To do transcription, the DNA strands have to be separated in order to provide a template and the
RNA polymerase then creates a new molecule using the base pairing rules and references the
template used prior.
To build the RNA molecule you must have phosphodiester bonds using either the 5’ or 3’ base
RNA polymerase – separates the DNA strands and builds the phosphodiester bonds using the
base pairing rules. It will only make one strand!
Combinatorial regulation or transcription
Multiple transcription factors are required for gene expression
Transcription factors activate or block gene expression in specific combinations
DNA sequences of promoter regions of genes, and the presence of absence of specific
transcription factors determined by gene expression.
Transcription factors – positive regulators of DNA transcription they are sequencespecific
DNA binding proteins. Through the use of enhancers or silencers, they regulate gene expression
Constitutive transcription factors – promote many different genes and do not seem to respond
to external signals
Regulatory transcription factors – promotes a limited number of genes and responds to
RNA falls off of the DNA and stops transcribing by forming a structure called a stem loop.
Stem loop (palindrome) – the space between the two structures so that the base pairing
sequences are perfectly arranged. When this forms its interacts with RNA polymerase and causes
it to fall off of the DNA. (TRANSCRIPTION STOP SIGNAL)
UTR – Un translated region, located in the RNA.
Upstream of the UTR – is not located in the UTR and downstream.
3’ hydroxyl – required to join nucleotides together in DNA
2’ hydroxyl – added into the loop in order to create 2 bases for the loop to form
Exons – the coding regions of RNA normally located at the ends of the DNA strand/fragment.
(5’ to 3’)
During alternate RNA processing differing exons can be connected together to form a laureate
(loop). In order to block a particular exon a blocking site on a donor site on the introns is formed.
Then the snRNP moves downstream to the next donor site.
Introns – the noncoding regions of RNA are located in between the exons and are eventually
removed from the fragment in order for the exon ends to be bound together and create a double
helix. (5’ to 3’) (A laureate is formed as the intron is being removed)
Typically the intron being with the GT sequence and end with the AG sequence (the GTAG rule) Splicing – mRNA processing removes the introns from the DNA fragment and splices or
attaches the exon ends together.
SnRNPs – the editors of the RNA. They work by binding to the donor and accepting sites,
forming a laurite (double bend or loops) and splice out the intron site.
A special base called the A nucleotide, is responsible for this and joining together the exon ends.
Needs a special double phosphodiester bond that joins the two exons together
By blocking acceptor sites, the donor site goes to the next one and acts like the one it skipped is
an intron and then it is removed. (Smaller mRNA)
If the donor site is blocked, nothing is scanned for removal and then the intron never gets
removed (bigger mRNA)
TATA box – at transcription start site that is 5’ – 3’ in nature and goes like: 5’TATAWAW3’ –
happens in transcription and allows transcription to happen.
Ribosome binding site – is located in front of the stop codon in the 5’ UTR, which allows
protein to be made.
Okazaki fragments – are joined together with DNA ligase and are at the end of the lagging
strands in RNA processing
Protein is made of chains of amino acids that fold up and can act as many things such as
collagen, keratin, kinases, receptors etc.
Amino acids (20 different ones) all have the same common cores, two abbreviations that are
either 3 letters or single letter code, which makes things easier for them.
Four types of charges: basic – positively charge, or acidic – negatively charged, polar – positive
or negative charge, and nonpolar –no charge given off – neutral.
Bonded together with a peptide bond.
Also they are formed from 5’ to 3’.
Translation making a sequence of amino acids in proteins by using the transfer RNA (tRNA)
through the use of messenger RNA (mRNA). By using anticodons it allowed to make sure that
the translation is correct.
Aminoacyl tRNA synthetase – is responsible for the correct matching of am