• Ribonucleic acid is a polymeric molecule essential in various biological roles
in coding, decoding, regulation, and expression of genes.
• Polymer of ribonucleotide held together by 3’ 5’ phosphodiester bridge
and are single stranded.
• RNA is the only molecule known to function both in the storage and
transmission of genetic information and in catalysis.
• All RNAs except the RNA genomes of certain viruses derive information
that is permanently stored in DNA.
5. Kinds of RNAs
• There are 4 types of RNA, each
encoded by its own type of gene.
• The genomic DNA contains all the
information for the structure and
function of an organism.
• In any cell, only some of the genes
are expressed, that is, transcribed
• mRNA - Messenger RNA: Encodes amino acid sequence of a polypeptide.
• tRNA - Transfer RNA: Brings amino acids to ribosomes during translation.
• rRNA - Ribosomal RNA: With ribosomal proteins, makes up the ribosomes, the
organelles that translate the mRNA.
• snRNA - Small nuclear RNA: With proteins, forms complexes that are used in
RNA processing in eukaryotes. (Not found in prokaryotes.)
9. Basic Structure of a Protein-Coding
• A protein-coding gene consists of a promoter followed by the coding
sequence for the protein and then a terminator.
• The promoter is a base-pair sequence that specifies where transcription begins.
• The coding sequence is a base-pair sequence that includes coding information for
the polypeptide chain specified by the gene.
• The terminator is a sequence that specifies the end of the mRNA transcript.
11. The Transcription Process
• RNA synthesis involves separation of the DNA strands and synthesis
of an RNA molecule in the 5' to 3' direction by RNA polymerase,
using one of the DNA strands as a template.
• In complementary base pairing, A, T, G, and C on the template DNA strand
specify U, A, C, and G, respectively, on the RNA strand being synthesized.
12. Features of Transcription
1. Highly Selective
• This selectivity is due to signals embedded in the nucleotide sequence of
• Specific sequences mark the beginning and the end of DNA segment which
is o be transcribed.
• This signal instruct the enzyme where to start and stop transcription, when
to start and how often to start.
2. Formation of Primary Transcripts
Many of RNA transcripts are synthesized as precursors known as
• On modification and trimming they are converted into functional RNA.
14. RNA polymerase
• RNA polymerases are enzymes that transcribe DNA into RNA.
• Using a DNA template, RNA polymerase builds a new RNA molecule through base
• For instance, if there is a G in the DNA template, RNA polymerase will add a C to
the new, growing RNA strand.
• RNA polymerase always builds a new RNA strand in the 5’ to 3’ direction. That is, it
can only add RNA nucleotides (A, U, C, or G) to the 3' end of the strand.
• RNA polymerases are large enzymes with
multiple subunits, even in simple
organisms like bacteria.
• In addition, humans and other eukaryotes
have three different kinds of RNA
polymerases: I, II, and III. Each one
specializes in transcribing certain classes of
16. Transcription initiation
• To begin transcribing a gene, RNA polymerase binds to the DNA of the gene at a
region called the promoter.
• Basically, the promoter tells the polymerase where to "sit down" on the DNA and
• Each gene (or, in bacteria, each group of genes transcribed together) has its own
• A promoter contains DNA sequences that let RNA polymerase or its helper
proteins attach to the DNA.
• Once the transcription bubble has formed, the polymerase can start transcribing.
18. Promoters in bacteria
• To get a better sense of how a promoter works, let's look an example from bacteria.
• A typical bacterial promoter contains two important DNA sequences, the -10 and -
• RNA polymerase recognizes and binds directly to these sequences.
• The sequences position the polymerase in the right spot to start transcribing a target gene,
and they also make sure it's pointing in the right direction.
• Once the RNA polymerase has bound, it can open up the DNA and get to work.
• DNA opening occurs at the -10 element, where the strands are easy to separate due to the
many As and Ts (which bind to each other using just two hydrogen bonds, rather than the
three hydrogen bonds of Gs and Cs).
20. Promoters in Humans
• In eukaryotes like humans, the main RNA polymerase in your cells does not attach directly
to promoters like bacterial RNA polymerase.
• Instead, helper proteins called basal (general) transcription factors bind to the promoter
first, helping the RNA polymerase in your cells get a foothold on the DNA.
• Many eukaryotic promoters have a sequence called a TATA box.
• It's recognized by one of the general transcription factors, allowing other transcription
factors and eventually RNA polymerase to bind.
• It also contains lots of As and Ts, which make it easy to pull the strands of DNA apart.
• Once RNA polymerase is in position at the promoter, the next step of
• Basically, elongation is the stage when the RNA strand gets longer, thanks to the
addition of new nucleotides.
• During elongation, RNA polymerase "walks" along one strand of DNA, known as
the template strand, in the 3' to 5' direction.
• For each nucleotide in the template, RNA polymerase adds a matching
(complementary) RNA nucleotide to the 3' end of the RNA strand.
• The RNA transcript is nearly identical to the non-template, or coding,
strand of DNA.
• However, RNA strands have the base uracil (U) in place of thymine (T), as
well as a slightly different sugar in the nucleotide.
• So, as in the diagram , each T of the coding strand is replaced with a U in
the RNA transcript.
25. • The picture shows DNA being
transcribed by many RNA
polymerases at the same time,
each with an RNA "tail" trailing
• The polymerases near the start
of the gene have short RNA
tails, which get longer and
longer as the polymerase
transcribes more of the gene.
26. Transcription termination
• RNA polymerase will keep transcribing until it gets signals to stop.
