Topic 5: Molecular Genetics

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Alfred Hershey and Martha Chase
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-Figured out DNA was the basis of genetic material -Used bacteriophages, viruses that infect bacteria
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James Watson and Francis Crick
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-Structure of DNA -Used X-ray crystallography
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X-ray crystallography
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-Process used to visualize molecules three-dimensionally
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4 Major features of DNA
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1. DNA is a double helix 2. Sugar (deoxyribose) attached to a nitrogen base 3. A to T, G to C 4. Antiparallel
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Double helix
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-Side of sugar-phosphate components, with rungs of nitrogenous bases
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Antiparallel
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-Left side runs 5′ to 3′ while the opposite strand runs 3′ to 5′
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Replication
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-Making of DNA from an existing DNA strand
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DNA polymerases
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-Catalyzes the elongation of new DNA at the replication fork
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Leading strand
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-DNA replication occurs continuously along the 5′ to 3′ strand
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Lagging strand
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-Runs 3′ to 5′ is copied in series of segments
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Okazaki fragments
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-Lagging strand is synthesized in separate pieces
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DNA ligase
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-Sealed together DNA
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Accuracy of DNA replication
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1. Specificity of base pairing 2. Mismatch repair 3. Nucleotide excision REPAIR
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Mismatch repair
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-Special repair enzymes fix incorrectly paired nucleotides
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Nucleotide excision repair
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-Incorrectly placed nucleotides are excised or removed by nucleases, and the gap left over filled in with the correct nucleotides
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Nucleases
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-Enzymes that remove incorrectly placed nucleotides
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Telomeres
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-Short, repetitive nucleotide sequences
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Chromatin
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-DNA and proteins packed together
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Euchromatin
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-Chromatin is in highly extended form
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Heterochromatin
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-Condensed chromatin
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Gene expression
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-Process by which DNA directs the synthesis of proteins
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One gene-one polypeptide hypothesis
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-Each gene codes for a polypeptide which can be a protein
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Transcription
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-Synthesis of RNA using DNA as a template
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Messanger RNA (mRNA)
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-Produced during transcription -Carries the genetic message of DNA to the protein-making machinery of the cell in the cytoplasm, the ribosome
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RNA processing
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-Turns pre-mRNA to mRNA
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Translation
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-Production of a polypeptide chain and are written as a series of three-nucleotide groups, called triplet code
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Template strand
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-Only one strand of the DNA is transcribed
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Codons
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-mRNA base triplets
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RNA polymerase
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-An enzyme that separates the two DNA strands and connects the RNA nucleotides as they base-pair along the DNA template strand
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Promoter
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-DNA sequence at which RNA polymerase attaches
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Terminator
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-DNA sequence that signals the end of transcription
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Transcription unit
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-Entire stretch of DNA that is transcribed into an RNA molecule
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3 main stages of Transcriptopn
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1. Initiation 2. Elongation 3. Terminatin
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Initiation
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-RNA polymerase recognizes and binds to the promoter
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Transcription factors
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-Assist the binding of RNA polymerase to the promoter and the initiation of transcription
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Transcription initiation complex
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-Whole complex of RNA polymerase II and transcription factors
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Elongation
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-RNA polymerase moves along the DNA untwisting the double helix -RNA nucleotides added to the 3′ end -Double helix re-forms, with the new RNA molecule strangling away from the DNA template
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Termination
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-After RNA polymerase transcribes a terminator sequence in the DNA, the RNA transcript is released, and the polymerase detaches
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Key post-transcriptional modifications
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-5′ cap -poly- A tail
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RNA Splicing
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-Large portions of the newly synthesized RNA strand are removed
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Introns
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-Sections of the mRNA that are spliced out
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Exons
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-Sections that remain and subsequently spliced together by a spliceosome
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Small nuclear RNA (snRNA)
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-Catalyzes the excision of the introns and joining of the exons
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Ribozyme
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-When RNA serves as a catalyst
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tRNA
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-Transferring amino acids from a pool of amino acids in the cell’s cytoplasm to a ribosome
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Anticodon
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-A nucleotide triplet allows it to pair specifically with a complementary codon on the mRNA
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Codon
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-An mRNA triplet -64 different codon
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rRNA
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-Complexes with proteins to form the two subunits that form ribosomes
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Wobble
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-Relaxation of base-pairing rules
