Ap Biology - Modern Genetics free essay sample

DNA is the template (3’ to 5’) ! 3. RNA Polymerase Binds to promoters, separates strands of DNA and ! hook together RNA nucleotides (only add to 3’ end) ! a. TATA Box Where RNA polymerase H binds (eukaryotes) ! ! b. Transcription Factors Aid polymerase in locating promoters ! ! such as the TATA Box ! ! c. Reads in sets of 3 called codons. ! 4. Termination site on DNA indicates end in prokaryotes ! 5. Eukaryotes Pre-mRNA separates from DNA at the polyadenylation ! signal, but RNA polymerase continues to transcribe until it falls off the ! DNA. C. Pre-mRNA processing in eukaryotes ! 1. Heterogenous nuclear RNA (hnRNA) contains introns and exons. ! ! a. Introns not used (stay IN nucleus) ! ! b. Exons used (EXIT nucleus) ! 2. Small nuclear ribonucleic proteins (snRNP’s/snurps) help excise introns ! and fuse exons. ! 3. Splicosomes Snurps and proteins working together ! 4. Poly A tail is added to 3’ end which a 5’ cap is added to the 5’ end. ! ! a. Prevent damage to mRNA as it leaves nucleus ! ! b. Helps mRNA leave nucleus ! ! c. Helps mRNA attach to ribosome. D. rRNA Formed in nucleoli, makes up part of ribosome. ! 1. Ribosomes Binding site for rRNA. E. Translation ! 1. Initiation Brings mRNA and tRNA together by means of factors (start ! codon is AUG) ! 2. Elongation Amino acids are added with aide of elongation factors. ! ! a. Codon Recognition mRNA codon on A site forms H bonds with ! ! anticodon of incoming tRNA. ! ! b. Aminoacyl tRNA synthetase matches amino acid with correct ! ! tRNA ! ! c. Peptidyl transferase catalyzes the formation of a peptide bond ! ! between polypeptide at P site and amino acids at A site. ! ! d. Wobble Effect Exact base pairing is not always necessary. ! 3. Translocation ! ! a. A site on ribosome holds tRNA carrying the next amino acid to be ! ! added. ! ! b. P site on ribosome holds tRNA carrying the growing polypeptide ! ! chain. ! ! c. E site is where it exits. F. Termination Indicated by termination codons (UAA, UAG, UGA) ! . Release Factor Protein which binds to termination codon on A site ! causing hydrolysis reaction and freeing the polypeptide. ! 2. Posttranslational modi? cations now take place Protein goes into ! secondary, and tertiary structure. AP Bio Modern Genetics IV. Mutations ! A. Point Mutations Chemical changes in one or a few nucleotides. ! ! 1. Base Pair Substitutions Replacement of one nucleotide and its partner ! ! from a complementary DNA strand with another pair of nucleotides. ! ! ! a. Missense Mutations Altered codons still code from amino acids ! ! ! but don’t always make sense. ! ! b. Nonsense Mutations Change amino acids codon to a stop ! ! ! signal (most result in nonfunctional codons) ! ! 2. Insertions and Deletions Additions or losses of one or more nucleotide ! ! pairs in a gene. ! ! ! a. Frameshift Mutation Alters reading from (usually nonfunctional) ! B. Mutagenesis Creation of mutations ! ! 1. Hermann Muller discovered that genetic changes occurred when fruit ! ! ? ies were exposed to X-Rays. ! ! 2. Spontaneous mutations result from errors in DNA replication, repair, or ! ! recombination. ! ! 3. Mutagens Physical and chemical agent which cause mutations. Chapter 18 The Genetics of Viruses and Bacteria I. Viruses ! A. Wendell Stanley (American-1935) crystallized particle, now called tobacco ! mosaic virus (TMV) ! B. Genomes May be double or single stranded DNA or RNA. ! C. Capsid Protein shell enclosing genome, built from capsomere ! D. Phages Virus which infects bacteria. ! E. Lack enzymes for metabolism and have no ribosomes, nonliving ! F. Vaccine Harmless variation which stimulates immune response (? rst made ! from cowpox) ! G. Viroids Tiny molecules of naked RNA, upset metabolism of plants ! H. Prions Infectious proteins ! ! 1. Often cause brain diseases like mad cow and scrapie in sheep ! ! 2. Not killed by heat, long incubation period II. Sources of New Viruses ! A. Mutations of current viruses ! B. Spread between species typically due to new exposure. ! C. Spread within species between a small population and the rest of the world. III. Replication and Infection ! A. Obligate intracellular parasites ! B. Basic Infection ! ! 1. Some recognize host by a â€Å"lock and key† ? t, and only infect certain cells ! ! of the body. ! ! 2. Genome Enters Cell Method varies (leaving ghost behind-empty ! ! capsid) AP Bio Modern Genetics ! ! ! ! ! ! ! ! ! ! ! ! ! 