Transcription
•The ___ ___ of molecular biology; DNA makes RNA makes protein •Transcription factors assemble at a specific ___ region along the DNA •The length of DNA following the promoter is a ___ and it contains the recipe for a protein •A mediator protein complex arrives carrying the enzyme ___ ___; it maneuvers the __ __ in to place, inserting it with the help of other factors between the strands of the DNA double helix •The assembled collection of all these factors is referred to as the __ ___ __, and now it is ready to be activated •The initiation complex requires contact with activator proteins, which bind to specific sequences of DNA known as __ regions; these regions may be thousands of base pairs distant from the start of the gene •Contact between the activator proteins and the initiation complex releases the ___ mechanism •The RNA polymerase ___ a small portion of the DNA helix exposing the bases on each strand •Only one of the strands is copied; it acts as a ___ for the synthesis of an RNA molecule which is assembled one sub-unit at a time by matching the DNA letter code on the ___ strand •The sub-units can be seen here entering the enzyme through its intake hole, and they are joined together to form the long ___ ___ chins snaking out of the top
central dogma promoter gene RNA polymerase RNA polymerase transcription initiation complex enhancer copying unzips template template messenger RNA
the template strand of DNA is the. opposite of the ___ strand
coding
___ strands are the same as DNA except has ___ instead of ___
coding Uracil Thymine
The ___ strand of DNA looks like the mRNA, the only difference is the mRNA has __ instead of ___
coding uracil thymine
DNA that is transcribed by RNA polymerase (aka open reading frame or "ORF")
coding sequence
what is the DNA that is made into a protein
coding sequence
RNA polymerase adds a ___ nucleotide according to the ___ template, which is read from 3' to 5'
complimentary DNA
RNA still has __ ___ __ with other nucleotides, but it si most stable when
complimentary base pairing it is single stranded
what is the first step of transcription
initiation
what is most important when it comes to preserving hereditary material
integrity of DNA sequence
how does alpha amantin cause comma or death in a few days?
it interferes with RNA polymerase alpha amantin is a small circular peptide that is able to bind to a place in RNA polymerase which changes the shape of the protein so that it cannot function; basically jams the mechanism of the enzyme
DNA is most stable when
it is in a double stranded double helix form
RNA polymerases are ___ and have lots of different ___
large subunits
___ also has a sugar-phosphate backbone, phosphodiester linkages, and bases. It is just unpaired because it is single stranded
mRNA
if a gene is coding for something, it means that the segment of DNA is going to become ___ which becomes ___ into a ____
mRNA translated protein
what type of RNA makes up the least percentage of a cell and why?
mRNA mRNA has important functions, but it only makes up 2.5% of the cell because tRNA and rRNA is a lot bigger in size (could be because they are necessary for translation)
termination sequences indicate to RNA polymerase to
stop transcribing
RNA polymerase ___ DNA during transcription
unzips
what is the structure of DNA defined by
which base it has in the sequence
what is the function of tRNA
works as a bridge between mRNA and amino acids
what is the non-coding sequence to initiate transcription
promoter
what is the upstream binding site for RNA polymerase
promoter
why is it called the M^7G cap?
because guanosine is methylated on the 7th position
What are the three modifications to make pre-mRNA mature?
1. add a m^7G cap (methyl cap) 2. polyadenylation at the 3' end (adding a poly(A) tail 3. RNA splicing: removal of introns and fusing of exons
what makes mRNA different from DNA
1. mRNA is a single-stranded nucleic acid 2. mRNA has a ribose sugar instead of a deoxyribose sugar like DNA 3. mRNA nucleotides have a uracil base instead of thymine
What are the basic steps of transcription
1.Binding of RNA polymerase and local DNA unwinding 2.Initiation of RNA synthesis 3.Elongation of RNA 4.Termination of RNA synthesis
What is the function of the m^7G cap?
1.Making mRNA distinguishable from other types of RNA molecules 2.Regulation of nuclear export 3.Prevention of degradation by exonucleases 4.Promotion of translation 5.Promotion of 5' proximal intron excision
RNA polymerase can only add RNA nucleotides to the
3' end
what is the template strand read from
3' to 5'
The __ __ is added to the first nucleotide in the transcript during transcription.
5' cap
translation cannot occur without the __ __
5' cap
what direction does RNA polymerase add nucleotides (RNA) in during elongation?
5' to 3'
What direction does RNA polymerase build new RNA in?
