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    I don't understand protein synthesis and my textbook doesn't make sense as it presents things in such a jumbled order that I can't piece it together.


    - RNA polymerase synthesises a template in 5'->3' direction starting at AUG. My textbook says there's RNA polymerase I, II and III but I'm not sure what they each do
    - I'm not sure of what mRNA, tRNA and rRNA do? I don't know whether mRNA is microRNA or messenger RNA as my book mentions both. Is mRNA basically the same as the non-template strand of DNA except there is Uracil instead of Thymine or are there other structural differences? Then mRNA goes to the ribosomes and amino acids attached to tRNA molecules bond to the mRNA by complementary base pairing? But I thought polypeptides are just long chains so do they detach from mRNA
    - I don't know how splicing works. I get that snRNPs are involved but I can't visualise how it works
    - Is it correct to say that tRNA 'find' AA (?) in the cytoplasm, bind to them and then the tRNA's anticodon binds to the codon on the mRNA
    - I don't understand this sentence: "Ribosomes exist as seperate large and small subunits. The first step in translation involves the binding of the small ribosomal subunit to the mRNA" I thought ribosomes were just where translation occurred? I don't undestand what the subunits are and why they are binding to mRNA.

    I also don't understand Seymour Benzer's work with E-coli and the T4 phage.

    Sorry for all the questions but my textbook is not very helpful and I can't find much stuff on the internet.

    Thank you.
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    All RNA polymerases work with a similar mechanism - the difference is the type of RNA they make. Polymerase I makes rRNAs (ribosomal RNAs), polymerase II makes mRNAs (messenger) and polymerase III makes some rRNA, some tRNA, sRNA and everything else.

    mRNA is messenger RNA. This is the one ribosomes bind to and move along in order to create a polypeptide chain. On a chemical level, it is basically a copy of the non-template DNA with U instead of T, but on a structural level mRNA can fold up into loops and various other structures by base pairing with itself. (Btw, microRNA would be abbreviated to "miRNA".)
    tRNA is transfer RNA, it binds to amino acids inside the "amino acid pool" in the cell, and brings them to the ribosome bound to mRNA to allow protein synthesis. The order in which amino acids are linked together depends on base pairing between tRNA and mRNA (different tRNAs with different anti-codons bind to different amino acids). At the end of protein synthesis, proteins called "release factors" will come along and mediate release of the ribosome, mRNA and polypeptide.
    rRNA is ribosomal RNA, which are RNAs that make up the ribosome.

    If you type "splicing" into Google images, literally the first image that comes up shows the chemical side of it quite well (in terms of the branch point A attacking the 5' splice site, formation of the lariat etc.). snRNPs bind to different parts of the intron in order to mediate this reaction, and also to bring both ends of the intron together - remember, introns can be really long.

    There is actually a separate enzyme called "tRNA synthetase" that is involved in attaching the correct amino acid to the correct tRNA. And yes, the anticodon interacts with the codon through base pairing.

    Ribosomes bind to mRNA and tRNA. The first step involves the ribosome attaching to the mRNA and positioning the codon at a specific site, to which the correct tRNA + amino acid also binds. Once the correct tRNA is in place, the ribosome moves one codon along, and the next tRNA and amino acid will bind. The ribosome also catalyses peptide bond formation between amino acids. Old tRNAs are released as the ribosome moves and new ones carrying new amino acids come in. As for the subunits, in bacteria for example you have a 70S ribosome, which is made up of 30S and 50S (I don't actually know why 30 + 50 = 70). These are usually floating around separated in the cytoplasm. When translation starts, the two subunits will come together to form an active ribosome.

    - I don't understand this sentence: "Ribosomes exist as seperate large and small subunits. The first step in translation involves the binding of the small ribosomal subunit to the mRNA" I thought ribosomes were just where translation occurred? I don't undestand what the subunits are and why they are binding to mRNA.

    You'll have to be a little more specific about Benzer's stuff. He did a lot of work on E.coli and T4.

    I've also tried to keep the explanations brief because I don't know how much you've been taught, so let me know if you want anything elaborated on.

    Edit: Which textbooks are you using?
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    (Original post by LeaX)
    - I don't understand this sentence: "Ribosomes exist as seperate large and small subunits. The first step in translation involves the binding of the small ribosomal subunit to the mRNA" I thought ribosomes were just where translation occurred? I don't undestand what the subunits are and why they are binding to mRNA,
    I think the problem is you are thinking of ribosomes as being organelles similar to mitochondria, ER or whatever. This is kind of how we were taught when they were introduced in school, so it's not surprising.

