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Biochemistry

1. Nucleic Acid BY: RINKU YADAV

2. There are two types of nucleic acids, namely (DNA) and (RNA). Primarily, nucleic acids serve as repositories and transmitters of genetic information. history DNA was discovered in 1869 by Johann Friedrich Miescher,. The demonstration that DNA contained genetic information was first made in 1944, by Avery, Macleod and MacCary.

3. Functions of DNA It carries and transfers the genetic information. The genetic information code of functional proteins. DNA transfers the genetic information from one generation to the next. It regulates the metabolic reactions of the cell. It helps in the synthesis of RNA by transcription. It is self-replicative i.e. DNA can make its copies. It controls all the aspects of an organism’s development.

4. It can be used for DNA fingerprinting during any crime or parental dispute. It can undergo abrupt changes or mutations due to any possible reason. It gives the required information to design gene-based therapy for disease.

5. Types of DNA Nuclear DNA ( nDNA ) : The eukaryotic cells have a nucleus that contains the genetic material of the cell i.e. the DNA. This form of DNA that controls all the general characteristics of cell is called nuclear DNA. Mitochondrial DNA ( mtDNA ):  Mitochondria are semi-autonomous as they possess their DNA, RNA, and ribosomes. This DNA is called mitochondrial DNA and it usually comes from the mother in case of sexually reproducing organisms .

6. A-DNA : These are right-handed double helical DNA that have 11 bases per complete turn with a 2.3 nm diameter of the helix. B-DNA : right-handed double helical DNA found in most of the cells. They have 10 bases per complete turn with a 1.9 nm diameter of the helix. C-DNA : It is right-handed double helical DNA that has 9.3 bases per complete turn with a 1.9 nm diameter of the helix.

7. D-DNA:  Lacks the Guanine (G) base unit making it an interesting variation and a rare form. It has 8 base pairs per complete turn with 2.3 nm diameter of the helix. E-DNA : It is an eccentric and extended form of DNA that is a right-handed helix. They have 7.5 bases per complete turn with a 2.3 nm diameter of the helix. Z-DNA : It has a zig-zag pattern with a left-handed helix that has 12 bases per complete turn with a 1.8 nm diameter of the helix.

8. SN B-Form A-Form Z-Form 1 helix sense Right Handed Right Handed Left Handed 2 base pairs per turn 10 11 12 3 vertical rise per bp 3.4 Å 2.56 Å 19 Å 4 rotation per bp +36° +33° -30° 5 helical diameter 19 Å 19 Å 19 Å

9. The interrelationship of these three classes of biomolecules (DNA, RNA and proteins) constitutes the central dogma of molecular biology or more commonly the central dogma of life.

10. Components of nucleic acids Nucleic acids are the polymers of nucleotides (polynucleotides) held by 3 prim and 5 prim phosphate bridges, nucleic acids are built up by the monomeric units—nucleotides NUCLEOTIDES : Nucleotides are composed of a nitrogenous base , a pentose sugar and a phosphate .

11. STRUCTURE OF DNA : DNA is a polymer of deoxyribonucleotides (or simply deoxynucleotides). It is composed of monomeric units namely deoxyadenylate (dAMP), Deoxyguanylate (dGMP), deoxycytidylate (dCMP) deoxythymidylate (dTMP)

12. The 3'-hydroxyl of one sugar is combined to the 5'-hydroxyl of another sugar through a phosphate group. the thymidine is attached to cytidine and then cytidine to adenosine through phosphodiester linkages. The deoxyribose and phosphodiester linkages are the same in all the repeating nucleotides. 5'P–Thymine–Cytosine–Adenine–3’OH

13. Watson-Crick Model of DNA Structure The salient features of Watson-Crick model of DNA 1. Right Handed Double Helix: DNA consists of two polydeoxy ribonucleotide chains twisted around one another in a right handed. The Base Pairing Rule : the two strands are complementary to each other.

14. strand, while guanine will pair with cytosine. The base pairing (A with T; G with C) is called Chargaff's rule, which states that the number of purines is equal to the number of pyrimidines . Hydrogen Bonding: The DNA strands are held together mainly by hydrogen bonds between the purine and pyrimidine bases. There are two hydrogen bonds between A and T while there are three hydrogen bonds between C and G .

15. Antiparallel The two strands in a DNA molecule run antiparallel, which means that one strand runs in the 5' to 3' direction, while the other is in the 3' to 5' direction. The spiral has a pitch of 3.4 nanometers per turn. Within a single turn, 10 base pairs are seen. Thus, adjacent bases are separated by 0.34 nm.

16. Chargaff’s rule of DNA composition Erwin Chargaff in late 1940s quantitatively analysed the DNA hydrolysates from different species. He observed that in all the species he studied, DNA had equal numbers of adenine and thymine residues (A = T) and equal numbers of guanine and cytosine residues (G = C). This is known as Chargaff’s rule of molar equivalence between the purines and pyrimidines in DNA structure.

