Questions tagged [proteins]

Biopolymers consisting of amino acids that fold into 3D shapes and perform a large number of functions in living organisms.

Filter by
Sorted by
Tagged with
2
votes
1answer
32 views

Fluorescent protein tags and colocalisation

We want study if 2 proteins A and B are co-located, for that we use 2 FTP(Fluorescent tag proteins) for each protein?and after the expirement these 2 FTP are co-located. Does that mean necessarily ...
3
votes
1answer
275 views

Why do bacteria need messenger RNA?

Why do bacteria need mRNA? Isn't the DNA free floating without nuclear membrane so why doesn't the tRNA read the code directly off of the split DNA strands? (ofcourse after helicase splits them). ...
1
vote
1answer
29 views

How many different chains exist within a specific pdb file?

More specifically, if we want to understand the different chains within a protein, is it enough to look at the fourth column of all the lines that start with "ATOM" in a pdb file, and see how many ...
6
votes
1answer
5k views

Is ATP Synthase a channel or an enzymatic protein?

Today in a biology lecture about plasma membranes and functions of proteins, we learned about channel and enzymatic proteins along other kinds of proteins. ATP synthase is considered an enzyme that ...
3
votes
2answers
97 views

Can a bacterium survive without GroEL protein?

In prokaryotes, GroEL protein (together with GroES) is required for protein folding. Question: Can a bacterium survive without GroEL protein?
0
votes
1answer
61 views

Homology modelling of protein with two identical subunits in its quaternary structure

I am using homology modelling to assign the 3D structure of Torpedo acetylcholine receptor (Unwin 2004, 2bg9 in RCSB) to human muscle nAChR. The problem is, both Torpedo receptor, and human receptor ...
4
votes
5answers
386 views

Why analyse transcriptome instead of proteome?

Analysing the transcriptome (RNA-Seq, microarrays, qPCR etc) is probably the most widely used technology to assess gene expression and dynamic cellular processes. The results are then extrapolated (...
1
vote
0answers
79 views

Tensile strength of collagen?

Really specific question, but what is the average tensile strength of human collagen, type I? I've tried looking for it online, and either my google-fu skills are weak, or I'm just unlucky. Also, is ...
1
vote
1answer
545 views

What does 'half life' of a protein mean?

Why do we use the term 'half life' for proteins? Here is a link to some information regarding this question, but I am unable to infer it.
-2
votes
1answer
113 views

Why do ADULTS need protein in their diet, if they are not growing? [duplicate]

Why do ADULTS need protein in their diet, assuming they are not growing? What happens to the amino acids already present in the body? Why don't our bodies conserve them?
2
votes
2answers
516 views

Coordinates of amino acids in a protein sequence

In PDB format, the coordinates of each of the atoms are available. Are the coordinates for the amino acids available separately? As in say a protein sequence consisting of a chain of amino acids MKL......
4
votes
2answers
422 views

Betaine HCl stomach pH

It seems betaine HCL is often recommended for those suffering from "low stomach acid" -- which, as I understand, is having too high stomach pH for proper digestion (especially for proteolysis via ...
6
votes
1answer
75 views

For Penicillin Binding Proteins, why is the enzyme-peptide complex less stable than the enzyme-β-lactam complex?

I'm trying to figure this out. I cannot find any publications that go into good detail about the chemistry of PBP inhibition by β-lactam antibiotics. PBPs cross-link adjacent pentapeptides to form ...
1
vote
1answer
151 views

Glucose Carrier Proteins in Cell Membranes

I'm using Campbell's Biology textbook, and it states that certain carrier proteins transport glucose across the cell membrane much faster than would occur normally. It states that the "glucose ...
0
votes
1answer
88 views

What is the difference between spidroin-1 and spidroin-2?

So I'm doing a research project for my school and I'm trying to decide on the exact nature of the project. My current plan is to try to genetically engineer E. coli or Yeast to produce spider silk ...
3
votes
1answer
2k views

Why does BLAST reduce word size for short proteins?

