Nucleic acids: structure and function

Question 1

each nucleotide contains 3 components

Answer 1

1. a nitrogenous heterocyclic base
   
   1. purine or pyrimidine
2. A pentose sugar
   
   1. ribose (RNA) or deoxyribose (DNA)
3. A phosphoric acid group in ester linkage to the 5’ carbon of the pentose

Question 2

describe the structure of purines and pyrimidines

Answer 2

• Purines are heterocyclic compounds consisting of a pyrimidine fused to a 5 member imidazole ring
• Pyrimidines are heterocyclic compounds containing N atoms at position 1 and 3 of a 6 member ring

Question 3

describe nucleosides

Answer 3

Nucleosides consist of a nitrogenous base and a ribose or deoxyribose sugar

Question 4

describe nucleotides

Answer 4

• Nucleotides consists of nitrogenous base, a ribose of deoxyribose sugar and a phosphate group

Question 5

explain when nucleosides 5’-triphosphates are acidic and negative and the functions

Answer 5

• Nucleosides 5’-triphosphates are acidic at neutral pH and possess 4 negative charges

1. Function
   
   1. Precursors of the nucleotides for RNA and DNA
   2. ATP - universal chemical energy
   3. GTP - protein synthesis
   4. UTP - biosynthesis
   5. CTP - phospholipid biosynthesis
   6. Formation of coenzymes

Question 6

explain what DNA/RNA polyermase does

Answer 6

• DNA/RNA polymerase catalyze the formation of a phosphodiester bond between the 3’ OH group of the deoxyribose/ribose on the last nucleotide and the 5’ phosphate of the dNTP/NTP precursor

Question 7

describe the function of DNA ligase

Answer 7

• DNA ligase is responsible for sealing nicks in DNA during replication and repair and creates phosphodiester bonds
• Creates phosphodiester bond between 3’OH and monophosphate

Question 8

describe the melting temperature (Tm) of DNA and what influences it

Answer 8

• Tm is the temp. at which 50% of the DNA becomes single stranded
• Tm increases with G-C content
• Tm is influenced positively by ionic strength

Question 9

describe annealing and the rate

Answer 9

• Single strands of complementary DNA Acan reanneal with each other by H-bond formation
• The rate of annealing is dependent on the size and complexity of the DNA strands

Question 10

describe the secondary structures of DNA

Answer 10

• B-DNA
  
  • Basis of Watson-Crick model
  • Right hand helix
  • Can contain considerable variations of structure depending on the nucleotides present. Important in influencing DNA-protein binding
• Z-DNA
  
  • Left hand helix
  • Seen in sequences containing alternating pyrimidine and purines
  • Maybe involved in gene regulation
• A-DNA
  
  • Right hand helix
  • Dehydrated state
  • No biological significance

Question 11

describe the different types of structures (primary, secondary…)

Answer 11

1. Primary structure
   
   1. The sequence of nucleotides (bases) along the polynucleotide chain
2. Secondary structure
   
   1. The 3D structure e.g. double helix of DNA
3. Tertiary structure
   
   1. Includes supercoiling of the secondary structure
4. Quaternary structure
   
   1. the interaction of nucleic acids with proteins

Question 12

describe the different types of RNA and their functions and percentage

Answer 12

• mRNA
  
  • Linear single stranded molecule
  • carries codon information for translation
  • 2% of total RNA
• tRNA
  
  • folded stem loop structures formed by intramolecular H-bonding
  • carries amino acid to ribosome
  • 16% of total RNA
• rRNA
  
  • linear single stranded, folded molecule
  • complexes with protein to form ribosome
  • 82% of total RNA

Question 13

describe the role of rRNA

Answer 13

• overall structure of ribosome
• catalytic activtiy (forming covalent peptide bonds)

Question 14

describe snRNA

Answer 14

• snRNA are small nuclear ribonucleic acid
• Involved in generation of mature mRNA transcripts
• Central components of the splicing apparatus
• Involved in regulation of:
  
  • transcription factors
  • RNA pol II activity
  • telomere maintenance

Question 15

describe miRNA

Answer 15

• microRNA
• Silencing of gene expression
• 1000 human genes that encode miRNAs (3% of genome)

Process

• primary miRNA transcript
  
  • undergoes nuclear processing
• pre miRNA
  
  • undergoes cytoplasmic processing
• mature miRNA
• miRNA + RNA-induced silencing complex (RISC)
  
  • 2 functions
    
    • translation of target DNA is repressed
    • target mRNAs are degraded

Question 16

describe what azidothymidine (AZT)/zidovudine/didanosine does

Answer 16

• It is utilized by the viral reverse transcriptase
• Upon incorporation into the ds DNA chain termination occurs due to lack of 3’OH
• Specificity for infected cells lies in the fact that these drugs have a 100-300 fold greater affinity for incorporation by reverse transcriptase than eukaryotic DNA polymerase
• Zidovudine can:
  
  • prolong life in HIV infected individuals
  • reduce mother to baby transmission by more than 20%

Question 17

describe what tenofovir does

Answer 17

• Tenofovir diphosphate competes with its natural nucleotide counterpart, deoxyadenosine 5’-triphosphate, for incorporation into newly forming HIV DNA
  
  • Once successfully incorporated, termination of the elongating DNA chain ensues and DNA synthesis is interrupted

Question 18

explain what cytosine arabinoside (araC) is and does

Answer 18

• It is a cytosine nucleoside analogue
• AraC has a 3’ OH group to act as an acceptor for further chain elongation. However the OH gap at position 2 prevents polymerase adding the next dNTP due to stereo restraints, which leads to chain termination
• This is important in the therapy of leukemia, in particular acute myeloid leukemia and lymphoma
• Instead of altering the base (like in nucleotide base analogues) AraC alters the sugar

Question 19

describe the function of acyclovir

Answer 19

• Viral thymidine kinase = much more effective in catalyzing 1st phosphorylation event thatn hose thymidine kinase
• Only infected cells possess the viral kinase, therefore, acyclovir is only activated in infected cells
• Causes chain termination due to lack of 3’OH 30x more potent against viral DNA polymerase than host
• Acyclovir has high specificity for herpes simplex and varicella zoster

Question 20

describe the process of cytidine analogues

Answer 20

• Once incorporated into DNA and RNA they cause hypomethylation as a methyl group cannot be added to the N at position 5. Additionally, these drugs are known to bind and inhibit DNA methyltransferase enzymes
• In eukaryotes, methylation of cytosine is an important mechanism of transcriptional regulation
• Decitabine
  
  • used in DNA
• 5-azacytidine
  
  • used in RNA

Question 21

what is an example of DNA hypomethylating agents in cancer

Answer 21

• Hypomethylation of CDKN2B correlates with response to decitabine
• Used in myelodysplastic syndrome and acute myeloid leukemia