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20

Well you are assuming one sequenced genome/proteome per NCBI tax id. That is no longer true. So if you click on the proteome filter it decreases by half. Which gets you into the 60,000 range. Now not all of these are "different" conceptual proteins, many are artifacts from the way GenBank/EMBL/DDBJ interact with the TrEMBL section of UniProtKB i.e. they are ...


13

Proteins can move around the membrane. The protein does move: the membrane is a liquid crystal and has fluid behaviour. Specifically this is due to the membrane being in a gel-state. This gel state allows phase behaviour which means that the protein is able to move around on the surface by a similar process. This is often referred to as the fluid mosaic ...


11

The paper's description is poor, but they seem to be describing an encoding where each of 20 possible amino acids are associated with a position within a string of 20 bits, e.g. alanine with offset 0, cysteine with offset 1, etc. With that representation, one amino acid residue within a window is encoded by a string of 20 bits, 19 of them being 0 and the ...


6

Introductory textbooks will not get into the details of the lac operon. Basically, the operon is expressed constitutively at a low level that means that Beta Galactosidase and Lactose Permease are expressed at low levels by the bacterium. This is because it takes a little bit of time to build up the concentration of LacI in the cell before it can start to ...


6

ATP synthase is an enzyme, a molecular motor, and an ion channel all wrapped together in one structure (Fig. 1). It is an enzyme, because it generates ATP. It is a molecular motor, because it the central rotor part turns about 150 times every second during ATP synthesis (Source: MRC mitochondrial Biology Unit). It is an ion channel, because it funnels ...


6

There are two major pathways through which proteins are degraded in your generic cell: In a lysosome or in a proteasome. The Lysosome It's considered an organelle. It has a lipid bilayer that encloses a potent cocktail of acid hydrolases working at a low pH. The pH is maintained by a Cl-/H+ antiporter(Ref). Acid hydrolases that are being processed in the ...


6

Each cell will indeed have the same DNA sequences and ability to produce any given protein. However, there are certain factors (transcription factors) and cellular conditions within a cell that dictate which proteins are produced. If the conditions are right then only certain proteins will be produced depending on what type of cell it is. This process by ...


5

I think you have misunderstood the "inside" part of the "positive-inside rule". Perhaps because "inside" is indeed an imprecise term (but now it is history and cannot be changed ;) ). In order to understand it a bit better it helps to think about the topology of the membrane. During synthesis most membrane proteins (ignoring peroxisomal and mitochondrial ...


5

I see no reason why not. Just to make sure, I decided to test. I ran a search on all human proteins (using the UniProt flat file) for all possible dipeptide combinations of the 20 standard amino acids (selenocysteine is also present in humans but only in 22--or so, depending on how you count them--proteins, so I wouldn't expect all possible sec-containing ...


5

Ribosome doesn't read DNA. Transcription adds several layers of regulation tactics: you can control transcription itself, you can control mRNA. mRNA amplifies genetic information that you need at the moment. Having many copies of a matrix really helps. Archaea have splicing. It's not a good idea to splice your DNA. EDIT per your request of some ...


5

In Kabash and Sander's paper related to DSSP (Biopolymers 1983 vol. 22 (12) pp. 2577-637) the following appears in the abstract: We have developed a set of simple and physically motivated criteria for secondary structure, programmed as a pattern-recognition process of hydrogen-bonded and geometrical features extracted from x-ray coordinates. Cooperative ...


5

There are only 26 letters in the English language, and more than 80% of words are under 10 letters. Yet there are over a million English words. Nonsense words don't count. Now imagine the possibilities of a 20 letter alphabet, where the average "word" length is about 375 letters, and where words of up to 800 letters are possible. And that also does not ...


4

A protein-protein interaction (PPI) binding site is a type of interface. If it has been established that the interface is a PPI binding site, then the terms can from that point forward be used interchangeably. But the word "interface" is very generic and does not have any specific scientific meaning so the nature of the interface must be defined or else the ...


4

With a few exceptions among some bacteria, all species on the planet make protein from the same 21 amino acids, and the relative abundances of amino acids is very similar in proteins from plants, animals, fungi and even prokaryotes. See for example this article (available as PDF here). So protein from pretty much any food provides the same amino acids. The ...


4

It's because E.coli BL21(DE3) are competent cells. The competent is the key here as the cells were chemically treated so the transfection can be performed by heat-shock with high efficiency. This means these bacteria are quite fragile, due to the chemical treatment, and therefore are very sensitive to both mechanical and thermal shocks. Pre-heating the ...


