Introduction to Biotechnology Midterm PDF

# Intro to Biotech ## Lec 1 **What is biotechnology?** - The manipulation of living organisms and organic material to serve human needs. **Antony van Leeuwenhoek** - Discovered cells using simple microscope. - Bacteria - Protists - RBCs **Robert Hooke** - 1665 - Invented the com...

# Intro to Biotech ## Lec 1 **What is biotechnology?** - The manipulation of living organisms and organic material to serve human needs. **Antony van Leeuwenhoek** - Discovered cells using simple microscope. - Bacteria - Protists - RBCs **Robert Hooke** - 1665 - Invented the compound light microscope. - First to observe cells in cork **Louis Pasteur** - Describing the role of bacteria in spoilage & the scientific basis for fermentation. - Created the rabies vaccine. **Ernst Ruska** - Invented the electron microscope. **Sir Alexander Fleming** - Discovered Penicillin. **Gregor Johann Mendel** - Discovered genetics. **Colors of Biotechnology** - **Red biotechnology** - Health, Medical, Diagnostic - **Green biotechnology** - Agricultural - **White biotechnology** - Industrial - **Brown biotechnology** - Food biotech, Nutrition - **Desert biotechnology** - - **Gold biotechnology** - Bioinformatics, Nanobiotech - **Blue biotechnology** - Aquaculture, Marin biotech - **Violet biotechnology** - Legal aspects related to bio - **Grey biotechnology** - Environmental biotech - **Dark biotechnology** - Bioterrorism, Biowarfare - **Purple biotechnology** - Patents, Publications, Inventions ## Lec 2 **Gene Knockout** - Disrupt a gene in the animal and look at what functions are affected in the animal as a result of the loss of this gene. - This allows researchers to determine the role and function of the gene. **Bioremediation (Environmental Biotechnology)** - Stimulated growth of bacteria that degrade components in crude oil. - (1989 Exxon Valdez oil spill in Alaska) - (2010 Deepwater Horizon Spill Promoted research into natural oil degrading organisms and enzymes) **Aquatic Biotechnology** **Genetic Engineering** - Vaccines against viruses that infect salmon. - Transgenic salmon that produce "GH". **BioPropecting** - Looking for rich and valuable sources of new genes, proteins, and metabolic processes with important applications for human benefits. - Marine plankton and snails were found to be rich sources of antitumor and anticancer molecules. **Medical Biotechnology** 1. Involved with the whole spectrum of human medicine: - Preventive medicine - Diagnosis of health and illness - Treatment of human diseases 2. New information from the Human Genome Project: - Gene therapy - Stem cell technologies **Stem Cells:** - Grown in a lab, treated with different chemicals (growth mediators) to allow them to develop into specific kinds of tissues needed for transplant. **Forensic Biotechnology** - **DNA Profiling:** Known as DNA fingerprinting, is a technique used to identify individuals based on their unique DNA sequence. - **Bloodstain Pattern Analysis:** Based on the patterns of bloodstains. **Forensic Toxicology** - Analysis of body fluids and tissues for the presence of drugs and poisons. **Forensic Entomology** - The use of insects to estimate the time of death, to identify the location of a crime scene, and to determine whether a body has been moved. ## Lec 3 **Genetic Engineering** - Comprises multiple techniques for the international manipulation of genetic material to alter, repair, or enhance form or function. - It's also called **Recombinant DNA technology**, involves a group of techniques used to cut up and join together genetic material, especially DNA from different biological species, and to introduce the resulting hybrid DNA into an organism to form new combinations of heritable genetic material. - It refers to the direct manipulation of DNA to alter an organism's characteristics in a particular way. **What is a Plasmid?** - A small, circular piece of DNA, it can replicate independently. **Four Main Areas of Biotechnology Genetic Engineering:** 1. Transgenic biotechnology 2. Reproductive cloning 3. Programming of cells 4. Forensic Biotechnology **Human gene** - Cut them by same restriction enzyme. - Same sticky ends **Plasmid** - Mixed together (DNA ligases) to form Recombinant Plasmid - Insert into bacteria or yeast fungus to be replicated with their own gene. - Treat DNA with some restriction enzyme to recover replicated DNA from plasmid. - "Centrifugation" to isolate DNA from Plasmid. ## Lec 4 **Intro to Biotech** **The Central Dogma** - **DNA Polymerase** - **DNA** - **RNA Polymerase** - **RNA** - **Ribosome** - **Protein** **Genetic Code** - Used by cells as a triplet codon, every 3 nucleotides or codon, is read from a specified starting point in the mRNA. - **Non-ambiguous & universal.