Biomolecules

1. Biomolecules

2. Atoms Atoms have 3 components: protons, neutrons, and electrons The type of element (carbon, iron, etc. ) is entirely determined by how many protons are in the nucleus. protons and neutrons are in the nucleus Protons have a +1 charge Neutrons have no charge Electrons circle around the nucleus, in a series of shells. Electrons have a -1 charge Chemical bonds are created by movements of the electrons between atoms The number of protons determines which element the atom is. Hydrogen: 1 proton, carbon = 6 protons, oxygen = 8 protons. Biological and chemical processes never change the number of protons in any atom. Normally, the number of electrons is equal to the number of protons, so the atom has no electrical charge: it is neutral.

3. Covalent Bonds Covalent bonds occur when 2 atoms share a pair of electrons. The electrons spend part of their time with both atoms. A molecule of hydrogen gas, H2, has 2 hydrogen atoms. Each atom provides 1 electron, so in the bond each atom shares 2. The bond is symbolized as a line connecting the 2 H’s: H-H ↑ In water (H2O), the oxygen has 6 electrons in its outer shell, and it shares one with each of the 2 hydrogens, giving 8 shared electrons for oxygen and 2 for each hydrogen. Each element has a characteristic number of bonds it forms: carbon = 4, nitrogen = 3, oxygen = 2, hydrogen = 1.

4. Polar Covalent Bonds Sometimes the electrons in a covalent bond aren’t shared equally, because one atom attracts electrons more strongly than the other. When this happens, the electrons spend more time with one atom, and that atom becomes slightly negatively charged. The other atom becomes slightly positively charged. This is a polar covalent bond, because the atoms form positive and negative poles. Bonds where the electrons are shared equally are called non-polar. Water is a polar compound, because the oxygen is slightly negative and the hydrogens slightly positive. Oxygen attracts electrons more than hydrogen Polar molecules attract each other: the opposite charges attract.

5. Water • Water forms many hydrogen bonds with other water molecules and with other polar substances. This causes water molecules to stick together (causing surface tension) and stick to other things (causing capillary action, how water gets from the roots to the top of trees). • Polar substances dissolve in water, because water forms hydrogen bonds with the polar molecules. Thus, polar substances are called hydrophilic, or “water-loving”. • Non-polar substances don’t dissolve in water because they can’t form hydrogen bonds, so they are called hydrophobic, or ‘water-fearing”. Oils and fats are examples of non-polar substances. • Soap works by having a non-polar end, which dissolves in grease, and a polar end, which dissolves in water. Soap causes tiny droplets of grease to be suspended in water, where they can be rinsed away.

6. Organic Compounds It used to be thought that only living things could synthesize the complicated carbon compounds found in cells German chemists in the 1800’s learned how to do this in the lab, showing that “organic” compounds can be created by non-organic means. Raw materials: coal and oil Organic compounds are those that contain carbon. (with a few exceptions such as carbon dioxide and diamonds)

7. Four Basic Types of Macromolecule Most organic molecules in the cell are long chains of similar subunits. Because they are large, these molecules are called macromolecules. Each macromolecule has a different type of subunit. The four types of macromolecule are: carbohydrates (sugars and starches), Subunit = simple sugar. lipids (fats). Subunits = fatty acids and glycerol proteins, Subunits = amino acids nucleic acids (DNA and RNA). Subunits = nucleotides The cell also contains water, inorganic salts and ions, and other small organic molecules. Plants often produce secondary metabolites: special compounds that attract pollinators, inhibit microorganisms, deter grazing animals, etc. We have found uses for many of these secondary metabolites as medicines, spices, and drugs.

8. Carbohydrates Sugars and starches: “saccharides”. The name “carbohydrate” comes from the approximate composition: a ratio of 1 carbon to 2 hydrogens to one oxygen (CH2O). For instance the sugar glucose is C6H12O6. Carbohydrates are composed of rings of 5 or 6 carbons, with –OH groups attached. This makes most carbohydrates water-soluble. Carbohydrates are used for energy production and storage (sugar and starch), and for structure (cellulose).

