Unit 3 – Freitag – Flashcards
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| Where does the energy needed to covalently bond ribonucleotides come from? |
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| Using the energy from the first phosphate bond of the ribonucleotide. |
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| Four type os RNA ribonucleotides |
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| rATP rUTP rGTP rCTP |
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| Primase Transcribes: RNA Polymerase Transcribes: |
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| Primase: RNA Primer RNA Poly: mRNA, rRNA, tRNA |
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| The strength of the promoter directly affects: |
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| The likelihood that transcription will take place. |
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| In bacteria this subunit of RNA polymerase is necessary for recognition of a promoter. |
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| Sigma Factor |
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| RNA Polymerase initially bonds to where? |
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| Promoter Sequences |
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| What enzyme synthesizes RNA |
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| RNA Polymerase |
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| Start Codon: |
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| AUG |
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| Stop Codons: |
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| UAA UAG UGA |
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| # of ribonucleotides in an tRNA molecule? |
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| 75 |
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| What is "Wobble" in reference to anticodon. |
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| Change of angle from normal axis that allows the third nucleotide to hydrogen bond to a nucleotide other than its compliment. |
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| Three sites on a ribosome involved in polypeptide formation. |
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| A - Amino Acid P - Polypeptide E - Exit |
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| Stages of Translation. |
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| Initiation Elongation Termination |
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| Steps of Translation Initiation: |
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| 1. Ribosomal subunit attaches to mRNA at a ribosome-binding site in a way that the start codon is in the P site. 2. tRNA attaches at the ribosome's P site. 3. The larger ribosomal subunit then attaches to form a complete initiaion complex. |
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| Steps of Translation Elongation: |
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| 1. The transfer RNA whose anticodon matches the next codon delivers its amino acid to the A site. 2. A peptide bond is formed between terminal amino acid of the growing chain and the newly introduced amino acid. 3. The ribosome then shifts the mRNA one position. 4. The ribosome releases the empty tRNA from the E site. |
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| Steps of Translation Termination: |
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| Proteins called release factors halt elongation and the ribosome dissociates into its subunits. |
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| Translation differences in Eukaryotes: |
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| 1. Initiation of translation in eukaryotes occurs when the small ribosomal subunit binds to the 5' guanine cap rather than a specific nucleotide sequence. 2. The first amino acid in eukaryotic polypeptides is methionine rather than formylmethionine. |
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| Two types of bacterial gene expression regulation: |
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| Induction Repression |
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| Inducible operons: |
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| Not usually transcribed and must be activated by inducers. |
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| Repressible Operons: |
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| Are transcribed continually until deactivated by a repressor. |
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| What are miRNA's? |
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| Micro RNA's made of 22 nucleotides that binds with RNA silencing complex either cleaves the mRNA molecule or binds to it blocking its entrance into a Ribosome. |
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| What are siRNA's? |
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| Double stranded RNA that binds with RNA silencing complex and blocks mRNA from binding with a ribosome. These are not natural, lab created. |
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| What is a riboswitch? |
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| A RNA molecule that changes shape in response to environmental conditions such as temp or concentration of nutrients. When activated it will fold to either favor or block translation. |
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| Example of an inducible operon: |
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| The lac operon - Lactose. |
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| Example of a repressible operon: |
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| The trp operon - Tryptophan. |
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| Define biotechnology: |
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| The use of microorganisms to make practical products. |
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| Tools of Genetic Engineering: |
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| 1. Mutagens 2. Reverse Transcriptase 3. Synthetic Nucleic Acids 4. Restriction Enzymes 5. Vectors |
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| What are mutagens? |
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| Physical and chemical agents that produce mutations. |
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| What is reverse transcriptase? |
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| Technique that creates a flow of genetic information in the opposite direction of conventional transcription. Therefore writing additional code to a cells DNA. |
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| What are synthetic nucleic acids? |
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| Lab grown nucleotides. |
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| What are restriction enzymes? |
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| Enzymes that cut DNA molecules at restriction sites (palindromes). |
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| Types of ends produced by restriction enzymes and a description. |
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| Sticky Ends: Ends are fragmented. CGA AGCTTCG GCTTCGA AGC Blunt Ends: Both strands cut at same point. CCCAAC GTTGGG GGGTTG CAACCC |
