What is Proteins: Definition and 77 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. nomadreid

    Distribution of amino acids in different proteins

    In https://en.wikipedia.org/wiki/Selenocysteine , I read: "As of 2021, 136 human proteins (in 37 families) are known to contain selenocysteine (selenoproteins)." This seems to indicate (my knowledge of biochemistry being close to zero) that this amino acid is not found throughout the human...
  2. mktsgm

    What is the role of insulin other than translocating GLUT-4 proteins?

    Insulin's role in glucose metabolism by translocating GLUT-4 proteins into the plasma membrane (thereby regulating the uptake of glucose), in the adipose and skeletal muscle cells, is rather well known. And in the liver, insulin aids to regulate gluconeogenesis and promoting glycogen synthesis...
  3. user366312

    How can I calculate hydrogen bonds in a specific direction w.r.t. a C-

    I need to calculate H-bonds in a specific direction of a C-alpha atom of a protein. And, I need to calculate that from a PDB file. Can anyone give me a general guideline/direction/idea regarding how to do that? N.B. I need to write a python program.
  4. P

    RNA coding sequence for proteins

    Simplistic Example Given - DNA - RNA AATGTA codes for a protein. 1. Does the inverse ATGTAA usually/ever code for a protein? 2. Does the reciprocal RNA TTACAT usually/ever code for a protein?
  5. Zohar

    How many proteins are coded by mitochondrial DNA compared to nuclear DNA?

    The mitochondria has DNA code which being translated to protein in a certain amount. So how many proteins are from the mitochondria compared to the nuclues?
  6. BillTre

    Preserved Dinosaur Cartilage: Proteins, Chromosomes and DNA Markers

    I found this article on https://www.researchgate.net/publication/339566392_Evidence_of_proteins_chromosomes_and_chemical_markers_of_DNA_in_exceptionally_preserved_dinosaur_cartilage. The reference is: Alida M. Bailleul, Wenxia Zheng, John R. Horner , Brian K. Hall, Casey M. Holliday and Mary H...
  7. TytoAlba95

    Do ESCs produce a large array of proteins?

    'Analyses of global histone modification patterns in ESCs have previously suggested that the ESC genome is subject to generalized histone acetylation and lysine 4 H3 methylation (H3K4me). As these are both transcription-activating modifications, these changes in global genomic architecture and...
  8. BillTre

    Ancient Jaw Found in Tibetan Cave Identified as Denisovan by Proteins

    Previously, Denisovans have been identified by their DNA sequence but since the DNA only came from a small distal pinky bone and teeth, their appearance was largely unknown. Science news article here. However DNA is not well preserved in many environments, so many potential fossils can not be...
  9. Navin

    What is the structural level of fibrous proteins: secondary or tertiary?

    My question is if fibrous proteins posess secandory or if they posess tertiary structure There is a fiery debate between me and one smart dude from my class.I believe(firmly) that proteins posess secandory structure while he is of that school of thought that believes fibrous proteins have a...
  10. Navin

    Origin Story Of The First Proteins

    Now i had a question,but before that look at this. Now by the central dogma DNA is transcribed by RNA polymerase onto mRNA and this leads to translation which creates Protiens. But hold on...The polymerase itself is an enzyme ie ;a protein . So to make proteins...you need proteins aldredy...
  11. Wrichik Basu

    Neutrophil nanosponges soak up proteins, reducing arthritis

    Have a look at the article here. From the article: Transmission electron microscopy of neutrophil nanosponges. Credit: Qiangzhe Zhang/Nature Nanotechnology
  12. mktsgm

    Can proteins and fats undergo fermentation like carbohydrates?

    Fermentation can be defined as the chemical conversion of carbohydrates into alcohols or acids. Here sugar is the main substrate which is converted to alcohol. Can such a process happen in proteins and fats also?
  13. T

    How does pH affect secondary structure of proteins?

    I understand that pH affect the tertiary structure as it will change the ionic interactions between the COO- and NH3+ groups, however, as the secondary structure is caused by hydrogen bonds, how does pH affect it? Is it because the change in tertiary structure will alter the shape of the protein...
  14. KenJackson

    How Can the Complex Evolution of Proteins Be Explained by Mathematical Theories?

    Our bodies are made up of tens of thousands of proteins, each of which is a long precise sequence of amino acid molecules ("residues"). Evolution requires them to be "formed by numerous, successive, slight modifications." Does this mean the code for one of the twenty residues was added...
  15. KenJackson

    Have Any New Proteins Evolved in Animals Over the Last 1000 Years?