3. Genome reprograms cell to copy viral genes and manufacture capsid ! proteins. ! ! a. DNA viruses use DNA polymerases of host cell ! ! b. RNA viruses contain their own enzymes to initiate replication. ! 4. Self Assembly Assembly of capsids and nucleic acid molecules into ! viruses. ! 5. Viruses leave host cell C. Bacteriophages Virus which infect b acteria ! 1. Lytic Cycle Reproductive cycle which ends with death of host cell ! 2. Lysogenic Cycle Reproduces viral genome without destroying host ! ! a. Viral DNA is incorporated into bacterial DNA (prophage) ! b. Prophage is replicated every time bacteria devices ! ! c. Eventually goes into lytic cycle. IV. Animal Viruses ! A. Viruses with Envelopes ! ! 1. Envelopes fuse with host membrane, inserting information ! ! 2. Enzymes remove capsid, genome replicates ! ! 3. Viral offspring are wrapped in a membrane and released ! ! 4. Provirus Some viruses become integrated into cell’s genome (infection ! ! tends to reoccur throughout life, HIV, herpes) ! B. RNA Viruses ! ! 1. Retroviruses Most complicated life cycle (HIV) ! ! ! a. Reverse Transcriptase Transcribes DNA from RNA template ! ! ! b. Newly formed DNA integrates as a provirus into a chromosome ! ! ! within the nucleus of the host cell. ! C. Viral Diseases ! ! 1. Vaccine Harmless variants or derivatives of pathogenic microbes ! ! which stimulate an immune response. V. Plant Viruses ! A. Horizontal Transmission Plant infected from external source ! B. Vertical Transmission Plant inherits infection from parent VI. Bacteria ! A. Single stranded, circular DNA, found in nucleoid region ! B. Plasmids Smaller circles of DNA, used in genetic engineering ! C. Replication of chromosome is followed by binary ? ssion (copying of DNA ! occurs in both directions) VII. Genetic Recombination of Bacteria ! A. Transformation Alteration of a bacterial cell’s genotype by the uptake of ! naked, foreign DNA from environment. ! B. Transduction Transfer of bacteria by means of a virus ! C. Conjugation Direct transfer of genetic material between two bacterial cells ! ! 1. Donor is â€Å"male† (requires F plasmid, F+), receiver is â€Å"female† (F-) AP Bio Modern Genetics ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! 2. Plasmid Not required for survival or reproduction, but can be ! advantageous in stressful environments. ! ! a. Episomes Can replicate as a free molecule in cytoplasm or as ! part of the main bacterial chromosome. ! 3. R Plasmids cause bacteria to be resistant to antibiotics D. Transposons Pieces of DNA which can move from one location to another in a cell’s genome (jumping genes) discovered by Barbara McClintock. ! 1. Conservative Transposition Genes are not replicated, number of ! copies is conserved (cut and paste) ! 2. Replicative Transposition Transposon replicates at original site and a ! copy inserts at another location (copy and paste) E. Insertion Sequences Simplest transposons, consist of only the DNA necessary for act of transposition itself. F. Barbara McClintock (1940’s-50’s) worked with Indian corn, based on observations, she believed there were mobile elements. VII. Operons Unit of genetic function common in bacteria and phages and consisting of regulated clusters of genes with related function. ! A. Jacob and Monod Discovered operon model in 1961 ! B. Operon is made of an operator, promoter and the genes they control ! C. Operator Switch which gets turned on ! D. Oppressor Segment of DNA, functions as an on/off switch for an operon ! E. Repressor Protein which turns off the operon (operator speci? c) ! F. Corepressor Metabolite that cooperates with a repressor protein to switch an ! operon off ! G. E coli Operons ! ! 1. Lac Operon ! ! ! a. Regulatory Gene gt; Repressor gt; Binds to Operator ! ! ! b. RNA Polymerase cannot transcribe structural genes needed to ! ! ! make enzymes break down lactose ! ! ! c. When lactose is present, some of the lactose attaches to the ! ! ! repressor and shuts it down allowing RNA polymerase to transcribe ! ! ! (example of an inducible operon Usually off but can be induced. ) ! ! 