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final week of bisc 130 notes

by: Victoria Kemp

final week of bisc 130 notes Bisc 130

Victoria Kemp
LA Tech
GPA 3.0

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these notes are the notes from monday and wednessday of the test 5 notes
Introduction to Biology
Dr. Kyle Kemege
Class Notes
25 ?




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This 7 page Class Notes was uploaded by Victoria Kemp on Sunday February 28, 2016. The Class Notes belongs to Bisc 130 at Louisiana Tech University taught by Dr. Kyle Kemege in Fall 2015. Since its upload, it has received 30 views. For similar materials see Introduction to Biology in Natural Sciences and Mathematics at Louisiana Tech University.

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Date Created: 02/28/16
Notes for Kemege test 5 Molecular cloning  Frequently used in molecular biology labs  Overview: 1. Isolate gene for protein of interest a. Need high concentration of gene DNA 2. Put gene into vector/Plasmid a. Plasmid: optional, additional small chromosome used in bacteria 3. Put plasmid into bacteria a. The commonly used one in lab is E-coli 4. Let bacteria grow a. Will express the gene and make the protein 5. Break open the bacteria and purify your protein from others How to get a high concentration of gene of interest?  Obtaining genome DNA from source organism cells 1. Problem: low yield of DNA 2. Solution: artificially amplify gene from source DNA  Like DNA replication but just for one gene 3. Polymerase Chain Reaction(PCR)  (PCR) has many applications beyond molecular cloning 4. PCR starting material  Source DNA  Can be low concentration  Nucleotides  DNA polymerase  DNA Primers  Complementary to sequences on either end of gene of interest 1. Heat to determine (unwind) double-stranded DNA a. DNA Pol. Needs a single-stranded template 2. Cool to allow DNA Primers to bind 3. Heat slightly to allow DNA Pol. To extend Primers replicate DNA a. Repeat 1)-3): dozens of cycles b. Use a thermal cycler machine to adjust temp. at timed intervals i. (Problem): DNA Pol. Denatures (unfolds) at high temp used in step 1) 1. No longer active a. (Solution): use DNA poly From an organism that lives in very hot environments i. Would’ve evolved enzymes that function at high temps ii. Hot spring bacteria 1. Ex. Thermus Aquaticus (Tac Pol) How to get plasmids?  Are naturally occurring in many bacteria  Easily purified from bacteria  Many have been artificially modified to be better for molecular cloning How to cut open plasmid and seal in Gene/Insert?  Restriction Endonucleases o AKA restriction enzymes  Cut DNA at a very specific sequence  Many restriction enzymes exist, have different sequences where they cut o Sequence is an inverted repeat palindrome o Live not on evil o Ex. GAATTC o CTTAAG o Opposite strands read backwards from one another o Cut between two specific bases in the sequence the example cuts between the G and the A  Makes uneven cuts creates sticky ends  Ex G AATTC  CTTA G  Pick a restriction enzyme that cuts Plasmid once  Cut end of insert gene with same restrictions-twice  Use DNA Ligase to seal plasmid to insert together How to get plasmid into bacteria? o Process called Transformation How to grow bacteria? o In liquid media in a shaking incubator o E-Coli are easy to take care of and grow quickly o Will express protein of interest How to purify the protein of interest?  Many methods  E.g Size Exclusion Chromatography o Run the protein solution over a column of porous beads o Small protein will get caught in the pores of beads o They will therefore travel slowly o Large proteins pass by unhindered o Travel quickly o SEPERATES PROTEINS BASED ON THEIR SIZE o Find protein in appropriate fraction Genetically engineered food  Manipulation of the genes in plants and animals  Herbicide: Compounds that kill plants o Want an herbicide that is safe, biodegradable, and kill weeds but won’t kill our crop plants  Glyphosate is an herbicide that is highly effective, biodegradable with fairly low human toxicity o May be a carcinogen with “occupational exposure” o Kills all plants o Herbicide-resistant plants  Solution: put gene for glyphosate resistance in crop plants so they will not be killed by glyphosate o Problem: millions of children worldwide suffer from vitamin A deficiency  Illness, blindness and /or death  Because diet is low of vitamin A  Dependent on inexpensive staple foods like rice  Rice has no vitamin A o Solution: make rice that contains vitamin A  Golden Rice  Add genes to the rice chromosome or enzymes that synthesize vitamin A  Genes from other plants and bacteria  Genetically engineered salmon o Express a gene for a growth hormone frm a related fish species o Not the same as human hormones o Fish can grow faster and larger o Recently approved for human consumption o ALLGENETICALLY MODIFIED ORGANISMS UNDERGO RIGOROUS TESTING BEFORE MARKETING Population: group of organisms of the same species living in same area at the same time Ecology:  Study of how organisms related to one another and to the environment  Population range: o Aka distribution o Area throughout which a population exists o Boundaries of population range can be not clear or not distinct or it is very distinct o Can be very limited or very wide o Can change over time o With climate change o By expansion of a population  In nature organisms reproduce exponentially, However limited resources constrains pop. size  Carrying capacity: the maximum number of individuals in a population that an environment can support because organisms cannot reproduce limitless for infinite time, we see logistic growth o Sigmoidal growth curve  Rapid growth that slows near carrying capacity, levels out o K-selected populations  Reproduce slowly  Gradually approach carrying capacity o R-selected populations  Reproduce rapidly  Overshoot their carrying capacity;  often leads to death (population reduction) until carrying capacity is reached  MOST POPULATIONS ARE AT OR NEAR THEIR CARRYING CAPACITY AT MOST TIMES. Human population:  We are at/near Carrying capacity for thousands of years  Advances in technology have increased our carrying capacity  Still growing WHAT IS OUR CARRYING CAPACITY?  