Download - Nucleic acid chemistry na 03
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Dr. Aga Syed SameerCSIR LecturerDepartment of Biochemistry,Medical College,Sher-I-Kashmir Institute of Medical Sciences, Bemina, Srinagar, Kashmir, 190018. India.
NUCLEIC ACIDS
ChemistryRNA: Structure & Functions
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• RNA (RiboNucleic Acid), like DNA, is a form of nucleic acid found in cells. RNA, like DNA, is a polymer composed of nucleoside monophosphates
• The bases in RNA are adenine (A), guanine (G), cytosine (C), and uracil (U)
• These are the same bases as DNA except that the base uracil is used in place of thymine (T)
• Unlike DNA, RNA is rarely composed of two strands base paired with each other.
• Instead, RNA exists as a single-stranded entity, though extensive regions of many RNAs may form double helices within themselves by the base pairing rules
RNA
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The three predominant forms of RNA are all involved in translating the genetic information in the sequence of bases in DNA to a sequence of amino acids in proteins.
They are called:
messenger RNA (mRNA),
transfer RNA (tRNA), and
ribosomal RNA (rRNA)
Types of RNA
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• mRNA is made directly from DNA, so mRNAcarries the genetic information in the DNA sequence from the cell nucleus to the ribosomes where proteins are made
• Thus, mRNA serves as the mediator in converting the information in DNA into the sequence of amino acids in proteins
• Information is organized in DNA (and mRNA) in a sequence of three nucleotides called as codons
• One codon specifies the incorporation of specific amino acid in protein
mRNA
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• tRNAs serve as adaptor molecules for the translation the genetic code
• One end of the tRNA contains a three nucleotide sequence called the anticodon loop that is complementary to the codon of the mRNA
• The other end of the tRNA is covalently attached to a specific amino acid
• Because the amino acid carried by a tRNA is specific for each anticodon and each anticodon is complementary to the codons in mRNA, thus tRNA provides the link between nucleic acid sequence and amino acid sequence for a protein during translation
tRNA
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• tRNAs are made up of 74- 95 nucleotides about 20% of which are modified bases found exclusively in its sequence.
• 50 different types of modified bases have been observed in several hundred characterized to date.
• All tRNAs have a common secondary structure formed due to complementary base pairing in the primary sequence of tRNA.
tRNA
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• tRNAs contain numerous chemical modifications to the bases within them.
• Pseudouridine,
• Ribothymidine,
• Dihydrouridine,
• Inosine
• Methyl cytidine
• Methyl guanosine
tRNA
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• The secondary structure of tRNA is called the cloverleaf structure as shown.
• It has a 5' -phosphate formed by RNase P cleavage and a 7 bp stem formed by base pairing between 5’- and 3'-ends of the tRNA
tRNA - Clover Leaf Model
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• The invariant residues 74-76 (i.e. the 5'-CCA-3') which are added during processing in eukaryotes are not included in this base pairing region
• This stem is called the amino acceptor stem as it is site for the amino acid binding during the process of translation
tRNA - Clover Leaf Model
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• The next secondary structure is D-arm which is composed of a 3 or 4 bpstem and a loop called the D-loop (DHU-loop) usually containing the modified base dihydrouracil.
• The next structural feature consists of a 5 bp stem and a seven residue loop in which there are three adjacent nucleotides called the anticodon which are complementary to the codon sequence (a triplet in the mRNA)that the tRNArecognizes
tRNA - Clover Leaf Model
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• The presence of inosine in the anticodon gives a tRNA the ability to base-pair to more than one codon sequence
• Next there is a variable arm which can have between three and 21 residues and may form a stem of up to 7 bp.
• The final major feature of secondary structure is the T -arm or TψC -arm which is composed of a 5 bp stem ending in a loop containing the invariant GTψC.
tRNA - Clover Leaf Model
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• The tertiary structure of the tRNA looks like the letter L, with the anticodon at one end & the amino acid acceptor site at the other
• There are nine hydrogen bonds (tertiary hydrogen bonds) that help 3-D structure of tRNA molecules. They mainly involve base pairing between several invariant bases
tRNA – 3D Structure
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There are nine bonds in tRNAtertiary structure:
Two are formed between DHU loop and TψC loop involving which G*=ψ and G=C respectively.
One within the TψC loop between T=A*.
One within anticodon loop between Y and purine.
The rest of the five bonds involve DHU arm; three of which are formed between the DHU arm and variable arm and two occur within the DHU loop
tRNA Molecule
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• rRNA is a component of the ribosomes where translation (protein synthesis) is occurring
• It is the most stable form of RNA and also the type which has got high half life
rRNA
Comparison between prokaryotic and eukaryotic rRNA
Prokaryotic Ribosome(2.7 x 106)
Eukaryotic Ribosome (4.2 x 106)
50S (1.8 x 106) 30S (0.9 x 106) 60S (2.8 x 106) 40S (1.4 x 106)
5S & 23S rRNA36 proteins
16s rRNA21 proteins
5S, 28S & 5.8S rRNA~49 proteins
18s rRNA~33 proteins
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rRNA
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• Another type of RNA in eukaryotic cells, called snRNA (for small nuclear RNA) helps process some RNAs after they are made
• Many eukaryotic RNAs have portions of them removed by a process called splicing. It is this process in which the snRNAs participate
snRNA
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• An RNA virus is a virus that has RNA (ribonucleic acid) as its genetic material
• This nucleic acid is usually
• single-stranded RNA (ssRNA)
• double-stranded RNA (dsRNA)
Viral RNA
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Viral RNA
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Viral RNA
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Questions?
Immunology