2.3

• The structure of DNA:

  • Two polynucleotide chains/strands hydrogen bond together to form a DNA double helix molecule
  • Phosphate and sugar groups make up the outside backbone
  • Bases hydrogen bond in the center
  • Adenine only pairs with thymine using two hydrogen bonds
  • Cytosine only pairs with guanine using three hydrogen bonds
  • Bases pair together due to complementary base pairing
  • Purines must pair with pyrimidines for the helix to be uniform
  • The two DNA strands are antiparallel, running in opposite directions (5' -> 3' and 3' -> 5')
  • The two polynucleotide strands twist to form a double helix
• Nucleic Acids:

  • The Central Dogma of molecular genetics: DNA -> RNA -> protein
  • The repeating unit of nucleic acids is a nucleotide
  • Monomer of nucleic acids: nucleotide
  • Polymer of nucleic acids: DNA or RNA
  • The structure of a generalized nucleotide:

  1. Phosphate group

  2. Pentose sugar (deoxyribose in DNA, ribose in RNA)

  3. Nitrogenous base (purine or pyrimidine)

  • Examples of nucleotides: ATP, ADP
• Specific examples of nucleotides in the cell:

  • ATP (adenosine triphosphate) is the energy currency of all cells
  • Cellular respiration converts consumed/stored energy into ATP
  • ATP structure involves the addition of a phosphate to ADP (adenosine diphosphate)
• Table of comparisons between nucleic acids and nucleotides:

  • Nucleotide components: phosphate group, pentose sugar, nitrogenous bases
  • As a monomer within DNA: deoxyribose sugar, adenine, thymine, cytosine, guanine
  • As a monomer within RNA: ribose sugar, adenine, uracil, cytosine, guanine
  • As ATP: adenine, ribose sugar, 3 phosphates
  • As ADP: adenine, ribose sugar, 2 phosphates
• Protein synthesis has 2 stages:

  • 1st Stage: Transcription:
  • The synthesis of RNA from DNA
  • DNA never leaves the nucleus
  • A copy of the gene must be made which can leave the nucleus (via the nuclear pores in the nuclear envelope)
  • This copy is called messenger RNA (mRNA)
  • The triplet code on the DNA is transcribed to the mRNA as codons
  • A codon is a sequence of 3 nucleotides/bases in mRNA which code for a specific amino acid
  • 2nd Stage: Translation:
  • The code carried by the mRNA is translated to the amino acid sequence of the protein
• Transcription:

  • The DNA helix is unwound
  • The H bonds between the 2 strands are broken
  • Unlike DNA replication, transcription involves only one template strand
  • Antisense strand acts as template strand during transcription (3' to 5')
  • Free RNA nucleotides will base pair with exposed antisense strand when DNA unzips
  • Thymine is replaced with uracil
  • Phosphodiester bonds form between RNA nucleotides by the enzyme RNA polymerase
  • DNA double helix reforms once mRNA forms and detaches from DNA template and leaves nucleus through a nuclear pore
• Translation:

  • mRNA binds to a specific site on the small subunit of a ribosome
  • tRNA is used (composed of a strand of RNA folded in such a way that 3 bases called the anticodon are at one end of the molecule
  • tRNA anticodons bind to complementary codons on mRNA strand bringing amino acids together by peptide bonds forming the primary structure of the protein coded for by the mRNA
  • Amino acids are added one at a time and the polypeptide chain grows as this happens
  • Ribosomes act as the binding site for mRNA and tRNA and catalyse the assembly of the protein
• The process of translation:

  • The anticodon on the first tRNA base pairs/hydrogen bonds to its complementary codon on the mRNA
  • The first tRNA detaches from its amino acid and moves out to the cytoplasm bonding the first and second amino acid in a peptide bond by a condensation reaction
  • A tRNA corresponding to the third codon brings amino acid 3 (aa3) to the ribosome and its anticodon hydrogen bonds with codon 3 in the mRNA
  • Translation is terminated and the ribosome separates from the mRNA: the primary structure of the polypeptide has been made
• Both DNA and RNA carry information: DNA holds genetic information, while RNA transfers this genetic information from DNA to ribosomes made of RNA and proteins
• DNA and RNA are polymers of nucleotides, which consist of pentose (a 5-carbon sugar), a nitrogen-containing organic base, and a phosphate group
• Components of a DNA nucleotide:

