Below is a list of these 20 amino acids:

1. 3. Proteins are the 3rd type of food. In order to understand proteins we have to define some other terms. Amino Acids are molecules that contain the acid functional group (COOH) and the amine functional group (NH2) in the same molecule. There are 20 amino acids found in Nature. In each case, the amine group is on the C atom next to the COOH carbon. This is called the -C and these amino acids are called -amino acids:

2. Only the R group differs in the various amino acids. • There is one exception to this basic structure; proline which is cyclic and has the structure: Below is a list of these 20 amino acids:

5. Our bodies can make 11 of these amino acids from other nutrients, but we cannot make 9 of these. We can only get these from eating protein that contains them. These are called the essential amino acids. There is some disagreement about the number and identity of the essential amino acids but we will follow your book.

6. 2 amino acids can combine together in a reaction called a condensation reaction. The bond formed is the same as the one formed in an amide. Biochemically this is called a peptide bond. 2 amino acids connected by one peptide bond form a molecule called a dipeptide. This molecule still has an amine group and a COOH group, so it can react with another amino acid, and so on and so on. The peptide bond is between the COOH group on one amino acid and the NH2 group on the other amino acid.

7. Peptide Bond; Also amide bond

8. A protein is a giant molecule (a polymer) composed of up to thousands of peptide bonds. It is estimated that the human body contains about 100,000 different proteins. Proteins are characterized by how the amino acids are arranged in the molecule. 1. Primary Structure – Simply the sequence of amino acids bonded together. 2. Secondary Structure – Protein molecules are so large that it doesn’t exist as a simple straight chain, but rather it twists around to allow hydrogen bonding between NH2 groups (the twisting allows 2 NH2 to get close enough for H-bonding to occur) The most common secondary structure is that of a helix:

10. 3. Tertiary structure refers to how a protein molecule folds over itself, forming structural fibers or other 3 dimensional shapes. 4. Quaternary Structure – Forms when more than one protein molecule chains bond together. An example is hemoglobin (red blood cells).

11. All proteins have primary and secondary structure, but only some have tertiary and quaternary structure. All the structure of a protein is critical to its function. Any chemical or physical process that changes the structure of a protein will prevent it from doing its normal function. This is called denaturation. Heat and chemicals commonly cause denaturation of proteins Examples: • Fever • Tanning

12. Humans eat protein in order to obtain the amino acids, especially the essential amino acids. Our bodies break down ingested protein to amino acids. A protein that contains all the essential amino acids is called a complete protein. These are usually found in animal products (meat, fish, milk, eggs), while incomplete proteins are common in plants. A vegetarian diet has to contain a variety of foods so that all the essential amino acids can be obtained.

13. Proteins perform different functions in our bodies. All enzymes are proteins. Enzymes are catalysts for almost all the biochemical processes taking place in our bodies. Proteins are also used for structure (muscle, ligaments, tendons). Also, hemoglobin carries O2 to cells and CO2 away from cells. Finally, protein can be metabolized to provide energy, if necessary.

14. Within the cells of living organisms are the substances that control our genetic make-up and control many of the biochemical reactions, most importantly, protein synthesis. These are huge polymers called nucleic acids. 2 general types: 1. Ribonucleic acid (RNA) 2. Deoxyribonucleic acid (DNA)

15. DNA exists in a central part of the cell, called the nucleus, (Like the nucleus of an atom). RNA exists in the portion outside the nucleus, however, as we will see some RNA molecules travel between the 2 areas. There are 3 major types of RNA: 1. Messenger RNA (mRNA) 2. Transfer RNA (tRNA) 3. Ribosomal RNA (rRNA)

16. There are 3 major components to these polymers, a simple sugar (either D-ribose or 2-deoxy-D-ribose), a phosphoric acid group and a group of ring molecules, containing N as part of the ring, referred to as the bases in nucleic acids. There are 5 of these bases: 1. Adenine (A) 2. Guanine (G) 3. Thymine (T) 4. Cytosine (C) 5. Uracil (U) Uracil is only found in RNA while thymine is only found in DNA.

