Evolution and Gene Regulation

• The theory of evolution by natural selection applies to the development and treatment of tumors.
• Cancer cells exhibit overproduction, genetic variability, and mutations that enhance survival.
• Evolution explains the difficulty in curing cancer and suggests novel therapies, such as priming tumors for treatment.

Gene Regulation

• Multicellular organisms have different cell types due to different combinations of genes being turned on and off.
• An operon is a cluster of genes with related functions controlled by a promoter and other DNA sequences.
• The lac operon in E. coli allows for lactose use only when lactose is present.
• In eukaryotic cells, gene expression is controlled at multiple points in the pathway in the nucleus.
• DNA packing blocks gene expression by preventing access of transcription proteins to the DNA e.g. X chromosome inactivation.
• Gene transcription is a control point that involves regulatory proteins interacting with DNA to turn genes on or off.
• Post-transcription control involves intron removal, RNA processing, and mRNA modification.
• In the cytoplasm, protein translation initiation is also a control point.
• The cell also regulates protein activation and breakdown.

Cell Signaling

• Cell-to-cell signaling uses signal transduction pathways to convert molecular messages to cell responses, such as gene transcription.

Homeotic Genes

• Homeotic genes are master genes that regulate other genes that control embryonic development.

DNA Microarrays

• DNA microarrays determine which genes are turned on in a particular cell type.

Cloning Plants and Animals

• Most differentiated cells retain a complete set of genes.
• Animals can be cloned through nuclear transplantation.

Reproductive Cloning

• Reproductive cloning involves inserting a donor cell nucleus into an egg from which the nucleus has been removed.

Therapeutic Cloning and Stem Cells

• Therapeutic cloning produces embryonic stem cells for medical uses.
• Embryonic, umbilical cord, and adult stem cells all show promise for therapeutic uses.

Cancer Genes

• Cancer cells divide uncontrollably due to mutations in genes that regulate the cell cycle.

Proto-oncogenes

• Proto-oncogenes and tumor-suppressor genes code for proteins active in signal transduction pathways regulating cell division, and mutations of these genes cause malfunction of the pathways.
• Cancer results from a series of genetic changes in a cell lineage.

Cancer Risk

• Reducing exposure to carcinogens and making healthful lifestyle choices can help reduce cancer risk.

DNA Technology

• DNA technology includes genetic engineering, DNA profiling and bioinformatics.

Biotechnology

• Biotechnology manipulates organisms or their components to make useful products.
• Ancient practices such as using yeast to make bread and selective breeding of livestock are examples of biotechnology.
• Modern biotechnology uses DNA technology, modern laboratory techniques for studying and manipulating genetic material.
• Organisms that have acquired one or more genes by artificial means are called genetically modified organisms.
• A transgenic organism is a recombinant organism with newly acquired genes typically from another species.

Recombinant DNA

• Recombinant DNA is constructed by combining pieces of DNA from two different sources.
• Recombinant DNA technology is widely used in genetic engineering, direct manipulation of genes for practical purposes.

Bacterial Plasmids for Gene Cloning

• Biologists often use bacterial plasmids, small circular DNA molecules that duplicate separately from the bacterial chromosome, to manipulate genes in the laboratory.
• Gene cloning is the production of multiple identical copies of a gene-carrying piece of DNA.
• Scientists have genetically engineered bacteria to mass-produce useful chemicals.
• Engineering can serve many purpose from basic research to medical applications.

Cloning a Gene

• Isolate bacterial plasmids (vectors) and DNA from another organism that includes the gene of interest.
• The DNA from the two sources is joined together resulting in Recombinant DNA plasmids.
• The recombinant plasmids are then mixed with bacteria.
• Under the conditions, the bacteria take up the recombinant plasmids.
• Transgenic bacteria with the gene of interest can be grown in large tanks, producing the protein in marketable quantities.
• The end products of gene cloning may be copies of the gene itself, or the protein product of the cloned gene.

Enzymes

• Bacterial enzymes called restriction enzymes are the cutting tools used for making recombinant DNA.
• A restriction site is the DNA sequence recognized by a particular restriction enzyme.
• After a restriction enzyme binds to its restriction site, it cuts the two strands of the DNA by breaking chemical bonds.
• Restriction fragments are the pieces of DNA produced when the restriction enzyme cuts the DNA strands.
• The staggered cuts yield two double-stranded DNA fragments with single-stranded ends.
• The single-stranded ends are called "sticky ends." because they can bond with complementary single-stranded stretches of DNA.
• DNA ligase, the "pasting" enzyme, connects the DNA pieces into continuous strands by forming bonds between adjacent nucleotides.

