Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
DNA-encoded chemical library wikipedia , lookup
Radical (chemistry) wikipedia , lookup
Photosynthesis wikipedia , lookup
Chemical biology wikipedia , lookup
Cell-penetrating peptide wikipedia , lookup
Protein adsorption wikipedia , lookup
Carbohydrate wikipedia , lookup
Biomolecular engineering wikipedia , lookup
Abiogenesis wikipedia , lookup
Evolution of metal ions in biological systems wikipedia , lookup
Welcome to Biology! Unit 1: Biochemistry Chapter 1: The Molecules of Life Chapter 2: The Cell and its Components Chapter 1: The Molecules of Life Molecules Interactions between and within molecules Structure and shape of molecules Macromolecules The 4 major types Roles in biological organisms Biochemical reactions The 4 major types The role of enzymes in reactions Section 1.1: Chemistry in Living Systems All matter is composed of elements Cannot be broken down into simpler substances by ordinary chemical methods Approximately 92 naturally occurring elements Only 6 elements serve as the chemical foundation for life Carbon Hydrogen Nitrogen Oxygen Phosphorous Sulfur Atoms An atom is the smallest particle of an element that retains the element’s properties Atomic mass = sum of protons and neutrons All atoms of an element have the same number of protons, but the number of neutrons can vary Isotopes Isotopes are atoms of the same element that have different numbers of neutrons Radioisotopes are unstable and their nucleus decays over time They are valuable diagnostic tools in medicine Studying the Interactions of Molecules A molecule is composed of two or more atoms and is the smallest unit of a substance that retains the chemical and physical properties of the substance Organic molecules are carbonbased Carbon atoms often bind to each other or hydrogen May also include nitrogen, oxygen, phosphorous, and/or sulfur Biochemistry Biochemists study the properties and interactions of biologically important organic molecules Biochemistry forms a bridge between chemistry (the study of the properties and interactions of atoms and molecules) and biology (the study of properties and interactions of cells and organisms). Understanding the physical and chemical principles that determine the properties of these molecules is essential to understanding their functions in the cell and in other living systems Interactions within Molecules Intramolecular forces (“intra” = within) hold the atoms within a molecule together These forces are generally thought of as the chemical bonds within a molecule Chemical bonds within a molecule are called covalent bonds. A covalent bond forms when the electrons of two atoms overlap so that the electrons of each atom are shared between both atoms Interactions within Molecules Some atoms attract electrons much more strongly than other atoms This property is referred to as an atom’s electronegativity Oxygen, nitrogen, and chlorine have high electronegativity Hydrogen, carbon, and phosphorus have low electronegativity When two atoms share electrons, the electrons are more attracted to the atom with the higher electronegativity Electrons have a negative charge, so that atom would assume a slightly negative charge (∂-) The atom with lower electronegativity assumes a partial positive charge (∂+) Interactions within Molecules This unequal sharing of electrons in a covalent bond creates a polar covalent bond Ex: A water molecule contains two polar covalent O-H bonds, where the electrons in each bond are more strongly attracted to the oxygen atom Molecules that have regions of partial negative and partial positive charge are called polar molecules Interactions within Molecules When covalent bonds are formed between atoms with similar electronegativities, the electrons are shared equally between the atoms These bonds are considered non-polar If these bonds predominate a molecule, the molecule is considered a non-polar molecule Ex: Carbon and hydrogen The polarity of biological molecules greatly affects their behaviour and functions in a cell Interactions between Molecules Intermolecular forces (“inter” = between) are forces between molecules They form between different molecules or between different parts of the same molecule (if it is very large) They are much weaker than intramolecular forces They determine how molecules interact with each other and with different molecules They play a vital role in biological systems Interactions between Molecules Intermolecular forces are usually attractive and make molecules associate together They can be broken fairly easily if enough energy is applied Intermolecular forces are responsible for many of the physical properties of substances Two types of intermolecular interactions are particularly important for biological systems: Hydrogen bonding Hydrophobic interactions Hydrogen Bonding A water molecule