DNA

EUKARYOTIC CELLS DOUBLE HELIX COILS AROUND HISTONE PROTEINS FORMING A NUCLEOSOME NUCLEOSOMES COIL AROUND H1 HISTONES INTO A SUPER COIL SUPER COILS WIND UP ON A PROTEIN SCAFFOLD TO FORM CHROMOSOMES CHROMOSOMES FORM CHROMATIN IN NUCLEUS SUPERCOIL

PRIMARY FUNCTIONS STORES AND TRANSMITS GENETIC INFORMATION WITHIN ORGANISM ALSO TO NEXT GENERATION CHEMICALLY CONTROLS THE SYNTHESIS OF ALL PROTEINS CHEMICAL PHENOTYPE: ENZYMES, HORMONES, HEMOGLOBIN, ETC STRUCTURAL PHENOTYPE: CHARACTERISTICS OF ORGANISMS-HAIR, WINGS, COLLAGEN, CLAWS, ETC

DeoxyriboNucleic Acid Made of repeating monomers: NUCLEOTIDES 5-carbon sugar Phosphate functional group 1 of 4 Nitrogen containing bases Adenine Cytosine Guanine Thymine

NITROGEN BASES PURINES PYRIMIDINES BASES WITH TWO CARBON RINGS BASES WITH ONE CARBON RING RNA THE PURINE AND PYRIMIDENE BASES ARE ISOMERS

BASE PAIR BONDING ONE PURINE BONDS WITH ONE PYRIMIDINE FORMING A COMPLIMENTARY BASE PAIR CHARGAFF RULE: A=T AND G=C ADENINE ALWAYS BONDS WITH THYMINE w/2 H bonds forming either: A-T OR T-A GUANINE ALWAYS BONDS WITH CYTOSINE w 3/H bonds forming either: G-C OR C-G

Determining Molecule’s Orientation The DNA molecule’s orientation is determined by the 5 carbons in the deoxyribose sugar. The carbon bonded to the base is #1, carbons are counted around the ring to the carbon bonded to the PO4, carbon #5. If the #5 carbon is ‘high’ and the corner #3 carbon is ‘low’ the strand is referred to as the 5 prime-3 prime or 5’-3’ strand. What would the other side of the molecule look like and what would be it’s orientation? This orientation of the two sides of the DNA molecule makes it antiparallel Knowing DNA’s orientation is important in understanding replication, protein synthesis and which alleles are coded. PO4 low, sugar “upside down” or 3’- 5’

To Summarize DNA LOOKS LIKE A LADDER SUGAR AND PHOSPHATE MAKES THE “FRAME” BASES FORM THE “RUNGS” ONE SIDE OF MOLECULE MUST “FLIP” IN ORDER FOR HYDROGEN BONDS TO FORM BETWEEN BASES, IT IS ANTIPARALLEL ALL BASE PAIRS, NO MATTER THE ORDER OR ORIENTATION, HAVE THE SAME STRUCTURAL SHAPE SO THEY STACK ON TOP OF EACH OTHER AND TWIST FORMING THE DOUBLE HELIX SINCE A ALWAYS BONDS WITH T, AND C WITH G, THEIR AMOUNTS MUST BE EQUAL TO EACH OTHER(Chargaff Principle) DNA’S STRUCTURE ALLOWS THE MOLECULE TO REPLICATE ITSELF QUICKLY, CODE FOR THE SYNTHESIS OF PROTEINS WITHIN ALL ORGANISMS THE SAME WAY EACH TIME.

DNA Replication - Occurs during S phase of Interphase. One strand of DNA has all of the information needed to reconstruct the other half through the mechanism of base pairing. During DNA replication, the DNA molecule is used to produce two new complementary strands. Each strand of the double helix serves as a template for the new strand.

DNA REPLICATION

3 Models for DNA Replication

Overview of DNA Replication

Enzymes in DNA Replication Topoisomerase: regulates the coiling and uncoiling of DNA Helicase: Unbinds a portion of the DNA double helix between bases RNA Primase: Attaches RNA primers to the replicating strands. DNA Polymerase delta (ä): Binds to the 5' - 3' strand in order to bring nucleotides and create the daughter leading strand. DNA Polymerase epsilon (å): Binds to the 3' - 5' strand in order to create discontinuous segments starting from different RNA primers. Topoisomerase

Enzymes in DNA Replication Exonuclease (DNA Polymerase I): Finds and removes the RNA Primers DNA Ligase: Adds phosphate in the remaining gaps of the phosphate - sugar backbone. Ligase means “to tie”. Nucleases: Remove wrong nucleotides from the daughter strand. “Proof-reader” enzyme Binding Proteins: Not enzymes. Stabilize the molecule once strands are separated for replication Topoisomerase Exonuclease: removes RNA primer

3. How is the DNA molecule stabilized after it is unwound? 1. Which enzyme unbinds the parental double helix? Where does this take place?   2. What is the area of unwound DNA where replication will take place called? 3. How is the DNA molecule stabilized after it is unwound? 4. In which direction does replication occur? Why is this a ‘problem’ for one side of the molecule? 5. How does replication differ for the leading and lagging strand? 6. What is the function of DNA polymerase? 7. What kind of fragments are constructed by the lagging strand? 8. How does the DNA polymerase ‘know’ where to begin construction of the lagging strand? 9. After the lagging strand fragments are constructed what two steps occur to complete the strand and link the fragments together? 10. Locate the enzyme topoisomerase on the diagram. Hypothesize the purpose for this enzyme. HELICASE, BETWEEN THE COMPLIMENTARY BASE PAIRS REPLICATION FORKS FORM REPLICATION BUBBLES ALONG THE STRAND STABILIZING PROTEINS ATTACH TO THE PO4 ALONG THE STRAND ON BOTH SIDES REPLICATION OCCURS FROM 3’ TO 5’ DIRECTION AS NUCLEOTIDES MUST BE ADDED IN A 5’-3’ ORIENTATION, SO THE 5’-3’ SIDE MUST BE REPLICATED “BACKWARDS” LEADING STRAND(3’-5’) IS REPLICATED CONTINUOUSLY, LAGGING STRAND(5’-3’) DISCONTINUOUSLY The DNA POLYMERASE ENZYMES BRING NUCLEOTIDES INTO PLACE OKAZAKI FRAGMENTS A SMALL PIECE OF DNA IS CONVERTED TO AN RNA PRIMER BY ENZYME PRIMASE THE RNA PRIMER IS CONVERTED BACK TO DNA(BY ANOTHER POLYMERASE) AND THEN DNA LIGASE CONNECTS THE FRAGMENT TO THE STRAND THIS ENZYME UNWINDS THE HELIX AHEAD OF HELICASE AND KEEPS THE STRAND ORIENTED CORRECTLY AND UNTANGLED

The speed of DNA replication for the humans is about 50 nucleotides per second per replication fork (low speed comparing to the speed of the bacterial DNA Replication). But the human genome can be copied only in a few hours because many replication forks take place at the same time (multiple initiation sites). DNA Rep

Replication and Cells Human body grows to 100 trillion cells DNA rep occurs about 100 quadrillion times Not all DNA sequences encode proteins, in fact most do not. Next Question: How are the sequences of DNA that encode proteins distinguished from those that do not?