NUCLEIC ACIDS for BSc Optometry (Bio-Chemistry)

for BSc Optometry (RGUHS)

1. NUCLEIC ACIDS

2. Nucleotide and Nucleic Acid Chemistry; Nucleotide chemistry : Nucleotide composition, functions of free nucleotides in body. Nucleic acid (DNA and RNA) chemistry : Difference between DNA and RNA , Structure of DNA (Watson and Crick model), Functions of DNA. Structure and functions of tRNA, rRNA, mRNA.

3. NUCLEOTIDES AND NUCLEOSIDES OF BIOLOGICAL IMPORTANCE Adenosine nucleotides: ATP, ADP, AMP and CyclicAMP . Guanosine nucleotides: GTP, GDP, GMP and cyclicGMP . Uridine nucleotides: UTP, UDP, UMP, UDP-G. Cytidine nucleotides: CTP, CDP, CMP

4. NUCLEOSIDES The nucleosides are composed of purine or pyrimidine base linked to either D-ribose (in RNA) or D-2-deoxyribose (in DNA). • NUCLEISIDES BASE + SUGAR Adenosine Adenine + Ribose • Deoxyadenosine Adenine + deoxyribose • Guanosine Guanine + Ribose • Deoxyguanosine Guanine + deoxyribose • Uridine Uracil + Ribose • Cytidine Cytosine + Ribose • Deoxycytidine Cytosine + deoxyribose • Thymidine Thymine + deoxyribose

5. NUCLEOTIDES A nucleotide is a nucleoside to which a phosphoric acid group has been attached to the sugar molecule by ‘ esterification ’ at a definite – OH group and thus has the general composition base – sugar – PO4 .

6. Neucleotide Base Sugar Phosphoric acid (a) Present in RNA • Adenylic acid or Adenylate (AMP) Adenine + Ribose + Phosphoric acid • Guanylic acid or Guanylate (GMP) Guanine + Ribose + Phosphoric acid • Cytidylic acid or Cytidylate (CMP) Cytosine + Ribose + Phosphoric acid • Uridylic acid or Uridylate (UMP) Uracil + Ribose + Phosphoric acid (b) Present in DNA • Deoxy adenylic acid or deoxy Adenylate ( dAMP ) Adenine + Deoxyribose + Phosphoric acid • Deoxy guanylic acid or deoxy guanylate (d GMP) Guanine + Deoxyribose + Phosphoric acid • Deoxy cytidylic acid Or deoxy cytidylate (d CMP) Cytosine + Deoxyribose + Phosphoric acid • Thymydylic acid or thymidylate (TMP) Thymine + Deoxyribose + Phosphoric acid Note 1. Uridylic acid occurs in RNA only, hence there will be only ribose. There is no deoxy uridylic acid . 2. There is no thymidylic acid in RNA.

7. Adenosine triphosphate (ATP) It is called as storage battery of the tissues. It is storehouse of energy. Functions: Two of the three phosphate residues are high energy “phosphates (~P)” and on hydrolysis each releases energy Many synthetic reactions require energy, e.g. arginine succinate synthetase reaction in the urea cycle ATP is also required in the synthesis of Phosphocreatine from creatine, synthesis of FA from acetyl CoA , synthesis of peptides and proteins from amino acids, formation of glucose from pyruvic acid, synthesis of glutamine, etc.

8. ATP is an important source of energy for muscle contraction , transmission of nerve impulses , transport of nutrients across cell membranes, motility of spermatozoa . ATP is required for formation of active methionine , which is required for methylation reactions.

9. GUANOSINE NUCLEOTIDES GTP : Guanosine Triphosphate The oxidation of succinyl-CoA in the citric acid cycle involves phosphorylation of GDP to form GTP. GTP is also required for protein synthesis GTP is required in rhodopsin cycle. Role of GTP in gluconeogenesis

10. URIDINE NUCLEOTIDES Uridine monophosphate (UMP) is obtained by the hydrolysis by RNAase and phosphodiesterase UMP is convertible to UDP and UTP by the enzyme nucleoside diphosphokinase ( nudiki ) in presence of ATP. UDPG is also required for UDP-Glucose-Galactose epimerase for the interconversion of glucose and galactose in the liver.

11. CYTIDINE NUCLEOTIDES These include CMP, CDP, and deoxy CDP—derivatives of glucose, choline, ribitol , glycerol, sialic acid, etc. • CDP-choline, CDP-glycerol, and CDP-ethanolamine are involved in the biosynthesis of phospholipids . • CMP-acetyl neuraminic acid is an important precursor of cell wall polysaccharides in bacteria. • CMP-Sialic acid is present in salivary glands and may be concerned with the biosynthesis of salivary mucin .

12. Deoxyribose nucleic acid (DNA)

13. Structure of DNA Deoxyribonucleic acid is a slightly acidic molecule originally identified in cell nuclei. Nucleotides are the building blocks of DNA. Each nucleotide contains a phosphate group , a five-carbon sugar , and a nitrogen base . The five-carbon sugar is called deoxyribose . Covalent bonds hold the sugar of one nucleotide to the phosphate group of another nucleotide to form chains.

