Biochemistry Lecture

by: Angela Marie Ferrer BSN 2B

ENZYMES Enzymes are the catalysts of biochemical reactions. Enzymes catalyze nearly all the myriad reactions that occur in living cells. Uncatalyzed reactions that require hours of boiling in the presence of a strong acid or strong base can occur in a fraction of a second in the presence of the proper enzyme. The catalytic functions of enzymes are directly dependent on their three-dimensional structures. Some Characteristics of a Chemical Reaction Every chemical reaction starts with at least one reactant and finishes with a minimum of one product. As the reaction proceeds, the reactant concentration decreases and the product concentration increases Reaction Rate - Defined as a change in concentration with time the rate at which the reactants of a chemical reaction disappear and the products formed. Transition state - The reactant must pass through a high energy transition state to be converted to a product. This transition state is an unstable structure with characteristics of both the product and the reactant Activation energy - The energy necessary to move a reactant to the transition state. The larger this energy barrier is, the slower the reaction rate will be. Each organism contains thousands of enzymes: 1. Some are simple proteins consisting of only amino acid units. 2. Others are conjugated and consist of a protein part, or apoenzyme, and a nonprotein part, or coenzyme. 3. A functioning enzyme that consists of both the protein and nonprotein parts is called a holoenzyme. 4. Apoenzyme + Coenzyme = Holoenzyme 5. Often the coenzyme is derived from a vitamin, and one coenzyme may be associated with different enzymes. 6. For some enzymes, an inorganic component such as a metal ion (e.g. Ca2+, Mg2+, or Zn2+) is required. 7. This inorganic component is an activator. 8. The activator is analogous to a coenzyme. 9. Another remarkable property of enzymes is their specificity of reaction that is, a certain enzyme catalyzes the reaction of a specific type of substance. e.g. lactase 10. The substance acted on by an enzyme is called the substrate. e.g. Sucrose is the substrate of the enzyme sucrase. Classes of Enzymes 1. Oxidoreductases: Enzymes that catalyze the oxidation-reduction between two substrates. 2. Transferases: Enzymes that catalyze the transfer of a functional group between two substrates. 3. Hydrolases: Enzymes that catalyze the hydrolysis of esters, carbohydrates, and proteins (polypeptides).

Oxidoreductase COOOH- C H + NAD+ OH- C = O CH3 reduced substrate oxidized coenzyme Transferase

COOLDH + NADH + H CH3 oxidized product

reduced coenzyme

Hexokinase is the enzyme that catalyzes the first reaction in glycolysis pathway. The reaction involves transfering a phosphate group (PO42-) from adenosine triphosphate (ATP) to glucose to produce glucose-6-phosphate and adenosine diphosphate (ADP)

Hydrolase Carbohydrases effect the breaking of glycosidic bonds in oligo- and polysaccharides, proteoses effect breaking of peptide linkages in proteins and lipases effect the breaking of ester linkages in triacylglycerols.

the

Lyase The reaction involves trans-addition of the elements of water across the double bond. A dehydratase effects the removal of the components of water from a double bond and a hydratase effects the addition of the components of water to a double bond

Isomerase Phosphate transfer to 2-Phosphoglycerate catalysed by phosphoglycerate mutase 3-Phosphoglycerate <=> 2-Phosphoglycerate

Ligase ATP involvement is required because such reactions are generally energetically unfavorable and they require the simultaneous input of energy obtained by a hydrolysis reaction which ATP is converted to ADP.

in

Predict the function of the following enzymes 1. Maltase 2. Lactose dehydrogenase 3. Fructose oxidase 4. Maleate isomerase 5. Cellulase

Answers: 1. 2. 3. 4. 5.

Hydrolysis of maltose Removal of hydrogen from lactate ion Oxidation of fructose Rearrangement or isomerization of maleate ion Hydrolysis of cellulose

1. 2. 3.

There are three common ways to increase a reaction rate: Increasing the reactant concentration Increasing the reaction temperature Adding a catalyst