has two polar O-H bonds and is a polar molecule The slightly positive hydrogen atoms of one molecule are attracted to the slightly negative oxygen atoms of other water molecules This type of intermolecular attraction is called a hydrogen bond. Hydrogen bonds are weaker than ionic and covalent bonds and are represented by a dotted line Many biological molecules have polar covalent bonds involving a hydrogen atom and an oxygen or nitrogen atom. Hydrogen Bonding A hydrogen bond is more easily broken than a covalent bond, but many hydrogen bonds added together can be very strong The cell is an aqueous environment so hydrogen bonding between biological molecules and water is very important They help maintain the proper structure and function of the molecules Hydrogen Bonding Ex: The 3-D shape of DNA, which stores an organism’s genetic information, is maintained by numerous hydrogen bonds The breaking and reforming of these bonds plays an important role in how DNA functions in the cell Hydrophobic Interactions Non-polar molecules do not form hydrogen bonds When non-polar molecules interact with polar molecules, they clump together Non-polar molecules are hydrophobic, literally meaning “water-fearing” Polar molecules have a natural tendency to form hydrogen bonds with water molecules and are hydrophilic, literally meaning “water-loving” Hydrophobic Interactions The natural clumping together of non-polar molecules is called the hydrophobic effect This effect plays a central role in how cell membranes form and helps to determine the 3-D shape of biological molecules as proteins Ions in Biological Systems When an atom or group of atoms gains or loses electrons, it acquires an electric charge and becomes an ion When it loses electrons, the resulting ion is positive and is called a canion. When it gains electrons, the resulting ion is negative and is called an anion. Ions can be composed of only one element, such as a sodium ion, Na+, or of several elements, such as a bicarbonate ion HCO3- Ions in Biological Systems Ions are an important part of living systems Hydrogen ions, H+, are critical to many biological processes, including cellular respiration (the process by which cells break down nutrients into energy) Sodium ions, Na+, are part of transport mechanisms that enable specific molecules to enter cells. Since the cell is an aqueous environment, almost all ions are considered free or disassociated ions (Na+(aq)) since they dissolve in water, rather than as ionic compounds such as sodium chloride (NaCl(s)). Functional Groups Organic molecules that are made up of only carbon and hydrogen atoms are called hydrocarbons Hydrocarbons share similar properties including: Non-polar Do not dissolve in water Relatively low boiling points (depending on size) Flammable The covalent bonds between carbon and carbon and between carbon and hydrogen are “energy-rich” Breaking them releases a great deal of energy Most of the hydrocarbons you encounter in everyday life, such as acetylene, propane, butane, and octane, are fuels Functional Groups Though hydrocarbons share similar properties, other organic molecules have a wide variety of properties Most organic molecules have other atoms or groups of other atoms attached to their central carbon-based structure. A cluster of atoms that always behaves in a certain way is called a functional group Functional groups contain atoms such as oxygen (O), nitrogen (N), phosphorus (P), or sulfur (S). Certain chemical properties are always associated with certain functional groups Table 1.1 Structures and Shapes of Molecules A molecular formula shows the number of each type of atom in an element or compound Ex: H2O, C3H7NO2, and C6H12O6 Structural formulas show how the different atoms of a molecule are bonded together When representing molecules using a structural formula, a line is drawn between atoms to indicate a covalent bond A single line indicates a single covalent bond, double lines indicate a double bond, and triple lines indicate a triple bond Structural Formulas Structural Formulas Structural formulas can also be presented in a simplified form, particularly for biological molecules Carbon atoms are indicated by a bend in the line Their symbol, C, is omitted Hydrogen atoms attached to these carbon atoms are omitted but are assumed to be present Shapes of Molecules Structural formulas are 2-D representations, but molecules take up space in 3 dimensions In fact, the 3-D shape of a molecule influences its behaviour Ball-and-stick Model Space-filling Model Section 1.2: Biologically Important Molecules Many of the molecules of living organisms are composed of thousands of atoms These are called macromolecules, which are large molecules that often have complex structures Many macromolecules are polymers Long chain-like substances composed of many smaller molecules linked together by covalent