What is Protein: Definition and 164 Discussions

Proteins are large biomolecules and macromolecules that are comprised of one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity.
A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides, or sometimes oligopeptides. The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residues in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the genetic code specifies 20 standard amino acids; but in certain organisms the genetic code can include selenocysteine and—in certain archaea—pyrrolysine. Shortly after or even during synthesis, the residues in a protein are often chemically modified by post-translational modification, which alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. Some proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors. Proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes.
Once formed, proteins only exist for a certain period and are then degraded and recycled by the cell's machinery through the process of protein turnover. A protein's lifespan is measured in terms of its half-life and covers a wide range. They can exist for minutes or years with an average lifespan of 1–2 days in mammalian cells. Abnormal or misfolded proteins are degraded more rapidly either due to being targeted for destruction or due to being unstable.
Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and participate in virtually every process within cells. Many proteins are enzymes that catalyse biochemical reactions and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape. Other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. In animals, proteins are needed in the diet to provide the essential amino acids that cannot be synthesized. Digestion breaks the proteins down for use in the metabolism.
Proteins may be purified from other cellular components using a variety of techniques such as ultracentrifugation, precipitation, electrophoresis, and chromatography; the advent of genetic engineering has made possible a number of methods to facilitate purification. Methods commonly used to study protein structure and function include immunohistochemistry, site-directed mutagenesis, X-ray crystallography, nuclear magnetic resonance and mass spectrometry.

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  1. S

    Biology Is a smeared band on a Western Blot a valid result?

    From this result, the conclusion is that MDCK-siNGT and MDCK-siB4Gal4 resulted in less keratin sulfate, while MDCK-RCA did not produce keratin sulfate at all. Looking at the gel, the band look very smeared, as if nothing was purified prior to blotting. I have noticed a similar looking gel in...
  2. user366312

    How can I compute energy from a protein PDB file?

    Suppose I have a protein PDB file and want to compute energy using the following formula from the coordinates in that file. How can I do that? Sometimes people suggest using the `CONECT` field for that purpose. However, some PDB files do not have this field. Example: 4OSK.pdb (Crystal...
  3. M

    Unimaginable Numbers: What is 1.36 x 10^495 times 20 Million?

    Kurzesagt in a Nutshell said that the number of possible protein combinations the human body can have is 6.8 x 10^495. I asked GPT to multiple it by 20 million (which is the hypothetical number of possible alien civilizations in the Milky Way galaxy give or take). The chatbot gave me 1.36 x...
  4. .Scott

    AlphaFold Catalogues 200 Million Protein Fold Predictions

    In their (AlphaFold) words: The value of this as a news story is directly proportional to the accuracy of the predictions. The AlphaFold Database includes information about their confidence for each protein segment, but I have not found an overall quantitativ assessment of its accuracy.
  5. A

    SARS CoV-2 link to Parkinson's, N protein α-synuclein interaction

    While researching S protein interactions I stumbled across a couple of recent papers studying the increased risk of developing Parkinson's after a Covid infection and the possible mechanism that plays a role there. https://pubmed.ncbi.nlm.nih.gov/34860005/ here is the full version of the study...
  6. A

    Spike protein level in blood, vaccinated vs. infected study

    So I'll try to be brief. There is a recent study that is titled "Immune imprinting, breadth of variant recognition, and germinal center response in human SARS-CoV-2 infection and vaccination" https://www.sciencedirect.com/science/article/pii/S0092867422000769 Among other stuff it has measured...
  7. jim mcnamara

    Exploring the Protein Diversity of 4n Wheat: A Global View of Pasta-Making

    @Bystander @fresh_42 pasta is normally made from tetraploid wheat ( 4n = 4 sets of chromosomes, humans are diploid with 2 sets. ) Semolina and durum are names you will encounter for 4n wheat cultivars. 6n (hexaploid) wheat is so-called bread wheat or sometimes modern wheat. 4n wheat crops...
  8. A

    COVID Spike protein stability, effects etc

    Before I say something I want to kindly ask any possible participants to refrain from attacking the personal symptom explanation as untrustworthy or made up as some have done before in another thread. Although I will express my personal side in the thread as such, I am looking for answers from...
  9. EFech

    How Do Configurational and Conformational Entropy Differ in Protein Folding?