5' to 3' direction
what is a polyadenylation signal
AAUAAA
what is the mRNA of the coding strand CGATT
CGAUU
what does RNA polymerase use to build a new RNA molecule through base pairing?
DNA template
what is transcription
DNA to RNA
what would the template strand be if the coding strand is CGATT
GCTAA
Why does it matter to control how much or how little of the gene we are making?
Having something like this under really tight control is very important because the amount of protein that you are making is just as important as making it in the first place
What is elongation in transcription?
RNA nucleotides are added to the 3' end of the new RNA RNA strand lengthens
What catalyzes the elongation reaction in transcription
RNA polymerase
__ __ is an enzyme used to transcribe DNA to RNA
RNA polymerase
the promoter is a binding site for
RNA polymerase
•The polyadenylation signal is recognized by an enzyme that cuts the RNA transcript nearby, releasing it from ___ ___
RNA polymerase
•In all eukaryotes, including us, the main ___ ____ in your cell does not attach directly to promoters like they do in bacterial RNA •It is much more ___ controlled in eukaryotes because of our complex system and cells
RNA polymerase tightly
what is TBP
TATA binding protein
Initiation: •First, we have helper proteins that are going to attach to the ___ ___. The majority of our genes is going to have the TATA box in the core region of the ___ region. •This is going to allow binding of something called the __ __ __, ___ which is the first __ ___ that is going to start setting the stage for recruiting__ ___. •Allows other factors, ___, that are going to be recruited to the sight based on the specific sequence of DNA •Then ___ ___ is recruited. It is not that RNA polymerase does not interact with DNA at all, it just cannot interact with DNA alone; needs these other proteins to bind to
TATA box promoter TATA-binding protein TBP transcription factor RNA polymerase TFIIs RNA polymerase
what is the TATA box
The core region of the promoter region that allows binding of proteins necessary to initiate transcription (TATAAA sequence in the promoter)
coding strand of DNA
The original strand off which the new nucleotide sequence is based. Almost the same as mRNA
what is the difference between thymine and uracil
Thymine has a methyl group while uracil only has an H group on C5
Describe the process of elongation in transcription
UTP is added, 2 phosphates are released, and a new phosphodiester bond forms with the previous nucleotide
functions of RNA polymerase
Unwinding DNA breaking hydrogen bonds adding in and catalyzing the reaction of the addition of nucleotides to growing RNA strand
what does the terminator signal begin with
a polyadenylation signal
when we say coding, we are always referring to makeing
a protein product
what percentage of tRNA makes up a cell
about 14%
what percentage makes up mRNA
about 2.5%
what percentage of rRNA makes up a cell
about 84%
what is the most important RNA polymerase that is most sensitive to alpha-amanitin
all protein-coding nuclear pre-mRNA (helps with transcription all over the body)
what is the toxin in death cap mushrooms that causes comma and or death in a few days
alpha amantin
•Remember: we have all of these phosphate groups, a phosphodiester backbone, the bases themselves that are in a __ __ formation, which creates unique binding sites based on the sequence of DNA that is present that is going to allow __ __ to attach
double helix RNA polymerase
What is the step that comes after the initiation step of transcription?
elongation
what is the function of mRNA
encodes for proteins
•RNA polymerase is an ___ •One of the reactions that catalyze in addition to winding and separating DNA is adding in the new RNA bases •These free nucleotides exist in the cell as __ ___ (or ___); this is seen in the animation where the little grey circles are the phosphate groups; lose ___ of them every time; only one of those phosphate groups are going to become part of the ___ bond that is creating the backbone that we are building as we are going •Remember: phosphodiester bonds are ___ bonds; that is the reaction that is being catalyzed: a ___ attachment of one nucleotide to the next one in a sequence •The base pair in the __ __ happen on their own (we do not need an enzyme to catalyze that reaction). They just occur due to being in proximity •The __ phosphate is being lent to the __ end of the growing mRNA strand which is why transcription occurs in a __ to __direction (remember RNA polymerase can only add to the ___ end)
enzyme nucleoside triphosphate NTPs two phosphodiester covalent covalent hydrogen bonds 5' 3' 5' to 3' 3'
Conformational shape of a protein is tied to its ___
function
•RNA polymerase has many ___: one being the enzyme that binds that actually initiates ___ and it is able to unwind and open up the DNA. It is able to break apart the ___ bonds in base pairs and give access to __ __ that are going to come in and be added to make the copy.
