Fundamentals of Biochemistry

I. Types of Chemical Reactions - biological compounds are typically synthesized and broken down in a very similar fashion.

A. Synthesis or condensation reactions – anabolic reactions •Biological macromolecules are generally considered polymers. Polymers are large molecules composed of repeating subunits called monomers. These monomers are linked together by by chemical reactions that may be termed as synthesis reactions, condensation reactions or anabolic reactions. These reactions form covalent bonds between hydrogens and hydroxyls of smaller substrate molecules, require ATP, release one molecule of water for each bond. I attempt to illustrate them below:

H-Mer-OH + H-Mer-OH + ATP -------> H-Mer-Mer-OH

(2 mono Mers) (A dimer)

You will note that the dimer in the diagram above still contains a hydroxyl, meaning that we could continue adding "Mers". When many "mers" are linked together, we have a polymer. Since energy is required in biological terms, this is an anabolic reaction.

 B. Biological molecules are broken down by reactions that may be termed Hydrolysis reactions or catabolic reactions. The polymers are broken down to their original monomers by the addition of a water molecule for each bond broken hence the term hydrolysis. Since energy is required to link the mers together, energy will be released as as the bonds are broken. Energy releasing reactions are called catabolic reactions. The energy released is typically captured to form ATP.

H-Mer-Mer-OH + H₂O ---->H-Mer-OH + H-Mer-OH + ATP

The 4 types of biological molecules: carbohydrates, lipids, proteins and nucleic acids differ only by their only by the monomers that comprise them.

II.Carbohydrates are commonly known as sugars or polysaccharides and have the General formula (CH₂O)n. This can be otherwise stated as Carbon, Hydrogen and Oxygen in a ratio of 1:2:1. The monomers of carbohydrates are known as monosaccharides. 3 common monosaccharides are shown below.

A. Disaccharides you should know. - the photo below is to emphasize synthesis. You should know the composition of Maltose, Sucrose and Lactose

B. Polysaccharides all of the polysaccharides discussed here are composed of glucose mononers.

1. amylose - aka starch. amylose is commonly thought of a a plant storage polysaccharide. Digestible by most humans.

2. cellulose. cellulose is commonly called plant fiber and is not digestible by humans. However, many microbes including bacteria and fungi are capable of digesting cellulose.

3. glycogen not shown in the pic below, glycogen is typically thought of an an animal storage carbohydrate. Most aminals store it in their livers and also in muscle cells and other cells as well.

III. Lipids. Very diverse group of compounds grouped together because they are all less polar to non polar, fats, steroids, waxes, oils. Generally composed of Carbon, Hydrogen, Oxygen and some have Phosphate (CHOP).

                   A. true fats - triglycerides - glycerol + 3 fatty acids linked together by dehydration/synthesis/anabolic reactions

  1. saturated fatty acid - one in which each C is covalently bonded to a full complement of H atoms or stated another way cannot accept any more hydrogen atoms

a. saturated fats are more common among mammals, or really any organism that lives at warmer temperatures

b. they generally have a higher melting point than unsaturated fatty acids and as we see them commercially they are typically solids. (ie butter, lard, etc.)

2. Unsaturated fatty acid - contains one or more C=C double bonds

                     a. generally liquids at room Temperature (oils)

                     b. more likely found in plant found products or

                     c. poikilotherms - organisms that do not regulate temperature

                     d. property of the fat is due to the fatty acids that that comprise it

e. are often hydrogenated in some commercial products "partially hydrogenated vegetable oils"

f. hydrogenation - the addition of hydrogen atoms increases the melting point so that products can remain solid or semisolid at refrigeration temperatures

 3. phospholipids - a diglyceride in which one of the glycerol binding sites contains a phosphate group

                             a. major component of cell membranes

                             b. amphipathic - a molecule which has both hydrophilic and hydrophobic groups.  The phosphate ion (hydrophilic) is attracted to polar water, while the fatty acid "tails" are non- polar and not attracted to water (hydrophobic)

 4. FUNCTIONS OF fats -

                             a. Energy storage - 9 kcal/gram

                             b. insulation

                             c. cushions internal organs - multicellular

                             d. hormones (steroids) such as estrogens, testosterone & prostaglandins and in animals

                             e. biological barriers -- cell membranes - regulate entry of substances into cells

 IV. Proteins, or polypeptides the shapers of life - very diverse group of compounds - composed of long chains of amino acids They may be called heteropolymers as they are composed of chains of amino acids. Since there are at least 20 different amino acids any of which may appear in a polypeptide they may have many different monomeric units. Hence the term heteropolymers. Their basic elements comprising amino acids (AAs) are Carbon, Hydrogen, Oxygen, Nitrogen, Phosphate and sometimes Sulfur (CHONPS)

                   A. amino acids and the formation of a peptide bonds

1. The NH2 group is called an amine or amino. The COOH is a carboxylic acid commonly just called an acid group. The amino group of the 2nd amino acid above reacts with the carboxylic acid group of the 1st amino acid splitting out a water molecule and forming a peptide bond.

