DNA

1. DNA

2. Bellwork! Happy Monday (eh)! Two more weeks until Spring Break! What is the shape of DNA? What are the four nitrogenous bases found in DNA? What does DNA code for?

3. DNA Function We need DNA to tell our bodies what proteins to make. These proteins make up EVERYTHING. DNA codes for protein synthesis by first coding for RNA. Hmm… you don’t know what protein synthesis is. Or do you? Either way, you will know a whole lot more by Friday 

4. DNA Structure • DNA is made up nucleotides • Nucleotides are made of deoxyribose (a sugar), a phosphate group, and one of four different nitrogenous bases. • Together, these nucleotides create a double helix, or spiral staircase shape

6. Adenine and guanine are purines. Purines are the larger of the two types of bases found in DNA. Cytosine and thymine are pyrimidines, which are the smaller of the two bases. Chargaff’s Rule: Adenine and Thymine are found in almost equal concentrations in DNA Cytosine and Guanine are found in almost equal concentrations in DNA Which begs the conclusion: • A pairs with T • C pairs with G

8. When A & T are paired, there are TWO hydrogen bonds linking them together.

9. When C & G are paired, there are THREE hydrogen bonds linking them together.

10. Each nucleotide consists of a 5-carbon sugar (deoxyribose), a nitrogen containing base attached to the sugar, and a phosphate group. There are four different types of nucleotides found in DNA, differing only in the nitrogenous base.

11. DNA Replication • In order for DNA to be passed down to future generations or even for new somatic cells to be made, it must replicate • Replication= making an exact copy

12. DNA replication occurs in a semi-conservative manner • The double helix “un-zips” so that a new complimentary strand can be made next to it

13. DNA Replication Vocabulary • Helicase: Enzyme required for DNA to unzip • Topoisomerase: Keeps the supercoiled DNA that is not replicating from breaking • Single Strand Binding Proteins (SSBs): Keep the DNA from zipping back up • DNA Polymerase III: Adds new complimentary nucleotides to the exposed DNA • Primase: Enzyme that creates an RNA primer which DNA Polymerase III will use to make complimentary nucleotides • RNA primer: Sequence of nucleotides laid down so that DNA Polymerase III can begin to add complimentary nuclotides • RNas H: Removes used RNA primers • Ligase: “Glues” together sections of newly synthesized DNA

14. DNA Replication http://www.wiley.com/college/pratt/0471393878/student/animations/dna_replication/index.html • DNA is unzipped by the enzyme Helicase as it enters the “replication factory” • It is important to note that the DNA itself moves through a region of the cell where free-nucleotides and important enzymes are located. The enzymes required for DNA replication do not move to the DNA. • Topoisomerase keeps the now supercoiled regions of DNA from snapping • A replication “bubble” forms where the DNA is open, and the two ends of the bubble where replication is actively taking place are known as the Replication Forks

15. The two strands of DNA that make up the double helix are lined up oppositely. One end of the strand is called the 5’ end and the other is the 3’ end • DNA Polymerase can only synthesize DNA in the 5’ to 3’ direction because it is the most stable for the phosphate backbone

16. An RNA primer lays down on the exposed DNA, laying a framework for the coming DNA Polymerase III to add complimentary nucleotides. • DNA Polymerase III moves down the strand of DNA with the help of the sliding arm. Here, it picks up a code left by an RNA primer that was laid down earlier by RNA Primase. • It is important to note that DNA Polymerase III cannot itself begin adding new nucleotides, it can only add to what the RNA primer has already set down. • Once replication is complete, RNase H removes the RNA primers. DNA Polymerase I fills their now empty area on the strand, and Ligase (another enzyme) “glues” together the pieces.

17. One strand of the unzipped DNA is in the right orientation to allow DNA Polymerase III to move freely down the unzipped strand. This strand is in the 3’ to 5’ direction, allowing DNA Polymerase III to move in the 5’ to 3’ direction. This easily replicated strand is the Leading Strand.