    Are there any proteins in any animals that are known to have completed their evolution in the last 1000 years? That is, are there any proteins that exist today that did NOT exist a millenia ago? If yes, are the mutation paths known for their origins?
  16. T

    What are some fertilizin and antifertilizin proteins?

    What are the fertilizin and antifertilizin proteins found in Human beings (and Sea urchins)? Thoughts: Is bindin an antifertilizin in Arbacia sp? And ZP3 a fertilizin in Human beings?
  17. I

    Why proteins and DNA aren't organelles?

    Hi, when I look up organelles listed, DNA and proteins are not in that list. How come? Aren't they "specialized subunit within a cell that have specific functions" too? Then I see ribosome made it to the list. Why is that protein more special than others? Why not put RNA Polymerase in there...
  18. 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...
  19. Neha98

    Medical DNA Codes: Examining How Proteins Differ Between Males & Females

    All of human beings receive half of their genetic material from one of the 2 parents and this genetic material has DNA codes which are transcribed into RNA and then start coding for proteins such as hormones. But hormones for example differ from one to another; for example females secrete high...
  20. 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...
  21. Priyadarshini

    Heat Shock Proteins & Protein Folding: How HSP Helps

    I was watching a video in which they said that HSP is produced to help proteins fold correctly and to prevent them from tangling up and misfolding. But, if the cell is producing another protein, wouldn't the chances of tangling up and misfolding increase (because now you have one extra protein...
  22. I

    Methionine and cysteine influence on proteins?

    Hello, I was just wondering what are the distinct features that methionine and cysteine add to proteins when they happen to be in them, as opposed to proteins that contain only non-sulfur-containing amino acids? I am especially if they create unique conformations for the proteins, that other...
  23. I

    Are chemical messages between proteins intermolecular forces

    This question might be a stretch, but I was just reading about inter- and intra-molecular forces. And I found that "Intermolecular forces (IMFs) are forces of attraction or repulsion which act between neighboring particles (atoms, molecules, or ions)"...
  24. Superposed_Cat

    How did the first dna produce proteins?

    Hey all, i get how evolution applies to things using DNA and reproduction, and i get the RNA world hypothesis, but what i don't understand is how the first DNA actually manged to produce the proteins that would later develop into cells without the surrounding machinery to process it, second...
  25. Logic Cloud

    Activation and deactivation of proteins

    I have come to understand that phosphorylation plays a significant role in the (de)activation of certain proteins. I'm now trying to understand this mechanisms in more detail. Specifically, how the addition of a phosphate group can regulate protein activity. Can anyone point me to a source where...
  26. R

    Are there two or three types of membrane proteins?

    Most sources I've read state that there are two types of membrane proteins: integral and peripheral. However, my lecturer has been saying there is a third type: lipid anchoring. Doing a search online, I've found many sources say that there are only two types, whilst others say there are three...
  27. 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...
  28. R

    What websites can tell me which proteins are found in crop

    There are 20 amino acids and 4 are essential. You can lookup the nutrition facts of anything on google and get results. What I don't like is that google does not tell me which proteins are found in these foods, it just tells you how many grams of anything the food contains.
  29. R

    Are Globular proteins red blood cells?

    So globular just means spherical, are globular proteins just red blood cells; then all red blood cells are considered globular proteins. Are all enzymes in the blood red blood cells? Are all red blood cells enzymes? What else in the blood is spherical? What is in the blood other than...
  30. R

    Why can proteins be considered as bionanomachines when

    ... something else (?) does the work. For example: For translocation the protein get unfolded and refolded when it gets to the other side of the membrane, but shouldn't the thing doing the work be considered the "machine". In our class the title was "The role of proteins as 'machines' in...
  31. R

    Extremophiles, how to relate to their (?) proteins?

    We have briefly being introduced to extremophiles in class in our lectures on proteins and I'm struggling to relate the two. For example say if you had an organism living in a high temperature environment what would be different about it's (?) proteins. Does that question even make sense? I'm...
  32. miles johnstone

    Basics for: Carbohydrates, Proteins, Amino Acids and Lipids

    I have been trying to get my head around the basics for these four (Carbohydrates, Proteins, Amino Acids and Lipids) for about a week and I just don't understand the basic structure, formulas and such. Help?!
  33. mark!

    Protein Competition in Our Body: Do They Compete?

