Nucleic Acid

Nucleic Acids – Structure, DNA Replication

Nucleic Acid Structure

Deoxynuclaic acid and Ribsonuclaic acid are two types of nucleic acids. They are unbranched polymers of repeating units known as nucleotide. Each nucleotide is made up of :

  • A base (Pyrimidine (cytosine and thyamine(DNA)/uracil (RNA)) or Purine(adenine and guanine))
  • 5 carbon sugar (Pentose Sugar = Ribose)
  • Phosphate group

Deoxy means without oxygen, no hydroxyl group. And no ‘O’ atom on carbon 2

Nucleic Acids:

  • Are large molecules that store information for cellular growth and reproduction.
  • Are DNA and RNA
  • Are long monomer chains called nucleotides

Chromosomes:

  • Make up DNA as individual molecules in pairs. Like a long strand of beads squished.
  • Contain the cells genes
  • 23 pairs in a human cell

Gene:

  • A gene is a segment of a DNA molecule that controls :protein production (the fundamental unit of hereditary).

Genome:

  • All Genetic material in the cell. Eukaryotes, DNA of the nucleus
  • Mitochondrial DNA – mitochondria have their own genomes

 

Nucleosides and Nucleotides

Nucleoside:

  • Has a nitrogen base linked by a glycosidic bond to Carbon 1 of a sugar.
  • Named by changing the ending of the nitrogen base ending in:

-osine for Purine and

-idine for Pyrimidine

Nucleotide:

  • Is a nucleoside with a phosphate ester with a carbon five – OH group of ribose or deoxyribose (sugar)
  • They are also held together by phosphodiester bonds (3’ =OH group of the sugar in a nucleotide forms and ester bond to the phosphate group in 5’ carbon of the sugar of the next nucleotide)
  • Named the same as nucleosides but has the additional: 5’-Monophosphate.

 

For Example:
Base Adenine DNA

  • Nucleoside = Deoxyadenosine
  • Nucleotide =Deoxyadenoside -5’-Monophosphate (dAMP)

Base Cytosine DNA

  • Nucleoside = Deoxycytidine
  • Nucleotide = Deoxycytidine-5’-Monphosphate (dCMP)

Base Adenine RNA

  • Nucleoside = Adenosine
  • Nucleotide= Adenosine -5’-Monophosphate (AMP)

Base Cytosine RNA

•              Nucleoside = Cytidine

•              Nucleotide = Cytidine-5’-Monphosphate (CMP)

Adding phosphate groups to AMP forms the diphosphate ADP and the triphosphate ATP

 

RNA

Structure:

A single strand of neucleotides. The bases, A, C, G and U are linked using ester bonds 3’ and 5’ between ribose (sugar) and phosphate.

Rna transmits info from DNA to make protiens

There are 3 types of RNA

  • Messenger RNA, mRNA, carries genetic info from DNA to ribosomes.
  • Transfer RNA, tRNA, brings amino acids to the ribosome to make protein.
  • Ribosomal RNA, rRNA,  2/3rds of the  robsomes where protein synthesis takes place.

DNA

Structure:

A,C,T and G are linked using Ester Bonds 3’ and 5’ between deoxyribose (sugar) and phosphate.

A double Helix has two strands of nucleotides that forma spiral. Hydrogen bonds form between A-T and G-C. One side is full of bases that complement the other strand. A-T use 2 hydrogen bonds. C-G use 3 hydrogen bonds.

DNA replication:

  • Occurs when the stands of the double helix unzip (Parent DNA unwinds using the enzyme : Helicase in several sections) and  the bases are separated and are given a new complementary strand each = two strands that are new that are exactly like the original.
  •   At each opening of the DNA strand (replication fork), DNA polymerase catalyzes the forming of the ester bonds that leads to the new strands being made to complement the open parent DNA of the leading strand.  (The polymerase synthesises the corresponding mRNA during transcription)
  • The lagging strand is synthesized in short segments (okazaki fragments). These are joined by DNA  ligase to give a single DNA strand. Synthesised in 5’ to 3’ direction.

Hydrolysis Energy: the energy from the hydrolysis of each nucleoside triphosphate  adding to the new complementary strand is used to form a phosphodiester bond.