I'm using BLAST to identify a short protein (BLASTp). If I check the short query then the word size reduces from 3 to 2. However the search will then be less ...
2
votes
1answer
75 views

When in Ampicillin degraded (gone) in liquid TB-media? Concerns about selectivity

Question: Specifically regarding Ampicillin; When growing cells in TB (terrific broth) for protein expression - when should I expect the ampicillin to be gone due to degradation by b-lactamases? (and ...
2
votes
3answers
717 views

Can the central dogma work in reverse?

Theoretically, is it possible to obtain the original gene from the protein’s amino acid sequence as its “template”, as in, the reverse of how gene’s codons were “templates” for the amino acid sequence ...
4
votes
3answers
6k views

Do the enzymes and compounds in saliva help with stain removal?

Does spitting on stains help with removal? Saliva is high in amylase that should help with the breakdown of protein rich stains like blood and semen. It also contains antimicrobial enzymes and ...
2
votes
1answer
81 views

What proportion of proteins require chaperone-assisted folding?

I am new to the field of biochemistry (I am a chemist, actually). I have long known the process of folding as the process that leads to the minimum energy conformation of a protein. Now, I am ...
2
votes
2answers
99 views

What is protein secondary structure?

Could someone please clarify what is protein secondary structure: https://en.wikipedia.org/wiki/Protein_secondary_structure I believe I understand the primary structure, I am not sure what's the ...
1
vote
0answers
424 views

Are microtubules in centrioles helical, like they are when in isolation?

Microtubules tend to be of a helical structure, do microtubules in centrioles also have a helical structure? The centriole is composed of nine circularly arranged triplet microtubules, one complete ...
1
vote
0answers
12 views

how long do chaperone proteins take to fold a protein? [closed]

how long do chaperone proteins take to fold a protein?
8
votes
3answers
3k views

Why don't membrane proteins move?

I understand that based on their tertiary structure, intrinsic proteins have hydrophobic non-polar R-groups on their surface and that they 'interact with the hydrophobic core of the cell membrane to ...
2
votes
1answer
28 views

Will the interaction of two proteins vary across different tissues? [closed]

Suppose protein A and B is both abundant in tissue X an tissue Y. Will A and B interact in X but not interact in Y? I guess A and B could be biomarkers of a certain disease, and in the pathological ...
2
votes
0answers
44 views

How are animal patterns encoded in the dna?

After seeing the patterns on the feathers of a argusianus argus pheasant (shown below), I am curious where is the information that encodes a pattern for a particular bird, and what form is this ...
21
votes
2answers
11k views

Do all proteins start with methionine?

Start codon AUG also codes for methionine and without start codon translation does not happen. And even the ambiguous codon GUG codes for methionine when it is first. So does this mean that all ...
2
votes
1answer
50 views

How do metal ions acting as enzyme cofactors “find” their respective enzymes?

Metalloproteins are metal-dependent proteins, i.e. they require certain metal ions (copper, magnesium, zinc, etc.) for their correct function in the body. Since proteins are manufactured inside cells ...
5
votes
4answers
188 views

Program (on Mac) to show 3D protein structures?

I have an assignment for 6th grade biology. I have to look at a 3D structure of a protein and manipulate it so it only shows the AA I’m interested in currently. what I already did I already looked up ...
1
vote
1answer
37 views

Is there a notion of RMSD for two different molecules?

The (least) Root Mean Square Deviation is used for comparing different conformations of the same molecule. However one may be interested in comparing the conformations of two different molecules e.g. ...
-1
votes
1answer
19 views

How does chemical shift assignment from NMR spectroscopy is translated to three dimensional structure of protein?

I am currently involved in determination of protein structure using NMR spectroscopy. As part of structure determination I have finished the chemical shift assignment. The chemical shift information ...
7
votes
3answers
1k views

What has caused life to choose this unfathomably tiny subset of all possible proteins?

I wonder why life uses the particular proteins that it does, about 10^6 different proteins, I think? Evolution cannot explain it because the number of possible proteins is far far too large to ever ...
0
votes
1answer
43 views

Can proteins structure change depending of alimentation of an organism? [closed]

In my understanding protein are built using information caring by RNA. So a given protein should always have the same structure in a given organism has the DNA of this organism does not change. I'm ...
3
votes
2answers
4k views

Why is pepsin able to operate at low pH?

