Vad är DNA-transkription?

DNA-transkription är processen där DNA omvandlas till RNA.

Vilka är de viktiga enzymerna i DNA-transkription för prokaryota celler?

RNA-polymeras holoenzym med core enzym och sigma subenhet.

Vad är en promotorregion?

En promotorregion är en nukleotidsekvens i DNA som tillåter bindning av RNA-polymeraser och transkriptionsfaktorer.

Vad är alternatv RNA-splitsning?

Alternativ RNA-splitsning är en process där samma gen kan ge upphov till olika proteinvarianter.

Varför är det viktigt med 5'-cap och poly-A-svans?

De skyddar RNA från nedbrytning och hjälper till att initiera translation.

Vad är rho-beroende och rho-oberoende terminering?

Rho-beroende terminering använder rho-proteinet för att avsluta transkriptionen, medan rho-oberoende bildar en hårnålsslinga som signalerar terminering.

Vad är post-transkriptionella modifieringar?

Modifikationerna inkluderar 5'-capping, poly-A-svans läggs till och splitsning av exoner/introner.

Vad påverkar hastigheten på DNA-transkription i eukaryoter?

Enhancers och silencers påverkar hastigheten på transkription genom att öka eller minska processen.

Vad är RNA-redigering?

RNA-redigering är en process där nukleotider i RNA kan modifieras för att påverka proteintranslation.

Cell Biology | DNA Transcription 🧬

01:25:28

https://www.youtube.com/watch?v=ZrCx98CtJ_4

Summary

TLDRVideon från Ninja Nerd handlar om DNA-transkription, vilket är processen där DNA omvandlas till RNA. Den täcker reglerande element och enzymer som deltar i processen, såsom RNA-polymeras och transkriptionsfaktorer. För prokaryoter sker transkriptionen med ett RNA-polymeras som består av core enzym och en sigma-enhet medan eukaryoter använder tre olika RNA-polymeraser och flera allmänna transkriptionsfaktorer. Videon diskuterar även post-transkriptionella modifieringar som capping, poly-A svans och splitsning av introner och exoner. Alternativ RNA-splitsning förklaras, där samma gen kan leda till olika proteiner beroende på hur mRNA splitsas. Skillnader i transkriptionella processer mellan prokaryoter och eukaryoter tas också upp, inklusive rho-beroende och rho-oberoende terminering samt eukaryotisk genreglering med enhancers och silencers. Videon avslutas med en diskussion om RNA-redigering, där exempel ges på hur samma RNA-sekvens kan modifieras för att producera olika proteiner i olika celltyper.

Takeaways

📘 Förståelse av DNA-transkription och dess definition.
🔍 Skillnad mellan prokaryotisk och eukaryotisk transkription.
🧬 Roller hos RNA-polymeras i transkription.
📍 Vikt av promotorregioner i transkription.
🛠 Funktion av 5'-cap och poly-A-svans i mRNA.
🔄 Alternativ RNA-splitsning och dess betydelse.
🚀 Roll av enhancers och silencers i genreglering.
🛑 Mekanismer för terminering av transkription.
🧪 Post-transkriptionella modifieringar i eukaryoter.
🌱 RNA-redigering och dess biologiska konsekvenser.

Timeline

00:00:00 - 00:05:00
Introduktion till DNA-transkription. Vi kommer att förklara processen där DNA omvandlas till RNA i både eukaryota och prokaryota celler. För att denna process ska ske behövs vissa proteiner eller enzymer.
00:05:00 - 00:10:00
Fokus på prokaryota celler och deras behov av RNA-polymeras holoenzym, som består av kärnenzym och en sigma-subenhet, för transkriptionen. Promotorregionens roll i DNA beskrivs.
00:10:00 - 00:15:00
RNA-polymeras holoenzym läser DNA:s templatsträng för att syntetisera RNA. Prokaryota celler kan producera mRNA, rRNA och tRNA från en enda RNA-polymeras.
00:15:00 - 00:20:00
I eukaryota celler krävs specifika RNA-polymeraser och transkriptionsfaktorer. Tre RNA-polymeraser (I, II och III) ansvarar för produktionen av olika typer av RNA.
00:20:00 - 00:25:00
Transkriptionsfaktorer och deras roll i bindningen till promotorregioner i eukaryota celler beskrivs. RNA-polymeras I producerar rRNA, polymeras II producerar mRNA, och polymeras III producerar tRNA.
00:25:00 - 00:30:00
Processen för initiering av transkription i eukaryota celler: polymeras II och generella transkriptionsfaktorer binder till promotorregioner. Jämförelse mellan prokaryota och eukaryota system.
00:30:00 - 00:35:00
Elongering i transkription: RNA-polymeras öppnar och stabiliserar DNA-strängar och syntetiserar mRNA genom att läsa DNA-templatsträngen i 3'-5'-riktning.
00:35:00 - 00:40:00
Förklarar 5'-3'-läsning och syntes av RNA med hjälp av diagram för att illustrera processen.
00:40:00 - 00:45:00
Diskussion om hur RNA-polymerasers funktion kan hämmas av olika ämnen och vilka konsekvenser det får för cellerna. Termineringsprocessen i transkriptionen introduceras.
00:45:00 - 00:50:00
Termineringsprocessen i prokaryoter kan ske via rho-beroende eller rho-oberoende mekanismer. Beskrivning av hur rho-protein och hårnålsslingor påverkar processens avslutning.
00:50:00 - 00:55:00
Eukaryota celler använder polyadenyleringssignal för att avsluta transkriptionen. Enzymer klipper bort RNA från DNA och RNA-polymeraset.
00:55:00 - 01:00:00
Post-transkriptionella modifieringar i eukaryota celler innebär 5'-capping och poly-A-svans för stabilitet och transport av mRNA.
01:00:00 - 01:05:00
Cappning av RNA hjälper till att starta translation och skyddar mot nedbrytning. Poly-A-svansens roll diskuteras i liknande termer.
01:05:00 - 01:10:00
Splitsning av pre-mRNA i eukaryota celler tar bort introner och fogar samman exoner. Detta görs med hjälp av snurps, bestående av snRNA och proteiner.
01:10:00 - 01:15:00
Exon/intron strukturen i pre-mRNA beskrivs. Splitsningsprocessen avlägsnar introner och fogar samman exoner för att bilda moget mRNA.
01:15:00 - 01:20:00
Alternativ rna-splitsning ger möjlighet att producera olika proteiner från samma gen genom att variera exonkombinationer.
01:20:00 - 01:25:28
RNA-editering kan leda till olika proteinprodukter från samma mRNA, ett fenomen exemplifierat med apob100 och apob48 i enterocyter och hepatocyter.

Mind Map

Frequently Asked Question

Vad är DNA-transkription?
DNA-transkription är processen där DNA omvandlas till RNA.
Vilka är de viktiga enzymerna i DNA-transkription för prokaryota celler?
RNA-polymeras holoenzym med core enzym och sigma subenhet.
Vad är en promotorregion?
En promotorregion är en nukleotidsekvens i DNA som tillåter bindning av RNA-polymeraser och transkriptionsfaktorer.
Vad är skillnaden mellan transkription i prokaryoter och eukaryoter?
Prokaryoter använder ett RNA-polymeras, medan eukaryoter använder tre olika RNA-polymeraser och allmänna transkriptionsfaktorer.
Vad är alternatv RNA-splitsning?
Alternativ RNA-splitsning är en process där samma gen kan ge upphov till olika proteinvarianter.
Varför är det viktigt med 5'-cap och poly-A-svans?
De skyddar RNA från nedbrytning och hjälper till att initiera translation.
Vad är rho-beroende och rho-oberoende terminering?
Rho-beroende terminering använder rho-proteinet för att avsluta transkriptionen, medan rho-oberoende bildar en hårnålsslinga som signalerar terminering.
Vad är post-transkriptionella modifieringar?
Modifikationerna inkluderar 5'-capping, poly-A-svans läggs till och splitsning av exoner/introner.
Vad påverkar hastigheten på DNA-transkription i eukaryoter?
Enhancers och silencers påverkar hastigheten på transkription genom att öka eller minska processen.
Vad är RNA-redigering?
RNA-redigering är en process där nukleotider i RNA kan modifieras för att påverka proteintranslation.