17. It could be shown that every cell in a particular living organism contained its own unique DNA, always the same for that organism. How could cells reproduce themselves and also reproduce (or replicate) the DNA molecule. 2 Internationally famous biochemists (James Watson and Francis Crick) solved the problem in 1953 and were awarded the Nobel Prize for their efforts. They wrote a popular book explaining the process simply enough for lay people to understand titled The Double Helix. DNA animation

18. The basis of their theory is that DNA is composed of 2 helical strands of sugar molecules bonded to each other forming a backbone with the bases attached to the outside. The bases point inwards and bond to each other via Hydrogen bonding (Think of a winding staircase), but only specific bases can bond this way: • 1. A to T • 2. G to C

19. When a cell divides, so does the DNA, into 2 strands. When the 2 new cells are formed, Each strand of DNA hydrogen bonds to the appropriate bases and thus a carbon copy of the original DNA is formed. See Figure 16.25 on page 480.

21. Using the base sequences on the DNA molecule and mRNA, rRNA and tRNA cells produce the proteins needed by the organisms. These nucleic acids direct which amino acids and in which order (remember primary protein structure) are needed for each protein. The amino acids are all either stored or made in the cells. RNA transcription Protein Synthesis

23. The information for each protein is a segment of DNA called a gene. The human DNA was thought to contain an estimated 80,000 to 100,000 genes. One of the largest combined scientific projects ever undertaken in this world is the Human Genome Project. This was an international collaboration of scientists around the world to identify all of the base sequences for all of the genes in human DNA. In 2003, the project was completed, about 5 years ahead of schedule, and only about 25,000 genes were found. It is thought that some genes produce more than one protein.

24. This knowledge is already being put to use in producing bio-engineered products, such as drugs and plants. Actually about 99.9% of all the DNA in all humans is the same from one human to the next.. The function of most of this is still unknown. The rest makes all the protein that is common to all humans. This is what was discovered in the Human genome Project.

25. Most of the remaining 0.1% of DNA in every human being is not the same for every human. This is what controls the differences between one person and the next. DNA profiling, which has become so important in solving crimes or proving family relationships, is done on this 0.1% of the DNA. It can only identify by comparison, because the parts analyzed do not tell scientists anything about the individual.

26. We mentioned antioxidants earlier, when we discussed REDOX reactions. An interesting example of the use of antioxidants is in the preservation of food. Many foods that contain fats and/or oils spoil because the fat turns rancid. This is the result of an oxidation reaction on the fat, in which O2 reacts with the fat and eventually a fatty acid is produced. Most fatty acids have a distinctly unpleasant taste and order, hence the spoilage of the food. Chemicals that prevent O2 from attacking the fat molecules are added to the food slowing down this process.

27. They work by reacting with an oxidation reaction intermediate, called a free radical. The free radical, if left on its own, would keep reacting with other fat molecules producing fatty acids and more free radicals. The antioxidants react with the free radicals instead, so the process doesn’t continue on its own. Two of the most common food additives are BHA (butylated hydroxyanisole) and BHT (butylated hydroxytoluene).

28. There is a theory that aging processes in living animals is aided by oxidation reactions leading to the formation of free radicals. Thus many people and nutritionists believe that eating foods high in natural antioxidants (such as vitamins C and E) or supplementing diets with these chemicals, will prolong a healthy life. Very recently, however, a study came out that said vitamin E supplements might increase the risk of heart disease and there is no hard, concrete evidence that antioxidant supplements prolong life.

29. We mentioned steroids earlier. Besides cholesterol, there are many important steroids produced by our bodies. Many hormones (which are chemicals produced in one gland in our bodies to be used elsewhere in our body, controlling many important functions in our bodies) are steroids. Some of the chemicals produced by the adrenal gland are steroids. There are many sex hormones, essential, not only for reproduction but as we are finding now for other important processes in our bodies. A list of some of the more important hormones is found in the next table.

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