibitor and Experiement 2 has a competitive inhibitor. A graph shows reaction velocity vs. substrate concentration for Experiments 1 and 2.

Question: What would happen if the enzyme concentration were NOT kept constant during measurement of reaction velociy as a function of substrate concentration?

A. Vmax would remain constant, but V would change.
B. Vmax would remain constant, but Km would change.
C. Vmax would change, but Km would remain constant.
D. It is not possible to predict what would happen.


The answer is C., but I don't understand how Km remains constant when Vmax changes...

In the PR sample Bio passages, there is a passage that deals with enzyme substrate interaction. Experiment 1 has no inhibitor and Experiement 2 has a competitive inhibitor. A graph shows reaction velocity vs. substrate concentration for Experiments 1 and 2.

Question: What would happen if the enzyme concentration were NOT kept constant during measurement of reaction velociy as a function of substrate concentration?

A. Vmax would remain constant, but V would change.
B. Vmax would remain constant, but Km would change.
C. Vmax would change, but Km would remain constant.
D. It is not possible to predict what would happen.


The answer is C., but I don't understand how Km remains constant when Vmax changes...

Vmax is enzyme concentration-dependent, which is why it changes if you change [E]. But I think you are really asking about the other part, which is why Km remains constant. This happens because Km is equal to the *ratio* of the enzyme-substrate complex's destruction/formation. So adding more enzyme will allow you to make more ES complex, but it will also allow you to destroy more of that ES complex, and the net ratio (Km) will stay the same.

Alternatively, you can consider it this way: Km can also be thought of as the concentration of substrate that results in a speed of 1/2 Vmax. But this is true only if your [E] remains constant. In this case, since you are not changing [S], you will not change Km, even though you are changing Vmax by changing [E].

Incidentally, unless you were given an explanation about all of this in the passage, this level of detail is way beyond what you'd be expected to know for the MCAT.

Vmax is enzyme concentration-dependent, which is why it changes if you change [E]. But I think you are really asking about the other part, which is why Km remains constant. This happens because Km is equal to the *ratio* of the enzyme-substrate complex's destruction/formation. So adding more enzyme will allow you to make more ES complex, but it will also allow you to destroy more of that ES complex, and the net ratio (Km) will stay the same.

Alternatively, you can consider it this way: Km can also be thought of as the concentration of substrate that results in a speed of 1/2 Vmax. But this is true only if your [E] remains constant. In this case, since you are not changing [S], you will not change Km, even though you are changing Vmax by changing [E].

Incidentally, unless you were given an explanation about all of this in the passage, this level of detail is way beyond what you'd be expected to know for the MCAT.


Thanks QofQuimica. Your *ratio* explanation helped me. I was originally thinking that a change in [E], say a reduction in [E], would have the same effect as a non-competitive inhibitor in that both instances would reduce Vmax. But now I see that in the case of the non-competitive inhibitor, the ratio is changed.

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This is from cellular pathway topic...

I just wanted to know why fermentation produces less ATP's (two ATP's per glucose) compared to cellular respiration (which produces 36 total ATP's including 2 from glycolysis). Does this have to do with the fact that, in cellular respiration, electron carriers such as NADH + H & FADH2 get oxidized by the respiratory chain? Also, I don't quiet understand a statement "fermentation is an imcomplete oxidation of glucose." Can someone clarify this? Thanks!

-passion2k7

I just wanted to know why fermentation produces less ATP's (two ATP's per glucose) compared to cellular respiration (which produces 36 total ATP's including 2 from glycolysis). Does this have to do with the fact that, in cellular respiration, electron carriers such as NADH + H & FADH2 get oxidized by the respiratory chain?
Yes. The NADH electrons get "wasted" in anaerobic respiration, but are used in the electron transport chain to produce ATP in aerobic respiration. Fermentation is done only to regenerate the NAD needed to continue with glycolysis. But if you look at where the majority of ATP are produced, they come from the electron transport chain. Thus, if a cell respirates anaerobically, it wastes most of the energy present in the glucose.
Also, I don't quiet understand a statement "fermentation is an imcomplete oxidation of glucose." Can someone clarify this? Thanks!

This is based on the different carbon-based products that are produced from glucose by each pathway. Anaerobic respiration oxidizes glucose up to lactic acid or ethanol. But aerobic respiration ultimately oxidizes all six carbons in the glucose as far as chemically possible, all the way up to carbon dioxide. If you look at the structures of each of these molecules, you will see that carbon dioxide is much more oxidized than either of the anaerobic compounds.

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1. why is dna phosphate group acidic?
Is it the the oxygens pulling all the electrons away?

2. Can someone explain to me how acidic and basic side chains of amino acids vs positive and negative charges and what kind of molecules they react with.

