Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation, and expression of genes. RNA and DNA are nucleic acids, and, along with proteins and carbohydrates, constitute the four major macromolecules essential for all known forms of life. Like DNA, RNA is assembled as a chain of nucleotides, but unlike DNA it is more often found in nature as a single-strand folded onto itself, rather than a paired double-strand.
2. Ribonucleic acid (RNA) is a polymeric molecule essential
in various biological roles in coding, decoding, regulation,
and expression of genes. RNA and DNA are nucleic acids,
and, along with proteins and carbohydrates, constitute the
four major macromolecules essential for all known forms of
life. Like DNA, RNA is assembled as a chain of
nucleotides, but unlike DNA it is more often found in nature
as a single-strand folded onto itself, rather than a paired
double-strand. Cellular organisms use messenger RNA
(mRNA) to convey genetic information (using the letters G,
U, A, and C to denote the nitrogenous bases guanine, uracil,
adenine, and cytosine) that directs synthesis of specific
proteins. Many viruses encode their genetic information
using an RNA genome.
3.
4. Each nucleotide in RNA contains a ribose sugar, with
carbons numbered 1' through 5'. A base is attached to the 1'
position, in general, adenine (A), cytosine (C), guanine (G),
or uracil (U). Adenine and guanine are purines, cytosine and
uracil are pyrimidines. A phosphate group is attached to the
3' position of one ribose and the 5' position of the next. The
phosphate groups have a negative charge each, making
RNA a charged molecule (polyanion). The bases
form hydrogen bonds between cytosine and guanine,
between adenine and uracil and between guanine and
uracil. However, other interactions are possible, such as a
group of adenine bases binding to each other in a bulge, or
the GNRA tetraloop that has a guanine–adenine base-pair.
5. An important structural feature of RNA that distinguishes it
from DNA is the presence of a hydroxyl group at the 2'
position of the ribose sugar. The presence of this functional
group causes the helix to mostly adopt the A-form
geometry, although in single strand dinucleotide contexts,
RNA can rarely also adopt the B-form most commonly
observed in DNA. The A-form geometry results in a very
deep and narrow major groove and a shallow and wide
minor groove.A second consequence of the presence of the
2'-hydroxyl group is that in conformationally flexible
regions of an RNA molecule (that is, not involved in
formation of a double helix), it can chemically attack the
adjacent phosphodiester bond to cleave the backbone.
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RNA functions
• Storage/transfer of genetic information
• Genomes
• many viruses have RNA genomes
single-stranded (ssRNA)
e.g., retroviruses (HIV)
double-stranded (dsRNA)
• Transfer of genetic information
• mRNA = "coding RNA" - encodes proteins
• Structural
• e.g., rRNA, which is major structural component of
ribosomes
• Catalytic
RNA in ribosome has peptidyltransferase activity
• Enzymatic activity responsible for peptide bond
formation between amino acids in growing peptide chain
• Also, many small RNAs are enzymes
"ribozymes”
7. REGULATORY
◦ Recently discovered important new roles for RNAs
◦ In normal cells:
• in "defense" - esp. in plants
• in normal development
e.g., siRNAs, miRNA
As tools:
• for gene therapy or to modify gene expression
• RNAi
• RNA aptamers
8. There are mainly 3 types of RNA:
mRNA-Messenger RNA
rRNA-Ribosomal RNA
tRNA-Transfer RNA
9.
10. mRNA accounts for just 5% of the total RNA in the cell. mRNA is the
most heterogeneous of the 3 types of RNA in terms of both base
sequence and size. It carries the genetic code copied from the DNA
during transcription in the form of triplets of nucleotides called codons.
Each codon specifies a particular amino acid, but one amino acid can
be coded by many different codons. Although there are 64 possible
codons or triplet bases in the genetic code, only 61 of them represent
amino acids; the remaining 3 are stop codons.
As part of post-transcriptional processing in eukaryotes, the 5’ end of
mRNA is capped with a guanosine triphosphate nucleotide, which
helps in mRNA recognition during translation or protein synthesis.
Similarly, the 3’ end of an mRNA has a poly A tail or multiple
adenylate residues added to it, which prevent enzymatic degradation of
mRNA. Both 5’ and 3’ end of an mRNA imparts stability to the mRNA.
11. rRNAs are found in the ribosomes and account for 80% of the total
RNA present in the cell. Ribosomes are composed of a large subunit
called the 50S and a small subunit called the 30S, each of which has its
own rRNA molecules. Different rRNAs present in the ribosomes
include small rRNAs and large rRNAs, which denote their presence in
the small and large subunits of the ribosome.
rRNAs combine with proteins in the cytoplasm to form ribosomes,
which act as the site of protein synthesis and has the enzymes needed
for the process. These complex structures travel along the mRNA
molecule during translation and facilitate the assembly of amino acids
to form a polypeptide chain. They bind to tRNAs and other molecules
that are crucial for protein synthesis.