bonds These smaller molecules are called monomers, which can exist individually or as units of a polymer The monomers in a polymer determine the properties of that polymer. Protein Nucleic Acid Carbohydrate Lipid Carbohydrates Carbohydrates contain carbon, hydrogen, and oxygen in the ratio of 2 hydrogen and 1 oxygen for every carbon The general formula for carbohydrates is (CH2O)n where “n” is the number of carbon atoms Sugar and starches are examples of carbohydrates They store energy in a way that is easily accessible by the body Most carbohydrates are polar and dissolve in water Due to high proportion of hydroxyl functional groups, and often carbonyl groups Monosaccharides and Disaccharides Monosaccharides are simple sugars that consist of 3 to 7 carbon atoms “Mono” = one and “saccharide” = sugar Common examples include: Glucose is the sugar the cells in the body use first for energy (i.e. blood sugar) Fructose is a principal sugar in fruits Galactose is a sugar found in milk Glucose Fructose Galactose Monosaccharides and Disaccharides These 3 simple sugars have the same molecular formula (C6H12O6) but the 3-D shapes of their structures and the relative arrangement of their hydrogen atoms and hydroxyl groups differ Molecules that have the same molecular formula but have different structures are called isomers Due to their different 3-D shapes, they’re treated very differently by your body and in the cell Ex: Your taste buds detect fructose as being much sweeter than glucose Monosaccharides and Disaccharides Two monosaccharides can join to form a disaccharide. The covalent bond between them is called a glycosidic linkage It forms between specific hydroxyl groups on each monosaccharide. Sucrose Common table sugar is the disaccharide sucrose (glucose and fructose) Lactose (galactose and glucose) is found in dairy products Glycosidic linkage Polysaccharides Many monosaccharides can join together by glycosidic linkages to form a polysaccharide (“poly” = many) Three common polysaccharides are starch, glycogen, and cellulose All three are composed of monomers of glucose, but they differ in the ways the glucose units are linked together This results in them having different 3-D shapes Starch and Glycogen The differences in their 3-D shapes also leads to them having different functions Plants store glucose in the form of starch and animals store glucose in the form of glycogen They provide short-term energy storage, whereby glucose can be easily accessed from their breakdown within the cell Starch and glycogen differ in their number and type of branching side chains Glycogen has more branches so it can be broken down much more rapidly than starch Cellulose Cellulose carries out a completely different function. It provides structural support in plant cell walls. The type of glycosidic linkage between monomers of cellulose is different from the type in starch and glycogen The hydroxyl group on carbon-1 of glucose can exist in 2 different positions These positions are referred to as alpha and beta The alpha form results in starch and glycogen, while the beta form results in cellulose. Lipids Like carbohydrates, lipids are composed of carbon, hydrogen, and oxygen atoms However, lipids have fewer oxygen atoms and a significantly greater proportion of carbon and hydrogen bonds As a result, lipids are non-polar and hydrophobic (they do not dissolve in water) Since the cell is an aqueous environment, the hydrophobic nature of some lipids plays a key role in determining their function Lipids The presence of many energy-rich C-H bonds makes lipids efficient energy-storage molecules Lipids yield more than double the energy per gram that carbohydrates do However, they store their energy in hydrocarbon chains so their energy is less accessible to cells than energy from carbohydrates Lipids provide longer-term energy and are processed by the body after carbohydrate stores are used up Lipids Lipids are crucial to life in many ways: Lipids insulate against heat loss Lipids form a protective cushion around major organs Lipids are a major component of cell membranes Lipids provide water-repelling coatings for fur, feathers, and leaves Triglycerides Triglycerides are composed Ester Linkages of 1 glycerol molecule and 3 fatty acid molecules The bond between the hydroxyl group on a glycerol molecule and the carboxyl group on a fatty acid is called an ester linkage because it results in the formation of an ester functional group 1 Glycerol 3 Fatty Acids Triglycerides: Fatty Acids A fatty acid is a hydrocarbon chain that ends with an acidic carboxyl group (-COOH) A saturated fatty acid has no double bonds between carbon atoms An unsaturated fatty acid has one or more double bonds between carbon atoms One double bond = monounsaturated Two or more double bonds = polyunsaturated Humans can’t synthesize polyunsaturated fats and