SCIMATB BLOCK1 REVIEWER

SCIMATB Q1 REVIEWER 

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I. INTRODUCTION

Development of tools and methodology  Expression systems, gene synthesis/sequencing, o purification process, formulation, bioassays, diagnosis, delivery 

 Definition  

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 Application of technology to improve a biological organism  The application of the technology to modify the biological function of an organism by adding genes from another organism  The techniques used by the biotechnology industry to modify  genes and introduce them into tran sgenic organisms

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Required Disciplines Integration of biology with engineering principles Cost-effectiveness o Process development/design/optimization o Basic biology  Mass/energy balance  Thermodynamics Physical, organic chemistry/Pharmacology  Biochemical engineering  Bioreaction engineering  

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 Why is Biotechnology needed? 

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Nature has a rich source of variation; however, nature does not have all of the traits we need Purposeful design and modifications/assembly of bio-oriented materials (proteins/enzymes, microorganisms, plant/animal cells, tissues, stem cells, etc) and unit processes to benefit humans or to make a profit  To produce valuable products at commercial scale and o to treat diseases  To discover and understand the underlying  o mechanisms of behaviors and disorders in living  organisms Cost-effectiveness  economically feasible

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Molecular Biology 

Biochemi stry 

Genetics

Biotechnology  

Definition of Biotechnology based on the use of techniques and methods  Traditional Biotechnology (before 1970) Broad definition of biotechnology  o Using a biological system to make products o Food Processing  o Fermented foods, brewery, dairy products,  etc. Brewing beer: conversion of starch to sugar  followed by the addition of a specific yeast  Agriculture o Modifications of living plants for improved  yield of food crops via artificial selection and hybridization Simple process o Direct use of or isolation from original  biological sources Fermentation  Modern Biotechnology  Use of recombinant DNA technology since 1973 o Stanly Cohen and Herbert Boyer perfected  techniques to cut and paste DNA (using  restriction enzymes and ligases) and reproduce the new DNA in bacteria Combined use of different disciplines o Biology-based knowledge  Knowledge linked with practical applications  (Biochem Eng, etc.) Use of genetically altered organisms o Enabling the production of existing   medicines or products easily and cheaply   Traditional Biotechnology industries  Adopts new approaches and modern techniques to o improve the quality and productivity of their products

Other traditiona l discipline s 

 Biotechnology focuses on… 

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Development of therapeutics based on underlying mechanisms of  diseases Development of new methods to cure diseases Gene and cell (stem cells) therapies o Production of valuable products at commercial scale Organic acids, antibiotics, amino acids, proteins o (enzymes), biofuels, vitamins, hormones, alcohol, fermented food, etc.

Major Application Areas Health Care/Diagnostics Development of therapeutics: efficacy, toxicity  o Diagnosis: early detection and prevention o Best solution compared to treatments  Prediction and treatment based on genomes  Invasive or non-invasive analysis or  detection of disease biomarkers  Agriculture Crop production with high yield and quality  o Bio-based processed Pollution, CO2 emission, global warming  o Bio-energy  Use of renewable sources o 

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Eng & Compute r Science

Microbiol ogy 

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Key Technologies and Fields Protein engineering  Design of proteins/enzymes based on structural and o mechanistic knowledge, molecular evolution and computational design Metabolic pathway engineering  Design of more efficient metabolic pathways; high o yield of target product, low by-product Computational modeling and optimization Systems biology  o Genome-wide analysis o Nano-biotechnology  For diagnosis and imaging  o Cell culture engineering  Microorganisms and mammalian cells o Hybridoma technology  o Forming hybrid cell lines (hybridomas) by   fusing a specific antibody-producing B cell  with a myeloma (B cell cancer) cell that is 

