Biolo1100 Chapter 5 DNA, Gene Expression, and Biotechnology
  1. DNA is a double helix   macromolecule made of nucleotides  .
    • DNA is made from nucleotide subunits, which is composed of
      • a five-carbon deoxyribose sugar
      • a phosphate group
      • a nitrogen-containing base

      Two chains of nucleotides twist around each other to form a double helix with sugar-phosphate backbones held together by hydrogen bonds between the nitrogen-containing bases.

      The hydrogen bonding between the nitrogen-containing bases occurs in complementary base pairs:

      • Adenine (A) always pairs with Thymine (T).
      • Guanine (G) always pairs with Cytosine (C).


  2. Sequences of nucleotides called genes   control cellular functions and make up an individual's genome.
    • The full set of genetic material in an organism's cells is called its genome.

      In eukaryotes, DNA in the nucleus is organized in linear strands called chromosomes.

      Sequences of nucleotide base pairs make up genes that code for proteins.

      Humans have 23 pairs of chromosomes, one of each pair inherited from our mother, one from our father, for a total of 46.

      You may inherit different versions of a gene from your parents.


    • Since 2000, the genomes of many organisms have been sequenced.

      A human cell has over 3 billion base pairs of DNA, for a total of 6 billion (6 x 109) nucleotides.

      Our genome size is relatively large among organisms, but not the largest.

      Some plants such as onion (Allium species) possess many times as much DNA as a human.

    • Alternative versions of a gene that code for different variations of a protein are called alleles.

      Different alleles may result in the production of different variants of a proteins and be observed as different traits of an organism, such as petal color.

      Thus you may inherit different alleles from your parents for any given trait, such as hair color.

      An observable trait is also called phenotype, while an individual's alleles make up its genotype (genetic makeup).

      The genotype determines the phenotype.

  3. Much of the human genome   are non-coding DNA that are not genes   .
    • Genes make up only about 2% of human DNA.

      The coding regions of genes provide instructions for synthesizing proteins that can often be observed as phenotypes, e.g. hair color.

      The genes of an individual make up its genotype and determine its phenotype.


  4. Gene expression   (exhibiting a phenotype) involves 2 steps:
    • Gene expression (exhibiting a phenotype)
      Messenger RNA (mRNA) molecules are produced by transcription from genes on the DNA.
      This occurs in the nucleus.
      Other types of RNA such as transfer RNA can also be transcribed.
      Proteins are produced by translation from the mRNA.
      This occurs on ribosomes in the cytoplasm. Quiz

    • Transcription involves copying genetic information on DNA   to a RNA   transcript.
      • Transcription

        1. RNA polymerase binds to DNA at a specific region called the promoter site and separates the double helix to single strands.

        2. One of the DNA strands on the gene is used as a template on which RNA nucleotides are built, using the base-pairing rules. Note:
          • Adenine (A) on the DNA pairs with Uracil (U) on the RNA.

        3. The mRNA (or other types of RNA) transcript is released when it reaches the end of the gene.


    • Translation involves the production of proteins   from nucleotide sequences copied onto the RNA   transcript.

    • Translation needs a a "dictionary": the genetic code.

      1. Ribosomes guide the translation process by binding to mRNA and loading tRNAs.

      2. An attachment site on the tRNA binds to three-base codons on the mRNA, adding amino acids to a growing protein chain, using the genetic code as a "dictionary".

      3. The protein is released from the complex when the ribosomes reads one of three stop codons on the mRNA.

      Codon pairing exercise:


    • Genetic Code (Codon Table)

      A codon is a triplet of 3 nucleotides on the mRNA that codes for an amino acid.

      Ribosomes translate each codon to an amino acid; most amino acids are specified by more than one codon.

      The codon AUG is both the "start" codon and also a codon for the amino acid Methionine.

      There are 3 "stop" codons.


    • A transfer RNA (tRNA) molecule is single-stranded;

      On one end is a three-base sequence that binds to a complementary codon on the mRNA, using base-pairing rules; remember A pairs with U.

      The other end carries a specific amino acid.

      The match between codon and amino acid is specified in the genetic code.

      For example, the codon "ACG" is code for the amino acid "Threonine".

      Types of RNA exercise:


  5. A mutation   is a change in the DNA sequence that may affect proteins.
    • A mutation is a change in the DNA sequence of an organism, due to errors in DNA replication or to damage from physical or chemical agents.

      The mutant fruit fly at the bottom has suffered a mutation in a gene regulating eye shape.

      The rate of mutations in cells is about 1 per 108 (hundred million) base pair of nucleotides.

    • Mutations that change a single base pair are called substitution mutations.

      The changed DNA sequence is reflected in a changed mRNA codon, leading to a possible change in the amino acid sequence of the translated protein, which may be defective.

