Lecture 3

1) Simple sugars differ in 3 respects – a) the location of the carbonyl group. b) the number of carbon atoms present c) the spatial arrangement of the atoms – particularly the relative positions of the hydroxyl groups.

2) Glycogen is used to store glucose. Its branched because it has to store glucose in an inactive form.

3) At neutral pH, a amino acid won’t remain unionized. Its amino group would attact a proton, causing it to positively charged, and its carboxyl group would release a proton causing it to be negatively charged. At very low pH, due to the large availability of protons, the inclination would be to attaching the proton to the carboxyl group. At very high pH, where the hydroxyl group is in predominance, they scavenge protons, and hence the amine group would be in its original state.

4) The amino acids exist in a  very specific 3d configuration. Mirror images called chirals

5) Amino acids polymerize through peptide bonds, hence proteins called polypeptides. If these chain lengths are small, we call them oligopeptides. Here again, we have the possibility of extending them infinitely. The side chains can be anything out of 20 R molecules.

6) There is a polarity. The new amino acid is always added on the carboxyl end. Hence, there is a N end and there is a C end. Things are growing at the C terminal end progressively.

7) Virtually every biochemical reaction is reversible. If one is able to form peptide bonds, one is able to break them as well, through hydrolysis. There are 20 R’s for proteins. 99.99% of all the proteins that is created is through the synthesis of these amino acids.

8) Since there are 4 distinct side chains around the central carbon, you’d expect to have handedness, but the glycine amino acid doesn’t exhibit chirality.

9) Side chains have quite distinct biochemical properties, proteins and then biochemical attributes can be dictated by the amino acids that are used to construct them. We can talk about non-polar vs. polar amino acids. Amino acids which have a poor affinity for water, hydrophobic. You would wonder how can they be hydrophobic, because the amine and carboxyl group is charged. But I am talking about them not as single form, but when they have polymerized. So when we talk about polar and non-polar amino acids, we are concentrating upon the side chain.

10) Polar side chains – serine with a hydroxyl group that can form hydrogen bonds with water. Threonine can form hydrogen bonds through hydroxyl, asparagine can form hydrogen bonds through carbonyl and amine group, as can glutamine.

11) When the side chains are charged, strongly hydrophilic.

12) Tyrosine has the strongly hydrophobic benzene ring, and the hydroxyl group which loves water. Cysteine has SH group which can form bonds with other SH groups from other cysteines, through a disulphide bond. This is a very strong bond in the absence of reducing agents. Thus polypeptide links can be covalently crosslinked. Conversely, if you add reducing agent, that will add protons back, and reduce the oxidation state of the sulphurs, causing the disulphide bonds to break apart. The disulphide bonds could be used to link two proteins together, but more often than not, there are intramolecular bonds, bonds from one domain of the protein to another. Why do we have these disulphide bonds? Because a protein can only function when it has a certain 3dimensional stereochemical configuration. This structural rigidity is maintained by these disulphide bonds, which link neighboring regions of a polypeptide chain, these intramolecular links.

13) There can also be intermolecular links between two polypeptide chains that are mediated by the disulphide bond.

14) In proline the side chain is covalent bonded to the amine group, it creates a 5 member ring. This amino acid when occurs in a polypeptide doesn’t have the flexibility of assuming certain configurations that the other ones have.

15) After we wrestle with the 3dimensional structure of the chain, we realize that after the initial chain is synthesized, its initially chaotic, and as it extends, it begins to assume a 3d molecular configuration.

16) If you knew the primary structure, the sequence of amino acids, you should be able to develop a computer algorithm that can predict the 3d configuration. This has not been possible yet because of the infinite no of intermolecular interactions that greatly complicate how the protein assumes its structure. And if this is the native state of the protein, there are ways of disrupting that, because much of this native state is created because of intramolecular hydrogen bonds. Hydrogen bonds are weak and we break the 3d structure when we heat. Some molecules upon cooling down will reassume their native structure. Most proteins however will not do so.

17) Primary structure is the amino acid sequence. Secondary structure represens structures containing the hydrogen bonds. (eg helix structure)

18) Prolene is known as a helix breaker, because it cannot twist itself around to form an alpha helix. So locally where there is a prolene, there won’t be a helix structure. So, secondary structure means, a certain segment can form alpha helix, another segment of the protein will form beta pleated sheets.

19) Tertiary structure – How the alpha helixes are disposed wrt one another.

20) Proteins act as catalysts in cells, as enzymes. Almost all biochemical reactions require an enzyme to propel them forward. Catalytic cleft – active site of the enzyme where the substrates are pulled in, and are manipulated and changed by the actions of the enzyme.

21) Proteins also have another function – to create a biochemical structures. Complex structures are formed out of proteins.

22) Hemoglobin is a tetromer. Two alpha helices and two beta pleated sheets, there are combined together through hydrogen bonds. If you break it apart into 4 pieces the individual parts are useless.

23) The hydrophobic proteins do not like water, therefore they are tucked inside the protein far away from the surfaces. They don’t have contact with water. The hydrophilic amino acids are tucking out from the surface.

24) Summary – there are disulphide bonds, there are hydrogen bonds, there are these hydrophobic and hydrophylic interactions, and there are also some VanderWaals interactions.

25) In carbohydrate, you have the same monomer in 100 or 500 stretches. Protein is much more interesting.

26) If the 3d structure is disrupted (denature) by heating, it loses its function irreversibly.

27) Nucleic acids – We start with two pentoses, recall they have 4 carbon atoms. Two basic kinds of pentose molecules that are present in nucleic acids. Nucleic acids are polymers just like proteins are polymers, but instead of being made of monomers called amino acids, they are made of nucleotides. A nucleotide contains a phosphate group, a sugar, and a nitrogenous base.

28) The two kinds of sugars define the essential difference between DNA and RNA. – ribose and deoxyribose. In carbohydrates, the hydroxyl groups represent opportunities for all kinds of dehydration reactions, which can enable one to build much more complex molecules. The nitrogenous base is attached to the sugar by a dehydration reaction. One of the things you are going to have to memorize is the numbering system here.

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