chapter 8 Flashcards

Question

Palindromic sequences can form  hairpins and cruciforms

Answer 1

Palindromes: words or phases that are the same when read backward or forward: Saippuakuppinippukauppias (Finnish word for “soap cup batch trader”) Νίψον ἀνομήματα, μὴ μόναν ὄψιν (Ancient Greek fountain text: “Wash the sin as well as the face”)

Answer 2

-Is synthesized using DNA template -Contains ribose instead of deoxyribose -Contains uracil instead of thymine -One mRNA may code for more than one protein -Together with transfer RNA (tRNA) transfers genetic information from DNA to proteins

Answer 3

Bacterial mRNA Schematic diagrams show: (a) monocistronic and (b) polycistronic mRNAs of bacteria. Red segments represent RNA coding for a gene product; gray segments represent noncoding RNA. In the polycistronic transcript, noncoding RNA separates the three genes.

Answer 4

The product of transcription of DNA is always single-stranded RNA, which tends to assume a right-handed conformation dominated by base-stacking interaction Typical right-handed stacking pattern of single-stranded RNA (Bases in yellow, Phosphorus atoms in orange, and riboses and phosphate oxygens in green)

Answer 5

The paired RNA with perfectly complementary seq is often an A-form right-handed double helix. B-form has not been observed, Z-form can be made in lab with high salt or high T. Secondary structure of RNAs. (a) Bulge, internal loop, and hairpin loop. (b) An A-form right-handed helix for a hairpin.

Answer 6

Base-paired helical structures in an RNA The secondary structure of the M1 RNA component of the enzyme RNase P of E. coli, with many hairpins. The two brackets: additional complementary sequences that may be paired in the 3D structure. The blue dots: non-Watson-Crick G=U base pairs (boxed inset). Note that G=U base pairs are allowed only when presynthesized strands of RNA fold up or anneal with each other. There are no RNA polymerases that insert a U opposite a template G, or vice versa, during RNA synthesis.

Answer 7

A t-RNA (with some unusual base-pairing pattern) A hammerhead ribozyme A segment of mRNA

Answer 8

Covalent bonds remain intact --Genetic code remains intact Hydrogen bonds are broken --Two strands separate Base stacking is lost --UV absorbance increases Denaturation can be induced by high temperature, or change in pH Denaturation may be reversible: annealing

Answer 9

-Native DNA at 25ºC and pH 7 is very viscous -When T > 80ºC or at extreme pH, viscosity decreases sharply -Disrupt H bonds but backbone covalent bonds remain intact -Renaturation is a rapid one step process if a section of DNA strands is undisrupted -IF completely denatured- 2 step process- --Requires a section of the double helix to reform by reuniting a dozen or more residues in the same area by random collisions- slow --Successive unpaired bases zipper to form a double helix- fast DNA Reversible denaturation and annealing (renaturation)

Answer 10

-DNA exists as double helix at normal temperatures -Two DNA strands dissociate at elevated temperatures -Two strands re-anneal when temperature is lowered -The reversible thermal denaturation and annealing form basis for the polymerase chain reaction -DNA denaturation is commonly monitored by UV spectrophotometry at 260 nm

Answer 11

-The midpoint of melting (Tm) depends on base composition --High CG increases Tm -Tm depends on DNA length --Longer DNA has higher Tm --Important for short DNA -Tm depends on pH and ionic strength --High salt increases Tm

Answer 12

Detection of a specific DNA molecule in complex mixture - radioactive detection - fluorescent DNA chips Amplification of specific DNA - polymerase chain reaction - site-directed mutagenesis -Evolutionary relationships -Antisense therapy

Answer 13

Two complementary strands have the ability to detect each other in solution. The complements can come from the same source, or they can be from different sources If they are from different sources they are hybrids

Answer 14

-Mutation – alternation in DNA structure that produce permanent changes in the genetic information encoded therein -Deamination – loss of the exocyclic amino group -Depurination/Depyrimidination – hydrolysis of the N-glycosidic bond between the base and the pentose, to create a DNA lesion called an AP (apurinic, apyrimidinic) site or abasic site -Cells have mechanisms to correct most of these modifications

Answer 15

-Loss of their exocyclic amino group -Very slow reactions -Some can be severe such as cytosine to uracil occurring about 1 in every 107 residues every 24 hours -Deamination of A and G: 1/100th of C to U -This may be one reason that uracil is not used in DNA, but T

Answer 16

-Process is slow and not considered physiologically significant -Can be accelerated by dilute acid. e.g. incubation at pH3 causes selective removal of the purine bases to give the apurinic acid -Does not break the covalent backbone but it causes a loss in information -Occurring rate: Purines > Pyrimidines

Answer 17

Oxidative damage -Hydroxylation of guanine -Mitochondrial DNA is most susceptible Chemical alkylation -Methylation of guanine Cells have mechanisms to correct most of these modifications

Answer 18

UV light induces dimerization of pyrimidines; this may be the main mechanism for skin cancers. Ionizing radiation (X-rays and γ-rays) causes ring opening and strand breaking . These are difficult to fix. Cells can repair some of these modifications, but others cause mutations. Accumulation of mutations is linked to aging and carcinogenesis.

Answer 19

Energy Source Some Coenzymes containing adenosine Acyl Group Transfer Electron Transfer Hydride Transfer

Answer 20

Regulatory Molecules Second Messengers Produced in bacteria in response to a slowdown in protein synthesis during AA starvation

Answer 21

Dideoxy Sequencing of DNA

Answer 22

Y-STR testing is useful for forensic, relationship and genealogy testing

Answer 23

Genomic DNA Can Be Edited Nowadays CRISPR: Clustered Regularly Interspaced Short Palindromic Repeats