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Subtitles

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00:00:14
what's up ninja nerds in this video
00:00:15
today we are going to be talking about
00:00:17
dna
00:00:17
transcription before we get started if
00:00:19
you guys do like this video please hit
00:00:21
that like button comment down in the
00:00:22
comment section
00:00:23
and please subscribe also down in the
00:00:25
description box we have links to our
00:00:26
facebook instagram patreon
00:00:28
all that stuff will be there all right
00:00:29
ninjas let's get into it all right ninja
00:00:31
so with dna transcription we have to
00:00:33
have a basic understanding of just the
00:00:34
definition what the heck is
00:00:36
transcription
00:00:37
and it's really a simple thing it's just
00:00:38
taking dna
00:00:40
okay double stranded dna with the
00:00:41
eukaryotic cells and even in prokaryotic
00:00:43
cells
00:00:44
and converting that into rna so it's
00:00:46
taking dna and making rna that's all
00:00:48
transcription is
00:00:49
but in order for transcription to occur
00:00:52
in order for it to take place
00:00:53
we need two particular types of proteins
00:00:56
or enzymes if you will
00:00:58
to facilitate this process and i want to
00:01:00
talk about those real quick
00:01:01
because these are very important now
00:01:04
transcription can be kind of different
00:01:07
okay and it's important to know the
00:01:09
differences
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between prokaryotic cells we'll consider
00:01:12
bacteria in this case
00:01:13
and eukaryotic cells human cells like me
00:01:15
and you
00:01:17
in prokaryotic cells there's a
00:01:19
particular type of protein
00:01:21
that is needed in order for
00:01:23
transcription to take place
00:01:25
what is that protein so let's say that
00:01:27
we take
00:01:28
this dna strand here right we have this
00:01:30
dna strand
00:01:31
on this dna strand we have these blue
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portions that i've highlighted here as a
00:01:35
box with some lines in it
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this right here for right now i want you
00:01:39
to know is what's called a promoter so
00:01:41
this is called
00:01:43
a promoter region now a promoter region
00:01:46
is a
00:01:47
particular nucleotide sequence within
00:01:49
the dna
00:01:51
and what it does is it allows for
00:01:53
particular proteins like
00:01:54
rna polymerases and transcription
00:01:56
factors
00:01:57
to bind onto the dna and then start
00:02:00
moving through the dna
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taking the dna and making rna so that's
00:02:04
the first thing you need to know is
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within the dna
00:02:07
there's a particular nucleotide sequence
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we'll talk about a little bit later
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called a promoter region and that's the
00:02:12
first thing that we need to
00:02:14
identify let's say that we take this
00:02:16
particularly for
00:02:19
prokaryotic cells so prokaryotic cells
00:02:23
and we'll just say like a bacterial cell
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okay prokaryotic cells use a
00:02:28
very particular type of enzyme what
00:02:31
is that enzyme it's called a
00:02:34
rna polymerase holoenzyme okay so it's
00:02:38
called an
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rna we're going to put poll polymerase
00:02:42
holo enzyme
00:02:46
now that's a lot of stuff let me explain
00:02:48
what this is and i'll show you the
00:02:49
structure of it a basic structure of
00:02:51
what the rna polymerase holoenzyme is
00:02:53
it's made up of two things one of the
00:02:56
components of this enzyme
00:02:59
is called the core enzyme
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and the core enzyme for this rna
00:03:04
polymerase holoenzyme
00:03:07
consists of multiple subunits that they
00:03:09
just love to ask you on your us mles and
00:03:11
other exams
00:03:12
and these are they contain two alpha
00:03:15
units
00:03:16
okay two alpha chains proteins it
00:03:18
contains
00:03:19
two beta units technically we say beta
00:03:22
and beta prime
00:03:23
if you really want to be specific and
00:03:25
then one more
00:03:26
which is called an omega unit okay
00:03:29
so these are the primary components of
00:03:31
the core enzyme which makes up rna
00:03:33
polymerase what's important to remember
00:03:36
is that these are what are going to
00:03:38
really read the dna
00:03:39
and make rna that portion of the enzyme
00:03:42
reads the dna
00:03:43
and makes rna the next component of the
00:03:45
rna polymerase holoenzyme is the portion
00:03:48
that we need in order to bind
00:03:50
to the dna to the promoter region
00:03:51
without it we won't be able to allow for
00:03:53
this rna polymerase to bind to the dna
00:03:55
and transcribe it this is called
00:03:58
the sigma right or you can represent it
00:04:02
like this
00:04:03
subunit or factor if you will okay
00:04:07
these two components the core enzyme
00:04:09
which is made up of the two alpha the
00:04:10
beta and the beta prime and the omega
00:04:12
sub unit
00:04:13
as well as the sigma subunit make up the
00:04:15
entire rna polymerase
00:04:16
now let me show you for example here
00:04:19
let's say i represent the core enzyme
00:04:21
as just this kind of blue circle with
00:04:23
lines in it
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and then we'll represent the sigma
00:04:26
subunit as kind of like a pink circle
00:04:27
with some lines in it right so let's
00:04:29
imagine here
00:04:30
we have that core enzyme which we're
00:04:33
going to represent like this
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and then the other component of it which
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is the sigma subunit which will
00:04:38
represent
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like this that sigma subunit will then
00:04:43
bind to the promoter region once it
00:04:45
binds to the promoter region
00:04:47
then this core enzyme of the rna
00:04:49
polymerase will then
00:04:50
release away from the sigma subunit
00:04:54
and it'll start moving down
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this dna and as it moves down the dna
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it'll read the dna
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from three to five and synthesize an rna
00:05:04
strand
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from that which we'll talk about more
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detail later
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from five to three
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so it'll read the dna and make rna
00:05:16
this rna that we make from in
00:05:18
prokaryotic cells with the rna
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polymerase holoenzyme
00:05:22
is very different from eukaryotic cells
00:05:25
in prokaryotic cells that mrna that we
00:05:27
made from this one rna polymerase
00:05:29
holoenzyme can make all the mr
00:05:31
all the rna we need whether that be rrna
00:05:34
within the prokaryotic cell whether that
00:05:36
be m
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rna within the prokaryotic cell or t
00:05:41
rna within the prokaryotic cells
00:05:44
so that's very important big thing i
00:05:47
really need you guys to take away from
00:05:48
that is
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prokaryotic cells they use one rna
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polymerase which is called a holoenzyme
00:05:54
made up of two components a core enzyme
00:05:56
made of these subunits
00:05:57
and a sigma subunit the core is what
00:06:00
reads the dna and makes the rna the
00:06:02
sigma subunit is what
00:06:04
binds the rna polymerase to the promoter
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region
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enabling it to transcribe the dna okay
00:06:11
and whenever you make rna within a
00:06:13
prokaryotic cell from this rna
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polymerase it makes
00:06:16
all the rnas within that prokaryotic
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cell in eukaryotic cells it's a little
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bit different
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so let's talk about that let's say here
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we have
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three promoter regions that i want us to
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focus on and this is all within
00:06:30
eukaryotic cells
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in eukaryotic cells we need
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two different things in order to allow
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for transcription to occur
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and this portion here right and this
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portion of prokaryotic cells we only
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need
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one enzyme which had two different
00:06:48
components
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within eukaryotic cells each process
00:06:52
requires
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a particular enzyme an rna polymerase
00:06:56
and a transcription factor let's let's
00:06:59
kind of write that down
00:07:00
so let's say that we take this first
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promoter we want to read this gene this
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portion of the dna
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and make rna and this is the rna that
00:07:08
we're actually going to
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synthesize right here okay from this
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gene
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a particular enzyme let's represent this
00:07:16
in blue since we've been kind of doing
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blue here there's going to be a
00:07:19
particular enzyme which is going to
00:07:21
read this dna okay
00:07:24
and make this rna there's a particular
00:07:26
enzyme what is that enzyme called it's
00:07:27
called rna polymerase
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but this is the first promoter within
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the eukaryotic cells that we're talking
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about right
00:07:35
so let's call it rna polymerase one
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rna polymerase one will read the dna and
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make a particular type of rna but in
00:07:44
order for it to do this
00:07:46
it needs a special protein that can bind
00:07:49
to the promoter region which allows for
00:07:51
the rna polymerase to bind to the dna
00:07:53
and read the dna
00:07:54
what is that particular protein that
00:07:57
protein
00:07:58
let's represent it here in let's do
00:08:01
green there's a particular protein
00:08:05
which will bind here to the rna
00:08:08
polymerase
00:08:09
and to the promoter and allow the rna
00:08:11
polymerase to
00:08:12
bind to the dna and start moving down
00:08:15
reading the dna and making this rna
00:08:17
what is this called this is called a
00:08:19
transcription
00:08:20
factor tf and there's many different
00:08:23
types of transcription factors the
00:08:26
particular thing that i need you to
00:08:27
remember for right now
00:08:29
is that we call these transcription
00:08:31
factors which are utilized by rna
00:08:33
polymerases
00:08:34
within eukaryotic cells we call these
00:08:38
general
00:08:40
transcription factors we'll talk about
00:08:41
very specific types
00:08:43
with an rna polymerase type 2 a little
00:08:45
bit later but for right now
00:08:47
two things i need in order for this rna
00:08:49
polymerase to be able to read the dna
00:08:51
and make this rna rna polymerase 1 needs
00:08:54
a general transcription factor
00:08:56
to bind to the promoter allowing the rna
00:08:58
polymerase 1 to
00:09:00
then bind into the dna read it and make
00:09:02
rna
00:09:03
what type of rna does it make i have all
00:09:06
the rnas within prokaryotic cells from
00:09:08
one rna polymerase
00:09:09
but rna polymerase 1 makes a very
00:09:12
particular type of rna
00:09:14
and this is called r rna
00:09:18
now rrna is very important because this
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is incorporated into what's called
00:09:23
ribosomes ribosomes and ribosomes are
00:09:27
utilized in the translation process
00:09:29
where we take
00:09:30
mrna and from that make proteins
00:09:34
so we'll talk about this later in
00:09:35
another video but for right now first
00:09:36
thing i need you know is rna polymerase
00:09:38
one
00:09:38
with transcription factors reads the dna
00:09:41
and makes
00:09:42
rrna now that makes everything else
00:09:44
pretty easy from this point
00:09:46
here's another promoter region of a
00:09:48
particular sequence of dna
00:09:50
right within a eukaryotic cell so this
00:09:53
is the second promoter region
00:09:54
another enzyme binds another rna
00:09:57
polymerase
00:09:58
and not only just that one rna
00:10:00
polymerase here but we also need
00:10:02