For the CO2 + H2 O reaction shown in Fig.30.3, predict which set of conditions will yield a faster reaction rate A)CO2 pressure = 100 torr T= 37oC Activation energy = 31 kcal / mol ________________________ B) CO2 pressure = 100 torr T= 37oC Activation energy = 31 kcal / mol A)CO2 pressure = 100 torr T= 37oC Activation energy =26 kcal / mol ________________________ B) CO2 pressure = 130 torr T= 37oC Activation energy = 31 kcal / mol Describe the effect that each of the following changes would have on the rate of a reaction that involves the substrate urea and the liver enzyme urease 1. Increasing the urea concentration 2. Increasing the urease concentration 3. Increasing the temperature from its optimum value to a value 106 higher than this value 4. Lowering the pH from the optimum value of 5.0 to a value of 3.0 Enzyme Kinetics Turnover Number An enzymes catalytic speed is also matched to an organisms metabolic needs. This catalytic speed is commonly referred to as turnover number the number of molecules an enzyme can react or turn-over in a given time span. ENZYME INHIBITION Enzyme inhibitors are molecules that interact in some way with the enzyme to prevent it from working in the normal manner. Types of Inhibitors Nonspecific and Specific Specific Inhibitors may be: Irreversible and reversible Competitive and noncompetitive. Poisons and drugs are examples of enzyme inhibitors. Non specific Inhibition A nonspecific inhibition effects all enzymes in the same way. Non-specific methods of inhibition include any physical or chemical changes which ultimately denatures the protein portion of the enzyme and are therefore irreversible. Specific Inhibitors Specific Inhibitors exert their effects upon a single enzyme. Most poisons work by specific inhibition of enzymes. Many drugs also work by inhibiting enzymes in bacteria, viruses, or cancerous cells Competitive Inhibitors A competitive inhibitor is any compound which closely resembles the chemical structure and molecular geometry of the substrate. The inhibitor competes for the same active site as the substrate molecule. A competitive inhibition is usually reversible if sufficient substrate molecules are available to ultimately displace the inhibitor. Therefore, the amount of enzyme inhibition depends upon the inhibitor concentration, substrate concentration, and the relative affinities of the inhibitor and substrate for the active site. Example: Ethanol is metabolized in the body by oxidation to acetaldehyde, which is in turn further oxidized to acetic acid by aldehyde oxidase enzymes. Normally, the second reaction is rapid so that acetaldehyde does not accumulate in the body. Non competitive Inhibitors

A noncompetitive inhibitor is a substance that interacts with the enyzme, but usually not at the active site. Non competitive inhibitors are usually reversible, but are not influenced by concentrations of the substrate as is the case for a reversible competive inhibitor.

Irreversible Inhibitors form strong covalent bonds with an enzyme. These inhibitors may act at, near, or remote from the active site. Consequently, they may not be displaced by the addition of excess substrate. In any case, the basic structure of the enzyme is modified to the degree that it ceases to work. Since many enzymes contain sulfhydral (-SH), alcohol, or acid groups as part of their active sites, any chemical which can react with them acts as an irreversible inhibitor. Heavy metals such as Ag+, Hg2+, Pb2+ have strong affinities for -SH groups. Oxalic and citric acid inhibit blood clotting by forming complexes with calcium ions necessary for the enzyme metal ion activator. Industrial Strength Enzymes Enzymes offer two major advantages to manufacturing processes and in commercial products: 1. Enzymes cause very large increases in reaction rates even at room temperature. 2. Enzymes are relatively specific and can be used to target selected reactants. 3. Proteases (proteolytic enzymes) break down proteins. 4. Lipases digest lipids. 5. Cellulases, amylases, lactases, and pectinases break down carbohydrates, cellulose, amylose, lactose, and pectin, respectively. Models of Enzyme Action Enzyme Active Site LOCK AND KEY MODEL In the lock and key model, the active site in the enzyme has a fixed, rigid, geometrical conformation. Only substrates with a complementary geometry can be accomodated at such a site, much as a lock accept only certain keys. Induced Fit Model Experimental evidences indicates that many enzymes have flexibility in their shapes. The induced fit model allows for small changes in the shape or geometry of the active site of an enzyme to accommodate a substrate. Temperature and pH Effects on Enzyme Catalysis Essentially, any change that affects protein structure also affects an enzymes catalytic function. If an enzyme is denatured, its activity will be lost. Thus, strong acids and bases, organic solvents, mechanical action, and high temperature are examples of treatments that decrease an enzymecatalyzed rate of reaction.

VITAMINS Vitamins are a group of naturally occurring organic compounds that are essential for good nutrition and that must be supplied in the diet.

They are often classified according to their solubility. Water Soluble Vitamins (B vitamins and Vitamin C) Absorption Directly into the blood Storage Storage Travel without carriers Circulate in the water-filled

Fat- Soluble Vitamins ( Vitamins A,D.E.K) First enter into the lymph system Many require protein carriers Found in the cells

Excretion Toxicity

Requirements Relationship to coenzymes

parts of the body Kidneys remove excess in the urine Not likely to reach toxic levels when consumed from supplements Needed in frequent doses Function as coenzymes

associated with fat Tend to remain in fatstorage sites Likely to reach toxic levels when consumed from supplements Needed in periodic doses Do not function as coenzymes

Vitamin C Vitamin C has the simplest structure of the 13 vitamins , exist in two active forms in the human body, an oxidized and the reduced form. We need vitamin C for the growth and repair of tissues in all parts of your body. It helps the body make collagen, an important protein used to make skin, cartilage, tendons, ligaments, and blood vessels. Vitamin C is needed for healing wounds, and for repairing and maintaining bones and teeth. Vitamin C is an antioxidant, along with vitamin E, beta-carotene, and many other plant-based nutrients. Antioxidants block some of the damage caused by free radicals, substances that damage DNA. The build-up of free radicals over time may contribute to the aging process and the development of health conditions such as cancer, heart disease, and arthritis. Vitamin B Selected Important Coenzymes in which B Vitamins are Present Vitamin B Complex The vitamin B complex consists of eight water soluble vitamins. The B vitamins work together to boost metabolism, enhance the immune system and nervous system, keep the skin and muscles healthy, encourage cell growth and division, and other benefits to your body. Brewer's yeast is one of the best sources of the B vitamins. Selected Important Coenzymes in which B Vitamins are Present B Vitamin 1. Vitamin B1 Thiamine 2. Vitamin B2 Riboflavin Coenzymes thiamin pyrophosphate (TPP) Flavin mononucleotide(FMN) Flavin adenine dinucleotide Nicotinamide adenine dinucleotide (NAD+) Nicotinamide adenine dinucleotide phosphate (NADP+) Pyridoxal-5-phosphate (PLP) Tetrahydrofolate(THF) 5deoxyadenosylcobalamin Coenzyme A (CoA) Acyl carrier protein biocytin Groups Transferred aldehydes Hydrogen atoms

