Biochemistry

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simsimjoey
Posts: 9
Joined: Wed Nov 22, 2017 9:59 am

Biochemistry

Post by simsimjoey » Wed Dec 13, 2017 1:06 pm

Hi,

I haven't taken biochemistry before so I'm struggling a bit understanding the materials on the review book.

Amino Acid

- I don't understand how pka and pH could be compared?
- Finding the charge of histidine in different pH seems to need knowledge of pKa values in order to solve them. Would they be given in the test?
- amino acids, do we have to memorize even the abbv and symbols?

Lipid

- It is mentioned that glycolipid forms the basis of ABO blood typing. Does this mean the ABO antigens on erythrocytes are glycolipids?
- correct me if I'm wrong, but i think you've mentioned on the content videos that glycoproteins are responsible for cell-signaling, which is sphingolipids do as well. What is exactly cell signaling?

Thnx in advance!
NS_Tutor_Sophia
Posts: 28
Joined: Tue Aug 01, 2017 11:49 am

Re: Biochemistry

Post by NS_Tutor_Sophia » Wed Dec 13, 2017 2:14 pm

Hi simsimjoey,

The relationship between pKa and pH is described by the Henderson-Hasselbalch equation: pH = pKa + log [base]/[acid]. Specifically, the pKa describes the pH at the half-equivalence point.

To determine the charge of histidine or most amino acids at a given pH with complete certainty, you would need to be provided its pKa values, which you would almost certainly be provided on Test Day along with most other constants. However, you can often make predictions at pH extremes.

You may be required to recognize 3-letter or 1-letter abbrevations for amino acids, so I definitely recommend familiarizing yourself with those.

Interestingly, ABO antigens are both glycoproteins and glycolipids, so you may see them described either way, though you don't need to know their structural details.

Cell signaling describes the processes by which external signals (which can include proteins, hormones, foreign particles, etc.) initiate a signaling cascade inside the cell. Often it involves a cell surface receptor that activates secondary messengers in the cell which amplify the signal and cause downstream mediators to effect some sort of intracellular change (such as regulating gene expression or protein synthesis or cell division).Of course there are many different examples of cell signaling, but this is a common example.

Great questions! We will be holding Chemistry Office Hours this Sunday (12/17) at 3-5 pm Eastern and Open Q&A Office Hours next Tuesday (12/19) at 5-7 pm Eastern, so you are more than welcome to join if you would like an even more in-depth review of biochemistry.
Sophia Stone
PCAT Content Manager
Next Step Test Prep
simsimjoey
Posts: 9
Joined: Wed Nov 22, 2017 9:59 am

Re: Biochemistry

Post by simsimjoey » Thu Dec 14, 2017 12:59 am

Hi, thank you for the explanation.

Correct me if I'm wrong, so one of the functions that glycoproteins and sphingolipids have is cell-signaling.

Does this mean glycoproteins and sphingolipids can both be cell surface receptors...?
If yes, how can sphingolipids act as receptors if there are protein compartments? Isn't it only protein that can recognize ligands?
Is it safe to think glycoprotein = gpcr?
NS_Tutor_Sophia
Posts: 28
Joined: Tue Aug 01, 2017 11:49 am

Re: Biochemistry

Post by NS_Tutor_Sophia » Thu Dec 14, 2017 10:09 am

Your questions show that you're definitely thinking about this at a deep level! Cell signaling is one of the most confusing topics in molecular biology as it's so broad (SO many aspects of cellular biology can contribute to cell signaling) with a lot of moving parts (what's a GPCR? what does cAMP do?), and in fact there's a lot we still don't know that remains elusive to scientists. On Test Day, you'll be responsible for understanding the fundamental features of cell signaling at a topical level. In other words: some sort of stimulus or ligand activates a receptor, which activates some other intracellular molecule, which then activates 10 other intracellular molecules, which then activate 1000 other intracellular molecules, and eventually this accomplishes some downstream effect, whether that be initiating cell division or transcribing genes for glucose metabolism, or mobilizing proteins for immune defense.

To answer your questions, receptors will almost always be proteins, at least for the purposes of the PCAT. "Receptor" is really just a term that means something that receives a signal (the "ligand"). This protein might be decorated with carbohydrates (glycoprotein) or be covalently linked to lipids (lipoprotein). Most commonly it will be found on the extracellular surface of a cell as a cell surface receptor, but there are also intracellular receptors that bind hormones that diffuse straight through the cell membrane (estrogen receptor is a good example of this).

Glycoproteins and sphingolipids can both absolutely be involved in cell signaling. Some cell surface receptors definitely include glycoproteins, but my understanding of the subject with regard to sphingolipids is that recent research has shown sphingolipids to contribute to cell signaling either extracellularly as a ligand that binds cell surface receptors or intracellularly as a secondary messenger that amplifies the initial signal, but not really as a cell surface receptor (as far as I know). That said, this is far beyond the scope of the PCAT. You can certainly read more on the subject in articles like this one: http://www.jbc.org/content/291/21/11460.full

Glycoproteins and G protein-coupled receptors are two categories of types of proteins. Glycoproteins are any protein with attached carbohydrate groups, so as you can imagine this class is pretty broad. GPCRs on the other hand are transmembrane proteins (in fact they have SEVEN transmembrane domains!) that are linked to an intracellular G protein that initiates a cell signaling cascade. It's possible there could be some overlap between the two if some GPCRs are in fact glycoproteins, but most are not.
Sophia Stone
PCAT Content Manager
Next Step Test Prep
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