MCB 250 1st Edition- Universal Tree of life: Carl Woese taught us how to look at life differently on the planet. By looking at the sequence of the small subunit of the ribosome (16s rRNA), you can look at the sequence and see evolution take place. This puts all the organisms of the planet into a tree. Woese taught us there are three large domains: bacteria, archaea, and eucarya.- Archaea is a branch between bacteria and eucarya, thus it shares characteristics of both domains.- Most of all organisms are fundamentally single-celled- The central dogma: found by Crick. DNA genetic material must be replicated, transcribed to RNA, and translated into protein.- Some organisms like HIV will take RNA and make DNA in reverse transcription- RNA can also have enzymatic and regulatory functions that can act alone, thus RNA does not always have to be translated in to proteino Proteins: Many proteins are enzymes. Proteins make up enzymes that catalyze reactions in the cell Metabolism: total of all the chemical reactions in the cell. - Catabolism: Breakdown food, making energy- Anabolism: synthesize components of cells so they can grow and divide, using energy.o Other proteins are important to move, regulate, or structure components of the cell- Two basic designs for cells: - Prokaryotes: (Bacteria and archae) They lack a nucleus. The DNA is in direct contact with the cytoplasm and all processes are essentially taken place in one compartment. Translation and transcription are simultaneouso Gram-negative organism: (E. Coli) Has peptidoglycan cell wall and a outer membraneo Gram-Positive organisms don’t have an outer membrane and has cytoplasm and a thick cell wall- Eukaryotes: (Plants and animals) They contain a nucleus and processes are divided into compartments. Translation and transcription are separated.o Eukaryotes contain organelles: Mitochondria are actually gram-negativebacteria. It was acquired through symbiosiso The sizes of gram-negative bacterium are about the same size of the mitochondria. Cells vary in size, however.These notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.o Eukaryotes are more complex: DNA is replicated and transcribed with a separation between the nucleus and cytoplasm. The transcript is processed then brought out to the cytoplasm to be translated- Chemistry’s importance in biology: Chemistry is what happens inside the cell- The DNA carries the cell’s genetic information: the chemical nature of DNA and its forcesthat determine the structure and properties- Proteins catalyze: the reactions that allow cells to fuction and what allows them to fold and maintain the structures- Biological processes: Protein-protein interaction and how they occur- Life is primarily the chemistry of the six elements: CHNOPSo However there are other elements in the body- Chemical Bonds: Covalent bonds (strong), ionic bonds, hydrogen bonds, Van der Waals interactions, and hydrophobic “bonds” (all weaker)o Covalent bonds: They are relatively stronger bonds resulting from shared electrons. G of -50- -110 kcal/mol. Weak bonds are <10kcal/molo Atoms want to share electrons to fill their outer orbitals with electrons. For example, hydrogen needs to 2 elecrons to fill its outer orbital. It shares its electronwith another atom (ex: another H)o Oxygen needs 2 electrons more to fulfill its outer shell, thus it has two bonds. It can share it with another oxygen or two hydrogeno Phosphate for most biological molecules have five and sulfur has two Rotation: Ethan has two carbon atoms and with three hydrogen bonds pereach carbon atom. The single bonds between the carbon are free to rotate. Every moment, it is spinning. Some states are more energetically favorable than others.  If hydrogen all separate at an equal distance, it is the most energetic state. This is all freely rotating around a single bond Ethylene has a double bond between its carbons. The pi orbitals are interacting with one another to create a double bond. The double bond CANNOT rotate. The molecule is fixed and planar because hydrogen is in the same plane Isomerism: if all four elements surrounding are not hydrogen (like dichloroethene, there can be two different forms because of the chloride on each carbon- CIS: 2 remarkable atoms (this case the Cl) are on the SAME side of the double bond- TRANS: 2 remarkable atoms (Cl) are on the OPPOSITE sides of the double bond1. Aromatic Rings- Benzene: has alternating/conjugating double bonds between the carbons. The electrons can be shared among all the carbons: aromatic compounds.- Two aromatic rings can interact with one another into ring stacks at over lapping pi bonds stabilize interaction of stacked aromatics. You see this in DNA- Butadiene has alternating double bonds and the entire molecule is planar because there is no rotation due to the electrons being delocalized. 2. Absorption of Light- Another important property is that atoms can absorb energy. The energy absorption is quantized because electrons are thought to be in shells. You can shine energy of a particular wavelength and can displace electrons into a higher energy state. This requiresa particular wavelength of light. The particular molecule can absorb it and you can calculate the absorption spectrum and see the peak of absorbance and the wavelength is equivalent to energy of which the molecule can absorb light.- All molecules can absorb light of some frequency. Aromatic compounds can absorb light in the UV light range. o B-Carotene has lots of conjugated double bonds and can absorb light in the visible range (orange) More conjugated double bonds mean that light of lower energy will be absorbed3. Chirality: Stereoisomerism- Biological molecules/organic molecules are based on carbon, which has 4 different bonds. If the 4 side groups differ from one another, that carbon is chiral.- The mirror image of that molecule is not the same molecule/not identical. Cannot rotatethe molecule around to match the mirror image (chiral)- If 2 or more are identical, then it is not chiral, so you can rotate the image around to get the mirror image- Evolution chooses particular ones, all the amino acids in proteins are the L. (mirror image is D)o L alanine is not the same as D-alanine It is not interchangeable. o Exception is Glycine, because 2 side groups are identical H.- L and d are found by