Questions tagged [proteins]

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

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1answer
2k views

How does temperature influence the rate of protein degradation?

For computer modeling purposes, I am looking for some referenced quantitative measurements of the effect(s) of temperature on biochemical reactions. Question In particular, my question is: How does ...
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Can proteins/peptides pass through the intestine?

I've heard somewhere said that : Stomach cells do not absorb anything larger than single amino acids. Is that wrong? How do biological toxins (peptides/proteins) from mushroom or bacteria like ...
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What inactivates pepsin in infants?

In infants, rennin helps in digestion of milk. Pepsin is also present in their stomach. Why do infants need rennin for milk digestion, at the first place? Why does pepsin not act on the milk ...
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Influence of temperature on protein binding and decay rates

For computer modeling purposes, I am looking for some referenced quantitative measurements of the effect(s) of temperature on the dynamic of biochemical reactions. Question In particular, my ...
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2answers
14k 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 ...
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Is there a difference between polarity and hydrophobicity?

From literature the two terms seem to be interchangeable when discussing protein domains and motifs. But biochemically, what are the specific differences between these two terms? For example what is ...
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How do DNA-binding proteins recognize the correct DNA base pairs?

My professor posed this question to the class today - "How do DNA binding proteins specifically bind to base pairs?" He alluded to the different arrangements of hydrogen-bond donor and acceptors in A-...
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Effect of 2,3-bisphophoglycerate (2,3-BPG) on haemoglobin

When 2,3-bisphophoglycerate (2,3-BPG) binds to haemoglobin, a higher partial pressure of oxygen is needed to bring about 50% saturation of with oxygen. What is the physiological significance of this ...
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What role does a protein's size have on protein-protein interactions?

Protein-protein interactions are when two or more proteins bind together, possibly for some important biological function. Recently, I'm starting to look more into proteins, and in particular, ...
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Visual maps of the neuronal membrane

There are lots of visual maps of the brain as a whole, especially the cortex, that show the distribution of "features" over a two-dimensional map, e.g. the Brodman areas (their morphology and their ...
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Why are 3 nucleotides used as codons for amino-acid mapping in DNA?

DNA is made of 4 unique nucleotides. When coding for a protein, a sequence of 3 nucleotides is used to code for each amino acid. Why are codons 3 nucleotides in length? A related question can be ...
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Macromolecule levels in daughter cells after fission

When a prokaryote undergoes binary fission, how are the non-DNA macromolecules distributed between the two daughter cells? This is motivated by comments on a previous question and a G+ discussion. I ...
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Are there any primary structure sequences that strongly suggest b-sheet or alpha helix?

Is there a particular sequence of amino acids that we know will take on a beta-sheet or an alpha helix or is it essentially random?
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How do we know if the folding@home project results are right?

Some of us are involved in the folding@home project, spending time, money, and resources. I would like to know the answer to two main questions: How do we know we fold it right? I mean, these models ...
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What are some examples of genes that code for multiple proteins?

The title pretty much says it all. It is widely taught that a gene in a eukaryotic system could produce more than one protein due to post-transcriptional modification, but I do not believe I have come ...
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How does protein denaturation work?

I was wondering how protein denaturation works. Are there covalent bonds, such as disulfide bridges involved, or is it based purely on non-covalent bonds such as hydrogen bonds? Why is denaturation ...
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Effect of mutation on phenotype

Is there a type of mutation that changes the phenotype of an organism, but not the protein sequence?
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Why are prions in animal diets not destroyed by the digestive system?

According to CBC: Mad cow disease is the common name for a condition known technically as bovine spongiform encephalopathy, or BSE. [...] The only known source of mad cow disease is from animal-...
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Do proteins generally contain phosphorus and sulfur?

I've heard that proteins generally contain six main elements - carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur. I know that proteins are made from amino acids. Amino acids are composed of ...
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Given ATP synthase's structure, how can 3.33 protons ultimately synthesize one and only one ATP?

I am familiar with the structure and function of ATP synthase, but one small detail doesn't seem to make sense. It also happens to be a detail that seems very hard to express. Depending on the ...
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Why and how does uniprot list around 150,000 proteins in the human genome?

Using organism:"Homo sapiens (Human) [9606]" as a query in uniprot returns about 146,000 proteins. I was under the impression that there were only 20-25,000 protein ...
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How many human proteins have a solved 3D structure?

I was wondering how many human proteins have a solved 3D structure. Is there a database with only human proteins? I looked at pdb but couldn't find a filter.
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Can you get enough water by eating only fish?

Scenario: In a boat in the middle of the sea, no freshwater or food stores, no desalination equipment, no rain, but you can catch fish and eat it raw. Can you get enough water this way to survive, let'...
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Why are transmembrane proteins difficult to crystallise?

I know that in vivo there are a lot fewer transmembranous proteins in general, and that they are produced at a lower rate than their free counterparts. This is mainly because transmembrane proteins ...
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Should there be separate Ramachandran plots for an amino acid in different contexts?

I understand the nomenclature of the phi and the psi angles of the alpha-Carbon atoms in protein stucture, but I am confused by the Ramachandran plot. Each alpha-Carbon atom (magenta) makes two ...
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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?
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What can cause the bloating in high protein diet of Whey proteins?