In bacteria, the small and large rRNAs contain about 1500 and 3000
nucleotides, respectively, whereas in humans, they have about 1800
and 5000 nucleotides, respectively. However, the structure and function
of ribosomes is largely similar across all species.
12.
13. • tRNAs serve as adapter molecules that couple
the codons in mRNA with the amino acids they
each specify, thus aligning them in the appropriate
sequence before peptide bond formation.
• Translation takes place on ribosomes, complexes
of protein and rRNA that serve as the molecular
machines coordinating the interactions between
mRNA, tRNA, the enzymes, and the protein
factors required for protein synthesis.
• Many proteins undergo posttranslational
modifications as they prepare to assume their
ultimate roles in the cell.
14. DNA
1. It usually occurs inside nucleus and
some cell organelles.
(Mitochondria and Chloroplast in
plants)
2. It is double stranded with exception of
some viruses (e.g., Øx174)
3. DNA contains over a million
nucleotides
4. The sugar portion of DNA is 2-
deoxyribose
RNA
1. Very little RNA occurs inside the
nucleus. Most of it is found in
the cytoplasm.
2. It is single stranded with exception of
some viruses (Reovirus)
3. Depending on the type, RNA contains
70-12,000 nucleotides.
4. The sugar portion of RNA is ribose
15. THE GENETIC CODE
• Most genetic code tables designate the codons
for amino acids as mRNA sequences. Important
features of the genetic code include:
• Each codon consists of three bases (triplet). There
are 64 codons. They are all written in the 5' to 3'
direction.
• 61 codons code for amino acids. The other three
(UAA, UGA, UAG) are stop codons (or nonsense
codons) that terminate translation.
• There is one start codon (initiation codon), AUG,
coding for methionine. Protein synthesis begins
with methionine (Met) in eukaryotes, and
formylmethionine (fmet) in prokaryotes.
• The code is unambiguous. Each codon specifies
no more than one amino acid.
16. • The code is degenerate. More than one codon can
specify a single amino acid.
• All amino acids, except Met and tryptophan (Trp),
have more than one codon.
• For those amino acids having more than one
codon, the first two bases in the codon are
usually the same. The base in the third position
often varies.
• The code is almost universal (the same in all
organisms). Some minor exceptions to this occur
in mitochondria and some organisms.
• The code is commaless (contiguous). There are no
spacers or "commas" between codons on an
mRNA.
• Neighboring codons on a message are non-
overlapping.
19. The central dogma of molecular biology is an explanation
of the flow of genetic information within a biological
system. It was first stated by Francis Crick in 1958
The Central Dogma states that once ‘information’ has
passed into protein it cannot get out again. In more detail,
the transfer of information from nucleic acid to nucleic
acid, or from nucleic acid to protein may be possible, but
transfer from protein to protein, or from protein to nucleic
acid is impossible. Information means here the precise
determination of sequence, either of bases in the nucleic
acid or of amino acid residues in the protein
20. Protein synthesis is one of the most fundamental
biological processes by which individual cells build
their specific proteins. Within the process are involved
both DNA (deoxyribonucleic acid) and different in
their function ribonucleic acids (RNA). The process is
initiated in the cell’s nucleus, where specific enzymes
unwind the needed section of DNA, which makes the
DNA in this region accessible and a RNA copy can be
made. This RNA molecule then moves from the
nucleus to the cell cytoplasm, where the actual
the process of protein synthesis take place.
21. Transcription is the first step of gene expression, in
which a particular segment of DNA is copied
into RNA (especially mRNA) by the enzymeRNA
polymerase. Both DNA and RNA are nucleic acids,
which use base pairs of nucleotides as
a complementary language. During transcription, a
DNA sequence is read by an RNA polymerase, which
produces a complementary, antiparallel RNA strand
called a primary transcript.
22. Stages of transcription
Transcription of a gene takes place in three stages:
initiation, elongation, and termination. Here, we will briefly
see how these steps happen in bacteria. You can learn more
about the details of each stage (and about how eukaryotic
transcription is different) in the stages of
transcription article.
1.Initiation. RNA polymerase binds to a sequence of DNA
called the promoter, found near the beginning of a gene.
Each gene (or group of co-transcribed genes, in bacteria)
has its own promoter. Once bound, RNA polymerase
separates the DNA strands, providing the single-stranded
template needed for transcription.
23. 2. Elongation. One strand of DNA, the template strand,
acts as a template for RNA polymerase. As it "reads" this
template one base at a time, the polymerase builds an RNA
molecule out of complementary nucleotides, making a
chain that grows from 5' to 3'. The RNA transcript carries
the same information as the non-template (coding) strand of
DNA, but it contains the base uracil (U) instead of thymine
(T).
