BIO311C_CH14_DNA Structure and Replication
Terms
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- Wilking, Franklin, Watson, Crick
- used X-ray crystallography to determine the three-d structure of DNA
- Origins of Replication
- are locations on DNA molecules with specific sequences that are recognized by enzymes involved in DNA replication. Bacterial chromosomes and plasmids contain a single origin of replication whereas eukaryotic chromosoems contain multiple origins of replication.
- Semiconservative
- refers to the fact that half of a newly made DNA is the old template.
- deoxy nucleoside triphosphates (dNTPs)
- The DNA synthesis always happens 5' to 3'. This is a result of the nature of the enzyme DNA polymerase to link new deoxyribose nucleoside triphosphates (dNTPs) only to the 3'-OH group.
- Hershey and Chase
- used a bacteriophage that was knwon to inject part of its contents into bacteria to program the cells to make more viruses. They wanted to find out if the injected material was protein or DNA. After infection, they mixed the contents vigorously in a kitched blender to shake off the phages from the bacteria. THe mixture was then centrifuged to peelet the bacteria and retain phages in the supernatant. THe pellet fraction contained the 32P and the supernatant contained 35S.
- DNA Replication
- 1) Initiation 2) Elongation
- DNA polymerase I
- DNA polyermae I removes the RNA primer and completes the DNA strand
- Supercoiling
- The double helix of DNA coils onto itself resulting in supercoiled DNA. This occurs in circular DNA and linear eukaryotic chromosomes. Supercoiling is important to keep the DNA compact in the cell and during DNA replication.
- Excision Repair
- occurs after a cell divides and is in the G1 phase or G2 phase. THis damage is caused by carcinogens and mutagenic radiations altering the baes of making pyrimidine dimers. Such mutations are constantly monitord by over 50 different enzyme and corrected by excising the damaged strand of DNA (by an endonuclease( and making a new matching stand (by DNA polymerase and DNA ligase) in its place. the disease xererma pigmentosum is cuased by lack of enzyme invovled in excision repair.
- Mismatch Repair
- is done to correct ethe errors made during DNA replication. DNA polmerase III proofreads the newly made DNA, removes the wrong baes, and remakes the DNA to minimize the errors to 1 to a billino These error corrections use the mismatch repair mechansism by checking the complementary base pairing. e.g., problem in mismatch repair causes colon cancer.
- Lagging Strand
- Since the opposite strand is not fully open to cotinue DNA synthesis int he 5' to 3' direction, DNA is synthesized in small fragments which are called Okazaki fragments.
- DNA gryase
- facilitates supercoiling of the DNA to c ompact the chromosomes into nucleosomes
- Denaturing/Renaturing DNA
- Because the two strands of DNA are bonded with H-bonds tehy can be separated by heating of exposure to alkaline condition. The same DNA can be renatured to its original form hybridization, they rejoin due to complementary basie pairing, by gradual cooling or neutralizing the alkaline solution with a mild acid.
- Initiation
- It starts with the relaxation of supercoiling at the origin of replication by topoisomerase. 2) The relaxed DNA helix is opened to make a replication fork and the resulting single-stranded DNA is stabilized by SSB proteins 3) Primase make an RNA primer (which provided a free 3' OH group and the primer needed for the DNA polymerase to work_ to start the new DNA synthesis
- SSN
- Single-stranded DNA binding protein, stabilizes the single-stranded DNA
- Primase
- Synthesizes RNA primers
- Griffith
- Rat experiment. S-strain killed. R-strain doesn't
- DNA gryase
- introduces supercoiling in the DNA
- DNA polymerases III Holoenzyme
- DNA repolication proof reading and repair
- DNA Polyermase III
- Once the new DNA strand is synthesized, DNA polyermase III proofreads it and make sure the errors are removed.
- DNA ligase
- Covalently joins free 3' and 5' ends of two stands
- DNA Ligase
- Once the small fragments are completed, DNA liagse joins the two ends of the DNA strands to complete DNA replication.
- Chargaff
- A and T; G and C ratio are equivalent
- DNA polyermase I
- eraes RNA primers and fills in the gaps
- DNA's Double Helix
- 1) DNA consists of two strands H-bonded together 2) THe two strands turn right to make a right-handed matrix 3) The hydrophilic sugar-phosphate is on the outside of the helix. THe negatively charged P-groups make DNA souluable in aqueous solution 4) The hydrophobic nitrogenous baes are stacked inside in a perpendicular manner to the strand. The distance between two base pairs is .34nm. 5) A pairs with T, 2 H-bonds G pairs with C, 3 H-bonds 6) The two strands run in opposite directions, i.e., antiparallel orientation. The beginning of the DNA strand has a phophate group attached to the fifth C of ribose and the other end has an -OH group attached to the third C of ribose
- Elongation
- DNA polymerase III ( a complex protein) binds to the DNA template + RNA-primer region and starts to add nucleotides that are complementary to the template strand. 2) The DNA synthesis always happens 5' to 3'. This is a reulst of the nature of the enzyme DNA polymerases to link new deoxyncleoside triphosphates (dNTPs) onl to the 3'-OH group.
- Helicase
- Unwiinds the double helix into single-stranded DNA
- Avery, McLeod, McCarty
- isolated pure DNA from the S-strain , mixed with R-strain to transform the latter into a disease-causing strain.
- Topoisomerase I
- Relaxes the supercoiled DNA
- Leading Strand
- is synthesized conitnously from 5' to 3' based on the template.