18. Problem: The other strand of unzipped DNA is laying in the 5’ to 3’ direction, which makes it difficult for DNA Polymerase III to move down the strand. Oops. This strand will be called the Lagging Strand. • RNA primer is still laid down on this section, but DNA Polymerase III must work in short “bursts” or sections. These short sections of newly replicated DNA are called Okazaki Fragments. After several of them are formed, Ligase must come in and glue them together.

19. Wednesday Bellwork! Half-way there people! • Get out your DNA Replication instructions/ summaries. • For your bellwork, try to do this without looking at notes: Define the following – HelicasePrimase Topoisomerase RNA Primer Single Strand Binding Proteins Rnase H DNA Polymerase III

20. DNA Review • Where is DNA located? • What are chromosomes made of? • What is DNA made of? • What are nucleotides made of? • What are the nitrogenous bases?

21. DNA >>>> RNA >>>>> Proteins If the entire point of having DNA is to make proteins that eventually make EVERYTHING about US, we need to talk about how to make those proteins from DNA.

22. First off, you need to remember that genes code for proteins. Genes are a region on a chromosome (DNA) that tell the cell what to do. In the beginning, we kind of simplified this by saying that genes were what caused traits, like dimples and freckles, and Hemophilia. Really, if we want to be grown up about it, we can realize that genes only actually code for a protein (genotype?) that then shows up as a phenotype such as dimples, freckles, and Hemophilia.

23. The entire process from DNA to Protein is called PROTEIN SYNTHESIS. DNA Transcription and Translation are the two steps of PROTEIN SYNTHESIS. Transcription: DNA to RNA Translation: RNA to Proteins Movie

25. TRANSCRIPTION • One gene codes for one protein. That’s a law. No questions. • Each gene is made of many nucleotides (that looks like TATAAGTCGAAGTTTCGA…..) • The gene has 3 regions: Promoter, Coding, and Terminator

26. TRANSCRIPTION • An initiation sequence tells RNA Polymerase where to bind on the DNA strand. This area where the RNA Polymerase binds is known as the promoter region. • Elongation: Transcription factors (proteins) bind to the DNA and begin to unzip it. RNA Polymerase will then “read” ONE of the coding regions in ONE of the strands. The strand that is read is the antisense strand. The non-read strand is the sense strand. During this elongation phase, RNA Polymerase is adding complimentary nucleotides to the opened DNA. Something is different: RNA doesn’t use the exact same nitrogenous bases as DNA. Instead of Thyamine, RNA uses Uracil. So the normal C=G still exists, but now T is replaced by U, so A=U. While not a huge difference, you won’t be able to transcribe DNA to RNA if youdon’tuse uracil. This new strand of information, properly called Messenger RNA or mRNA (not just plain ole’ RNA) keeps growing and growing. It isn’t attached to the DNA stand though, it is off to the side. It will fall off in a minute and do it’s own thing. Just wait! 3. RNA polymerase keeps growing until it reaches the terminator sequence, which causes the newly formed mRNA strand to fall off. This event is called termination.

27. TRANSCRIPTION ANIMATIONS http://www-class.unl.edu/biochem/gp2/m_biology/animation/gene/gene_a2.html http://bcs.whfreeman.com/thelifewire/content/chp12/1202001.html http://www.youtube.com/watch?v=5MfSYnItYvg&feature=related

28. REPLICATION V. TRANSCRIPTION

29. WHILE WE’RE AT IT. LETS COMPARE AND CONTRAST RNA AND DNA!

30. TRANSLATION RNA TO PROTEINS First of all, Translation happens in the Cytoplasm of the cell. DNA Replication and Transcription happen in the nucleus. Frankly, DNA is too big to move out of the Nucleus of the cell. Just can’t fit out the door. But also, it SHOULDN’T. DNA is safer in the nucleus than in the cytoplasm.