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| What are vectorsExamples of Vectors: |
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| Nucleic acid molecules used to transport and insert genes into cells. Examples: Viral Genomes, Transposons, and Plasmids |
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| Techniques of Genetic Engineering: |
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| 1. Polymerase Chain Reaction 2. Gel Electrophoresis 3. Southern Blot 4. DNA Microarrays 5. Inserting DNA into Cells |
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| What is Polymerase Chain Reaction? |
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| Technique by which scientists produce a large number of identical molecules of DNA in vitro. |
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| What is Gel Electrophoresis? |
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| Technique used to isolate fragments of DNA molecules that can be inserted into Vectors. |
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| What is Southern Blot? |
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| A method to transfer DNA from agarose gels to nitrocellulose membranes. |
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| What are DNA Microarrays? |
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| An array consisting of molecules of single-stranded DNA, which is immobilized on glass slides, silicon chips, or nylon membranes. |
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| Three artificial techniques for introducing DNA into cells: |
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| 1. Electroporation: Usage of electrical current to puncture tiny holes in the cells membrane so DNA can enter. 2. Protoplast fusion: Combining of DNA by increasing rate of fusion. 3. Injection: By micropipette. |
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| Some products produced by recombinant DNA Technology: |
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| Vaccines, DNA fingerprinting, Herbicides |
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| Parts of DNA: |
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| Deoxyribose Sugar Nitrogenous Base Phosphate Group |
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| Eukaryotic Genomes: Shape - Contained Within - |
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| Linear Shape Contained within the nucleus |
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| What are nucleosomes? |
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| DNA and Histones wrapped together. |
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| What are chromatin fibers? |
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| Nucleosomes clumped together with other proteins. |
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| Other than the nucleus where else can Eukaryotic DNA be found? |
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| Within mitochondria or chloroplasts. |
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| Define: Gene |
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| Specific sequences of nucleotides that code for polypeptides or RNA molecules. |
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| Describe: Base Pairs |
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| The specific way which one of 5 nitrogenous bases are hydrogen bonded to one another. |
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| Which base pair are triple bondedWhich are double bonded? |
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| Triple = Guanine and Cytosine Double = Adenine and Thymine |
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| The two strands of DNA are called(Hint: orientation) |
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| Antiparallel |
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| Which bacteria have histones? |
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| Archaea |
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| Direction of DNA synthesis: |
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| 5' to 3' direction |
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| Why is DNA replication called semi-conservative? |
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| New DNA is composed of 1 original strand and 1 daughter strand. |
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| What is a Heterochromatin? |
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| Closed, inactive DNA |
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| What is a Euchromatin? |
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| Open, active DNA. |
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| Genetic Recombination: Transduction and Steps |
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| The transfer of DNA from one cell to another via a replicating virus. 1. Phage injects its DNA 2. Phage enzymes degrade host DNA 3. Cell synthesizes new phages with phage and host DNA. 4. Transducing phage injects donor DNA into new cell. 5. Donor DNA is incorporated into recipient chromosome by recombination. |
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| Genetic Recombination: Transformation |
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| Recipient cell takes up DNA from the environment, such as DNA from dead organisms. -Mouse Experiment |
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| 3 Effects of Mutations |
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| Silent Mutation Missense Mutations Nonsense Mutations |
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| What is a Silent Mutation |
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| No change to amino acid sequence due to redundancy of genetic code. |
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| What is a Missense Mutation |
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| Triplet still codes a protein but is not the correct protein in the sequence, can prevent protein from forming correctly if in a critical area. |
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| What is a Nonsense Mutation |
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| Changes an amino acid into a stop codon. |
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| Types of Mutations |
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| Point Mutations Framshift Mutations Gross Mutations |
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| What are point mutations? |
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| One nucleotide base pair is affected. |
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| What are frameshift mutations? |
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| When insertions or deletions cause the entire sequence to shift. |
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| What are gross mutations? |
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| Large deletions, transpositions, or inversions of genetic sequences. |
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| Define: Mutation |
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| A permanent change in the nucleotide base sequence of a genome. |
