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IB Biology HL Transcription and Translation
The document outlines the processes of transcription and translation in molecular biology, highlighting differences between DNA and RNA, as well as the steps involved in synthesizing polypeptides from mRNA. Key concepts include transcription initiation, elongation, termination, and the role of ribosomes in translation, where mRNA codons are decoded into amino acids. Additionally, it discusses gene expression regulation through mechanisms such as the operon model exemplified by the lac operon in E. coli.
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Introduction to transcription and translation processes, focusing on DNA and RNA structures.
Introduction to transcription and translation processes, focusing on DNA and RNA structures.
Comparative structure of DNA and RNA, highlighting differences in sugar, strands, base composition, and forms.
Overview of transcription, copying DNA sequences to mRNA, and the concept of introns and exons.
Overview of transcription, copying DNA sequences to mRNA, and the concept of introns and exons.
Description of translation, decoding mRNA to form polypeptides, continuation of translation details.
Description of translation, decoding mRNA to form polypeptides, continuation of translation details.
Description of translation, decoding mRNA to form polypeptides, continuation of translation details.
Details of transcription initiation, including binding of RNA polymerase to promoter and unwinding DNA.
Elongation of RNA strand and termination of transcription at terminator sequences.
Elongation of RNA strand and termination of transcription at terminator sequences.
Explanation of sense vs. antisense DNA strands and their roles in mRNA synthesis.
Process of RNA splicing, distinguishing introns and exons in eukaryotic cells, and the maturation of pre-mRNA.
Introduction to translation including ribosomal structure, binding sites for tRNA and mRNA.
Explanation of the genetic code, codon structure, and the coding process for amino acids.
Function and structure of tRNA, its role in translation and attachment to mRNA codons.
Steps of translation initiation, including assembly of ribosomal subunits at start codon.
Elongation steps in translation, including amino acid addition and translocation of tRNA.
Completion of translation process upon reaching stop codons, freeing polypeptide.
Introduction to gene expression regulation, on/off states of genes and clone E. coli example.
The lac operon model for gene expression in E. coli, detailing its function in response to lactose.
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IB Biology HL Transcription and Translation
- 1.
- 3.
- 4. Structures of DNAand RNA
- 5. DNA containsdeoxyribose while RNA contains ribose;
- 6. DNA isdouble-stranded while RNA is single-stranded;
- 7. the basethymine found in DNA is replaced by uracil in RNA;
- 8. one form ofDNA (double helix) but several forms of RNA (tRNA, mRNA and rRNA);
- 9. Transcription: Transcription: Processof copying a sequence of DNA bases to mRNA
- 14.
- 15.
- 17. Translation: decodingof mRNA at a ribosome to produce a polypeptide
- 20.
- 21.
- 24.
- 25. Transcription initiation complex-the area where transcription factors and RNA polymerase are bound to the promoter TATA box -promoter DNA sequence -the actual sequence is 5'-TATAAA-3' -RNA polymerase binding site After polymerase is bound to the promoter DNA, the two DNA strands unwind and the enzyme starts transcribing the template strand
- 26.
- 27. A. RNA polymerasemoves along DNA template B. It unwinds 10-20 DNA bases at a time C. RNA polymerase adds nucleotides in the 5’→3’ direction D. As RNA polymerase moves along, the DNA double helix reforms E. The new section of RNA ‘peels away’ as the double helix reforms
- 29.
- 30.
