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RNA vs. DNA
• RNA contains the sugar ribose; DNA contains deoxyribose.
• RNA contains the base uracil; DNA contains thymine instead.
• RNA is usually single stranded; DNA is usually double stranded.
• RNA is short: one gene long at most; DNA is long, containing many genes.
• RNA contains A,U,G and C; DNA contains A,T,G and C.
Types of RNAs
• mRNA: A copy of the gene that is being expressed. Groups of 3 bases in mRNA, called “codons”
code for each individual amino acid in the protein made by that gene.
“In eukaryotes, the initial RNA copy of the gene is called the
“primary transcript”, which is modified to form mRNA”.
• rRNA: Four different RNA molecules that make up part of the structure of the ribosome. They
perform the actual catalysis of adding an amino acid to a growing peptide chain.
• tRNA: Small RNA molecules that act as adapters between the codons of messenger RNA and the
amino acids they code for.
• In prokaryotes, the RNA copy of a gene is messenger RNA, ready to be translated into protein. In fact,
translation starts even before transcription is finished.
• In eukaryotes, the primary RNA transcript of a gene needs further processing before it can be translated.
• This step is called “RNA processing”. Also, it needs to be transported out of the nucleus into the cytoplasm.
• Steps in RNA processing:
1. Add a cap to the 5’ end (7-methyl G)
2. Add a poly-A tail to the 3’ end
3. splice out introns.
• In eukaryotes, RNA polymerase produces a “primary transcript”, an exact RNA
copy of the gene.
• A cap (guanine nucleotide) is put on the 5’ end as a triphosphate linkage by
• The RNA is terminated and poly-A tail is added (having multiple Adenosine
monophosphate) to the 3’ end.
• All introns are spliced out.
• At this point, the RNA can be called messenger RNA. It is then transported out
of the nucleus into the cytoplasm, where it is translated.
Structure of tRNA
• The tRNA molecule has a distinctive folded structure
with three hairpin loops that form the shape of a
• At the 3' end of the tRNA molecule, opposite the
anticodon, extends a three nucleotide acceptor site
that includes a free -OH group.
• A specific tRNA binds to a specific amino acid through
its acceptor stem.
• Translation of mRNA into protein is accomplished by the ribosome, an RNA/protein hybrid.
Ribosomes are composed of 2 subunits, large and small.
• Ribosomes bind to the translation initiation sequence on the mRNA, then move down the RNA in
a 5’ to 3’ direction, creating a new polypeptide.
• The first amino acid on the polypeptide has a free amino group, so it is called the “N-terminal”.
The last amino acid in a polypeptide has a free acid group, so it is called the “C-terminal”.
• Each group of 3 nucleotides in the mRNA is a “codon”, which codes for 1 amino acids. Transfer
RNA is the adapter between the 3 bases of the codon and the corresponding amino acid.
• In eukaryotes, ribosomes bind to the 5’ cap, then move down the mRNA
until they reach the first AUG, the codon for methionine. Translation starts
from this point. Eukaryotic mRNAs code for only a single gene.
• Note that translation does not start at the first base of the mRNA. There is
an un-translated region at the beginning of the mRNA, the 5’ un-translated
region (5’ UTR).
• The initiation process involves first joining the
mRNA, the initiator methionine-tRNA, and the
small ribosomal subunit.
• Several “initiation factors”(eIF 1-6) additional
proteins are also involved.
• The large ribosomal subunit then joins the
• The ribosome has 2 sites for tRNAs, called P (peptide) and A (aminoacyl). The initial tRNA with attached amino acid is in the P site
and new tRNA, corresponding to the next codon on the mRNA, binds to the A site.
• The ribosome catalyzes a transfer of the amino acid from the P site onto the amino acid at the A site, forming a new peptide bond.
The ribosome then moves down one codon.