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selected for its ability to grow in tissue culture Separation technology  Recovery and purification of a target product o Synthetic biology  Creation of new biosystems o Systematic, hierarchal design of artificial, bio-inspired o system using robust, standardized and wellcharacterized building blocks Branches of Biotechnology  Blue biotechnology  o Marine and aquatic  Green biotechnology  o  Agricultural  Red biotechnology  o Medical   White biotechnology  o Industrial 

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Shift from petroleum-based economy  Exhaustion and soaring price of petroleum o Environmental issue o Global warming and pollution pollution  Development of renewable source-based Bioprocess Replacement of chemical processes with Bio-based ones Key role of enzymes Use of enzymes in Biofuel production from renewable o biomass

Production of biofuels from natural resources Increase in the yield and alcohol to lerance o Redesign of pathway for the ethanol  production in yeast to use raw materials Elucidation of enzyme mechanisms  Redesign of pathway to increase the yield  and to reduce by-products Design of critical enzymes in the pathway   Process development: fermentation process o Separation and concentration o

Carbohydrates Serve as quick energy and short-term energy storage Play a structural role in plants, bacteria and insects Monomers are monosaccharides Glucose (C6H12O6 )  ) o Fructose o Galactose o Disaccharides Glucose + Fructose = Sucrose o Glucose + Galactose = Lactose o Glucose + Glucose = Maltose o Larger polysaccharides are made from linking many monomer molecules together through condensation synthesis Starch o Polysaccharide composed of glucose  Predominantly made by plants  Oligosaccharides 3-12 monosaccharides with proteins o Polysaccharides 12 monosaccharides o 

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 Alternative Energy Sources 

Organic Molecule Contains carbon Macromolecules 

 Bio-based Economy: Impact on Global Economy  

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Lipids    

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 Therapeutic Proteins  

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Frozen water is less dense

High specificity and less toxicity  –   – high safety and efficacy   Therapeutic proteins  Antibodies, proteins, enzymes, peptides, etc. o  Therapeutic proteins will form the back-bone of future medicinal therapy 

Serve as long-term energy stores in cells and form membranes Serve as hormones and insulation Do not dissolve in water Fats and oils are formed from a glycerol molecule and three fatty  acid molecules Fatty acids – long chains of hydrocarbons ending in  – COOH Saturated (without double bonds) o  Animal fats  Coconut and palm oil  Unsaturated (with double bonds, low melting point, o fluid nature, sensitive to oxidation) Corn, soybean, olive, canola oil 

 Perspectives 

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Biotechnology will have an impact on human’s health, life-style, and economy. Modern biotechnology constitutes a variety of diverse areas and technologies, requiring interdisciplinary collaborations.

II. CHEMICAL COMPONENTS  Water   

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Most abundant molecule Has special traits that make it important to life Polar molecule Oxygen atoms are large and hydrogen are small o Characteristics Liquid at room temperature o Universal solvent for polar molecules o  Water molecules are cohesive o  Temperature of water changes changes slowly  o High heat of vaporization o

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Food rich in plant sterols and sterolins  Avocado, walnuts, almonds, soybeans, cold-pressed o olive oil, peanuts, sunflower seeds, wheat germ oil, sesame seeds  Types of oil Fixed o Palm, soybean, sunflower seed, tuba-tuba,  kasuy (cashew), corn Fats o  Avocado, cacao   Waxes o

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Saging butuan, sisal

 Volatile 

Lavender, pine needle, rosemary, jasminol (jasmine), geraniol (rose), citral (oranges), citronella, camphor (sambong, manzanilla), safrol (cinnamon)

 Proteins 

Functions Serve as structural proteins  Act as enzymes to speed reactions reactions Serve as transport carriers o  Allow materials to cross cell membranes o Expression of our genes o Proteins are polymers of amino acids Peptide bonds join amino acids o o

