Biology 1000 Lecture #3-2 PDF

Lecture #3 Chemical Reactions and Organic Chemistry Textbook Chapter #3 3.1-3.7  Organic Compounds All organic compounds contain carbon Carbon is an excellent molecular component because of its ability to form large and diverse mo...

Lecture #3 Chemical Reactions and Organic Chemistry Textbook Chapter #3 3.1-3.7  Organic Compounds All organic compounds contain carbon Carbon is an excellent molecular component because of its ability to form large and diverse molecules These abilities of carbon are the reasoning behind the many different organic molecules that are necessary for every day life Carbohydrates Lipids Proteins Nucleic acids Carbon has four electrons in its outer shell: To achieve a complete outer shell containing 8 electrons carbon forms four covalent bonds with other atoms  Organic Compounds Compounds composed only of carbon and hydrogen are referred to as hydrocarbons The chain of carbon atoms in an organic molecule is referred to as the carbon skeleton The carbon skeleton may be: Branched: example isobutane Unbranched: example butane Both butane and isobutane have the same chemical formula meaning that they both consist of four carbons and ten hydrogens but these atoms are connected to one another differently Atoms with the same chemical formula but different connectivity are called isomers Isomers have different chemical properties because of their different shapes  Functional Groups The size, shape and the chemical groups that are attached to an organic molecule determine the molecule’s unique properties Chemical groups that are polar and affect a molecule’s reactivity are referred to as functional groups These functional groups are polar because the oxygen or nitrogen present within the group has a very strong pull on the electrons that are shared in the covalent bond These groups are water loving or hydrophilic because of their polarity Since these molecules are so important for life function it is a key characteristic that they be water soluble  Functional Groups The methyl group (# 6 on chart) is non- polar and therefore non-reactive It still affects molecular shape and thus function 1. Hydroxyl Group: This is composed of a hydrogen atom bound to an oxygen atom This hydrogen-oxygen group (hydroxyl group) is then bound to a carbon skeleton Example: ethanol (shown on table) Groups containing a hydroxyl group are called alcohols  Functional Group 2. Carbonyl Groups: These consist of a carbon atom joined by a double bond to an oxygen atom If the carbonyl group is at the very end of the chain it is called an aldehyde If the carbonyl group is anywhere in the middle of the chain (ex) not at the end it is called a ketone Sugars have one carbonyl groups and several hydroxyl groups 3. Carboxyl Group: These groups have carbon double bonded to an oxygen and single bonded to a hydroxyl group The OH group behaves as an acid, ionizing and donating H+ to solution Compounds with carboxyl groups are called carboxylic acids  Functional Groups 4. Amino Groups: These are composed of a nitrogen bonded to two hydrogen atoms and a carbon skeleton This group acts as a base by picking up H+ from solution Organic compounds containing the amino group are called amines Amino acids which are the protein building blocks contain both an amino group and a carboxyl group 5. Phosphate Group: Consists of a phosphorous atom bound to four oxygen atoms It is attached to the carbon skeleton by one of its four oxygen atoms Involved in energy transfers from the ATP molecule Compounds containing the phosphate group are called organic phosphates  Functional Groups The figure below illustrates the different chemical properties that two molecules can have because of a change in a functional group  Polymers There are four main classes of biological molecules referred to as macromolecules 1. Carbohydrates 2. Proteins 3. Lipids 4. Nucleic acids When larger molecules are formed by joining smaller molecules together the larger molecules are called polymers Polymers are large molecules consisting of many identical or very similar building blocks The individual units (building blocks) of the polymer are called monomers  Polymers Polymers are made via dehydration reactions Two monomers are joined to one another by the removal of water One of the unlinked monomers has a free – OH group and the other unlinked monomer has a free –H group The H and the OH are removed forming: A water molecule A covalent bond between the two monomers  Polymers Breaking polymers occurs via a hydrolysis reaction: Hydrolysis is the addition of water to the molecule This occurs when carbohydrates that you eat are broken down