Depends on desired way of life  Depends on future advances of technology How population growth is mostly in developing countries Community: all the species of organisms living together in same area Ecological niche: all the ways an organism/population uses resources of environment  Use of space,food,water,light,etc  Usually very specific  Because of natural selection  DIFFERENT ENVIRONMENTS,DIFFERENT NICHES,DIFFERENT RESOURCES, DIFFERENT COMMUNITIES Competitive exclusion: no two species with the same niche can coexist  One species will outcompete the other  Leads to exstinction of one species in that community  Predation: consuming of one organism(prey) by another (predator) o Affects prey population size/levels o Prey population size can affect predator population size o Predation provides selective pressure for prey tp evolve defenses o Prey defenses provide selective pressure for predators to evolve ways to overcome  Coevolution: evolution of predators and prey together o Many prey species hAve evo;ved chemical defenses to discharge predators o Often advertised by bright colors  Batesian mimcry: nonharmful species evolves physically resemble a harmful species  Imitates warning signals  Symbiosis: two or more organisms interacting in a long-term relationship o 3 types: o Mutualism: both species benefit from relationship o Parasitism: one species benefits at expense of one another o Commensalism: one species benefits while the other is neither directly helped nor harmed Ecosystem : community of organisms plus non-living component(e.g. atoms, river, rocks, energy,etc.)  Biogeochemical cycles o Matter is neither created or destroyed o Certain compounds and elements are re-used in cycles  Carbon cycle o Organic molecules are based on carbon or built primarily on carbon o CO2 in the air, bicarbonate in water o Fixed into organic compounds by photosynthesis o Heterotrophes eat photosynthetic organisms or their products o Cellular respiration releases carbon as CO2 o When organisms die, decomposition releases carbon as CO2  Water cycle o Living things absolutely need water o Its our Solvent o Water evaporates from lakes to oceans etc. o Heat (energy from the sun) causes this evaporation o Water vapor in the air condenses to rain  Nitrogen cycle o Proteins and nucleotides contain nitrogen o Vital element o Nitrogen in the air (N2)is fixed into usable form(NH3-amonia) by special bacteria o N2 is highly abundant in air but NH3 is often limited in soil o Decomposing bacteria convert fixed nitrogen back to N2  Phosphorus cycle o Phosphorus needed for nucleic acids, lipids, ATP, etc o Vital to element o No gas form, no fixation required o Used by living organisms, broken down to soluble phosphate  LIMITS ON GROWTH ON LIFE IN AN ECOSYSTEM ARE DEFINED BY THE NUTRIENT OR COMPOUND THAT IS MOST LIMITED  Trophic levels o Position of an organism in a food chain o 1) primary producers  Are autotrophs: makes organic compounds from in organics compounds o 2) herbivores  Are heterotrophs: get organic compounds from other organics o 3) primary carnivores  Heterotrophs  Eat herbivores o 4)secondary carnivores  Heterotrophs  Eat primary carnivores o X) detrivores  Heterotrophs  Feed on/break down dead organic matter  ENERGY ENTERS MOST SYSTEMS FROM SUN WITH EACH STEP OF FOOD CHAIN, ENERGY IS CONVERTED TO HEAT o Because of the chemical reactions in cellular respiration  Trophic cascade: species in one trophic level of an ecosystem can affect species in other trophic levels o Top-down trophic cascade  Initial effect on an upper trophic level affects lower trophic levels o Bottom-up trophic cascade  Initial effect on lower trophic level affects higher trophic levels o FOOD CHAINS AND TROPHIC CASCADES CAN BE VERY COMPLEX WITH MANY DIFFERENT SPECIES INVOLVED/AFFECTED The relationship between the species in an ecosystem can be disrupted by invasive species. Invasive species: non-native species that have been introduced into an ecosystem (usually by human actions) and cause harm to the native species  Invasive can: o Out compete the native species for resources  Kudzo intodused to prevent soil erosion but it just took over and covers everything o Damage the non-living components of an ecosystem o Be toxic to local predators o Spread rapidly throughout an introduced area o Prey on native species that are not accustom to a certain kind of predator  Prey can be plants or animals o Isolated island ecosystems (e.g austrailia) are particularly affected by invasive species o Directly affect human activities  IMPORTANT FOR HUMANS TO NOT INTRODUCE MORE POTENTIALLY INVASIVE SPECIES TO THE ECOSYSTEM  INTRODUCED SPECIES: non-native species that have been introduced into an ecosystem (usualy by human actions) but do not cause harm to native species


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