** - **Amino acids** have only one code: - Methionine (start codon) - Tryptophan - **Stop codons:** - UAA - UAG - UGA **Proteins** - Polymers of α-amino acids - Are synthesized from 20 amino acids - Nitrogen forms about 16% of their weight. **Biological Importance of Proteins** - Plasma membrane proteins - Receptors - Enzymes - Antibodies - Some hormones - Some protective proteins - Keratine - Some supportive proteins - collagen - Actin & myosin - Responsible for muscle contraction - Some amino acids are converted to other nitrogenous substances: - Creatine - Histamine - Heme - Purines & Pyrimidines ## Lec 5 **Intro to Biotech** **Structure of Microorganisms** 1. **Cell wall:** Inhibition of cell wall synthesis. 2. **Cell membrane:** Disruption of cell membrane function. 3. **Folic acid:** Block pathways and inhibit metabolism. 4. **DNA:** Inhibition of nucleic acid synthesis. 5. **Ribosomes:** Inhibition of protein synthesis. **Microbial Genomes** - 1994, Microbial Genome Program (MGP) - To sequence the entire genomes of microorganisms that have potential applications in environmental biology, research, industry, and health as well as genomes of protozoan pathogens. **Why sequence microbial genomes?** - Find new strains - For bioremediation or other tasks - Disease causing organisms - Find rapid diagnostic methods, vaccines - Identify genes involved in bacterial cell metabolism, cell division, and genes that cause human and animal illness. - Synthesis of novel products from microbes. **Metagenomics** - Involves the sequencing of genomes for entire communities of microbes. - Jovishas has sequenced over 6 billion bp DNA from 400 uncharacterized microbial species, containing 7.7 million previously uncharacterized sequences encoding more than 6 million different potential proteins. - 5-year project to sequence 1,000 genomes of microorganisms that live on and inside humans. **E. coli** - *Escherichia coli* bacteria **Streptococcus Pneumoniae** - Causes ear and lung infections, kills 3 million children worldwide each year. - Many of the vaccines are ineffective in children. **Microbiome** - A term that describes the genome of all microorganisms (symbiotic and pathogenic, living in or on all vertebrates). **The Gut Microbiome:** - Consists of the collective genome of microbes inhabiting the gut, including bacteria, archaea, viruses, and fungi. - Plays a very important role in your health by helping control digestion and benefiting your immune system and other aspects of health. - An imbalance of unhealthy and healthy microbes in the intestines may contribute to weight gain, high blood sugar, high cholesterol, and other disorders. **Microbial Diagnostics** - Techniques used to detect and track microbes. - Bacterial detection strategies - RFLP analysis, PCR, and DNA sequencing. - Databases are available for comparison of clinical samples - Used to detect and track bacterial contamination of food. **Goals of the Human Microbiome Project** 1. Determine if individuals share a core human microbiome. 2. Understand how we acquire and maintain microbial communities. 3. Understand how changes in the microbiome can be correlated with changes in health and conditions that affect the microbiome. 4. Develop new methods for the analysis of the microbiome. 5. Address ethical, legal, and social implications raised by human microbiome research. ## Lec 6 **Intro to Biotech** **The Central Dogma** - DNA Polymerase - DNA - RNA Polymerase - RNA - Ribosome - Protein **Genetic Code** - Used by cells as a triplet codon, every 3 nucleotides or codon, is read from a specified starting point in the mRNA. - **Non-ambiguous & universal.