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| What is an Operon? |
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| Section of DNA that includes a promoter, operator, and subsequent genes. Operon [----------------------------------------] {AAAA}{=Promotor=}{=Operator=}{=Gene1=}{=Gene2=}{AAAAAAA} |
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| What are triplets? |
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| A sequence of 3 nitrogenous bases. |
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| What are codons? |
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| Triplets of mRNA that code for a specific anti-codon or amino acid. |
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| What are anti-codons? |
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| Matching base pairs to codons, located on tRNA. |
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| What bases are methylated in: Bacteria Eukarya |
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| Bacteria: Adenine and rarely Cytosine Eukarya: Cytosin only. |
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| Differences in Eukaryotic and Bacteria DNA replication: |
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| 1. Eukaryotic uses four different polymerases. 2. Eukaryotic Okazaki fragments are shorter than bacterial. 3. Plants and animals methylate cytosine bases exclusively. 4. Large size of Eukaryotic chromosomes requires thousands of origins instead of one like bacterial cells. |
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| 4 Types of Eukaryotic Polymerases |
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| Alpha(1) - Initiates Delta(4) - Elongates Leading Strand Epsilon(5) - Replicates Lagging Strand Gamma(3) - Replicates Mitochondrial DNA |
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| Bacteria Archaea Eukarya # Chromo Plasmids DNA Shape DNA Locale Histones? |
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| |Bacteria | Archea | Eukarya |___________|___________|_________ # Chromo| Haploid | Haploid | Diploid |___________|___________|_________ Plasmid?| In some | In Some |FungiPro |___________|___________|_________ DNA Shp | Circular | Circular | Linear |___________|___________|_________ DNA Loc | Nucleoid | Nucleoid | Nucleus | Plasmids | Plasmids | Mitochon |___________|___________|_________ Histones| No | Yes | Yes |___________|___________|_________ |
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| Topoisomerase |
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| Removes supercoils during DNA replication of bacteria, and unwinds DNA for replication in eukaryotes. |
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| DNA Ligase |
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| Seals gaps between Okazaki Fragments of lagging strand. |
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| RNA Primer (Primase) |
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| Provides 3' hydroxyl group required by DNA polymerase. |
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| DNA Polymerase I |
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| Replaces RNA primer w/DNA |
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| DNA Polymerase III |
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| The usual enzyme of DNA replication in bacteria and mitochondria. |
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| DNA Polymerase |
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| Adds new nucleotides into open DNA strands. |
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| DNA Helicase |
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| Breaks hydrogen bonds. |
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| Why is one strand of DNA called the 3' strand? |
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| Because it ends with a hydroxyl group bound to the 3' carbon. |
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| Why is one strand of DNA called the 5' strand? |
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| Because it ends with a phosphate group attached to the 5' carbon. |
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| Roles of Methylation in Bacteria (4) |
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| 1. Control genetic expression 2. Initiation of DNA replication 3. Protection against viral infection 4. Repair DNA |
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| DNA Replication: Steps (5) Lagging Strand |
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| 1. Primase synthesizes RNA primers, instead of 1 like leading strand it inserts one every 1000-2000 DNA base pairs. 2. Nucleotides pair up compliments. 3. DNA Polymerase 3 joins nucleotides into Okazaki fragments. 4. DNA polymerase 1 replaces RNA primers of okazaki fragments and proofreads. 5.DNA ligase seals gaps between okazaki fragments. |
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| DNA Replication: Steps (5) Leading Strand |
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| 1. Enzyme primase synthesizes a short RNA molecule complementary to DNA strand. 2. Triphosphate deoxyribonucleotides form compliments. 3. Using energy from Triphosphate deoxyribonucleotides, DNA polymerase 3 forms covalent bonds. 4. DNA Polymerase 3 proofreads the strand. 5. DNA polymerase 1 replaces RNA primer w/DNA. |
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| Enzyme responsible for Proofreading Replicated DNA and correcting errors? |
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| Proofreading Exonuclease |
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| DNA Replication: Initial Steps (4) |
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| 1. Proteins and histones are removed. 2. DNA Helicase separates strands. 3. DNA Polymerase binds to each strand. 4. Begin leading and lagging strand synthesis. |
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| Types of Plasmids and their Functions |
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| Fertility - instructions for conjugation Resistance - carry genes for resistance to drugs. Bacteriocin - produce toxins to kill competititve bacteria. Virulence - carry instructions for structures, enzymes, or toxins that enable it to be pathogenic. |
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| Prokaryotic Genomes: Where is DNA storedWhere are chromosomes located? |
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| In Chromosomes or plasmids. Within the nucleoid region. |
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| Define: Genome |
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| The entire genetic compliment of a cell or virus. Including its genes and nucleotide sequences. |
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| Genetic Recombination: Conjugation (Process) |
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| 1. Bacteria connect via pili. 2. One strand of F plasmid DNA transfers to the recipient. 3. A single strand of plasmid DNA is synthesized to compliment the transfered single strand DNA. 4. The new double strand DNA is now a fully formed plasmid within the recipient cell. |
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What is gene therapy?