3. Vitamin B3 Niacin

Hydride ion (H+)

4. Vitamin B6 Pyridoxine 5. Folate 6. Vitamin B12 Cobalamin 7. Vitamin B 5 Pantothenic Acid 8. Biotin

Amino groups One carbon groups other than CO2 Alkyl groups, Hydrogen atoms Acyl groups Carbon dioxide

Colorado State University

Fat Soluble Vitamins Small amounts of vitamins A, D, E and K are needed to maintain good health. Foods that contain these vitamins will not lose them when cooked. The body does not need these every day and stores them in the liver when not used. Most people do not need vitamin supplements. Megadoses of vitamins A, D, E or K can be toxic and lead to health problems. J. Anderson and L. Young Functions Deficiency symptoms Poor growth, night blindness, blindness, dry skin, People at risk Rare in United States but common in Sources Daily recommended intakes Infants: 400500 mg RAE Children: 300400 mg RAE Adolescents: Toxicity

Vitamin

Vitamin A Preformed retinoids and provitamin

Vision in dim light and color vision, cell differentiation and growth,

Preformed vitamin A: liver, fortified milk, fish

Headache, vomiting, double vision, hair loss, dry

A carotinoids

immunity

Xerophthalmia

preschool children living in poverty in developing countries, alcoholics

liver oils Provitamin A: red, orange, dark green, and yellow vegetables, orange fruits

600-900 mg RAE Adult men & women: 700900 mg RAE Pregnant women: 750770 mg RAE Lactating women:12001300 mg RAE

mucous membranes, bone and joint pain, fractures, liver damage, hemorrhage, coma, teratogenic effects: spontaneous abortions, birth defects. Upper level is 3000 mg of preformed vitamin A based on risk of birth defects and liver toxicity. Toxicity

Vitamin

Functions

Deficiency symptoms Rickets in children, osteomalacia in older adults

People at risk Dark skinned individual s, older adults, breastfed infants from vitamin D deficient mother

Sources

Vitamin D Cholecalci ferol Ergocalcif erol

Maintainenc e of intracellular and extracellular calcium concentratio ns

Vitamin D fortified milk, fish oils

Daily recommended intakes 0-50 years: 5 mg 51-70 years: 10 mg, >70 years: 15 mg

Calcificatio n of soft tissues, growth restriction, excess calcium excretion via the kidney. Upper level is 50 mg based on the risk elevated blood calcium. Toxicity

Vitamin

Functions

Deficiency symptoms Hemolysis of red blood cells, degeneration of sensory neurons

People at risk

Sources

Vitamin E Tocopherols Tocotrienols

Antioxidant, prevention of propagation of free radicals

Patients with fat malabsorption syndromes, smokers [overt deficiency is rare]

Plant oils, seeds, nuts, products made from oils

Daily recommended intakes Infants: 4-5 mg Children: 6-7 mg Adolescents:1115 mg Adult men & women: 15 mg Pregnant women: 15 mg Lactating women: 19 mg Daily recommended intakes Infants: 2-2.5 mg Children: 30-55 mg

Inhibition of vitamin K metabolism. Upper level is 1000 mg based on the risk of hemorrhage.

Vitamin

Functions

Deficiency symptoms Hemorrhage , fractures

People at risk

Source s Green vegeta bles,

Toxicity

Vitamin K Phylloquino ne

Synthesis of blood clotting

Those taking antibiotics for a long period

No upper level has been set

Menaquino ne

factors and bone proteins

of time; older adults with scant green vegetable intake

liver synthes is by intestin al microo rganis ms

Adolescents: 60-75 mg Adult men: 90 mg Adult women: 120 mg Pregnant/lactat ing women: 7590 mg

Minerals A number of inorganic elements are needed for good health. These minerals include: 1. sodium 2. potassium 3. calcium 4. magnesium 5. chloride 6. phosphate The body does not synthesize minerals.

The stepwise oxidation of sugars begins with glycolysis. Each of the 10 steps of glycolysis is catalyzed by a different enzyme. Note that step 4 cleaves a six-carbon sugar into two three-carbon sugars, so that the number of molecules at every stage after this doubles. As indicated, step 6 begins the energy-generation phase of glycolysis, which causes the net synthesis of ATP and NADH molecules.. Glycolysis is also sometimes referred to Embden-Meyerhof pathway.

Krebs cycle