L3 - Nucleic acids

• What is DNA

  Deoxyribonucleic acid, a biological macromolecule that carries hereditary information in a cell
• What is RNA?


  • a class of nucleic acids characterized by the presence of the sugar ribose and the pyrimidine uracil. 

  
• What is a nitrogenous base  


  • nitrogen-containing molecules having the chemical properties of a base that are components of nucleotides.

  
• Nucleoside


  • a nitrogenous base chemically linked to one molecule of a five-carbon sugar, either ribose (RNA) or deoxyribose (DNA).

  
• Nucleotide 


  • one of the structural components, or building blocks, of DNA and RNA, composed of three parts: a five-carbon sugar, a phosphate group, and a nitrogenous base

  
• Replication fork (Draw it)

  • the point where the two parental DNA strands separate to allow replication.
  • DNA helicases unwind DNA on both sides
  • DNA polymerases synthesise new DNA off the parental strand in a bidirectional fashion

  
• DNA polymerase


  • an enzyme that synthesizes DNA by linking together deoxynucleoside monophosphates in the order dictated by the complementary sequence of nucleotides in a template DNA strand. 

  
•  Primer 


  • short sequence (often of RNA) that is paired with one strand of DNA and provides a free 3-OH end at which a DNA polymerase starts synthesis of a deoxyribonucleotide chain.

  
• Draw a Ribose 


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• Draw a deoxyribose


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• Which is more stable DNA or RNA?

  Why?

  DNA because of one less functional group than the RNA .
• What is the charge of the phosphate group + what's its significance ?


  • Negatively charged, polar and repel each other. Maintains double helix structure.
  • Connects to the 5' carbon of one deoxyribose sugar and the 3' carbon of the next sugar
  • Forms phosphodiester bonds and backbone

  
• What are the pyramidine bases of DNA and RNA ?

  • The smaller, single-ring structures
  • DNA : T , C
  • RNA : U, C
• What are the purine bases of DNA and RNA?


  • larger double ring structures
  • DNA and RNA : A , G
• Describe base pairing 


  DNA : Adenine + thymine with 2 hydrogen bonds.

  Guanine + cytosine with 3 bonds.

  RNA : Adenine + Uracil with 2 hydrogen bonds

  
• Number of strands in DNA and RNA

  • DNA : 2
  • RNA : 1
• Types of DNA

  • Mitochondrial DNA
  • Genomic DNA
• Types of RNA

  • mRNA
  • tRNA
  • rRNA
• Describe the frequency of the bases in DNA 


  • pair of bases are always present in roughly equal amounts
  • This is because DNA must exist as complementary strands
  • This is also due to specific hydrogen bonds between the bases
• How is DNA antiparallel + importance 


  • One strand runs from the 5' end to 3' end while the other complementary strand runs from 3' to 5'.

  Importance

  • Allows each base to align properly via hydrogen bonding
  • Keeps DNA strands stable in double helix + minimises repulsion between negatively charged phosphate groups = more efficient DNA packaging
  • During replication, one strand (the leading strand) synthesized continuously, while the other (the lagging strand) synthesized in short fragments (Okazaki fragments) because it runs in the opposite direction.
• What is genetic code

  • Sequence of 3 nucleotide bases, codons
  • is universal in all organisms, code for same amino acids
  • Is degenerate, multiple codons can code for same amino acid
• RNA polymerase binds to the promoter region on the template strand of DNA and begins transcribing RNA using mRNA as the template.
• DNA replication occurs when the two strands separate, new nucleotides are added to form complementary strands, and then the two strands come back together.
• What is the origin of DNA replication characterized by?

  An A-T rich area
• Why is the A-T rich area significant in DNA replication?

  It requires less energy to break 2 hydrogen bonds
• How many origins of replication are there in eukaryotic cells?

  Multiple origins of replication
• What is the role of the pre-replication protein complex in DNA replication?

  It binds to the origins of replication and separates the strands of DNA
• What is formed when the strands of DNA are separated during replication?

  A replication bubble
• What is the function of single-stranded binding proteins (S.S.B.P) during DNA replication?

  They bind to parental strands and prevent reannealing
• How do single-stranded binding proteins protect the DNA during replication?

  They protect from nucleases that want to break phosphodiester bonds
• What structures are formed as DNA unwinds during replication?

  Replication forks
• What is the role of helicase in DNA replication?

  It unwinds the DNA at the replication forks
• What energy source does helicase require to function?

  ATP
• What problem arises as DNA is unwound at the replication fork?

  The strands bunch up distal to the replication fork, creating supercoils
• How do supercoils affect the process of DNA replication?

  They impede helicase from unwinding the DNA
• What is the function of topoisomerases during DNA replication?

  They cut the DNA strand to let it unravel
• What are the two domains of topoisomerases involved in DNA replication?

  Nuclease domain and ligase domain
• What does the ligase domain of topoisomerase do after cutting the DNA strand?

  It reconnects the area that had been cut
• What are the different types of Topoisomerases?

  Topoisomerase I

  • Function: Topoisomerase I creates a single-strand break (nick) in one of the DNA strands, allowing it to unwind by rotating around the uncut strand. This process releases supercoils and relieves torsional stress without requiring ATP (energy).

  Topoisomerase II

  • Function: Topoisomerase II creates a double-strand break in the DNA, allowing one DNA helix to pass through another. This process is crucial for resolving tangling between DNA helices, especially during cell division. It requires ATP.
• Where is topoisomerase I primarily found?


  • In the nucleus of eukaryotic cells
  • Essential for transcription, replication, recombination in eukaryotic chromosomes