chemical paper topic of your choice, something in the Lectures in each module that you found interesting.

CHE 102: LECTURE 6 Polymers to Proteins to Nucleic Acids to Covid-19

In December 2019, a new coronavirus Covid-19 (a protein) caused an outbreak of pulmonary disease in the city of Wuhan, the capital of Hubei province in China, and has since spread globally. 

POLYMER A polymer is composed of many simple molecules that are repeating structural units called monomers. A single polymer molecule may consist of hundreds to a million monomers and may have a linear, branched, or network structure. Examples of naturally occurring polymers are silk, wool, DNA, cellulose and proteins. Natural polymers occur in nature and can be extracted. They are often water-based. Examples of synthetic polymers include nylon, polyethylene, polyester, Teflon, and epoxy. The process by which a polymer is synthesized, called polymerization, is illustrated by the formation of polyethylene from n molecules of ethylene. See Lecture 5 for the structure of ethylene.

STRUCTURE of SOME COMMON POLYMERS

Some Common Addition Polymers
Name(s)	Formula	Monomer	Properties	Uses
Polyethylene low density (LDPE)	–(CH2-CH2)n–	ethylene CH2=CH2	soft, waxy solid	film wrap, plastic bags
Polyethylene high density (HDPE)	–(CH2-CH2)n–	ethylene CH2=CH2	rigid, translucent solid	electrical insulation bottles, toys
Polypropylene (PP) different grades	–[CH2-CH(CH3)]n–	propylene CH2=CHCH3	atactic: soft, elastic solid isotactic: hard, strong solid	similar to LDPE carpet, upholstery
Poly(vinyl chloride) (PVC)	–(CH2-CHCl)n–	vinyl chloride CH2=CHCl	strong rigid solid	pipes, siding, flooring
Poly(vinylidene chloride) (Saran A)	–(CH2-CCl2)n–	vinylidene chloride CH2=CCl2	dense, high-melting solid	seat covers, films
Polystyrene (PS)	–[CH2-CH(C6H5)]n–	styrene CH2=CHC6H5	hard, rigid, clear solid soluble in organic solvents	toys, cabinets packaging (foamed)
Polyacrylonitrile (PAN, Orlon, Acrilan)	–(CH2-CHCN)n–	acrylonitrile CH2=CHCN	high-melting solid soluble in organic solvents	rugs, blankets clothing
Polytetrafluoroethylene (PTFE, Teflon)	–(CF2-CF2)n–	tetrafluoroethylene CF2=CF2	resistant, smooth solid	non-stick surfaces electrical insulation
Poly(methyl methacrylate) (PMMA, Lucite, Plexiglas)	–[CH2-C(CH3)CO2CH3]n–	methyl methacrylate CH2=C(CH3)CO2CH3	hard, transparent solid	lighting covers, signs skylights
Poly(vinyl acetate) (PVAc)	–(CH2-CHOCOCH3)n–	vinyl acetate CH2=CHOCOCH3	soft, sticky solid	latex paints, adhesives
cis-Polyisoprene natural rubber	–[CH2-CH=C(CH3)-CH2]n–	isoprene CH2=CH-C(CH3)=CH2	soft, sticky solid	requires vulcanization for practical use
Polychloroprene (cis + trans) (Neoprene)	–[CH2-CH=CCl-CH2]n–	chloroprene CH2=CH-CCl=CH2	tough, rubbery solid	synthetic rubber oil resistant

For more details, there are multiple websites. See the listing at the end of this Lecture.

PROTEINS

We begin by identifying the monomers or “building blocks” ( the 20 naturally occurring amino acids) of class of biopolymers called proteins. Proteins that play a catalytic role in metabolism are called enzymes. Following are questions often asked by students followed by my response. 1. What is a protein?

Proteins are a class of organic compounds that consist of large molecules composed of one or more long chains of amino acids. They are an essential part of all living organisms, especially as structural components of body tissues such as muscle, hair, collagen, etc., and as enzymes and antibodies. Proteins are simply biopolymers, with the monomers or “building blocks ” making up the protein called amino acids. 2. What is an amino acid? Amino acids are organic compounds containing both a carboxyl (- COOH) functional group and an amino functional group (- NH2) group. See Lecture 5. There are 20 amino acids occurring nature which are central to life. Each has the following structure with only the “R group” differentiating one amino acid from another.

The 20 amino acids are: 3. What are some examples of proteins? Some proteins provide structural support in our bodies, for example, the proteins in our connective tissues, such as collagen and elastin. Hormone proteins co-ordinate bodily functions. For example, insulin controls our blood sugar concentration by regulating the uptake of glucose into cells The metal ions in insulin (purple “balls” in the structure) are zinc (Zn) and  manganese (Mn).

Hemoglobin is the protein that carries oxygen to the cells in our body. It is comprised of four chains two having 141 residues (amino acids) and two chains having 146 residues.

hemoglobin (heterotetramer, (αβ)2)

Structure of human hemoglobin. α and β subunits are in red and blue, and the iron-containing  heme  groups in green. From  PDB :  1GZX ​  Proteopedia   Hemoglobin

.

