molecular biology Flashcards

Question

dna the double helix

Answer 1

described by Watson and crich received the 1962 noble proze 3 forms, b-dna most commonly found in nature complimentary: TA and CG antiparallel, 3'-5', 5'-3' stabilized by chemical reactions base pairs - hydrogen bonds provide weak electrostatic attraction between electronegative atoms base stacking involves hydrophobic interactions between adjacent base pairs, provides stability to double helix van der Waals forces - aromatic ring stacking forces vetween base oairs hydrophobic effects non polar, uncharged bases are present in the interior of structure while negatively charged phosphates are on the outside important because in aqueous environment

Answer 2

most basic complex of the chromosome is the dsdna dsdna is wound around proteins called histones small +. charged proteins because phosphate backbone is negative nucleosomes are made up of dsdna complexed with hsitones further compacted into chromatin fiber each chromosome contains a large number of looped domains of chromatin fibers attached to a protein scaffold

Answer 3

occurs when hydrogen bonds between base pairs are disrupted and strands separated melting curve obtained by measuring dna denaturation by slowly heating a solution of dna melting temp tm the temp at which 50% of dna strands is denatured salt conc can affect tm nucleotide content can affect tm lots of CG increases TM because there's more H bonds length of molecule can affect tm ph can affect tm

Answer 4

also called reannealing under certain conditions single strands of dsdna can reform 2 requirements much be met salt conc high enough to neutralize the negative charges of the phosphate groups that would otherwise repel each other temp must be high enough to sufficiently disrupt h bonds that randomly formbetweenm bases of the same strand, pinloop but not too high that they can't form between complimentary strands

Answer 5

an enzyme that synthesizes long chains of nucleic acids always moves in 5'-3' direction synthesis is continuous on the leading strand and discontinuous on the lagging strand, creating Okazaki fragments dna replication requires a primer a short single stranded DNA sequence that is complimentary to a specific target sequence of dna primers indicate the starting point for the synthesis of the new strand by the polymerase enzyme

Answer 6

gyrase, topoisomerase relieves positive supercoils ahead of fork, physics helicase unwinds the dsdna helix dna primase - a type of RNA polymerase which catalyzes the synthesis of a short ran primer complimentary to ssdna dna polymerase II synthesizes dna using ran primers dna polymerase I removes the primer on the lagging strand and replaces it with dna dna ligase seals gaps between Okazaki fragments dna synthesis occurs at multiple locations at a time in vivo bubbles and forks meet each other coalesce

Answer 7

initiation/regulation how and where polymerization is activated and how its cntrolled polymerization rate - number of nucleotides polymerized per second error rate - # of incorrect nucleotides processivity number of nucleotides added per binding event proofreading functions - does it have an error-correcting function primer specificity ABI Amplitaq Gold was gold standard has a hot start modification added to allow room temp set up optimal operating temp is 72

Answer 8

utliizes synthetic primers to target specific areas of the genome uses the polymerase chain reaction makes millions of copies of target sequences from one strand of dna

Answer 9

temps not specific, depends on dna 3 basic steps denaturations (96) heat is added to separate or denature dna strands, providing ss dna templates annealing (55-65) reaction is cooled to allow primers to bind to their complimentary sequences depends on the tm of primers extension 72 temp is raised again so that taq polymerase extends the primers, synthesizing new dna strands (specific temp is based on the optimal operating temp of polymerase being used) repeats the steps 25-35 times, 2- 4 hours not just the original dna is used as a template each cycle uses the new dna strands in addition copies of copies

Answer 10

reaction buffer (salt) reduces Tm of DNA because negative charge of the phosphate backbone MgCl2 improves primer binding primers - target areas of DNA and primes the synthesis of DNA dNTP's Polymerase template DNA