- 31. A. Transcription stopswhen RNA polymerase reaches a section of DNA called the terminator B. Terminator sequence = AAUAAA C. Next, the RNA strand is released and RNA polymerase dissociates from the DNA D. The RNA strand will go through more processing
- 34. Transcription (termination) A. Transcriptionstops when RNA polymerase reaches a section of DNA called the terminator B. Terminator sequence = AAUAAA C. Next, the RNA strand is released and RNA polymerase dissociates from the DNA D. The RNA strand will go through more processing
- 35. Sense vs. AntisenseDNA strandsA. The DNA double helix has two strands B. Only one of them is transcribed C. The transcribed strand is the antisense strand D. The non transcribed strand is the sense strand E. mRNA is complementary to the anitsense strand
- 36. Sense vs. AntisenseDNA strands F. The 5’ end of the RNA nucleotides are added to the 3’ end of the growing chain G. RNA nucleotides are linked together in the same fashion as DNA molecules
- 37. RNA splicing (ineukaryotes) A. In eukaryotes RNA transcripts have long non-coding stretches of nucleotides -these regions will not be translated B. The non-coding sections are dispersed between coding sections C. Introns-non-coding sections of nucleic acid found between coding regions D. Exons-coding regions of nucleic acids (eventually these are expressed as amino acids)
- 38. RNA splicing (ineukaryotes) E. RNA polymerase transcribes introns and exons, -this is pre-mRNA F. Pre-mRNA never leaves the cell’s nucleus G. The introns are excised and exons are joined together to form mRNA H. pre-mRNA I. Mature mRNA
- 39. Translation A. Translation-forming ofa polypeptide -uses mRNA as a template for a.a. sequence -4 steps (initiation, elongation, translocation and termination) -begins after mRNA enters cytoplasm -uses tRNA (the interpreter of mRNA)
- 40. Translation B. Ribosomes -made ofproteins and rRNA -each has a large and small subunit -each has three binding sites for tRNA on its surface -each has one binding site for mRNA -facilitates codon and anticodon bonding -components of ribosomes are made in the nucleus and exported to the cytoplasm where they join to form one functional unit
- 41. 8. Translation B. Ribosomes(continued) -the three tRNA binding sites are: 1. A site=holds tRNA that is carrying the next amino acid to be added 2. P site= holds tRNA that is carrying the growing polypeptide chain 3. E site= where discharged tRNAs leave the ribosome
- 42. Ribosomal structure E P A Largesubunit Peptidyl-tRNA binding site Aminoacyl-tRNA binding site mRNA 5’ Exit site Small subunit 3’
- 43. Translation C. The geneticcode Four RNA nucleotides are arranged 20 different ways to make 20 different amino acids Nucleotide bases exist in triplets Triplets of bases are the smallest units that can code for an a.a. 3 bases = 1 codon = 1 a.a. There are 64 possible codes (64=43 )
- 44. Translation C. The geneticcode Most of the 20 a.a. have between 2 and 4 possible codes The mRNA base triplets are codons In translation the codons are decoded into amino acids that make a polypeptide chain It takes 300 nucleotides to code for a polypeptide made of 100 amino acids (Why?)
- 45. Translation C. The geneticcode (continued) 61 of 64 codons code for a.a. Codon AUG has two functions -codes for amino acid methionine (Met) -functions as a start codon mRNA codon AUG starts translation The three ‘unaccounted for’ codons act as stop codons (end translation)
- 46. Translation D. How itworks DNA (antisense) A C C A A A C C G mRNA (transcription) U G G U U U G G C polypeptide (translation) Trp - Phe - Gly-
- 47. Translation E. More ontRNA tRNA is transcribed in the nucleus and must enter the cytoplasm tRNA molecules are used repeatedly Each tRNA molecule links to a particular mRNA codon with a particular amino acid When tRNA arrives at the ribosome it has a specific amino acid on one end and an anticodon on the other Anticodons (tRNA) bond to codons (mRNA) p. 304 (red book)
- 48. Where the a.a.attaches Hydrogen bonds Anticodon = tRNA diagrams Although we draw tRNA in a clover shape it’s true 3-D conformation is L-shaped.