9. Sugars Monosaccharides, or simple sugars, like glucose and fructose, are composed of a single ring. Glucose is the primary food molecule used by most living things: other molecules are converted to glucose before being used to generate energy. Glucose can also be assembled into starch and cellulose. Fructose is a another simple sugar found in plants, It is sweeter than glucose and is used to sweeten may food products. Disaccharides are two simple sugars joined together. Most of the sweet things we eat are disaccharides: table sugar is sucrose, glucose joined to fructose. Plants use photosynthesis to make glucose, but convert it to sucrose for ease of transport. Maltose, malt sugar, consists of two glucoses joined together. It is a breakdown product of starch, which yeast converts to ethanol when beer is brewed.

10. Complex Carbohydrates = polysaccharides (many sugars linked together). Can be linear chains or branched. Some polysaccharides are used for food storage: starch. Starch is a glucose polymer, we have enzymes that easily digest starch. Starch is a convenient way to store glucose in both plants and animals. Some polysaccharides are structural: the cellulose of plant cell walls and fibers is a polysaccharide composed of many glucose molecules, but linked together differently than starch. We don’t have enzymes that can digest these polymers. Cows and termites depend on bacteria in their guts to digest cellulose, producing methane as a byproduct.

11. Lipids Lipids are the main non-polar component (hydrophobic) of cells. Mostly hydrocarbons—carbon and hydrogen. They are used primarily as energy storage and cell membranes. 4 main types: fats (energy storage), phospholipids (cell membranes), waxes (waterproofing), and steroids (hormones). Waxes: waterproof coating on plants and animals. Composed of fatty acids attached to long chain alcohols. The ability of plant to coat themselves in waxes was crucial to the ability to live on dry land. Steroids have carbon atoms arranged in a set of 4 linked rings. Cholesterol is steroid; it is an essential component of cell membranes (along with the phospholipids). Many human hormones are steroids

12. Triglycerides and Phospholipids Triglyceridesare the main type of fat. A triglyceride is composed of 3 fatty acids attached to a molecule of glycerol. Fatty acids are long hydrocarbon chains with an acid group at one end. Fats store about twice as much energy per weight as carbohydrates like starch. Phospholipids are the main component of cell membranes. they have a glycerol with 2 fatty acids attached, plus a phosphate-containing “head” group instead of a third fatty acid. The head group is hydrophilic, while the fatty acids are hydrophobic. Cell membranes are 2 layers, with the head groups facing out and the fatty acids forming the interior of the membrane.

13. Proteins The most important type of macromolecule. Roles: Enzymes: all chemical reactions in the cells are catalyzed by enzymes, which are proteins: building up, rearranging, and breaking down of organic compounds,, generating energy Structure: collagen in skin, keratin in hair, crystalline in eye. Also, movement of materials inside the cell. Transport: everything that goes in or out of a cell (except water and a few gasses) is carried by proteins. All organisms contain protein, but animals have much more protein than plants: most of the animal body is composed of protein, while most of the plant body is carbohydrate. Proteins are 1/3 nitrogen. Acquiring this nitrogen and getting rid of nitrogenous waste is a big problem animals face.

14. Amino Acids Amino Acids are the subunits of proteins. Each amino acid contains an amino group (-NH2) and an acid group (COOH). Proteins consist of long chains of amino acids, with the acid group of one bonded to the amino group of the next. There are 20 different kinds of amino acids in proteins. Each one has a functional group (the “R group”) attached to it. Different R groups give the 20 amino acids different properties, such as charged (+ or -), polar, hydrophobic, etc. The different properties of a protein come from the arrangement of the amino acids.

15. Protein Structure A polypeptide is one linear chain of amino acids. A protein consists of one or more polypeptides, and they sometimes contain small helper molecules such as heme. Many co-factors are vitamins: molecules our body can’t make for itself, so we have to get from our food. After the polypeptides are synthesized by the cell, they spontaneously fold up into a characteristic conformation which allows them to be active. The proper shape is essential for active proteins. For most proteins, the amino acids sequence itself is all that is needed to get proper folding. The joining of polypeptide subunits into a single protein also happens spontaneously, for the same reasons. Denaturation is the destruction of the 3-dimensional shape of the protein. This inactivates the protein, and makes it easier to destroy. Heat is the easiest way to denature proteins: this is the effect of cooking foods.