must consume them in their diet Triglycerides: Saturated and Unsaturated Fats The double bonds in a triglyceride affects its 3-D shape, which alters its behaviour in the body Triglycerides containing saturated fatty acids are generally solid fats at room temperature Ex: lard and butter Triglycerides containing unsaturated fatty acids are generally liquid oils at room temperature Ex: olive oil and canola oil Triglycerides: Health Saturated fat is linked with heart disease, while some unsaturated fats, particular polyunsaturated fatty acids, are known to reduce the risk of heart disease A food preservation process called hydrogenation involves chemical addition of hydrogen to unsaturated fatty acids of triglycerides to produce saturated fats A by-product of this reaction is the conversion of cis fats to trans fats, whereby remaining double bonds are converted to a trans conformation Consumption of trans fats is associated with increased risk of heart disease Phospholipids Phospholipids are the main components of cell membranes They are similar in structure to triglycerides, but a phosphate group replaces the third fatty acid Attached to the phosphate group is an R group which defines the type of phospholipid The “head” portion is polar and hydrophilic The lower “tail” portion is non-polar and hydrophobic Phospholipids In aqueous environments phospholipids form a lipid bilayer In a phospholipid bilayer, the hydrophilic heads face the aqueous solution on either side of the bilayer, while the tails form a hydrophobic interior The inside of a cell is an aqueous environment, as is the extra-cellular fluid surrounding cells Therefore the membranes of cells, which are made of phospholipids, adopt this bilayer structure Other Lipids Steroids are a group of lipids that are composed of 4 carbon-based rings attached to each other Steroids differ depending on the arrangement of the atoms in the rings and the types of functional group Other Lipids: Steroids Cholesterol is a steroid that is: A component of cell membranes Present in the blood of animals The precursor of several other steroids, such as sex hormones testosterone and estrogen. Testosterone regulates sexual function and aids in building bone and muscle mass Estrogen regulates sexual function in females and acts to increase the storage of fat Mammals make cholesterol and it also enters the body as part of the diet Other Lipids: Steroids In medicine, steroids are used to reduce inflammation Ex: Topical steroid ointments to treat skin conditions and inhalers to treat asthma. Anabolic steroids are synthetic compounds that mimic male sex hormones They are typically used to build muscle mass in people who have cancer and AIDS, but are also frequently misused by athletes Other Lipids: Waxes Waxes have a diversity of chemical structures, often with long carbon-based chains, and are solid at room temperature They are produced in both plants (ex: carnauba wax) and animals (ex: earwax, beeswax, and lanolin) In plants, waxes coat the surfaces of leaves, preventing water and solutes from escaping and helping to repel insects In animals, waxes are present on the skin, fur, and feathers of many species and on the exoskeletons of insects Proteins Proteins represent an extremely diverse type of macromolecules that can be classified into groups according to their function Some of the functions of proteins include: Catalyzing chemical reactions Providing structural support Transporting substances in the body Enabling organisms to move Regulating cellular processes Providing defense from disease The functions of proteins depend on their 3-D structures Amino Acids: Monomers of Proteins A protein is a macromolecule composed of amino acid monomers An amino acid contains a central carbon atom that is bonded to the following four atoms or group of atoms: A hydrogen atom An amino group A carboxyl group An R group (which is also called a side chain) The distinctive shape and properties of an amino acid depend on its R group Amino Acids All amino acids are somewhat polar, due to the polar C=O, C-O, C-N, and N-H bonds Some amino acids are more polar than others, depending on the polarity of the R group There are 20 common amino acids that make up most proteins 8 of these are essential amino acids and can’t be produced by the human body and must be consumed as part of the diet These are isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. Amino Acids In proteins, amino acids are joined by covalent bonds called peptide bonds Form between the carboxyl group on one amino acid and the amino group on another A polymer composed of amino acid monomers is called a polypeptide Proteins are composed of one or more polypeptides Amino acids can occur in any sequence in a polypeptide and since there are 20 possible amino acids for each position, an enormous variety of proteins are possible