- 49. Translation (Initiation) A. Initiation 1.Brings together mRNA, tRNA (w/ 1st a.a.) and ribosomal subunits 2. Small ribosomal subunit binds to mRNA and an initiator tRNA -start codon= AUG -start anticodon-UAC -small ribosomal subunit attaches to 5’ end of mRNA
- 50. #9. Translation (Initiation) B.Initiation 2. (continued) -downstream from the 5’ end is the start codon AUG (mRNA) -the anticodon UAC carries the a.a. Methionine 3.After the union of mRNA, tRNA and small subunit, the large ribosomal subunit attaches 4. Initiation is complete
- 51. Translation (Initiation) B. Initiation 5.The intitiator tRNA and a.a. will sit in the P site of the large ribosomal subunit 6. The A site will remain vacant and ready for the aminoacyl-tRNA
- 52.
- 53. Translation (Elongation) A. Aminoacids are added one by one to the first amino acid (remember, the goal is to make a polypeptide) B. Step 1- Codon recognition a. mRNA codon in the A site forms hydrogen bonds with the tRNA anitcodon C. Step 2- Peptide bond formation a. The ribosome catalyzes the formation of the peptide bonds between the amino acids (the one already in place and the one being added) b. The polypeptide extending from the P site moves to the A site to attach to the new a.a.
- 54. Translocation A. The tRNAw/ the polypeptide chain in the A site is translocated to the P site B. tRNA at the P site moves to the E site and leaves the ribosome C. The ribosome moves down the mRNA in the 5’→3’ direction
- 55. Termination A. Happens atthe stop codon B. Stop codons are UAA, UAG and UGA -they do not code for a.a. C. C. The polypeptide is freed from the ribosome and the rest of the translation assembly comes apart
- 56. Gene expression A. Jacoband Monad (1961) -studied control of protein synthesis in E. coli and lactose digesting enzymes -found that E. coli do not produce lactose digesting enzymes when grown in a medium without lactose -when bacteria were placed in a lactose environment, enzymes were found within minutes
- 57. Gene expression B. Genescan be switched on or off as necessary -a gene that is ‘on’ will be transcribed -in E.coli, the enzyme lactase will be produced if the gene is ‘on’ -if the gene is ‘off’ mRNA will not be created and translation can not occur
- 58. Gene expression C. Theoperon model -proposed by Jacob and Monad -explains how genes switch on and off -operon=promoter, operator and structural genes -lac operon is found in E.coli
- 59. Gene expression D. Thelac operon
- 60. Gene expression D. Thelac operon (no lactose) -lactose is absent, repressor is active, operon is off, no mRNA is produced, RNA polyermase cannot bind because it is blocked by the repressor that has bound to the operator
- 61. Gene expression D. Thelac operon (lactose is present) -lactose is present, repressor is inactive, operon is on, mRNA is transcribed, RNA polymerase binds to operator -an isomer of lactose binds to the repressor and changes its shape -this prevents it from binding to the operator -lactase is produced
Editor's Notes
- #3 So we have DNA goes to DNA. DNA makes RNA, RNA makes protein. This, by the way, gets the name the central dogma of molecular biology. Due to Francis Crick, and as an aside, Francis actually never said DNA goes to RNA goes to protein. What he said was nucleic acids go to protein. The information flows from nucleic acids to proteins. He never actually said DNA goes to RNA goes to protein, and that's an important point. And we'll come to it at some point, probably next time. So, transcription. Here's my genome.
- #4 Lets look at these assessment statements, and know what IB expects from us.
- #5 So what's the difference between DNA and RNA? 4 differences. One, this is two prime deoxyribose. This is ribose. It's not two prime deoxy. It's truly ribose. The other difference, where DNA has T, RNA, has U, uracil. The difference, what's the difference between T and U? The difference is a methyl group. It's a methyl group in an unimportant position for the base paring. It doesn't matter. It has an extra methyl group.
- #6 OH, H Difference
- #7 Single-Double Stranded
- #8 Difference between thymine and uracil is just one methyl group.
