Notes biochemistry2010

Editor's Notes

1. The term “macromolecule” means large molecule.
2. Why do we study carbon -- is it the most abundant element in living organisms? H & O most abundant C is the next most abundant
3. Carbon chemistry = organic chemistry Why is it a foundational atom? What makes it so important? Can’t be a good building block if you only form 1 or 2 bonds.
4. • great variety of polymers can be built from a small set of monomers • monomers can be connected in many combinations like the 26 letters in the alphabet can be used to create a great diversity of words • each cell has millions of different macromolecules
5. Most macromolecules are polymers • build: condensation (dehydration) reaction • breakdown: hydrolysis An immense variety of polymers can be built from a small set of monomers
6. carb = carbon hydr = hydrogen ate = oxygen compound
7. maltose
8. sucrose = table sugar
9. Polysaccharides are polymers of hundreds to thousands of monosaccharides
10. Can you see the difference between starch & glycogen? Which is easier to digest? Glycogen = many branches = many ends Enzyme can digest at multiple ends. Animals use glycogen for energy storage == want rapid release. Form follows function. APBio/TOPICS/Biochemistry/MoviesAP/05_07Polysaccharides_A.swf
11. Starch = all the glycosidic linkage are on same side = molecule lies flat Cellulose = cross linking between OH (H bonds) = rigid structure
12. Cross-linking between polysaccharide chains: = rigid & hard to digest The digestion of cellulose governs the life strategy of herbivores. Either you do it really well and you’re a cow or an elephant (spend a long time digesting a lot of food with a little help from some microbes & have to walk around slowly for a long time carrying a lot of food in your stomach) Or you do it inefficiently and have to supplement your diet with simple sugars, like fruit and nectar, and you’re a gorilla.
13. Made of same elements as carbohydrates but very different structure/ proportions & therefore very different biological properties
14. Look at structure… What makes them hydrophobic? Note functional group = carboxyl
15. BIG FAT molecule!!
16. Pulling the water out to free up the bond
17. What happens when you add oil to water Why is there a lot of energy stored in fats? • big molecule • lots of bonds of stored energy So why are we attracted to eating fat? Think about our ancestors on the Serengeti Plain & during the Ice Age. Was eating fat an advantage?
18. Mostly animal fats
19. Mostly plant lipids Think about “natural” peanut butter: Lots of unsaturated fats Oil separates out Companies want to make their product easier to use: Stop the oil from separating Keep oil solid at room temp. Hydrogenate it = chemically alter to saturate it Affect nutrition?
20. Storage: beans (seed proteins) Movement: muscle fibers Cell surface proteins: labels that ID cell as self vs. foreign Antibodies: recognize the labels ENZYMES!!!!
21. Rubisco = 16 polypeptide chains Hemoglobin = 4 polypeptide chains (2 alpha, 2 beta)
22. free COOH group on one end is ready to form another peptide bond so they “grow” in one direction from N-terminal to C-terminal
23. Hemoglobin Hemoglobin is the protein that makes blood red. It is composed of four protein chains, two alpha chains and two beta chains, each with a ring-like heme group containing an iron atom. Oxygen binds reversibly to these iron atoms and is transported through blood. Pepsin Pepsin is the first in a series of enzymes in our digestive system that digest proteins. In the stomach, protein chains bind in the deep active site groove of pepsin, seen in the upper illustration (from PDB entry 5pep), and are broken into smaller pieces. Then, a variety of proteases and peptidases in the intestine finish the job. The small fragments--amino acids and dipeptides--are then absorbed by cells for use as metabolic fuel or construction of new proteins. Collagen– Your Most Plentiful Protein About one quarter of all of the protein in your body is collagen. Collagen is a major structural protein, forming molecular cables that strengthen the tendons and vast, resilient sheets that support the skin and internal organs. Bones and teeth are made by adding mineral crystals to collagen. Collagen provides structure to our bodies, protecting and supporting the softer tissues and connecting them with the skeleton. But, in spite of its critical function in the body, collagen is a relatively simple protein.
24. Sickle cell anemia: 1 DNA letter changes 1 amino acid = serious disease Hemoglobin mutation: bends red blood cells out of shape & they clog your veins.
25. It’s a helix or B sheet within a single region. Can have both in one protein but a specific region is one or another
26. How the whole thing holds together
27. Structure equals function wonderfully illustrated by proteins Collagen is just like rope -- enables your skin to be strong and flexible.
28. sequence determines structure and… structure determines function. Change the sequence & that changes the structure which changes the function.
29. glutamic acid is acidic & polar valine is non-polar = tries to “hide” from water of cell by sticking to another hemoglobin molecules.
30. Isn’t this a great illustration!?
31. DNA & RNA are negatively charged: Don’t cross membranes. Contain DNA within nucleus Need help transporting mRNA across nuclear envelope. Also use this property in gel electrophoresis.
32. The 2 strands are complementary. One becomes the template of the other & each can be a template to recreate the whole molecule.
33. H bonds = biology’s weak bond • easy to unzip double helix for replication and then re-zip for storage • easy to unzip to “read” gene and then re-zip for storage
34. when cells divide, they must duplicate DNA exactly for the new “daughter” cells Why is this a good system?
35. when cells divide, they must duplicate DNA exactly for the new “daughter” cells Why is this a good system?
36. The greatest understatement in biology!
37. Discovered & published in 1953 Nobel Prize in 1962: Watson, Crick, Wilkins
38. A chemist by training, Franklin had made original and essential contributions to the understanding of the structure of graphite and other carbon compounds even before her appointment to King's College. Unfortunately, her reputation did not precede her. James Watson's unflattering portrayal of Franklin in his account of the discovery of DNA's structure, entitled "The Double Helix," depicts Franklin as an underling of Maurice Wilkins, when in fact Wilkins and Franklin were peers in the Randall laboratory. And it was Franklin alone whom Randall had given the task of elucidating DNA's structure. The technique with which Rosalind Franklin set out to do this is called X-ray crystallography. With this technique, the locations of atoms in any crystal can be precisely mapped by looking at the image of the crystal under an X-ray beam. By the early 1950s, scientists were just learning how to use this technique to study biological molecules. Rosalind Franklin applied her chemist's expertise to the unwieldy DNA molecule. After complicated analysis, she discovered (and was the first to state) that the sugar-phosphate backbone of DNA lies on the outside of the molecule. She also elucidated the basic helical structure of the molecule. After Randall presented Franklin's data and her unpublished conclusions at a routine seminar, her work was provided - without Randall's knowledge - to her competitors at Cambridge University, Watson and Crick. The scientists used her data and that of other scientists to build their ultimately correct and detailed description of DNA's structure in 1953. Franklin was not bitter, but pleased, and set out to publish a corroborating report of the Watson-Crick model. Her career was eventually cut short by illness. It is a tremendous shame that Franklin did not receive due credit for her essential role in this discovery, either during her lifetime or after her untimely death at age 37 due to cancer.