  • Deoxyribose
  • Phosphate group
  • Organic bases: adenine, cytosine, guanine, or thymine
• Components of an RNA nucleotide:

  • Ribose
  • Phosphate group
  • Organic bases: adenine, cytosine, guanine, or uracil
• Nucleotides join together by phosphodiester bonds formed in condensation reactions
• DNA is a double helix composed of two polynucleotides joined by hydrogen bonds between complementary bases, while RNA is a relatively short single polynucleotide chain
• Adenosine triphosphate (ATP) consists of ribose, adenine, and three phosphate groups
• Energy is released when ATP is hydrolyzed to form ADP and a phosphate molecule, catalyzed by ATP hydrolase
• Inorganic phosphate from ATP hydrolysis can phosphorylate other compounds, making them more reactive
• Condensation of ADP and inorganic phosphate, catalyzed by ATP synthase, produces ATP during photosynthesis and respiration
• A gene is a sequence of bases on DNA that codes for a sequence of amino acids in a polypeptide chain
• Genetic code features:

  • Non-overlapping
  • Degenerate (multiple triplets code for the same amino acid)
  • triplet code
  • universal
• Transcription occurs in the nucleus and involves DNA and mRNA, while translation involves mRNA, tRNA, and ribosomes
• During transcription:

  • DNA uncoils
  • RNA polymerase uses one DNA strand as a template to make mRNA
  • Free nucleotides line up by complementary base pairing
  • Adjacent nucleotides join by phosphodiester bonds to form a single-stranded mRNA molecule
• During translation:

  • mRNA attaches to a ribosome
  • tRNA collects amino acids and carries them to the ribosome
  • tRNA attaches to mRNA by complementary base pairing
  • Amino acids join by peptide bonds
  • tRNA molecules detach, leaving the amino acids behind
  • Process repeats until a stop codon is reached on mRNA, ending protein synthesis
• DNA and RNA are nucleic acids made up of nucleotides, which consist of:

  • A pentose sugar
  • A nitrogen-containing organic base
  • A phosphate group
• DNA nucleotides consist of:

  • Deoxyribose sugar with hydrogen at the 2' position
  • Phosphate group
  • Adenine (A), cytosine (C), guanine (G), or thymine (T)
• RNA nucleotides consist of:

  • Ribose sugar with a hydroxyl (OH) group at the 2' position
  • Phosphate group
  • Adenine (A), cytosine (C), guanine (G), or uracil (U)
• Purines (adenine and guanine) have a double ring structure, while pyrimidines (cytosine, thymine, and uracil) have a single ring structure
• DNA and RNA are polynucleotides joined by phosphodiester bonds formed between the phosphate group of one nucleotide and the pentose sugar of the next
• ATP (adenosine triphosphate) is a phosphorylated nucleotide used as the universal energy currency in cells
• DNA is a double helix structure formed by two antiparallel polynucleotide strands held together by hydrogen bonds between complementary base pairs (A-T, C-G)
• In DNA, the number of hydrogen bonds between different base pairs is crucial
• Bases in DNA are complementary: A pairs with T and C pairs with G
• Knowing the complementary base pairs is important as it helps determine the number of bases present in a DNA molecule if given the number of one of the bases
• DNA purification involves isolating DNA from cells through a process like the 'Marmur preparation'
• The 'Marmur preparation' involves three basic steps:

  1. Breaking (lysing) the cells and disrupting the nuclear membranes to release the DNA

  2. Using enzymes to denature and remove the proteins (histones) associated with the DNA

  3. Precipitating the DNA using an organic solvent (e.g. ethanol)
• In DNA replication, the process of semi-conservative replication ensures genetic continuity between generations of cells
• Semi-conservative replication involves:

  • Unwinding the DNA double helix by helicase
  • Using free nucleotides to form new strands
  • Joining new nucleotides together by DNA polymerase
  • Forming hydrogen bonds between base pairs to create the new DNA molecule
• During DNA replication, mutations can occur, leading to errors in the genetic code
• A gene is a sequence of nucleotides that forms part of a DNA molecule
• One DNA molecule contains many genes