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3

Entropy is a measure for the number of states accessible to a system. The more states available, the higher the entropy. If you think of an atom confined in a volume V, then, without further restrictions, the atom can be anywhere inside that volume, i.e. the number of states will be a function of the volume V. The bigger the volume, the bigger the entropy. ...


3

Ahh entropy. The bane of many undergraduates. You won't need a lot of mathematical rigor needed to solve for absolute entropies in most biological fields so it's best to think of it abstractly. Consider the atom. What can it do? Well if you remember from chemistry class, it can bounce around a process we call translate, and the electrons can basically ...


2

As this table shows, the more complex a molecule is (in general) the more entropy it has. Entropy is an absolute quantity which is zero at $0^o K.$ When an atom or molecule has no way to rotate (is 'frozen') there is only one state in which it can exist. An atom of a gas or a molecule of a diatomic gas at $25^oC$ is also somewhat constrained compared to a ...


1

It seems to me that you're asking about homology modelling. In that case, yes you need to compare your protein of interest to a protein (or proteins) of known structure. Homology modelling in a nutshell includes three (four?) steps: template identification/template alignment, modelling, quality assessment. You start with finding a template for your ...


2

Why bother predicting proteins badly from DNA sequence when you could have just as well downloaded the manually curated human proteome? As to your questions: Are you asking about human genomes or genomes in general? The vast majority of the variance in human genomes is in non-coding sequence. As to genomes in general, they vary in pretty much every ...


7

No, your approach will not work, you are taking a very simplistic view of an extremely complex system. Some of the problems you are ignoring are: Genes (eukaryotic genes anyway) are spliced to produce mRNA, a process that removes introns and leaves only the exons. If you just translate the entire chromosome file you will get noise. Splicing also changes ...


1

Your problem will finally boil down to searching your sequence in the Blast databases. Performing Blast seems to be probably the best way to find out if your bacteria has that specific protein expressed or not. If you could not find it in the nearest species using Blast, then try running PSI-BLAST, which would return you distant homologs, by which you can ...


3

The condensation is not done in water alone - the enzymatic function of the ribosome plays the essential part here. And in the active center of the ribosome where the formation of the peptide bond takes place, no water is present, only the growing peptide chain and the single amino acid (bound to the tRNA). See this schematic image from the Wikipedia: If ...


3

You are correct, the 368 stands for the position of the amino acid in the protein's sequence - this particular serine is the 368th residue in the protein counting from the amino-terminal end.


7

Those (really cool) pictures are created by David Goodsell using custom-written software. From an interview to the artist: PDB: How do you create the illustrations? Goodsell: Most of the pictures are created with a computer program that I developed back when I was doing postdoctoral work with Dr. Art Olson here at The Scripps Research Institute. ...


1

As others have said, although certain amino acid substitutions are considered to be conservative, the effect of a particular substitution will very much depend upon the context. Here are some examples: gly>ala can change stability of glyceraldehyde-3-phosphate dehydrogenase gly>ala mutations in a fungal glucoamylase increase thermostability asp>glu in a ...


3

There are twenty standard amino acids, and some of them are structurally/functionally similar to each other, such as aspartate and glutamate, or asparagine and glutamine, or glycine and alanine. In general, mutations that cause these amino acid switches don't change the function of the protein, but that's just a general rule - it also depends on where these ...


-1

I think the term you are looking for is Single Nucleotide Polymorphism (SNPs). This is when there is a change in a single nucleotide of a gene thus altering its expression. When there is no particular change in the organism from the mutation, it is called a silent mutation. One famous example of SNP is sickle cell anaemia where a change (A to T) of the ...


1

I think you are referring to the concept of conserved substitution, which tends not to change the property/function (http://en.wikipedia.org/wiki/Sequence_alignment) of a protein although thats not necessarily true if the mutated AA (point mutation) changes a functional residue in an enzymatic domain such as GAP or kinase domains or even certain residues ...


5

This question is based upon a wrong inference about the work that forms the basis of the National Geographic article, which includes this statement: All species in all three domains share 23 universal proteins, though the proteins' DNA sequences—instructions written in the As, Cs, Gs, and Ts of DNA bases—differ slightly among the three domains (quick ...



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