Lesson 10 Biochemistry

A study of Proteins, Enzymes, Carbohydrates, & Lipids (The branch of chemistry dealing with compounds produced by living organisms.) Print and Save for Board Exam Preparation

I. Proteins
A. Definitions & Characteristics
1. Protein - A biological compound that is a polymer of many amino acids. (Proteins are polymers made by linking together (in various combinations) a number of similar but different amino acids.) The fundamental building blocks of living matter. a. Essential elements include: carbon, hydrogen, oxygen, and nitrogen. (some proteins may contain iron, sulfur, and phosphorus) 2. Amino Acid The building blocks of proteins; a compound containing an amino group (-NH2), and a carboxyl group (-COOH), and a radical. a. General Formula (the Alpha Amino Acid) H O | || H - N - C - C - OH | | H R (1). Observe the two functional groups: NH2 and COOH (2). R is the radical. Since there are 30 identified amino acids, there are 30 possible R groups. b. Glycine is the simplest amino acid. c. Amino acids are amphoteric and may act as blood buffers. (1) Amphoteric (definition) A compound that can act as both an acid and a base. (2). Buffers (definition) Substances that in solution are capable of neutralizing, within limits, both acids and bases and thereby maintaining the original or a constant solution pH. d. Peptide linkage (peptide bond) (definition) A bond formed from a dehydration reaction between the amino group on one amino acid with the carboxyl group on another amino acid. (The link holding two amino acids together.) CONH are the elements forming the peptide bond. e. Simple Protein Example: Glycine (amino acid) and Alanine (amino acid) combine to form the protein (dipeptide) known as glycylalanine.

B. Protein Structure
Some proteins are composed of one polypeptide chain. Others consist of two or more

chains. The chains may form coils, sheets, or take on three dimensional shapes. The types of protein structures include: 1. Primary Structure The sequence of amino acids in a protein (one single chain). 2. Secondary Structure The protein chain forms a coil (alpha helix) or a beta pleated sheet.. The text includes the triple helix of collagen as a secondary structure, also. 3. Tertiary Structure A folding of the coiled protein chain. Think of a coiled alpha helix folding over. 4. Quaternary Structure Those proteins with more than one polypeptide chain may have quaternary structure. Here, the chains are arranged in three dimensional shapes. For example, one hemoglobin molecule (with four chains) takes on the shape of a tetrahedron. a. Hemoglobin Facts: (1). The lifespan of red blood cells is approx. 120 days. Normal degradation occurs in the spleen. (2). During life, hemoglobin will decompose to: (a) Globin - (protein) The amino acids that comprise globin are re-used by the body. (b). Heme - (non-protein) The heme degrades to: aa. Biliverden (biliverden is green in color). bb. Biliverden is reduced to bilirubin (yellow in color) in the spleen. cc. Bilirubin is carried by serum albumin to the liver. dd. Bilirubin is found in bile (bile is secreted by the liver). ee. Bile is a normal secretion that aids in fat digestion. The normal concentration of bilirubin in blood serum is approx. .1 to 1.5 mg/ml. When the bilirubin concentration reaches a level above 2.5 or 3.0 mg/ml, the yellow discoloration of jaundice may be evident. b. Hemoglobin & Embalming Concerns (1). Postmortem Staining: Heme (from degraded hemoglobin) may cause postmortem staining. Following hemolysis, the heme seeps into tissue resulting in a postmortem stain. Said stain will remain in tissues during arterial injection of embalming solution. (No displacement or removal occurs) (2). Jaundice: Patients dying with higher than normal concentrations of bilirubin in blood will exhibit jaundice (characterized by a yellow discoloration of tissues). Jaundice may be the result of the following pathological conditions: aa. Bile duct obstruction bb. Excessive red blood cell hemolysis cc. Liver cell damage (e.g., cirrhosis of the liver) (3). Some formaldehyde based arterial embalming fluids may be responsible for the conversion of yellow bilirubin to green biliverden. aa. One school of thought suggests that formaldehyde acts as a reducing agent that causes the change in color. bb. Another school of thought suggests that the acidic condition created by the presence of unbuffered formaldehyde solutions spur said color

change.

