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

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19 views

Why are the hydrogen bonds between the backbones not straight down in a parallel B-sheet?

I am not sure why the hydrogen bond patterns in a parallel beta sheet are not straight down and why they are offset by about ~0.5 Angstroms. Is there any significance to this difference?
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0answers
26 views

How does a human body differentiate between fat vs protein vs carbohydrates vs sugar? [on hold]

I would like to know how the human body differentiate between fat vs protein vs carbohydrates vs sugar. In a simple sentence, how does our body know if a food is protein, carbohydrate, fat or sugar. ...
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1answer
40 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 ...
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1answer
12 views

is a-keratin a fully functional protein?

is a-keratin before it coils with another polypeptide, makes chains, and build intermediate fillaments a fully functioal protein? I mean, is the single monomer of a-keratin a protein or it has to ...
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0answers
16 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 ...
0
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1answer
16 views

What's a good reference for learning about recombinant proteins?

I'm looking for books and articles that can bring me up to speed on the design, expression, and purification of mammalian proteins in recombinant systems, both in E. coli and in more complex systems ...
4
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5answers
110 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 (...
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1answer
54 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?
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1answer
47 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.
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2answers
53 views

Molecular animations of, say, protein synthesis, are simplified, but how exactly?

In several animations of biological processes (eg protein synthesis (go to frame 1.20mins), DNA replication, etc), molecules such as amino acids are shown heading straight to the replicating protein ...
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0answers
17 views

Proline flexibility

I was reading about the role of proline-rich domains in proteins. There seem to be two schools of thought. One is that proline has 2 degrees of freedom instead of 4, making it more rigid. This makes ...
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0answers
17 views

How did self-replicating molecules distinguish between regular nucleic acid and the first codons?

I've read that the first protein synthesis has likely included translation by readily formed tRNA-like adapters. The other alternative is that primordial 'mRNA's didn't need adapters and instead ...
1
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1answer
16 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
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1answer
20 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 ...
0
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0answers
7 views

False positives in TAP - MS experiments

Is anyone aware of a website where they show common false positives often found when doing a TAP-MS experiment to find protein-protein interaction experiments? Particularly the Acs1 protein (Acetyl-...
0
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0answers
14 views

Removing signal peptide enough to prevent protein from going to membrane?

I am trying to perform a yeast two hybrid and one of my proteins of interest has a single peptide and several transmembrane domains. Now for the yeast two hybrid it is of course better that the ...
2
votes
1answer
38 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
159 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 ...
2
votes
1answer
61 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
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2answers
57 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
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0answers
52 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 ...
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0answers
11 views

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

how long do chaperone proteins take to fold a protein?
2
votes
1answer
22 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
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0answers
28 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 ...
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2answers
919 views

Is Tyrosine considered hydrophobic or hydrophilic?

I’ve seen Tyrosine classified as a hydrophobic amino acid due to its benzene ring in some textbooks and as hydrophilic due to its hydroxyl group in other textbooks. How does Tyrosine actually ...
2
votes
1answer
28 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
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4answers
94 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 ...
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1answer
30 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. ...
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votes
1answer
12 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 ...
3
votes
2answers
345 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 ...
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votes
1answer
30 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 ...
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0answers
32 views

How to calculate the amount of protein synthesized knowing the amount of essential amino acids ingested?

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
30 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
66 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 ...
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0answers
21 views

Can a frameshift mutation into the open reading frame not affect the stop codon?

I'm having trouble understanding a practice test question that is as follows: https://imgur.com/a/AeXPK#yXx9W8G So they insert a nucleotide to the mRNA of an open reading frame (so it starts with ...
1
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0answers
12 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 ...
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0answers
60 views

How to characterize stability of a protein from Trp fluorescence vs [denaturant] curves?

A colleague of mine has taken Trp fluorescence measurements from a dimer in combination with various ligands, over a range of denaturant concentrations. The idea is that ligands which bind more ...
3
votes
2answers
43 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 ...
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1answer
109 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
38 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 ...
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1answer
36 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
40 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: ...
1
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1answer
46 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-...
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0answers
15 views

Which among the seven secretion systems in gram-negative bacteria are pathogenic?

Among the 7 secretion systems of a gram-negative bacteria, do all the systems secrete pathogenic proteins that harm the host into which the protein is secreted? Or is it the type 3, type 4 and type 6 ...
1
vote
1answer
28 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 ...
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votes
1answer
39 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 ...
8
votes
4answers
964 views

What is the difference between a protein and a factor?

In terms of nomenclature/semantics, why are some proteins named proteins, and some named factors? I've been revising on eukaryotic DNA, and I've come across some proteins that seem to serve roughly ...
3
votes
2answers
325 views

What is C-terminal tryptic peptide?

A biologist wrote to me: ... C- or N-terminus,... For example, a C-terminal tryptic peptide like AGWRGSDSHSR, would be... I don't have any idea what that is. When ...
2
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2answers
53 views

Ribosomes producing proteins, but need proteins to be produced?

So according to my textbook: RNA is used to create ribosomal RNA (known as rRNA) which is then combined with proteins to form the ribomsomes necessary for protein synthesis. I'm a bit confused ...
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1answer
23 views

Is it possible to induce protein activation via frequency-specific mechanical waves? [closed]

Would it be possible to induce shape changes in specific proteins by providing specific frequencies of mechanical waves in a thermostatically controlled environment such that those proteins may be ...