I am thinking what can cause the swelling of gastrointestinal system i.e. bloating after high protein diet of Whey proteins. Liver does breaks those proteins to branched chain amino acids (BCAA), ...
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Recombinant protein fraction in E. coli

If a protein is heterologously expressed in E. coli under the T7 promoter, what fraction of the total protein concentration in the cell is the heterologously expressed protein? What could be its ...
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Lac operon: How can lactose enter the cell in the absence of lactose permease?

My textbook states that lactose permease...transports lactose into the cell and When lactose is added to the growth medium, the lactose molecules bind to the other site on the repressor protein ...
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Turning publicly available genome data into proteins

I'm a computer scientist who is starting to dabble with biology. My eventual goal is to model different kinds of cells with a computer program. As of right now, I'm just trying to take some smaller ...
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Mechanism of Muscle Growth

According to this video (sorry for the poor reference but it represents my level of understanding in physiology), muscle grow as a consequence of repairing micro-lesions. How are these micro-lesions ...
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How can one create images like those in the PDB ‘Molecule of the month’?

I am impressed by the illustrations for the Protein Data Bank ‘Molecule of the month’, e.g. the gorgeous image of DNA Helicase below. Does anyone know how they were made or how one might create ...
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Why does protein folding not depend on the order in which it is synthesized?

I read an article recently, written by researcher from Department of Biochemistry, University of Washington, which stated that: Similarly, success in de novo protein design bears on the question I ...
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How do proteins and genes participate in learning?

I am a computer scientist that studies biology and bioinformatics. In the last weeks, I have been trying to study new research directions, and I would like to deepen my knowledge on the role and ...
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The meaning of the $\alpha$ helix and $\beta$ sheets in proteins [duplicate]

I asked this question to my Biology teacher and he, in collaboration with a Chemistry teacher, couldn't find the answer. My question is the following: "What does the $\alpha$ and $\beta$ represent in ...
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Why cooked food considered nutritious if proteins decompose at much lower temperatures?

Food is cooked/baked at temperatures that are significantly higher than what's considered normal for proteins/amino acids (40°C). Why is it, then, that such food is still considered nutritious ...
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Why do three nucleotides code for one amino acid? Why not 5 nucleotides? [duplicate]

We all know why there are 3-base codons, and why there aren't any 2-base codons. But why is there not a 4-base a 5-base codon?
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Why does it matter to predict protein structure?

And how do you predict it ? What is your input data (sequence of amino acids, temperature, pH, ...) ? Is there a "standardized" input that scientists agree on ? Moreover, I've read that knowing the ...
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Mass Spectrometry (proteomics): How isotopes can be used to to determine charge of the peaks?

I'm trying to understand how isotopes can tell me something about the charge of the different peaks. This pdf file mentioned the following about isotopes in correlation with the charge of the peaks: ...
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Doubts regarding definition of upstream/downstream genes and cognate protein

With respect to the research paper, there are a few things I didn't understand: 1. What is upstream and downstream gene 2. This paper identifies proteins that help in secretion, but does not identify ...
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Protein in fruits

Why do fruits have such a low protein content (with a few exceptions) ? Don't seeds need protein while growing up? In comparison, the egg of a hen contains lots of protein, used to make a chick.
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Can concentration of a protein be determined from a gel quantitatively (rough estimation)?

I've got a His-tagged protein in 6M urea, 500 mM imidazole buffer that needs to be quantified before dialysis to ensure there's enough protein worth dialysing. I ran out of my elution buffer which ...
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What are the various types of protein-protein interactions

I understand there are a number of protein-protein interactions, but what types of interactions exist? and what are the characteristics of them?
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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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Why don't amino acids get linked in the functional groups of acidic and basic amino acids?

There are 'acidic' and 'basic' amino acids like aspartate and histidine. When protein is synthesized with those amino acids, what ensures that the to-be-assembled amino acids will not bond to the ...
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position of cell penetrating peptide

I'd like to add a cell penetrating peptide to my custom peptide (30aa). Can I just add it to the end of the peptide sequence or does it have to be positioned on an outward facing external chain?
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Influence of temperature on transcription, protein binding and decay rates

I am the kind of biologist who doesn't know much about molecular genetics and about the dynamic of biochemical reactions. Question My question concerns the influence of temperature on the dynamic of ...
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1answer
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What buffer should I choose for IEX chromatography for purifying IgY

I will use ion exchange chromatography with an anion exchange column to purify chicken IgY. Prior to this I did dialysis to remove salts from previous purification steps, is it possible after this ...
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Is there an optimal composition and length for protein linkers in FRET?

I'm designing a protein that I'd like to use in FRET reporting. General idea on the shape is: FRETprotein1--Linker--CleavageSite--Linker--FRETprotein2. I would like to know what AA are best for the ...
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Why is Cysteine and Tyrosine used to calculate a sequence isoelectric point?

Why are the amino acids - cysteine and tyrosine used in isoelectric point calculations for a protein sequence, yet neither of them are positively charged molecules? and are not used in net charge ...