Unraveling DNA: The Molecule of Life

1. The Molecule of Life

2. DNA DNA is the molecule of life. All living things contain DNA. DNA is found in the nucleus of cells. DNA contains genetic codes that determine physical features.

3. DNA DNA stands for deoxyribonucleic acid. It may sound gibberish, but the name actually tells us two things: • DNA contains deoxyribose (a 5-carbon sugar) • DNA is a nucleic acid (molecule made up of nucleotides) Nucleotide 

4. Nucleotides consist of a sugar molecule attached to a nitrogen base and a phosphate group. Phosphate Nitrogen Base Sugar • Nucleotides have 3 parts: • Sugar • Nitrogen Base • Phosphate

5. The Nitrogen Bases There are 4 possible different nitrogen bases: -adenine -guanine -cytosine -thymine These 4 different bases allow for genetic diversity

6. Base-pairing rules DNA is a double stranded molecule – the two strands are connected by the nitrogen bases. Adenine can only pair with thymine (and vice versa). Guanine can only pair with cytosine (and vice versa). C G T A

7. Purines vs. Pyrimidines The molecular structure of the 4 bases fall under two categories: • Purines- double ring structures - adenine and guanine are purines 2) Pyrimidines- single ring structures - thymine and cytosine are pyrimidines Purines always bond with pyrimidines (as per the base pairing rules). Think OPPOSITES- The BIGGER word is the smaller molecule; the smaller word is the BIGGER molecule. HINT:

8. Chargaff’s Rule Chargaff's rules states that DNA from any cell should have a 1:1 ratio of pyrimidine and purine bases (as per the base pairing rules). • In other words, the amount of guanine is equal to cytosine and the amount of adenine is equal to thymine. Erwin Chargaff developed Chargaff’s rules through careful experimentation. His discoveries helpedWatson and Crick develop their model of the double helix.

9. Chargaff’s Rule Example: If a DNA molecule contains 28% cytosine, we can figure out how much guanine, thymine,and adenine are present in the molecule. According to Chargaff’s rule, how much guanine is present? How much of the DNA have we accounted for so far? 28% + 28% = 56% This tells us that 44% of the molecule must be made up of adenine and thymine.

10. Watson and Crick The shape of DNA is very complex. In 1953, James Watson and Francis Crick determined the shape of DNA based on X-ray diffraction.

11. The Structure of DNA: Discovery Though Watson and Crick tend to get most of the credit for discovering the structure of DNA, their discovery was more of a puzzle completion. • The work and information of other scientists was used to determine the structure of DNA, namely Rosalind Franklin.

12. The Structure of DNA: Discovery Rosalind Franklin was a very methodical and esteemed scientist. • Franklin was offered a position at Kings College in London to help Maurice Wilkins perfect X-ray crystallography. • Franklin and Wilkins allegedly did not get along. • Wilkins showed Watson and Crick Rosalind’s work, namely her famous “Photo 51”, which confirmed the helical structure of DNA.

13. DNA- The Double Helix Watson and Crick discovered that the shape of DNA was a double helix. Double= 2 strands of nucleotides Helix= twisted Picture a twisted ladder or staircase.

14. The Double Helix If DNA is straightened out and flattened, it looks like a ladder.

15. The sides of the ladder are composed of sugar (deoxyribose) molecules and phosphates. This is called the “sugar-phosphate backbone”. The nitrogen bases make up the rungs (steps) of the ladder.

16. The two strands of DNA are connected to each other at the bases. The bases bond together using hydrogen bonds. Adenine and thymine have two hydrogen bonds. Guanine and cytosine have three hydrogen bonds.

17. Hydrogen bonds are the weakest type of bond. You might think that DNA should be strongly held together- but it does need to unzip- and quite often! DNA comes apart during DNA Replication.

18. DNA Replication Recall that DNA is found in the nucleus of all cells. In order to make more cells (which you are constantly doing), you must make a copy of DNA first! DNA Replication occurs during the synthesis phase of the cell cycle (before the cell actually divides).

19. DNA Replication- Step 1 The first step required in order for DNA to make a copy of itself is to break those hydrogen bonds between the bases. An enzyme called DNA helicase breaks the hydrogen bonds and unzips the original parent DNA molecule.

20. DNA Replication- Step 2 Once the DNA strands are unzipped, the nucleotides are exposed. The second step involves another enzyme called DNA Polymerase. This enzyme reads the DNA and determines which NEW nucleotides to add to the parent strand. 1 1 2 3

21. Replication Forks DNA is a very long molecule that must be tightly coiled and packed into our cells. If the enzymes had to go from one end of DNA all the way to the other, it would take too long! Replication forks form at multiple points in the DNA to speed up replication. Replication fork 2 3

22. Two replication forks make replication “bubbles”.

23. 5’ and 3’ Since DNA is a 3-Dimensional molecule made of linked nucleotides, it really doesn’t have a “left” or “right”; “up” or “down”. If we have to refer to DNA’s direction we use 5’ and 3’ (5 prime and 3 prime). Recall that deoxyribose is a 5-carbon sugar. These numbers (5,3) are in respect to the position on the 5-carbon sugar.

24. Antiparallel DNA molecules are antiparallel- meaning the two strands run parallel to one another, but in different directions. (It always looks like one strand is up-side down relative to the other).