Levels of Protein Organization The structure of a protein can be divided into 4 levels of organization Primary structure The linear sequence of amino acids The peptide bonds linking the amino acids are the backbone of a polypeptide chain Since the peptide bonds are polar, hydrogen bonding is possible between the C=O of one amino acid and the N-H of another amino acid. Levels of Protein Organization Secondary structure The result of the hydrogen bonds between amino acids A polypeptide can form a coil-like shape (alpha helix) or a folded fan-like shape (beta pleated sheet) Levels of Protein Organization Tertiary structure The 3-D shape of proteins that results from a complex process of protein folding This folding occurs naturally as the peptide bonds and the different R groups interact with each other and with the aqueous environment of the cell The hydrophobic effect had a large effect on structure The polar hydrophilic groups direct towards the aqueous environment and non-polar hydrophobic groups direct towards the interior of the proteins 3-D shape Hydrogen bonding and electrostatic attractions between R groups of different amino acids also add stability One class of proteins have molecular chaperones that interact with the polypeptide chain and produce the final folded protein Levels of Protein Organization Quaternary structure The association of two or more polypeptides to form a protein Protein Denaturation Under certain conditions, proteins can completely unfold in a process called denaturation This occurs when the normal bonding between R groups is disturbed Intermolecular bonds break, potentially affecting the secondary, tertiary, and quaternary structures Conditions that cause denaturation include extremes of hot and cold temperatures and exposure to certain chemicals Once a protein loses its normal 3-D shape, it is no longer able to perform its usual function Nucleic Acids There are two types of nucleic acids: DNA (deoxyribonucleic acid) RNA (ribonucleic acid) DNA contains the genetic information of an organism, which is interpreted and decoded into particular amino acid sequences of proteins, which carry out numerous functions in the cell This conversion is carried out with the assistance of different RNA molecules The amino acid sequence of a protein is determined by the nucleotide sequences of both DNA and RNA Nucleic Acids DNA and RNA are polymers made of thousands of repeating nucleotide monomers A nucleotide is made up of 3 components that are covalently bonded together A phosphate group A sugar with 5 carbon atoms A nitrogen-containing base The nucleotide make-up of DNA and RNA differs The nucleotides in DNA contain the sugar deoxyribose The nucleotides in RNA contain the sugar ribose Nucleic Acids There are 4 different types of nitrogenous bases in DNA: Adenine (A) Thymine (T) Guanine (G) Cytosine (C) In RNA all the same bases are used, except thymine, which is replaced with Uracil (U) Nucleic Acids A polymer of nucleotides is often referred to as a strand The covalent bond between adjacent nucleotides is called a phosphodiester bond It occurs between the phosphate group on one nucleotide and a hydroxyl group on the sugar of the next nucleotide A nucleic strand has a backbone made up of alternating phosphates and sugars with the bases projecting to one side of the backbone Nucleic Acids DNA is composed of 2 strands twisted about each other to form a double helix When unwound, it resembles a ladder The sides of the ladder are made up of alternating phosphate and sugar molecules, and the rungs of the ladder are made up of pairs of bases held together by hydrogen bonds Nucleotide bases always pair together in the same way: Thymine (T) pairs with Adenine (A) Guanine (G) pairs with Cytosine (C) These bases are said to be complementary to each other RNA is single-stranded Section 1.3 Biochemical Reactions The chemical reactions that are associated with biological processes can be grouped in several types The four main types of chemical reactions that biological molecules undergo in the cell are: Neutralization Oxidation-reduction Condensation Hydrolysis Neutralization (Acid-Base) Reactions In the context of biological systems, acids and bases are discussed in terms of their behaviour in water An acid is a substance that produced hydrogen ions, H+, when it dissolves in water It increases the concentration of hydrogen ions in an aqueous solution A base is a substance that produces hydroxide ions, OH-, when it dissolves in water It increases the concentration of hydroxide ions in an aqueous solution Neutralization (Acid-Base) Reactions The pH scale ranks substances according to the relative concentration of their hydrogen ions Substances that have a pH lower than 7 are classified as acids Substances that have a pH higher than 7 are classified as bases Substances that have a pH of 7 (that