HONR 210-01A: FALL 1997


Dr. Henry Jakubowski

Day 1, Wed, September 3: Introduction to course: syllabus, philosophy, backgrounds

Day 2, Fri, September 5: Discussion of the nature of truth, knowledge; the role of science and religion in understanding the world. Video Question: How does a sperm fertilze an egg and no other cell.

Day 3, Tue, September 9: The molecular view of fertilzation. Van Helmont Experiment - What is the source of the acquired mass of a tree? Historical view of the nature of matter.

Day 4, Thur, September 11:

Day 5, Mon, September 15:



Day 6, Wed, September 17

We reviewed the rules for drawing molecular structures for molecules and molecular ions. Some key points to remember:

In chemical reactions, ionic or covaelent bonds are broken. If a covalent bond is broken, the electrons either are split equally between the two separating atoms, or both leave with one of the atoms. If an O-H bond is broken, the electrons usually stay with oxygen, since O is electronegative and likes electrons more than H, and both atoms depart with a full outshell of electrons (O has an octet, and a - charge, while H leaves with no electrons (in a way a filled outer shell? and with a positive charge.).

Day 7, Fri, September 19

Are there really atoms and molecules? Modern Evidence

Intermolecular Forces (IMF): Molecules must attract each other. If there were no IMF, there would be no solids or liquids, in which the particles seems to "stick" to each other. The extent of IMF must vary among molecules. Hence liquid nitrogen (N2) evaporates quite readily (it boils at room temperature), compared to acetone and finally water which evaporates least readily of the three. This suggests that water molecules attract each other more tightly than nitrogen or acetone.

We next discussed the types of IMF. The force that attracts molecules to each other must be based on the attraction of + and - charges, hence they are like the source of the force in ionic and covalent bonds. It is important to remember that IMF are much weaker, and can be broken readiliy at normal temperatures.. The H-bond is a type of IMF in which the H (slightly positive) covalently bonded to a F, O, or N on one molecule, attracts an F, O, and N (slightly negative) covalently bonded to an H on another molecule. The H-bond is not a covalent bond, but rather a type of IMF.

Since liquid nitrogen , a molecule with all nonpolar covalent bonds, exists, there must be attractive forces between these nonpolar molecules. Remember the electrons are moving rapidly around the nuclei of the molecule. If at one instanteous point of time, more of the electrons are on one side of the molecule, that side will develop a transient partial negative charge while the far side will have a temporay slight positive. If this side of the molecule comes close to another molecule, it will pull the electron clouds of that molecule toward it, inducing a slight negative on the side of the second molecule near the slight positive on the first. This induce-dipole (a separation of charge) on each molecule leads to an attractive force, called a London Force. The bigger the nonpolar molecules, the greater surface area for possible induction of dipoles exists, so the London Forces are greater. Likewise, when a nonplar gas like nitrogen is cooled and put under high pressure, the molecules bump into each other more often which leads to longer-lastting IMF, and possible liquefication.

Day 8,Tues, September 23

We showed in lab that the solubiity properties of a substance can be explained by IMF. Like molecules dissolve like. Water, a polar molecule with all polar covalent bonds, attracts polar covalently or ionically bonded substances, interacting with the substance to be dissolve through H-bonds. Hexane, in contrast, dissolves nonpolar molecules by interacting with them through London Forces.

Some solutes (substances to be dissolved) have both polar and nonpolar parts. The larger the nonpolar part, the less likely it would dissolve in water, and the more likely it will dissolve in hexane. The converse is true as well. In addition, some substances with both polar and nonpolar parts can interact with each other in water to produce sphererical structues that act like detergents or biological membranes.

We then introduced the central dogma of molecular biology, using the metaphor of a language. DNA, the molcule holding the blue-print of life, is transcribed into RNA, which is then translated into a protein . Each part of the DNA that has the informaton for a protein is called a gene. There about 100,000 genes in the human DNA and hence about 100,000 different proteins. Each protein has a unique shape.

DNA, RNA, and proteins are all polymers in which monomers covalently link together to form polymers. The backbone chain of the polymer contains the bases A, G, C, and T projecting from it for DNA, A, G, C, and U for RNA, and 1 of 20 different amino acid side chains for protein. The monomer that make up DNA are called deoxyribonucleotiodes, ribonucleotides for RNA and amino acids for proteins.

Day 9, Thur, September 25

Today we discussed the structures of DNA, RNA, and proteins. All are biological polymers consisting of monomers. The backbone of DNA and RNA consists of a repeating sugar - phosphate backbone, with the negatively charged phosphate linking the adjacent sugars. The bases, which have atoms that an form Hydrogen bonds point away from the backbone. The DNA strand has a direction, much like a shoe lace with a plastic protector on one end with the other plastic end removed. DNA strands run from 5' to 3' direction. DNA is nuclei and chromosomes consists of a double strand of DNA in which the two strands are held together by IMF between the atoms on the bases on adjacent strands that can base pair by forming H bonds. The double helix is like a twisted ladder in which the rungs are the base pairs pointed towards each other. T always base pairs with A through 2 specific H-bonds, while C base pairs with G through 3 H-bonds. DNA can be replicated by separating the strands and the using a protein called DNA polymerase which synthesizes complementary strands to the two separated stands. DNA can be transcribed by RNA polymerase. The DNA strands separate and a single strand of RNA is made complementary to the template strand of the DNA. RNA is synthesized in the 5' to 3' direction, and reads the template strand in the 3' to 5' direction. Hence the RNA strand is actually identical to the nontemplate DNA strand, which is usually called the coding strand. The only difference is that a U is used in place of a T.

Proteins are polymers of amino acids. The covalent link between amino acids consists of a C=O and N-H, which allows H-bonds from the backbone of the protein to other parts of the backbone within the same protein. The twenty different side chains can interact through IMF's within the same molecule, along with H bonds between the linkage of the backbone, to cause the protein to fold to a unique 3D shape. Structures such as alpha helices and beta sheets (held together by H bonds between the linkage groups in the backbone) are common in proteins. Distal side chains can interact through H-bonds, + /- i nteractions, and London forces, when the side chains are nonpolar and hydrophobic.

In the process of transcription, a triplet of contiguous bases (or codon) of the RNA molecule is read in the process of transcription (done on a large structure in the cytoplasm called a ribosome) and leads to the insertion of 1 amino acid in the growing protein. For a problem set, you were asked to determine from the DNA sequence, the corresponding protein sequence using a table of the genetic code.

Day 10, Mon, September 29

We also discussed how to determine the amino acid sequence given the dsDNA sequence, using the Genetic Code. A couple hints: The two strands of DNA in a gene are called the template and coding strand. The template strand is read in a 3' to 5' direction as a complementary strand of RNA is made in the 5' to 3' direction. This RNA strand is read in triplets, from the 5' to 3' end, using the Genetic Code, to get the amino acid sequence of the protein.

Last update on September 29, 1997