Risks? Benefits? Limitations? |
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A process where missing or defective genes are replaced with normal copies.
Risks: Unexpected Results Benefits: Curing "uncurable" diseases. Limitations: Limited to only certain diseases. |
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| Human genetic defects targeted by gene therapy. |
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| Cystic Fibrosis Sickle-cell anemia Hemophilia Diabetes |
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| What is DNA Fingerprinting |
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| Technique to identify unique sequences of DNA. |
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| What are some applications for DNA Fingerprinting? |
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| Paternity Investigations Crime Scene Forensics Diagnostic Microbiology Epidemiology |
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| What is "Antisense" DNA Technology? |
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| The technique of using nucleic acid molecules that have nucleotide sequences that bind to and interfere with genes and mRNA molecules. |
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| What is a GMO? |
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| Genetically modified organism, used to produce proteins and enzymes not typically found within said organism. |
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| Novel properties of Viruses: |
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Inert outside of a cell, becomes active inside. Do not divide or grow. Acellular Obligate intracellular parasites. Contain either DNA or RNA, never both. Genome can be dsDNA, ssDNA, dsRNA, ssRNA. Ultramicroscopic. Have a proteinaceous capsid around genome. Replicate in an assembly-line manner using host cell functionality. |
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| General size of a virus is measured in? |
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| Nanometers |
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| When a virus is outside of a cell it is referred to as a? |
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| Virion |
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All virions have these basic parts:
Some also have: |
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All: Capsid and a Nucleic Acid Core
Some: Envelope (Phospholipid membrane)
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| The term referring to a capsid and its nucleic acid core is: |
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| Nucleocapsid |
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| The outermost layer of a virus, either the capsid or envolope provides these funcitons: |
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| Protection and recognition sites for specific hosts. |
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| Define: Capsid |
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| Protein coating surrounding nucleid acid core of a virus. |
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| Define: Capsomere |
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| The proteinaceous subunits of a capsid. |
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| A virus that infects bacteria is called? |
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| Bacteriophage |
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| Name given to viruses that will infect many types of cells in many different hosts. |
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| Generalists |
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| Virus is latin for: |
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| Poison |
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| Smallest Virus size: Largest Virus size: |
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| Smallest: 10nm Largest: 400nm |
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| Define: Matrix Protein |
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| Proteins that fill the region between capsid and envelope. |
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| Define: Viral Envelope |
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| A membrane located externally to the viral capsid. |
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| How does a capsid acquire a viral envelope? |
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| When a virus is released from a host cell it is coated with a portion of the host cells external membrane. |
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| In addition to the viral envelope what else does the virus pick up while being exocytosed? What are these used for? |
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| Glycoproteins, used for recognition of like cells. |
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| Chemical Composition of Capsomer: |
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| Protein |
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| Chemical Composition of Capsid: |
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| Protein |
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| Chemical Composition of Viral Genome: |
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| Nucleic Acid |
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| Chemical Composition of Viral Envelope: |
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| Phospholipid Bilayer and Proteins |
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| Chemical Composition of Viral Spike: |
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| Glycoprotein |
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| Five stages of viral replication: |
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| 1. Attachment 2. Entry 3. Synthesis 4. Assembly 5. Release |
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| Viral Replication: Explain Attachment |
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| Connecting of the virion to a host cell. |
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| Viral Replication: Explain Entry |
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| A virion or its genome entering a host cell. |
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| Viral Replication: Explain Synthesis |
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| Creation of new nucleic acids and viral proteins by the host cell's enzymes and ribosomes. |
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| Viral Replication: Explain Assembly |
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| Building of new virions within the host cell. |
