Essay Exam 1- Ch. 5,7,8 – Flashcards
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| Catabolism |
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| breakdown of molecules release of energy |
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| Anabolism |
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| building of molecules energy investment |
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| Oxidation |
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| removal of electrons (often in the form of H atom) |
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| Reduction |
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| gain of electrons net loss of charge |
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| Electron carrier molecules (2 types) |
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| NAH+ and FAD (become NADH and FADH2) |
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| Metabolism |
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| All chemical reactions within a living organism |
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| Activation Energy |
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| energy needed to start a reaction. This energy investment is the reason for slow reaction rate. |
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| Substrate Specificity |
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| 3D structure of enzyme makes active site that only specific substrates can bind to. |
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| co-enzyme |
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| non-protein portion that enables substrate to bind to the enzyme. |
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| What is the role of ATP in the cell? |
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| energy bridge between catabolic and anabolic reactions- redox |
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| What are the three parts of ATP? |
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| pentose sugar, phosphate groups, and adenosine base |
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| Cellular Respiration |
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| redox reaction where the energy released in the transfer of electrons (oxidation) from one compound to another is stored in the bonds of phosphates creating ATP |
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| 3 energy sources |
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| carbohydrates fats proteins |
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| Cellular respiration |
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| complete breakdown of carbs- max ATP |
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| What defines if you have aerobic or anaerobic respiration? |
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| presence or absence of final electron acceptor |
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| Where does prokaryote carbohydrate catabolism (respiration) occur? |
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| cyctoplasm |
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| Where does eukaryote carbohydrate catabolism occur? |
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| Partially in cyctoplasm (glycolysis) and the rest in the mitochondria. |
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| What are the two steps in glycolysis? (give steps and their investments or byproducts) |
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| Energy investment (2 ATP) Lysis (create two pyruvate which generates 2 ATP and 2 NADH) |
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| what type of phosphorylation is used in glycolysis? |
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| substrate level |
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| Define substrate level phosphorylation |
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| inorganic phosphate is directly attached to ADP with the help of an enzyme |
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| what are the end products for ONE molecule of glucose through glycolysis? |
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| 2 ATP 2 NADH 2 pyruvic acid |
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| What organisms most commonly use fermentation for energy generation? |
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| prokaryotes and single celled organisms |
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| What is the purpose of Fermentation in cells? |
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| Regenerate the NADH formed in glycolysis so it can return to accept the electrons from the cleaved glucose and generate the 2 ATP. 2 H are added to pyruvate to make lactic acid/ethanol |
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| What are the byproducts of fermentation(for both prokaryotes and eukaryotes) |
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| Prokaryotes: 2NAD+, 2 CO2, 2 ethanol (or other acidic molecule) Eukaryotes: 2NAD+, 2 Lactic acid |
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| List the steps or cellular respiration |
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| 1. glycolysis 2. Acetyl Co A production 3. Krebs Cycle 4. ETC (electron transport chain) |
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| What happens to pyruvate before it enters the krebs cycle? |
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| It is converted to Acetyl CoA by bonding to CoA. One CO2 is removed resulting in net 2 CO2 and 2 NADH from one glucose entering the Krebs cycle |
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| Where does Krebs occur in eukaryotes? |
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| Matrix of the mitochondria with the ETC located on the cristae of the mitochondria membrane |
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| What are the end products for Krebs cycle per ONE glucose? |
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| 2 ATP 2 FADH2 6 NADH 4 CO2 |
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| What are the 4 transport proteins of the ETC? |
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| flavoproteins ubiquinones metal-containing proteins cytochromes |
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| What is the goal of the ETC? |
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| reduce NADH and FADH2 by accepting their electrons and using them to pump H ions out of the mitochondrial cristae. |
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| What happens to the electrons as they reach the final ETC protein? |
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| The e- is attached to a final electron acceptor such as Oxygen which generates a much less harmful water molecule. |
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| How is ATP made from the high H concentration generated by the ETC? What is this process called? |
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| H+ ions move through ATP synthase due to proton motive force (high to low conc) which adds inorganic phosphate to ADP. Called chemiosmosis |
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| How many ATP are made by the ETC? Net ATP from cellular respiration? |
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| approx 34 ATP for ETC and 38 total ATP |