into sugars This reaction is the reverse of a dehydration reaction A hydroxyl group joins to one of the monomers and a hydrogen to the other monomer  Monosaccharides Carbohydrates are a class of molecules that include small sugars found in things that we drink and large sugars such as starch in foods such as potatoes Carbohydrate monomers are called monosaccharides An example of a monomer is glucose Monosaccharides generally have the formula CnH2nOn n=6 for glucose (C6H12O6) Monosaccharides can be linked together by a dehydration reaction in order to form more complex molecules Honey is a mixture of the monosaccharides glucose and fructose  Disaccharides Disaccharides are constructed from a dehydration reaction between two monosaccharides Maltose is formed from dehydration of two glucose monomers Table sugar is called sucrose and is made by joining a glucose monomer and a fructose monomer together via a dehydration reaction  Polysaccharides Polysaccharides are the polymers of monosaccharides linked together via dehydration reactions These can be used either as storage molecules or structural molecules Starch is a storage polysaccharide used in plants Starch is composed entirely of glucose molecules linked to one another Glycogen is used by animals (including humans) to store glucose Glycogen is a more highly branched structure than starch When glucose is needed by the body, the glycogen is broken down via a hydrolysis reaction  Polysaccharides Cellulose is a polysaccharide found in plant cell walls Also made entirely from glucose but they are linked to one another in a distinct fashion Animals do not have the enzymes necessary to digest cellulose Cellulose passes through the human digestive tract undigested Referred to as dietary fiber Some animals such as cows are able to digest cellulose because they have the necessary enzymes  Lipids Lipids are grouped together because they mix poorly (or not at all) with water They are different than carbohydrates and most other organic molecules because they are composed mainly of non-polar carbon-hydrogen bonds As a consequence lipids are hydrophobic Example: salad dressing, oil separates from vinegar Example: water on a feather Oils are liquid fat Fat is a large lipid made of glycerol and fatty acids  Lipids Glycerol is an alcohol with three carbons each bearing a hydroxyl group A fatty acid has a carboxyl group and a hydrocarbon chain: Hydrocarbon chain is usually 16-18 carbons in length Carbons are bound to one another and to hydrogens by non-polar covalent bonds The hydrocarbon chain is therefore hydrophobic Fats primarily function to store energy: 1 gram of fat stores twice as much energy as one gram of carbohydrate (ex: starch) Also functions to cushion vital organs and insulates the body  Lipids Fatty acids are linked to glycerol via a dehydration reaction Fat is produced when 3 fatty acids are linked to glycerol Fat is therefore also called triglyceride Three fatty acids in fat are often all different from one another Fatty acids can sometimes contain a double bond Double bonds add a kink or a bend to the carbon chain These double bonds prevent the maximum number of hydrogen atoms from binding to the carbon skeleton Carbon forms bonds to achieve the 4 extra electrons needed to have 8 electrons in its outer shell This can be done by forming 4 single bonds (4x1=4) This can also be done by forming 2 single bonds and 1 double bond (2x1 + 1x2=4) This can also be done by forming 2 double bonds (2x2=4)  Lipids Fats (fatty acids) containing double bonds have fewer than the maximum number of hydrogens bound and are therefore referred to as unsaturated Fats (fatty acids) with the maximum number of hydrogens bound are said to be saturated Kinks present in unsaturated fatty acids prevent the molecules from packing tightly together in the solid state at room temperature and as a result unsaturated fats are often liquid at room temperature Example: oil Hydrogenated fats have hydrogen added to the double bonds of the fat Allows the fat to be solid at room temperature Downside: also gives way to trans fats which have been found to associate with heart disease Most plant fats are unsaturated and most animal fats are saturated  Phospholipids These are the major component of the cell membrane Structurally similar to fats but rather than three fatty acids, phospholipids have only two fatty acids attached to glycerol A negatively charged phosphate group replaces the third fatty acid in phospholipids The hydrophilic regions and the hydrophobic regions of phospholipids associate to form a bilayer: Hydrophilic regions face to the inside and the outside Inside and outside areas