DNA Strcuture and Replication (PART 2) Ms. Gaynor AP Biology

DNA and Its Structure From 1953

What is the Double Helix? Shape of DNA Looks like a twisted ladder 2 coils are twisted around each other Double means 2 Helix means coil

The Structure of DNA Made out of nucleotides Includes a phosphate group, nitrogenous base and 5-carbon pentose sugar Nucleotide Structure 1 “link” in a DNA chain

Nucleoside Structure

DNA has a overall negative charge b/c of the PO4-3 (phosphate group) A Polynucleotide MANY nucleotides (“links”) bonded together Nucleotide Structure DNA has a overall negative charge b/c of the PO4-3 (phosphate group)

The Structure of DNA Backbone Backbone = alternating P’s and sugar Held together by COVALENT bonds (strong) Inside of DNA molecule = nitrogen base pairs Held together by HYDROGEN bonds (weaker) Backbone

The covalent that holds together the backbone Phosphodiester Bond The covalent that holds together the backbone Found between P & deoxyribose sugar STRONG!!!

Minor Groove Major Groove

DNA is antiparallel Antiparallel means that the 1st strand runs in a 5’ 3’ direction and the 2nd 3’ 5’ direction THEY RUN IN OPPOSITE or ANTIPARALLEL DIRECTIONS P end is 5’ end (think: “fa” sound) -OH on deoxyribose sugar is 3’ end 5’ and 3’ refers to the carbon # on the pentose sugar that P or OH is attached to

DNA Bonding Purines (small word, big base) Pyrimidines Adenine Guanine Pyrimidines (big word, small base) Cytosine Thymine Chargaff’s rules A=T, C=G Hydrogen Bonds attractions between the stacked pairs; WEAK bonds

Why Does a Purine Always Bind with A Pyrimidine?

DNA Double Helix LET’S PRACTICE… Watson & Crick said that… http://www.sumanasinc.com/webcontent/animations/content/DNA_structure.html Watson & Crick said that… strands are complementary; nucleotides line up on template according to base pair rules (Chargaff’s rules) A to T and C to G LET’S PRACTICE… Template: 5’AATCGCTATAC3’ Complementary strand: 3’ TTAGCGATATG5’

REVIEW… ______ discovered the double helix structure of DNA and won a Nobel prize for this work in 1962 ______ made photo 51, which helped discover the correct helical shape of DNA ______ worked with pneumococcus bacteria and mice to conclude an inheritance molecule is present in cells ______ worked with fruit flies and discovered genes are linked (connected to) chromosomes (chunks of DNA) ______ worked with bacteriophages and discovered that DNA not protein is the inheritance molecule in cells ______ worked with pneumococcus bacteria and test tubes to discover DNA not RNA or protein is a transforming agent ______ worked with x-ray crystallography and created pictures of DNA; won a Nobel prize in 1962 for this work ______ discovered DNA in any species contains equal amounts of adenine and thymine and equal amounts of guanine and cytosine; credited with forming the “base pair rules” ______ worked with garden pea plants and was the first scientist to study inheritance patterns

Label the DNA strands shown below. Label a deoxyribose sugar molecules a phosphate molecules (PO43-) Hydrogen bonds Label the phosphodiester bonds The 5’ and 3’ ends Label the bases that are not already labeled Purines Pyrimidines 5. (3’ end) 5. (5’ end) 3. (2 bonds) 6. T 1. 2. 6. A 3. (3 bonds) 6. C 4. 6. G A and G C and T 5. (5’ end) 5. (3’ end)

A nucleotide is made of three parts: a ________ group, a five carbon __________________, and a nitrogen containing _____________________. Nucleotides are monomers for _______ and ________. In a single strand of DNA, the phosphate group binds to the _______ of the next group to form the _____________ of the molecule. What bond holds together the sugars and phosphates in DNA? _______________ The _______ _______ form the middle of the DNA molecule (rungs or steps of the ladder) and are held together by _________________ bonds. Purines have _____ rings of carbon, and pyrimidines have ______ ring. Purines include ___________ base and ____________ base. Pyrimidines include __________ base and ____________ base. In DNA, thymine is complementary to ________________ ; cytosine is complementary to _____________. Thymine and _____________________ are _____ hydrogen bonds together. Cytosine and _____________________ are _____ hydrogen bonds together.

DNA Replication (initiation)

DNA Replication DNA Replication = DNA  DNA Parent DNA makes 2 exact copies of DNA Why?? Occurs in Cell Cycle before MITOSIS so each new cell can have its own FULL copy of DNA

Models of DNA Replication http://www.sumanasinc.com/webcontent/animations/content/meselson.html

DNA Replication How does it occur? Matthew Meselson & Frank Stahl Discovered replication is semiconservative PROCEDURE  varying densities of radioactive nitrogen (Nitrogen is in DNA)

Meselson & Stahl Experiment **DNA is semiconservative http://highered.mcgraw-hill.com/sites/0072437316/student_view0/chapter14/animations.html

DNA Replication: a closer look http://henge.bio.miami.edu/mallery/movies/replication.mov

DNA Replication Steps: Initiation involves assembly of replication fork (bubble) at origin of replication sequence of DNA found at a specific site Elongation Parental strands unwind and daughter strands are synthesized. the addition of bases by proteins Termination: the duplicated chromosomes separate from each other. Now, there are 2 IDENTICAL copies of DNA.

