Nucleic Acids -Bio-Molecules Chemistry Notes | EduRev

Organic Chemistry

Chemistry : Nucleic Acids -Bio-Molecules Chemistry Notes | EduRev

The document Nucleic Acids -Bio-Molecules Chemistry Notes | EduRev is a part of the Chemistry Course Organic Chemistry.
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Nucleic Acids

What do they do?

  • Dictate amino-acid sequence in proteins
  • Give information to chromosomes, which is then passed from parent to offspring
  • The 4th type of macromolecules
  • The chemical link between generations
  • The source of genetic information in chromosomes

Two types (depending on the sugar they contain)

1. RNA (Ribonucleic acids): The pentose sugar is Ribose (has a hydroxyl group in the 3rd carbon)

2. DNA (Deoxyribonucleic acids): The pentose sugar is Deoxyribose (has just an hydrogen in the same place). Deoxy = “minus oxygen”

Nucleotides and Nucleosides

Nucleic Acids -Bio-Molecules Chemistry Notes | EduRev

  • Nucleotide = Nitrogeneous base, Pentose sugar, Phosphate
  • Nucleoside = Nitrogeneous base, Pentose sugar

Nucleic Acids -Bio-Molecules Chemistry Notes | EduRev

Bases (Purine and Pyrimidine)

  • Pyrimidine contains two pyridine-like nitrogens in a six-membered aromatic ring.
  • Purine has 4 N’s in a fused-ring structure. Three are basic like pyridine-like and one is like that in pyrrole.

Nucleic Acids -Bio-Molecules Chemistry Notes | EduRev

Purines:

Nucleic Acids -Bio-Molecules Chemistry Notes | EduRev

Pyrimidines:

Nucleic Acids -Bio-Molecules Chemistry Notes | EduRev

Pentose Sugars: There are two related pentose sugars:

  • RNA contains ribose
  • DNA contains deoxyribose

“The sugars have their carbon atoms numbered with primes to distinguish them from the nitrogen bases”

Nucleic Acids -Bio-Molecules Chemistry Notes | EduRev

Double helical structure of DNA:

Two polynucleotide strands, running in opposite directions (anti-parallel) and coiled around each other in a double helix. The strands are held together by complementary hydrogen- bonding between specific pairs of bases. Weak forces stabilize DNA.

  • Stacking interactions (Van Der Waals forces)
  • Hydrophobic effect
  • Charge-charge
  • Hydrogen bonding

✔ Little contribution to stability

✔ Large contribution to selectivity

Nucleic Acids -Bio-Molecules Chemistry Notes | EduRev.


Tertiary Structure of DNA: It is supercoiled. Each cell contains about two meters of DNA. DNA is “packaged” by coiling around a core of proteins known as histones.

The DNA-histone assembly is called a nucleosome. Histones are rich is lysine and arginine residues.

Nucleic Acids -Bio-Molecules Chemistry Notes | EduRev


Processes in the transfer of genetic information

Nucleic Acids -Bio-Molecules Chemistry Notes | EduRev


1. Replication: Identical copies of DNA are made. DNA is replicated by the coordinated efforts of a number of proteins and enzymes. For replication, DNA must be unknotted, uncoiled and the double helix unwound. Topoisomerase is an enzyme that unknots and uncoils DNA. Helicase is a protein that unwinds the DNA double helix. DNA polymerase is an enzyme that replicates DNA using each strand as a template for the newly synthesized strand. DNA ligase: enzyme that catalyzes the formation of the phosphodiester bond between pieces of DNA. Replication process is semi-conservative: Each new strand of DNA contains one parental (old, template) strand and one daughter (newly synthesized) strand. Unwinding of DNA by helicases is exposed by the DNA bases so that replication can take place. Helicase hydrolyzes ATP in order to break the hydrogen bonds between DNA strands.

Nucleic Acids -Bio-Molecules Chemistry Notes | EduRev


2. Transcription:

Stages of Transcription-

  • Promoter Recognition
  • Chain Initiation
  • Chain Elongation
  • Chain Termination

a) Promotor Recognition

Transcription factors bind to promoter sequences and recruit RNA polymerase. DNA is bound first in a closed complex. Then, RNA polymerase denatures a 12–15 bp segment of the DNA (open complex). The site where the first base is incorporated into the transcription is numbered “+1” and is called the transcription start site. Transcription factors that are required at every promoter site for RNA polymerase interaction are called basal transcription factors. Promoter sequences vary considerably.