are full of water Hydrophobic regions face to the inside of the bilayer Inside areas lack water  Steroids Steroids are lipids The carbon skeleton contains four fused rings Each point in the diagram on the right represents a carbon atom Hydrogen atoms are also omitted but are bound to each carbon atom in order to satisfy the required four bonds to carbon Cholesterol is a steroid that is commonly found embedded in the cell membrane Cholesterol is also used as a starting point to build other hormones such as estrogen and testosterone Different functional groups attached to the steroid ring change its chemical properties which in turn affects the molecule’s function  Anabolic Steroids Anabolic steroids are synthetic variants of the male hormone testosterone Testosterone causes a build up of muscle and bone mass in males during puberty and maintains male sex traits throughout life Anabolic steroids mimic testosterone Therefore they also have some of the same effects Anabolic steroids can be produced to correct the loss of muscle mass and general anemia Overdose can cause violent mood swings called “steroid rage” and deep depression Liver damage can occur leading to liver cancer Can alter cholesterol levels leading to high blood pressure and cardiovascular problems Causes the slow down of production of natural testosterone leading to shrunken testicles, reduced sex drive, infertility and breast enlargement in men  Proteins Proteins are polymers made from amino acid monomers Each individual protein has a unique three dimensional structure Proteins are structurally important to cells and whole organisms Enzymes are proteins Enzymes are chemical catalysts that speed up and regulate all cellular chemical reactions Structural proteins are found in hair and the fibers that compose connective tissues, ligaments, tendons and muscles Muscles are specifically made up of contractile proteins Defensive proteins are proteins produced by the immune system: Example: antibodies Signal proteins are hormones and other messengers necessary for communication between different cells in the body Receptor proteins are usually located in the cell membrane and bind to signal proteins  Proteins Proteins are the most diverse biological molecules in terms of structure and function Proteins are based on differing arrangements of amino acids There are 20 amino acids known, different combinations of these create different proteins Amino acids consist of an amino group and a carboxyl group The carboxyl group makes the amino acid an acid The R group is what makes each amino acid different from one another and determines the chemical properties of the acid  Proteins A dehydration reaction between the carboxyl group of one amino acid and the amino group of another amino acid occurs Water is removed and a peptide bond is formed Two amino acids linked together is called a dipeptide Many amino acids linked together is called a polypeptide A water molecule can be added to the peptide bond in order to break it apart (hydrolysis reaction)  Proteins Protein shape determines protein function Proteins found in hair and tendons are usually fibrous (long and thin) Most enzymes and other proteins are globular Denaturation of protein indicates the importance of the protein shape on protein function This ruins the protein shape resulting in a loss of function Heat, salt and pH changes can denature proteins Example: frying an egg and the visible changes in the egg white from the heat Also reasoning behind the danger of fevers which can denature key bodily enzymes  Nucleic Acid The amino acid sequence of a protein is determined by the gene sequence of the gene Genes are made of DNA (deoxyribonucleic acid) DNA is a nucleic acid DNA is not directly made into protein but must first be converted into RNA (ribonucleic acid) DNA Transcription RNA Translation Protein  Nucleic Acid Nucleic acid polymers (DNA and RNA) are made up of nucleotide monomers Each nucleotide is composed of three parts A five carbon sugar (deoxyribose in DNA, ribose in RNA) A phosphate group A nitrogenous base: structure containing carbon and nitrogen Adenine, guanine, cytosine and thymine in DNA Adenine, guanine, cytosine and uracil in RNA  Nucleic Acid Nucleic acid polymers are joined to one another by covalent bonds via a dehydration reaction The phosphate group of one nucleotide bonds to the sugar of the next nucleotide (monomer) This results in a repeating sugar-phosphate backbone in the polymer Blue in diagram below represents sugar (deoxyribose) Yellow in diagram below represents phosphate groups  Nucleic Acid DNA is always double stranded and is found as a double helix Two