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Proteins have levels of organization Primary structure o Peptide bonds  Secondary structure o 3D structure  3.6 amino acids per turn   Alpha-helix stabilized by hydrogen bonds  H bonds between NH and CO   Tertiary structure o Formation of domains  Functional unit of proteins  Made up of about 200 amino acids  Stabilized by bonds  Disulfide Hydrophobic Hydrogen Ionic interactions Quaternary structure o Several subunits of proteins  Held together by hydrophobic bonds, H  bonds, ionic bonds Protein denaturation Unfolding and disorganization of the protein structure o Destroys up to secondary structure o Peptide bonds not hydrolyzed o Heat, organic solvents, mechanical mixing  o    

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Nucleic Acid Polymers of nucleotides Deoxyribonucleic Acid (DNA) o Double-stranded with complementary base  pairing  Strands are antiparallel  G-C pairs have 3 hydrogen bonds   A-T pairs have 2 hydrogen bonds  One strand is the complement of the other  Major and minor grooves present different  surfaces Cellular DNA is almost exclusively B-DNA  B-DNA has ~10.5bp/turn of the helix  

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III. CELLS 

Animal cells

Ribonucleic Acid (RNA)

 Plant cells

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Function   

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 Water, salts, crystals, starch, protein bodies, granules/fibrous materials Storage of nutrient reserves and waste materials Digestive organelle Impermeable to wastes

Ribosomes Sites of protein synthesis o In plants, only few ribosomes except in legumes and o insectivorous plants  A cluster is called a polysome o

IV. CELL DIVISION  Interphase 

G1 phase

Period before DNA synthesis gap between cell o division and DNA synthesis Cell makes ER, o ribosomes, and cytosol to make functional cells S phase DNA synthesis o Replicates its o DNA for the next 6-8 hours o

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Cell wall o

Primary wall Microfibrils attached to the cell membrane  Polysaccharide  Celluloses – polymers of glucose Hemicelluloses  –  akali-soluble portion Pectin – hot water-soluble portion Secondary wall Lignin   Aromatic polymer that rigidifies secondary cell walls Stained red by phloroglucinol solutions Mid lamella Pectin   

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Goal of replication is o to accurately copy the genetic information so that each daughter cell will have an exact copy of the parental DNA Steps

 Compartmentalization

Eukaryotic cells are full of membrane-enclosed compartments Separates incompatible chemical and physical o conditions Proteins can be both synthesized and hydrolyzed in a o single cell  Parts of the cell (incomplete :o) Nucleolus Holds the genetic information of the cell o Endoplasmic Reticulum Rough and Smooth o Ribosomes attached outside = rough  Protein synthesis within endomembrane  system Protein synthesis for secretion  Integral membrane protein syntheshis  Protein modification (Golgi also)  Membrane assembly   Golgi Apparatus Packages proteins before they are sent to their o destination Mitochondria o  The cell’s “powerhouse”, “powerhouse”, as it produces ATP Chloroplasts Contains chlorophyll, which is a catalyst for o photosynthesis Central Vacuoles  Tonoplast o Single membrane  Contents o 

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Spans the time from the completion of DNA synthesis to the onset of cell division Spends 2-5 hours making proteins before mitosis o Cell performs all of its regular functions and gets ready to divide High metabolic activity  DNA is duplicated DNA is in the form of chromatin o

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G2 phase

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Chromosomes Before a cell starts dividing, the chromosomes are duplicated (refer to S phase) Produces sister chromatids o Structure Homologous chromosomes = identical pairs o One inherited from mother, and one from father o Made of of sister chromatids joined at the centromere o 

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 M phase (Mitosis) o o

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Purpose: to make copies of cells and their DNA Events Replicated chromosomes align at the  metaphase plate Sister chromatids separate and move to  opposite poles Nuclear membranes form around each new   nucleus Division of cytoplasm or cytokinesis  Stages

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Cell Cycle Control Checkpoint proteins monitor progression through t he cell cycle 

Note: 

Please don’t rely on this reviewer alone! This is just a summarized  version of the PowerPoints we got from the FIRST HALF of the term.  Good luck!