Nucleic Acids – Protein Synthesis

Genetic Code

  • The sequence of amino acids in mRNA  decides which amino acids are needed for a protein
  • 3 base triplets (a codon)
  • A different codon for each protein
  • Special codons are on and off.

tRNA

  • tNA has a triplet called :Anticodon, it complements a codon on mRNA
  • binds to a certain amino acid at the acceptor stem
  • the activation of tRNA  happens when a synthetase usues ATP hydrolysis enery to attatch an amino acid to a to a certain tRNA. The activated tRNA prepares each tRNA to use a anticodon to complete a codon on mRNA.

mRNA Processing

  • The DNA of eukaryotes contain exons that code for proteins, along with introns that don’t.
  • mRNA starts off as PRE-RNA (initial stages) and includes noncoding introns. In the nucleus, the introns are removed from PRE-RNA. The exons that remain are attached to form mRNA that allows the nucleus to have enough info to synthesis the protein.

Protein Synthesis – Transcription and Translation

Transcription:

  • mRNA is formed from a gene on a DNA strand.
  • A section of DNA that contains the gene  unwinds
  • One strand of DNA is copied starting at the initiation point: sequence: TATAAA.
  • mRNA is synthesised using complementary bases, using U instead of T.
  • The new mRNA moves from nucleus to ribosomes (located in cytoplasm)
  • mRNA is released at the termination point.
  • When the cell requires a specific protein a specific mRNA will synthesise it.
  • The end products control the speed (feedback control)
  • Transcription can be induced to provide enzymes.

Translation:

  • tRNA molecules bring amino acids to mRNA to build protein.
  • Activation, initiation, elongation and termination.

Initiation of Protein Synthesis:

•              mRNA attaches  to a sugar (ribosome)

•              start codon binds to tRNA

•              second codon attaches to tRNA with next amino acid.

•              A peptide bond forms between adjacent amino acids at 1st and 2nd codons (elongaition step)

Termination of Protein Synthesis:

•              When a polypeptide has all the synthesised amino acids for protein

•              When a ribosome reaches the stop codon. (there is no tRNA anticodon for stop.)

•              The polypeptide lets go from the ribosome and the ribosome seperates into 2 sperate smaller units.

Translocation:

  • first tRNA detaches from ribosome
  • the ribosomes shift to the adjacent codon on the mRNA
  • a new amino acid / tRNA attaches to the open binding site
  • peptide bond forms and tRNA lets go.
  • ribosomes move along  the mRNA to read the next codon.

Antibiotics:

  • Antibiotics inhibit protein synthesis in bacteria: by attatching to ribosomes of bacteria and not human cells.

Mutations

  • Change the nucleotide sequence in the DNA… so a wrong codon is produced in the corresponding mRNA.. so a protein with wrong amino acids = genetic disease that makes enzymes and proteins that don’t work as they should.
  • Can happen because of radiation, chemicals and free radicals.
  • Source of genetic variation, sometimes good sometimes bad.

Substitute Mutation:

  • Has a different base used as the proper DNA base.
  • A change in the codon mRNA – wrong amino acid is attatched to polypeptide. Eg C is now T.

Frame Shift:

  • An extra base is either added or removed from a regular DNA sequence.
  • All codons in mRNA  and amino acids are wrong from the base change.

Genetic Engineering

Recombinant DNA:

  • Scientists cut and rearage/recombine DNA fragments, eg to code for insulin or growth hormone.

Cloning:

  • Produces lots of identical copies of the same recombinant DNA
  • Can be done in vitro by PCR (polymerase chain reaction) : PRC produces multiple copies od DNA quickly – separates the DNA stands with heat, then mixes the separate strands with enzymes and nucleotides to get a complementary strand.
  • Can be done in vivo in unicellular prokaryotes, unicellular eukaryotes

Viruses

  • Small particles of DNA or RNA and require a host cell to replicate. Cause a viral infection they enter a host cell. Are synthesised  in the host cell from the viral RNA produced by DNA

Reverse Transcription:

  • A retrovirus (has viral RNA but no viral DNA ) enters a cell
  • The viral RNA uses reverse transcription to produce Viral DNA
  • The viral DNA strand now produces a complementary strand of DNA, this uses the nucleotides and enzymes in the host cell to make new virus particles.

We can’t forget to praise Endeavour College of Natural Health for their fantastic Lecturers who very fabulously verbalise and impart the understanding of Chemistry. And Of course Karen Timberlake for her awesome book, and the chapters I have read tirelessly trying to understand chemistry. Specifically chapter 21 about Nucleic Acid.

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