a set of general transcription factors
00:10:06
to bind to this promoter region so
00:10:09
general transcription factors we need to
00:10:11
bind to the promoter region
00:10:12
enabling this rna polymerase to bind to
00:10:15
the dna
00:10:15
read it and then make what make these
00:10:19
particular types of rna we have here
00:10:23
this is well this was the first promoter
00:10:26
this is the second one
00:10:27
all right so we're going to call this
00:10:29
rna polymerase
00:10:31
2 rna polymerase 2 will bind to this
00:10:35
promoter via the transcription factor
00:10:37
read the dna and make rna what kind of
00:10:39
rna is it going to be making
00:10:41
big thing i need you to remember is it's
00:10:43
making m
00:10:45
rna mrna you'll see later again
00:10:48
is the component it'll have to go
00:10:50
through some very specific modifications
00:10:54
that we'll talk about in great detail
00:10:56
and then eventually
00:10:57
it'll be translated with
00:11:00
the help of rrna and another thing
00:11:02
called trna
00:11:04
at the ribosomes and making proteins
00:11:06
okay the other thing that
00:11:08
you guys can remember if you guys want
00:11:09
to be scholarly or ninja nerdy
00:11:11
there's another rna that's made here and
00:11:13
we'll talk about it a little bit later
00:11:15
with what's called splicing
00:11:17
and these are called small nuclear rnas
00:11:21
and these are involved in what's called
00:11:23
splicing and we'll get into that a
00:11:25
little bit more in detail later okay
00:11:27
but big thing rna polymerase ii with the
00:11:29
help of general transcription factors
00:11:31
makes mrna
00:11:32
and snrnas rna polymerase one with the
00:11:34
help of general transcription factors
00:11:36
makes
00:11:36
rnas when the heck do you think this
00:11:38
last promoter region of this
00:11:40
sequence of dna within this eukaryotic
00:11:42
cell is going to make
00:11:44
trnas and it's the same process what do
00:11:46
i need here
00:11:47
i need general transcription factors to
00:11:49
bind to the promoter region
00:11:51
when that binds that facilitates or it
00:11:53
helps to
00:11:54
allow the rna polymerase
00:11:57
type what
00:12:00
three two
00:12:04
bind to the dna and then read the dna
00:12:07
and then synthesize what rna
00:12:12
what type of rna is it making the type
00:12:14
of rna that is being synthesized from
00:12:16
rna polymerase iii is
00:12:18
primarily trna but
00:12:22
a teensy little bit of snra is
00:12:25
also made by rna polymerase type 3.
00:12:28
and if you guys really want to be extra
00:12:30
ninja nerdy technically
00:12:32
even a teensy bit of
00:12:36
rna is also made here as well okay
00:12:39
now trna what the heck does this do
00:12:41
you'll see later
00:12:42
that this is also involved in the
00:12:44
translation process
00:12:46
it carries a particular amino acid and
00:12:48
an anticodon
00:12:50
which is going to be involved in that
00:12:51
process and we'll talk about that in a
00:12:52
separate video
00:12:53
so i know this was a lot of stuff to
00:12:54
take away and take away from this but
00:12:56
the big
00:12:56
overall theme that i really just out of
00:12:58
all of this what i want you to take away
00:13:00
from this is this quick little thing
00:13:01
here
00:13:02
that rna polymerases 1
00:13:06
2 3 remember
00:13:10
r m t
00:13:14
rna polymerase 1 primarily gives way to
00:13:16
rrna
00:13:17
rna polymerase 2 primarily gives way to
00:13:20
mrna
00:13:22
and then rna polymerase 3 primarily
00:13:24
gives way to
00:13:25
t rna these are the big things that i
00:13:28
want you to take away from all this if
00:13:29
you want to go the extra mile be extra
00:13:31
ninja nerdy
00:13:32
two and 3 also can give way to what
00:13:36
small nuclear rna if you really want to
00:13:37
go the extra mile technically three can
00:13:39
also give way to
00:13:40
rrna but this is the basic thing to take
00:13:42
away from what we just talked about
00:13:45
and then the other thing is in
00:13:47
prokaryotic cells we don't need all of
00:13:48
these
00:13:49
we need one rna polymerase holoenzyme
00:13:53
to make all the rnas one last thing is
00:13:57
you notice in eukaryotic cells that we
00:13:58
have particular transcription factors
00:14:00
that are going to be needed for each rna
00:14:02
polymerase
00:14:03
the transcription factor in prokaryotes
00:14:05
technically if you want to be specific
00:14:08
is the sigma subunit because it's the
00:14:09
portion that's binding to the promoter
00:14:11
to allow
00:14:12
the core enzyme of the rna polymerase to
00:14:14
read the dna
00:14:15
okay so that kind of covers the basic
00:14:17
concepts of the two main things that we
00:14:18
need
00:14:19
in order for this transcription process
00:14:21
to occur now
00:14:23
there's one other thing that i want to
00:14:24
talk about very quickly before we really
00:14:26
start talking about
00:14:27
mrna because that's going to be the
00:14:28
primary topic here i want to have a
00:14:31
quick little discussion on how we can
00:14:33
modulate
00:14:34
the rate of transcription either
00:14:36
speeding it up or slowing it down
00:14:38
okay so the next thing i want to talk
00:14:39
about is very very briefly
00:14:41
on eukaryotic gene regulation so i want
00:14:44
to have a quick
00:14:45
quick tiny little discussion on gene
00:14:46
regulation
00:14:48
okay and the only reason i want to
00:14:49
mention this is because this is very
00:14:51
easy and it kind of makes sense along
00:14:53
with what we're talking about
00:14:55
but we're not going to talk about it in
00:14:56
prokaryotic cells we're primarily going
00:14:58
to talk about this gene regulation
00:15:00
and eukaryotic cells we're going to have
00:15:02
a separate video because it's more
00:15:03
involved
00:15:04
we'll talk about gene regulation and
00:15:06
prokaryotic cells with the lac operon
00:15:07
and the tryptophan operon we'll get into
00:15:09
that
00:15:09
but in eukaryotic cells there's two ways
00:15:12
that we can modulate and it's really
00:15:13
easy
00:15:14
one way that we can modulate
00:15:17
transcription is we have particular dna
00:15:19
sequences
00:15:20
particular sequences of dna particularly
00:15:22
palindromic sequences
00:15:24
which are called enhancers and enhancers
00:15:28
are basically dna sequences and
00:15:30
the big thing i want you to take away
00:15:32
from this they can increase
00:15:34
the transcription rate so they increase
00:15:37
the
00:15:38
rate of transcription or the process of
00:15:39
transcription okay we'll talk about how
00:15:41
they do that
00:15:43
the other thing that can regulate the
00:15:45
the transcription process or gene
00:15:47
regulation in a way
00:15:48
is something called silencers
00:15:52
in silencers they do what they decrease
00:15:55
the transcription rate or the
00:15:57
transcription process
00:15:59
now it's really straightforward it's
00:16:02
relatively simple let me explain
00:16:04
what i mean let's say here we have a
00:16:06
strip of dna we're going to explain how
00:16:08
this happens so here's our strip of dna
00:16:10
and remember this blue region what did
00:16:12
we call this blue region that we talked
00:16:13
about above
00:16:14
this was called our promoter region and
00:16:17
do you guys remember let's take
00:16:19
eukaryotic cells in this case what we
00:16:21
needed in order for this process to
00:16:24
occur
00:16:25
we needed a particular transcription
00:16:27
factor to bind to that promoter region
00:16:29
and then what else did we need in order
00:16:31
for that to read the dna and make rna
00:16:33
you needed a particular rna polymerase
00:16:37
right so we need an
00:16:38
rna polymerase depending on which one
00:16:40
we're talking about
00:16:41
would depend on the type of rna that we
00:16:43
want to make
00:16:44
and then a transcription factor okay
00:16:48
now this is going to go read the dna
00:16:50
this rna polymerase will read the dna
00:16:52
and then make rna right now here let's
00:16:55
say that we have the promoter
00:16:56
and you can have this enhancer upstream
00:17:00
from the promoter or it could be down
00:17:02
here downstream where we can't see it in
00:17:03
this
00:17:04
diagram but it would be all the way down
00:17:05
here regardless of where it is it's
00:17:08
usually can be close to the promoter or
00:17:10
it can be far to the promoter so you're
00:17:11
probably asking the question how the
00:17:13
heck would an enhancer that's really far
00:17:15
away
00:17:16
influence a promoter that's all the way
00:17:18
down here how that does it do that
00:17:20
there's particular structures there's
00:17:22
different things
00:17:24
that can activate enhancers and cause
00:17:27
conformational changes of the dna
00:17:30
and these are called specific
00:17:32
transcription factors you know why i
00:17:34
really frustrate i got
00:17:35
really deep into talking about specific
00:17:37
and general transcription factors
00:17:39
the general transcription factors are
00:17:40
what bind to the promoter region
00:17:42
specific transcription factors which
00:17:45
we're going to really kind of do a
00:17:46
different color here let's do purple
00:17:48
specific transcription factors
00:17:51
will bind to this enhancer region so
00:17:54
this let's put specific
00:17:56
transcription factors these will bind
00:17:59
to the enhancer when they bind
00:18:02
to the enhancer region it causes a
00:18:06
looping of the dna to where now the
00:18:09
promoter was far
00:18:10
downstream from this enhancer but when
00:18:13
this
00:18:14
specific transcription factor binds to
00:18:16
the enhancer
00:18:18
it causes the dna to loop in a way that
00:18:20
it's in very close proximity to the
00:18:23
promoter region even though it's far
00:18:24
upstream from it
00:18:26
and then what was bound to this promoter
00:18:28
region here do you guys remember
00:18:31
the general transcription factors
00:18:34
and what else the rna
00:18:38
polymerase so now that these are in
00:18:42
close proximity guess what this
00:18:44
general trans this uh specific
00:18:46
transcription factor can do to this area
00:18:48
over here
00:18:49
it can act on these proteins and
00:18:53
stimulate this reading of the dna
00:18:56
the rna polymerase is to read the dna
00:18:58
and to do what
00:19:00
make rna
00:19:04
whether it be mrna rrna trna so the
00:19:06
whole point here is that
00:19:08
enhancers can be either far upstream or
00:19:10
far downstream which makes it hard to
00:19:12
interact with the promoter
00:19:13
but if a specific transcription factor
00:19:15
binds to that enhancer it creates a
00:19:17
looping process
00:19:18
bringing it in close proximity which can
00:19:21
then stimulate the
00:19:22
specific transcription factors and the
00:19:24
rna polymerases which are bound to the
00:19:26
promoter
00:19:27
to increase the transcription of rna
00:19:30
what do you think silencers do
00:19:32
the exact same process we're not going
00:19:34
to go into detail of it
00:19:35
but if you imagine i did the same thing
00:19:37
i put the silencer here
00:19:39
and i have a specific transcription
00:19:41
factor that bound here it's going to
00:19:42
fold it in a particular way bringing it
00:19:44
close to the promoter
00:19:45
inhibiting that promoter region and
00:19:47
slowing down the transcription process
00:19:50
it doesn't make sense it's pretty cool
00:19:52
too right so i need you guys to ask
00:19:53
yourself the questions because we're
00:19:54
going to talk about these
00:19:56
these general transcription factors what
00:19:58
in the world
00:20:00
are these specific transcription factors
00:20:02
and i know that if you guys are the og
00:20:04
ninjas
00:20:05
you'll know these processes in and out
00:20:08
you guys know when we make a protein
00:20:10
whenever we have like a cell
00:20:12
signaling response we've talked about
00:20:13
this a million times here an engineer
00:20:15
right
00:20:16
let's say that we take a hormone like
00:20:18
tsh which stimulates thyroid hormone
00:20:20
synthesis right tsh will act on a
00:20:23
particular receptor we call these
00:20:25
g-protein-coupled receptors right like
00:20:27
g-stimulatory proteins
00:20:29
those g-stimulatory proteins will
00:20:31
activate something called
00:20:33
cyclic amp cyclic amp will then activate
00:20:37
something called
00:20:38
protein kinase a protein kinase a
00:20:43
depending upon what type of you know
00:20:46
transcription factor you need in this
00:20:48
case
00:20:48
we're going to activate a very specific
00:20:51
transcription factor
00:20:52
for making what thyroid hormone
00:20:55
so some type of thyroid hormone
00:20:57
transcription factor
00:20:58
that'll be needed to bind to the
00:21:00
enhancer change the shape of it
00:21:02
activate the promoter have the rna
00:21:05
polymerase
00:21:06
read the gene that makes what hormone
00:21:09
thyroid hormone
00:21:10
and so you'd have this get read you'd
00:21:12
make an mrna
00:21:13
that would then get translated and make
00:21:17
thyroid hormone doesn't that make sense
00:21:20
how that process occurs
00:21:22
so we can increase the transcription and
00:21:25
protein formation of thyroid hormone
00:21:26
through this process the same thing
00:21:28
exists
00:21:28
with steroid hormones if i took for
00:21:31
example testosterone
00:21:33
you guys know testosterone right
00:21:35
testosterone does what
00:21:38
testosterone will move across
00:21:41
the cell membrane it'll bind onto a
00:21:44
intracellular receptor when testosterone
00:21:48
binds onto the intracellular receptor
00:21:49
what will that intracellular receptor do
00:21:52
bind to the enhancer when it binds to
00:21:54
the enhancer
00:21:55
loops it brings it close to the promoter
00:21:56
stimulates the transcription to make