2. Trp Operon (Tryptophan is an amino acid) ! ! ! a. Regulatory Gene gt; Inactive repressor that doesn’t attach to the ! ! ! operator so RNA polymerase can transcribe. ! ! ! b. Increased levels of trp combine with repressor to make it active ! ! ! and the RNA polymerase can’t transcribe (example of corepressor) ! ! ! c. Repressible Operon Transcription usually on but can be ! ! ! repressed Chapter 19 Eukaryotic Genomes: Organization, Regulation, and Evolution I. Key Terms ! A. Cellular Differentiation Process of cells becoming specialized and therefore ! only parts of genes expressed. AP Bio Modern Genetics ! ! ! ! ! ! ! ! ! B. Histones Positively charged proteins which bind to negative DNA and â€Å"package it together† C. Nucleosome Basic unit of DNA packaging in eukaryotes, consisting of DNA around a protein core (2 copies of each of the 4 types of histones) D. Multigene Families Collections of identical or similar genes (hemoglobin alpha and beta are expressed at different times) E. Pseudogenes Similar to functioning genes but are lacking some essential part. F. Heterochromatin, euchromatin, telomere. II. Gene Control Eukaryotes ! A. Transcriptional Control Factor which tell where to start and stop ! B. Posttranscriptional Splicing, cap and tail ! C. mRNA Degradation ! ! 1. Prokaryotic mRNA are usually broken down within minutes of use ! ! 2. Eukaryotic mRNA can live hours to weeks before being broken down by ! ! enzymes. ! D. Chromosomes Puffs In insects, regions of intense transcription, chemicals ! signal when they should form. ! E. Steroids in Humans ! ! 1. Steroid diffuses through cell (lipid soluble) into cytoplasm and binds to ! ! receptor. ! ! 2. Binding to an enhancer then occurs and activates transcription. ! ! 3. Steroid acts as a signal to turn on speci? c gene. ! F. Hormones bind to outside of cell (not lipid soluble) and operate with the help of ! receptor protein on the outside of the cell. ! G. Gene Ampli? cation Selective replication of certain genes. ! H. Immunoglobulin Proteins which speci? cally recognize and help ? ght viruses, ! bacteria and invaders. ! ! 1. Made by B lymphocytes ! ! 2. Antibody variation results from different combinations of variable and ! ! constant regions of immunoglobulin polypep tides. ! I. DNA Methylation III. Abnormal Expression of Genes ! A. Oncogenes Cancer causing genes found in RNA viruses ! B. Proto-Oncogenes Found in human cells, normal genes which may become ! oncogenes. ! ! 1. Increased activity may cause change ! 2. Gene Ampli? cation ! ! 3-5. Translocation, Gene Transposition, and Point Mutation ! C. Tumor Suppressor Genes Normally prevent cell division and may produce ! proteins which repair damaged DNA. ! D. The more mutations throughout life, the greater the chance of cancer. AP Bio Modern Genetics Chapter 20 DNA Technology I. Gene Manipulation ! A. Restriction Enzymes Bacterial enzymes which cut up foreign DNA forming ! sticky ends. ! ! 1. Sticky ends can be used to join DNA pieces originating from different ! ! sources. ! ! 2. Restriction fragments can be separated by gel electrophoresis ! ! ! a. Brief electric pulse is applied to a solution of DNA to separate ! ! ! DNA. ! ! ! b. DNA is negative and moves towards positive end ! ! ! c. Can be used to compare DNA of different species. ! B. Gene Cloning in a Plasmid ! ! 1. Isolate bacterial plasmid and eukaryotic DNA with gene desired ! ! 2. Both are treated with same restriction enzyme ! ! ! a. Plasmid DNA Cut at restriction site ! ! ! b. Eukaryotic DNA Generates thousands of fragments ! ! 3. Two types of DNA are mixed Sticky ends of each pair up ! ! 4. DNA ligase joins molecules (called recombinant DNA) ! ! 5. Recombinant DNA is introduced into a bacterial cell ! 6. Gene Cloning Production of multiple copies of desired gene ! C. Inserting DNA into Cells ! ! 1. Cloning Vectors Carriers for moving recombinant DNA (plasmids, ! ! phages-transformation) ! D. Sources of Genes for Cloning ! ! 1. DNA isolated directly from organism ! ! 2. Complementary DNA (cDNA) made in a lab from mRNA templates. ! E. Probes Nucleic molecules w hich will hydrogen bond speci? cally to a desired ! gene, location traced by labeling ! F. Sanger Method of Sequencing ! ! 1. Synthesizing in vitro DNA strands complementary to one of the strands ! ! being sequenced. ! G. Amplifying DNA ! ! 1. Polymerase chain reaction (PCR) technique by which any piece of DNA ! ! can be quickly ampli? ed in vitro ! ! ! a. DNA is incubated with DNA polymerase and primers. II. Applications ! A. Human Genome Project Mapping of entire human genome ! B. Analyzing genomes of other species ! C. Human Gene Therapy Correct Disorders ! D. Vaccines ! E. Mammalian Hormones and Proteins Growth hormones, clotting factor, insulin ! F. Treating Farm Animal with vaccines, antibodies and growth hormones ! G. Transgenic Organisms Contain genes from another species ! H. Manipulating Plant Genes Herbicide resistance, better foods