Answer 11

each chromosome has a short arm (p) and a long arm (q) separated by a centromere centromeres are the dense DNA sequences found near the points of attachment of mitotic or meiotic spindle fiber telomeres are the ends of the chromosomes, help stabilize chromosome and play a role in replication cytogenetic mapping - chemical staining of metaphase chromosomes resulting in an alternate banding pattern, can be seen under a microscope, used to identify locations on a chromosome ex: AmelY (amelogenin, Y-linked) is Yp11.2 which indicates its location on chromosome Y, short arm, band 11, sub band 2 gametes are haploid (22 autosomes + 1 sex chromosome) in ova always X in sperm can be X or Y formed by germ cells fertilization results in a zygote diploid most somatic cells are diploid some hav eno nucleus hair epithelial skin nails result = 46 chromosomes homologous chromosomes the two chromosomes of a pair in a diploid cell, one inherited from sperm, the other egg karyogram shows chromosomes

Answer 12

genetic expression to code for proteins needed for survival replication (mitosis) to propagate the hereditary material during development of an individual recombination (meiosis) to shuffle hereditary material between successive generations these are exploited by forensic dna analysis

Answer 13

locus (plural loci) the chromosomal location of a dna marker in a non-coding region gene: the segment of dna which codes for a functional ran or a protein product allele the alternate form of a gene or genetic locus homozygous: identical alleles at a locus on homologs chromosomes heterozygous different alleles at a locus on homologous chromosomes genotype (spelling) the characterization of the allies present at a genetic locus phenotype (what it is saying) the physical manifestation of a genotype: visible trait

Answer 14

3.2 billion base pairs (haploid) genes and related sequences + intergenic noncoding sequences human genome project initiated in 1990 and completed in April 2003

Answer 15

25 % human genome are genes or related sequences 1.5% is coding DNA ~25000-30000 genes 23.5% non-coding regions (promoter, introns, pseudogenes, etc.) encode the information for the synthesis of proteins most human genes are discontinuous exons, introns during gene expression the primary mRNA contains both introns and axons throughout the process of splicing the introns are removed and the axons are joined together messenger RNA can be used for protein synthesis via translation process

Answer 16

DNA transcription and mRNA processing mRNA translation protein post-translational modifications active protein

Answer 17

75% of human genome located between genes 20% is single copy sequences with unknown function 55% is repetitive DNA 2 categories Intersprersed repeats randomly located throughout the genome SINEs - short interspersed elements ~300kb LINEs - long-interspersed elements ~ 6-8kb LTR elements - long terminal repeats, telomeric regions DNA transposons (floating) or tandem repeats smaller, back to back satellite: centromeric, long chunks mini satellite: forensic VNTRs (variable # tandem repeats) and RFLP micro satellite: Forensic STRs forensics utilizes mini satellite and micro satellite

Answer 18

mini satellites - variable nucleotide tandem repeats (VNTRs_ banding, first DNA typing located in subtelomeric region end of chromosome core repeat size = 10-100 bp overall size = 500 bp-30kb repeated in tandem, over and over obey hardy Weinberg equilibrium example D1S80 - 16bp repeat OJ Simpson one of 1st DNA cases size not ideal for forensics, very long not good with degraded DNA need a large amount of sample 50-1000 ng DNA needed micro satellites - short tandem repeats (STRs) ~3% of genome, dispersed throughout )genie and extragenic) core repeat size - 2bp-6bp (1/2 size of smallest VNTRs overall size = 50bp - 350bp obey hardy Weinberg equilibrium example: original codes 13 loci smaller size, large # in genome, polymorphic (diff alleles, diff versions at different loci) multiplexing capabilities, PCR with diff primers, all in 1 chem reaction HWE made ideal for forensics .5-2ng DNA needed

Answer 19

types of markers: length and sequence polymorphisms polymorphism the existence of two or more alleles at significant frequencies in the population repeat length polymorphisms: STR/VNTR sequence variation: single nucleotide polymorphism (SNPs) diff version, same loci