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| What are some of the final electron acceptors for anaerobic respiration? |
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| nitrates, nitrites, sulphates, CO2, Iron3, etc. |
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| How are lipids used in cellular respiration? |
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| Fatty acid chains are broken down into 3 carbon chains of pyruvic acid which enter the Krebs cycle. |
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| How are proteins used in cellular respiration? |
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| Proteases (outside the cell) break down proteins and remove amine (N) to be recycled or disposed of. Carbon molecules enter the Krebs cycle. |
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| Purine N bases |
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| Adenine Guanine |
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| Pyrimidine N bases |
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| Thymine Cytosine |
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| How are chromosomes and bacterial DNA packaged? |
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| around protein histones |
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| Genotype |
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| linear composition of genetic information made of nucleic acids |
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| Phenotype |
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| physical characteristic that results from the genotype. |
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| What are three differences between DNA and RNA |
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| RNA is single stranded Uracil instead of Thymine Ribose instead of deoxyribose |
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| 3 types of RNA |
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| ribosomal RNA (rRNA) messenger RNA (mRNA) transfer RNA (tRNA) |
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| which way to you read DNA and which way do you make DNA? |
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| read 3 to 5 create 5 to 3 |
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| What is the role of DNA helices? |
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| unwinds DNA. DNA gyrase removes super coils |
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| Role of Primase in DNA replication |
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| Adds a short RNA primer for DNA Polymerase to attach to for replication |
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| Role of DNA Polymerase |
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| Adds nucleotides starting at the RNA primer. Read DNA in the 3 to 5 direction and creates a new strand in the 5 to 3 direction |
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| What happens to DNA after it is replicated? |
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| form of DNA polymerase edits and repairs the new strand. Once the editing is completed, the daughter strand is methylated by adding a methyl group added throughout the strand |
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| what is the central dogma? |
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| DNA specifies the sequence of RNA which specifies proteins |
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| Where does RNA synthesis begin and what directions is it made? |
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| Begins at initiation site (promoter) on coding strand of DNA and synthesizes in 5 to 3 direction |
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| How is RNA processed after synthesis? |
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| Ribozymes remove introns from segment so you are only left with coding RNA. (this happens BEFORE the RNA leaves the nucleus) |
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| What direction do ribosomes read mRNA? |
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| 5 to 3 |
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| 2 ways mutations can occur |
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| errors during replications recombination (crossing over) |
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| 3 types of mutations (classes) |
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| neutral (silent) harmful beneficial |
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| Neutral (silent) mutation |
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| single base change (substitution) where no change in AA sequence results (due to redundant code) |
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| Harmful Mutations (3 types) |
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| 1. Missense (substitution)- change in nucleotide that results in different AA 2. Nonsense (substitution)- change in nucleotide that results in appearance of stop codon 3. Frameshift- insertion or deletion of nucleotide that results in shift in the reading frame of codons |
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| Beneficial Mutations (examples) |
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| sickle cell resulting in malaria resistance drug resistance |
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| Genetic recombination |
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| exchange of DNA segments of homologous sequences of DNA (recombinants). Known as crossing over |
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| Vertical gene transfer |
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| passing genes to the next generation |
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| Horizontal gene transfer |
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| transfer of genes among members of the same generations (donor sometimes dies) |
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| Transformation |
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| Competent cells pick up DNA from environment Discovered by Griffith in 1928 |
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| Griffith's Experiment |
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| mixed heat treated cells (S) with capsule plasmid with living R strain cells (typically not deadly) and the R cells were able to pick up the capsule plasmid to kill the host (demonstrates transformation) |
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| Transduction |
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| Transfer of host DNA via bacteriophage vector |
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| Conjugation |
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| transfer of cellular plasmids through pili. Must contain F+ plasmid to form sex pili |
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| HFr (high frequency recombination) |
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| If plasmid integrates with genomic DNA, it results in Hfr cell. During conjugation, cells can transfer their plasmid and genomic DNA- usually incomplete due to large size. |
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| DNA recombination |