polynucleotides are wrapped around one another Nitrogenous bases always protrude from the sugar phosphate backbone into the center of the double helix Nitrogenous bases on one strand always pair with nitrogenous bases of the second strand according to the following rule: A::T C:::G Adjacent strands are held together by hydrogen bonds Most DNA molecules have thousands or even millions of base pairs RNA is always single stranded  Enzymes Enzymes are protein molecules that act to increase the rate of a chemical reaction All chemical reactions have a particular activation energy that must be overcome in order for the reaction to proceed Enzymes function to decrease this activation energy If heat were added to increase the rate of a reaction it would work, however heat is non-specific and would act to simultaneously increase the rate of all chemical reactions  Enzymes Enzymes act to increase the rate of a chemical reaction: They are not consumed during a chemical reaction They work to lower the activation energy of the reaction They are specific to a particular chemical reaction  Enzyme Specificity Enzymes are proteins with unique three dimensional shape Enzymes act on specific reactants called substrates The substrate fits into a particular region on the enzyme called the active site which is a groove on the surface of the enzyme The remainder of the protein maintains the active site shape Enzymes act specifically on a particular target because the shape of the active site caters to the shape of the specific substrate  Enzyme Specificity The enzyme sucrase catalyzes the breakdown of the disaccharide sucrose Enzymes usually have the ending ase and are named after their substrate Example: the enzyme maltase catalyzes the breakdown of the disaccharide maltose 1. Sucrase begins with an empty active site 2. Sucrose enters into the active site, attaching with weak bonds The induced fit hypothesis refers to the fact that the active site changes shape slightly in order to fit the substrate more closely This also functions to strain substrate bonds making them easier to break It also places amino acids of the active site in proper position to catalyze the reaction  Enzyme Specificity 3. The strained substrate bond reacts with water converting sucrose to glucose and fructose 4. The enzyme releases the newly formed products and is released unchanged from the reaction ready to catalyze a new reaction **a single enzyme may act on thousands or even millions of substrate molecules per one second  Optimal Enzyme Conditions The shape of an enzyme is critical to its function The environment of an enzyme may act to alter the enzyme shape and thus its function Certain parameters of an environment affect its function if they are not optimal: 1. Temperature 2. pH 1. Temperature: The optimal temperature for a particular enzyme maximizes contact between the enzyme active site and substrate molecules Temperatures that are higher than optimal function to denature the enzyme rendering it non-functional Example: most human enzymes function best at 37oC 2. pH: Most human enzymes function best near neutral pH (pH=7) At pH values higher and lower than 7, enzyme function may be impaired  Enzymes and Cofactors In order to function, most enzymes require non-protein molecules called cofactors Cofactors can be either organic or inorganic Inorganic cofactors are usually ions of zinc, copper or iron Organic cofactors are called coenzymes Vitamins that are essential dietary components often function as coenzymes  Enzyme Inhibitors Any chemical that interferes with an enzymes activity is called an inhibitor Inhibitors bound to the enzyme by tight covalent bonds are irreversible inhibitors Inhibitors that are only weakly associated with the enzyme are reversible Some inhibitors resemble the substrate of the enzyme: These inhibitors compete with substrate for the enzymes active site and are called competitive inhibitors These inhibitors block substrate from entering the enzyme’s active site This form of inhibition can be overcome by increasing the amount of substrate present so that it outcompetes the inhibitor Other inhibitors do not resemble the substrate: Non-competitive inhibitors bind to the enzyme in a different spot than the active site and cause a change in the enzyme’s active site so that it no longer fits the substrate  Feedback Inhibition When a cell produces more product than it needs, the product can act to inhibit an enzyme that works to produce one of the substrates early on in the pathway When a metabolic reaction is blocked by one of its products it is called feedback inhibition Feedback inhibition is an important metabolic regulator