00:21:58
proteins within muscle so that you can
00:21:59
get direct
00:22:00
right that's the whole process of how we
00:22:03
increase
00:22:04
transcription and the same thing would
00:22:06
happen if we wanted to decrease it just
00:22:08
we would have some type of
00:22:10
repressing transcription factor binding
00:22:13
to the silencer
00:22:14
that would inhibit the transcription
00:22:15
process so i think we have a pretty good
00:22:17
idea now of the basic concepts of
00:22:19
eukaryotic gene regulation
00:22:21
now spend most of our time talking about
00:22:23
the transcription particularly of
00:22:26
mrna all right so when we talk about
00:22:28
transcription we've had a basic concept
00:22:29
of it right that we need rna polymerases
00:22:31
and transcription factors to read the
00:22:32
dna and make the
00:22:34
rna but the real one that i want us to
00:22:36
primarily focus on
00:22:38
which is primarily important with
00:22:40
transcription of dna
00:22:41
is mrna that was the real important one
00:22:45
now that's in eukaryotic cells with
00:22:46
utilizing the what
00:22:48
rna polymerase type 2 in prokaryotic
00:22:50
cells we would just be using the
00:22:52
rna polymerase holoenzyme so what i want
00:22:54
us to do is i want us to go through
00:22:56
particularly and more d we already have
00:22:57
a basic concept of how this is going to
00:22:59
work
00:22:59
but let's go into the stages of
00:23:01
transcription particularly for
00:23:03
mrna within prokaryotic cells in
00:23:05
eukaryotic cells
00:23:06
the first stage that is involved here is
00:23:09
called initiation
00:23:11
of transcription so the first step that
00:23:13
we have to talk about is called
00:23:15
initiation of transcription now this is
00:23:18
the part that we've pretty much already
00:23:20
familiarized ourselves with
00:23:22
okay now within this let's have our two
00:23:26
cells
00:23:26
okay that we're going to do initiation
00:23:28
with we're going to have our prokaryotic
00:23:30
cells here
00:23:31
on this left side of the board
00:23:34
and then over here we're going to have
00:23:37
the eukaryotic cells here on the right
00:23:40
side of the board
00:23:41
what i want us to do is to have kind of
00:23:42
a comparison a side-by-side comparison
00:23:45
of the initiation process the first
00:23:48
thing that we need to know
00:23:49
is we've talked a little bit about this
00:23:51
already but this blue region what did we
00:23:53
call this blue region here again
00:23:55
this blue region was called the promoter
00:23:58
region
00:23:59
now the promoter region i told you is a
00:24:01
particular kind of like nucleotide
00:24:03
sequence that is very very specific and
00:24:05
allows transcription factors and rna
00:24:07
polymerases to bind to the dna
00:24:09
it's kind of a signal if you will it's
00:24:10
like hey here i am come bind to me
00:24:13
in prokaryotic cells the promoter
00:24:16
region has particular types of like
00:24:19
names and just
00:24:20
weird stuff that they can ask you in
00:24:22
your exams
00:24:24
so in the prokaryotic cells they call
00:24:26
this the third negative 35 region
00:24:29
which means from the start point at
00:24:31
which the rna polymerase starts reading
00:24:33
the dna and making rna
00:24:35
if you go back 35 nucleotides that's
00:24:37
kind of the
00:24:38
point at which the rna polymerases will
00:24:40
bind
00:24:41
in prokaryotic cells another one is
00:24:44
called the negative 10 region
00:24:46
but they wanted to give this one a name
00:24:48
so they called it the pribno box
00:24:50
just meaning that it's negative it's 10
00:24:52
nucleotides away from that startup
00:24:54
transcription right
00:24:56
and then the last one here is called the
00:24:58
plus one region which is also called the
00:25:01
transcription
00:25:02
start site so it's going to be pretty
00:25:03
much the nucleotide at which you just
00:25:05
read
00:25:06
and start making the whole process of
00:25:09
rna
00:25:10
so these are the regions that you guys
00:25:12
need to remember within prokaryotic
00:25:13
cells these are the kind of
00:25:14
specific promoter regions and eukaryotic
00:25:18
cells
00:25:19
the promoter regions have particular
00:25:23
nucleotide sequences that we need to be
00:25:24
aware of
00:25:26
these are called the top box which means
00:25:28
that you would have thymine adenine
00:25:29
thymine adenine
00:25:30
that would be a particular recognition
00:25:32
sequence within the promoter and
00:25:33
eukaryotic cells
00:25:35
or cat c-a-a-t so cytosine adenine
00:25:39
adenine thymine
00:25:40
and the last one is a gc box
00:25:43
so if there's a tata box a cap box or a
00:25:46
gc
00:25:47
box these are identify identifying
00:25:49
nucleotide areas at which the rna
00:25:51
polymerase is type 2
00:25:53
and transcription factors will bind to
00:25:56
that is the important thing okay now the
00:25:59
next thing here is
00:26:00
the polymerases the rna polymerase is
00:26:03
within prokaryotic cells it's just
00:26:05
one it's rna polymerase
00:26:09
holoenzyme right we already kind of
00:26:12
talked about that with the core enzyme
00:26:14
two alpha beta beta prime omega and then
00:26:16
the
00:26:16
the sigma subunit all of that's needed
00:26:19
to bind to the promoter region
00:26:21
and eukaryotic tells us a little bit
00:26:22
more right we said that we needed two
00:26:24
things we needed an rna polymerase
00:26:26
and which what are we making here
00:26:28
initiation and we're going to say that
00:26:30
we're trying to make what
00:26:31
we're trying to make mrna transcription
00:26:34
so we're doing
00:26:34
transcription but we're making mrna so
00:26:37
what was the particular rna polymerase
00:26:39
1 2 3 r m m is
00:26:44
for r for the mrna so rna polymerase
00:26:46
type 2 is one of the things that i need
00:26:48
the second thing that i need is the
00:26:52
general transcription factors
00:26:55
and there's just so many of these that i
00:26:57
don't know how important and how
00:26:59
specific we really need to go into these
00:27:01
i'll give you some of them but i just
00:27:03
want you to know
00:27:04
that there's so many different types of
00:27:06
them the main one if you had to remember
00:27:09
one specific out of the tons of them i
00:27:12
want you to remember transcription
00:27:14
factor
00:27:14
2 d this is the one that i really want
00:27:17
you to remember and the reason why is
00:27:20
this contains a structure called the
00:27:22
tata binding protein so this
00:27:23
transcription factor 2d has a particular
00:27:25
protein portion
00:27:27
which binds to the promoter region the
00:27:30
tata box
00:27:31
but there's many other reasons region
00:27:34
transcription factors and you can
00:27:36
remember these by transcription factor
00:27:38
2 and there can be h there can be e
00:27:41
there can be f there can be a there can
00:27:43
be b so there's tons of these dang
00:27:45
things
00:27:46
so i don't know how important it really
00:27:47
is to know that but the main one i want
00:27:49
you to remember
00:27:50
is the transcription factor 2d all right
00:27:54
so these are the things that we need in
00:27:55
order for initiation to occur
00:27:57
so let's take for example we're going to
00:27:58
have on one side
00:28:00
eukaryotic cells will the eukaryotic
00:28:02
enzymes will bind
00:28:03
and on this side the prokaryotic will
00:28:05
bind right so let's say here we take for
00:28:07
example we'll make this prokaryotic rna
00:28:09
polymerase
00:28:11
we'll make this one blue
00:28:14
and we'll make the rna polymerase over
00:28:16
here for the eukaryotic cells just for
00:28:18
the heck of it
00:28:19
we'll make it orange okay just so we can
00:28:21
distinguish the difference between these
00:28:23
so what will happen this whole rna
00:28:26
polymerase holoenzyme will do what
00:28:31
bind to the promoter what will allow it
00:28:32
to bind what
00:28:34
subunit of it the sigma subunit and if
00:28:37
you really wanted to go back
00:28:38
you guys remember we made that pink
00:28:42
okay for the eukaryotic cells
00:28:45
what do we need we need the rna
00:28:47
polymerase type 2. we said we're going
00:28:48
to represent that with
00:28:50
orange so here's going to be the rna
00:28:53
polymerase
00:28:54
type 2 and then what else do we need we
00:28:57
need those
00:28:58
general transcription factors there's a
00:29:00
bunch of them but what's the particular
00:29:02
one that i really want you to remember
00:29:04
here
00:29:04
transcription factor 2 d
00:29:08
which contains the tata binding protein
00:29:10
so it binds to the tata box which is the
00:29:12
promoter region in the eukaryotic cells
00:29:14
then allows the rna polymerase 2 to bind
00:29:17
to the dna
00:29:18
now once the rna polymerase is bound to
00:29:20
the dna it's going to start
00:29:22
moving down the dna strands reading it
00:29:25
and making rna
00:29:26
so we've now started the process of
00:29:28
transcription that's all that's
00:29:29
happening here
00:29:31
the next step is that once we've bound
00:29:34
had
00:29:34
this rna so let's write these down here
00:29:36
for the prokaryotic cell this would be
00:29:38
the
00:29:38
we'll put rna polymerase and we'll put h
00:29:42
for the holoenzyme and for that one up
00:29:45
here this is going to be
00:29:47
rna polymerase type 2
00:29:50
right once this is bound and it's in the
00:29:53
dna it's going to start
00:29:54
reading the dna as it reads the dna
00:29:58
it'll make mrna that process by which it
00:30:01
does that is called
00:30:03
elongation so let's write that down now
00:30:06
so the next step
00:30:07
is elongation to make
00:30:11
the mrna now within elongation a couple
00:30:16
different things happens
00:30:18
and this is thankfully the same in
00:30:20
prokaryotic cells and eukaryotic
00:30:22
cells so thank the lord for that right
00:30:23
so let's just say that we take
00:30:25
either one of these rna polymerases
00:30:27
let's just for the heck of it we'll say
00:30:29
here's your rna polymerase ii okay
00:30:33
here's your rna polymerase two and it's
00:30:34
reading the dna
00:30:36
the dna we already know has two strands
00:30:39
we're going to call this top strand here
00:30:42
this top strand sonogram this top strand
00:30:44
up here we're going to call this the
00:30:46
template strand so the template strand
00:30:50
also sometimes referred to as the
00:30:55
anti-sense
00:30:57
strand this strand down here we're going
00:30:59
to call
00:31:00
the coding strand
00:31:04
now when rna polymerases read dna
00:31:07
the strand that they read is the
00:31:10
template strand or the antisense strand
00:31:13
so that's the first thing i really need
00:31:15
you guys to remember
00:31:16
is that the rna polymerases
00:31:20
what strand do they read they read
00:31:24
we're going to put the template strand
00:31:27
or also referred to as what else
00:31:30
the antisense strand and that's the
00:31:32
strand that they use to make the mrna
00:31:34
they do not use the coding strand
00:31:37
so let's kind of put a little asterisk
00:31:38
here that this is the strand that we're
00:31:39
gonna read
00:31:40
now when it reads it it does it in a way
00:31:43
that you guys if you guys watch our dna
00:31:44
replication video this should be
00:31:46
so darn easy let's say here
00:31:50
this end of the dna is the three
00:31:53
prime end that means that this end is
00:31:56
the
00:31:57
five prime end and remember one strand
00:32:00
of dna
00:32:01
on this side should have a complementary
00:32:04
anti-parallel strand on the other side
00:32:06
which means that this is the three and
00:32:08
on here
00:32:08
this has to be the five end on this side
00:32:11
and this has to be the
00:32:13
three end on that side what happens is
00:32:16
this rna polymerase when it binds into
00:32:18
the dna
00:32:19
it does something very interesting it
00:32:21
binds to the dna through the initiation
00:32:23
process
00:32:23
and then opens up the dna who opened up
00:32:27
the dna before it was that whole
00:32:29
in replication it was that whole like
00:32:30
replication complex
00:32:32
rna polymerase does that so the first
00:32:33
thing we need to know is that rna
00:32:35
polymerase does what
00:32:37
it opens the dna
00:32:40
now in replication what else happened
00:32:41
you opened the dna and you had those
00:32:42
single stranded binding proteins which
00:32:44
keep it stable and kept it open right
00:32:46
rna polymerase does that on its own so
00:32:48
it also
00:32:49
stabilizes the single
00:32:53
stranded dna molecules right so it
00:32:55
stabilizes the single strands
00:32:57
then what was the enzyme in replication
00:33:00
that opened up to unwound the dna
00:33:02
helicase rna polymerase has its
00:33:05
intrinsic helicase activity so it also
00:33:08
unwinds the dna
00:33:12
after it unwinds the dna then it starts
00:33:14
reading the dna
00:33:15
so let's say here as it reads the dna in
00:33:18
this direction
00:33:19
three to five it'll make mrna
00:33:24
that'll be going in the opposite
00:33:26
direction so it's going to read this 3
00:33:28
all the way to the 5 direction and as it
00:33:31
does that it starts synthesizing
00:33:33
mrna right and this mrna
00:33:37
will be synthesized in what direction
00:33:38
what will this be this starting point
00:33:41
the five end and what would be this
00:33:43
point
00:33:44
the three end so we know the next thing
00:33:46
that the rna polymerase does
00:33:48
whether it be in prokaryotic cells or
00:33:50
eukaryotic cells
00:33:52
is it reads the dna
00:33:55
from three to five
00:33:58
then it synthesizes
00:34:02
rna from what direction guys
00:34:07
five to three very
00:34:10
very important the last thing that you
00:34:12