• The now-empty tRNA at the P site is displaced off the ribosome, and the tRNA that has the growing peptide chain on it is moved
from the A site to the P site. The process is then repeated:
the tRNA at the P site holds the peptide chain, and a new tRNA binds to the A site.
the peptide chain is transferred onto the amino acid attached to the A site tRNA.
the ribosome moves down one codon, displacing the empty P site tRNA and moving the tRNA with the peptide chain from the A site
to the P site.
• Three codons are called “stop codons”. They code for no amino acid,
and all protein-coding regions end in a stop codon.
• When the ribosome reaches a stop codon, there is no tRNA that binds
to it. Instead, proteins called “release factors” bind, and cause the
ribosome, the mRNA, and the new polypeptide to separate. The new
polypeptide is completed.
• Note that the mRNA continues on past the stop codon. The remaining
portion is not translated: it is the 3’ un-translated region (3’ UTR).
Post translational modifications
• The chemical modification of a protein after its translation is known as Post-Translational Modification.
• Some amino acids might be changed and carbohydrates or lipids can be added.
• Peptide can be activated by addition or removal of some residue (acetate, phosphate, methyl etc.)
• Changes in the Hydrogen bond proclivity which results in secondary and tertiary structures.
• Some of the proteins might remain in cytosol while others are transported across the membrane or even
imported into cellular organelles (mitochondria or chloroplasts) to accomplish their functions
Importance of PTMs
• Play a crucial role in generating the heterogeneity in proteins.
• Help in utilizing identical proteins for different cellular functions in different cell types.
• Regulation of particular protein sequence behavior in most of the eukaryotic organisms.
• Play an important part in modifying the end product of expression.
• Contribute towards biological processes and diseased conditions.
• Translocation of proteins across biological membranes.
Types of PTMs
• Trimming; in which part of the translated sequence is removed.
• Covalent modification include:
• Lipoylation and Sulfationand Acetylation.
• Glycosylation:- The addition of saccharide to a protein or a lipid molecule.
• N-Linked Glycosylation:- Amide nitrogen of Asparagine.
• O-Linked Glycosylation:- Hydroxyl oxygen of Serine and Therionine.
• Hydroxylation:- The addition of hydroxyl group to proline of protein.
• Carboxylation:- The addition of carboxyl group to glutamate.
• Biotinylation:- The addition of biotin to protein or nucleic acid.
• Acetylation:- The addition of an acetyl group, usually at the N-terminus of the protein.
• Methylation:- The addition of a methyl group, usually at lysine or arginine residues.
• Alkylation:- The addition of an alkyl group (e.g. methyl, ethyl).
• Glutamylation:- Covalent linkage of glutamic acid residues to tubulin and some other.
• Lipoylation:- The attachment of a lipoate functionality
• Sulfation:- The addition of a sulfate group to a tyrosine.
• Ubiquitination:- Highly specific degradation of protein can be achieved through the
addition of one to several ubiquitin molecules to a target protein.
Protein synthesis Inhibitor
• A protein synthesis inhibitor is a substance that stops or slows the growth or proliferation of cells
by disrupting the processes that lead directly to the generation of new protein.
• Antibiotics are biochemically or fungally produced substances that inhibit the growth of other
organisms. Most antibiotics, like many pharmaceuticals, block translation in protein synthesis.
• These substances are effective because they take advantage of the tremendous complexity
involved in the synthesis of proteins.
• Some examples are Puromycin, Streptomycin, Erythromycin, Tetracyclin, Penicillin,
Chloramphenicol, Rifampin, Fusidic Acid and Thiostrepton.
• Chemical modification involves three steps:
• Modification of amino acid residues into other types,
• Addition of organic units (such as sugars or lipids) to specific amino
• Enzymatic cleavage of one or more amino acids from a region of the
Diseases caused by PTMs
• The abundance of collagen in the extracellular structures of humans and other
mammals makes disorders of collagen deposition.
• Atherosclerosis: A disease involving stiffening of the arteries, is related to an
over-deposition of collagen.
• Fibrosis: A disease involving hardening of the tissues, is related to excessive
• Progressive Systemic Sclerosis (Scleroderma): A disease of the vascular and
immune systems, and a severe connective tissue disorder.