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P site
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-Holds the tRNA that carries the growing polypeptide chain
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A site
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-Holds the tRNA that carries the amino acid that will be added to the chain next
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E site
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-Exit site for tRNA
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3 stages of Translation
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1. Initiation 2. Elongation 3. Termination
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Initiation (Translation)
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Elongation (Translation)
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1. Codon recognition 2. Peptide bond formation 3. Translocation
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Termination (Translation)
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-A stop codon in the mRNA is reached and translation stops -Release factor binds to the stop codon and the polypeptide is freed from the ribosome
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Signal peptide
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-Sequence of the leading 20 or so amino acids directing proteins to their final destination
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Mutation
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-Alterations in the genetic material of the cell
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Point mutation
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-Alterations of just one base pair of a gene
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Nucleotide-pair substitution
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-Replacement of one nucleotide and its partner with another pair of nucleotides
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Missense mutations
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-Substitutions that enable the codon to still code for an amino acid, may not be correct one
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Nonsense mutations
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-Substitutions that change a regular amino acid codon into a stop codon, ceasing translation
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Insertions
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-Additions of nucleotide pairs in a gene
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Deletions
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-Losses of nucleotide pairs in a gene
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Frameshift mutation
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-Causes the mRNA to be read incorrectly
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Mutagens
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-Substances or forces that interact with DNA in ways that cause mutations
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Operon
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-Genes are often clustered into units
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Operator
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-Controls the access of RNA polymerase to the genes -Found within the promoter site or between the promoter and the protein coding genes of the operon
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Promoter of operon
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-Where RNA polymerase attaches
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Genes of the operon
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-Entire stretch of DNA required for all the enzymes produced by the operon
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Regulatory genes
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-Produce repressor proteins that may bind to the operator site
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Repressible operon
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-Normally on but can be inhibited -Normally anabolic, building an essential organic molecule
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Corepressor
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-Binds to the repressor protein, activating it
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Inducible operon
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-Normally off but can be activated -Normally catabolic, breaking down food molecules for energy
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Inducer
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-A specific small molecule binds to and inactivates the repressor protein
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Differential gene expression
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-Expression of different genes by cells with the same genome
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DNA methylation
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-Addition of methyl groups to NA -Causes DNA to be more tightly packed, reducing gene expression
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Histone acetylation
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-Acetyl groups are added to amino acids of histone proteins, making the chromatin less tightly packed and encouraging transcription
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Epigenetic inheritance
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-Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence
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Transcription initiation
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-Control point in gene expression -DNA control elements that bind transcription factors are involved in regulation
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Transcription initiation complex
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-Enhances gene expression
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Enhancer regions
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-DNA sequences from the gene
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Activators
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-Proteins that bind DNA sequences to the promoter region
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micro RNAs (miRNA)
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-Bind to mRNA and degrade the mRNA or bind to mRNA and block its translation
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small interfering RNAs (siRNAs)
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-Bind to mRNA and degrade the mRNA or bind to mRNA and block its translation
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Zygote transformations
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1. Cell division 2. Cell differentiation 3. Morphogenesis
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Cell division
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-Series of mitotic divisions that increases the number of cells
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Cell differentiation
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-Process by which cells become specialized in structure and finction
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Morphogenesis
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-Gives an organism its shape
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Cytoplasmic determinants
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-Maternal substances in the egg that influence the course of early development
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Cell-cell signals
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-Result from induction
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Induction
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-Molecules produced by one cell influencing neighboring cells, causing cells to differentiates
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Determination
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-A series of events that lead to observable differentiation of a cell -Caused by cell-cell signals and is irreversible
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Pattern formation
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-Set up the body plan and is a result of cytoplasmic determinants and inductive signals
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Morphogens
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-Plays a role in establishing differing features
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Homeotic genes
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-Master control genes that control pattern formation
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Oncogenes
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-Cancer-causing genes
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Proto-oncogenes