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| Viral Replication: Explain Release |
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| Virions leaving the host cell either by lysing or exocytosis. |
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| How does lysogenic replication differ from lytic replication? |
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| During lysogenic replication the viral DNA/RNA remains inert until and environmental trigger activates it. While inert it is inserted into the DNA of the host and is replicated with each cell division. |
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| An inactive bacteriophage is called: |
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| Prophage |
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| 3 Ways animal viruses can penetrate a host cell? |
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| 1. Direct Penetration 2. Membrane Fusion 3. Endocytosis |
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| Additional step that animal viruses must do after entering host cell: |
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| Uncoating the Capsid. |
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| For the genome: dsDNA How is mRNA synthesizedWhat molecule is template for Genome Replication? |
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| mRNA Synth: RNA Polymerase (in nucleus or cytoplasm) Molecule: Each strand of DNA serves as template for its compliment. |
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| For the genome: ssDNA How is mRNA synthesizedWhat molecule is template for Genome Replication? |
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| mRNA Synth: RNA polymerase (in nucleus) Molecule: Complementary strand of DNA is synthesized. |
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| For the genome: +ssRNA How is mRNA synthesizedWhat molecule is template for Genome Replication? |
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| mRNA Synth: Genome acts as mRNA Molecule: -RNA complementary to the genome is synthesized to act as template. |
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| For the genome: +ssRNA (Retroviridae) How is mRNA synthesizedWhat molecule is template for Genome Replication? |
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| mRNA Synth: DNA from RNA using reverse transcriptase. mRNA is transcribed from DNA by RNA polymerase. Molecule: DNA |
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| For the genome: -ssRNA How is mRNA synthesizedWhat molecule is template for Genome Replication? |
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| mRNA Synth: RNA dependent RNA transcriptase Molecule: +mRNA (compliment to viral genome) |
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| For the genome: dsRNA How is mRNA synthesizedWhat molecule is template for Genome Replication? |
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| mRNA Synth: Positive strand of genome acts as mRNA. Molecule: Each strand acts as template. |
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| Steps of Animal Virus Replication: (6) |
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| 1. Attachment 2. Penetration 3. Uncoating 4. Synthesis 5. Assembly 6. Release |
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| What term describes a nonenveloped virus? |
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| Naked |
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| Name given to viruses that shed from host cell slowly and relatively steadily without killing the host cell. |
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| Persistent infections. |
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| Two ways naked viruses are released from host cells: |
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| Exocytosis or by cell lysis. |
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| Examples of latent viruses: |
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| Herpes and Chicken Pox |
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| Define: Lysogenic Conversion |
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| Conversion of a harmless form of bacteria to a pathogenic form. |
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| Difference in Latency vs. Lysogeny |
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| In latency the viral DNA does not necessarily become incorporated into the host DNA. |
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| Uncontrolled cell division in a multicellular animal is called: |
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| Neoplasia |
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| Define: Oncogenes |
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| Active genes that control cell division rate. |
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| Factors that contribute to the inhibition of oncogene repressors and the activation of oncogenes: |
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| UV Light Radiation Carcinogens Viruses |
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| How are viruses classified? |
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| DNA or RNA strand type. |
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| Define: Viroids |
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| Extremely small, circular pieces of RNA that are infectious and pathogenic to plants. |
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| Define: Prions |
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| Proteinaceous infective particles. |
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| How do Prions infect cells? |
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| By hijacking the cellular membrane protein PrP of the host and converting it to prion PrP. |
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| Examples of diseases associated with Prions: |
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| Mad Cow Disease (Bovine Spongiform Encephalitis) Scrapie in sheep. Kuru Chronic Wasting Disease in deer and elk. Creutzfeldt-Jakob disease in humans. |
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| A virus that is specific for a bacterial host is called a: |
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| Phage |
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| Name 3 criteria for specific family classification of viruses: |
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| 1. Type of nucleic acid. 2. Envelope Structure 3. Capsid Type |
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| A clear zone of phage infection in a bacterial lawn is: |
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| A Plaque |
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