C. Protein Reactions
1. Denaturation A protein is denatured when its structure is changed in a way that modifies its properties. a. Methods to Denature Proteins (1). Alcohol (2). Salts of heavy metals (e.g., compounds containing lead, arsenic, mercury, and silver.) Arsenic salts and bichloride of mercury have been prohibited as embalming ingredients. (3). Heat (4). Acids & Bases 2. Protein Hydrolysis In the presence of water, peptide linkages are broken, liberating amino acids. Water splits apart during the process. 3. Imbibition Proteins have the ability to absorb moisture. 4. Putrefaction (definition) - Decomposition of proteins by the action of enzymes of anaerobic bacteria. a. Putrefaction involves three major chemical reactions: (Hydrolysis, Deamination, & Decarboxylation.) (1). Hydrolysis - Reaction in which water is one of the reactants and compounds are often broken down. In the hydrolysis of proteins, the addition of water accompanied by the action of enzymes results in the breakdown of protein into amino acids.
Enzymes

Protein + Water ----------------> Amino Acids

(2). Deamination - The removal of an amino group (-NH2) from a compound.

Deamination

Amino Acid --------------------> Ammonia + Carboxylic Acid Note: The carboxylic acid can further decompose to CO2 + H2O

(3). Decarboxylation - The removal of a carboxyl group (-COOH) from a compound.

Decarboxylation

Amino Acid ---------------------> Carbon Dioxide

Water

+ Amine

Note: Amines may further decompose to ammonia and various end products.

Summary During putrefaction, deamination and decarboxylation may occur at the same time. Here is a flow chart to illustrate this point.

CO2 & H2O are end products

______________________________________________________________________

End Products of Putrefaction:

CO2 H2O Ammonia Others: hydrocarbons,

H2S mercaptans (thiols) H2

D. Glossary Terms
1. Protein, amino acids, amphoteric, buffers, peptide bond, coagulation, deamination, decarboxylation, denaturation.

II. Enzymes
A. Definitions
1. Enzyme A protein that acts as a biological catalyst. 2. Substrate The material upon which an enzyme works. 3. Catalyst A substance that changes the rate of a chemical reaction but undergoes no net change itself during the reaction

B. Example of Enzyme Action

1. Goal: Split sucrose.

Sucrose

Sucrase (Enzyme )

Water

--------> Fructose

Glucose + Sucrase (Enzyme)

(Substrate )

( Products )

Note: When sucrose (disaccharide) and sucrase combine, they initially form a complex. Next, sucrose will split into two monosaccharides (fructose & glucose). Sucrase remains unchanged.

C. Chemical Properties of Enzymes

1. Enzymes are Specific Enzymes are very specific concerning the type of reactions they catalyze and what substrates they bind. There are varying degrees of specificity among enzymes. (See text for lock and key theory & induced-fit theory.) 2. Enzymes are Proteins 3. Enzymes are Chemically Labile (unstable) Since enzymes are proteins, they can be denatured. 4. Enzymes are Affected by Changes in pH and Temperature. They operate within a minimum and maximum pH range & temperature range. They work best under an optimum pH and temperature.

D. Enzymes Are Involved In Blood Clotting

Prothrombin (inactive enzyme) is converted to thrombin (active enzyme). Thrombin

serves as the catalyst to convert the soluble protein fibrinogen to the insoluble protein fibrin. Fibrin forms the tangled threads that capture red blood cells, hence forming a blood clot.

E. Two Sources of Enzymes That Catalyze Human Decomposition

1. Saprophytic Bacteria Bacteria that use dead organic matter as a source of nutrition (e.g., E. Coli). 2. Lysosome of Cells During autolysis, enzymes (e.g., cathepsin) catalyze cell self digestion. The lysosome contains this enzyme before releasing it. a. Autolysis (definition) Self digestion or self destruction of the body by autolytic elements.

III. Carbohydrates
A. Definition A compound of hydrogen, carbon, and oxygen that is an aldehyde or
ketone derivative of a polyhydroxy alcohol. Examples are sugars, starches and glycogen. 1. Glossary Terms to Know: Monosaccharide, disaccharide, polysaccharide, aldose, ketose, pentose, hexose, glucose, glycogen, hydrolysis. 2. Uses: A stored form of energy, a source of carbon for synthesis of cell compounds, and a part of the structural elements of some cells and tissues.