    Are proteins in our body competition with each other? It is known that bacteria in our intestines compete, but regarding proteins I only found here: "RNA transcripts, both protein-coding and non-coding, thus have the ability to compete for microRNA binding and co-regulate each other in complex...
  34. R

    Molecular sensing fluorescent proteins and FRET pairs

    Hope this is in the right place, apologies if not. We have studied green flourescent protein GFP and others (RFP, CFP etc) as a means of analysing an organism / sample, you need two that have unique fluorophores. We have also studied the use of FRET pairs such as florecein-florescien or...
  35. L

    Resolving proteins with UV microscope

    Homework Statement Your molecular biology lab studies proteins, and you're frustrated because your microscopes can't quite resolve crystallized proteins. A sales rep touts the advantages of an expensive microscope using 200-nm ultraviolet light, saying you'll be able to resolve structures less...
  36. L

    Side chains numeration of proteins (example Cytochrome C)

    Hi everybody, I hope I'm in the right forum. I have a question concerning the side chain numeration. I was reading the following paper http://www.ncbi.nlm.nih.gov/pubmed/22927377 and they used the some of the following names for the side chains: M65, H33 etc. What does that mean...
  37. T

    How do proteins get into the blood stream?

    Hi there, So I'm asking this in reference to the injection of insulin, which is commonly done subcutaneously (in the hypodermis, a fatty part of skin). Now I know proteins usually get into the blood when digested through the stomach/intestines - but I was wondering how they manage to get into...
  38. O

    Exploring Protein Entropy: The Curious Case of Collagen Binding to Bone

    When collagen binds to bone, the entropy of the system increases. Why does the entropy not decrease, since it seems more logical that the entropy decreases since it seems to become more ordered?
  39. Gliese123

    Will all proteins fall apart by exaggerated heat?

    Like the topic; if you boil proteins (or vitamines for that matter), will the molecular structure break? For example warm milk etc.
  40. P

    Building a quantum computer from living parts (FMO proteins)

    The most serious challenge to engineering a quantum computer is protecting it from decoherence. But FMO proteins in photosynthetic complexes can exhibit entanglement for a few picoseconds as reported here and here, among other places. So would it be possible to build a working, useful quantum...
  41. M

    What is the relationship between cloudiness and coagulation in proteins?

    Coagulation of Proteins -- please help We have a report tomorrow about this and I am not so sure of my results: (coagulation by heat) Milk - no cloudy appearance, soluble in water Egg white - with cloudy appearance, insoluble in water Flour - no cloudy appearance, slightly soluble I...
  42. B

    How do superparamagnetic micro-beads attract proteins in immunoprecipitation?

    Immunoprecipitation is a technique used to separate proteins from organic samples for investigation. Initially, rough and porous sepharose and agarose polymers were utilized to isolate proteins and they used adhesion to their rough surfaces, gaps and hollow spaces inside them to capture the...
  43. U

    Quantum Coherence in Transmembrane Proteins?

    I am presently in a Biophysics lab, and am formulating a project wrt transmembrane protein association in lipid bilayers (based on the 4 stage model of membrane protein folding, i.e. partitioning, folding, insertion, association). I was wondering if anyone on here has heard of any decent...
  44. H

    Exploring Mutations in Enolase Gene Expression: A Western Blot Analysis

    Hello Forum, please have a look at this image http://imageshack.us/photo/my-images/98/0bigg.jpg/ There are two proteins A and B in the right column. Marker B is the protein´s length of healthy people. But as you can see there are two different markers for this protein (the western...
  45. J

    Identifying proteins by structure

    Identifying proteins by structure Can proteins be identified by their structural image alone? What do i mean by that? Well i understand the basics of protein folding and protein structure. I have a basic understanding of primary, secondary and tertiary structure of DNA/RNA. But i want to...
  46. K

    IHC detection of proteins in mitochondrial matrix

    I'm specifically wondering: Can proteins in the mitochondrial matrix be detected by immunohistochemistry? I am familiar with the general techniques required for IHC, and I believe the procedures vary depending on what you're looking for. I do think that IHC can stain within the mito-matrix...
  47. C

    Chemistry Molecular Biology (Molecular Chaperone Proteins)

    The study of viral particles has revealed significant information regarding protein folding. Many proteins hae been shown to often spontaneously fold into their functional structures and give an active viral particle. Yet some are incapable of proper folding on their own. It was shown in 1973...
  48. L

    Synthesis of proteins in Euk. cells

    Homework Statement I'm a little confused as to how the nucleolus in a eukaryotic cell manages to synthesize proteins. For example, in the nucleolus, does it contain DNA that it uses to synthesize ribosomal RNA, which then synthesizes ribosomal subunits? Then the ribosomal subunits go out into...
  49. E

    Wilson's Heart: amantadine binds to proteins in the kidney

    I was watching the Last episode of House for season 4 a few months back, where Amber receives damage to her kidneys making them unable to adequately filter out amantadine she took for a flu. They put her on dialysis and had her cryogenically frozen in an attempt to buy them more time for a...