    I have been reading about protein thermodynamics and found different types and models for entropy calculation before and after protein folding. I understand Vibrational, conformational, configurational entropy are some of the most studied "types" of protein folding entropy. My questions is...
  10. BWV

    AI-Powered AlphaFold 2: Revolutionizing Protein Folding

    This is cool - AI is the future of biology, humans just arent smart enough https://deepmind.com/research/case-studies/alphafold https://predictioncenter.org/casp14/doc/presentations/2020_12_01_TS_predictor_AlphaFold2.pdf Deepmind trained on 100K proteins and is now in the second iteration of...
  11. S

    Question about antibody affinity chromatography

    I am learning about protein purification in my Biochemistry class, and I have a question about protein elution in antibody affinity chromatography. My understanding of the mechanism for the technique is that proteins that do not bind to the antibody will be separated first as it runs down the...
  12. epenguin

    Protein folding AI: "Will Change Everything"

    Google’s deep-learning program for determining the 3D shapes of proteins stands to transform biology, say scientists...
  13. docnet

    Asking questions about protein structure determination

    Hi, I tend to write down questions/thoughts that come to me as I read articles that are interestsing. I'm reading the intro to solution state NMR in a biophysics textbook. Any there any purely theoretical approaches to determine protein structure / dynamics ? The 1 dimensional digital code...
  14. littledog

    The meaning of protein phosphorylation to bioscience?

    Many researchers have mentioned in their researches that protein phosphorylation take a decisive position to regulate various physiological activity, from prokaryote to eukaryote. So did anyone has taken the research on control the protein phosphorylation in wildtype microorganisms with...
  15. allisrelative

    Scientists Claim to Have Found The First Known Alien Protein

    I think this is important not just for the extraterrestrial part but it can help explain how life starts on planets through Panspermia. https://www.sciencealert.com/scientists-claim-to-have-found-the-first-known-extraterrestrial-protein-in-a-meteorite This could really be groundbreaking. If...
  16. TytoAlba95

    Biology MCQ- Insertion of a protein into a liposome membrane

    Please give me clues as to how to solve this question. The answer provided is (c).
  17. TytoAlba95

    Biology MCQ-Effect of a scaffolding protein on Signaling

    My understanding: A) As in RTK signalling in which Raf-MEK-ERK are bound to KSR, they are close enough and in proper orientations to transduce the signal faster than when they are not in a complex. So A is correct. B) Correct. Because to cross-link with other signalling pathways the kinases have...
  18. M

    What does HC3 mean in 'His HC3'?

    My lecturer said it means: "3rd residue, C-terminal to Helix 'H'" but that makes no sense. If it's the 3rd residue then it can't be on the C-terminal, because the C-terminal is at the end of a massively long sequence of residues. Visa versa if it's on the C-terminal then it can't be the 3rd...
  19. .Scott

    Harvard Team Discovers 'Hemolithin' Protein Series on Asteroid

    A Harvard teams believe they have found a protein series they call "Hemolithin" in an asteroid. Isotopes and other evidence indicates that it is not from a terrestrial source."Astrobiology Web" link arxiv pdf link
  20. jim mcnamara

    Protein nanowires + Geobacter + humidty = electric potential

    https://phys.org/news/2020-02-green-technology-electricity-thin-air.html I am not competent to judge this (what seems very edgy to me) article. Basically it says: a ten micron thick protein layer with Geobacter on the surface and protein nanowires arranged in a mesh, when exposed to...
  21. hagopbul

    COVID About the protein shape of Covid-19

    hello i came across an old article about crystalline shape of AEC2 receptor that is been some how associated with covid-19 my question dose knowing the crystalline profile of protein receptors some how can help with finding a better aid against this kind of outbreaks and how crystalline...
  22. TytoAlba95