guys should be asking is okay zach you
00:34:14
also
00:34:15
said that in replication the dna
00:34:18
polymerases read the dna
00:34:20
and then if there was an accident or a
00:34:22
mistake they would proofread it and then
00:34:24
cut out the nucleotide
00:34:25
what about rna polymerases do they do
00:34:26
that as well because it looks like
00:34:27
they've done everything that was similar
00:34:29
in dna replication
00:34:30
that's the one thing that's
00:34:31
controversial so the only thing that's
00:34:33
kind of relatively controversial
00:34:35
is is there a proof reading function we
00:34:38
don't really know it's still subject to
00:34:39
study
00:34:40
so that's one thing to remember if you
00:34:42
want to compare this
00:34:43
the proofreading function is somewhat
00:34:46
uncertain
00:34:47
at this point in time all right so we
00:34:50
have an idea now we've
00:34:51
read this dna and we've made rna
00:34:54
i know we talked about this a lot in dna
00:34:56
replication we're talking about it here
00:34:58
and sometimes it really can be confusing
00:35:00
when you're saying
00:35:01
five end three and i don't i don't i
00:35:03
don't freaking get what you're talking
00:35:04
about zach
00:35:04
so i want to take a quick little second
00:35:06
and explain what the heck i mean when i
00:35:08
say it reads it from three
00:35:09
to five and synthesizes it from five to
00:35:11
three a diagram i really think will
00:35:13
clear this up for you
00:35:14
let's take a second to understand what i
00:35:16
mean by reading the dna three to five
00:35:18
and then
00:35:19
synthesizing it five to three i think
00:35:20
it's really important to understand that
00:35:22
so let's say here we have this strand of
00:35:25
dna so this is
00:35:26
this is going to be our dna
00:35:30
template if you will
00:35:33
okay so this is our dna template on this
00:35:35
side the blue one
00:35:36
and then this is going to be the rna
00:35:39
that we're going to synthesize utilizing
00:35:41
the rna polymerase type 2 and eukaryotes
00:35:43
are the rna polymerase hollow enzyme and
00:35:44
prokaryotes
00:35:46
now when we're making this rna we have
00:35:48
to read
00:35:49
the dna in what direction the three end
00:35:52
to the five and what is the three and
00:35:54
you guys remember the video on dna
00:35:55
structure
00:35:56
it's the oh so this is going to be the
00:35:59
three end
00:35:59
what's the five end it's the phosphate
00:36:02
group
00:36:02
so the phosphate group is going to be
00:36:04
the five and so i have to read this
00:36:06
starting at the o h portion towards the
00:36:09
five end where the phosphate is so the
00:36:13
rna polymerase let's pretend i'm the rna
00:36:15
polymerase i'm walking right
00:36:16
to do i find the three prime and i'm
00:36:18
like oh there it is okay i'm gonna move
00:36:20
up oh i found the
00:36:21
three prime five prime let me just fill
00:36:22
this up oh i feel my nitrogenous base
00:36:25
the nitrogenous base that it feels is
00:36:27
adenine so it picks into its little
00:36:29
satchel of nucleotides it's like okay
00:36:31
this is adenine
00:36:32
the complementary base for is thymine uh
00:36:35
oh no that's not correct because you
00:36:37
guys know
00:36:38
that if we're taking dna making rna
00:36:41
what's the one nucleotide that
00:36:42
switches from dna and rna adenine is no
00:36:46
longer complementary to thymine
00:36:48
in the rna it is uracil
00:36:52
so the dna the rna polymerase will come
00:36:54
read find the three end
00:36:56
read the nucleotide and say oop okay
00:36:58
this is an adenine
00:36:59
reach into its satchel of a bunch of
00:37:01
nucleotides and pull out
00:37:03
uracil when it pulls that out it then
00:37:06
puts the nucleotide in a particular
00:37:08
orientation
00:37:10
what's the orientation we said it reads
00:37:11
it from three to five
00:37:13
and synthesizes it from five to three
00:37:15
what's the five
00:37:16
end here's the nucleotide the five end
00:37:19
is this
00:37:19
phosphate group the three end
00:37:22
is this oh group so it's going to kind
00:37:24
of flip the nucleotide the opposite
00:37:27
direction
00:37:28
and make sure that the nitrogenous base
00:37:30
here is what
00:37:31
uracil then when it does that it's going
00:37:34
to go to the next one so it's going to
00:37:35
continue it's going to go to the next
00:37:36
point
00:37:37
here's where the next oh group would be
00:37:38
right the three prime end
00:37:40
reads it finds that finds the nucleotide
00:37:42
it says oh the nitrogenous base here is
00:37:45
t let me reach into my satchel of a
00:37:47
bunch of different uh
00:37:49
good old nucleotides i'm going to read
00:37:50
it t goes with a
00:37:52
i'm going to put my nucleotide and i'm
00:37:53
going to flip it where it's five prime
00:37:55
end
00:37:56
going down three prime end pointing up
00:37:59
and then the nitrogenous base which is
00:38:02
complementary to the t
00:38:03
is a when it does that
00:38:06
it then fuses the three prime end
00:38:10
and the five prime end together making a
00:38:13
bond what is that bond called
00:38:14
the phosphodiester bond and the same
00:38:17
process occurs
00:38:18
so then it'll do what let's fix this
00:38:21
three prime in there
00:38:22
it'll then go go to the next nucleotide
00:38:24
here's the three prime end where the oh
00:38:26
group is
00:38:26
reads it finds the nucleotide says that
00:38:29
it's a g reaches into its satchel pulls
00:38:31
out a nucleotide
00:38:32
with the cytosine when it does it it
00:38:34
flips it to where the five
00:38:35
end is on this side there's my phosphate
00:38:38
the three prime end is upwards
00:38:40
and it says oh the nucleotide that goes
00:38:42
with this
00:38:43
is with the nitrogenous base c then it
00:38:46
says oh
00:38:46
i have my phi prime n situated close to
00:38:49
the three prime end of the preceding
00:38:51
nucleotide
00:38:52
let me fuse these two together and make
00:38:54
my phosphate ester bond
00:38:56
and just for the heck of it because
00:38:57
repet repetition i guess is helpful
00:38:59
we go reads this says okay next one
00:39:02
here's my three prime end where the oh
00:39:03
group is
00:39:04
read it find the nitrogenous base it's a
00:39:06
cytosine
00:39:09
digs into its satchel pulls out the
00:39:10
nucleotide guanosine
00:39:13
sorry the guanine nitrogenous base then
00:39:15
when it does that
00:39:16
it situates it where the five prime end
00:39:19
is situated down
00:39:21
three prime n is situated upwards in
00:39:22
this case and then
00:39:24
the nitrogenous bases on guanine
00:39:28
then it says oh my five prime n i can
00:39:30
stitch it to the three prime end of the
00:39:32
preceding nucleotide
00:39:33
and form my phosphodiester bond and
00:39:35
that's how we make rna
00:39:37
reading it three to five and
00:39:40
synthesizing it from five to
00:39:42
three dang we good all right
00:39:45
now that we've done that the last thing
00:39:47
i need you to understand is that
00:39:48
rna polymerase is a very important
00:39:50
enzyme within eukaryotic and prokaryotic
00:39:52
cells
00:39:54
a question that can come up and it's so
00:39:56
dumb and annoying but you should know it
00:39:59
is that in eukaryotic cells
00:40:02
we can inhibit the rna polymerase
00:40:06
by using a kind of toxin amanitin it's
00:40:10
for mushrooms
00:40:11
and this can inhibit the rna polymerase
00:40:14
within we'll put eukaryotic cells
00:40:18
okay there's another drug
00:40:21
which they love to ask in the exams as
00:40:23
well called rifampicin it's an
00:40:24
antibiotic
00:40:27
and this inhibits the rna polymerase
00:40:31
within if it's an antibiotic that's good
00:40:33
against bacteria prokaryotic cells
00:40:35
so this will inhibit the rna polymerase
00:40:37
within prokaryotic cells
00:40:39
which would inhibit what the part of the
00:40:42
initiation
00:40:43
the elongation basically making rna if
00:40:45
you can't make rna you can't make
00:40:46
proteins
00:40:47
if you can't make proteins you can't
00:40:48
perform the general functions of the
00:40:50
cell
00:40:51
so this is kind of from a poisonous
00:40:54
mushroom which is stupid to know that
00:40:55
but they like to ask it on your exams
00:40:57
and then rifampicin is an antibiotic
00:40:58
which they also love to ask
00:41:00
okay now we've talked about elongation
00:41:03
we've made the dang rna
00:41:05
rna polymerase is working real hard the
00:41:08
last thing we got to do is we got to
00:41:09
just
00:41:09
end it we don't need any more rna we've
00:41:11
made the rna that we need to make the
00:41:12
protein
00:41:13
that is called termination all right so
00:41:16
we talked about elongation the next step
00:41:18
the last step really that we got to
00:41:20
discuss here is
00:41:21
termination we've got to end this whole
00:41:23
transcription process so the last step
00:41:25
is
00:41:25
termination now unfortunately
00:41:27
termination is probably one of the more
00:41:29
annoying and complicated ones
00:41:31
unfortunately
00:41:32
and it is different in prokaryotes and
00:41:34
eukaryotes that's why it kind of makes
00:41:35
it a little bit frustrating
00:41:37
but termination is basically where we've
00:41:40
already made our rna transcript and we
00:41:43
just need to
00:41:44
detach it or disassociate it away from
00:41:46
the dna and
00:41:47
prevent that rna polymerase from reading
00:41:50
any more of the dna and making any more
00:41:51
rna so just stop
00:41:52
transcription how do we do that in
00:41:55
prokaryotes there's two mechanisms
00:41:58
one of the ways that this happens is
00:42:00
through what's called
00:42:02
road dependent termination so one is via
00:42:04
this process called row
00:42:07
dependent termination and it's really
00:42:10
simple believe it or not
00:42:12
so let's say here we take the
00:42:13
prokaryotics we we picked blue for our
00:42:16
rna polymerase so the rna polymerase
00:42:18
here's our rna polymerase
00:42:20
it's reading this dna as it's reading
00:42:23
the dna again what is it making from it
00:42:26
you guys remember it's making the rna in
00:42:29
this case
00:42:30
it could be any rna it could be the mrna
00:42:32
trna rna whatever
00:42:35
as it does this there's a protein called
00:42:37
rho
00:42:38
and what rho does is this rho protein
00:42:42
will start moving up the mrna
00:42:45
and as it moves up the rna that's being
00:42:47
synthesized by the rna polymerase as it
00:42:49
gets to this rna polymerase it basically
00:42:53
says hey
00:42:54
it just punches the rna polymerase off
00:42:56
the dna
00:42:58
if you punch the rna polymerase off the
00:43:01
dna
00:43:02
is it going to be able to continue to
00:43:03
keep breeding the dna and making
00:43:05
any more rna no so that terminates the
00:43:08
transcription process
00:43:10
so the big thing i need you guys to know
00:43:11
here is that with the road dependent
00:43:13
termination
00:43:14
is rho protein
00:43:17
causes rna polymerase
00:43:21
uh to break away to disassociate if you
00:43:25
will
00:43:25
okay to break
00:43:29
away from the dna okay
00:43:32
all right beautiful the next mechanism
00:43:35
within prokaryotes
00:43:37
is rho independent termination so we
00:43:40
don't use the row protein
00:43:41
so we call this row
00:43:45
independent termination now with this
00:43:48
process it's a little bit more
00:43:49
complicated and a little annoying
00:43:52
let's say here we have the dna right and
00:43:54
within the dna we're going to mark these
00:43:56
here we're going to say this is our
00:43:57
template strand right so this strand is
00:43:59
the template strand
00:44:01
right or the antisense strand and then
00:44:03
this is going to be our coding strand
00:44:05
so which one does the rna polymerase
00:44:08
read it reads the
00:44:09
template strand or the antisense strand
00:44:12
there's a particular like thing called
00:44:14
inverted repeats that form within the
00:44:17
dna that the rna polymerase is reading
00:44:20
so what happens is this rna polymerase
00:44:22
will bind
00:44:23
to that template strand and it'll start
00:44:25
reading it
00:44:26
making the rna as it starts making this
00:44:29
rna
00:44:30
it it encounters a particular sequence
00:44:33
of
00:44:34
of dna called inverted repeats let's
00:44:37
write these inverted repeats out in kind
00:44:38
of a nice little color let's do let's do
00:44:40
orange
00:44:42
and let's say here we have an inverted
00:44:43
repeat where we have c
00:44:45
c g g and then a bunch of nucleotides
00:44:48
that we don't care about
00:44:50
and then here we'll have ggcc
00:44:55
okay then we're just going to have this
00:44:57
is the template again
00:44:58
on the coding strain it would just be
00:45:00
the complementary base so if this was cc
00:45:02
this would be gg
00:45:04
cc we don't really care about these
00:45:06
nucleotides cc
00:45:08
gg right the rna polymerase is going to
00:45:11
read this template strand what happens
00:45:13
is right you're going to get this kind
00:45:15
of strand here where you'll have
00:45:17
a bunch of nucleotides already kind of
00:45:18
made up here
00:45:20
and then it reaches this kind of like
00:45:21
inverted repeat area
00:45:23
and what happens is it reads this and
00:45:25
then basically everything you read
00:45:27
within the template strand should be the
00:45:28
same as it is in the coding strand
00:45:30
because it's the complementary base
00:45:31
so you'll have g g c
00:45:34
c that it'll make a bunch of nucleotides
00:45:36
we don't care about
00:45:37
and then c c g g
00:45:41
what happens is whenever this
00:45:44
rna is kind of coming and being
00:45:46
transcribed from the rna polymerase
00:45:48
something interesting happens where some
00:45:50
of these c's and some of these g's on