1. why is dna phosphate group acidic?
Is it the the oxygens pulling all the electrons away?

2. Can someone explain to me how acidic and basic side chains of amino acids vs positive and negative charges and what kind of molecules they react with.
See if this helps answer your question: http://forums.studentdoctor.net/showpost.php?p=3359304&postcount=258

I don't understand exactly what you're asking in your second question. Are you asking what the charge is on acidic and basic side chains? Acidic groups will be deprotonated, and therefore negatively charged. Basic groups will be protonated, and therefore positively charged.

are u sure it's the phosphoric acid thats acidic? isnt there only one H+ throughout the chain. Wouldn't the electro negative oxygens make the every phosphate in the esster groups all somewhat positive.

As for the second question, I actually wanted to know more like the isoletric point and so on, and how that relates to charges.

are u sure it's the phosphoric acid thats acidic? isnt there only one H+ throughout the chain. Wouldn't the electro negative oxygens make the every phosphate in the esster groups all somewhat positive.

As for the second question, I actually wanted to know more like the isoletric point and so on, and how that relates to charges.
Are you asking about the individual phosphorus atoms? :confused: Phosphoric acid is the whole *molecule*, not just one atom. The phosphate group *as a whole* is acidic. You are seeing the O's with negative charges because they have been deprotonated. In other words, the pKa of phosphoric acid is lower than 7, so at neutral pH, they will get deprotonated. Remember that the def. of an acid (Bronsted Lowry) is that the compound will donate an H. You are seeing the negatively charged phosphate conjugate bases left behind after the proton transfer has occurred.

An amino acid reaches its isoelectric point when it's a zwitterion. In other words, the amino group will be protonated and the acid group will be deprotonated so that the molecule is not charged overall. This will happen at a different pH for each amino acid, which is how isoelectric focusing (where you subject the aa's to a charge and run them through a gel) works. A few aa's have charged side chains, and they will reach their isoelectric point when they have one positive basic group, one negative acidic group, and the third group (acidic or basic) is neutral.

Ok I understand now. So just to clarify the the phosphate chain originally all contained protons, that dissociated at physiological pH correct? But then are the phosphourus atoms somewhat positive as well or not?

This also helps me a lot about the amino acid questions. So are acidic amino acids negative at physiological pH and bind to positive molecules because the side chain carboxyl group loses deprotonates? and the opposite with basic groups?

The side chains in both single and polypeptides are the only thing that binds to other molecules right as opposed to the amide NH3 and COOH groups?

Ok I understand now. So just to clarify the the phosphate chain originally all contained protons, that dissociated at physiological pH correct?
yes

But then are the phosphourus atoms somewhat positive as well or not?
Yes, the phosphorus atoms will have a partial positive charge on them due to their being bonded to the more electronegative oxygen atoms. There is an inductive withdrawal of electron density from P due to the electronegativity difference.

This also helps me a lot about the amino acid questions. So are acidic amino acids negative at physiological pH and bind to positive molecules because the side chain carboxyl group loses deprotonates? and the opposite with basic groups?
yes

The side chains in both single and polypeptides are the only thing that binds to other molecules right as opposed to the amide NH3 and COOH groups?
That is often true because the amide backbones tend to participate in secondary structure formation. In other words, the amides will hydrogen bond to one another to form alpha helices and beta sheets. There are probably some examples where the backbone also can interact with other molecules though, so I'd hesitate to say "only."

so to be a bother, but back to the positive phosphorus question, would it be acidic? Since the it does get positive, does histidine and other basic amino acid bind to it during regular cell cycles. Also is the basicity of the bases neutralized by the overall phosphoric acidic nature?

hey i need help on something. I am confused about the whole equation:
H+ + HCO3- --> H2CO3 --> H20 + CO2

what happens when there is excess/or not enough H+ or excess CO2 in terms of respiration (hyperventilate, hypoventilate) and in terms of the hemoglobin saturation curve?? i cant seem to get this, please help.

It is my understanding that the Bohr Shift applies to the hemoglobin binding curve and its reaction to varying conditions ie. it shifts right under hot acidic environments and left in cold basic environments.

As you can see from your equation and Le Chatlier's Principle during hyperventilation you breathe off all of your CO2. This causes a shift to the right (in the equation) to make up for the lost CO2 making your blood more basic. In hypoventilation the opposite is happening. You keep the CO2 in your lungs and drive the equilibrium to the left creating more acid (this is why you breathe into a paper bag - to breathe in CO2 and make your blood more acidic to get back to physiological pH.

hey i need help on something. I am confused about the whole equation:
H+ + HCO3- --> H2CO3 --> H20 + CO2

what happens when there is excess/or not enough H+ or excess CO2 in terms of respiration (hyperventilate, hypoventilate) and in terms of the hemoglobin saturation curve?? i cant seem to get this, please help.