      Insertions and deletions of nucleotides lead to frame-shift mutations that change many more amino acids in the protein.

      genetic code

      • What is a substitution mutation in the DNA that causes the illustrated amino acid change from cys (Cysteine) to ser (Serine)?
        • ACA -> TCA (or ACG -> TCG) hint


      1. A mutated gene codes for a defective protein, sometimes an enzyme such as aldehyde dehydrogenase.

      2. The defective enzyme fails to carry out a chemical reaction.

      3. Molecules fail to be processed and accumulates.

      4. The accumulated chemical may be toxic, such as the byproduct of alcohol breakdown acetaldehyde.

    • Insertion mutation

      Use the genetic code to follow the insertion of a nucleotide in DNA.


    • Deletion mutation

      Use the genetic code to solve this problem.

      What caused this deletion?

      A wrong solution.

  6. Genetic engineering   technologies have introduced genetically modified   organisms that provide new opportunities and risks.
    • Genetic engineering allows genes from one species to be expressed in another.

      Human insulin has been produced by bacteria - a transgenic, or Genetically Modified Organism (GMO).

      Restriction enzymes allow a desired piece of DNA from one species to be inserted into that of another - producing recombinant DNA.

    • Human insulin has been produced by bacteria - a transgenic, or Genetically Modified Organism (GMO).

    • Restriction enzymes can be used to isolate genes of interest.

      1. A gene of interest from a target organism is identified.

      2. A restriction enzyme can cut DNA double helixes at specific restriction sites that contain a palindrome sequence.

      3. The restriction enzyme binds and cuts DNA at the restriction sites.

      4. DNA fragments with complementary single-stranded ends are produced. Some of these fragments contain the genes of interest.

      After isolation, restriction fragments can reform double helixes with other sources of DNA to produce recombinant DNA.



    • Polymerase Chain Reaction (PCR) is used to amplify small amounts of DNA.

      1. The target DNA double helix is denatured by heat and separated into single strands.

      2. Cooling allows the enzyme DNA polymerase to work on nucleotides added to the mix.

      3. The DNA polymerase reconstitutes the double helix on each of the single strands by base-pairing.

      4. After one cycle, the original DNA has been doubled (21); 2 cycles amplifies the DNA 4 times (22).



    • Bacteria often possess circular pieces of DNA called plasmids that are useful for producing recombinant DNA.

      1. The same restriction enzyme used to isolate the gene of interest is now used to cut plasmid DNA.

      2. This yields complementary single-stranded ends that can base-pair with those of the target fragments.

      3. Some of the plasmids are now recombinant: the DNA is a combination of target and plasmid DNA.

      The recombinant plasmids is inserted back into bacteria; if the gene of interest is expressed in the transgenic bacteria, it may produce useful proteins.

    • Humans have long used artificial selection techniques to enhance crops and animals.

      Genetic engineering has allowed the development of Genetically Modified Organisms (GMOs) that has radically sped up this process.

      • Bt corn

      • Golden rice

    • Golden Rice is a variety with genes from other organisms added to it to produce beta-carotene, which is a precursor for vitamin A.

      This transgenic crop (or genetically modified organism - GMO) has the potential for reducing vitamin A deficiency in developing countries where the major staple food is rice.

    • Caterpillars can damage corn crops.
      Bt extracted from a bacterium (Bacillus thuringiensis) is a pesticide that is toxic to caterpillars.
      The Bt gene can be inserted into the corn genome to yield a GMO corn with built-in pest resistance. Farmers no longer need to spray crops with the Bt pesticide. Quiz

  7. Mammals can be cloned by nuclear   transfer.
    • Cloning Dolly by nuclear transfer

      1. The nuclei are removed from a mammary cell of a female lamb and an egg cell from a different female.

      2. The nucleus from the mammary cell is implanted into the egg cell.

      3. An electric shock is applied to the egg to trigger cell division, which can happen in culture for a few divisions.

      4. The embryo is implanted into a living uterus; a 3rd lamb serves as the surrogate mother.

      5. The cloned Dolly is identical in genetic makeup to the mammary cell donor.

      • What's wrong with this picture?
        • Dolly should look identical to the mammary cell donor. Tutorial:


  8. DNA fingerprinting   makes use of several genetic technologies.
    • Short tandem   repeats provide genetic markers.
      • Among non-coding regions of the DNA are short tandem repeats (STRs).

        The number of repeats vary greatly among individuals, yielding many different alleles of each STR in the population.

        A total of 13 different STR locations can be used to uniquely identify an individual based on the combination of her STRs.

        (tandem: one following or behind the other)

    • Gel electrophoresis   separates DNA fragments.
      • Gel electrophoresis

        DNA samples are cut into fragments by restriction enzymes.

        The fragments are placed in a semifluid gel apparatus and an electrical charge is applied.

        The negatively charged DNA fragments move toward the positive end at different speeds, based mainly on fragment size.

        The separated fragments can be visualized with dyes.


    • DNA fingerprints   can identify individuals based on their DNA.

    • DNA fingerprints

      1. DNA samples are cut by restriction enzymes to yield many fragments.

      2. Fragments containing STRs are amplified by PCR.

      3. Fragments are sorted by size using gel electrophoresis

      4. The separated fragments are analyzed to identify an individual.