2. Basic Biology & some calculations [Read Chpt 1 of Berg et al.: lots of important things about Molecular Binding, Central Dogma, Entropy,  G] 1. Living is made up of complex polymers organized in one or more cells. 2. Central Dogma of Biology DNA  RNA  Proteins 2a. Why “junk” DNA become hot. 3.How to calculate stability of DNA 4. What introns and exons lead to tremendous genetic variability

3. All living organisms consist and make complex, heterogeneous macromolecules. They do this by ingesting the necessary substituents and make them from simple compounds. It has a way of reproducing itself, although any one member of the species need not be able to reproduce. At the molecular level, the definition of life becomes somewhat simpler.

4. 4 Large [Macro]Molecules (from small molecules) Biological polymers (Large molecule made from many smaller building block) DNA & RNA  Nucleotides Proteins  Amino Acids Carbohydrates  Sugars Lipids (Fats)  Fatty acids Example: a.Make Proteins, Enzymes, Hair… Each is used to: a.Make macromolecules/structural b.Energy Source c.Information– Storage/signaling b. Break down yields energy; c. amino acids used as nerve impulses (your brain largely runs on a.a. glutamate.)

5. Major Classes of Macromolecules DNA fragment (nucleic acid) Hemoglobin (protein) Lipid Polysaccharide (carbohydrate) An atomic scale representation of each 0.34 nm between base pairs

6. We are mostly made of water (H 2 O): ≈75% C —very versatile: everything made of: Nucleic acids, Proteins, Lipids (fat), Carbohydrates. (Remember these families)! O —bonding, proteins, fats, nucleic acids N — proteins, genetic material Ca, P — bones Atoms: What are we made of? Campbell

7. The Fundamental Unit of Life is the Cell 3 types (not two!) Archea and Bacteria most ancient: without a nucleus (special place to put its genetic material, DNA). Otherwise bacteria and archea look a lot alike. Eukaryotes have a nucleus. Here at U of Illinois, Carl Woese in the 1970s made claim that 3 branches of life based on RNA What caused split? Don’t know but…Possibly the ingestion of a bacteria to become a mitochondria (specialized to make energy—ATP) http://bio1903.nicerweb.com/ Locked/media/ch25/25_18Tr eeOfLife.jpg

8. Bacteria Prokaryotes (No nucleus) Eukaryotic cell (us) (Has nucleus)  1  m   10-30  m   10-100  m  (Nucleus 3-10  m) Most Biopolymers in Body are in Cells Yet there are  200 different types of cells in body. (Heart cell not equal to a brain cell…)  10 14 (100 billion!) cells in body… …more stars than in Milky Way Galaxy.

9. Nucleus contains DNA Blueprint of cell Each cell type expresses only a part of information in DNA (Brain cell differs from a heart cell….) Every cell (which has nucleus) has identical DNA [A few types, like red blood cells, are made with a nucleus but gets de-nucleated.] So a meter of DNA must be packed in 3-10  m! How much DNA? 3 billion base pairs 1 meter In humans 46 pieces: chromosomes What does this tell about bendability of DNA? Highly flexible. Persistence Length = 50 nm (~150 bp.) How this is measured? Use magnetic tweezers (Yet can unwind and very robust in storing genetic information over a lifetime) What is persistence length? Walk in one direction: how long headed in that direction

10. DNA is a double helix of anti-parallel strands DNA uses a 4 letter sequence, A, T, G, C Must come apart for bases to be read. 3.4 Å 3.4 nm per ~10 base-pairs = 1 turn (360º)

11. Minimal knowledge about Nucleotides 4 nucleotides: A,T,G,C A=T ≈ 2kT two hydrogen bonds G=C ≈ 4kT three hydrogen bonds Many weak bonds…very strong overall structure. DNA is stable. We’ll calculate this in a few minutes. (Boltzman constant.) To unzip, takes energy, ATP and proteins that act like a wedge. Also takes proteins that act to unwrap the DNA and then act like a wedge

12. Need to know Chemical Bonding – 100kT. Sharing of electrons. C-H –kT (weakest, but many of them together--significant). Two neutral atoms have instantaneous dipoles, and attract. 1.Hydrogen attached to a very electro- negative elements, (O, N) causing the hydrogen to acquire a significant amount of positive charge. 2.Lone pair– electrons in relatively small space, very negative. Result is H is (+) and O is (-). Will bind to other molecules www.chemguide.co.uk/atoms/bonding/hbond.html#top Neon: -246°C; Xenon: -108°C Is light enough to break covalent bond? 1um=1eV; kT=1/20eV. 1um= 20kT: close (yup) – varies tremendously, 100kT to few kT. + and – attract, but depends on solvent. Na + Cl - = few kT (break up easily) – few kT, up to 5kT 4 types: what are they? 1. Covalent 2. Ionic 3. Hydrogen 4. Van der Waals

