Nucleic Acids Information storage 2006-2007

Nucleic Acids Function: genetic material stores information genes blueprint for building proteins DNA  RNA  proteins transfers information blueprint for new cells blueprint for next generation DNA proteins

Nucleic Acids Examples: Structure: RNA (ribonucleic acid) single helix DNA (deoxyribonucleic acid) double helix Structure: monomers = nucleotides DNA RNA

Nucleotides 3 parts nitrogen base (C-N ring) pentose sugar (5C) ribose in RNA deoxyribose in DNA phosphate (PO4) group Nitrogen base I’m the A,T,C,G or U part! Are nucleic acids charged molecules? DNA & RNA are negatively charged: Don’t cross membranes. Contain DNA within nucleus Need help transporting mRNA across nuclear envelope. Also use this property in gel electrophoresis.

Types of nucleotides 2 types of nucleotides different nitrogen bases Purine = AG Pure silver! 2 types of nucleotides different nitrogen bases purines double ring N base adenine (A) guanine (G) pyrimidines single ring N base cytosine (C) thymine (T) uracil (U)

Dangling bases? Why is this important? Nucleic polymer Backbone sugar to PO4 bond phosphodiester bond new base added to sugar of previous base polymer grows in one direction N bases hang off the sugar-phosphate backbone Dangling bases? Why is this important?

Pairing of nucleotides Nucleotides bond between DNA strands H bonds purine :: pyrimidine A :: T 2 H bonds G :: C 3 H bonds The 2 strands are complementary. One becomes the template of the other & each can be a template to recreate the whole molecule. Matching bases? Why is this important?

H bonds? Why is this important? DNA molecule Double helix H bonds between bases join the 2 strands A :: T C :: G H bonds = biology’s weak bond • easy to unzip double helix for replication and then re-zip for storage • easy to unzip to “read” gene and then re-zip for storage H bonds? Why is this important?

Matching halves? Why is this a good system? Copying DNA Replication 2 strands of DNA helix are complementary have one, can build other have one, can rebuild the whole when cells divide, they must duplicate DNA exactly for the new “daughter” cells Why is this a good system? Matching halves? Why is this a good system?

When does a cell copy DNA? When in the life of a cell does DNA have to be copied? cell reproduction mitosis gamete production meiosis when cells divide, they must duplicate DNA exactly for the new “daughter” cells Why is this a good system?

DNA Replication 2007-2008

Directionality of DNA You need to number the carbons! nucleotide it matters! nucleotide PO4 N base 5 CH2 This will be IMPORTANT!! O 4 1 ribose 3 2 OH

Sounds trivial, but… this will be IMPORTANT!! 5 The DNA backbone PO4 Putting the DNA backbone together refer to the 3 and 5 ends of the DNA the last trailing carbon base CH2 5 O 4 1 C 3 2 O –O P O Sounds trivial, but… this will be IMPORTANT!! O base CH2 5 O 4 1 3 2 OH 3

Anti-parallel strands Nucleotides in DNA backbone are bonded from phosphate to sugar between 3 & 5 carbons DNA molecule has “direction” complementary strand runs in opposite direction 5 3 3 5

Bonding in DNA 5 3 3 5 hydrogen bonds covalent phosphodiester ….strong or weak bonds? How do the bonds fit the mechanism for copying DNA?

Base pairing in DNA Purines Pyrimidines Pairing adenine (A) guanine (G) Pyrimidines thymine (T) cytosine (C) Pairing A : T 2 bonds C : G 3 bonds

Copying DNA Replication of DNA base pairing allows each strand to serve as a template for a new strand new strand is 1/2 parent template & 1/2 new DNA semi-conservative copy process

DNA Replication Large team of enzymes coordinates replication Let’s meet the team… DNA Replication Large team of enzymes coordinates replication Enzymes more than a dozen enzymes & other proteins participate in DNA replication

Replication: 1st step Unwind DNA helicase enzyme I’d love to be helicase & unzip your genes… Replication: 1st step Unwind DNA helicase enzyme unwinds part of DNA helix stabilized by single-stranded binding proteins helicase single-stranded binding proteins replication fork

Where’s the ENERGY for the bonding! We’re missing something! Replication: 2nd step Build daughter DNA strand add new complementary bases DNA polymerase III Where’s the ENERGY for the bonding! But… We’re missing something! What? DNA Polymerase III

Leading & Lagging strands Okazaki Leading & Lagging strands Limits of DNA polymerase III can only build onto 3 end of an existing DNA strand  5 Okazaki fragments 5 5 3 5 3 5 3 ligase Lagging strand 3 growing replication fork 3 5 Leading strand  3 5 Lagging strand Okazaki fragments joined by ligase “spot welder” enzyme 3 DNA polymerase III Leading strand continuous synthesis

direction of replication Replication fork DNA polymerase III lagging strand DNA polymerase I 3’ primase Okazaki fragments 5’ 5’ ligase SSB 3’ 5’ 3’ helicase DNA polymerase III 5’ leading strand 3’ direction of replication SSB = single-stranded binding proteins

DNA polymerase III enzyme DNA polymerases DNA polymerase III 1000 bases/second! main DNA builder DNA polymerase I 20 bases/second editing, repair & primer removal DNA polymerase III enzyme In 1953, Kornberg was appointed head of the Department of Microbiology in the Washington University School of Medicine in St. Louis. It was here that he isolated DNA polymerase I and showed that life (DNA) can be made in a test tube. In 1959, Kornberg shared the Nobel Prize for Physiology or Medicine with Severo Ochoa — Kornberg for the enzymatic synthesis of DNA, Ochoa for the enzymatic synthesis of RNA.

Editing & proofreading DNA 1000 bases/second = lots of typos! DNA polymerase I proofreads & corrects typos repairs mismatched bases removes abnormal bases repairs damage throughout life reduces error rate from 1 in 10,000 to 1 in 100 million bases