2. you will note that the tripeptide above has an amino group at one end. At the other end there is a carboxylic acid.  We could therefore keep adding amino acids to that end of the molecule to form a polypeptide. Polypeptides found in proteins can be hundreds of amino acids long.              

3. protein diversity - Since there are at least 20 different AA's if we were to assume that any of which can occupy any position in the polypeptide chain the number of different proteins is almost infinite. Hair is protein. T

 4. levels of protein structure

               a. primary - linear sequence of AA's which AA acid occupies a position on the polypeptide chain

b. secondary - alpha helix or pleated sheet due to regular Hydrogen bonding between adjacent peptide bonds

                c. tertiary structure - 3D folding of polypeptide chain due to interaction of R groups

                d. quaternary structure - interaction of 2 or more polypeptide chains to form the functional protein

5. functions of proteins -

          a. enzymes - biological catalysts - control chemical reactions in cell or body. By definition enzymes increase the rate of chemical reactions by lowering the amount of energy required to start the reaction (Activation Energy). Enzymes are neither products nor reactants and they are not consumed in the reaction. They remain active and are therefore effective in low concentration. They are often named by their substrate + the suffix ' ase.

            b. The lock and key model of enzyme activity demonstrates why protein shape is important. The enzyme has an active site that is an exact fit for the substrate. That means enzymes are highly specific for the substrate and particular reaction. The further may be specific for a wide range of environmental conditions like pH, temperature, osmotic pressure among others. As an example many enzymes in the acid pH of your stomach do not function in the small intestine which is slightly alkaline. THE LOCK AND KEY MODEL IS ILLUSTRATED BELOW

c. 1 Mechanism of Enzyme Control --- Competitive Inhibition occurs when a molecule very similar to size, shape or charge of the substrate competes with the "normal substrate" for access to the active site.

d. Another mechanism of Enzyme Control is known as Allostearism. In allostearic control mechanisms a product of the enzymatic reaction binds to a site other than the active site of the enzyme and changes the shape of the enzyme either activating or inactivating enzyme activity. Systems that activate are called inducible systems while systems that deactivate are said to be repressible. COMPETITIVE INHIBITION AND REPRESSIBLE ALLOSTEARISM ARE SHOWN BELOW.

e. Denaturation - enzyme (protein) shape can be permanently altered by heat or changes in pH

Enzymatic Allostearism Competetive Inhibition Noncompetitive inhibition

Denaturation

f. other enzyme functions

 ` 1) structure - proteins form structures of cells, and in tissues and organs and systems of all organisms

       2). Cellular ID . Cells of multicellular organisms and in the environment recognize each other by the proteins they express. for example your blood type is an expression of modified proteins present on the surface of your red blood cells. Administering and wrong blood type activates an immune recognition system with dire consequences.

       3). transport enzymes - allow entry into cells

       4) Proteins can also serve as a source of energy. Like carbohydrates they are worth 4.5 kcal/gram

V. Nucleic acids - universal in all known cells and viruses nucleic acids important information molecules that contain the "code of life" - "master computer of cells"

       1. 2 types

a. DNA - deoxyribonucleic acid

            b. RNA - ribonucleic acid

2. Composed of long chains of nucleotides. The components of a nucleotide are:

                             a. nitrogen base

                             b. 5C sugar

                             c. phosphate 

A. DNA contains Adenine (A) a Purine that forms hydrogen bonds with the pyrimidine Thymine (T). The Purine Guanine (G) hydrogne bonds with the pyrimidine Cytosine (C).

B. RNA is typically, but not always, single stranded. RNA has no Thymine (T). Instead, it utilizes the pyrimidine Uracil (U).

C. The Central Dogma of Biology - most biological entities, excluding some viruses, functions are encoded in DNA which is then TRANSCRIBED to RNA. Then the 3 types of RNA are TRANSLATED to protein.

1. Transcription - the production of RNA from a DNA template

2. Translation - the production of protein (polypeptides) from RNA

D. Adenosine Triphosphate (ATP) The Energy molecule of cells is a ribonucleotide. It is composed of Adenine (A), ribose and 3 phosphates. ATP belongs to a group of high energy molecules including Guanine Triphosphate (GTP) that give off energy when a bond is broken between the second and third phosphates to produce Adensosine Diphosphate (ADP). This is how cells fuel energy requiring reactions. Think of ATP as a very short term energy storage molecule. We often call it "energy currency" I think as a reference to money. How long does your money last? Cells must always be making more ATP.