BODY CHEMISTRY
Chapter 2

Inorganic Chemistry

Elements: basic substances that cannot be broken down into simpler substances by ordinary chemical means.

Atoms of elements combine chemically to form molecules.

Compounds are composed of molecules with more than one kind of element linked by chemical bonds.

Bonds

Common Elements (Know these!)

     Hydrogen (H): water and in organic molecules.

     Oxygen (O): water, oxygen gas, and in most organic molecules.

     Carbon (C): all organic molecules

     Nitrogen (N): in amino acids (proteins) & nucleic acids (DNA & RNA).

     Calcium (Ca + +): bone, cell membrane, nerve & muscle

     physiology, and bloodclotting.

     Phosphorus (P): bones, nucleic acids, phosphate (PO4) is an important buffer.

     Potassium (K +): cell membrane, nerve and muscle physiology.

     Sodium (Na+): cell membrane, nerve and muscle physiology.

     Chlorine (Cl) or chloride (Cl-): cell membrane and nerve physiology.

     Magnesium (Mg+ +): cofactor for some enzymes.

     Sulfur (S): found in some proteins

     Iron (Fe): In hemoglobin (for oxygen transport)

     Iodine (I): in thyroxine (thyroid gland)

 

Chemical Reactions

Combining or breaking apart two or more atoms that brings about a chemical change is called a chemical reaction.

Metabolism: includes all the chemical reactions that occur in the body.

Anabolism: building-up metabolic reactions. "Anabolic steroids."

Catabolism: tearing-down metabolic reactions.

Hydrolysis and Condensation

Water

Acids, Bases, Salts, & Buffers

Organic Compounds

Organic compounds always contain carbon and hydrogen.

Common "Optional elements" are oxygen, nitrogen, and sulfur.

4 Macromolecular Classes: Carbohydrates, Lipids, Proteins and Nucleic Acids.

Carbohydrates

General formula is CH2O or CnH2nOn

Functions:

     Sources of energy.

     Water retention (e.g., cartilage of joints and between cells).

     Cell-cell recognition

Saccharides are subunits:

     Monosaccharides: 5-6 carbon rings. E.g., glucose, fructose,

     ribose, galactose. (Note: -ose endings)

     Disaccharides: 2 monosaccharides condense to form 1

     disaccharide. E.g., sucrose, maltose, lactose.

     Polysaccharides: 3 or more monosaccharides. E.g., starch, glycogen.

 

Lipids

Fatty acids: chains of CH2 groups with a terminal carboxylic acid.

Basic building blocks of most complex lipids.

Saturated: no double bonds; "saturated" with hydrogen. Saturated fats are solids at room temperature.

Example: palmitate

Unsaturated: one or more C=C double bonds (loss of hydrogen). Generally liquid at room temperature.

Example: oleate

Polyunsaturated and Monounsaturated oils.

Not all unsaturated fats are the same. Cis fatty acids are more fluid than trans fatty acids.

Some simple fatty acid amides can act as hormones -- e.g., recently identified sleep inducing hormone.

Triglycerides: glycerol linked to 3 fatty acids

Phospholipids: 2 fatty acids linked to glycerol + phosphate group +

alcohol. Phospholipids are "bipolar" -- compound has a charged end and uncharged end. Phospholipids make up most of cell membranes.

Steroids: Fats in ring form. In cell membranes; cholesterol, hormones such as Estradiol (Estrogen) and Testosterone

Eicosanoids: Most abundant are prostaglandins -- prostaglandins are typically "local hormones" since they are nvolved in local reactions such as smooth muscle contraction (e.g., labor), mucus production in the stomach, blood clotting, and inflammation.

Proteins

Large complex molecules composed of subunits called amino acids

Amino: amine group --NH2.

Acid: carboxyl group -- COOH.

"R" group is different in the 20 common amino acids that make up proteins.

Amino acids are joined together by peptide bonds (via condensation reaction)

Amino acids linked by peptide bonds are called Peptides.

Levels of Protein organization

Primary -- linear arrangement of amino acids.

Secondary -- interactions between differ amino acids (hydrogen bonds) result in the formation of helices and sheets.

Tertiary -- interactions between different parts of a helix cause the protein to fold in different ways.

Quaternary -- separate helices interact forming complex structures; form taken can mean the difference between active and inactive proteins.

Protein types: Globular and fibrous.

Change in a single amino acid can result in a cascade of changes in protein structure -- Sickle cell anemia would be an example of how such a subtle change causes a serious disease.

Substitution of one amino acid in beta-hemoglobin chain (charged glutamic acid replaced by neutral valine) causes hemoglobin to form rod-like filaments when oxygen is low. The filaments cause red blood cells to sickle. Sickled cells block small capillaries and the spleen works overtime removing abnormal cells.

Functional Classifications:

Structural, contractile, transport, buffers, enzymes, coordination (hormones), and antibodies.

Enzymes: act as catalysts for reactions

     a) Can be quite specific for the type of reaction they catalyze.

     b) They are not changed as a result of the reaction.

     c) They have temperature and pH optima

Enzyme nomenclature: -ase suffix is common, e.g., protease breaks down protein, lipase breaks down lipids.

" -in" suffix was used for some of the first enzymes characterized, e.g., pepsin, trypsin since "-in" was the common suffix for proteins.

Enzymes may require cofactors or coenzymes to function properly -- common examples of cofactors are magnesium, calcium, zinc. Many vitamins are coenzymes.

Enzymes have important technological uses: Glucose-test strips and meters along with Industrial enzymes.

 

Nucleic Acids

2 types: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) DNA and RNA differ in the type of simple sugar they have -- deoxyribose or ribose. They also differ in structure and function.

Subunits are nucleotides:

Nucleotide = Base + sugar + phosphate

Adjacent nucleotides are linked together via sugar-phosphate bonds, making a "backbone" for the large molecule 5 different bases: Adenine (A) Guanine (G) Thymine (T): only in DNA Cytosine (C) Uracil (U): only in RNA

Other nucleotides: ATP, (adenosine triphosphate) and GTP have "high energy" phosphate bonds. Used as energy sources in the cell -- "cell money."

ATP ---> ADP + P + energy (The terminal high energy phosphate bond of ATP is broken, producing adenosine diphosphate, a free phosphate, plus free energy which can then be used to power other reactions in the cell).

DNA

DNA is the genetic code of most organisms -- its structure is the code for the different proteins that an organism manufactures. Double helix -- the double helix is the basic form of DNA. Two strands of DNA are held together by hydrogen bonds which form between the base (base pairing). Adenine pairs with thymine, cytosine pairs with guanine.

The sequence of bases is a linear code.....

opposite strand: -T-A-C-G-G-C-A-T-T-A-A-C-C-T-A-

A chromosome is condensed chromatin, a collection of proteins and DNA (many genes).

A gene is a sequence of nucleotides which the cell can decode to form

a protein (or a non-translated form of RNA) -- details to be covered in next chapter.

DNA serves as a template for RNA. "DNA codes for RNA"

one strand DNA: A-T-G-C-C-G-T-A-A-G-T-C-G-A-T

complementary RNA: U-A-C-G-G-C-A-U-U-C-A-G-C-U-A

DNA is found in the nucleus, but proteins are formed in the cytoplasm.

Genetic code is transferred from the nucleus to cytoplasm via RNA.

RNA serves as the direct code for protein synthesis. RNA is single stranded whereas DNA is double-stranded.