• The process of ending transcription is called termination, and it happens
once the polymerase transcribes a sequence of DNA known as
27. Termination in bacteria
• There are two major termination strategies found in bacteria: Rho-dependent and Rho-
• In Rho-dependent termination, the RNA contains a binding site for a protein called
Rho factor. Rho factor binds to this sequence and starts "climbing" up the transcript
towards RNA polymerase.
• When it catches up with the polymerase at the transcription bubble, Rho pulls the RNA
transcript and the template DNA strand apart, releasing the RNA molecule and ending
• Another sequence found later in the DNA, called the transcription stop point, causes
RNA polymerase to pause and thus helps Rho catch up.
• Rho-independent termination depends on specific sequences in the DNA
• As the RNA polymerase approaches the end of the gene being transcribed, it
hits a region rich in C and G nucleotides.
• The RNA transcribed from this region folds back on itself, and the
complementary C and G nucleotides bind together.
• The result is a stable hairpin that causes the polymerase to stall.
• In a terminator, the hairpin is followed by a stretch of U nucleotides in the
RNA, which match up with A nucleotides in the template DNA.
• The complementary U-A region of the RNA transcript forms only a weak
interaction with the template DNA.
• This, coupled with the stalled polymerase, produces enough instability for the
enzyme to fall off and liberate the new RNA transcript.
32. What happens to the RNA
• After termination, transcription is finished.
• An RNA transcript that is ready to be used in translation is called a messenger
• In bacteria, RNA transcripts are ready to be translated right after transcription. In fact,
they're actually ready a little sooner than that: translation may start while transcription is
still going on!
• In the diagram , mRNAs are being transcribed from several different genes. Although
transcription is still in progress, ribosomes have attached each mRNA and begun to
translate it into protein.
• When an mRNA is being translated by multiple ribosomes, the mRNA and ribosomes
together are said to form a polyribosome
34. Why can transcription and translation happen
simultaneously for an mRNA in bacteria?
• One reason is that these processes occur in the same 5' to 3' direction.
• That means one can follow or "chase" another that's still occurring.
• Also, in bacteria, there are no internal membrane compartments to separate
transcription from translation.
35. Complete Transcription of an RNA
Transcription begins at the promoter, proceeds through the coding
region, and ends at the terminator.
36. mRNA in Prokaryotes
• The sequence of a prokaryotic protein-coding gene is colinear with the translated mRNA;
that is, the transcript of the gene is the molecule that is translated into the polypeptide.
37. mRNA in Eukaryotes
• The sequence of a eukaryotic protein-coding gene is typically not colinear with the
translated mRNA; that is, the transcript of the gene is a molecule that must be
processed to remove extra sequences (introns) before it is translated into the
• Most eukaryotic protein-coding genes contain segments called introns, which break up the
amino acid coding sequence into segments called exons.
• The transcript of these genes is the pre-mRNA (precursor-mRNA).
• The pre-mRNA is processed in the nucleus to remove the introns and splice the exons
together into a translatable mRNA. That mRNA exits the nucleus and is translated in the
39. Key points
• Transcription is the process in which a gene's DNA sequence is copied
(transcribed) to make an RNA molecule.
• RNA polymerase is the main transcription enzyme.
• Transcription begins when RNA polymerase binds to a promoter sequence near the
beginning of a gene (directly or through helper proteins).
• RNA polymerase uses one of the DNA strands (the template strand) as a template
to make a new, complementary RNA molecule.
• Transcription ends in a process called termination. Termination depends on
sequences in the RNA, which signal that the transcript is finished.
40. Post Transcriptional modifications
• The primary transcript needs to be modified to become functional tRNAs,
rRNAs and mRNAs.
• Post Transcriptional modifications include
• Addition of 5’ cap
• Creation of Poly A tail
• RNA editing.
41. Pre-mRNA Processing (Splicing)
• Eukaryotic pre-mRNAs typically include introns.
• Introns are removed by RNA processing in which the intron is looped out and
cut away from the exons by snRNPs, and the exons are spliced together to
produce the translatable mRNA.
• The steps of pre-mRNA splicing (intron removal) are as follows:
• The intron loops out as snRNPs (small nuclear ribonucleoprotein particles, complexes
of snRNAs and proteins) bind to form the spliceosome.
• The intron is excised, and the exons are then spliced together.
• The resulting mature mRNA may then exit the nucleus and be translated in the
43. Addition of 5’ cap
• At the end of transcription, the 5' end of the RNA transcript contains a free
triphosphate group since it was the first incorporated nucleotide in the chain.
• The capping process replaces the triphosphate group with another structure
called the "cap".
• The cap is added by the enzyme guanyl transferase.
• This enzyme catalyzes the reaction between the 5' end of the RNA transcript
and a guanine triphosphate (GTP) molecule.
44. The Poly A Tail
• Post-transcriptional RNA processing at the opposite end of the transcript comes in the
form of a string of adenine bases attached to the end of the synthesized RNA chain.
• This string of adenine is called the "poly A tail".
• The addition of the adenines is catalyzed by the enzyme poly (A) polymerase, which
recognizes the sequence AAUAAA as a signal for the addition.
• The reaction proceeds through mechanism similar to that used for the addition of
nucleotides during transcription.
• The poly A tail is found on most, but not all, eukaryotic RNA transcripts. Its significance
46. RNA editing
• RNA (ribonucleic acid) editing is a post-transcriptional alteration of RNA
sequences and structures via modification, deletion or insertion of nucleotides.
• This process has been detected in eukaryotes ranging from single-celled protozoa
to plants and mammals; as a result, functionally distinctive proteins can be
processed from a single gene.
• RNA editing occurs concurrently with transcription and splicing processes in the
nucleus or mitochondria.
• It comes in a myriad of different natures, with all of the diverse editing types
distributed intermittently across the phylogenetic spectrum.