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14

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 ...


7

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

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 ...


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

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

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

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

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

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. The ...


4

Yes, there are certain amino acid sequences that tend to form alpha-helices, and others that prefer to form beta-sheets. There is no perfect correspondence between sequence and structure, but there is a statistical relation where presence of certain amino acids in particular sequences makes one conformation or the other more likely. For example, alanine, ...


4

2-mercaptoethanol (2ME) reduces the disulphide bonds in proteins. If disulphide bonds are connecting two polypeptide chains ("intermolecular") then 2ME would cause them to separate and therefore instead of a higher molecular weight (MW) band you would get one or more lower MW bands. However, if there are disulphide bonds in the same polypeptide chain, they ...


4

I used to work for a company well-known for its modification state-specific antibodies, including phospho-specific ones, and they actually performed extensive in-house testing of PBST vs. TBST in Western blotting. Part of the reason the company chose to recommend the use of Tris-buffered saline over phosphate-buffered saline based buffers was the clearly-...


4

Ar means aromatic and + means positively charged residues. However, this is not a standard code (as of now). From the same paper: Sequences closely matching these optimal binding motifs, R-X-[Ar/S]-[+]-pS-[LEAM]-P and R-[S/Ar]-[+]-pS-[LEAM]-P, denoted as mode 1 and mode 2 consensus sequences, were found to be present in many known 14-3-3 ligands ( Yaffe ...


3

BACKGROUND We should first understand what activation energy really is and what does Arrhenius equation mean. For any chemical reaction to happen you need to break some existing bonds in order to form new bonds. Breaking existing bonds consumes some energy; in other words you have to convert the reactant to an active form which undergoes a reaction readily. ...


3

There are different kinds of DNA binding domains; the ones involved in base identification in the major groove can differentiate between different base pairs of the same nucleotides i.e. AT vs TA because they bind to functional groups on a nucleotide and not the base-pair per se. The stereochemistry i.e. which nucleotide is in the major groove, is important. ...


3

TLDR; Answer: You could consider this particular residue to belong to both structural elements, but it's a tricky call and depends on the method of secondary structure assignment. Ambiguous secondary structure allocation comes up fairly often. Whilst obviously, not many people will be able to use this protein specifically, the below approach could be ...


3

The term isoform has become a little ambiguous over the years (see http://blogs.cornell.edu/collinslab/2012/05/30/protein-isoform/)... still some things are consistent: In some genetics literature 'isoform' has been used in the place of allele when talking about the allele states at a locus for a gene Typically a gene isoform is equivalent an alternate ...


3

Proteins often undergo conformational changes. The activation energy required to undergo a conformational change in a protein with only covalent interactions would be much higher compared to that of a protein with weaker bonding forces. An example of a conformational change seen in enzymes is the change in conformation during allosteric regulation, in which ...



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