- #11 Just a jist of what’s transcription, and then we’ll dive into the details. Here's my double helix. I'm going to stop wrapping around itself, just because it's tedious. And here's a chunk of DNA that encodes a gene. Maybe it's a gene that makes our enzyme for arginine biosynthesis. But what happens is it has a starting point, it has a stopping point. Five prime to three prime. What happens is there is a signal in the DNA that the cell knows how to read called a promoter. And under certain circumstances, this promoter invites an enzyme to sit down, and the enzyme starts copying. Which direction does this enzyme go? Five prime to three prime. They all go five prime to three prime. But it makes RNA. Okay? And then it gets to certain point, and it stops copying. This process of copying is called transcription, because it's just a direct transcribing.
- #12 An enzyme takes nucleotides, RNA nucleotides here, with their triphosphates, and sticks them on, just like we saw with DNA. And it makes a polymer of RNA. And the enzyme is called RNA polymerase, right? This is all pretty logical stuff. RNA polymerase comes along and does that. So we get RNA polymerase. Now, when I am a cell, and this is my genome, I have a gene that goes this way. Here's its promoter, here's its transcriptional stop. I could also have a gene that goes this way. Here's its promoter, here's its transcriptional stop. Directionality could go in either direction. RNA polymerase comes along, and with the help of friends, knows where to start. 2 Those friends could be other proteins that are sitting down there that RNA polymerase likes to associate with. And which strand is being transcribed? The bottom strand, or the top strand? Matters. You get a different single stranded RNA. So RNA, when it floats off, is single stranded.
- #13 Transcribing DNA into mRNA in prokaryotes At the start of transcription, the DNA molecule is separated into two strands by the enzyme RNA polymerase, which binds to the DNA near the beginning of a gene. Hydrogen bonds between the bases are broken and the double helix unwinds (Figure 7.6). Transcription begins at a speci c point on the DNA molecule called the promoter region. Only one of the two strands is used as a template for transcription and this is called the antisense strand. The other DNA strand is called the sense strand. RNA polymerase uses free nucleoside triphosphates (NTPs) to build the RNA molecule, using complementary base pairing to the DNA and condensation reactions between the nucleotides. This produces a primary mRNA molecule that is complementary to the antisense strand being transcribed, and has the same base sequence as the sense strand (except that it contains the base U in place of T). RNA polymerase moves along the antisense DNA strand in a 3' → 5' direction. As it does so, the 5' end of a nucleotide is added to the 3' end of the mRNA molecule so that the construction of the mRNA proceeds in a 5' → 3' direction. RNA polymerase checks the mRNA molecule as it forms to ensure that bases are paired correctly. As the mRNA molecule is extended, the DNA is rewound into a helix once a section has been transcribed. Eventually RNA polymerase reaches another speci c sequence on the DNA called the terminator region or the transcription stop signal, which indicates the end of the gene. The RNA polymerase releases the completed RNA strand and nishes rewinding the DNA before breaking free.
- #14 Some exam prep for us.. So , I have a past paper question.
- #15 In eukaryotes, many genes contain sequences of DNA that are transcribed but not translated. These sequences, which appear in mRNA, are known as introns. After transcription of a gene, the introns are removed in a process known as post-transcriptional modi cation. The sequences of bases that remain are known as exons and these are linked together to form the mature mRNA that is translated (Figure 7.7). Mature mRNA leaves the nucleus via the nuclear pores and moves to the cytoplasm.
- #16 Now, lets move on to Translation
- #17 These are the syllabus requirements for the HL part, the requirements for SL is complete.