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| intentionally modifying the genomes or organisms for practical purposes- artificial or natural processes. |
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| 3 goals of DNA recombination |
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| 1. eliminate undesirable phenotypic traits (humans, animals, plants, etc.) 2. Combine beneficial traits of two or more organisms 3. create organisms that synthesize products humans need (insulin) |
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| examples of genetic engineering (3) |
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| diabetes/insulin Growth Hormone Pest resistant foods |
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| Basic process for genetic modification |
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| 1. observe a trait of interest 2. change or insert a gene in an attempt to modify the organism 3. Look for phenotypic changes 4. repeat or modify as needed. |
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| Reverse transcriptase |
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| retrovirus enzyme that converts RNA to DNA (cDNA). Used because we can harvest RNA (which lacks introns) and can convert back to DNA for insertion into the genome. |
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| Synthetic Nucleic Acids- define and give uses (4) |
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| produce synthetic DNA and RNA probes -locate sequences on genes (fluorescent DNA probes) -determine genetic code of an organism -create genes for specific proteins -create antisense DNA to interfere with genes |
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| Restriction Enzymes (what do they do, where do they come from, what are they used to do, what are the two types?) |
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| 1. Bacterial enzymes that cut DNA at specific locations (restriction sites) 2. Found in bacteria- defense against phages 3. used to cut desired DNA and insert into host or vector DNA 4. Sticky and blunt ends |
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| Gel Electrophoresis |
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| separating molecules of DNA based on charge, size, and shape. Allows isolation of specific DNA segments. |
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| Gel Electrophoresis - what is the charge of DNA and what is the DNA drawn toward? |
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| DNA has negative charge and is drawn toward positive electrode |
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| What is the gel material used in Gel Electrophoresis? |
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| Agarose |
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| Gel Electrophoresis - determining fragment size |
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| smaller fragments migrate further. can determine size by comparing distances migrated to curve of standards |
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| Southern Blot (what is it and what is it used to do?) |
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| DNA is transferred from gel to nitrocellulose paper Used for: -genetic fingerprinting -diagnosis of infectious diseases -demonstrate prevalence of an organism that cannot be cultured -DNA microarrays |
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| PCR (Polymerase Chain Reaction) |
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| used to replicate DNA molecules in high numbers |
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| PCR materials |
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| -DNA sample -Primers -Nitrogenous bases -Heat resistant DNA polymerase (Taq polymerase) -Thermocycler |
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| Heat-resistant DNA Polymerase (Taq)- where is it found and why do we use it? |
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| found in thermophilic bacteria -used because it is not denatured by the heat of the thermocycler |
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| 3 steps of PCR |
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| 1. Denaturation 2. Annealing of Primers- Priming 3. Extensions |
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| PCR- Step 1 (Denaturation) |
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| DNA sample heated to 94 degrees C to denature the dsDNA. This allows binding of primer |
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| PCR- Step 2 (Annealing of Primers) |
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| Temp lowered to 55-65 degrees C- Allows primers to bond to target DNA |
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| PCR - Step 3 (Extension) |
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| Temp raised to 72 degrees C (optimum for Taq polymerase) Taq binds to DNA which synthesizes new strands using old templates. |
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| Plasmids (natural vectors)- why are they useful? 4 |
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| 1. Easily picked up by bacteria 2. can be isolated from bacteria 3. can be generically engineered outside the bacteria 4. can be manipulated in the lab |
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| How do you manipulate a plasmid? |
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| Use an endonuclease to cleave the plasmid and DNA in the same place and then the DNA may recombine into the plasmid. |
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| Natural Methods of Plasmid Insertion |
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| Transformation Transduction Conjugation |
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| Artificial Methods of Plasmid Insertion |
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| Electroporation (electrical shock to induce competency for DNA uptake) Protoplast fusion (remove cell walls from protoplasts and merge cells using polyethylene glycol) Injection- gene gun and microinjection |
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| Uses for Recombinant DNA Technology |
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| Pharm applications- protein synthesis, vaccines Genetic Screening (checking family mutations) DNA fingerprinting (crime scenes and paternity testing) Gene Therapy (replacing defective genes with normal copies- immunodeficiency and other diseases) Xenotransplant (growing human organs and tissues on animals) |
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| Agricultural Application of genetic engineering |
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| -Transgenic organisms -herbicide resistance -salt tolerance -freeze resistance -pest resistance -improve nutritional value and yield |
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| What are the major differences between eukaryotic and prokaryotic protein synthesis? |
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| 1. prokaryotes can form chains of ribosomes that process a single strand of RNA as it's being transcribed 2. Eukaryotes edit mRNA before sending outside the nucleus for translation 3. 70s vs 80s ribosomes |
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| what is added to mRNA before translation? (eukaryotic) |
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| cap and poly A tail |