BEGINNING OF DNA REPLICATION Segments of single-stranded DNA are called template strands. Copied strand is called the complement strand (think “c” for copy) BEGINNING OF DNA REPLICATION (INITIATION) Gyrase (type of topoisomerase) relaxes the supercoiled DNA. DNA helicase (think “helix”) binds to the DNA at the replication fork untwist (“unzips”) DNA using energy from ATP Breaks hydrogen bonds between base pairs Single-stranded DNA-binding proteins (SSBP) stabilize the single-stranded template DNA during the process so they don’t bond back together.

Supercoiled DNA relaxed by gyrase & unwound by base pairs 5’ 3’ Supercoiled DNA relaxed by gyrase & unwound by helicase SSB Proteins Helicase ATP Gyrase SSB Proteins http://media.pearsoncmg.com/bc/bc_campbell_biology_7/media/interactivemedia/activities/load.html?16&F

DNA Replication (elongation)

DNA Replication (Elongation) After SSBP’s bind to each template… RNA Primase binds to helicase primase is required for DNA synthesis Like a “key” for a car ignition makes a short RNA primers Short pieces of RNA needed for DNA synthesis DNA polymerase adds nucleotides to RNA primer  makes POLYNUCLEOTIDES (1st function) After all nucleotides are added to compliment strand… RNA primer is removed and replaced with DNA by DNA polymerase (2nd function) DNA ligase “seals” the gaps in DNA Connects DNA pieces by making phosphodiester bonds

Supercoiled DNA relaxed by gyrase & unwound by base pairs 5’ 3’ Supercoiled DNA relaxed by gyrase & unwound by helicase + proteins: SSB Proteins Helicase ATP DNA Polymerase 1 2 Gyrase RNA primer replaced by DNA Polymerase & gap is sealed by ligase RNA Primer primase DNA Polymerase Leading strand http://media.pearsoncmg.com/bc/bc_campbell_biology_7/media/interactivemedia/activities/load.html?16&F

Elongation 5’  3’ direction only!!! Antiparallel nature: Sugar (3’end)/phosphate (5’ end) backbone runs in opposite directions one strand runs 5’  3’, other runs 3’  5’ DNA polymerase only adds nucleotides at the free 3’ end of NEW STRAND forming new DNA strands in the 5’  3’ direction only!!!

Elongation (con’t) Leading (daughter) strand NEW strand made toward the replication fork (only in 5’  3’ direction from the 3’  5’ master strand Needs ONE RNA primer made by Primase This new leading strand is made CONTINOUSLY

Elongation (con’t) Lagging (daughter) strand NEW strand synthesis away from replication fork Replicate DISCONTINUOUSLY Creates Okazaki fragments Short pieces of DNA Okazaki fragments joined by DNA ligase “Stitches” fragments together Needs MANY RNA primer made by Primase

Supercoiled DNA relaxed by gyrase & unwound by base pairs 5’ 3’ Supercoiled DNA relaxed by gyrase & unwound by helicase + proteins: SSB Proteins DNA Polymerase Lagging strand Okazaki Fragments 1 Helicase ATP 2 3 Gyrase RNA primer replaced by DNA Polymerase & gap is sealed by DNA ligase RNA Primer primase DNA Polymerase 5’  3’ Leading strand http://media.pearsoncmg.com/bc/bc_campbell_biology_7/media/interactivemedia/activities/load.html?16&F

DNA Replication: Elongation http://highered.mcgraw-hill.com/sites/0072437316/student_view0/chapter14/animations.html

DNA Replication (termination)

Telomeres Euchromatin = coding region of DNA; contains active genes (in both prokaryotes & eukaryotes) Not all euchromatin is necessarily transcribed THINK: “Eu” need Euchromatin Heterochromatin = noncoding region of DNA; contains active genes (only in eukaryotes) Thought to protect the genes while they are not in use/ “turned on” in transcription

Termination (Telomeres) Short repeats of “G” base found at END of LINEAR chromosomes in eukaryotes protect ends of linear chromosomes The repeated sequence of GGGTTA make up the human telomeres. Telomerase is the enzyme that makes telomeres.

http://spine.rutgers.edu/cellbio/assets/flash/tel.htm

Telomeres, Aging & Cancer Telomeres get shorter as cell divides leads to aging??? Most cancers come from body cells. Cancers cell have ability to divide indefinitely. Normal cells limited to ~50-75 divisions  stop making telomerase. 85–90% cancer cells continue to make high levels of telomerase & are able to prevent further shortening of their telomeres. Leads to “immortality”

Mistakes Made during DNA Replication Mutation Change in DNA (genetic material) Frameshift(s) extra or missing base(s). Substitutions when the wrong nucleotide is incorporated (mismatch mutation). Deletions Nucleotides are deleted shortening the DNA

DNA Repair Errors occur 1/10 billion nucleotides Mismatch repair (Humans have 3 billion base pairs in their DNA) Mismatch repair DNA polymerase (yes…it’s 3rd function) “Proofread” new DNA Like the “delete” key on computer Excision (“cut out”) repair Nuclease

DNA Repair