Module 2.1.3- Nucleotides and nucleic acids

• What are the 2 types of nucleic acids

  DNA and RNA
• 3 components of a nucleotide

  pentose monosaccharide sugar

  phosphate group

  nitrogenous base
• How are nucleotides linked together

  Through condensation reactions to form phosphodiester bonds
• How are phosphodiester bonds broken


  by hydrolysis
• Phosphodiester bonds


  A bond formed between adjacent nucleotides which consists of a phosphate group that links the sugars of two nucleotides
• Pyrimidines


  Single carbon ring structures

  Thymines and Cytosines
• Purines


  Double carbon ring structures

  Adenines and Guanines
• Number of hydrogen bonds between A-T and C-G

  A-T : 2 hydrogen bonds

  C-G : 3 hydrogen bonds
• DNA vs RNA

  deoxyribose sugar vs. ribose sugar

  thymine vs. uracil

  double strand vs. single strand
• DNA double helix


  DNA polymer strands held together by H bonds

  the two DNA strands run antiparallel

  2 strands of polynucleotides are coiled into a helix
• RNA function


  protein synthesis

  essential role in the transfer of genetic information from DNA to the proteins
• Why is RNA useful?


  Since DNA is a very long molecule, a short section of a gene can be transcribed into an mRNA molecule which is small enough to leave the nucleus
• DNA extraction

  
• Semi-conservative replication


  In each new DNA double helix, one strand is from the original molecule, and one strand is new
• DNA helicase


  An enzyme that unwinds the DNA double helix during DNA replication by catalysing the reaction of breaking hydrogen bonds
• DNA polymerase


  Catalyses the formation of phosphodiester bonds between the free nucleotides which pair up with the newly exposed bases on the template strands
• Semi-conservative replication process


  1. DNA helicase breaks down hydrogen bonds that link base pairs

  2. double helix separates into two strands

  3. each exposed polynucleotide strand acts as a template where free complementary nucleotides bind by specific base pairs

  4. nucleotides join together by DNA polymerase in a condensation reaction to replace missing nucleotides forming two strands in the end
• Mutation


  Occur randomly and spontaneously and lead to a change in the sequence of bases
• What direction does DNA polymerase travel in and what strand can be replicated continuously?

  3' to 5' direction

  The leading strand
• Okazaki fragments


  Small fragments of DNA produced on the lagging strand during DNA replication, joined later by DNA ligase to form a complete strand.
• Genetic code


  the ordering of nucleotides in DNA molecules that carries the genetic information in living cells
• Triplet code


  3 bases of DNA that code for a single amino acid
• Codon


  A specific sequence of three adjacent bases on a strand of DNA or RNA that provides genetic code information for a particular amino acid
• Gene


  sequence of DNA that codes for a protein and thus determines a trait
• Degenerate code


  there are more codons (64) than there are amino acids to be coded, so multiple codons encode a single amino acid
• Transcription


  (genetics) the organic process whereby the DNA sequence in a gene is copied into mRNA
• Sense strand


  the strand of DNA that runs 5' to 3' and contains the genetic code for a protein.
• Anti-sense strand


  The DNA strand that serves as the template for synthesis of mRNA. It is complementary to the sense strand.
• Transcription process


  1) the segment of DNA to be transcribed unwinds by DNA helicase

  2) free RNA nucleotides pair with the complementary DNA bases on the antisense strand (template) and are linked by RNA polymerase

  3) the RNA detaches from the DNA template and leaves the nucleus through nuclear pores

  4) mRNA molecule travels to ribosome in cell cytoplasm
• Translation


  decoding of a mRNA message into a polypeptide chain
• ribosomal RNA


  type of RNA that combines with proteins to form ribosomes, important in maintaining the structural stability of the protein synthesis sequence
• structure of tRNA

  "T"-shaped, has anticodons complementary to the mRNA opposite of the amino acid

  
• Translation process


  1) mRNA binds to a specific site on the small subunit of a ribosome. ribosome holds it in place.

  2) tRNA with complementary anticodon binds to mRNA start codon

  3) This is then repeated and a maximum of 2 tRNAs can be bound at the same time

  4) First AA is then transferred to AA on the second tRNA by the formation of a peptide bond. Through enzyme peptidyl transferase

  5) Ribosome moves along the mRNA releasing the first tRNA.
• What enzyme catalyses the peptide bond formation between adjacent amino acids


  Peptidyl transferase
• Components of ATP (Adenosine Triphosphate)


  Adenine

  Ribose

  3 phosphate groups
• ATP vs DNA vs RNA structure

  ribose vs deoxyribose vs ribose

  energy currency of the cell vs DNA/protein synthesis

  adenine vs ATCG vs AUCG

  5 carbon sugar all
• How much energy is approximately released from the hydrolysis of ATP

  30.6 kJ mol-1
• Hydrolysis of ATP

  ATP + H2O -> ADP + Pi + energy

  
• Phosphorylation


  the addition of a phosphate group to a molecule. condensation reaction
• ATP is a good immediate energy store and not a good long-term energy store because...

  ... interconversion of ATP and ADP is happening constantly so a large store of ATP is not needed. Furthermore it is not a good long-term energy store because of the instability of the phosphate bonds in ATP