    In actual fact ribosomes are just proteins, so they should be thought of in the same way as any other heteromeric protein complex, and one of the subunits binds to mRNA. In bound form it is now considered rRNA.

    It's awkward because it kind of doesn't make sense to draw ribosomes as organelles in school unless you're also going to draw proteasome complexes, G proteins, and whatever else. But it also doesn't make sense to not draw them and have no explanation for where proteins are synthesised, so A level and GCSE biology teachers are stuck a bit between a rock and a hard place.

    I hope this helps, I'm going a little out on a limb about how you were taught and what your problem might be. Let me know if it is or isn't helpful.
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    (Original post by kanra)
    All RNA polymerases work with a similar mechanism - the difference is the type of RNA they make. Polymerase I makes rRNAs (ribosomal RNAs), polymerase II makes mRNAs (messenger) and polymerase III makes some rRNA, some tRNA, sRNA and everything else.

    mRNA is messenger RNA. This is the one ribosomes bind to and move along in order to create a polypeptide chain. On a chemical level, it is basically a copy of the non-template DNA with U instead of T, but on a structural level mRNA can fold up into loops and various other structures by base pairing with itself. (Btw, microRNA would be abbreviated to "miRNA".)
    tRNA is transfer RNA, it binds to amino acids inside the "amino acid pool" in the cell, and brings them to the ribosome bound to mRNA to allow protein synthesis. The order in which amino acids are linked together depends on base pairing between tRNA and mRNA (different tRNAs with different anti-codons bind to different amino acids). At the end of protein synthesis, proteins called "release factors" will come along and mediate release of the ribosome, mRNA and polypeptide.
    rRNA is ribosomal RNA, which are RNAs that make up the ribosome.

    If you type "splicing" into Google images, literally the first image that comes up shows the chemical side of it quite well (in terms of the branch point A attacking the 5' splice site, formation of the lariat etc.). snRNPs bind to different parts of the intron in order to mediate this reaction, and also to bring both ends of the intron together - remember, introns can be really long.

    There is actually a separate enzyme called "tRNA synthetase" that is involved in attaching the correct amino acid to the correct tRNA. And yes, the anticodon interacts with the codon through base pairing.

    Ribosomes bind to mRNA and tRNA. The first step involves the ribosome attaching to the mRNA and positioning the codon at a specific site, to which the correct tRNA + amino acid also binds. Once the correct tRNA is in place, the ribosome moves one codon along, and the next tRNA and amino acid will bind. The ribosome also catalyses peptide bond formation between amino acids. Old tRNAs are released as the ribosome moves and new ones carrying new amino acids come in. As for the subunits, in bacteria for example you have a 70S ribosome, which is made up of 30S and 50S (I don't actually know why 30 + 50 = 70). These are usually floating around separated in the cytoplasm. When translation starts, the two subunits will come together to form an active ribosome.

    - I don't understand this sentence: "Ribosomes exist as seperate large and small subunits. The first step in translation involves the binding of the small ribosomal subunit to the mRNA" I thought ribosomes were just where translation occurred? I don't undestand what the subunits are and why they are binding to mRNA.

    You'll have to be a little more specific about Benzer's stuff. He did a lot of work on E.coli and T4.

    I've also tried to keep the explanations brief because I don't know how much you've been taught, so let me know if you want anything elaborated on.

    Edit: Which textbooks are you using?
    Thank you so much, that was soo helpful. The textbook I'm using is Bios Instant Notes Genetics by Hugh Fletcher and Ivor Hickey.

    As for Benzer's work, it was to do with experimentally demonstrating a non-overlapping DNA code. He used a mutant T4 phage (called FC0) to infect E.coli and selected for phages that had reverted to a wild type phenotype. It also mentions something about rll+ and rll-? Sorry if that's a bad explanation

    (Original post by SmashConcept)
    I think the problem is you are thinking of ribosomes as being organelles similar to mitochondria, ER or whatever. This is kind of how we were taught when they were introduced in school, so it's not surprising.

    In actual fact ribosomes are just proteins, so they should be thought of in the same way as any other heteromeric protein complex, and one of the subunits binds to mRNA. In bound form it is now considered rRNA.

    It's awkward because it kind of doesn't make sense to draw ribosomes as organelles in school unless you're also going to draw proteasome complexes, G proteins, and whatever else. But it also doesn't make sense to not draw them and have no explanation for where proteins are synthesised, so A level and GCSE biology teachers are stuck a bit between a rock and a hard place.