14. DNA is a polymer of about 10 10 deoxyribonucleotides . Normally there are only four different types of deoxyribonucleotides that are found in DNA molecule, Deoxyadenylate ( dAMP ), Deoxyguanylate ( dGMP ), Deoxycytidylate( dCMP ) and Deoxythymidylate (dTMP)

15. The "5 prime end" has a free hydroxyl (or phosphate) on a 5' carbon and the "3 prime end" has a free hydroxyl (or phosphate) on a 3' carbon (carbon atoms in the  sugar  ring are numbered from 1' to 5'; ).

16. DNA DOUBLE HELIX The double helical structure of DNA was proposed by lames Watson and Francis Crick in 1953 (Nobel Prize, 1962). The DNA is a right-handed double helix. It consists of two polydeoxyribonucleotide chains (strands) twisted around each other on a common axis. The two strands are antiparallel , i.e., one strand runs in the 5' to 3' direction while the other in 3' to 5'direction .

17. The width (or diameter) of a double helix is 20 Ao (2 nm). Each turn (pitch) of the helix is 34 A" (3.4 nm) with 10 pairs of nucleotides , each pair placed at a distance of about 3.4 A Each strand of DNA has a hydrophilic Deoxyribose phosphate backbone( 3'-5' phosphodiester bonds)on the outside (periphery)of the molecule while the hydrophobic bases are stacked inside (core). This is comparable to two parallel adjacent roads carrying traffic in opposite direction.

18. The two strands are held together by hydrogen bonds formed by complementary base pairs. The A-T pair has 2 hydrogen bonds while G-C pair has 3 hydrogen bonds. The G = C is stronger by about 50% than A=T. The hydrogen bonds are formed between a purine and a pyrimidine only. lf two purines face each other, they would not fit into the allowable space . And two pyrimidines would be too far to form hydrogen bonds. The only base arrangement possible in DNA structure, from spatial considerations is A-T, T-A, G-C and c-c.

19. The two polynucleotide chains are not identical but complementary to each other due to base pairing. The complementary base pairing in DNA helix proves Chargaff’s rule . The content of adenine equals to that of thymine (A = T) and guanine equals to that of cytosine (G = C). The genetic information resides on one of the two strands known as template strand or sense strand . The opposite strand is antisense strand . The double helix has (wide) major grooves and (narrow) minor grooves along the phosphodiester backbone. Proteins interact with DNA at these grooves, without disrupting the base pairs and double helix.

20. DNA Types There are three different DNA types: A -DNA, B -DNA Z -DNA The most common conformation is B-DNA

21. Functions of DNA DNA has three roles/purposes/functions: 1. Storing information – genes are segments of DNA that carry messages to make proteins. 2. Copying information – so that when cells divide, all cells get a complete copy of the genetic material. 3. Transmitting information – DNA is passed from parents to offspring.

22. RIBONUCLEIC ACID (RNA)

23. RNA is made up of  ribonucleotides ,  each containing a phosphate group , a 5-carbon sugar , and a nucleotide base. The four types of nitrogenous base found in RNA molecules are: Uracil Adenine Guanine Cytosine Thymine is absent in RNA. The pentose sugar of the nucleotide is D-ribose .

24. Therefore, the four types of RNA nucleotide are: A nucleotide (containing  adenine ) U nucleotide (containing  uracil ) G nucleotide (containing  guanine ) C nucleotide (containing  cytosine ) RNA is found in the nucleolus , ribosomes , mitochondria and cytoplasm. Like in DNA molecules , these ribonucleotides are joined together by  phosphodiester bonds   that form between the 3’ carbon of one sugar and the 5’ carbon of another. Unlike DNA, RNA is a single-stranded molecule

25. Types of RNA There are mainly three types of RNA found in human beings. These are: 1. Messenger RNA or m-RNA : 5-1O % 2. Transfer or soluble RNA or t-RNA : 10-20 % 3. Ribosomal RNA or r-RNA : 50-80 % The main function of each of these RNA is protein synthesis. Other RNAs are also present in the cells. These include heterogeneous nuclear RNA ( hnRNA ), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA) and small cytoplasmic RNA ( scRNA )

26. mRNA carries a copy of the instruction from the DNA in the nucleus to the ribosome rRNA is a major component o f ribosome-the site of protein synthesis t-RNA carries the amino acids which are added to the polypeptide chain (protein) being synthesized. FUNCTION OF RNA

27. 1. Messenger RNA (m-RNA) 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. The mRNA carries genetic information from DNA.

28. The genetic information carried by the mRNA is called genetic code. The genetic code is the sequence of nitrogen bases in mRNA. Each codon is a sequence of 3 nitrogen bases. As each codon is formed of three nitrogen bases, it is called triplet code.