13. Note: Student mentioned metallic bonds Metallic bonding is the bonding within metals. It involves the delocalized sharing of free electrons between a lattice of metal atoms. Thus, metallic bonds may be compared to molten salts. e.g. Iron (Fe)... Why is it so strong? Of course, metallic bonding. Metal atoms typically contain a small amount of electrons in their valence shell compared to their period or energy level. These become delocalised and form a Sea of Electrons surrounding a giant lattice of positive ions. Metals seem to have higher boiling and melting points which might suggest stronger bonds between the atoms. Metallic bonding, as with covalent bonding is non-polar, in that there is no (for pure elemental metals) or very little (for alloys) electronegativity difference among the atoms participating in the bonding interaction, and the electrons involved in that interaction are delocalized across the crystalline structure of the metal. The metallic bond accounts for many physical characteristics of metals, such as strength, malleability, ductility, conduction of heat and electricity, and luster. See also chemical bond. Metallic bonding is the electrostatic attraction between the metal atoms or ions and the delocalised electrons. This is why atoms or layers are allowed to slide past each other, resulting in the characteristic properties of malleability and ductility. Metallic bond are different from chemical bonds. Ionic and covalent bonds are chemical bonds. Covalent bonding is a common type of bonding, in which the electronegativity difference between the bonded atoms is small or non-existent. In the latter case, the bond is sometimes referred as purely covalent. See sigma bonds and pi bonds for current LCAO-explanation of non-polar bonds. e.g. CH4 (methane) Ionic bonding is type of electrostatic bond between atoms which have an electronegativity difference of over 1.6 (this limit is a convention). These form in a solution between two ions after the excess of the solvent is removed. e.g. NaCl (common salt). https://answers.yahoo.com/question/index?qid=1006020202026

14. Covalent bonds holding bases together —very strong

15. If add salt to solution, what is effect on melting Temp? Melting temp = Temp. at which DNA strands come apart. 3’3’ 5’5’

16. If you have many weak bonds (e.g. each bond only few kT) you can get a biomolecule that will not fall apart. Zipped vs. unzipped What if 10 weak bonds? H bonded ~ -2 kT What if just one bond? Bond/unbound? DNA double helix: Many weak (H-bonds), makes for very stable structure. Many base pairs, essentially completely stable. We note that these numbers are completely unrealistic because our calculation doesn’t include the entropy. That is, it should be based on the free-energy (  G), not the energy, but the trend we see here, is still qualitatively correct. Still have end-fraying, but probability that whole thing comes apart– essentially zero. Say the unbound case has E= 0 The bound case therefore has E = - 2kT. (Notice that the energy is negative, i.e. it’s more stable if a bond is formed) e 2 ~ 8 e 20

17. DNA  RNA  Proteins Central Dogma of Molecular Biology http://learn.genetics.utah.edu/units/basics/transcribe/ DNA: linear series of 4 nucleotides (bases): A,T,G,C RNA: linear series of 4 nucleotides (bases): A,U,G,C   Transcription [DNA & RNA similar] Translation [RNA & Proteins different] Proteins: linear series of 20 amino acids: Met-Ala-Val-… each coded by 3 bases  amino acid AUG  Methionine; GCU  Alanine; GUU  Valine Proteins are 3-D strings of linear amino acids Do everything: structure, enzymes…

18. DNA  RNA U U U Must uncoil the DNA, separate the strands, and use one of strands as a template to make a RNA strand. RNA: uses U instead of T, uses ribose instead of deoxyribose The RNA that codes for proteins are called messenger RNA is an exact copy of DNA.

19. RNA  Proteins 3 nucleotides codes for 1 amino acid. Proteins are made up for a linear string of 20 different amino acids. Also need to know where to start making the protein, and where to stop making the protein. U U U    Histidine Cysteine Glycine If you can sequence all your DNA, how can you tell how many genes are there? Gene = sequence of DNA (or RNA) that makes a protein

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

21. If 3 bases make a codon, how many amino acids might there be? Answer: 4 3 = 64 Have redundancy, typically in the last nucleotide

22. The Central Dogma of Biology Each time a cell divides, entire DNA gets replicated. For us, that’s 3 billion base pairs. nucleus cytoplasm

23. Splicing is fundamental for Gene Expression

25. Alternative Splicing Adds Complexity 1 Gene, many proteins DSCAM = 1 pre-mRNA = 38,000 potential mRNAs Down Syndrome Cell Adhesion Molecule

26. 1 mm____ Now you understand why we’re not just a tiny worm. Why little worm (19,735 genes, 97 MB) has as many genes as a human (~21k, 3,000 MB = 3 GB)! A lot of “genes” are alternatively spliced, can produce more than one protein. Until very recently, used to call DNA which didn’t code for a protein “junk DNA”

27. Class evaluation 1.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.