RNA polymerase binds to different promoters with different strengths; binding strength relates to the level of gene expression. Eukaryotic genes may also have enhancers.Enhancers can be located at great distances from the gene they regulate, either 5´ or 3´ of the transcription start, in introns or even on the noncoding strand. One of the most common ways to identify promoters and enhancers is to use a reporter gene.

b) Chain Iniation

RNA polymerase locally denatures the DNA. The first base of the new RNA strand is placed complementary to the +1 site. RNA polymerase does not require a primer. The first 8 or 9 bases of the transcript are linked. Transcription factors are released, and the polymerase leaves the promoter region.

c) Chain Elongation

RNA polymerase moves along the transcribed or template DNA strand. The new RNA molecule (primary transcript) forms a short RNA-DNA hybrid molecule with the DNA template.

e) m-RNA synthesis/processing

In eukaryotic cells, the primary RNA transcript must be processed and transported to the cytoplasm before translation (protein synthesis) can begin. The DNA of eukaroytic genes contains noncoding sequences (introns) and coding sequences (exons). Introns must be removed from the RNA transcript by a process called splicing. Additionally a methylguanoisine cap is added to the 5´ end of the transcript, and a polyadenosine tail (polyA) is added to the 3´ end. The 5´ cap aids in transport of the completed mRNA from the nucleus, and the polyA tail helps to determine the stability of the mRNA molecule.

3. Translation: Genetic messages are decoded to make proteins. Translation, or protein synthesis, is directed in eukayotic cells by an mRNA molecule. Translation can be seen to occur in two phases: (1) information transfer, in which RNA base sequence of the mRNA determines the sequence of amino acids and (2) chemical processes, in which the peptide bonds between the adjacent amino acids are formed. The components required for translation include: mRNA, ribosomes, tRNA, aminoacyl tRNA synthetases, and accessory proteins involved in initiation, elongation and termination.

Components required for translation:

1. mRNA

2. Ribosomes

3. tRNA

a). Initiation:

Ribosome small subunit binds to mRNA. Charged tRNA anticodon forms base pairs with the mRNA codon. Small subunit interacts with initiation factors and special initiator tRNA that is charged with methionine. mRNA-small subunit-tRNA complex recruits the large subunit. The large subunit of the ribosome contains three binding sites: Amino acyl (A site), Peptidyl (P site), Exit (E site). At initiation, the tRNAfMet occupies the P site. A second, charged tRNA complementary to the next codon binds the A site.

b). Elongation

Ribosome translocates by three bases after peptide bond formed. New charged tRNA aligns in the A site. Peptide bond between amino acids in A and P sites is formed. Ribosome translocates by three more bases. The uncharged tRNA in the A site is moved to the E site. EF-Tu recruits charged tRNA to A site. Requires hydrolysis of GTP. Peptidyl transferase catalyzes peptide bond formation (bond between aa and tRNA in the P site converted to peptide bond between the two amino acids). Peptide bond formation requires RNA and may be a ribozyme-catalyzed reaction.

c). Termination

Elongation proceeds until STOP codon reached UAA, UAG, UGA. No tRNA normally exists that can form base pairing with a STOP codon; recognized by a release factor. tRNA charged with last amino acid will remain at P site. Release factors cleave the amino acid from the tRNA. Ribosome subunits dissociate from each other.


Bonding in DNA

Nucleic Acids -Bio-Molecules Chemistry Notes | EduRev

Why does DNA not contain U?

  • DNA damage from UV light, hydrolysis, oxidation
  • If DNA contained U, it would be unable to recognize a hydrolyzed cytosine
  • In RNA, damage not as important, and T production is costly.

Nucleic Acids -Bio-Molecules Chemistry Notes | EduRev

RNA (Ribonucleic Acid)

RNA contains ribose rather than 2-deoxyribose and uracil rather than thymine. RNA usually exist as a single strand. There are three major kinds of RNA

1. Messenger RNA (m-RNA):

2. Ribosomal RNA (r-RNA)

3. Transfer RNA (t-RNA)

DNA is found in the cell nucleus and mitochondria while RNA is more

disperse in the cell.

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