00:45:53
this portion have a strong affinity for
00:45:56
some of the c's and some of the g's
00:45:58
in this portion of the rna and as they
00:46:01
start having this affinity they start
00:46:02
approaching and kind of wanting to
00:46:04
interact with one another via these
00:46:05
hydrogen bonds
00:46:07
and so it creates this really
00:46:09
interesting kind of like hairpin loop if
00:46:11
you will
00:46:12
where there's a bunch of g's and c's
00:46:15
within this kind of hairpin loop
00:46:19
that are kind of interacting with one
00:46:21
another and what happens
00:46:23
is that hairpin loop is what
00:46:26
triggers the rna polymerase to pretty
00:46:29
much
00:46:30
hop off of the dna and terminate the
00:46:32
transcription process
00:46:34
because what happens is once you form
00:46:35
this hairpin loop what will happen is
00:46:37
there's going to be particular enzymes
00:46:39
that will
00:46:39
bind to that portion and cleave the d
00:46:42
the rna
00:46:43
away from the rna polymerase so the big
00:46:46
thing i need you to
00:46:47
know within row independent termination
00:46:50
is that you'll hit this area the rna
00:46:51
polymerase will be transcribing
00:46:53
reading the dna making rna it'll hit
00:46:55
these areas of inverted repeats
00:46:58
when these inverted repeats are made
00:47:00
they create this thing called a
00:47:03
hairpin loop this hairpin loop
00:47:07
will then trigger particular cleavage
00:47:10
enzymes
00:47:11
to come and cleave a couple nucleotides
00:47:15
after that hairpin loop
00:47:16
to cleave that away from the rna
00:47:19
polymerase
00:47:20
and then here you have your rna that you
00:47:23
formed
00:47:24
so that is one of the ways that we have
00:47:25
termination road
00:47:27
independent via prokaryotes the last
00:47:30
termination mechanism is going to be
00:47:32
eukaryotic cells now how does this work
00:47:36
this one's actually relatively simple so
00:47:38
we had the rna polymerase in eukaryotes
00:47:40
and this was orange
00:47:42
okay it's binding to the dna it's
00:47:44
reading the dna
00:47:45
as it's reading the dna it's making rna
00:47:50
as it starts making this rna it hits a
00:47:52
particular sequence
00:47:54
where when it starts reading the dna and
00:47:56
makes rna
00:47:58
it makes a particular sequence of
00:48:01
a a u a a
00:48:04
a okay so what are the what is the
00:48:06
nucleotide sequence here let's write it
00:48:08
out
00:48:08
this portion here will be double a u
00:48:11
triple a this is what's called a
00:48:14
polyadenylation signal
00:48:16
so what is this called here this is
00:48:18
called a poly
00:48:19
adenylation signal
00:48:24
and once this kind of nucleotide
00:48:27
sequence occurs
00:48:28
so it's kind of now that we know what
00:48:29
that nucleotide sequence is let's kind
00:48:30
of just put like this
00:48:33
here's that nucleotide sequence that
00:48:34
polyadenylation signal
00:48:36
that's been synthesized or formed by the
00:48:38
rna polymerase with the eukaryotes
00:48:40
once that happens it activates
00:48:42
particular
00:48:43
enzymes and those enzymes will come to
00:48:46
the area here
00:48:49
and cleave the rna away from the rna
00:48:52
polymerase
00:48:53
separating out this rna away
00:48:58
from the dna and the rna polymerase and
00:49:00
then again what will i have at this
00:49:01
portion here
00:49:02
just as kind of a diagrammatic portion
00:49:05
here this will be my
00:49:06
polyadenylation signal this is important
00:49:09
because we're going to talk about
00:49:10
post-transcriptional modification in a
00:49:11
second
00:49:12
so i know this was a lot of crap just
00:49:14
really quickly
00:49:15
recap because this is one of the
00:49:16
toughest parts of transcription
00:49:18
is termination prokaryotes there's two
00:49:20
ways road dependent row independent
00:49:23
with this one you need a row protein to
00:49:25
knock the rna polymerase off if you
00:49:26
don't have him he can't make any more
00:49:28
rna
00:49:29
the other one is row independent you
00:49:30
don't have a row protein
00:49:32
the rna polymerase is reading the dna
00:49:34
making rna and it hits these areas of
00:49:37
inverted repeats these inverted repeats
00:49:40
when they're made within the
00:49:41
rna it creates a hydrogen bond
00:49:44
interaction between them
00:49:46
which causes it to loop forming a
00:49:47
hairpin loop that
00:49:49
signals particular enzymes to break the
00:49:52
rna
00:49:53
away from the rna polymerase and we've
00:49:55
made our rna there
00:49:56
the last one is in eukaryotes the rna
00:49:59
polymerase is reading the dna
00:50:01
and it reaches a particular sequence of
00:50:02
nucleotides where it reads
00:50:04
and then makes a a u
00:50:08
triple a a polyadenylation signal which
00:50:11
activates enzymes to come
00:50:12
cleave the rna away from the rna
00:50:14
polymerase terminating
00:50:16
the transcription process that really
00:50:19
hammers this home let's now talk about
00:50:21
post-transcriptional modification
00:50:22
we know at this point how to take dna
00:50:25
make rna
00:50:26
right we talked about all the different
00:50:27
types of rna utilizing rna polymerases
00:50:29
utilizing the transcription factors we
00:50:30
talked a little about a gene regulation
00:50:32
we even went through all the stages of
00:50:34
transcription
00:50:36
taking the dna and making the mrna
00:50:39
all the way up until the point where we
00:50:41
finally made the mrna and broken it away
00:50:44
from the dna
00:50:45
unfortunately that's not it for
00:50:47
transcription
00:50:48
now we have this mrna right so we
00:50:51
basically what have we covered up to
00:50:53
this point
00:50:54
we took the dna
00:50:57
we read let's just say here
00:51:01
at this portion i'll just put here's our
00:51:03
promoter
00:51:04
our rna polymerase has read this gene
00:51:06
sequence
00:51:08
we hit a termination sequence let's say
00:51:10
here's our termination sequence
00:51:12
that we talked about here and once we
00:51:15
hit that termination sequence
00:51:17
the rna polymerase will fall off and
00:51:19
then from this you'll make the
00:51:21
rna so this was pretty much the basic
00:51:23
aspects of the transcription
00:51:26
but now we got to modify this now here's
00:51:28
the thing
00:51:30
it's actually kind of a misnomer to say
00:51:32
that this
00:51:33
is mrna it's technically not mrna right
00:51:37
now
00:51:37
so this piece of rna that we made okay
00:51:41
and this is this process of
00:51:42
post-transcriptional modification
00:51:44
this only occurs it's very important let
00:51:46
me actually write this down
00:51:47
this only occurs in
00:51:50
eukaryotic cells so that's nice
00:51:53
all this stuff that we're going to talk
00:51:54
about here is only in eukaryotic cells
00:51:56
it doesn't happen in prokaryotic cells
00:51:57
so they just make their rna and that's
00:51:59
it so technically
00:52:01
this immature mrna if you will we
00:52:03
actually give it a very specific name we
00:52:05
call it heterogeneous
00:52:07
nuclear rna now
00:52:10
this heterogeneous nuclear rna is kind
00:52:12
of an immature
00:52:14
mrna that has to go through some
00:52:15
modifications to really make mature
00:52:18
mrna that then can be translated to make
00:52:20
proteins
00:52:21
what are those modifications the first
00:52:24
thing that we have to do
00:52:26
is we have to put something on one of
00:52:29
these ends so now we got to know a
00:52:30
little bit about the
00:52:31
terminology of the ends of this immature
00:52:35
mrna or hn rna on this end
00:52:38
we're going to call this the five prime
00:52:41
end what's on that five prime end do you
00:52:42
guys remember
00:52:43
the phosphate groups what's on this end
00:52:46
the three prime end what's on the three
00:52:47
prime mint
00:52:48
the oh group okay now
00:52:51
something very interesting is on the
00:52:52
five prime end on the five prime end of
00:52:55
this heterogeneous nuclear rna or the
00:52:57
hrna
00:52:58
you have a triphosphate which we're
00:53:00
representing here with these
00:53:02
orange circles an enzyme
00:53:05
comes to the rescue and cleaves off
00:53:09
one of those phosphate molecules what is
00:53:11
that enzyme called
00:53:12
it's this orange little cute enzyme this
00:53:15
orange enzyme is called
00:53:17
rna tri-phosphatase
00:53:23
and what it does is it comes and cleaves
00:53:26
off
00:53:27
what portion it cleaves off one of these
00:53:31
phosphate groups it's going to cleave
00:53:33
off one of the phosphate groups
00:53:34
so now i only have two phosphates on the
00:53:37
end
00:53:38
of this five prime end then another
00:53:41
enzyme comes in
00:53:42
and it says hey there's only two
00:53:44
phosphates here
00:53:45
i can now add something on here and i'm
00:53:49
going to add on what's called a
00:53:52
gmp molecule what am i going to add on
00:53:54
again
00:53:55
i'm going to add a gmp molecule which is
00:53:58
guanosine monophosphate so we're going
00:54:01
to represent that here which
00:54:03
we add on the phosphate for the
00:54:05
guanosine monophosphate
00:54:07
and then we're going to just represent
00:54:08
this as the guanosine so this is our
00:54:10
guanosine and that blue circle there is
00:54:12
the phosphate on the guanosine
00:54:14
so what does he add on technically
00:54:17
he adds on to this little two phosphates
00:54:20
right
00:54:21
it adds in gtp but
00:54:24
when it does that two phosphates are
00:54:27
released
00:54:28
in the form of pyrophosphate which then
00:54:31
get broken down by pyrophosphatase into
00:54:34
individual phosphates so if i took gtp
00:54:37
and i removed two phosphates what am i
00:54:39
left with
00:54:40
gmp so it adds on this gmp group
00:54:43
onto that two phosphate end on the five
00:54:46
prime end
00:54:47
so this enzyme that adds that gmp on in
00:54:50
the form of gtp is called
00:54:52
guanolile
00:54:55
uh transferase
00:54:58
guanalyl transferase beautiful
00:55:02
so this last enzyme here which is
00:55:03
involved in this step here on the five
00:55:05
prime n
00:55:06
is going to add on a methyl group onto
00:55:09
one of the
00:55:10
components of the guanosine
00:55:11
monophosphate it's actually like one of
00:55:14
the seventh
00:55:14
components on that structure it adds on
00:55:17
a methyl group
00:55:19
and so at the end of this this enzyme
00:55:23
which adds a methyl group on what do you
00:55:24
think it's called methyltransferase
00:55:30
at the end of this process where you
00:55:32
took the prime end which had three
00:55:33
phosphates got rid of one
00:55:36
took the guanola transfers added on the
00:55:37
gmp took the methyl transferase added on
00:55:40
that methyl group
00:55:41
you formed this complex here and we call
00:55:43
this whole complex that we just added on
00:55:46
a seven methyl guanosine group
00:55:49
okay and that's on that five prime end
00:55:53
this is called capping
00:55:57
this is called capping so whatever we've
00:55:59
just done on this
00:56:00
five prime end is called capping what
00:56:03
the heck do we do all this stuff for
00:56:05
the whole purpose of capping
00:56:08
is to help to initiate
00:56:13
translation so this sequence this kind
00:56:15
of five prime end
00:56:16
with that seven methyl guanosine or that
00:56:18
five prime capping if you will
00:56:21
it's kind of a signal sequence if you
00:56:23
will that allow for it to interact with
00:56:25
the ribosome
00:56:26
and undergo translation the other thing
00:56:28
it does is it
00:56:30
prevents degradation by
00:56:33
nuclease enzymes that want to come and
00:56:35
break down
00:56:36
the rna so it helps to prevent
00:56:38
degradation helps to initiate the
00:56:40
translation process
00:56:43
one more thing that they it's a dumb
00:56:45
thing to know but they love to ask it
00:56:47
is that there is a particular molecule
00:56:51
that this methyltransferase
00:56:52
uses to add that methyl group on and
00:56:55
sometimes it's really important to know
00:56:56
it
00:56:57
and this is called s adenosyl methionine
00:57:00
also known as
00:57:01
sam sam carries a methyl group it's like
00:57:04
a methyl donor if you will
00:57:06
it gives that methyl group to the methyl
00:57:09
transferase
00:57:10
and the methyl transferase adds that
00:57:12
methyl group onto the guanosine
00:57:13
monophosphate forming the
00:57:15
7-methylguanosine
00:57:17
or that 5-prime cap okay
00:57:20
so that's the first thing that happens
00:57:22
now we got to talk about the 3-prime end
00:57:24
on the three prime end we had that oh
00:57:26
group right that's the ohn but do you
00:57:28
remember
00:57:30
in eukaryote there was a particular
00:57:32
signal
00:57:33
that prevent that generated that
00:57:36
terminated transcription what was that
00:57:38
nucleotide signal do you guys remember
00:57:40
test your knowledge guys
00:57:42
a a u
00:57:45
triple a right that was that
00:57:47
polyadenylation signal do you guys
00:57:49
remember that the polyadenylation
00:57:50
segment we talked about in eukaryotes
00:57:53
that polyadenylation signal is
00:57:55
recognizable
00:57:56
by this cute little purple enzyme here
00:57:59
this cute little purple enzyme is called
00:58:01
poly a
00:58:04
polymerase it's called
00:58:08
poly a polymerase what it does is on
00:58:11
this
00:58:11
hand it has a bunch of
00:58:15
adenine
00:58:19
nucleotides right so it can eat a lot of
00:58:21
nucleotides containing the adenine
00:58:22
nitrogenous base
00:58:24
it takes one end and identifies that
00:58:27
polyadenylation signal
00:58:28
takes the other end and adds on
00:58:32
all of those adenine nucleotides a bunch
00:58:37
of them
00:58:37
sometimes up to 200 adenine nucleotides
00:58:41
when it does that this forms a tail
00:58:44
