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.

1. Oh that’s how you
make a cake!
The fundamentals of going
from gene to protein
Bri Bibel (aka the Bumbling Biochemist)

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. Different genes are like recipes for
different proteins

4. humans have
23 pairs of
chromosomes
recipes are in
combined into
“cookbooks”
called
chromosomes

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. 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. these
generic parts
DeoxyriboNucleic Acid
hydroxyl
deoxyribose
deoxyribose
phosphate(s)
allow for linking letters
into chains
+
+

8. DeoxyriboNucleic Acid
nitrogenous base
allows for pairing
between chains
ACGT
and this unique part

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. 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. 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. 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. 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. 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. 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. 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. 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. 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. an individual exon can get duplicated
double chocolate cake
so instead of this
you now get this

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. 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. 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. 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. 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. and unique “side
chains” with different
properties
amino acids have…
a generic
backbone
allows for linking into chains

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. 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. This dictionary’s “universal” - chefs can read them in
any type of cell

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. 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. To review…

33. Thanks for watching.
Hope this was helpful!
And you can find out more about
these topics and more at
thebumblingbiochemist.com