    Biology Solubility of protein in supernatant

    Answer: (d) My understanding: 1. At pH 6.4 i.e. less than 6.5, protonation or deprotonation will just begin (if we imagine that we are adding an acid to the protein soln), so not many protein molecules will be there in the supernatant 2. Glycerol interacts through H-bond with surface polar...
  23. cobalt124

    Protein Folding and NP-Completeness

    I'm looking to understand how protein folding has been shown to be NP-complete, but from the computational side rather than the biological side (if this is possible). Is there an analogous NP-complete problem that is similar? I read that self avoiding random walks might have something to do with...
  24. Igor 77

    A Radioisotope-induced radioactivity in a protein molecule

    Dear Forum Members, I am a molecular biologist. One of my projects is focused on the identification of a protein that interacts with a known organic molecule. Namely, I try to chase a transmembrane protein that is known to transport one organic acid. If possible, I would like to get an idea on...
  25. Eagle9

    Inverted Protein: Does Sequence Matter?

    Good day! :oldsmile: Imagine the mRNA with some nucleotide sequence that (after translation) will give us such polypeptide chain: L-Alanine (first, in the beginning of translation) - L-Arginine - L-Asparagine - L-Aspartic acid - L-Cysteine - L-Glutamic acid - L-Glutamine - Glycine (last, in...
  26. I

    Different folding options for a protein?

    Hello, I was wondering whether one same protein can assume different foldings that can do different functions in the organism? (each folding still having the usual active/inactive state) And if the is a specific example for this? Many thanks for any thoughts!
  27. Joppy

    MHB Surface of protein channel in membranes

    Do we know roughly what the surface of a protein channel looks like? In most of the diagrams they are depicted as a sort of cylindrical tube with a smooth surface, but I'm curious if there are some more detailed documentations somewhere? For example I know they aren't rigid objects and may be...
  28. I

    Different lengths of genes expressed

    I was wondering whether it can ever happen that only a certain "length" of the same gene gets expressed in different species? Or perhaps even within the same species? (Without it being a random mutation) Basically, can a part of a gene be expressed, and still have some functionality in the...
  29. BillTre

    Brave New World of Protein Design

    Here is an NY Times article by Carl Zimmer, describing recent advances in predicting protein design. This involves going from an amino acid sequence to a predict a protein 3D structure or going from what you want in a protein to the amino acid sequence that can generate it. This has long been...
  30. Greg Bernhardt

    Life’s First Molecule Was Protein, Not RNA

  31. P

    Protein melt temp/half life relation?

    Is anyone familiar with a way to determine the half-life of a protein from its melt temperature (Tm)? It seems like there ought to be some sort of correlation, be it theoretical or empirical.
  32. B

    Other So I have three weeks to learn about protein dynamics

    Hello there, Situation I got a research position at my university in studying amyloidogenic proteins, which are associated with many different neuro-degenerative diseases. The professor has a NovoControl Dielectric Spectrometer in the lab, which will be the main equipment used to gather data...
  33. N

    Chemistry Estimating number of amino acids with protein molecular mass

    Homework Statement Suppose you were told you had a protein with molecular mass of 65,000 g/mol. Show how you would estimate the number of amino acids present in this protein. Keep in mind that you cannot calculate the exact number, the point of this is to approximate how many amino acids are...
  34. mktsgm

    Medical Are there any other Macronutrients?

    I have a few questions on energy from foods. Do we have any other macronutrients that contribute energy to the body other than carbohydrates, proteins and fats in our body? What is the role of Hydrochloric acid (HCL) in our stomach? Is the HCL involved in all three above macronutrient digestion?
  35. S

    Ionic bond strength in protein folding?

    Our text says that ionic bonds are much weaker in aqueous solutions than covalent bonds, due to the dissociative properties of most ionic compounds in water. I read elsewhere though, that in general, ionic bonds are stronger due to the increased polarity. So, in protein folding, when different...
  36. I

    What is the term for a gene and its corresponding protein?