16. Nucleic Acids Nucleotides are the subunits of nucleic acids. Nucleic acids store and transmit genetic information in the cell. The two types of nucleic acid are RNA (ribonucleic acid) and DNA (deoxyribonucleic acid). Each nucleotide has 3 parts: a sugar, a phosphate, and a base. The sugar, ribose in RNA and deoxyribose in DNA, contain 5 carbons. They differ only in that an –OH group in ribose is replaced by a –H in DNA. The main energy-carrying molecule in the cell is ATP. ATP is an RNA nucleotide with 3 phosphate groups attached to it in a chain. The energy is stored because the phosphates each have a negative charge. These charges repel each other, but they are forced to stay together by the covalent bonds.

17. DNA and RNA DNA uses 4 different bases: adenine (A), guanine (G), thymine (T), and cytosine (C). The order of these bases in a chain of DNA determines the genetic information. DNA consists of 2 complementary chains twisted into a double helix and held together by hydrogen bonds. DNA is a stable molecule which can survive thousands of years under proper conditions The DNA bases pair with each other: A with T, and G with C. RNA consists of a single chain that also uses 4 bases: however, the thymine in DNA is replaced by uracil (U) in RNA. RNA is much less stable than DNA: it is used to convey information for immediate use by the cell.

18. Human Nutrition • To make all those molecules, we need various raw materials. The absence of any essential nutrient leads to disease and death. • Sufficient food molecules to supply our energy needs: calories. These can be carbohydrate, protein, or fat. • Fat has about twice the calories pr weight as carbohydrates or protein. • Protein generates ammonia waste (urine). • Some amino acids and fatty acids we can’t make for ourselves • Amino acids: 10 of the 20 are required in the diet. • Fatty acids: omega-3 (linolenic acid) and omega-6 (linoleic acid) fatty acids are required. • Small amounts of small complex molecules used by enzymes to catalyze chemical reactions. There are 15 known vitamins. • Elements in a usable form: these are called minerals: phosphorus, calcium, iron, zinc, magnesium, manganese, a total of 17 elements, not including carbon, hydrogen, oxygen, and nitrogen.

19. Some Deficiency Diseases • Undernutrition: not enough calories. Mostly in young children, and mostly they die of other diseases that would be easily overcome by the well-nourished. • Protein deficiency diseases. Some get sufficient calories (as form a starchy diet) but not enough complete protein: some essential amino acids are insufficient. • Vitamin deficiencies: • Vitamin A. Used in visual pigment and in skin. Permanent blindness can result from deficiency. Made from carotene. • Vitamin C. Needed to make collagen in skin. Scurvy. • Vitamin D. Used as a hormone that regulates calcium levels in the body. Deficiency leads to rickets: malformed bones, especially legs. Precursor made in liver, then transported to skin so UV can convert it to active form. Darker skinned people need more sunlight than lighter skinned • Thiamine. Used in breakdown of carbohydrates. Beriberi, seen in people who live on polished rice. Japanese sailors in 1880’s. Brown rice cures it.

20. Some Deficiency Diseases • More vitamins: • Niacin. Used in electron transport, essential for energy generation. Can be made from the amino acid tryptophan, which is lacking in maize. Pellagra leads to insanity: in the early 20th century, half the patients in mental hospitals in the US South had pellagra. • Vitamin B12 (cobalamin). Only bacteria make it. Plants don’t use it or contain it. Herbivores get it from their gut bacteria, and we get it by eating meat and dairy products. Pernicious anemia. • Minerals: • Sodium. Plants have very little of it. It has been a valuable commodity: salt mines. • Calcium. Used in many places, especially muscle and bone. Osteoporosis. • Iron. Needed for hemoglobin in the blood. Iron deficiency anemia is the most common form of nutrient deficiency. Rather hard to absorb. • Iodine. Part of thyroid hormone. Not used in plants, but lots in the sea, so seaweed and other marine things have a lot of it. Goiter: swollen thyroid glands, used to be common in the Midwest, but now we use iodized salt.