Answer 20

SNPs substitution of a single nucleotide, point mutation occurs ~ every 1000 bases markers for ethnicity, phenotype, lineage, and identity

Answer 21

length, repeats simple, compound, or complex

Answer 22

RFLP: restriction fragment length polymorphisms 1st described by Alec Jeffreys PhD in 1985 and used in forensic casework in 1986 Pitchfor murders in Leicestershire England Colin Pitchfork was identified as a primary suspect when he asked a friend for a blood sample uses restriction endonuclease - cuts DNA at specific target sequence size polymorphism VNTR, minisatellites

Answer 23

DQ-alpha polymarker sequence polymorphism reverse dot blot D1S80 VNTR size polymorphism PolyMarker 6 plex PCR for SNPs Singleplex STRs with silver staining

Answer 24

banding no statistics good for exclusions

Answer 25

papers with dots that turn a certain color for positive PCR on each dot location with specific primers not multiplex

Answer 26

of repeats indicates allele an accordion like DNA sequence that occurs between genes number of consecutive repeat units can vary between people FBI selected 13 core STR loci that must be run in all DNA tests in order to provide a common currency with DNA profiles

Answer 27

28 cycles 2^28 from one strand of ds DNA over 268 mil copies from one dsDNA <1ng target DNA we don't need that much quant system goes down to 50pg, about 9 haploid cells

Answer 28

multiplex PCR fast and efficient, robotic friendly very sensitive <1ng DNA high power of discrimination PD>10^21 DNA profile is 23 autosomal STR loci Promega PowerPlex Fusion 6c ABI GlobalFIlerTM polymorphic, diff alleles per loci loci - locations on chromosomes so you can see differences in genetic profiles, but how do you give it weight what's the frequency of this profile in a population mathematically speaking

Answer 29

1st law of segregation diploid organism passes a randomly selected allele for a trait to its offspring such that the offspring receives one allele from each parent half the parental gametes carry one allele and the other half carry the other allele 2nd law of independent assortment the alleles of two or more difference genes get sorted into gametes independently of one another the alleles;e a gamete receives for one gene does not influence the allele received for another gene

Answer 30

p^2 + 2pq + q^2 = 1 1 in population p^2 is dominant heterozygous frequence q^2 is recessive homozygous frequency 2pq is heterozygous frequency population assumptions for equation to be true random mating no natural selection large population, no isolation, lots of possible allele combinations no mutation/migration no new alleles being introduced or leaving allele frequencies remain constant generation to generation

Answer 31

Mendel's laws of segregation nd independent assortment are the basis for linkage equilibrium and hardy-weonberg equilibrium HWE deals with mendelian genetics in the context of populations of diploid, sexually reproducing individuals p^2 + 2pq+ q^2 = 1 are the expected genotype frequencies in a random-mating population for two alleles these are tested when creating dna population databases

Answer 32

genes in random association inherited independently of each other

Answer 33

each parent could five either an A or a allele to the next generation in the gamete there is an equal chance for giving either 1st law of segregation p+q=1 allele frequency (p+q)^2 = p^2 + 2pq + q^2 genotype frequencies HWE is a simple way to relate allele frequencies to genotype frequencies

Answer 34

generate data with set of samples from desired population groups generally only 100-150 samples are needed to obtain reliable allele frequency estimates determine allele frequencies at each locus count number of each allele seen there is a mathematical eq to deal with new alleles migration of new allele mutation allele frequency info is then used to estimate a genotype freq at a locus and the rarity of a particular DNA profile homozygous (p2) and heterozygous (2pq) use product rule (multiple locus freq estimates) apply to all loci

Answer 35

13 codes core str loci D13S317 chromosome 13 317th location on chromosome that they looked at to determine if it was k for forensics not how chromosomes should be labeled codes core 20 loci effective jan 2017 codes core 13 t minimum is required for NDIS upload any 13 core 20 loci

molecular biology Flashcards

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