29. One end of mRNA is called 5’ end and the other end is called 3’ end. At the 5’ end a cap is found in most eukaryotes. The cap is formed by the condensation of a guanylate residue. The termination codon At the 3’ end of mRNA, there is a polyadenylate sequence. It contains of 200 to 250 adenylate nucleotides (AAAAAA……)..

30. The non coding region is followed by the initiation codon. It is made up of AUG. The initiation codon is followed by the coding region which contains the code for protein. The coding region is followed by termination codon. It completes the translation.

31. The role of mRNA is to  carry protein information from the DNA in a cell's nucleus to the cell's cytoplasm  (watery interior), where the protein-making machinery reads the mRNA sequence and translates each three-base codon into its corresponding amino acid in a growing protein chain.

32. Functions of RNA The primary functions of RNA: Facilitate the translation of DNA into proteins Functions as an adapter molecule in  protein synthesis Serves as a messenger between the DNA and the ribosomes. They are the carrier of genetic information in all living cells Promotes the ribosomes to choose the right amino acid which is required in building up of new proteins in the body.

33. Transfer RNA (tRNA)

34. t-RNA (transfer RNA) is also named as S-RNA (soluble or supernatant RNA) and adaptor RNA . 10 – 20 % of total cellular RNA is t-RNA. t-RNAs are small molecules with about 74 – 95 ribonucleotides . Molecular weight – nearly 25,000 – 30,000 Dalton. t-RNAs are made up of a single stranded polynucleotide chain

35. Unique feature of tRNA Presence of unusual base pairs In addition to usual N-bases (A,U,G,C) tRNA contains number of unusual bases . These unusual bases are important as they protect t-RNA molecules from dehydration by Rnase , when tRNAs are floating freely in cytoplasm.

36. Protects mainly by methylation Inosine (I) – Adenine Pseudouracil (y) - Uracil Dihydroxyuridine - urdine Thymine are present in one loop. Structure of tRNA : Primary structure - linear sequence of nucleotides Secondary structure -Clover leaf model Tertiary structure - 3-D structure of tRNA ,

37. Robert Holley proposed clover leaf model for the first time in 1968. t RNA contains mainly four arms , each arm with a base paired stem . 1. The acceptor arm 2. The anticodon arm 3. The D arm 4. The T ѱ C arm 5. The variable arm

38. D arm • DHU or D arm – This arm consists of stem and loop with unusual pyrimidine nucleotide dihydrouracil . • 4 bp stem with a loop contain dihydrouridine • Recognition site for the specific enzyme aminoacyl-tRNA synthetase that activate the amino acid The acceptor arm : This arm is capped with a sequence CCA (5' to 3' ) . The amino acid is attached to the acceptor arm.

39. T y C arm • TψC arm is named for the presence of sequence TψC (thymine – pseudouridine (ψ) – cytosine), where pseudouridine is unusual base. • This arm also consists of stem and loop . • Stem contains 5 base pairs and Loop contains 7 unpaired nucleotides • This loop contains a ribosome recognition site This arm also contains stem and loop. • Stem consists of 5 base pairs and loop (called as anticodon loop or loop II) contains 7 unpaired nucleotides. • Out of these 7 unpaired nucleotides the middle three form anticodon. • Anticodon recognizes and codon of mRNA and binds to it.

40. Variable arm • The variable arm has between 3 and 21 nucleotides , depending on which amino acid the tRNA encodes. • Between anticodon loop and TΨU loop • This tRNA's variable arm is very short so it looks quite different from the other arms of the molecule.

41. Functions of tRNA  Help in the recognition of Aminoacyl tRNA synthetase enzyme    Picks up specific amino acid from cytoplasm and carries to site of protein synthesis    Attaches itself to ribosome in accordance with sequence specified by mRNA    Transmits amino acid to polypeptide chain    Participate in non protein synthetic processes such as a primer during reverse transcription in retrovirus life cycles

42. ribosomal RNA

43. rRNA This is the Ribosomal RNA. The rRNA is synthesized in the nucleus , they are transported to the cytoplasm , where they combine with a specific proteins to form a ribosome. In the cytoplasm, ribosomal RNA and protein combine together to form a nucleoprotein called a ribosomes.

44. The ribosomes and mRNA bind to carry out protein synthesis. rRNA is very abundant in the cell and forms about 80% of the total RNA. Ribosomes are attached to the surface of branches of endoplasmic reticulum (RER), in the matrix of organelles like mitochondria and chloroplasts . It is also found attached to the nuclear membrane and inside the nucleolus.

45. Each ribosome is composed of two subunits, a larger one and a smaller one In prokaryotes, the ribosomal RNA (rRNA) has three types: 23S, 5S, and 16S. The unit " S " stands for Svedberg , which is a measure of the sedimentation rate.  In prokaryotes , the size of a ribosome is 70S, consisting of two subunits: 50S and 30S. 

46. In mammals , four types of rRNA have been found : 28S, 5.8S, 5S and 18S.  The size of a mammalian ribosome is 80S, comprising a 60S and a 40S subunit.  Function : Ribosomal RNA (rRNA) is  responsible for the translation of mRNA to protein .

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