on that three prime end with a bunch of
00:58:47
adenine nucleotides and we call this the
00:58:50
poly a tail
00:58:54
so the poly a tail what's the purpose of
00:58:58
this
00:58:58
it's the exact same thing helps to
00:59:01
initiate
00:59:02
the translation process
00:59:06
and helps to decrease degradation
00:59:10
by what kind of enzymes nucleases that
00:59:13
will try to come and break down that end
00:59:15
okay the other thing that they do is
00:59:17
they help transport this
00:59:20
hn rna eventually they're going to help
00:59:22
to transport the
00:59:24
hnrna which will become mrna out of the
00:59:26
nucleus into the cytosol so they also
00:59:28
play a little bit of a role in
00:59:29
transport out of the nucleus and into
00:59:32
the cytosol
00:59:34
okay so within this first step what did
00:59:37
we do
00:59:38
we did five prime capping we went over
00:59:40
that part and the three prime
00:59:42
poly a tail that we did okay now we have
00:59:46
this so after we did all of this massive
00:59:48
mess
00:59:49
we've come to this point
00:59:53
okay on this part what do we have
00:59:57
we're just going to write these we're
00:59:58
going to circle it here this is our
01:00:00
five prime cap with the
01:00:01
7-methylguanosine
01:00:03
and on this end we already have kind of
01:00:05
formed our
01:00:07
polyetail the next thing that happens is
01:00:11
what's called
01:00:12
splicing and this can be sometimes a
01:00:14
little annoying
01:00:15
but it's not too bad i promise let's say
01:00:19
here
01:00:20
this is the sequence of nucleotides
01:00:22
within this
01:00:23
rna okay we're not at mrna yet we're
01:00:27
still at this h in rna we're still kind
01:00:29
of at this h
01:00:30
in rna at this point we haven't made
01:00:32
mrna yet
01:00:34
within this hn rna there's particular
01:00:37
nucleotides that will be read translated
01:00:41
and actually will code for particular
01:00:43
amino acids
01:00:45
there's other nucleotides within this h
01:00:48
rna
01:00:48
that will not be read and they do not
01:00:51
code for a particular amino acid
01:00:53
we give those very specific names i'm
01:00:56
going to highlight them
01:00:57
in different colors so let's say i
01:01:00
highlight this one here
01:01:02
and pink and then i will highlight
01:01:05
this one here in this kind of maroon
01:01:07
color
01:01:09
and then i'll pick here a blue
01:01:13
and then we'll do another maroon color
01:01:14
and then we'll do one more color after
01:01:16
this here's another maroon
01:01:18
and then we will do just for the heck of
01:01:21
it black
01:01:23
okay these portions here
01:01:27
the pink one this is actually going to
01:01:29
code
01:01:30
for an amino acid if it codes for an
01:01:33
amino acid we give a very specific name
01:01:35
for that
01:01:36
and we call it exons so exons
01:01:39
code for an amino acid
01:01:43
okay particularly amino acids will make
01:01:46
proteins
01:01:47
these other portions and again that's
01:01:49
going to be or we'll
01:01:51
i'll mention which ones are exons and
01:01:52
which ones are the next thing which is
01:01:54
called
01:01:54
introns introns are basically
01:01:57
nucleotide sequences that
01:02:01
do not code
01:02:05
for amino acids which will help to make
01:02:08
proteins
01:02:09
very important i'm going to call this
01:02:12
pink portion of the h and rna
01:02:15
i'm going to call this an exon but we
01:02:16
have a bunch of them in this h and rna
01:02:18
so i'm going to call this exon one
01:02:20
okay that's going to code for some amino
01:02:22
acids
01:02:24
i'm going to have this portion here
01:02:25
which is going to be in the maroon i'm
01:02:26
going to call this
01:02:27
an intron but you can have multiple
01:02:29
introns so i'm going to call this intron
01:02:31
1.
01:02:32
same thing here this is going to be
01:02:34
coding
01:02:35
so if it codes it's what it's an exon
01:02:38
well we have multiple types so we're
01:02:39
going to call this exon 2.
01:02:42
then i'm going to test you again this
01:02:44
one does not code for amino acids
01:02:46
so this is going to be a intron but we
01:02:49
have already intron once we're going to
01:02:50
call this
01:02:51
intron 2 and you guys already kind of
01:02:52
get the the pattern that i'm going with
01:02:54
here
01:02:55
this one does code so it's going to be a
01:02:58
exon
01:02:59
and we already have 1 2 so this will be
01:03:01
three
01:03:02
okay we're going to do something called
01:03:05
splicing
01:03:06
where let's think about this if the
01:03:09
introns don't
01:03:10
code for any amino acids do we even need
01:03:12
them
01:03:13
no let's get rid of them that's all that
01:03:15
splicing is
01:03:16
it's getting rid of these introns or
01:03:18
also known as intervening sequences
01:03:21
and then stitching together the exons
01:03:25
now in order for that process to occur
01:03:29
we need very specific molecules and we
01:03:32
talked about it before
01:03:33
let's see if you guys remember him rna
01:03:36
polymerase two and three they made
01:03:38
another very interesting small little
01:03:39
rna what was that rna called
01:03:42
small nuclear rna right
01:03:45
original right so small nuclear rna
01:03:48
is gonna combine we haven't used this
01:03:50
color yet so let's add this
01:03:53
these brown proteins okay so you're
01:03:56
gonna have some proteins
01:03:57
and some small nuclear rna together
01:04:01
these two things make up a very weird
01:04:04
name
01:04:05
called a snurp
01:04:08
okay snurps small nuclear
01:04:12
ribo ribonuclear proteins so our small
01:04:14
nuclear ribonuclear proteins and what
01:04:16
they do
01:04:16
is these snurps are going to bind
01:04:21
to this hn rna and they're going to
01:04:24
cleave
01:04:25
out the introns in this this actual rna
01:04:29
and then they're going to stitch
01:04:30
together the exons
01:04:32
so let's show that in a very basic way
01:04:34
of how that happens
01:04:35
so these snares which are the snra and
01:04:38
your proteins
01:04:40
are going to perform splicing so what
01:04:44
would that look like let's let's take
01:04:45
here
01:04:47
our transcript here and bring it down
01:04:49
here all the way down
01:04:50
to this portion here
01:04:54
so here we're going to make our
01:04:55
functional mrna so at this point in time
01:04:57
we've actually made what
01:04:59
at this point we've made the mature
01:05:02
mrna and
01:05:05
if i were to show kind of what was the
01:05:09
end result what am i going to have here
01:05:11
let's say here i have a sequence that's
01:05:12
in pink that's exon one
01:05:15
i got rid of intron one so what should
01:05:17
be next
01:05:18
i should have exon two
01:05:22
i got rid of intron too so watch what
01:05:24
should be left
01:05:25
we're gonna expand it a little bit here
01:05:27
get rid of that one
01:05:29
exon three so all i did was i
01:05:33
took and got rid of each exon i mean
01:05:36
each
01:05:36
in intron and stitch together
01:05:40
only the exon so now let's show kind of
01:05:43
coming out of this process here what am
01:05:45
i going to have kind of
01:05:46
popping out off of this the introns
01:05:50
and when the introns pop off this can be
01:05:53
intron
01:05:56
one and then you can have another one
01:05:59
let's say intron two these are going to
01:06:02
get popped off
01:06:04
we don't need these dang things anymore
01:06:06
so since we don't need them we're just
01:06:08
going to spit them off during that
01:06:10
splicing process and
01:06:11
only lead to the formation of exons now
01:06:14
within this
01:06:15
mrna i have my five prime cap
01:06:18
i have my poly a tail i have only the
01:06:22
nucleotide sequence which is going to
01:06:23
code for amino acids
01:06:25
and then if you really want to go the
01:06:27
extra mile we said this is the five
01:06:28
prime in
01:06:29
this is the three prime end i'm not
01:06:31
representing any kind of like
01:06:33
dashes here so this portion here
01:06:36
and this portion here doesn't get
01:06:39
translated or red at all by the
01:06:40
ribosomes
01:06:41
and so we call these regions since they
01:06:44
don't get translated
01:06:45
the five primes it's near the five prime
01:06:47
untranslated region
01:06:49
and this one doesn't get translated so
01:06:50
it's called the three prime
01:06:52
untranslated region the only portion
01:06:54
that gets translated is the
01:06:56
axons now
01:06:59
i don't know why but they love to ask
01:07:02
this stuff
01:07:02
in your exams where you actually go
01:07:05
through the specific mechanism
01:07:07
of how the snurps truly do pull the
01:07:10
n-trons out and splice together the
01:07:12
axons
01:07:13
so let's say we take just exon one
01:07:17
let's write this one as exon one
01:07:21
and this one is going to be exon two
01:07:25
and then here in the middle we're going
01:07:27
to make this
01:07:31
intron 1.
01:07:34
so let's kind of show you how these
01:07:36
snurps
01:07:37
again the snurps which is the s rna and
01:07:40
the proteins do this
01:07:41
so if you really wanted to show it let's
01:07:43
just represent the snurps as kind of a
01:07:45
black blob if you will
01:07:46
they're going to kind of bind
01:07:50
near this portion here so here's my
01:07:51
snurp
01:07:54
within this portion here right at the
01:07:56
intron at this portion
01:07:58
let's say here is the three prime end of
01:08:00
this exon
01:08:01
five prime end of this exon and let's
01:08:04
say that here is going to be the five
01:08:05
prime end of exon two and then the three
01:08:09
prime end
01:08:10
of exon two okay and then here's going
01:08:13
to be the intron inside
01:08:16
within this intron you have a very
01:08:18
specific nucleotide sequence that's near
01:08:20
the
01:08:20
three prime splice site near exon 1
01:08:24
and the beginning of intron 1 and then
01:08:26
you have a very specific nucleotide
01:08:28
sequence near the 5
01:08:29
prime splice site at exon 2 and at the
01:08:32
end of intron 1.
01:08:33
what are that nucleotide sequence it's
01:08:36
dumb
01:08:36
but it helps me to remember it so i say
01:08:39
i'm a g
01:08:40
how about you i'm a g so you remember
01:08:43
g u i'm a g how about you
01:08:47
i'm a g that's the basic way that i
01:08:50
remember the nucleotide sequence at the
01:08:52
three prime splice site
01:08:54
and then the one at the five prime
01:08:56
supply site between exon one exon two
01:08:58
and intron one in this example
01:09:01
at the there's another one right smack
01:09:03
dab in the middle let's make him a
01:09:04
different color so we don't confuse
01:09:06
it smack dab in the middle there's a
01:09:08
branch point which is an
01:09:10
adenine okay there's an adenine right at
01:09:12
this branch point
01:09:14
and it has a very specific oh group kind
01:09:16
of hanging from it
01:09:18
okay so this is called your branch point
01:09:21
what happens is is the snurps will come
01:09:24
in
01:09:26
and they're gonna cleave at that three
01:09:28
prime splice site
01:09:30
okay they're gonna cleave this portion
01:09:31
off so what would that look like
01:09:32
afterwards
01:09:34
so the snurps come in and they cleave at
01:09:36
that three prime prime splice site
01:09:38
and so what's going to be left over here
01:09:41
is we're going to have
01:09:44
exon 1 somewhat separated here and
01:09:47
coming off here what's the three prime
01:09:49
end contain
01:09:50
an oh group right and again this is exon
01:09:53
one then the next thing you have here is
01:09:57
intron one and it's going to have that
01:10:00
kind of
01:10:01
portion here kind of split off if you
01:10:02
will right kind of broken off here
01:10:05
and then again over here we're going to
01:10:06
have still fused at this end
01:10:10
exon 2.
01:10:14
so again this is my three prime end
01:10:16
which has that o h
01:10:17
this is the five prime end of that
01:10:18
portion of the axon
01:10:20
and then again same thing over here this
01:10:22
is the five prime n of x on two
01:10:24
three prime n of x on two and then again
01:10:27
what kind of nucleotides do we have
01:10:29
in here we have that gu which was pretty
01:10:31
much the marker which the snurp would
01:10:33
cut at that three prime site
01:10:35
then on this five prime splice side i
01:10:38
still have the ag
01:10:40
and then here in the middle i have that
01:10:41
branch point with the adenine with the
01:10:43
oh group
01:10:45
here's the next thing that happens the
01:10:47
oh
01:10:48
group of that branch point will then
01:10:51
bind or attack that gu site
01:10:56
and pull it in to where it kind of fuses
01:10:58
at this point so it makes kind of like a
01:11:00
little loop if you will
01:11:01
so let's show that if it attacks the gu
01:11:04
and pulls it in
01:11:05
after that happens you kind of form this
01:11:07
weird little like loopy structure if you
01:11:09
will
01:11:09
so what would that look like if we kind
01:11:11
of droon after we had that attack
01:11:13
after that attack point it's going to
01:11:15
kind of look somewhat
01:11:18
like this if you will where we have now
01:11:22
that portion where what would be here
01:11:24
what would be the kind of the nucleotide
01:11:26
sequence at that point right there g
01:11:30
and u was attacked at that point
01:11:33
by the o h at that branch point
01:11:36
then the next thing happens this is
01:11:40
crazy
01:11:41
this three prime o h of exon one
01:11:45
will then see that five prime splice
01:11:48
site
01:11:49
and it'll attack the five prime splice
01:11:53
site at exon two
01:11:55
when it attacks it it then breaks away
01:11:59
the nucleotide sequence ag of this
01:12:01
intron away from exon two
01:12:04
so okay now let's show what that would
01:12:06
look like
01:12:09
so if the three prime o h attacks the
01:12:12
five prime n