** - **Amino acids** have only one code: - Methionine (start codon) - Tryptophan - **Stop codons:** - UAA - UAG - UGA **Proteins** - Polymers of α-amino acids - Are synthesized from 20 amino acids - Nitrogen forms about 16% of their weight. **Biological Importance of Proteins** - Plasma membrane proteins - Receptors - Enzymes - Antibodies - Some hormones - Some protective proteins - Keratine - Some supportive proteins - collagen - Actin & myosin - Responsible for muscle contraction - Some amino acids are converted to other nitrogenous substances: - Creatine - Histamine - Heme - Purines & Pyrimidines **Poly Peptide Backbone** - Is the repeating sequence of C and N atoms linked by peptide bonds. - The R group gives the amino acid its unique property and isn't part of the backbone or the peptide bond. **Structural Organization** - Each polypeptide assumes at least three levels of structural organization: - Primary - Secondary - Tertiary - **Proteins** which possess more than one polypeptide chain in their molecule also possess a fourth structure called **quaternary structure**. - Proteins can be folded spontaneously or facilitated by proteins called **Chaperons**. - Final shape is called conformation which has the lowest free energy possible. **Chaperons** - small proteins that help guide the folding and can help keep the new protein from associating with the wrong partner. **Types of Proteins** - They are classified according to their shape depending on the axial ratio of proteins (i.e., length divided by width of the protein) into: - **Globular protein** - **Fibrous protein** **Introns:** Non-coding **Exons:** Coding **Complementary DNA** - It's synthesized in a lab from mRNA. - cDNA isn't genomic DNA because the transcript of genomic RNA has been processed (it lacks promoters and introns.) **Some Enzymes & their Industrial Applications** | **Enzyme** | **Application** | |:----------------|:------------------------------------------------------------------------------| | Amylases | Digest starch in fermentation & processing. | | Proteases | Digest proteins for detergents, meat/leather, cheese, brewing, baking, animal/human digestive aids | | Lipases | Digest lipids (fats) in dairy and vegetable oil products. | | Pectinases | Digest enzymes in fruit juice/ pulp. | | Lactases | Digest milk sugar. | | Glucose isomerase | Produce ↑ fructose syrups. | | Cellulases/hemicellulases | Produce animal feeds, fruit juices, brewing converters | | Penicillin acylase | Produce penicillin. | **Biotechnology Drugs & Other Medical Applications** - Produced through microbial fermentation or mammalian cell culture. - Cells are stimulated to produce the target proteins through precise culture conditions that include a balance of temperature, oxygen, acidity, and other variables. - At an appropriate time, the proteins are isolated from the cultures, tested at every step of purification, and formulated into pharmaceutically active products. - Must strictly comply with FDA regulations at all stages of the procedure. **FDA** - Food & Drug Administration. **Screening molecules associated with disease** - Identify early predictor biomarker proteins to aid in the diagnosis of specific diseases. - Insulin once had to be harvested from pigs and cows. **Applications of Proteins in Industry** - Food processing. - Textiles & leather goods. - Bioremediation - Some microorganisms have sticky coats of **metallothioneins** - proteins that actually capture heavy metals. **Restriction Enzymes** - Are enzymes that bind to specific recognition sequences to cleave double-stranded DNA. - Used to cut out a gene. **Insulin** - A peptide hormone (protein) ensures that glucose is taken up by the cells for cellular respiration. - Using genetic engineering techniques, scientists were able to use *E. coli* to bioengineer synthetic insulin in 1977. - Yeast (*Saccharomyces cerevisiae*) and safflower plants (*Carthamus tinctorius*) are used to produce insulin today. **Golden Rice** - A genetically modified food fortified with Beta Carotene, which the human body converts to vitamin A. - It's the result of mixing genes from daffodils into the rice genome. **What is a Clone?** - An exact genetic replicate of another cell or organism. **Somatic Cell Nuclear Transfer** - Animal 1 - Mammary cell donor - Animal 2 - Egg cell donor - Remove nucleus from egg cell 4 from somatic cell - Animal 2 - Put the nucleus of animal 1 in the empty egg cell of animal 2 - Leave it to grow in culture - Implant it in uterus of animal 3 (surrogate mother) - Embryonic development identical to animal 1 **What Have We Cloned so Far?** - DNA (Polymerase Chain Reaction (PCR)) - Cells (creating tissue culture or stem cell lines) - Whole organisms **Somatic Cell Nuclear Transfer** - A technique used to clone organisms. - Requires the transfer of a nucleus from a somatic cell (any cell other than a sperm or egg cell) into an egg cell whose nucleus has been removed. - This creates a genetically identical copy of the original organism. ==End of OCR==