DNA REPLICATION NOTES
The Central Dogma
Replication Facts DNA has to be copied before a cell divides DNA is copied during the S or synthesis phase of interphase New cells will need identical DNA strands Synthesis Phase (S phase) S phase during interphase of the cell cycle Nucleus of eukaryotes DNA replication takes place in the S phase. S phase G 1 interphase G 2 Mitosis -prophase -metaphase -anaphase -telophase 3
DNA Two strands coiled called a double helix Sides made of a pentose sugar Deoxyribose bonded to phosphate (PO 4 ) groups by phosphodiester bonds Center made of nitrogen bases bonded together by weak hydrogen bonds 4
DNA Phosphate Group Stands for Deoxyribonucleic acid Made up of subunits called nucleotides Nucleotide made of: 1.Phosphate group 2.5-carbon sugar 3.Nitrogenous base O O=P-O O Sugar (deoxyribose) 5 CH2 C 4 O C 3 C 2 C 1 N Nitrogenous base (A, G, C, or T) 5
Pentose Sugar 5 O 3 Carbons are numbered clockwise 1 to 5 P 3 O 5 P 5 Sugar (deoxyribose) CH2 O C 4 C 3 C 2 C 1 P 5 4 5 3 O O 1 2 T G A C 2 3 1 O 3 4 5 P P 3 O 5 P 6
Antiparallel Strands One strand of DNA goes from 5 to 3 (sugars) The other strand is opposite in direction going 3 to 5 (sugars) 7
Semiconservative Model of Replication Idea presented by Watson & Crick The two strands of the parental molecule separate, and each acts as a template for a new complementary strand New DNA consists of 1 PARENTAL (original) and 1 NEW strand of DNA DNA Template Parental DNA New DNA 8
DNA Replication As the 2 DNA strands open at the origin, Replication Bubbles form Prokaryotes (bacteria) have a single bubble Eukaryotic chromosomes have MANY bubbles Bubbles Bubbles 9
DNA Replication Begins at Origins of Replication Two strands open forming Replication Forks (Y-shaped region) New strands grow at the forks 3 5 3 Parental DNA Molecule Replication Fork 5 10
DNA Replication Driven by Enzymes Enzyme Helicase unwinds and separates the 2 DNA strands by breaking the weak hydrogen bonds Single-Strand Binding Proteins attach and keep the 2 DNA strands separated and untwisted Primase (an RNA primer) fills in areas to start replication; these must be present to start the addition of new nucleotides DNA polymerase can then add the new nucleotides in the 5 to 3 direction ONLY. #1 #2 #3 #4 #5 #6
DNA Replication Driven by Enzymes Enzyme Exonuclease then remove the primers and inserts the correct bases. Enzyme Ligase glues/seals the two strands together #1 #2 #3 #4 #5 #6
Step #1 - Helicase Helicase splits DNA into two separate strands within a replication bubble; creating a replication fork.
Step #2 - Primase Primase inserts short RNA fragments that is a message that says Yo, start replicating DNA right here.
Step #3 DNA Polymerase After Primase inserts RNA fragments, DNA polymerase knows where to start adding nucleotides. This enzyme begins adding nucleotides in the 5 to 3 direction
The problem with DNA Polymerase
DNA Polymerase is picky It can only add nucleotides in the 5 to 3 direction. Meaning that the two stands of DNA are going to have to be treated differently. Leading Strand: can be replicated in one continuous 5 to 3 direction Lagging Strand: must be replicated in segments using Okazaki FRAGMENTS
Lagging Strand: must be replicated in segments using Okazaki FRAGMENTS On the lagging strand Primase makes several start here, bro locations. It creates a 5 end that DNA polymerase can attach to and start adding nucleotides. DNA Polymerase will add these fragments (100-200 nucleotides long) in short bursts, making the name lagging a very honest name. Guy who discovered these fragments was a Japanese molecular biologist: Reiji Okazaki
Step #4 Exonuclease RNA segments that were added by Primase do not belong in DNA. So they HAVE GOT TO GO. Enzyme Exonuclease removes the primers and DNA polymerase fills in these gaps with DNA nucleotides. Exonuclease with the aide of all three different DNA polymerases helps proofread the DNA to ensure that mistakes were not made.
Step #5 Ligase Now that everything is replicated and double checked for spelling errors, the Ligase enzyme glues or seals the two new strands together (effectively printing and stapling your English paper together).
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DNA Replication Leading Strand 1. Helicase unzips the DNA 2. DNA primase preps for the start of replication 3. DNA polymerase slides along the leading strand in the 3 to 5 direction synthesizing the matching strand in the 5 to 3 direction 4. The Primase is discarded and nucleotides are added by DNA polymerase, and then DNA ligase connects the fragment at the start of the new strand to the end of the new strand
DNA Replication Lagging Strand 1. Helicase unzips the DNA 2. DNA primase preps for the start of replication 3. DNA polymerase slides along the leading strand in the 3 to 5 direction synthesizing the matching Okazaki fragments in the 5 to 3 direction 4. The Primase is discarded and nucleotides are added by DNA polymerase. 5. DNA ligase connects the Okazaki fragments to one another
Proofreading New DNA DNA polymerase initially makes about 1 in 10,000 base pairing errors Enzymes proofread and correct these mistakes The new error rate for DNA that has been proofread is 1 in 1 billion base pairing errors DNA Damage & Repair Chemicals & ultraviolet radiation damage the DNA in our body cells Cells must continuously repair DAMAGED DNA Excision repair occurs when any of over 50 repair enzymes remove damaged parts of DNA DNA polymerase and DNA ligase replace and bond the new nucleotides together 24
Wednesday, February 15 th As you come in, grab the Replication Bubble from the back cabinet!
1. COLOR the existing bases on your replication bubble according to the following rules: A = Red T = Pink G = Blue C = Purple 2. FIND the complementary base pairs in the baggies around the room (BE CAREFUL NOT TO SPILL!) 3. PASTE the complementary base pairs to your replication bubble (watch out for those Okazaki Fragments on the LAGGING strand!) 4. When you are finished POST the replicated DNA to the BLUE wall as designated by Mrs. Tupper Okazaki Fragments DNA Replication Activity NITROGEN BASES
Thursday, February 16 th As you come in, grab your plicker card. You will have the first 10 minutes to work on your Replication Bubble. (IF you have FINISHED, get out your REPLICATION PRACTICE).