01:12:13
three prime o h of x on one attacks the
01:12:15
five prime n of x on two
01:12:17
now what do we have here
01:12:20
exon one fused
01:12:25
with exon two and we just
01:12:29
fused the exons and then what do we spit
01:12:32
out
01:12:32
after we break this off
01:12:37
the intron lariat which i showed you
01:12:40
like that before
01:12:43
that is how this whole splicing process
01:12:45
technically occurs
01:12:47
super quick again snurps bind
01:12:51
what do they do cut the three prime
01:12:52
splice side on between exon one
01:12:54
intron one when it does that the
01:12:57
o h of the uh adenine at the branch
01:13:00
point
01:13:00
attacks the gu site pulls it in creates
01:13:03
this loop
01:13:04
the three prime oh of axon one attacks
01:13:07
the five prime man of axon two
01:13:09
which snaps the intron out and stitches
01:13:12
together
01:13:13
exon one and exon two that is splicing
01:13:16
you're like zach why the heck do i need
01:13:18
to know all this crap
01:13:20
there's a reason why whenever there's
01:13:22
abnormalities within splicing it can
01:13:24
produce a various amounts of diseases
01:13:26
because think about it
01:13:27
if i don't cut out the introns properly
01:13:31
and i have introns mixed in with the
01:13:33
exons and
01:13:34
introns don't code for amino acids am i
01:13:37
going to make a proper protein
01:13:39
no because i'm going to have areas that
01:13:40
will code free amino acids in areas that
01:13:42
don't code for amino acids
01:13:44
you know there's a very devastating
01:13:46
condition called spinal
01:13:48
muscular atrophy where they
01:13:51
are deficient in an smn protein you want
01:13:54
to know why
01:13:56
because the snurps aren't working
01:13:58
properly
01:13:59
so there's a deficiency or there's a
01:14:01
problem
01:14:02
with the snurps not performing the
01:14:05
proper splicing
01:14:06
you know what else there's another
01:14:08
disease called beta thalassemia
01:14:11
beta thalassemia guess what you don't
01:14:13
remove a particular intron
01:14:15
and because you don't remove that intron
01:14:16
you make a protein that's abnormal
01:14:18
and it produces beta thalassemia so
01:14:21
there's
01:14:21
reasons to know this stuff and again if
01:14:24
someone has spinal muscular atrophy
01:14:26
do you know what that affects the
01:14:28
anterior gray horn neurons and then they
01:14:30
develop lower motor neuron lesions
01:14:32
hypotonia hyperreflexia
01:14:34
floppy baby syndrome right so it's a
01:14:35
dangerous condition that can be traced
01:14:37
back to something at the molecular level
01:14:39
all right now that we talked about this
01:14:41
there's two more things and i promise
01:14:43
we're done all right nature so i want to
01:14:44
talk about two more things and then
01:14:45
we're done the first thing i want to
01:14:46
talk about because it's
01:14:47
very pretty much similar to what we
01:14:49
talked about over here with splicing
01:14:52
i want to talk about something called
01:14:54
alternative
01:14:56
rna splicing we understand the
01:14:59
specific reason for splicing it's making
01:15:01
sure that we
01:15:02
only utilize exons to code for proteins
01:15:05
and there's no introns because if we
01:15:06
have introns in there
01:15:07
it's going to frack up the whole protein
01:15:09
production process we'll get an abnormal
01:15:11
protein
01:15:12
with alternative rna splicing
01:15:15
it gives variance
01:15:19
of a protein and i'll give you guys an
01:15:23
example
01:15:24
in just a second but let me kind of talk
01:15:26
about how this works it's literally the
01:15:27
same thing
01:15:28
we're not going to go too ham on this
01:15:31
let's use the same colors here
01:15:33
here was exon one and then here we had
01:15:37
intron 1 and we'll just skip this part
01:15:39
here where that was intron 2
01:15:41
and then blue here we had x on 2
01:15:45
and then at the end here we had in black
01:15:50
exon 3 okay
01:15:53
so let's say that we take an example
01:15:55
here of of of
01:15:57
this kind of hn rna right so here's our
01:16:00
h
01:16:02
and rna and we want to make different
01:16:04
mrnas
01:16:05
that'll give variance of proteins so
01:16:08
let's say here that we have
01:16:09
i'm just going to put x on one i'm going
01:16:12
to do all the same color here exon 2
01:16:15
exon 3 and then here in between we're
01:16:18
going to have
01:16:20
intron 1 and intron 2.
01:16:24
here's what i can do which is really
01:16:26
interesting and it's very
01:16:28
cool when it comes to plasma cells and
01:16:30
antibodies
01:16:32
so let's say i use those snurps right so
01:16:35
let's say here i put
01:16:36
my snurpees right my snurps which are my
01:16:39
small
01:16:40
nuclear rival nuclear proteins with the
01:16:41
snra and the proteins
01:16:43
they're going to splice but they're
01:16:45
going to do it in a very interesting way
01:16:47
so let's say that the first one over
01:16:48
here we get the same thing that we did
01:16:50
with that whole process of splicing
01:16:51
where we got rid of
01:16:53
all the introns and we only have in
01:16:55
exons
01:16:56
and let's say that we have exon one
01:17:01
let's say that we have exon two
01:17:05
and then we have exon three right so we
01:17:08
have all those exons here exon one x on
01:17:10
two and exon three
01:17:12
so we'll put these exon three exon two
01:17:16
exon one so that's one this is going to
01:17:18
be mrna right
01:17:19
after we've kind of done that process
01:17:21
and it'll give way to a particular
01:17:22
protein
01:17:23
and we'll call this protein
01:17:27
a if you will okay then
01:17:31
we're going to go through the same thing
01:17:32
the snurps are going to cleave out the
01:17:34
entrons and only leave in the exons but
01:17:36
let's say
01:17:37
for this example we pop out so this one
01:17:40
we popped out introns
01:17:43
but let's say with this one we pop out
01:17:45
both the introns
01:17:46
and let's say that we pop out x on two
01:17:49
let's say that we don't want
01:17:50
x on two in this one so then what am i
01:17:53
going to be left with
01:17:56
i'm going to be left with only exon 1
01:18:00
and exon 3. and by doing that that's
01:18:04
going to give me
01:18:05
an mrna that'll code for another protein
01:18:09
let's call this protein b and then last
01:18:12
but not least you guys can already
01:18:13
probably see where i'm going with this
01:18:15
let's say that this last one example
01:18:17
three again we cut out the entrance we
01:18:18
always got to cut out those introns
01:18:20
but in this case we cut out
01:18:24
exon three i don't want that one in the
01:18:26
diagram i don't want this one in that
01:18:27
mrna
01:18:28
so what am i left with i'll be left with
01:18:32
exon one and i'll be left with
01:18:35
exon two and what will this code for
01:18:39
this will code for this will give an
01:18:42
mrna
01:18:44
that'll then do what code four another
01:18:46
protein and let's call this protein
01:18:49
c from one
01:18:52
h and rna we made three
01:18:55
different mrnas and made three proteins
01:18:59
from the same h and rna or from the same
01:19:02
kind of
01:19:03
a gene if you will that means it's going
01:19:06
to be the same
01:19:07
protein if it's coming from the same
01:19:08
gene but it's a variant of that protein
01:19:11
you know what this is examples of think
01:19:13
about it guys
01:19:15
think about plasma cells
01:19:18
which make antibodies when they make
01:19:21
antibodies you can have antibodies
01:19:24
that can be secreted or you can have
01:19:27
antibodies that are different
01:19:28
and they're expressed on the cell
01:19:29
membrane that could be one example
01:19:32
so antibodies differences in antibodies
01:19:35
would be an example of how that works
01:19:36
from
01:19:37
alternative rna splicing because i'm
01:19:38
making one protein that'll bind to the
01:19:40
membrane
01:19:40
and one protein that can be secreted
01:19:42
think about neurons
01:19:44
let's say here's one neuron and this
01:19:46
neuron
01:19:47
has a dopamine receptor dopamine 1
01:19:50
receptor
01:19:52
but then you have another neuron
01:19:56
and this has a dopamine 2
01:19:59
receptor it's the same gene that's
01:20:02
making these proteins but just a variant
01:20:04
of it
01:20:05
and then the last thing is take an
01:20:06
example of a muscle within the heart
01:20:10
called tropomyosin and the muscle
01:20:13
and then within the skeletal muscles
01:20:15
tropomyosin they're different they're
01:20:18
small
01:20:18
changes or variants within the protein
01:20:20
that are coming from the same
01:20:22
gene so one of the things that they'll
01:20:24
love to ask on your exam questions is
01:20:25
alternative rna splicing
01:20:27
gives you takes one gene one h and rna
01:20:30
gives you multiple
01:20:31
mrnas and variants of the same protein
01:20:33
if you give examples something like
01:20:35
immunoglobulins dopamine receptors of
01:20:38
the brain
01:20:39
or tropomyosin variant within cardiac
01:20:41
and skeletal muscle
01:20:42
all right engineers i promise i'm so
01:20:44
sorry for this being so long but there's
01:20:45
one last thing that i want us to talk
01:20:47
about
01:20:48
the last thing that i want us to discuss
01:20:49
is called rna editing
01:20:51
this is also mentioned a lot
01:20:54
in your exams and the reason why is
01:20:58
it's it's really interesting kind of how
01:21:00
this happens
01:21:01
there's two different types of rna
01:21:03
editing i only want to mention really
01:21:05
one of them
01:21:05
because it's the most relevant to your
01:21:07
usmles and in kind of a clinical setting
01:21:11
so let's say here we have our mrna right
01:21:13
so this is an
01:21:14
hn rna we've already at this point in
01:21:16
time for rna editing we've already
01:21:18
formed
01:21:18
our functional mrna so at this point in
01:21:21
time
01:21:22
this structure here is a mrna
01:21:26
okay this mrna
01:21:30
can have a particular nucleotide
01:21:33
sequence
01:21:34
that a special enzyme can read and
01:21:37
sometimes
01:21:38
switch nucleotides with what is that
01:21:41
nucleotide sequence which can be seen in
01:21:42
this
01:21:43
mrna which we really want to know it's c
01:21:46
a a we're going to be talking about
01:21:48
apoproteins that's why i'm mentioning
01:21:50
caa
01:21:51
so this is our signal which is really
01:21:54
really important within this
01:21:56
mrna which is going to be making april
01:21:58
proteins a particular protein called
01:22:00
let's say that this mrna is going to
01:22:01
code for a particular protein called apo
01:22:06
b100 if you guys watch our lipoprotein
01:22:09
metabolism video
01:22:10
this will sound familiar right but
01:22:13
april b100 this is going to be the mr
01:22:15
enable that will code for that protein
01:22:16
and here's a particular nucleotide
01:22:17
sequence that we're going to modify
01:22:20
in the hepatocytes this nucleotide
01:22:22
sequence
01:22:24
is not altered in any way it's kept the
01:22:26
same
01:22:27
so it's not going to be changed it's
01:22:29
still going to be c a a
01:22:31
and whenever this mrna is translated by
01:22:33
ribosomes
01:22:34
it makes a particular protein that we
01:22:36
already talked about called apob
01:22:38
100 but in enterocytes
01:22:43
okay your gi cells what are these cells
01:22:46
here called these are called your
01:22:47
enterocytes they have a very special
01:22:51
enzyme
01:22:52
where they can modify the same gene that
01:22:56
makes april b100 but make a different
01:22:58
protein how the heck
01:23:00
how do they do that let me explain
01:23:03
there's this cute little blue
01:23:04
enzyme in the enterocytes called
01:23:07
cytidine
01:23:11
d-aminase
01:23:14
and what the cytidine deaminase does is
01:23:17
is it deaminates the cytodine right here
01:23:20
or the
01:23:21
cytosine nitrogenous base and
01:23:24
switches it with uracil
01:23:27
so now let's switch it here where we're
01:23:29
going to have this as switching c
01:23:32
and putting u a a
01:23:35
if you guys know anything about your
01:23:38
codons
01:23:39
there's a little trick to remember your
01:23:40
stop codons you guys remember the
01:23:42
the little way to remember them you
01:23:44
remember by
01:23:46
you go away you are away
01:23:49
you are gone these are the easy ways to
01:23:52
remember your stop codons does any of
01:23:54
these look like a stop codon
01:23:56
yes uaa ua that's a stop codon
01:24:00
so what's going to happen is when you
01:24:02
have the ribosomes which will be reading
01:24:04
this let's say here i kind of put like a
01:24:05
little ribosome
01:24:07
it's going to be reading this and making
01:24:09
a particular protein
01:24:10
as it gets to this point where it's
01:24:12
going to translate it that's a stop
01:24:14
codon
01:24:15
will it then read the rest of the rna
01:24:17
and translate that into a long protein
01:24:19
no so at this point translation will
01:24:23
stop
01:24:23
you won't read all the rest of the mrna
01:24:26
and make the full protein
01:24:28
instead you'll make a smaller protein
01:24:32
and this small protein is called apo
01:24:35
b-48
01:24:37
this is something that they love to ask
01:24:40
on your exams because
01:24:41
you're taking the same mrna just
01:24:44
modifying it a little bit
01:24:47
to produce a different protein that is a
01:24:50
completely different sized protein
01:24:52
so that's really cool definitely wanted
01:24:54
you guys to know that
01:24:55
and that finishes our lecture on dna
01:24:57
transcription all right ninja nurse so
01:24:59
in this video we talk a ton about dna
01:25:01
transcription i hope it made sense and i
01:25:02
hope that you guys did enjoy it
01:25:04
as always ninja nerds until next time
01:25:12
[Music]
01:25:28
you