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CU-Boulder MCDB 2150 - Exam 2 Study Guide

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MCDB 2150 1st EditionExam # 2 Study Guide Lectures: 12 - 22Lecture 12 (2/09)Chromosomal problems & mutations3 Types- Chromosome rearrangement- Aneuploidy (+1) / monosomy (-1)- PolyploidyChromosome rearrangement:- Duplication = increased expression of some gene products- Deletion = decreased expression of some gene products- Unbalanced gene dosage can cause abnormal developmento Usually occurs during crossing over = unequal crossing over Chromosomes didn’t line up properly Wrong genes switchGene Duplication as material for evolutionPARALOGS = homologous genes (duplicated) – over time they mutate & change independently of each otherEg. Hemoglobin genes – different genes are activated in different times of human developmentRhodopsin = at 1 point there was only 1 rhodopsin gene, now there are 4 -> 1 for each different part of the color spectrumDuplications & deletions in meiosis- Chromosomes w/ duplications/deletions CAN ALIGN CORRECTLY DURING MEIOSIS = NORMAL GAMETESo Crossing over is not affectedChromosome rearrangement:- Inversions & Translocationso Results in normal gene dosage :)o Phenotypes occur if break occurs within gene or gene regulatory regionInversions & Translocations inmeiosis:- Trouble lining up during crossing over = non-viable gametes :(Lecture 13 (2/11)Bacterial & Microbial Genetics- Circular DNA/chromosome (NOT diploid – 1 copy of each gene)- Can contain plasmidsPlasmids = extra chromosome, small circular DNA pieceEpisome = freely replicating plasmid: F (fertility) factorF Factor plasmid contains genes for:- Regulation of plasmid transfer to other cells- Regulation of its insertion into bac. Chromosome- Regulation of plasmid replicationTechniques for the study of bacteria:- Complete media (prototrophs& autotrophs grow – contains all needed nutrients)- Minimal media (only prototrophs grow, not autotrophs)o Min media trp ->trp autotrophs don’t grow- Prototroph – can synthesize all needed nutrients (grows in minimal media)- Autotroph – needs a supply of a certain nutrientGenetic exchange (recombination) can take place and turn autotrophs into prototrophsGene transfer in bacteria (horizontal gene transfer):- Conjugation – direct transfer of DNA- Transformation – bacterium takes up free DNA- Transduction – phage take DNA from one bacterium to anotherConjugation:- Direct contact between cells- Gene material is transferred through sex pilius- One way transfer (donor cell) -> recipient cell)F-factor (plasmid) contains genes for sex piliusTransfer begins at ‘ori’ site of F-factorSingle strand is transferred (only f-factor is transferred)HIGH FREQUENCY OFRECOMBINATION = Hfr cells (F-factorplasmid is integrated into genome)**when an Hfr cell & other cellis undergoing conjugation,more than the plasmid istransferredTransformation:- Bacteria take up DNA from the environment (lysed cells)- Recombination takes place between genes and bacterial chromosomeUsing co-transformation (two genes at once) for mapping:Lecture 14 (2/13)Co-transformation cont., transduction & bacteriophage lifecyclesTransduction:Phage (viruses that infect bacteria)take up some DNA from one bacterium andit is inserted into another bacteriumgenemapping using co-transduction is done in the same way as co-transformationBacteriophage lifecycles:Lysogenic – phage DNA is integrated into bacteria DNA (making the bacterium a prophage)Lytic – phage particles are assembled and bacteria destroyed (lysed)attachmententryintegrationsynthesis of viral componentsviral assemblyreleaseRNA virusesUses reverse transcriptase (enzyme) to turn RNA into DNARetrovirus (like HIV) – has envelope & 2 copies of single stranded RNAProtease = breaks down protein into amino acidsAntigenic Drift:- Different types or strains of a virus that circulate at the same time- Over time, mutations accumulate in viral RNAo Leads to changes in the antigens on the virus’ surface- Major change in viral protein structureo Due to co-infection -> recombination of two strains in a hosto New strains that can jump species = dangerousLecture 15 (2/16)DNA replication, PCR & non-coding sequencesDNA replication- During S phase of cell cycle- DNA unwound, antiparallel strands are used as templateso Leading & lagging- The 5”-phosphate group of incoming dNTP (1 nucleotide) is added to the 3’-OH group o new nucleotides are only added onto the 3’ endo phosphodiester bond forms between nucleotidesprimase = adds theprimersPolymerase chain reaction (PCR)- mimics normal DNA rep.- makes multiple copies of specificDNA sequence- usesprimers:o short segments of DNA thatbind to the edges of the desiredDNA section1.) DNA is unwound with heat2.) Primers bind (initiate DNA rep)3.) DNA polymerase does it’s thaang (using nucleotides)Non-coding sequences (microsatellites/short tandem repeats)- Inherited like other genes (but non-coding)- Easy to determine differences b/c different lengths- Used to determine matches & used in evolutionary evidenceBecause everyone has 2 chromosomes*Multiply the frequencies together*Lecture 16 (2/18)DNA, STRs & RFLPsGel Electrophoresis separates DNA by sizeAmplified DNA (PCR product) is tagged with something visible like: Ethidium BromideGel is a MESH of material- Remember DNA is negatively charged (phosphate groups on backbone)So when you run electrical current through the gel material, charged particles move to other side (away from negative electrode)- Smaller pieces of DNA move faster & farther than larger pieces of DNA Back to STRs (short tandem repeats) o = non-coding regions of short repeatsSTRs are non-genic but can be near a disease allele- It will segregate during crossing over with disease allele- So you can find co-localization of an STR (if they segregate together, theyare very close together on the chromosome)Restriction Fragment Length Polymorphisms (RFLPs)These are single base changes in DNA that happen to be in the site of a restriction enzyme- you can use this to identify the single base change- restriction enzyme = proteins from bacteria that cut DNA in specific locations (always palindromes)CA|ATTGGTTA|ACSo when one letter is changed, the restriction enzyme won’t recognize it to cut it*Restriction fragment length polymorphism (RFLP)Lecture 17 (2/20)Transcription & TranslationTranscription:- RNA is transcribed from 5’ -> 3’o Reads template DNA strandeither side of our double stranded DNA can be a template, making either side a coding regionORF = open reading frame = mature


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