The heme (or haem) group in hemoglobin is the red pigment in blood.

The heme group is a coordination compound, a complex consisting of an iron (Fe) ion coordinated to a molecule called a porphyrin (see below) acting as a tetra-dentate ligand. A ligand is a molecule or ion attached to a metal atom by coordinate bonding. Tetra-dentate means four sites are coordinated. One or two axial ligands are above and below the plane of the porphyrin.

Importantly, a change of just one amino acid in this protein results in an inherited blood disorder, Sickle Cell Anemia (SCD), that affects over 100,000 people of all ages in the U.S. Healthy red blood cells are round and flexible. They move through your small blood vessels and bring oxygen to all parts of your body. With SCD, red blood cells are misshapen, hard and sticky. They get stuck in your blood vessels and clog them. This can cause pain, infection, organ damage, low blood count, strokes and other serious health problems.

People with sickle cell trait get the sickle cell gene from one parent but not both. Most people with sickle cell trait don’t have any symptoms of SCD.

Later in this Lecture we will discuss the genetic code, the nucleotide triplets of DNA and RNA molecules that carry genetic information in living cells. The mutation causing sickle cell anemia is a single nucleotide substitution (A to T) in the codon for amino acid 6. The change converts a glutamic acid codon (GAG) to a valine codon (GTG). while sickle beta chain has the amino acid valine.

It is this change in sickle cell hemoglobin (HbS), in which glutamic acid in position 6 (in beta chain) is mutated to valine, which causes the deoxygenated form of the hemoglobin to stick to itself. In sickle cell anemia, abnormal hemoglobin cause red blood cells to become rigid sticky and misshapen. The sickle cell gene is passed from generation to generation in a pattern of inheritance called autosomal recessive inheritance.

I have studied structural stability of the related heme protein cytoglobin (h-Cygb), the predicted function of which is the transfer of oxygen from arterial blood to the brain. The crystal structure of this protein has 2464 atoms in the unit cell (see Lecture 4), not including hydrogen.

It is interesting that the chemical “neighborhood” surrounding the iron atom (Fe) in hemoglobin is reminiscent of the chemical “neighborhood” of magnesium (Mg) in the molecule chlorophyll, the molecule central to photosynthesis. There is similarity in structure of the iron binding site in hemoglobin and magnesium binding site in chlorophyll (which is not a protein). Planar arrays of chlorophyll comprise the “light harvesting” system ( the so-called chlorophyll antenna network ) that captures sunlight and initiates the conversion of radiant energy from the Sun into chemical energy. This will be discussed in Lecture 7.

Chlorophyll a

NUCLEIC ACIDS A second class of biopolymers essential for life are the nucleic acids: DNA and RNA. 1. What are the “building blocks” or monomers that constitute DNA and RNA? The monomers or nucleotides found in the two nucleic acid types are different: adenine, cytosine, and guanine are found in both RNA and DNA, while thymine occurs in DNA and uracil occurs in RNA.

2. What is the structure of DNA? Deoxyribonucleic acid (DNA) is a molecule composed of two chains that coil around each other to form a double helix carrying the genetic instructions used in the growth, development, functioning and reproduction of all known living organisms and many viruses, such as coronavirus. The structure of DNA was proposed by James Watson, an American biologist born and raised in Chicago, and Francis Crick, an English physicist, in the journal Nature (April 25, 1953). See the end of this Lecture for a website that gives an historical perspective.

3. What is the genetic code? The genetic code is the set of rules used by living cells to translate information encoded within genetic material (DNA) into proteins. The code is a triplet code.

4. Why is the genetic code a triplet? Since there are only four nucleotides, a code of single nucleotides would only represent four amino acids, but there are 20 amino acids that are needed as “building blocks “ for the proteins necessary for life. A doublet code could code for 16 amino acids (4 x 4). A triplet code could provide a code for 64 different combinations (4 x 4 x 4), and provide plenty of information in the DNA molecule to specify the placement of all 20 amino acids. When experiments were performed to crack the genetic code it was found that the code was indeed a triplet. These three letter codes of nucleotides (AUG, AAA, etc.) are called codons. The “inverse” table to the above one is: CODON TABLE

GENETIC ENGINEERING Genetic engineering is the process of using knowledge of biochemistry and experimental techniques to change the genetic makeup (the DNA) of an organism, be it an animal, plant a bacterium or a virus.

This change can be achieved by using a technique known as “recombinant DNA”, or making use of DNA that has been isolated from two or more different organisms and then incorporating it into a single molecule.  This results in a mutation, something that Mother Nature has been doing since life evolved on Earth. An example in human history is the mutation that led to Emmer wheat. See Lecture 1.

Polymers

https://www.ch.ntu.edu.tw/~sfcheng/HTML/material94/Polymer-1.pdf

Polymer - Wikipedia

https://en.wikipedia.org/wiki/Polymer

Watson and Crick https://doi.org/10.1164/rccm.2302011        PubMed:  12684243