functions transcription hydrogen RNA nucleotides
instead of starting with ___ that unwinded DNA and ___ that separated the DNA in DNA replication, transcription has ___ __ that caries out those functions to separate the DNA strand so that it has access to add the mRNA that matches
gyrase helicase RNA polymerase
•RNA polymerase is an enzyme caries out the function of ___ in DNA
helicase
•Unlike ___ that opens up a complete section and creates a replication fork, ___ ___ opens up a little bubble that is going to be present while the RNA polymerase is bound. As soon as RNA polymerase is gone, __ __ that hold base pairing come back together. This is also important because we want our DNA to stay ___ and return back to the state it was in before we started transcription (we do not want to alter anything while we are transcribing- just want to copy it)
helicase RNA polymerase hydrogen bonds stable
•Although RNA polymerase is not classified as DNA ___, it includes ___ activity •can unzip or unwind DNA but only ___ and usually only for small ___.
helicase helicase locally lengths
___ ___ need to be broken for the DNA to be accessible just like in DNA replication
hydrogen bonds
RNA transcript is nearly ___ to the non-template, or ___ strand of DNA. However, RNA strands have the base ___ in place of thymine , as well as a slightly different ___ in the nucleotide.
identical coding uracil sugar
what is translation
mRNA to protein
what are the three main types of RNA
mRNA, tRNA, rRNA
alpha amantin is ___ actually involved with where RNA polymerase binds to the DNA
not
single stranded RNA is ___ as stable as double stranded DNA
not
what are the results of transcription?
original DNA is returned to double-stranded DNA that has not been altered in any way new nucleotide sequence where the pre-mRNA transcript. matches the coding strand of DNA for that gene (except has U's instead of T's
Termination begins when a ____ signal appears in the RNA transcript
polyadenylation
the RNA transcript is what is turned into a
polypeptide
___ is very important for initiation
promoter
•Every gene has a ___ for RNA polymerase and other proteins to enhance or disrupt transcription •RNA polymerase is always going to ____ transcription, but you can have regions in your promoter that can ___ transcription because it recruits other proteins that are repressors and slow the process down
promoter enhance dampen
what is TFII
proteins that bind to promoter (A-J)
which type of RNA is most present in a cell
rRNA
what is the initiation step of transcription?
recruitment of RNA polymerase to the sit where you want your gene transcribed
•as each RNA polymerase moves along DNA, the ___ gets longer and longer because it has ___ more and more of the sequence
tail copied
the ___ strand is the opposite of the DNA strand
template
After the mRNA is created from the __ strand, we end up with a ___ which should match the __ strand except it has ___ instead of ___
template transcript coding Uracil Thymine
RNA polymerase will stop transcribing at the ___ (end of coding sequence)
terminator
how does RNA polymerase know when to stop?
terminator sequence
why is RNA not as stable as DNA
the 2' hydroxyl group can be deprotonated and act as a nucleophile
what makes the M^7G cap unusual
the 5'-5' phosphate linkage because it is not a common chemical bond that is seen)
template strand of DNA
the DNA strand that is copied into mRNA and has the complementary sequence to the mRNA
what is the function of rRNA
the structural part of the ribosome
what allows the mRNA to mimic the coding strand of DNA?
the template strand of DNA
why do you want stability in preserving hereditary information
to keep viable offspring and have cells divide successfully
•In our bodies, we do not have any cells that are ___ everything or making use of all of our genes. They are going to be very ___ chosen based on what cell type we have and the environmental conditions around it
transcribing selectively
•In eukaryotic cells we are going to have ___ occur in the nucleus. Translation does not occur until the mRNA is in the ____
transcription cytosol (can also occur as far as the ER or mitochondria)
the promoter is where
transcription is initiated and located upstream of the gene
•Why would lots of Ts and As be beneficial for RNA polymerase?
•If we are using an enzyme that is going to require energy to try to break apart these bonds, it makes sense that we are going to want to start in a place that is easier to do that. Thus, having these Ts and As rich sequences have only two hydrogen bonds holding them together which is easier and requires less energy for the RNA polymerase to start doing its job and separate the DNA (in comparison to the 3 hydrogen bonds for Gs and Cs rich areas)
what is the 5' cap?
•The cap is a modified guanine (G) nucleotide, and it protects the transcript from being broken down. •It also helps the ribosome attach to the mRNA and start reading it to make a protein.
Why do most organisms use DNA as their hereditary material?
•The primary advantage of DNA over RNA as a genetic material is the greater chemical stability of DNA •2'-OH in RNA may be deprotonated and act as a nucleophile