4

Given your background (not a biologist or chemist) you would probably find the introductory material in a biochemistry "lite" textbook more accessible/useful than a hardcore text for specialists. As a co-author of a biochemistry textbook, I can tell you that there are essentially three different classes, or types of texts. Comprehensive textbooks, of ...


4

There are 20+ thousand genes in the genome, but each of these can produce multiple proteins. In addition to this, you have protein fragments and cleavage products further increasing the number of entries.


4

It sounds like you have considered most of the obvious alternatives (and thank you for clarifying the question). I suppose the first question in an alternatively spliced transcript with a retained intron is whether the open reading frame of the protein is maintained. If there is a termination codon that now becomes in-frame due to the intron then the ...


4

Substituting a single amino acid and checking the effect this has on a protein is a method to determine what this specific amino acid does in the protein. For example, substituting an amino acid that is part of the catalytic core would almost always make the protein non-functional. Alanine scanning is a technique that methodically replaces amino acids in a ...


4

Are multi-chain proteins synthesized as one biological unit? Sometimes yes but mostly not. Some proteins are synthesized as one long polypeptide pre-protein which is cleaved by some proteases to yield multiple chains. After cleavage the intramolecular interactions become inter-molecular or inter-chain interactions. Insulin is a good example of this ...


4

When cells run out of amino acids, more and more of their tRNAs remain uncharged. This elevated ratio of uncharged/charged tRNAs trigger complex signalling pathways that control amino acid biosynthesis, general reduction of translation, halting ribosome biosynthesis, autophagy (includes ribophagy - digestion of ribosomes) to recycle cells' components, etc. ...


4

Yes, there are well established methods for synthesizing DNA with any sequence you want. Several commercial companies will accept DNA sequence (a text file) and generate the DNA for you. Genscript for example is well known. Synthesizing the protein can be bit more tricky, depending on what it looks like and what you want it for --- proteins are way more ...


4

Asparagine (Asn) and glutamine (Gln) are derived forms of the amino acids aspartic acid (Asp) and glutamic acid (Glu). Both amino acid pairs (Asn/Asp, Gln/Glu) consist of the same carbon backbone, their side chains only differ in their functional group. Aspartic and glutamic acid include a carboxylic acid (-COOH), whereas asparagine and glutamine are ...


4

The abbreviation Asx (B) is used if it is uncertain whether the amino acid at a given position in a peptide sequence is Asparagine or Aspartate. Similarly, Glx (Z) is used when there is uncertainty between Glutamine / Glutamate. These two pairs of amino acids can be ambiguous in peptide sequences because Asp/Asn and Glu/Gln differs only by a terminal amide ...


4

No, carriers are not the same as pumps. Carriers may or may not carry out active transport and pumps always use energy. Carriers, for example, can make use of the concentration gradient of a certain ion built up by pumps to transport other molecules actively against their gradient. For example, the glucose transporter uses the sodium gradient to transport ...


4

The structural model of a protein is obtained using both experimental data and prior knowledge about geometry of macromolecules. As a structural model is refined, interatomic distances are also restrained. So, the C-N distance isn't really predicted. Alternatively, knowledge about this distance is used to construct reasonable model. In response to the ...


4

Firstly, is important to remember that protein structures are dynamic due to the torsion angles between the N-terminal and C-terminal bonds. There are different conformations to expose different sequences to the outside of the protein to react/catalyze. So there is no one perfect conformation for a protein in a biological system. The best models we have ...


4

Are there any proteins in the body whose surface is hydrophobic? Sure. Although you are right in thinking that most proteins have hydrophilic surfaces, some are very hydrophobic. My favorite example is Elastin, it is the main component of the skin which grants it elasticity. In fact, the hydrophobic nature of elastin is what confers it its function. ...


3

Cooking is just a form of digestion. What is digestion? Digestion is the process of breaking down big molecules into smaller molecules. When you cook food you break down big molecules into its small components. Why do we digest food? Think about a long sequence of DNA for example. You eat corn and you have in your body a long sequence of corn ...


3

This has been studied by some of my labmates in Why is the biological hydrophobicity scale more accurate than earlier experimental hydrophobicity scales? I am not involved in their research, but here is the gist of the paper: Different scales are, as you say, developed based on different criteria. In particular, Eisenberg scale is one of the consensus ...



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