BMP: Biosynthesis of Nucleic acids

Question 1

What is the centeral dogma?

Answer 1

The process by which DNA is replicated, transcribed and translated to form a protein

DNA —> RNA —> Protein

Question 2

What is the difference between a nucelic acid, nucleotide and nucleoside?

Answer 2

• Nucelic acid (polynucleotide): A linear sequence of nucleotide monomers
• Nucleotide: Phosphate esters of nuclosides. Contain a nitrogenous base (pyrimidine or purine), pentose sugar (deoxyribose or ribose) and a phosphate group
• Nucleoside: Contain a pentose sugar joined to a nitrogenous base by a glycosidic bond

Question 3

What are different types of bases, examples of each and their structures

Answer 3

• Pyrimidine:
  
  • Aromatic hetreocyclic compounds with a Nitrogen at position 1 and 3 of the ring structure
  • Cytosine
  • Thymine
  • Uracil
• Purine:
  
  • Aromatic hetreocyclic compund composed of a pyrimidine ring fused to an imidazole ring
  • Adenine
  • Guanine

Question 4

What are the corresponding neuclosides called?

What can the nucleotides be esters off?

Answer 4

1. Guanosine
2. Adenosine
3. Thymidine
4. cystidine

Nucleotides can be mono, di or tri phosphate esters of Nucleosides e.g. ATP or AMP

Question 5

What is the difference between Ribose and deoxyribose?

Answer 5

• Ribose is found in RNA an is the ‘normal’ sugar. It has an O2 on each carbon
• Deoxyribose is found in DNA and is modified sugar and is missing an O2 on the 2nd carbon

Question 6

What is DNA?

Answer 6

• A molecule of DNA consists of 2 polynucleotide strands joined by hydrogen bonds between the bases.
• Phosphodiester bonds between the 3’OH of one nucleotide and the 5’OH of the group of the next nucleotide join the nucleotides in one strand together
• Anti-parallel nature - both strands extend in opposite directions (3’ to 5’ and 5’ to 3’)
• Phosphate-sugar back bone and varibailty provided by the bases
• Right handed double stranded helix with base paris stacked like steps on a spiral stair case
• Geometry results in major and minner grooves

Question 7

Describe base pairing

Answer 7

• Guanine ALWAYS pairs with Cytosine (3 Hbonds)
• Adenine ALWAYS pairs with Thymine (2 Hbonds)
• Therefore the strands of DNA are always complemetary

Question 8

What are grooves and what do they do?

Answer 8

• Voids adjacet to base pairs
• Provide binding sites (e.g. proteins e.g. transcription factors)
• The major grooves are more acessible due to the narrowness of minor grooves. More likely to bind to major grooves for this reason

Question 9

Describe the structure of RNA

Answer 9

• Although similar to DNA, in RNA
• Thymine is replaced by uracil (U).
• The pentose is ribose.
• RNA chains are single-stranded
  
  • extensive secondary structure where complementary base pairs form within the molecule e.g. tRNA ‘cloverleaf’ structure.
• Three major categories exist
  
  • messenger, ribosomal and transfer RNA

Question 10

What is mRNA?

Describe the structure of mRNA

Answer 10

mRNA is a sequence of nucleotides which is converted to AA sequence of a protein

1. 5’ Guanosine Cap
   
   • ​​Specially altered nucleotide. mRNA capping is vital in creatino of stable and mature mRNA which is able to undergo transaltion during protein synethsis
2. 5’ UTR
   
   • ​​5’ Untranslated region
   • Directly upstream from initation codon
   • Important in regulation of translation of the transcript
3. Ribosome binding site (kozak sequence)
4. Coding Region
5. 3’ UTR​​
   
   • 3’ untranslated region
   • direcly follows transaltion termination codon
   • Contains regulatory regions that post-transcriptionally influence gene expression
6. 3’ Polyadenosine tail
   
   • ​​Polyadenylation is the addition of Poly(A)tail to mRNA. Helps produce mature mRNA
   • poly(A) tail consists of multiple adeonsine monophosphates

Question 11

Describe

Answer 11

• Very large
• Makes up ribosomes
• Different species of rRNA:
  
  • Prokaryote: 5s, 16s, 232
  • Eukaroyes: 5s, 18s, 28s
• Eukaryotes have 80s ribosomes, each consisiting of small (40S) and large (60S) subunits.
• Small subunits monitor complemenrairty between tRNA anticodon and mRNA codon
• Larger subunit catalyses peptide bond formation

Question 12

Describe tRNA

Answer 12

• Small
• Complex secondary structure - clover shape
• During translatino carries AA from cytoplasm to ribosome to incoperate them during protein synthesis
• tRNA’s can bepost-transctiptionally modified producing unsual nucleotides e.g. duhydrouridine (D)

Question 13

What is the function of the D loop in tRNA?

Answer 13

The D loop’s main function is that of recognition. It is widely believed that it acts as a recognition site for aminoacyl‐tRNA synthetase, an enzyme involved in the aminoacylation of the tRNA molecule. Aminoacyl‐tRNA (aa‐tRNA) is tRNA to which its cognate amino acid is chemically bonded (charged). This matching is crucial, since it ensures that only the particular amino acid matching the anticodon of the tRNA, and in turn matching the codon of the mRNA, is used in protein synthesis.

Question 14

Describe what Dihydrouridine is and its use

Answer 14

Dihydrouridine (D) is a pyrimidine contained within tRNA which is the result of adding two hydrogen atoms to a uridine, making it a fully saturated pyrimidine ring with no remaining double bonds. Transcriptionally modified nucleotides, such as D, are less spatially confined therefore allowing greater opportunity for pairing of the anticodon contained within tRNA and the codon contained within mRNA. Similarly, the modified nucleotide Inosine (I) can pair with A,U or C. Modified nucleotides are only ever found in tRNA, never in mRNA, as this would result in distortion of the code contained within DNA (see sections 3A and B for information on why this is important for protein synthesis).