25. During DNA replication, DNA polymerase READS the parent molecule in the 3’  5’ direction. New DNA is synthesized in the 5’  3’ direction (opposite). (How to Remember? When you READ a book you would read chapters 3 to 5)

26. Leading and Lagging Daughter Strands DNA Polymerase moves from 3’ to 5’ One new strand will move continuously TOWARD the replication fork- this is known as the leading strand. Because the strands are anti-parallel, the other strand will move AWAY from the replication fork- this is the lagging strand.

27. Leading and Lagging Daughter Strands The leading strand has continuous replication - it goes along with the replication fork. The lagging strand has discontinuous replication- it moves against the replication fork.

28. Lagging Strand Since the lagging strand is traveling away from the fork, as the fork continues to open up, the lagging strand needs to jump backwards to adjust (discontinuous). Okazaki fragments are the short segments of new DNA on the lagging strand. Replication fork

29. Final Product- DNA Replication The final product of DNA replication is two molecules of DNA (4 strands total since each molecule is double stranded). However, it would not be appropriate to call the molecules “new”.

30. DNA Replication is semi-conservative (semi= half; conserve= to save) Each time DNA is copied, the original DNA molecule is saved. DNA is never destroyed during replication! • Each new molecule consists of one parental strand, and one (new) daughter strand.

31. Summary Videos http://www.youtube.com/watch?v=aSILNKbhNLg

32. DNA Replication Video • DNATube- DNA Replication

33. Self Check Quiz Deoxyribonucleic acid Double helix • The letters D.N.A. stand for ___________________________. • DNA is shaped like a _______ _______. • The four nitrogen bases are: adenine, ___________, _________, ____________. • Adenine always bonds with ____________. • Cytosine always bonds with ____________. • DNA is important because it determines your physical _______________. • DNA replication is _______- _________________. 8. DNA replicates (circle one) [before | after] cell division. 9. DNA replicates using specific [enzymes | carbohydrates]. 10. Thymine and cytosine are [purines | pyrimidines]. 11. Nitrogen bases are paired together using [hydrogen | covalent] bonds. thymine cytosine guanine thymine guanine traits semi conservative

34. Why DNA is important: DNA is important because it holds the “recipe” for making proteins. Your entire body is made out proteins! DNA is your personalized instruction manual and yours is unique to you (though everyone in this room shares about 99% of the same DNA, that’s what makes us human!)

35. DNA is very important; it controls the workings of the cell. However, it is trapped inside the nucleus. (Like a mob boss in jail?) In order to get all of its instructions to the rest of the cell, DNA relies on its trusty sidekick....

36. (R.N.A.)

37. Ribonucleic Acid R.N.A. is also a nucleic acid- it is made out of linked nucleotides (like DNA). Recall that nucleotides are made of a sugar, phosphate, and nitrogen base.

38. DNA vs. RNA RNA and DNA are very similar, but there are some differences. First of all, DNA is double stranded, and RNA is single stranded. This means that RNA is SMALLER than DNA.

39. RNA contains 4 nitrogen bases: adenine, guanine, cytosine and URACIL. *Thymine is NOT present in RNA. Uracil is complementary to adenine in DNA. It essentially takes the place of thymine.

40. The last major difference between DNA and RNA is that RNA contains the 5-carbon sugar ribose. (Recall DNA contains deoxyribose). Ribose has one more oxygen atom than deoxyribose. Ribose Deoxyribose

41. Recap RNA is single stranded, so it is smaller than DNA. This means it can leave the nucleus (which DNA cannot). RNA contains the sugar ribose. RNA has 4 bases: A, T, C, and U. The base pairing rules are as follows: NO thymine in RNA

43. 3 Types of RNA RNA’s job is to help DNA make proteins. DNA must deliver its code to the remainder of the cell- it relies on 3 molecules: • Messenger RNA (mRNA) • Transfer RNA (tRNA) • Ribosomal RNA (rRNA)

44. Messenger RNA mRNA is complementary to the original strand of DNA. mRNA is first created in the nucleus and then travels to the ribosomes out in the cytoplasm. mRNA uses the DNA’s code (or message) to make proteins! Example) DNA Strand: G GCT T A mRNA strand: C C GA A U

45. Proteins Recall that proteins are made up of smaller parts called amino acids. Another word for protein is “peptide”. Individual DNA codes are called “codons”. The codons correspond to specific amino acids. mRNA also has codons, which are complementary to DNA codons.

46. Codons Codons consist of groups of 3 nucleotides called triplets. Example) DNA codon: cytosine-cytosine-adenine (CCA for short) Each codon codes for one amino acid. This is where we need RNA’s help. A C C

47. DNA Template Strand: A C G T T A G C C mRNA strand: U G C A A U C G G mRNA is always complementary to the template DNA strand. How many codons are there? What does the other DNA strand look like?

48. Three DNA codons are transcribed into three mRNA codons. mRNA codons are specific to amino acids. This is the beginning step of PROTEIN SYNTHESIS. Protein= well, protein synthesis= to make

49. DNA Template Strand: A C G T T A G C C mRNA strand: U G C A A U C G G • UGC • AAU • CGG Which three amino acids do these mRNA codons code for?

50. Amino Acids Though there are only 20 different amino acids, they are sequenced differently and come in different shapes to make for thousands of different proteins.