- #18 Its defined as: decoding of mRNA at a ribosome to produce a polypeptide
- #19 So, in translation, you have a particular RNA that has been made by the cell. Here's my RNA. It goes five prime to three prime. That's always the way we write these things. And it has some particular sequence. I'll make up a sequence here. A, U, A, C, G, A, U, G, A, A, G, A, G, G, C, C, C, dot dot dot dot dot, U, A, G, dot dot dot dot, three prime. All right. Somehow, that's going to be translated into a protein. It's translated 1 according to a fantastic look-up up table. This look-up table is called the genetic code. And the rule, the algorithm-- and it's a fairly simple algorithm, well, nothing's ever really simple in biology, but it's close to simple-- is you run along the sequence from the beginning. Run along the sequence and find the first occurrence of A, U, G. Why A, U, G? Because A, U, G is the place you start. That's how life worked it out, and that's what it does. After that, you parse the sequence in triplets. These triplets get the name codons. And then you keep going until you hit one of three possible triplets. U, A, G. U, A, A. U, G, A. And you stop there. Basically for computer programmers its like an algorithm that takes a string, finds the first occurrence of U, A, G, breaks it up into triplets passed there, keeps going until you encounter one of these three stop triplets. How many three-letter words are there with the four nucleotides? 64. That’s 4^3 right? And 3 of them are stop codons so, subtracting 3 from 64, we are left with 61 amino acids. But you know what? How many amino acids are there? 20. And there are 61 possible codons, so that implies there is some redundancy. Some codons-- some amino acids are coded for by the same codon. Okay. You may also look up the genetic code that is the look-up table on the internet which would tell you what triplet codes for what amino acid. That's the order in which you make the proteins. So you send off an order written in RNA, you send it off to the factory, the 2 factory sends you back a protein
- #20 Schematic Representation of what is exactly happening.
- #21 You know what?? This genetic code is essentially universal amongst all of life. That's pretty stunning. What does that tell you? The fact that all of life uses virtually the identical genetic code? There's actually a tiny difference between prokaryotes and eukaryotes affecting a codon and there's a tiny difference somewhere else. But essentially, it's the exact same genetic code that all of life uses. It's very unlikely that this genetic code is the only possible way you could make a genetic code, right? So the fact that all of life uses, essentially, exactly the same code is pretty strong evidence that all currently existing life descends from a common ancestor. Because if these were evolved independently, it's extremely unlikely that you would have gotten exactly the same genetic code. So that's an interesting point that you can see from just the fact that everybody uses essentially the same genetic code. It's a universal genetic code The reason that cells are unable to write C code is C wasn't really developed until the last several decades, and cells, pretty sure, precede the development of C code by Kernighan and Ritchie. So it's got to be the case that it's done some other way.
- #22 How is it done? Well, it's done like this. And I'll just be very schematic and you'll get it in your book. There's a big machine. The big machine here is called the ribosome. It consists, itself, of proteins and RNAs, and it's a huge structure. The huge structure needs to read codons. And this is a case where Francis Crick drove everybody nuts. Francis Crick, back in the 1950s, just sat at his desk and thought. He was terrible at doing experiments-- nobody really wanted to let him do experiments. Francis was a great thinker. He thought. He said, golly, how can this sequence be translated into amino acids? Well, people at the time had all sorts of nutty ideas. Some of the nutty ideas was that the sequence of the RNA folded up into pockets that just fit a proline. And another pocket that just an arginine. And if you just think about the constraints to get that to work, it's nuts. That the sequence itself would form perfect binding pockets for the necessary amino acids. Crick said impossible. He said the really sensible way to do this, if I were running life, what I would do is I would have an adapter molecule. The adapter molecule would be some kind of a nucleic acid, and the nucleic acid would kind of match the codon on one end and have the amino acid on the other end. And then there'd be another adapter, and the adapter would have the next amino acid. And then you would catalyze a bond between them. Therefore, I predict, says Francis, there will be small adapter molecules, probably made out of RNAs themselves. And Francis called this the Adapter Hypothesis. It drove people crazy because, of course, he was right. People found the adapters and they would use transfer things that transfer information-- get called transfer RNAs. What happens is the ribosome has pockets in which these transfer RNAs basically come in, match their sequence, there's