Lec 4: RNA (and Proteins)

1. Homework Lec 4: RNA (and Proteins) HW#2: Due Monday Reading, ECB, Chpt 2: Due Wednesday. Quiz next Wednesday

2. A vs. B vs. Z-DNA B “normal” configuration; A,Z- unusual, not-normal configuration” Figure 3-B-3.  The normal right-handed "double helix" structure of DNA, also known as the B form. In a solution with higher salt concentrations or with alcohol added, the DNA structure may change to an A form, which is still right-handed, but every 2.3 nm makes a turn and there are 11 base pairs per turn. Another DNA structure is called the Z form, because its bases seem to zigzag.  Z DNA is left-handed.  One turn spans 4.6 nm, comprising 12 base pairs.  The DNA molecule with alternating G-C sequences in alcohol or high salt solution tends to have such structure. http://www.web-books.com/MoBio/Free/Ch3B3.htm http://www.tulane.edu/~biochem/nolan/lectures/rna/DNAstruc2001.htm

3. Major vs. Minor Axis of DNA Sequence-specific DNA-binding proteins generally interact with the major groove of B-DNA, because it exposes more functional groups that identify a base pair. Major axis more likely to be accessible to proteins Cro protein complex with DNA Lambda repressor protein bound to a lambda operator DNA sequence http://commons.wikimedia.org/wiki/File:Cro_protein_complex_with_DNA.png http://en.wikipedia.org/wiki/DNA

4. Major vs. Minor Axis of DNA Structural proteins that bind DNA are well-understood examples of non-specific DNA-protein interactions. Within chromosomes, DNA is held in complexes with structural proteins. These proteins organize the DNA into a compact structure called chromatin. DNA that is not n x 3 bases in length? “There *must* be. For example, many stretches of DNA code for RNAs -- including ribosomal RNAs, tRNAs, newly discovered microRNAs, and many many others. All of these have particular requirements for what the RNA is -- including conservation of many of their bases -- yet these will not in general have lengths = 3*n. --Jonathon Widom, Northwestern Univ.

5. RNA has 3 different uses, called 3 different names, (mRNA, tRNA, rRNA) 1. Messenger RNA (mRNA) [~copy of DNA] 2. transfer RNA (tRNA) [binds to amino acid and codon for mRNA] 3. ribosomal RNA (rRNA) [Makes up Ribosome, along with protein. Has catalytic activity– can form peptide bond. RNA is catalytic!] http://en.wikipedia.org/wiki/Messenger_RNA

6. Why is RNA & DNA different? Probable Answer: RNA came first. RNA is capable of storing information (though not great cause of U) and can catalyze reactions. Later, split off—Long-term storage given to DNA because it’s more stable. (T instead of U) Catalysis mostly given to proteins—more diverse, efficient.

7. What is a Catalyst/Enzyme? For now just pretend that ΔG is equal to ΔE. (In-fact ΔG= ΔH- TΔS ≈ ΔG≈ ΔE- TΔS)  X+ Y Z  The starting and final reaction energies are the same, but the activation barrier is lowered. If Ea low enough (≈ kT), it will happen spontaneously

8. Ribozyme(ribonucleic acid + enzyme)Example of a biocatalyst, i.e. an enzyme http://en.wikipedia.org/wiki/Ribozyme RNA can be catalytic! 1989 Nobel Prize—Altman & Cech

9. RNA is likely predecessor of DNAFrom Nobel Lecture The discovery of catalytic properties in RNA also gives us a new insight into the way in which biological processes once began on this earth, billions of years ago. Researchers have wondered which were the first biological molecules. How could life begin if the DNA molecules of the genetic code can only be reproduced and deciphered with the aid of protein enzymes, and proteins can only be produced by means of genetic information from DNA? Which came first, the chicken or the egg? [Sid] Altman and [Tom] Cech have now found the missing link. Probably it was the RNA molecule that came first. This molecule has the properties needed by an original biomolecule, because it is capable of being both genetic code and enzyme at one and the same time. Presentation Speech by Professor Bertil Andersson of the Royal Swedish Academy of Sciences, December 10, 1989

10. Evidence that RNA have these properties? The Ribosome is an RNA-based catalytic machine– Big surprise!

11. Ribosome, i.e. Translation, is RNA catalyzed! Proteins; 23SrRNA; 5S rRNA (at the top) A-sitetRNA P-site tRNA T. Steitz, 2000, Science A ribosome's true colors. (Top) The large subunit of the ribosome seen from the viewpoint of the small subunit. (Bottom) The peptidyl transfer mechanism catalyzed by RNA (2). The general base (adenine 2451 in Escherichia coli 23S rRNA) is rendered unusually basic by its environment within the folded structure; it could abstract the proton at any of several steps, one of which is shown here. RNA is an enzyme! Nobel Prize 2009: Atomic Structure of Ribosome (Steitz, Ramakrishnan, Yonath)

12. In prokaryotes (messenger) In eukaryotes intron –”non-coding region” deleted 1993 Nobel Prize in Medicine to Phillip Allen and Richard J. Roberts RNA is made from DNA Introns vs. exons in Eukaryotes prokaryotes introns are only found in tRNA and rRNA http://en.wikipedia.org/wiki/Intron

14. What is siRNA? Small interfering RNA (siRNA), sometimes known as short interfering RNA or silencing RNA, is a class of double-stranded RNA molecules, 20-25 nucleotides in length, that play a variety of roles in biology. Most notably, siRNA is involved in the RNA interference (RNAi) pathway, where it interferes with the expression of a specific gene. dsRNA can also activate gene expression (RNAa). MicroRNAs (miRNA) tend to be ssRNA…Long dsRNA cleaved by Dicer…. http://en.wikipedia.org/wiki/Small_interfering_RNA siRNAs can also be exogenously (artificially) introduced into cells by various transfection methods to bring about the specific knockdown of a gene of interest. Essentially any gene of which the sequence is known can thus be targeted based on sequence complementarity with an appropriately tailored siRNA. This has made siRNAs an important tool for gene function and drug target validation studies in the post-genomic era. 2006 Nobel Prize on RNA interference Fire and Mello

15. What is Entropy?∆S Qualitative: Degree of disorder Gas will expand from a bottle at finite temperature because there are more accessible states available to it, than staying put. (Temperature gives molecules a little bit of energy to access states) Quantitative: ∆S = kBln W where W = # accessible states. Reaction that produces H2O, which, in general, is free to diffuse everywhere, is highly favorable.

16. How to make nucleotide(Example of condensation reaction, like amino acids & peptide bonds) Free H2O : lots of entropy gained Reaction wants to go.

17. Amino acids <a.a.> ~110 grams/mole (or about 100g/mole) hydrophilic R=CH3 Fairly hydrophilic Hydrophobic

18. Amino Acids undergo condensation reaction to form peptides Free H2O : lots of entropy gained

19. Can get enormous diversity and function with Proteins Linear sequence of ~ 20 amino acids

20. Secondary Structurea-helix, b-sheets a-helix, b-sheets depends on specific amino acids

21. Typical size of genes & proteins

22. Class evaluation • What was the most interesting thing you learned in class today? • 2. What are you confused about? • 3. Related to today’s subject, what would you like to know more about? • 4. Any helpful comments. Answer, and turn in at the end of class.