Pepsin is a protease that operates in the acid pH of the stomach. Many proteins are denatured at low pH, and most enzymes — whether or not they denature — require a higher pH for activity. Why is ...
-1
votes
1answer
38 views

How to estimate the amount of protein that are going to be synthesized?

I'm studying protein synthesis to understand how the body use the different amino acids to build proteins. In particular I would like to learn how to (roughly) calculate the total amount of protein ...
3
votes
0answers
56 views

How can I differentiate between polysaccharide bands and protein bands on SDS-PAGE? [closed]

I tried to extract bacterial polysaccharide but after running a SDS-PAGE I couldn't differentiate between the polysaccharide band and protein ones. I face a problem of moving up of the samples from ...
1
vote
2answers
75 views

mRNA and Protein relation [closed]

A and B are two different proteins: 1- can they have same mrna 2- is it possible that the gene types which encoding the synthase are same ? my answer is yes to both . because after protein synthased ...
1
vote
0answers
49 views

What prevents a density gradient made of sucrose from mixing through diffusion?

Based on what I've read, density gradients are used to facilitate separation in ultracentrifugation and prevent convective mixing of the molecular species from different locations in the gradient. But ...
3
votes
2answers
96 views

NAG, FUC molecules in PDB files

In some proteins (such as 4ZXB, 6CE9 which are respectively apo and halo forms of insulin receptors), I see ligands such as FUC (ALPHA-L-FUCOSE) and NAG(N-Acetylglucosamine). No matter which paper I ...
1
vote
1answer
43 views

What are the types of interactions in biological network (protein networks)?

In the KGML files, the types of relations between genes or proteins are precisely activation, inhibition, expression, repression, indirect effect, state change, binding/association, dissociation, ...
2
votes
1answer
214 views

How is the urea cycle regulated with respect to protein deficit?

Proteins cannot be stored in the body. Excess proteins from the diet are deaminated in the urea cycle that takes place in the liver. The liver is the first contact since these amino acids are ...
1
vote
1answer
2k views

What is the difference between Integrin to Cadherin?

My question is probably very basic but i couldnt get it in lecture and not from looking in the net. What is the difference between Integrin to Cadherin. By difference I am looking for say: ...
2
votes
1answer
91 views

Can two proteins have equal primary structure but different secondary structure?

I've been reading lately about primary (which I understand completely) and secondary (which I do not understand that well since I'm not very good at chemistry) structure of proteins. My question is: ...
4
votes
2answers
31k views

Importance of Double Helix DNA Structure

Gene expression involves transcribing only one strand of DNA molecule. So i was wondering what are some biological advantages of the double stranded DNA?
1
vote
1answer
71 views

Is protein folding symmetric with respect to reversing the sequence order?

Suppose that I have two proteins, protein A and protein B, and suppose that the sequence of amino acids of protein B is exactly the reverse of the sequence of protein A. For example (these are made-...
2
votes
1answer
196 views

How can carnitine enter the mitochondrial matrix without OCTN2?

Some people have defects on the gene SLC22A5, giving them problems with their OCTN2 transport protein (Organic cation transport). OCTN2 transports carnitine into the mitochondial matrix where it can ...
11
votes
4answers
62k views

Differences Between Protein Motifs and Protein Domains?

I am in a 300-level molecular biology class and am unclear about this concept and how to delineate motifs versus domains of proteins. Any suggestions would be much obliged.
1
vote
1answer
112 views

Could the protein dystrophin be artificially synthesised?

Could the protein dystrophin be artificially synthesised and if so could patients with DMD (Duchenne Muscular Dystrophy) benefit from it? //Now I don't have much scientific background other than a ...
1
vote
1answer
36 views

gel band contrast

Is there any way to increase the contrast of my SDS PAGE gel. I want to increase the coomassie stained gel contrast of my gel bands a little bit as it looks little less for my thesis. Ive heard that ...
-1
votes
1answer
85 views

Where different types of proteins can be found in food?

According to https://www.youtube.com/watch?v=KSKPgaSGSYA (created by one of the largest supermarket chains in the UK), different proteins have different roles in human body: (Group 1) They’re like ...