is, they have an equal concentration of hydrogen and hydroxide ions) are classified as neutral Neutralization (Acid-Base) Reactions When an acid chemically interacts with a base, they undergo a neutralization reaction that results in the formation of a salt (an ionic compound) and water The acid loses its acidic properties and the base loses its basic properties i.e. their properties have been cancelled out, or neutralized Neutralization (Acid-Base) Reactions The normal pH of human blood ranges from 7.35-7.45 If blood pH increases to 7.5 it can cause dizziness and agitation This condition is called alkalosis If blood pH decreases to 7.3-7.1 it can cause disorientation, fatigue, severe vomiting, brain damage, and kidney disease This condition is called acidosis Blood pH that falls below 7.0 or rises beyond 7.8 can be fatal Neutralization (Acid-Base) Reactions To maintain optimum pH ranges, organisms rely on buffers Substances that resist changes in pH by releasing hydrogen ions when a fluid is too basic and taking up hydrogen ions when a fluid is too acidic Most buffers exist as specific pairs of acids and bases Ex: One of the most important buffer systems in human blood involves the pairing of carbonic acid, H2CO3(aq), and hydrogen carbonate ion, HCO3-(aq) Oxidation-Reduction Reactions Another key type of chemical reaction is based on the transfer of electrons between molecules When a molecule loses electrons it becomes oxidized and has undergone a process called oxidation Electrons are highly reactive and do not exist on their own or free in the cell so when a molecule undergoes oxidation, the reverse process must occur in another molecule When a molecule accepts electrons from an oxidized molecule, it becomes reduced and has undergone a process called reduction Because oxidations and reductions occur at the same time, the whole reaction is called an oxidation-reduction reaction, or redox reaction Oxidation-Reduction Reactions A common type of redox reaction is a combustion reaction Ex: In the combustion of propane in your barbeque, the propane becomes oxidized and the oxygen is reduced This reaction releases a lot of energy that is used to cook food on the barbeque. Redox reactions also occur in cells, such as cellular respiration Sugars such as glucose are oxidized through a series of redox reactions to produce carbon dioxide and water. Condensation and Hydrolysis Reactions The assembly of all four types of biological macromolecules involves a condensation reaction between the monomers of each polymer In a condensation reaction, an H atom is removed from a functional group on one molecule, and an OH group is removed from another molecule The two molecules bond to form a larger molecule and water Condensation reactions are also called dehydration reactions because the reaction results in the release of water Condensation and Hydrolysis Reactions The breakdown of macromolecules into their monomers involves the addition of water to break the bonds between the monomers In a hydrolysis reaction, an H atom from water is added to one monomer, and an OH group is added to the monomer beside that one The covalent bond between these monomers breaks and the larger molecule is split into two smaller molecules Condensation Enzymes Catalyze Biological Reactions A certain amount of energy is required to begin a reaction, which is referred to as the activation energy of a reaction If the activation energy for a reaction is large, the reaction will occur very slowly One of the methods to speed up reactions is to increase the temperature of the reactants However, the temperatures that chemical reactions would need to reach in order to proceed quickly enough to sustain life are so high that they would permanently denature proteins This is why long-lasting high fevers are so dangerous, as the high temperature can cause major disruptions to cellular reactions Enzymes Catalyze Biological Reactions A catalyst is a substance that speeds up a chemical reaction but is not used up by the reaction Catalysts function by lowering the activation energy of a reaction Cells manufacture specific proteins that act as catalysts, called enzymes Ex: In red blood cells an enzyme called carbonic anhydrase enables carbon dioxide and water to react to form about 600,000 molecule of carbonic acid each second! Enzymes facilitate almost all chemical reactions in organisms, and each type of reaction is carried out by its own characteristic enzyme Enzymes Bind with a Substrate Like other proteins, enzymes are composed of long chains of amino acids folded into particular 3-D shapes, with primary, secondary, tertiary, and often quaternary structures Most enzymes have globular shapes, with pockets or indentations on their surfaces called active sites The unique shape and function of an active site are determined by the sequence of amino acids in that