3.Termination. Sequences called terminators signal that
the RNA transcript is complete. Once they are transcribed,
they cause the transcript to be released from the RNA
polymerase. An example of a termination mechanism
involving formation of a hairpin in the RNA is shown
below.
24.
25.
26.
27. In bacteria, RNA transcripts can act as messenger
RNAs (mRNAs) right away. In eukaryotes, the transcript of a
protein-coding gene is called a pre-mRNA and must go through
extra processing before it can direct translation.
Eukaryotic pre-mRNAs must have their ends modified, by
addition of a 5' cap (at the beginning) and 3' poly-A tail (at the
end).
Many eukaryotic pre-mRNAs undergo splicing. In this process,
parts of the pre-mRNA (called introns) are chopped out, and the
remaining pieces (called exons) are stuck back together
End modifications increase the stability of the mRNA, while
splicing gives the mRNA its correct sequence. (If the introns are
not removed, they'll be translated along with the exons,
producing a "gibberish" polypeptide.)
28.
29. In translation, messenger RNA (mRNA) is decoded by
a ribosome, outside the nucleus, to produce a
specific amino acid chain, or polypeptide. The
polypeptide later folds into an active protein and
performs its functions in
the cell. The ribosome facilitates decoding by inducing
the binding
of complementary tRNA anticodon sequences to
mRNA codons. The tRNAs carry specific amino acids
that are chained together into a polypeptide as the
mRNA passes through and is "read" by the ribosome
30. The basic process of protein production is addition of one amino acid at
a time to the end of a protein. This operation is performed by
a ribosome. A ribosome is made up of two subunits, a small subunit and
a large subunit. these subunits come together before translation of
mRNA into a protein to provide a location for translation to be carried
out and a polypeptide to be produced.The choice of amino acid type to
add is determined by an mRNA molecule. Each amino acid added is
matched to a three nucleotide subsequence of the mRNA. For each
such triplet possible, the corresponding amino acid is accepted. The
successive amino acids added to the chain are matched to successive
nucleotide triplets in the mRNA. In this way the sequence of
nucleotides in the template mRNA chain determines the sequence of
amino acids in the generated amino acid chain. Addition of an amino
acid occurs at the C-terminus of the peptide and thus translation is said
to be amino-to-carboxyl directed.
31. cells are making new proteins every second of the day. And each
of those proteins must contain the right set of amino acids, linked
together in just the right order. That may sound like a challenging
task, but luckily, your cells (along with those of other animals,
plants, and bacteria) are up to the job.
To see how cells make proteins, let's divide translation into three
stages: initiation (starting off), elongation (adding on to the
protein chain), and termination (finishing up).
Getting started: Initiation
In initiation, the ribosome assembles around the mRNA to be
read and the first tRNA (carrying the amino acid methionine,
which matches the start codon, AUG). This setup, called the
initiation complex, is needed in order for translation to get
started.
32. Extending the chain: Elongation
Elongation is the stage where the amino acid chain gets longer. In
elongation, the mRNA is read one codon at a time, and the amino acid
matching each codon is added to a growing protein chain.
Each time a new codon is exposed:
A matching tRNA binds to the codon
The existing amino acid chain (polypeptide) is linked onto the amino
acid of the tRNA via a chemical reaction
The mRNA is shifted one codon over in the ribosome, exposing a new
codon for reading
During elongation, tRNAs move through the A, P, and E sites of the
ribosome, as shown above. This process repeats many times as new
codons are read and new amino acids are added to the chain
33. Termination is the stage in which the finished
polypeptide chain is released. It begins when a stop
codon (UAG, UAA, or UGA) enters the ribosome,
triggering a series of events that separate the chain
from its tRNA and allow it to drift out of the ribosome.
After termination, the polypeptide may still need to
fold into the right 3D shape, undergo processing (such
as the removal of amino acids), get shipped to the right
place in the cell, or combine with other polypeptides
before it can do its job as a functional protein.
34. Processing
Our polypeptide now has all its amino acids—does that mean it's
ready to to its job in the cell?
Not necessarily. Polypeptides often need some "edits." During
and after translation, amino acids may be chemically altered or
removed. The new polypeptide will also fold into a distinct 3D
structure, and may join with other polypeptides to make a multi-
part protein.
Many proteins are good at folding on their own, but some need
helpers ("chaperones") to keep them from sticking together
incorrectly during the complex process of folding.
Some proteins also contain special amino acid sequences that
direct them to certain parts of the cell. These sequences, often
found close to the N- or C-terminus, can be thought of as the
protein’s “train ticket” to its final destination.
