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Oh, that's how you make a cake! The fundamentals of going from gene to protein.


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Animated slides covering the fundamentals of protein expression as a bakery analogy. Covers concepts including transcription, translation, alternative splicing, exon shuffling, recombinant protein expression, and more.

Published in: Science
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Oh, that's how you make a cake! The fundamentals of going from gene to protein.

  1. 1. Oh that’s how you make a cake! The fundamentals of going from gene to protein Bri Bibel (aka the Bumbling Biochemist)
  2. 2. The recipes for proteins NUCLEUS are written in genes & (in eukaryotes like us) housed in a membrane- bound room in the cell called the nucleus
  3. 3. Different genes are like recipes for different proteins
  4. 4. humans have 23 pairs of chromosomes recipes are in combined into “cookbooks” called chromosomes
  5. 5. and the whole collection of cookbooks is called the genome humans have 23 pairs of chromosomes recipes are in combined into “cookbooks” called chromosomes
  6. 6. each chromosome is 1 long strand of DNA it coils up tightly with the help of proteins called histones and is written in nucleotides
  7. 7. these generic parts DeoxyriboNucleic Acid hydroxyl deoxyribose deoxyribose phosphate(s) allow for linking letters into chains + +
  8. 8. DeoxyriboNucleic Acid nitrogenous base allows for pairing between chains ACGT and this unique part
  9. 9. But the “chefs” (ribosomes) are in the cytoplasm CYTOPLASM All that’s in the nucleus, And the nucleus is like a reference section of a library - you can’t check recipes out but you can make copies so we need to get the recipe to them So, in order to make a protein, a cell first makes an RNA copy of it.
  10. 10. DNA & RNA are both written in the nucleic acid alphabet but RNA has an “extra” oxygen in its sugar They're really similar, with the same general phosphate-sugar-base layout ribose RNA deoxyribose DNA
  11. 11. but U can still pair with A And RNA has a “U” instead of a T” so the DNA gene can act as a template for making the RNA copy speaking of which…
  12. 12. In order to make a protein, a cell first makes a messenger RNA (mRNA) copy of its gene. well, first it makes a pre-mRNA which needs editing before it can leave the nucleus since DNA & RNA are both in the nucleic acid language, going between them is called transcription DNA letters gene RNA letters mRNA transcription editing&
  13. 13. DNA and its pre-mRNA copy have EXONS & INTRONS EXONS have the product-making instructions that the chefs need. Different exons have instructions for different “parts” INTRONS have regulatory “notes” that “upper- management” needs make on Rosalind’s birthday: July 25 if you’re making this, you might also want to make some ice cream instructions for vanilla layer instructions for strawberry layer instructions for chocolate layer
  14. 14. INTRONS get removed through RNA splicing to make mature messenger RNA (mRNA) mRNA only has EXONS but it might not have them all as we’ll see… pre-mRNA has EXONS & INTRONS splicing
  15. 15. splicing leaves on the “front & back matter” - untranslated regions (UTRs) which have regulatory information for the chefs the chefs also need some regulatory notes, so 5’ UTR 3’ UTR This is called alternative splicing pre-mRNA can get edited in different ways to get different mature mRNA products
  16. 16. Alternative Splicing removes introns from the pre-mRNA in different ways to make different mRNAs from the same gene so you can make different proteins from the same gene RNA splicing translationpre-mRNA mRNA protein
  17. 17. splicing only affects the RNA copy -> the genomic gDNA version stays the same No DNA was harmed in the making of this protein! but the gDNA can get edited… in which case we call it mutation and it's not all bad!!!!
  18. 18. sometimes in the course of evolution, a whole gene gets duplicated so you have 2 DNA copies of a recipe in your cookbook evolution can then (through random mutations) “play around with” 1 copy to make a new protein while the other copy’s “safe” EXON SHUFFLING can mix n’ match exons & it occurs in the DNA version so it’s long-lasting
  19. 19. an individual exon can get duplicated double chocolate cake so instead of this you now get this
  20. 20. and exons from multiple genes can combine recipe for frosted cookie frosted cake instructions for sugar cookie instructions for frosting it doesn’t always work out so well…
  21. 21. it doesn’t always work out so well… … which is where natural selection comes to the rescue crunchy cake instructions for sugar cookie instructions for frosting
  22. 22. cap and tail added for protection and to help out the chefs In addition to that editing, there’s some “generic editing” that’s kinda like giving the recipe copy the nuclear stamp of approval to leave the restricted section 5’ mG cap 3’ poly-adenosine tail
  23. 23. then it’s taken out into the cytoplasm where the “chefs” are waiting to follow its instructions adding the specified ingredients to make protein
  24. 24. since that’s a different language from the nucleic acid one RNA's in, going from mRNA to protein is called translation These “ingredients” are amino acids amino acid letters protein translation RNA letters mRNA DNA letters gene transcription editing& the letters of the protein “alphabet"
  25. 25. and unique “side chains” with different properties amino acids have… a generic backbone allows for linking into chains
  26. 26. The chefs (ribosomes) travel along the recipe (mRNA), reading the instructions and having their servants, (tRNAs) bring them the matching ingredients (amino acids)
  27. 27. 3-nucleotide codons (mRNA words) correspond to 1 amino acid tRNAs provide the link between the nucleic acid language of RNA and the amino acid language of proteins mRNA has a codon tRNA has a matching anti-codon Arginine each amino acid has at least one & you can find them in a dictionary called a codon table and carries the corresponding amino acid Oh that’s how you make a cake!
  28. 28. This dictionary’s “universal” - chefs can read them in any type of cell
  29. 29. So, if we want to study a protein, we can use molecular cloning to stick its recipe into a circular piece of DNA called a plasmid that acts as a little extra cookbook. Then stick that plasmid into cells to have them make the protein for us. we call that recombinant protein expression because we’ve recombined cookbooks
  30. 30. But the cells also have a lot of other recipes of their own and make lots of other proteins As a protein biochemist, my goal is to separate the one I want from all the others so I can play with them & figure out how they work Instead of tasting them, I take advantage of some other types of differences charge size etc.
  31. 31. To review…
  32. 32. Thanks for watching. Hope this was helpful! And you can find out more about these topics and more at