Biomolecules 3 Nucleic Acids

Nucleic acids in living organisms

Nucleic acid comes in two forms: DNA (deoxyribonucleic acid) RNA (ribonucleic acid) In living organisms these molecules hold the coded information to build that organism

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Nucleic acids in living organisms

Almost all the DNA in a eukaryotic cell is found in the nucleus, which acts as the information store. DNA is also found in the cytoplasm of bacterial and archaeal cells, mitochondria and chloroplasts.

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Nucleic acids in living organisms

RNA is found in three different forms. All three are needed to read and translate the information in order to produce the proteins that make up a living functioning organism.

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The structure of DNA

1953 James Watson and Francis Crick proposed a model for the structure. They used the evidence from the X-ray diffraction patterns produced by Rosalind Franklin and Maurice Wilkins.

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The structure of DNA

DNA contains the genetic code which dictates all the inherited characteristics of an organism. It does this by controlling the manufacture of protein. Your proteins coded for by your DNA make you unique. They make you a human being and not pine tree or a Gorilla.

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Genes and genome

A gene is a sequence of bases on a DNA molecule coding for a sequence of amino acids in a polypeptide chain. Each chromosome found in a cell nucleus contains a large amount of DNA and carries numerous genes. All the genes in an individual(or a species) are known as a genome.

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DNA chain of nucleotides

A mononuceotide contains three molecules linked together by condensation reactions. Deoxyribose (5 carbon sugar) Phosphate group Organic base containing nitrogen. Mononucleotides link by condensation reactions between the sugar of one nucleotide and the phosphate of the next one

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Formation of a mononucleotide

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Nitrogen containing bases found in DNA

Adenine (A) Cytosine (C) Guanine (G) Thymine (T)

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Bases found in DNA

Purines: double ring structures Pyrimidines: single ring structures

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Structure of DNA
In a DNA molecule there are two long strands of nucleotides twisted around each other to form a double helix. Sugars and phosphates form the backbone on the outside. The bases point inwards horizontally like the rungs of a ladder. The two strands run in opposite directions are know as antiparallel strands and are held together by hydrogen bonds between base pairs.

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Chargaff Rule

DNA of any cell of any organism For every mole of Purine you get one mole of Pyrimidine For every mole of Adenine you get one mole of Thymine For every mole of Guanine you get one mole of Cytosine Erwin Chargaff in the late 1940's investigated the biochemistry of DNA and published certain facts that he did not himself interpret but that were explained by the Watson-Crick structure.
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Complementary Base Pairing

Adenine with thymine Cytosine with Guanine Three rings for each rung of the DNA ladder The shape and chemical structure dictates how many hydrogen bonds are formed. A with T (two hydrogen bonds) C with G (three hydrogen bonds) This is referred to as complementary base pairing
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RNA
Ribose (3 carbon sugar) Phosphate Organic base containing nitrogen Four possible bases: Adenine (A) Cytosine (C) Guanine (G) Uracil (U)

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RNA
Messenger RNA (mRNA) made as a strand complementary to one strand of DNA (template strand) it is therefore a copy of the other DNA strand (coding strand) of the double helix Transfer RNA (tRNA) carries amino acids to the ribosomes Ribosomal RNA rRNA is found in ribosomes

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RNA

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ATP (adenosine tri phosphate)

Energy transfer molecule within cells Organic base (adenine) Ribose (5C sugar) 3 phosphates

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ATP
ATP in water ADP + hydrated Pi + energy ATP is created from ADP by the addition of inorganic phosphate (Pi) This process is known as Phosphorylation ATPase catalyses the breakdown of ATP to ADP ADP + Pi ATP, where ADP and Pi are joined together by ATP synthase

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cAMP
Cyclic adenosine monophosphate is a second messenger important in many biological processes. cAMP is derived from adenosine triphosphate and used for intracellular signal transduction Cyclic AMP is believed to mediates the action of many hormones on their target cell. The mechanisms by which the nucleotide controls glycogen metabolism in liver and skeletal muscle has been established.

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DNA replication
When a cell divides an exact copy must be produced so that each daughter cell receives a copy This process is called replication. The DNA double helix unwinds from one end and the two strands split apart as the hydrogen bonds break. Free DNA nucleotides line up alongside each DNA strand Hydrogen bonds form between complementary bases
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DNA replication
DNA polymerase links adjacent nucleotides to form a complementary. Each DNA strand acts as a template on which a new strand is built. Two complete DNA strands are formed. The two strands are identical to each other and to the original DNA molecule. Each of the two DNA strand contains one old strand and one new strand. Process is known as semi-conservative replication
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DNA replication

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How do we know that DNA replication is semi-conservative?

There are three possible ways that DNA could replicate: In a fragmentary way In a conservative way In a semi-conservative way

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Three possible models of DNA replication (old yellow, new red)

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Meselson and Stahl Experiment

Used heavy and light strands of DNA Used Escherichia coli bacteria grown in a medium containing only heavy isotopes of nitrogen,15N All nucleotides at the start of the experiment contained heavy nitrogen (yellow in diagram). Then moved bacteria into a medium of normal 14N All nucleotides incorporated into replicated DNA were light but the original DNA nucleotides were heavy. Bacteria allowed to divide then DNA extracted and centrifuged
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Meselson and Stahl Experiment

Heavy DNA (15N) sinks to the bottom Light DNA (14N) collects in a band near the top Medium density collects in the middle it has some light and some heavy.

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Where would you expect the band of DNA to be after one round of replication

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Where would you expect the band of DNA to be after one round of replication
Conservative replication: light and heavy band at top and bottom of the tube Fragmentary and semi-conservative replication: medium band in the middle of the tube

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Meselson and Stahl result

A single medium band formed therefore reject conservative replication

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Which model was correct Semi-conservative or fragmentary?

Let the bacteria undergo two rounds of replication The result was one medium and one light band The presence of both light and medium confirmed semi-conservative replication Fragmentary would only produce one type of DNA a mixture of heavy and light molecules. Therefore Semi-conservative replication
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Enzymes involved in replication

Helicases separate the two DNA strands DNA polymerase form the nucleotide chain in the 5 to 3direction allowing one strand (leading strand) to be replicated continuously Other strand (lagging strand) not replicated continuously small sections made (Okazaki fragments) joined by the enzyme ligase DNA replicates at a number of sites at the same time called replication forks

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