    Hello again! Is there a common word/term for a gene and the protein that it codes for? I know there is signal transduction, but that would be for a whole set of genes and proteins doing a stream of functions. But would there be a name for the specific gene/protein "bundle"?
  37. C

    Other Statistical Physics and Biology

    I'm undergrad physics student and I have read some statistical physics like equilibrium statistical physics, Langevin model and Fokker-Planck equation. I have developed interest in application of statistical physics in biology like protein folding. So what are the other research topics that lie...
  38. I

    Proteins that duplicate the DNA in interphase

    For some reason, I can't seem to be able to find this answer easily on the internet. Or it is there and I somehow I can't see the wood for the trees. I know that in transcription (when DNA is read for protein production), "RNA polymerase" is the protein that creates the mRNA by creating the new...
  39. A

    2 Biochemistry MC Questions - Protein Structure, Enzymes

    1. A substrate molecule may be bound to the active site of an enzyme by all of the following EXCEPT A. Hydrogen Bonds B. Peptide Bonds C. Ionic Bonds D. Van der Waals Interactions E. Hydrophobic Interactions 2. Which of the following components is the most important in determining the 3-D...
  40. jdawg

    Lab Report: Significance of Protein Tests

    Homework Statement Hi! So I'm trying to write a lab report about testing BSA solutions for protein concentrations using a Biuret reagent and a spectrophotometer. There is a portion that asks you to give some practical applications for this test and how it applies to biology. The only thing I...
  41. I

    How many times does an average protein fold?

    Does anyone know how many times would an average protein fold in its lifetime? And how long do proteins live on average? Also, another quick question, somewhat related, any knowledge on how many "cascades" of different proteins making a conformational change on different new proteins can there...
  42. I

    Do Genes Code for Specific Types of Cells?

    My understanding is that genes code for proteins that then do a certain function. Apart from mitosis in an organism, I heard that cells (in forms of stem cells) are also produced and released into the body. I guess these would be all the floating around the body cells? Or the nerve cells that...
  43. nisler.1

    Trying to run QM/MM simulation with calcium binding protein

    Hello everyone, I'm a graduate student in a biophysics lab. I'm trying to run a QM/MM simulation with a protein that binds 3 Ca2+ ions, and as such I am having a devil of a time getting the SCF to converge. I've tried DIIS, KDIIS, damping, and a few other methods to try to get convergence with...
  44. Doktor Mabuse

    Temperature at which pea protein is destroyed?

    I am taking a protein supplement that has far too much sodium in it. If I took the amount I need every day, I would far surpass the safe upper limit of daily sodium intake. I had the idea of dissolving the pea protein powder in water, filtering out the sodium, and then evaporating the water...
  45. F

    Are Amino Acids and Proteins the Same Thing?

    I got a question, consuming amino acid and consuming protein is the same thing right? Protein is a chain of amino acids but it does not really change their properties by becoming protein right?
  46. I

    What happens to a protein built from mutated RNA?

    I was wondering if anyone knew what happens to a protein that gets wrongly assembled due to a mutated RNA? Does it just do a slightly different or very destructive action in the organism, or does the organism catch it and kick it out? Also an extra side question: Speaking of mutations of RNA...
  47. I

    Genes and protein they code size relation?

    If the gene is smaller, is the protein that it codes for smaller too? Vice versa?
  48. R

    Biology Point mutation, change in rna and protein

    Homework Statement UV Rays is said to induce point mutations which get incorporated during the DNA replication process. These mutations are corrected by the excision repair mechanism of the DNA polymerase but sometimes they might be left out. In one of such cases, point insertions were...
  49. G

    Methods of Regulating Proteins

    I have been looking into different methods of regulating protein activity for a project. I think it is pretty interesting and I want to learn more about this. I want to learn about the different methods out there, if you know of any cool or helpful regulation techniques I would certainly...
  50. T

    Centripetal acceleration in separating protein

    Homework Statement Two protein having same density 1.35 g /cm^3 but with different diameter 4nm and 5nm. They are mixed at the top of a centrifuge tube that is of length 1cm. What is the centripetal acceleration needed to separate them before they move to the end of the tube? Homework...