DNA-RNA

 

  1. Molecular biology- the study of DNA and RNA biochemistry.
    1. The major role of DNA is to lead to protein synthesis:
      1. Transcription (the code from DNA is transcribed into RNA):

        2. DNA

        enzymes

        RNA nucleotides --------------> RNA (ribonucleic acid)

        ATP

      2. Translation (the code on RNA is translated into a sequence of amino acids: i.e. a protein):

      ribosomes

      enzymes

      t-RNA

      m-RNA

      amino acids +(ATP + GTP) ---------------> protein            

      m-RNA => messenger RNA (carries the code)

      t-RNA => transfer RNA (transfers the amino acid to the ribosome)

      r-RNA => ribosomal RNA (part of the ribosome; the ribosome is

      made of r-RNA and protein)

    2. These concepts are usually written in the following way, which is often referred to as the central dogma:

      3.

      Remember that the proteins (enzymes) dictate all of the cellular activities.

    3. The whole scheme can be written more elaborately as we have learned more:

      4.  

      1. Notice that special enzymes are required for some of these reactions. On an evolutionary scale, one has to question how this whole system got started. It is not likely that the enzymes evolved first. Replication, transcription and translation all require enzymes.
      2. A significant amount of processing occurs. This means a molecule is altered (by enzymes) after it is made to make it into its final functional form. This is known to particularly happen frequently with proteins, but it is now also known to happen with t-RNA, DNA, and m-RNA!.
  2. Molecular makeup of DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).
    1. DNA is a polymer of the four nucleotides: adenine (A), guanine (G), cytosine (C), and thymine (T).
      1. All of the nucleotides have a sugar structure plus nitrogenous base ring structures.
        1. the sugar is a five carbon sugar called ribose (that is why DNA and RNA have 'ribo' in their names).
        2. There are two types of nitrogen containing ring structures.
          1. Adenine and guanine have a double ring (purines)
          2. Cytosine and thymine have a single ring (pyrimidines).
      2. The free nucleotides have an acidic phosphate group, and this is where the 'nucleic acid' part of their name comes from.
      3. DNA has an -H group instead of an -OH group on the 2' carbon (that is where the 'deoxy' part of its name comes from).
      4. In the polymerized form, the nucleotides are linked together by phosphate groups to the 3' carbon OH group of the next nucleotide in a linear fashion. One linear structure of DNA is called a strand.
      5. DNA usually exits with two complimentary strands twisted upon each other: called a double helix. (see more on this subject below).
    2. How does RNA differ from DNA?
      1. They are actually quite similar in structure, with the following exceptions:
      2. RNA is a polymer of the four nucleotides: adenine (A), guanine (G), cytosine (C), and uracil (U). That is, thymine is not one of the nucleotides, but the closely related uracil is.
      3. The 2' carbon of the ribose sugar has an -OH group rather than an -H group for all four nucleotides.
      4. It usually exists as a single strand rather than a double helix. However it can have some complicated secondary and tertiary structure.
      5. It is usually a much smaller molecule than DNA. That is, the number of nucleotides that make it up are quite a bit fewer.
      6. RNA exists in three functional forms: transfer RNA (t-RNA), messenger RNA (m-RNA), and ribosomal RNA (r-RNA). t-RNA carries amino acids, m-RNA transfers the code from DNA, and r-RNA helps ribosomes work (all of this will be discussed more later).
  3. What do we basically know about this stuff called DNA.
    1. Double stranded helix of four types of nucleic acids where the two strands are held together by hydrogen bonds.
      1. Adenine always hydrogen bonds with thymine. A--T or T--A

        2. Guanine always bonds with cytosine. C--G or G--C (Show transparency)

        Thus if one strand is A-G-G-C-T-A-A-T-C-C-G then the complimentary

        strand is ....T-C-C-G-A-T-T-C-G-G-C....
      2. In RNA, uracil will always associate with adenine (i.e., takes thymine's role).
      3. The strands are antiparallel.
    2. DNA replicates by splitting of the double helix by the enzyme helicase, and each strand then accepts nucleic acids to form a total of two double helices. Each new DNA has one old and one new strand (semiconservative).
      1. Messelson and Stahl showed this in 1958.
      2. It is known that enzymes are needed in the replication process (to split the double helix, to add on new nucleic acids, and to covalently link the new nucleic acids together)
      3. In prokaryotes the process starts at one end and sequentially goes to the other end (zipper hypothesis). In eukaryotes can start and occur at several places simultaneously (bubble hypothesis)

       

       

       

    3. Rules regarding the genetic code:
      1. Each amino acid is coded by a triplet of nucleic acids. (There are 64 possible codes=> four to the power of 3). Nirenberg and Khorana received the Nobel Prize in 1968 for breaking the code.
        1. A triplet code will code for one and only one amino acid. (e.g., CAT means valine and only valine) = unambiguous.
        2. An amino acid may be coded for by more than one triplet code. (e.g., valine is coded by CAT, CAG, CAC, and CAA). This phenomenon has been termed 'degenerate'.
        3. Some triplet codes are used for punctuation (e.g., to a ribosome, UAG means stop).
      2. As the ribosome translates m-RNA it reads the code in a non-overlapping way.

        3.  

      3. The code is earthly. The exact same code applies for every organism on earth. That is, CAT means valine in your brain cells, means valine in the floppy ear of your dog, means valine in the tulips in your garden, means valine in the E. coli, means valine in phage and means valine in my cat, Widgets.
    4. Transcriptional rules and characteristics.
      1. The mRNA is read in sequential groups of three. Nothing separates one triplet code from the next triplet code. It looks at the first three nucleotides, then the next three, etc. Because of this, a deletion of three nucleotides is a more favorable mutation than a deletion of a single nucleotide!
      2. The linear order is conserved from DNA to mRNA to protein. (except for processing)
      3. Transcription occurs only on one of the two strands (single stranded transcription).
      4. Transcription can start and occur at various specified points along a DNA molecule.
      5. Transcription from DNA to m-RNA requires an enzyme: RNA polymerase, which happens to be the same enzyme for all m-RNA genes.