17. STRUCTURE OF RNA: RNA is a polymer of ribonucleotides held together by 3prim ,5prim -phosphodiester bridges. Pentose : The sugar in RNA is ribose 2. Pyrimidine : RNA contains the pyrimidine uracil in place of thymine 3. Single strand : RNA is usually a singlestranded polynucleotide. 4. Chargaff’s rule: Due to the single-stranded nature, there is no specific relation between purine and pyrimidine contents. Thus the guanine content is not equal to cytosine

18. TYPES OF RNA : The three major types of RNAs Messenger RNA (mRNA) : 5–10% 2. Transfer RNA (tRNA) : 10–20% 3. Ribosomal RNA (rRNA) : 50–80%

19. Messenger RNA (mRNA): The mRNA is synthesized in the nucleus (in eukaryotes) as heterogeneous nuclear RNA ( hnRNA ). hnRNA , on processing, liberates the functional mRNA which enters the cytoplasm to participate in protein synthesis. mRNA has high molecular weight with a short half-life.

20. mRNA of eukaryotes is more stable with longer half-life, compared to prokaryotic mRNA. The eukaryotic mRNA is capped at the 5prim-terminal end by 7-methylguanosine triphosphate . this cap helps to prevent the hydrolysis of mRNA by 5prim-exonucleases . The 3prim-terminal end of mRNA contains a polymer of adenylate residues (20-250 nucleotides) which is known as poly (A) tail.

21. This tail may provide stability to mRNA, besides preventing it from the attack of 3prim-exonucleases. mRNA molecules often contain certain modified bases such as 6-methyladenylates in the internal structure Functions of mRNA mRNA carries genetic information from DNA to  ribosomes , which are used as a template to assemble the amino acid sequence of a protein.

22. Transfer RNA (tRNA) Transfer RNA molecule contains 71-80 nucleotides (mostly 75) with a molecular weight of about 25,000. There are at least 20 species of tRNAs, corresponding to 20 amino acids present in protein structure. The structure of tRNA was first explained by Holley. The structure of tRNA, resembles that of a clover leaf. tRNA contains mainly four arms, each arm with a base paired stem.

23. Cloverleaf Model tRNA molecule consists of 70-80 nucleotides that fold like a clover leaf. As clove has the following ends, the t-RNA molecule also has four ends: Acceptor end:  it accepts the specific amino acid. It is made up of 7-9 nucleotides. It has two ends- 3′ and 5′.   It is the 3’ end that consists of a base triplet CCA with OH group

24. the 5′ end consists of a phosphate group. At this OH at the 3′ end, the COOH group of amino acids joins. 2.Anti-codon end:   It is made up of 5 base pairs and consists of codons that are complementary to the codon present on mRNA, therefore known as an anticodon. Anticodon is the triplet base sequence in tRNA which binds with the codon at the time of translation. There is specific tRNA for a particular amino acid.

25. Base pairing between the codon and anticodon helps in the synthesis of proteins. There are no tRNAs for stop codons but have specific tRNAs for initiate codons . 

26. Enzyme site/DHU end:  It is present on the lateral side of the molecule that recognizes aminoacyl-tRNA synthetase that activates the amino acids and catalyzes the binding of a specific amino acid to a tRNA molecule. It consists of 3- 4 base pairs and is called a D loop because it consists of a modified nucleotide called dihydrouridine . TΨC Loop end:  It is known as T arm.  It consists of 4-5 base pairs and a loop consisting of modified uridine called pseudouridine .it is Ribosome recognition end

27. Variable Loop:  This loop is of variable size and ranges from 3-21 base pairs. It is present between the anticodon and TΨC loop. It recognizes tRNA molecules. L-shaped model 3D tRNA looks like an L-shaped molecule that has two functional ends:  The acceptor stem:  Site of attachment of specific amino acid (3’ end of the molecule) Anticodon loop:  Site where codons are read on mRNA (5’ end of the molecule)

28. L-shaped model

29. t-RNA Functions It helps in the synthesis of proteins. It helps in aminoacylation which is the first step of protein synthesis.  It transfers the specific amino acid from the amino acid pool to the mRNA to form a polypeptide to make proteins. It helps amino acids link with mRNA to form proteins.  5.It consists of anticodon which decodes the amino acid code for a specific amino acid present in mRNA .  etc

30. Ribosomal RNA : (rRNA) The ribosomes are the factories of protein synthesis. The eukaryotic ribosomes are composed of two major nucleoprotein complexes–60S subunit and 40S subunit. The 60S subunit contains 28S rRNA, 5S rRNA and 5.8S rRNA the 40S subunit contains 18S rRNA. The function of rRNAs in ribosomes is not clearly known. It is believed that they play a significant role in the binding of mRNA to ribosomes and protein synthesis

31. How does tRNA work? The anticodon site of tRNA has complementary nucleotides that code for specific amino acids. For example-AUG is coded for methionine amino acid and the tRNA anticodon site has a complementary code for it which is UAC. Once, the amino acid is coded, now it has been sent to the DHU site that recognizes the methionine amino acid from the amino acid pool.  This is done with the help of the  enzyme  aminoacyl-tRNA synthetase. After recognition, methionine will be accepted at the carrier end of tRNA and finally sent to the ribosome recognition site where it will get attached to the ribosome.