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Nucleotides and Nucleic Acids


 
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Nucleic acids contain genetic information and enable synthesis of proteins. Nucleotides are used to make Nucleic Acids.

     
    Nucleotides are the subunit that is polymerized (connected into a long chain) to make nucleic acids (DNA and RNA). Nucleotides consist of three smaller components: a ribose sugar, a nitrogenous base, and phosphate group(s).
    Generic nucleotide structure. The "nitrogenous
    base" varies in different nucleotides.
       
      Ribose is the sugar component of nucleotides. One of the main chemical differences between DNA and RNA is that in RNA, the sugar is ribose, but in DNA, the sugar is deoxyribose, in which an oxygen has been removed. (compare the bottom right corners of the two structures - you'll see that the "OH" side group of ribose has been replaced with an "H" ).
    • Nitrogenous Bases are Adenine, Guanine, Cytosine, and Thymine in DNA. One of the chemical differences between DNA and RNA is that in RNA, the nitrogenous base Uracil is used instead of Thymine. 
    • Phosphate group(s)
      • Nucleotides may have one, two, or three phosphate groups attached.
      • If there is one phosphate, the nucleotide is a monophosphate
        If there are two phosphates, the nucleotide is a diphosphate
        If there are three phosphates, the nucleotide is a triphosphate 

        Click to enlarge.
      • If there are NO phosphate groups, the molecule is called a nucleoside, not a nucleotide.
  • Naming Nucleotides: Nucleotide names are a three letter abbreviation. The first letter refers to the nitrogenous base, the third letter refers to the phosphate, and the second letter refers to the number of phosphates. For example: 
    •  
      ATP Adenosine Tri-Phosphate
      AMP Adenosine Mono-Phosphate
      TTP Thymidine Tri-Phosphate
      GDP Guanosine Di-Phosphate
      NOTE: If you're paying attention, you probably noticed that the nitrogenous bases have names like Adenine, Thymine, and Guanine. Are you wondering why the nucleotides are called Adenosine, Thymidine, and Guanosine? "Adenosine" is the name for a nucleoside of adenine + ribose. Likewise, "thymidine" and "guanosine" refer to the nucleosides - the combination of ribose sugar and nitrogenous base.
  • Nucleotides can be connected to make nucleic acids. 
    •  
    • The connection that forms between nucleotides is between the sugar of the first nucleotide and the phosphate group of the second.
    • Each connection between nucleotides is a covalent bond, so the nucleic acids have a covalently attached sugar-phosphate backbone.

    •  

       
       
       
       
       
       
       
       
       
       
       

      In this figure, the nitrogenous bases are representated as squares labeled T, C, and G, respectively.
       

    • Nucleic Acid Synthesis: Connecting nucleotides to make nucleic acids requires: 
      • Specific enzymes - DNA polymerase connects nucleotides to make DNA, and RNA polymerase connects nucleotides to make RNA.
      • A pre-existing nucleic acid molecule to serve as a template - a model or mold that determines the sequence of the strand being made. Nucleotides are added based on complementary base-pairing (discussed below).
    • RNA is a long single chain of nucleotides. 
      • Each sugar is ribose.
      • The nitrogenous bases are Adenine, Cytosine, Guanine, and Uracil.
      • The process of RNA synthesis is called transcription.
      • RNA, like DNA (see below) is a long chain of individual nucleotides. Unlike DNA, RNA is a single strand of nucleotides. In nature, parts of an RNA molecule often base-pair with other parts of the same RNA molecule, as depicted in the diagram (red lines indicating hydrogen bonds between the base pairs C-G, A-U, and U-A).

        To see an enlarged version of this figure, click here.

    • DNA is a pair of long chains of nucleotides. 
      • Each sugar is deoxyribose.
      • The nitrogenous bases are Adenine, Cytosine, Guanine, and Thymine.
      • The process of DNA synthesis is called replication.

      DNA Structure. At left is an "unfolded" view of a double-stranded DNA molecule, showing the two chains of nucleotides, connected in the center by a series of hydrogen bonds between nitrogenous bases. At right, a schematic illustration showing the arrangement of the two strands in the double-helix configuration. The "backbone" on the outside is the sugar-phosphate chain, and the nitrogenous bases form the bridges across the middle. For an enlarged version, click here.

      DNA structure. The two strands of DNA backbone are visible as red and grey balls; the nitrogenous bases are the blue and grey regions in the center of the double helix.
       