Gel Electrophoresis

• Gel electrophoresis is a method for sorting macromolecules based on their electrical charge and size.
• DNA fragments are placed in wells, and an electrical current is applied.
• The negatively charged DNA fragments move toward the positive pole.
• Shorter DNA fragments move more quickly through the gel than longer DNA fragments.
• Gel electrophoresis separates DNA fragments by length.

Pharmaceutical Applications of Recombinant DNA Technology

• Human insulin (Humulin) is produced by genetically modified bacteria.
• Human growth hormone (HGH) is also produced.
• Tissue plasminogen activator (tPA) is another recombinant pharmaceutical product.
• The hormone erythropoietin (EPO) is produced by genetically modified mammalian cells.
• In vaccination, a harmless variant or derivative of a disease-causing microbe such as a bacterium or virus is used to prevent an infectious disease.

Genetically Modified Organisms

• Today, DNA technology is quickly replacing traditional breeding programs as scientists work to improve the productivity of agriculturally important plants and animals.

Genetic Modification Risks

• Genetically modified crops reduce the need for chemical insecticides.
• They can also produce proteins that act as a natural antifreeze, protecting the delicate plants from the damages of cold weather.
• "Golden rice 2," contains genes from daffodils and corn and could help prevent vitamin A deficiency and resulting blindness.
• Pigs have been genetically modified to carry a roundworm gene whose protein converts less healthy fatty acids to omega-3 fatty acids.

Human Gene Therapy

• Human gene therapy treats disease by introducing new genes into an afflicted person.
• The procedure closely resembles the gene cloning process and can be used to supplement or replace a single defective gene that causes a disorder.
• A gene from a normal individual is cloned, converted to an RNA version, and then inserted into the RNA genome of a harmless virus
• Bone marrow cells are taken from the patient and infected with the recombinant virus.
• The virus inserts a DNA copy of its genome, including the normal human gene, into the DNA of the patient's cells.
• The engineered cells are then injected back into the patient.
• The normal gene is transcribed and translated within the patient's body, producing the desired protein.
• Bone marrow cells are prime candidates.

DNA Profiling

• DNA profiling is the analysis of DNA samples to determine whether they come from the same individual.
• Forensic scientists compare DNA sequences that vary from person to person.
• DNA samples are isolated from the crime scene, suspects, victims, or other evidence.
• Selected sequences from each DNA sample are amplified to produce a large sample of DNA fragments.
• The amplified DNA fragments are compared.

PCR

• The polymerase chain reaction (PCR) is a technique for amplifying a specific segment of DNA.
• Primers mark the start and end points for the PCR reaction.
• In the treatment and diagnosis of disease PCR can be used to amplify and thus detect HIV in blood or tissue samples. It can also be used to diagnose hundreds of human genetic disorders.

STR Analysis

• STR analysis is a method of DNA profiling that compares the lengths of STR sequences at specific sites in the genome.
• In the United States, the number of repeats at each site is entered into a database called CODIS (Combined DNA Index System).

Bioinformatics

• Bioinformatics is the application of computational methods to the storage and analysis of biological data.

DNA Sequencing

• Exploits complementary base pairing to determine the complete nucleotide sequence of a DNA molecule.
• Third-generation sequencing involves moving a single strand of a DNA molecule through a nanopore and detecting the bases one by one by their interruption of an electrical current.

Genomics

• Genomics is the study of complete sets of genes (genomes).

Genome Mapping Techniques

• Genomes are often sequenced using the whole-genome shotgun method.
• The first step is to chop the entire genome into fragments using restriction enzymes.
• The DNA sequences determined by many research groups are deposited in GenBank.

Human Genome Project

• The Human Genome Project was a massive scientific endeavor to determine the nucleotide sequence of all the DNA in the human genome and to identify the location and sequence of every gene.
• Several years into the project, private companies joined the effort
• The chromosomes in the human genome contain approximately 3 billion nucleotide pairs of DNA.
• The human genome has a relatively small number of human genes.
• Scientists have even begun to gather sequence data from our extinct relatives.

Systems Biology

• Systems biology aims to model the dynamic behavior of whole biological systems based on the study of the interactions among the system's parts.