Lecture 9: DNA Flashcards

Question

Hydrogen bonds in dsDNA

Answer 1

> Hydrogen bonds are weak -It takes 4-21 kJmol-1 of energy to break them > How is the dsDNA so stable? -The large numbers of hydrogen bonds within the helix gives stability -Forms a double helix

Answer 2

> Two, right-handed, helical polynucleotide chains are coiled around a common axis > The chains run in opposite directions -Anti-parallel > The purine and pyrimidine bases are on the inside of the helix, the sugar-phosphate backbone is on the outside > The planes of the bases are nearly perpendicular to the helix axis, the planes of the sugars are nearly perpendicular to the helix axis, the planes of the sugars are nearly parallel to the helix axisrly parallel to the helix axis.

Answer 3

> Adjacent bases are separated by 0.34nm > There are 10 bases per turn of the helix > The helical structure repeats every 3.4 nm > The helix diameter is 2nm

Answer 4

> The two chains are complementary due to the sequence of bases > The bases stack almost on top of each other giving stability due to 2 reasons: -Hydrophobic effect -stacking interactions called van der Waals forces occur between bases

Answer 5

> Stacked bases absorb less UV than unstacked bases (hydrochromism) > Absorption is maximal at 260nm

Answer 6

> Separating dsDNA into ssDNA is necessary for: -the transcription into mRNA -the copying of the DNA strand during replication -the copying of the DNA molecular during PCR > Separation occurs by disrupting hydrogen bonds between base pairs > Separation is called melting because it occurs abruptly at a certain temperature > Melting temperature (Tm) is defined as the temperature at which half of the helical structure is lost

Answer 7

> The higher the GC content, the higher the Tm > Single strands reassociate (anneal or hybridise) when Tm is lowered

Answer 8

> Ribose not deoxyribose, U instead of T > Usually single-stranded -fold back on themselves >>'self-complementary' regions form hairpin loops which are double helical -Random coil

Answer 9

> Requires in protein synthesis -messenger RNA (mRNA) -transfer RNA (tRNA) -ribosomal RNA (rRNA) > Required in other functional roles -small nuclear RNA (SnRNA) -micro RNA (MiRNA)

Answer 10

> Active during transcription -complementary to DNA sequence -codes for protein -Specific to gene -varies in quantity dependent on gene

Answer 11

> Physical link between mRNA and amino acids -linked to each amino acid -3 base pair anti-codon

Answer 12

> Forms ribosome with protein -interacts with both mRNA and tRNA -active during transcription

Answer 13

> A loose term to describe a specific piece of DNA that gives a unique piece of information > There are hundreds of different molecular markers used in forensic science > They belong to distinct 'classes' and are detected using different methods > Analysis over time shows variation > Increasing use in STRs and DNA sequencing > Around same time as the field of forensic genetics was born > Each marker has its benefits and disadvantages > Three main markers -gene regions -SNPs -STRs

Answer 14

> An entire gene or part of a gene sequence > Little variation in nuclear gene sequences as they're coding -Good for identifying different genes -example application- body fluid identification > mtDNA gene sequences show more variation -Good for identifying differences between species -examples application- wildlife forensics > Genes of closely related individual will be similar -can be used to track ancestry

Answer 15

> Single nucleotide Polymorphisms (SNPs) > Can occur In coding and non-coding regions > Some are highly informative others are not > Use of a SNP panel can be very powerful > SNPs occur through mutation events > Most common at position 3 in triple code

Answer 16

> STRs are co-dominant > Inherited in a mendelian fashion > 2 copies of a STR for each chromosome pair > STRs can exist as a number of different repeat units -Dinucleotide -Trinucleotide -Tetranucleotide -Pentanucleotide -Hexanucleotide > Heterozygote if fragments are different sizes > Heterozygote observed as two peaks on Genetic Analyser > Homozygote if fragments are same size > Homozygote observed as single peak on genetic analyser

Answer 17

> Basis of all DNA detection approaches > Increases the number of copies of the molecular marker > Allows detection through fluorescence

Answer 18

> DNA can't be observed directly > Detection is done by measuring fluorescence > Mechanism of fluorescence detection similar

Answer 19

> Most basic approach -detects genes (if primers are specific) -detects different sizes fragments > DNA is negatively charged > DNA is run through a matrix (agarose) > DNA is separated according to its relative mobility through the matrix > Small bands travel quickly > Large bands travel slowly > Compared to a ladder > Precision is poor > The agarose gel contains an intercalating dye > The dye binds in the groves of the double helix > The dye fluoresces in UV light when bound

Answer 20

> Same principles as agarose > Sizing accuracy is better > Can be used to detect STRs > Use a genetic analyser

Answer 21

> Same principles as FLA > Uses a Genetic Analyser > Requires detection of single base pairs > Up to 800p reads > Detects SNPs and Gene regions > First PCR produces DNA fragment > Second (sequencing) PCR adds fluorescent ddntp > Results in multiple different length DNA strands > Each strand has different terminal coloured dye

Answer 22

> Combined the principles of PCR and agarose gel > Fluorescence is detected as DNA is amplified > Fluorescence is detected by using an intercalating dye > Detects Gene regions (is primers are specific) > Or molecular probe (TaqMan) Detects Gene regions as probe is highly specific to gene

Answer 23

> Uses the same PCR instrument > Fluorescence is detected at the end of the PCR > Detects Gene regions and SNPs > Fluorescent probes bind to all the dsDNA that has been produced > The probe fluoresces when bound > The mix is then heated > At a specific temperature the probe 'melts' away from the DNA > A reduction In fluorescence is observed > Used in body fluid identification