Think about the answers to your questions in terms of LeChatlier's principle. In the equation(s) that you wrote above, an excess of H+ will tend to push the reaction to the right. This is one way in which the body deals with acidosis (acidic blood) by forming more H2CO3 from H+ and HCO3-, which subsequently decomposes in the lungs, releasing CO2. Excess CO2 (like in the tissues) would tend to push the reaction to the LEFT. The CO2 will dissolve in the blood as H2CO3 (which may dissociate to H+ and HCO3-).

The Bohr shift is the tendency for Hemoglobin to have a reduced affinity for oxygen at low pH (one cause of low pH could be high CO2, but there are others.) The lower affinity for O2 would cause the hemoglobin saturation curve to shift to the RIGHT.

Does that make sense?

Jota

What is the difference between phase of mitosis and meiosis??? stupid question, but a refresher for me... i know meisosis skips something though

What is the difference between phase of mitosis and meiosis??? stupid question, but a refresher for me... i know meisosis skips something though
Maybe you're thinking that meiosis II does not have a round of DNA replication preceding it like mitosis and meiosis I both do? The phases are the same: prophase, metaphase, anaphase, and telophase. One key difference is that in meiosis I, the chromosomes line up double-file in homologous pairs along the metaphase plate instead of single-file like they do in mitosis and meiosis II.

Maybe you're thinking that meiosis II does not have a round of DNA replication preceding it like mitosis and meiosis I both do? The phases are the same: prophase, metaphase, anaphase, and telophase. One key difference is that in meiosis I, the chromosomes line up double-file in homologous pairs along the metaphase plate instead of single-file like they do in mitosis and meiosis II.

ohhhhhhhhhh now i remember...thanks thanks...yes, metaphase is different in both stages--the answer i was lookin for!!!

Maybe you're thinking that meiosis II does not have a round of DNA replication preceding it like mitosis and meiosis I both do? The phases are the same: prophase, metaphase, anaphase, and telophase. One key difference is that in meiosis I, the chromosomes line up double-file in homologous pairs along the metaphase plate instead of single-file like they do in mitosis and meiosis II.

don't forget there is also crossing over in meiosis between homologous pairs when the chromosomes line up double-file...

hey i need help on something. I am confused about the whole equation:
H+ + HCO3- --> H2CO3 --> H20 + CO2

what happens when there is excess/or not enough H+ or excess CO2 in terms of respiration (hyperventilate, hypoventilate) and in terms of the hemoglobin saturation curve?? i cant seem to get this, please help.

to build on what others have said about the bohr shift... you can also think of H+ in terms of an allosteric regulator of hemoglobin. when there is a lot of H+ around, it binds hemoglobin and decreases its affinity for oxygen. if the affinity for oxygen is decreased, the curve will shift to the right. this means it will take a higher partial pressure of oxygen (more oxygen) in order for Hb to bind it. physiologically, it makes sense. if your muscles are working really hard, they need oxygen, so you don't want the Hb to be bound to oxygen in the muscles, you want it to be released and utilized by the muscles. hope that makes some sense.

I have a question about animal viruses. I know they contain a lipid/protein envelope (similar to a plasma membrane), but does this mean that they lack a capsid that bacteriophages have?

I have a question about animal viruses. I know they contain a lipid/protein envelope (similar to a plasma membrane), but does this mean that they lack a capsid that bacteriophages have?

Viruses accomplish the "capsid" that bacteriophages have by using an envelope. Some families of viruses, have capsids (Bunyavirus, Paramyxovirus) and others do not (Adeno, Picorona). I believe that the capsid of a bacteriophage and the envelope of a virus are analogous in that they both attempt to provide protection from the immune system and also contain binding proteins.

I have a question about animal viruses. I know they contain a lipid/protein envelope (similar to a plasma membrane), but does this mean that they lack a capsid that bacteriophages have?
No, as far as I know, all viruses contain genetic material in the center, surrounded by a protein capsid. Some also have an envelope as well, surrounding the capsid. If any of the biologists know of an exception, please feel free to educate us all. :)

No, as far as I know, all viruses contain genetic material in the center, surrounded by a protein capsid. Some also have an envelope as well, surrounding the capsid. If any of the biologists know of an exception, please feel free to educate us all. :)

As always, Q is correct, unless the OP is thinking of viriods (associated with plant disease). Of course, there are no known human pathogenic viriods. But there is one that resembles a viriod and that is hepatitis delta agent. However, unlike true viriods it is packaged.