B. Classification
1. Monosaccharides - The simplest form of a carbohydrate consisting of a single sugar molecule such as glucose or fructose. They cannot be hydrolized to a smaller carbohydrate molecule. a. Types: Triose (3 carbons), Tetrose (4 carbons), Pentose (five carbons), Hexose (six carbons) b. Examples of hexose carbohydrates: (these are isomers) (1). Glucose C6H12O6 (2). Fructose C6H12O6 (3). Galactose C6H12O6 2. Disaccharides - A carbohydrate formed by the linking of two monosaccharide units. These are double sugars. Upon hydrolysis, disaccharides will yield two simple sugars. a. Examples: (these are isomers) (1). Sucrose C12H22O5 (2). Maltose C12H22O5 (3). Lactose C12H22O5 b. Hydrolysis (1). Lactose + Water ---> Galactose + Glucose (2). Maltose + Water ---> Glucose + Glucose (3). Sucrose + Water ---> Fructose + Glucose

3. Polysaccharides A polymer made by linking together a number of simple sugar molecules. Starches and cellulose are examples. Complex sugars. Upon hydrolysis, polysaccharides will yield many simple sugars. a. Examples: general formula is (C6H10O5)x (1). Starch (2). Cellulose (3). Glycogen

C. Reactions of Carbohydrates
1. Some carbohydrates act as reducing agents. 2. Polysaccharides and disaccharides undergo hydrolysis. 3. The complete oxidation products of monosaccharides (during life) are carbon dioxide, water, and energy. 4. Monosaccharide can decompose by way of fermentation. In the presence of a catalyst, the sugar will convert to ethyl alcohol and carbon dioxide.

IV. Lipids
A. Classification
1. Method # 1 a. Lipids that contain fatty acids in their structure. (1). Fats (2). Oils (3). Waxes (beeswax, lanolin, carnouba) b. Lipids that do not contain fatty acids in their structure. (1). Steroids (cholesterol, testosterone, estrone, cortisone) (2). Fat soluble vitamins (A, D, E, & K) 2. Method # 2 (your text uses this method) a. Simple Lipids (AUpon hydrolysis, simple lipids produce fatty acids and an alcohol.) (1). Fats (2). Oils (3). Waxes b. Compound Lipids (A Upon hydrolysis, compound lipids produce fatty acids, an alcohol, and other compounds@) (1). Phospholipids (glycerol, two fatty acids, one phosphoric acid, amino alcohol) (a). Examples: cephalin & lecithin (both found in brain and nerve tissue) (2). Sphingolipids (amino alcohol, fatty acid, phosphoric acid, one or more cholines) (a). Example: sphingomyelin (found in brain tissue and myelin sheath) (3). Glycolipids (a sugar unit , usually galactose, either glycerol or sphingosine, and fatty acids) c. Miscellaneous Lipids (do not undergo hydrolysis; these are classified as lipids because they are extracted from plant and animal tissues by non-polar solvents)

(1). Examples: steroids, bile salts, hormones, fat soluble vitamins

B. Fat v. Oil
1. Fat (e.g., glycerol tristearate; a.k.a. Atristearin@) a. Solid at room temperature b. Fats contain a higher percentage of saturated fatty acids c. As a result, fats tend to be more saturated with hydrogen d. Sometimes fats are known as triglycerides. 2. Oil a. Liquid at room temperature b. Oils contain a higher percentage of unsaturated fatty acids

C. Fat & Oil v. Wax

1. Fats and oils contain three fatty acids and glycerol 2. Waxes contain three fatty acids and some other type of alcohol a. Example: the alcohols are usually higher in molecular weight (trimethylhydroxy alcohol)

D. Properties of Fats & Oils

1. Physical Properties a. Solubility (Not water soluble; soluble in organic solvents) b. Forms emulsions (definition) A mixture of two insoluble liquids, one being dispersed throughout the other in small droplets. Emulsification (definition) The act of mixing two insoluble liquids. c. Physical state (at room temperature): Fats solid; Oils liquid. 2. Chemical Properties a. Know the final hydrolysis products of each (see above) b. Saponification: What are the products? What is adipocere? (see below)

E. Reactions of Fats & Oils

1. Hydrolysis 2. Saponification (definition) The reaction between a fat and a strong base to produce glycerol and the salt of a fatty acid (soap). Adipocere (definition) Gravewax. A wax-like material produced by saponification of body fat when a body is buried directly in alkaline soil 3. Hydrogenation 4. Rancidity

F. Glossary Terms to Know:

1. Simple lipids, fats, oils, emulsification, adipocere, saponification, waxes, & compound lipid.