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-Genes that code for proteins that are responsible for normal cell growth
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Cancer
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-Caused by a mutation in a gene whose products normally inhibit cell division
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Tumor-suppressor genes
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-Genes that inhibit cell division
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p53 gene
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-Tumor-suppressor gene
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Apoptosis
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-Cell programed death
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Capsid
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-Protein shell that surrounds the genetic material
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Viral envelopes
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-Surround the capsid and aid the viruses in infecting their hosts
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Bacteriophages or Phages
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-Viruses that infect bacterial cells
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Host range
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-Viruses can infect only a very limited variety of hosts
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Lytic cycle
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-Ends in the death of the host cell by rupturing it (lysis) -Bacteriophage injects its DNA into a host cell and takes over the host cell’s machinery to synthesize new copies of the viral DNA
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Lysogenic cycle
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-Bacteriophage’s DNA becomes incorporated into the host cell’s DNA and is replicated along with the host cell’s genome
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Prophage
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-Viral DNA
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Retroviruses
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-RNA viruses that use reverse transcriptase to transcribe DNA from an RNA template
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Viroids
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-Circular RNA molecules several hundred nucleotides in length that infect plants -Causes errors in plant growth
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Prions
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-Misfolded, infectious proteins that cause the misfolding of normal proteins they contact in various animal species
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Genetic engineering
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-Process of manipulating genes and genomes
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Biotechnology
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-Process of manipulating organisms or their components for the purpose of making useful products
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Recombinant DNA
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-DNA that has been artificially made, using DNA from different sources
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Gene cloning
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-Process by which scientists can produce multiple copies of specific segments of DNA that they can work with in the lab
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Restriction enzymes
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-Used to cut strands of DNA
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Restriction sites
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-Specific locations where DNA is cut
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Restriction fragments
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-A set of DNA molecules after they have been cut by restriction enzymes
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Sticky ends
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-Single-stranded end
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Cloning vector
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-Carries the DNA sequence to be cloned and is often a bacterial plasmid
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Nucleic acid hybridization
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-Used to find the gene
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Genomic library
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-Set of thousands of recombinant plasmid clones, each of which has a piece of the original genome being studied
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cDNA library
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-Made up of complementary DNA made from mRNA transcribed by reverse transcriptase
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PCR
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-Method used to amplify a particular piece of DNA without the use of cells -Used to amplify DNA when the source is impure or scanty
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Gel electrophoresis
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-Lab technique used to separate macromoleculees
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Microarray assays
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-Genome-wide studies
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Restriction fragment length polymorphisms (RELPs)
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-Result from small differences in DNA and can be detected by electrophoresis -Allows for diagnosis of disease and answers paternity and identity questions
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Nuclear transplantation
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-Nucleus of an egg is removed and replaced with the diploid nucleus of a body cell
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Stem cells
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-Goal of human cloning
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Embryonic stem cells
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-Pluripotent, which means capable of differentiating into many different cell types -Use them for the repair of damaged or diseased organisms
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Uses of DNA tech
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1. Diagnosis of disease 2. Gene therapy 3. The production of pharmaceuticals 4. Forensic applications 5. Environmental cleanup 6. Agricultural applications -GM organisms
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Bioinformatics
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-Use of computers, software, and mathematical models to process and integrate the incredible volume of data from these sequencing projetcs
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Proteomics
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-Protein interactions are analyzed
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Systems biology
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-Aims to model the behavior of entire biological systems and is enhanced by bioinformatics
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Repetitive DNA
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-Sequences that are present in multiple copies in the genome
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Transposable elements
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-Repetitive DNA -Move from one location to another in the genome with the aid of transposase
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Transposons
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-Moves by means of a DNA intermediate
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Retrotransposons
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-Move by means of a RNA intermediate, and leave a copy at the original site -Involves reverse transcriptase
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Multigene families
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-Collections of two or more identical or very similar genes
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Evo-devo
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-A field of biology that compares developmental processes to understand how they may have evolved and how changes can modify existing organismal features or lead to new ones
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Homeotic genes
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-Master regulatory genes that control placement and spatial organization of body parts by controlling the developmental fate of groups of cells
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Homeobox
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-Widely conserved 180-nucleotide sequence found with homeotic genes -Found in many genes

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