section of the protein Enzymes Bind with a Substrate An active site on an enzyme interacts in a specific manner with the reactant of a reaction, called the substrate During the reaction, the substrate joins with the enzyme to form an enzyme-substrate complex The substrate fits closely into the active site because enzymes can adjust their shapes slightly Intermolecular bonds, such as hydrogen bonds, form between the enzyme and the substrate as the enzyme adjusts its shape This change in shape is called induced fit Enzymes Bind with a Substrate Enzymes lower the activation energy of the reaction by changing the substrate, its environment, or both To accomplish this, the active site may: Contain amino acid R groups that cause bonds in the substrate to stretch or bend, making the bonds weaker and easier to break Bring two substrates together in the correct position for a reaction to occur Transfer electrons to and from the substrate (reduce or oxidize it), destabilizing it and making it more likely to react Add or remove hydrogen ions to or from the substrate (i.e. act as an acid or base), destabilizing it and making it more likely to react Enzymes Bind with a Substrate Once the reaction takes place, the products of the reaction are released and the enzyme is able to accept another substrate and begin the process again This cycle is known as the catalytic cycle Some enzymes require the presence of other molecules or ions, known as coenzymes, to catalyze a reaction Some enzymes require the presence of metal ions, such as iron or zinc, which are referred to as cofactors This is why your body requires small amount of minerals and vitamins to stay healthy Enzyme Classification Enzymes are classified according to the type of reaction they catalyze The shape of an enzyme must match its substrate exactly, so most enzymes catalyze only one specific reaction There are thousands of different enzymes to catalyze the numerous reactions that take place within an organism, each with a specific name to identify it The names of many enzymes consist of the first part of the substrate’s name, followed by the suffix “-ase” Ex: The enzyme that catalyzes the cleavage of the glycosidic linkage in lactose is named lactase. Enzyme Activity and Surrounding Conditions Enzyme activity is affected by any change in conditions that alters the enzyme’s 3-D shape Temperature and pH are two important factors When temperatures are too low, the bonds that determine enzyme shape are not flexible enough to enable substrate molecules to fit properly When temperatures are too high, the bonds are too weak to maintain the enzyme’s shape The optimal temperature and pH ranges of most enzymes are fairly narrow Most human enzymes work best within the pH range of 6-8. There are exceptions though (ex: stomach enzymes) Enzyme Activity and Surrounding Conditions The number of substrates available also affects the rate of enzyme activity If there are too few substrates present, enzymes and substrates will encounter each other much less frequently, and the rate of reaction will decrease Therefore, enzyme activity increases as substrate concentration increases This is true up to a point where the enzymes are working at maximum capacity, after which adding more substrate will not affect the rate of the reaction Enzyme Activity Regulation Inhibitors are molecules that interact with an enzyme and reduce its activity They reduce the enzyme’s ability to interact with its substrate This can occur by two different mechanisms: Competitive inhibition Non-competitive inhibition Competitive Inhibition These inhibitors interact with the active site of the enzyme When both the substrate and inhibitor are present, they will compete to occupy the active site When the inhibitor is present in high enough concentration, it will out-compete the substrate and block it from binding This prevents the reaction that the enzyme usually catalyzes from occurring Non-competitive Inhibition These inhibitors bind to an allosteric site, altering the conformation or 3-D shape of the enzyme, which decreases the activity of the enzyme Many biochemical reactions are grouped together in pathways where the product of one reaction acts as a substrate for the enzyme that catalyzes the next reaction in the pathway These pathways are regulated by feedback inhibition The product of the last reaction in a pathway is a noncompetitive inhibitor of the enzyme that catalyzes the reaction at the beginning of the pathway This ensures that the products of a pathway are not produced unnecessarily Enzyme Activity Regulation Activator molecules can also bind to an allosteric site In this case, the conformation of the enzyme alters in such a way as to cause an increase in enzyme activity The regulation of enzyme activity by activators and inhibitors binding to allosteric sites is called allosteric regulation