    I hope this helps, I'm going a little out on a limb about how you were taught and what your problem might be. Let me know if it is or isn't helpful.
    Thank you, I think that might be a big reason to my trouble understanding lol.
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    (Original post by LeaX)
    Thank you so much, that was soo helpful. The textbook I'm using is Bios Instant Notes Genetics by Hugh Fletcher and Ivor Hickey.

    As for Benzer's work, it was to do with experimentally demonstrating a non-overlapping DNA code. He used a mutant T4 phage (called FC0) to infect E.coli and selected for phages that had reverted to a wild type phenotype. It also mentions something about rll+ and rll-? Sorry if that's a bad explanation.
    If you're finding it hard to understand the text you're using, it's probably a good idea to try other books. Molecular Biology of The Cell by Alberts is one of the main textbooks for undergrads in my uni. Molecular Biology by Weaver is also really good for explanations.

    The rII+ rII- system was used to show that rII consists of two genes, and that you can get recombination within and between genes. He also used recombination of rII to create a genetic map to show the location of different mutations. I'm afraid I'm not familiar with the FC0 experiments, but I can talk you through rII+/rII- if it's relevant to your course.
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    (Original post by kanra)
    If you're finding it hard to understand the text you're using, it's probably a good idea to try other books. Molecular Biology of The Cell by Alberts is one of the main textbooks for undergrads in my uni. Molecular Biology by Weaver is also really good for explanations.

    The rII+ rII- system was used to show that rII consists of two genes, and that you can get recombination within and between genes. He also used recombination of rII to create a genetic map to show the location of different mutations. I'm afraid I'm not familiar with the FC0 experiments, but I can talk you through rII+/rII- if it's relevant to your course.
    Thank you, I just checked and our library has Molecular Biology of the Cell by Alberts so I'll get that out the library this week.
    If you could briefly explain what rll+/rll- is I would appreciate it, but if it's quite complicated I'm not sure that we'd need to know it completely. Also, do you know what it means by reverting to a more wild type phenotype?
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    (Original post by LeaX)
    Thank you, I just checked and our library has Molecular Biology of the Cell by Alberts so I'll get that out the library this week.
    If you could briefly explain what rll+/rll- is I would appreciate it, but if it's quite complicated I'm not sure that we'd need to know it completely. Also, do you know what it means by reverting to a more wild type phenotype?
    rII+ and rII- just refer to two different strains of T4 phage. +/- is a standard nomenclature when you're dealing with mutants: the normal/wild type is + and the mutant is -. The difference between them is that rII+ produces small, fuzzy plaques when plated on E.coli B and E.coli K (B and K are just different strains of E.coli), whereas rII- produces larger, clearer plaques on B and no plaques on K.

    One of the key experiments he carried out was recombination, where he would take two strains of rII- with different parts of the rII gene mutated, mix them together, and plate on E.coli B. He then left them alone for a while so the phage could replicate and cause cell lysis. During replication, you can get recombination events (which involve swapping of bits of DNA between strains), and this can lead to formation of a wild type rII+, these could be tested for by plating on E.coli K (wild type = plaques). The frequency of wild type formation is related to position in the genome; the further apart two mutations are, the more frequently recombinant wild types form.

    "Reversion" in terms of mutations refers to when a mutant reverts back to the normal type. If you consider point mutations, a mutation in the gene can cause a normal type to become mutant. But because mutations are generally random, that mutation can theoretically mutate back to what it originally was by pure chance (or mutate again and create something that is more like the wild type).
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    (Original post by kanra)
    rII+ and rII- just refer to two different strains of T4 phage. +/- is a standard nomenclature when you're dealing with mutants: the normal/wild type is + and the mutant is -. The difference between them is that rII+ produces small, fuzzy plaques when plated on E.coli B and E.coli K (B and K are just different strains of E.coli), whereas rII- produces larger, clearer plaques on B and no plaques on K.

    One of the key experiments he carried out was recombination, where he would take two strains of rII- with different parts of the rII gene mutated, mix them together, and plate on E.coli B. He then left them alone for a while so the phage could replicate and cause cell lysis. During replication, you can get recombination events (which involve swapping of bits of DNA between strains), and this can lead to formation of a wild type rII+, these could be tested for by plating on E.coli K (wild type = plaques). The frequency of wild type formation is related to position in the genome; the further apart two mutations are, the more frequently recombinant wild types form.

    "Reversion" in terms of mutations refers to when a mutant reverts back to the normal type. If you consider point mutations, a mutation in the gene can cause a normal type to become mutant. But because mutations are generally random, that mutation can theoretically mutate back to what it originally was by pure chance (or mutate again and create something that is more like the wild type).
    Ahh thank you! I finally understand the experiment
 
 
 
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