      For more on DNA structure, scroll down or click here.
  • Nitrogenous bases can form hydrogen bonds. 
    • Adenine, Thymine, and Uracil can form TWO hydrogen bonds
    • Guanine and Cytosine can form THREE hydrogen bonds.
    • In nucleic acids (DNA and RNA), nitrogenous bases can bind to each other by hydrogen bonding. 
      • Guanine binds to Cytosine, and Cytosine binds to Guanine
      • In DNA, Adenine binds to Thymine. In RNA, Adenine binds to Uracil.


  • These hydrogen-bond interactions between nucleotides C-G and A-T or A-U are referred to as base-pairing or complementary base-pairing
    • Base-pairing holds the double-stranded DNA molecule together.
    • Base-pairing is necessary for DNA synthesis, RNA synthesis, and Protein synthesis to occur.
    • Base-pairing can occur between two strands of DNA, between two strands of RNA, or between one strand of DNA and one strand of RNA.
  • Some Nucleic Acids are RNA, which stands for ribonucleic acid. RNA contains the nitrogenous bases Adenine, Cytosine, Guanine, and Uracil. 
    • All RNA is single-stranded (a single long chain of nucleotides). However, one section of the RNA molecule can base-pair with another section.

    • This molecule, called tRNA base-pairs with itself to form a cloveleaf structure. Each circle represents a single nucleotide (A, U, c, or G). Lines that connect different nucleotides represent the hydrogen bonds of base-pairing. 


      In nature, the cloverleaf folds up into a "L" shape. This is the same molecule represented in the figure at left. The inset is another kind of depiction of the structure of tRNA, called a space-filling model.

    • There are three kinds of RNA; the main purpose of all of these is protein synthesis
      • rRNA = ribosomal RNA - part of the ribosome. Ribosomes are large complexes consisting of multiple different RNA molecules and many different protein molecules.
      • mRNA = messenger RNA - This long RNA molecule is an RNA copy of a gene (a region of DNA that contains the instructions for synthesis of a particular kind of protein).
      • tRNA = transfer RNA - during protein synthesis, carries amino acids to the ribosome, where the amino acids are attached in a growing chain that becomes the new protein. tRNA binds to mRNA by complementary base-pairing, so tRNA also serves as a "bridge" between the information code of DNA and RNA (the order of the nucleotides) and the code of protein (the order of amino acids). To learn more about this process, read about protein synthesis

      •  
  • Some Nucleic Acids are DNA, which stands for deoxyribonucleic acid. Nitrogenous bases in DNA are Adenine, Cytosine, Guanine, and Thymine. 
    • All DNA is double-stranded. The two strands are antiparallel (pointing in opposite directions). The backbone of each strand is the chain of sugars and phosphates. The nitrogenous bases of each strand are in the center, pointing toward the other strand. Each nitrogenous base forms hydrogen bonds with the complementary base pair on the opposite strand. Because the double-stranded DNA molecule twists around, it actually looks more like a spiral staircase than like a ladder. DNA is referred to as the "double-helix" because of this twist. 
    • Click Here for an enlarged DNA structure image.
    • DNA is the genetic material in cells - the essential part of the chromosomes. 
      • Chromosomes are very long double-helixes of DNA - a long pair of chains of nucleotides. The number of nucleotides in each strand is different for each chromosome, but is generally MILLIONS of nucleotides long. More on chromosomes.
      • Chromosomes in eukaryotic cells are linear - they have two ends. Chromosomes in bacteria are circular - the two ends are attached.
      • Genes are regions of the DNA on chromosomes. DNA is simply a long chain of A, T, C, and G nucleotides in a particular order. Genes are particular regions of DNA (A, T, C, and G nucleotides in a particular order) that contain the instructions for making RNA and protein molecules. For example, human genes contain thousands of genes, including the gene for beta-globin (part of the hemoglobin protein, which transports oxygen in the blood) and the gene for insulin (a hormone involved in regulation of glucose levels). On a specific part of one human chromosome, the gene for beta-globin is found: a specific sequence of A, T, C, and G nucleotides that contains the information required for the cell to make beta-globin. On another chromosome is a specific site where the sequence of nucleotides that encodes insulin is found. 


      If you want to know more about DNA, chromosomes, and genes,
      one link to try is:
      http://www.rothamsted.bbsrc.ac.uk/notebook/courses/guide/dnast.htm


Back: Sugars and Polysaccharides

I. The Chemistry of Life

A. The Basic Chemistry of Biology

B. The Molecules of Biology

1. Water - Structure and properties, hydrogen bonding, hydrophilic and hydrophobic, diffusion, osmosis

2. Amino Acids and Proteins; Protein structure and conformation (and allosteric modification

3. Sugars and Polysaccharides

4. Nucleotides and Nucleic Acids (you are here)

5. Lipids and Membranes (general information; more detail on membranes) 

II. The Cell
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