DNA - Biophysics 4

    Cards (50)

    • Macromolecules
      Large polymers (sometimes called biopolymers) of many similar subunits (monomers)
    • Most important macromolecules
      • Nucleic acids (which polymerise to form RNA and DNA)
      • Amino acids (which polymerise to form proteins)
      • Sugars (which form carbohydrates – starches, cellulose and others)
    • Titin = C132983H211861N36149O40883S693
    • Titin ~ 3 MD
    • Nucleus
      Contains DNA in the form of Chromosomes which store the genetic code. The nucleus is where DNA replication, repair and transcription occur. Surrounded by the nuclear membrane which contains nuclear pores which tightly regulate what can get in and out. The nucleus also contains the nucleolus – responsible for generating ribosomes and regulating the function of proteins in the nucleus
    • Nucleic acids
      Polymeric macromolecules made from monomers called nucleotides. There are two main types: DNA and RNA. Like proteins, DNA and RNA are unbranched polymers
    • Role of DNA
      To store genetic information and thus allow heredity
    • Role of RNA
      To transmit information between the information store (DNA) in the nucleus and the ribosomes where proteins are produced
    • Nucleic acids (DNA and RNA) are essential for all known life
    • DNA is arranged into large strands called chromosomes. In humans, the largest chromosome is a polymer of 220 million nucleotides
    • Nucleotide
      Has 3 main components: a phosphate group, a sugar (ribose in RNA, deoxyribose in DNA), and a base. The phosphate and sugar form the backbone of the molecule while the base encodes the genetic information
    • It is the phosphate group that makes nucleic acids acidic
    • Ribose
      The sugar used in RNA
    • Deoxyribose
      The sugar used in DNA
    • Deoxyribose is technically 2-deoxyribose
    • Possible bases in nucleic acids
      • Purines: Adenine, Guanine
      • Pyrimidines: Cytosine, Thymine (in DNA), Uracil (in RNA)
    • Nucleotide polymerisation
      The phosphate attached to the 5' position of one nucleotide bonds to the 3' position of the next. This is called a condensation reaction (because water is released) and the new bond is called a phosphodiester bond
    • The polymer has directionality – a 5' end and a 3' end. By convention, the sequence of bases (e.g. ATCCTTGCA) is read in the 5' to 3' direction
    • Base pairing
      Bases can interact through Hydrogen bonding. In DNA and RNA bases pair in specific ways: A always bonds with T (or U in the case of RNA), G always bonds with C. A-T form 2 Hydrogen bonds whereas G-C form 3 Hydrogen bonds
    • DNA
      • Consists of two anti-parallel strands held together by the base-pair hydrogen bonds. The sugar-phosphate backbone is on the outside with the base pairs in the centre. The two strands then wind into a right-handed double helix. One full turn of the helix contains 10 base pairs and is around 3.4 nm in length
    • RNA
      • Has 3 important differences from DNA: Ribose instead of deoxyribose in the backbone, Uracil takes the place of Thiamine as a base, and RNA generally does not form a double helix, but instead exists as a single strand. Small portions of the strand might be self-complimentary – causing the RNA to fold into complex formations. RNA can have a structural role e.g. in ribosomes
    • Main types of RNA
      • Messenger (mRNA) – a copy of a section of DNA to take the information to the ribosome
      • Transfer (tRNA) – a small RNA segment used to identify the right amino acid to for the protein
      • Ribosomal (rRNA) – a structural component of the ribosome
    • The basic genetic process
      1. DNA Replication
      2. Transcription (DNA to mRNA)
      3. Translation (mRNA to Protein)
    • DNA Replication
      1. DNA Topoisomerase unwinds the DNA helix
      2. DNA Helicase splits the two strands by breaking the hydrogen bonds, using ATP as a source of energy
      3. Single strand binding proteins (SSBP) stop the two strands re-joining
      4. DNA Polymerase adds nucleotides to create the complimentary strand and the DNA rewinds up
    • DNA Replication
      • DNA Polymerase can only add nucleotides in the 5' to 3' direction and can only elongate a chain – not start a new one because it also does proof-reading
    • Solution to DNA Replication problems
      1. DNA Primase forms a new chain from RNA not DNA. It forms a chain ~10 nucleotides long which DNA Polymerase can then extend. This chain is called a primer and is ultimately replaced by a DNA version by an enzyme called Exonuclease
      2. The primer is extended by DNA polymerase into small sections called Okazaki fragments which are then join together by an enzyme called DNA Ligase
    • DNA Replication
      1. DNA Topoisomerase
      2. SSBP
      3. DNA Helicase
      4. DNA Polymerase adds nucleotides to create the complimentary strand and the DNA rewinds up
    • DNA Polymerase can only add nucleotides in the 5' to 3' direction and DNA polymerise can only elongate a chain – not start a new one because it also does proof-reading
    • DNA Replication

      1. DNA Primase forms the new chain from RNA not DNA
      2. DNA Primase forms a chain ~10 nucleotides long which DNA Polymerase can then extend
      3. The primer is extended by DNA polymerase into small sections called Okazaki fragments
      4. Okazaki fragments are then joined together by an enzyme called DNA Ligase
    • Primer
      A chain of ~10 nucleotides formed by DNA Primase, which DNA Polymerase can then extend
    • Okazaki fragments
      Small sections of DNA formed when the primer is extended by DNA polymerase
    • Transcription
      1. RNA Polymerase splits the DNA strand
      2. RNA Polymerase creates an mRNA strand by adding nucleotides in the 5' to 3' direction complimentary to one of the DNA strands (the Template Strand)
      3. RNA Polymerase splits the base-base hydrogen bonds so the mRNA strand becomes free
      4. The mRNA strand then exits the nucleus through a nuclear pore in the nuclear membrane and travels to the ribosomes
    • Transcription
      • It has to regulate which gene is expressed and when
      • It has to carry the information from the nucleus to the ribosomes where proteins are made
    • Promoter
      Specific sections of DNA upstream of the required gene where RNA polymerase can first bind
    • Transcription
      1. RNA Polymerase binds to the promoter
      2. RNA Polymerase moves along the DNA strand creating a mRNA copy
      3. RNA Polymerase passes a specific DNA START sequence - ATG
      4. RNA Polymerase continues to a DNA Termination sequence at which point it detaches
    • The DNA polymerase then forms the mRNA strand until a specific STOP sequence is encountered – TAA, TAG or TGA
    • Codon
      A sequence of 3 bases in DNA that codes for a specific amino acid
    • There are 64 possible codons but only 20 amino acids, so the DNA code contains redundancy
    • The START codon is ATG which codes for Methionine – all proteins start with a Methionine
    • There are 3 possible reading frames – but only one gives a meaningful amino acid sequence. It is the job of RNA Polymerase to get the right reading frame
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