a codon each of these transfer RNAs has a matching anticodon that matches the triplet, and it has already attached to it an amino acid-- the right amino acid for that anticodon. How does that right amino acid get attached to the right tRNA? There's an enzyme. The job of that enzyme is to attach this amino acid, proline, to this transfer RNA. It's a Prolyl-tRNA synthetase. And its job is to put proline on the right tRNAs. There's another one that puts arginine on the right tRNAs. There's a whole business that's set up to get the right tRNAs, have the right amino acids attached to them through a bunch of enzymes floating around. So then these tRNAs with the amino acid attached drop in, they drop into the next position, and a bond-- the peptide bond-- is catalyzed. The catalysis, this enzymatic catalysis to join together those amino acids is actually carried out not by the proteins in a ribosome, but actually by RNA in the ribosome. The RNA is the enzyme. You know why that's kind of cool? If this bothers you, just forget it, but one of the mysteries about how you ever go from 4 DNA to RNA to protein and all of that is how the whole thing ever got started. How could you possibly have gotten protein synthesis started if the things that were needed to make protein synthesis were proteins? So this is actually an echo of an ancient world 3 billion years ago, where this was all probably carried out by RNAs. RNA was probably the early catalysts for most things, and we still see evidence of the fact that even today your peptide bonds are catalyzed actually by RNA and they're doing the enzymatic work. So then what happens after you attach the first two amino acids? Well, the ribosome chugs down here and grabs the next code-- these two shift over. You can either think about the ribosome moving this way or the RNA moving that way. The next tRNA drops in, the next bond gets made, chugs over, the next one drops in, the next one gets made, and onward like that until it hits a stop codon at which, it releases it. The ribosome knows to release it. There's actually a little factor that drops in and tells it to release it there. And that's how you make proteins– really interesting, isn’t it?. It works very well. It chugs along in that fashion.
- #23 As you can see this is tRNA,. tRNA is made of a single strand of nucleotides that is folded and held in place by base pairing and hydrogen bonds (Figure 7.8). There are many different tRNA molecules but they all have a characteristic ‘clover leaf ’ appearance with some small differences between them. At one position on the molecule is a triplet of bases called the anticodon, which pairs by complementary base pairing with a codon on the mRNA strand. At the 3' end of the tRNA molecule is a base sequence CCA which is the attachment site for an amino acid. An amino acid is attached to the speci c tRNA molecule that has its corresponding anticodon, by an activating enzyme.
- #24 Translation is the process that decodes the information of mRNA into the sequence of amino acids that eventually form a protein. Translation consists of four stages:
- #25 Initiation Translation begins at a start codon (AUG) near the 5' end of the mRNA strand. This codon codes for the amino acid methionine and is a signal to begin the process of translation (Figure 7.10). This is called initiation. The mRNA binds to the small subunit of a ribosome. Then an activated tRNA molecule, carrying the amino acid methionine, moves into position at site 1 of the ribosome. Its anticodon binds with the AUG codon using complementary base pairing. Hydrogen bonds form between the complementary bases of the mRNA and tRNA and, once this has happened, a large ribosomal subunit moves into place and combines with the small subunit.
- #27 Elongation Initiation is followed by elongation and the formation of peptide bonds (Figure 7.11). tRNA molecules bring amino acids to the mRNA strand in the order speci ed by the codons. To add the second amino acid, a second charged tRNA with the anticodon corresponding to the next codon enters site 2 of the ribosome and binds to its codon by complementary base pairing. The ribosome catalyses the formation of a peptide bond between the two adjacent amino acids, The ribosome and tRNA molecules now hold two amino acids. The methionine becomes detached from its tRNA. Now the ribosome moves along the mRNA and the rst tRNA is released to collect another methionine molecule. The methionine becomes detached from its tRNA. Now the ribosome moves along the mRNA and the rst tRNA is released to collect another methionine molecule.
- #29 Representation of how elongation occurs.
- #30 Translocation Translocation is the movement of the ribosome along the mRNA strand one codon at a time. As the ribosome moves, the unattached tRNA moves into the exit site and is then released into the cytoplasm, where it will pick up another amino acid molecule. The growing peptide chain is now positioned in site 1, leaving site 2 empty and ready to receive another charged tRNA molecule to enter and continue the elongation process. The Figure shows how translocation occurs as mRNA is translated.
- #33 Again we have a Past Paper question…