Nucleic Acids and the RNA World. Pages Chapter 4

Transcription

1 Nucleic Acids and the RNA World Pages Chapter 4

2 RNA vs. Protein Chemical Evolution stated that life evolved from a polymer called a protein. HOWEVER, now many scientists question this. There is currently a large scientific motion towards a polymer called a Nucleic Acid. Specifically, a RiboNucleic Acid RNA

3 RNA World Hypothesis This proposal is called the RNA World Hypothesis Again, this is still very HYPOTHetical THIS IS THE DELEMA OF

4 What is Life????? This is an age old question that scientists still debate! We don t have a simple explanation, and therefore discussing the origin of life is nearly impossible There are 2 versions of the story We will need to use the 2 nd version

5 Version 1 (The easy version) 1. All life is made of cells 2. Life reacts to its environment 3. Life reproduces 4. Life uses energy 5. Life grows at some point Sadly..it isn t so cut and dry!

6 Version 2 (Our version) Because scientists constantly debate this issue, we only use two of these rules to discuss LIFE in high end Biology 1. The ability to reproduce! 2. The ability to acquire particular molecules and use them in CONTROLLED CHEMICAL REACTIONS that maintain conditions suitable for life & contribute to growth!

7 What About the Other 3 Requirements They are there. They are just used as subcategories at this level of Biology. IE: Chemical reactions (Rule 2) are precisely controlled because chemicals and reactants are bound by a Plasma Membrane. Therefore, it is required for life it is just no longer the rule! The problem is that if it is debated, it becomes an uncertain theory Remember, even the rules are JUST theories

8 All Polymers are Proteins? Thus far, every polymer we have learned about IS a protein. HOWEVER, we now are learning of a new polymer. Proteins are the result of polymerization of monomers called Amino Acids Nucleic Acids are the result of polymerization of monomers called Nucleotides

9 Amino Acid

10 Nucleotide

11 Components of a Nucleotide 3 components Phosphate group Sugar Nitrogenous (Contains a nitrogen) Base PAGE 75

12 Sugar Your sugar is an organic compound with a carbonyl group C=O

13 How do Nucleotides Polymerize Figure 4.2 on page 76 It starts with a phosphodiester linkage This condensation reaction is the formation of the bond between the phosphate group of one nucleotide and the hydroxyl group of the sugar component. If the nucleotides involved contain the sugar RIBOSE, the polymer is called RNA If the nucleotides involved contain the sugar DEOXYRIBOSE, the polymer is called DNA

14 DNA s Sugar-Phosphate Backbone

15 RNA s Sugar Phosphate Backbone

16 Count Your Primes

17 Base Pairs

18 Base Pairs

19 Base Pairs

20 Base Pairs

21 Base Pairs

22 Base Pairs

23 Chargaff s Theory Found that the #of bases (Purines & Pyrimidines) are the same The # of A s = # of T s The # of C s = # of G s Found that these bases must be relavent to its matching pair

24 WATSON and CRICK Announced in 1953 Used the results of other scientists to figure out the structure of DNA

25 Watson & Crick Model Chemists found that DNA polymerized through the formation of phosphodiester linkages This concluded a sugar-phosphate backbone By analyzing the total number of purines and pyrimidines it was found that the number of A s and T s were equal to the number of C s and G s This was called Chargaff s rule after Erwin Chargaff X-ray diffraction showed a repeating scatter pattern (.34 nm, 2.0nm, 3.4nm) This repeating pattern only makes sense if the molecule is shaped as a double helix Pages 79-82

26 Scatter Pattern X-ray Diffraction

27 Scatter Pattern X-ray Diffraction Watson & Crick began to analyze the size and geometry of deoxyribose, phosphate groups, and nitrogenous bases. Using things like bond angles, and measurements, they were able to devise 2.0nm probably represented the width of the helix, and.34 was likely the distance between bases stacked in the spiral They arranged two strands of DNA running in opposite directions (5`-3` and 3`-5`)

28 Base Pairing Using the x-ray diffraction patterns and measurements, it was found only to work if: Adenine always bonded with Thymine Guanine always bonded with Cytosine This phenomena is called Complimentary Base Pairing

29 Polarity of DNA DNA is put together like a ladder with the sugar-phosphate bonds form the supports and the base pais form the rungs of the ladder The tight packing of the nitrogenous bases are the hydrophobic interior that is hard to break apart The exterior, sugar-phosphate backbone IS, however, hydrophilic, causing the molecule to be water soluble

30 Major vs. Minor Grooves

31 Letters of a Book Watson & Cricks Model of DNA was revolutionary because it explained how DNA worked In the structure of DNA alone we can see how the different sequences of bases in DNA act like the letters in a book =

32 DNA Size Width of the helix = 2.0nm Length of one full complete turn of helix = 3.4nm Distance between bases =.34nm

33 DNA Size

34 PROBLEM with DNA As we have mentioned, DNA seems like a great suspect for the first polymer to reproduce itself ONE PROBLEM DNA is WAYYYYYyyyyy to simple and staple of a template act as a catalyst and fuel self replication In fact, never has it been observed to act as a good enough catalyst to convince scientists that it alone could do this And with the problem that DNA doesn t just replicate what could it be???

35 RNA as a suspect for life RNA now surfaces as a possible suspect for life s roots So what is RNA??

36 DNA vs. RNA Both have a sugar phosphate backbone formed by phosphodiester linkages However there are 2 main differences: The pyrimidine base THYMINE does not exist in RNA. Instead, RNA contains the the closely related pyrimidine base URACIL The sugar in the sugar-phosphate backbone of RNA is RIBOSE, not deoxyribose as in DNA

37 RNA The second point is CRITICAL when comparing the two (and understanding RNA) The hydroxyl group on the 2`-carbon of RIBOSE is MUCH more reactive This is the main difference that makes DNA stable and RNA reactive The absence of Thymine and presence of Uracil makes them easy to distinguish

38 RNA Hairpin Another difference between RNA and DNA is in their secondary structures Very often, RNA is denoted as a single strand (where DNA is a double strand) However, RNA can appear to be a double stranded helix during what is called a Hairpin This is when the secondary structure of RNA loops and forms a double stranded stem

39 RNA Hairpin

40 Hairpins These form WITHOUT energy input because they energetically Hydrogen bond formation is exothermic and exergonic Though they do release the entropy of the strand, this is a flag for being the first reproducing molecule

41 RNA Contains Information RNA contains a sequence of bases that is analogous to the letters in a word This allows it to carry information Because hydrogen bonding occurs specifically between A-U and G-C in RNA, it is THEORETICALLY possible that it can make a copy of itself Figure 4.14

42 Template & Complimentary When considering the replication process, it is important to know the terminology for each strand Template Strand: Original strand Complimentary Strand: New strand being created It is called this because it needs to match the template as a perfect compliment

43 The Ribozyme So as long as RNA is catalytic, then it does make sense that it is possible to replicate itself if the perfect situation arises RNA is catalytic through RNA enzymes called RIBOZYMES. It has been observed in an experiment that the ribozymes that were isolated had the ability to catalyze BOTH the hydrolysis and condensation reaction of phosphodiester linkages This is why the majority of scientific evolutionists believe in RNA as the first LIFE This is called the RNA WORLD HYPOTHESIS This has still never been successfully shown in a laboratory