What is leakage? it is a heading in the aamc topic headings, but I could not find this anywhere. :confused:

thx

What is leakage? it is a heading in the aamc topic headings, but I could not find this anywhere. :confused:

thx
Please don't start new threads; just post in the appropriate existing question thread.

Genetic leakage is when genes flow from one species to another. This is a concern for things like GM foods or antibiotic resistance, where genes are able to cross species.

WTF is "selected against" and "selected for" nonsense?

"If none of the Xi-bearing genotypes is selected against, then the frequency of Xi is expected to increase to 100%, unless other genes act to suppress expression of e and f."

WTF is "selected against" and "selected for" nonsense?

"If none of the Xi-bearing genotypes is selected against, then the frequency of Xi is expected to increase to 100%, unless other genes act to suppress expression of e and f."
A trait that is "selected against" is one that is unfavorable for reproductive success, while one that is "selected for" allows for greater reproductive success. Probably the most famous example of this is with pepper moths. These moths can be either white or black. Originally, the white moths were most successful, because they could blend in with the bark of trees. In contrast, the black moths were readily eaten because the bird predators could easily see them. So white color was selected for, and black color was selected against. After the industrial revolution, the tree trunks became sooty. Now black moths could hide, while white moths stood out, and their roles reversed; black color became selected for, and white color selected against. Apparently nowadays the white color is again selected for due to anti-pollution laws.

I have some questions about intersitial fluid.

I suppose my first question is: What is interstitial fluid? It was glossed over in EK as "the fluid between cells", but AAMC 9R had about 6 or 7 questions in which I wasn't sure what interstitial fluid was doing, how increasing albumin concentration affected interstitial fluid, how it plays in to the capillaries and tissue (relative pressures), and other such annoyances. What do we have to know about it? I really appreciate any help.

I have some questions about intersitial fluid.

I suppose my first question is: What is interstitial fluid? It was glossed over in EK as "the fluid between cells", but AAMC 9R had about 6 or 7 questions in which I wasn't sure what interstitial fluid was doing, how increasing albumin concentration affected interstitial fluid, how it plays in to the capillaries and tissue (relative pressures), and other such annoyances. What do we have to know about it? I really appreciate any help.
Interstitial fluid is outside of cells, yes, but more importantly, it's outside the blood. It's the liquid in your tissues. Too much interstitial fluid will cause edema (swelling).

You don't need to know very much about interstitial fluid. A lot of questions asking you about how things like the albumin concentration affect the interstitial fluid are really testing you on your understanding of membrane transport (osmosis, diffusion). For example, if the blood albumin level goes down, the blood will not be hypertonic enough to reabsorb enough water from the tissues, and edema will result. If you need to know about the interstitial fluid in more detail, the passage should give you that info.

Interstitial fluid is outside of cells, yes, but more importantly, it's outside the blood. It's the liquid in your tissues. Too much interstitial fluid will cause edema (swelling).

You don't need to know very much about interstitial fluid. A lot of questions asking you about how things like the albumin concentration affect the interstitial fluid are really testing you on your understanding of membrane transport (osmosis, diffusion). For example, if the blood albumin level goes down, the blood will not be hypertonic enough to reabsorb enough water from the tissues, and edema will result. If you need to know about the interstitial fluid in more detail, the passage should give you that info.

Thank you so much! :thumbup:

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:luck: Hi, this might be a basic question, but what does plasma consist of and what's its function? My idea of plasma was a cell present in blood containing blood cells and proteins. What is the exact function of plasma and is it present in all blood (meaning in all blood vessels)? Thanks!!!!

:luck: Hi, this might be a basic question, but what does plasma consist of and what's its function? My idea of plasma was a cell present in blood containing blood cells and proteins. What is the exact function of plasma and is it present in all blood (meaning in all blood vessels)? Thanks!!!!

Hey. Plasma is the liquid portion of blood and is where red blood cells are suspended. The constituents of plasma include: fibrinogen (a clotting factor synthesized by the liver), water, blood proteins like albumin (which maintains oncotic pressure in the blood) and globulins, and inorganic electrolytes. Plasma serves as the medium of transport of a variety of materials like glucose, hormones and lipids. Good luck! :luck:

Hey. Plasma is the liquid portion of blood and is where red blood cells are suspended. The constituents of plasma include: fibrinogen (a clotting factor synthesized by the liver), water, blood proteins like albumin (which maintains oncotic pressure in the blood) and globulins, and inorganic electrolytes. Plasma serves as the medium of transport of a variety of materials like glucose, hormones and lipids. Good luck! :luck:

Hey BioMedEngineer. Thanks again. So plasma is the complete liquid portion of blood.. Is it true that only smooth muscles surround blood vessels? Also, is blood vessel phospholipid bilayer? Thanks!