Biology II – Chapter 2 & 3: Water and Biological Molecules Why Is Covalent Bonds and Water So Important in Biological Molecules? o Most Biological Molecules Utilize Covalent Bonding Covalent bonds are crucial to life on Earth Since biological molecules must function in a watery environment in which ionic bonds rapidly break apart – the atoms in most biological molecules are joined by covalent bonds Example: proteins, sugars, and cellulose Hydrogen, carbon, oxygen, nitrogen, phosphorus, and sulfur are the most common atoms found in biological molecules. Have the ability to form numerous bonds depending on the atom: o Hydrogen – 1 bond o Oxygen & Sulfur – up to 2 bonds o Nitrogen – up to 3 bonds o Carbon – up to 4 bonds o Phosphorus – up to 5 bonds The diversity of bonding arrangements allows the construction of biological molecules that have enormous variety and complexity. o Electron Sharing Determines Whether a Covalent Bond Is Nonpolar or Polar When two atoms are identical and the shared electrons spend equal time near each nucleus, the molecule is electrically neutral and so are the poles Electrically symmetrical bonds are called nonpolar covalent bonds Example: hydrogen gas (H2) and oxygen gas (O2) In many molecules, one nucleus has a larger positive charge than the other Attracts the electrons more strongly – produces a polar covalent bond Although the molecule as a whole is electrically neutral, it has charged parts: o The stronger attracted atoms carry a slightly negative charge o The other atom carries a slightly positive charge Example: water molecule o Oxygen attracts electrons more strongly than does hydrogen Oxygen end – negatively charged Hydrogen end – positively charged o Free Radicals Are Highly Reactive and Can Damage Cells Some reactions, such as those that occur as a cell processes energy, give rise to molecules that have atoms with one or more unpaired electrons in their outer shells – this type of molecule is called a free radical Very unstable and react readily with nearby molecules – capturing electrons to complete its outer shell Stealing electrons from the molecule it attacks, created a new free radical and begins a chain reaction that can lead to the destruction of the biological molecules crucial for life Cell death caused by free radicals contributes to a variety of human ailments – including heart disease, Alzheimer’s and cancer Materials from the environment can also generate free radicals Radiation from the sun X-rays Chemicals Industrial metals (lead and mercury) Antioxidants – a molecule that reacts with a free radical and neutralizes it Our bodies produce several antioxidants Healthy diets provide the rest Examples: Vitamins C & E o Hydrogen Bonds Are Weaker Electrical Attractions Between or Within Molecules with Polar Covalent Bonds Because of the polar nature of H2O’s covalent bonds nearby water molecules attract each other The negative oxygen of water molecules attract the positive hydrogen of nearby water molecules This attraction creates a hydrogen bond Hydrogen bonds give water several unusual properties that are essential to life on Earth. Also common and important in biological molecules Occur whenever polar covalent bonds produce slightly negative and slightly positive charges that attract one another Although individual hydrogen bonds are quite weak, many of them working together are quite strong Hydrogen bonds play crucial roles in shaping the 3-dimensional structures of proteins Why Is Water So Important to Life? o o o o Abundant on Earth – essential to life – unusual properties Life is very likely to have arisen in the waters of primeval Earth Living organisms contain about 60% to 90% water All life depends intimately on water’s properties o Water Interacts with Many Other Molecules Involved in many chemical reactions that occur in living cells Oxygen produced during photosynthesis by green plants comes from water Protein, fat, nucleic acid, and sugar manufacturing by the body produces water Digestion of proteins, fats, and sugars uses water in the reactions Water is an extremely good solvent – capable of dissolving a wide range of substances Water that contains dissolved substances is called a solution Water dissolves molecules held together by polar covalent bonds Ions and polar molecules are called hydrophilic – water loving – because of their attraction to water molecules Water’s positive and negative poles are attracted to oppositely charged regions of dissolving molecules Example: sugars, amino acids, oxygen gas and carbon dioxide gas Uncharged and nonpolar molecules are called hydrophobic – water fearing – because they do not dissolve in water Example: fats and oils Oils form globules when spilled into water o They disrupt the hydrogen bonding in water molecules o When oil molecules encounter one another in water, their nonpolar surfaces nestle together – surrounded by water molecules that form hydrogen bonds with one another but not with the oil The tendency for oil molecules to clump together is called a hydrophobic interaction o Water Molecules Tend to Stick Together Liquid water has high cohesion – water molecules tend to stick together Cohesion among water molecules at the water’s surface produces surface tension – the tendency for the water surface to resist being broken A crucial role of cohesion in water occurs in the life of land plants Plants absorb water through their roots – water molecules are pulled up by the leaves through the tiny tube system running throughout the plant Water molecules that evaporate from the leaves pull water up the tubes because the hydrogen bonds are stronger than the weight of the water itself Without cohesion in water, there would be no land plants as we know them, and terrestrial life would probably have evolved quite differently. Water exhibits another property called adhesion – the tendency to stick to polar surfaces having slight charges that attract polar water molecules. Helps water move in small spaces – such as the tubes in plants that carry water from roots to leaves – sticks to the sides (surface) of the tubes while the strength of the water molecules is provided by cohesion o Water-Based Solutions Can Be Acidic, Basic, or Neutral Water molecules can become ionized – broken apart into hydrogen ions (H+) and hydroxide ions (OH-) A hydroxide ion is negatively charges because it has gained an electron from the hydrogen atom – the hydrogen atom is converted into a positive charged hydrogen ion Pure water contains equal amounts of hydroxide ions and hydrogen ions – therefore is neutral If the concentration of H+ is greater than OH-, the solution is acidic. An acid is a substance that releases hydrogen ions when it is dissolved in water. Examples: lemon juice, vinegar - Sour taste – receptors on the tongue respond to the excess of H+ Molecules of different acids can ionize to form different numbers of H+ ions. Both HCl and HNO3 are examples of monoprotic acids, which yield one H+ per molecule of acid. Sulfuric acid, H2SO4, is an example of a diprotic acid, one that yields two H+ per molecule of acid. The ionization of H2SO4 and other diprotic acids occurs in two steps: Although H2SO4 is a strong electrolyte, only the first ionization is complete. Thus, aqueous solutions of sulfuric acid contain a mixture of H+(aq), HSO4–(aq), and SO42–(aq). If the concentration of OH- is greater than H+, the solution is basic. A base is a substance that combines with hydrogen ions, reducing their number Examples: baking soda, household ammonia - Slick feel when rubbed between the fingers Any substance that increases the concentration of OH–(aq) when added to water is a base. Ionic hydroxide compounds such as NaOH, KOH, and Ca(OH)2 are among the most common bases. When dissolved in water, they dissociate into their separate ions, introducing OH– ions into the solution. Compounds that do not contain OH– ions can also be bases. For example, ammonia, NH3, is a common base. When added to water, it accepts an H+ ion from the water molecule and thereby increases the concentration of OH– ions in the water (Figure 4.6): The degree of acidity is expressed on the pH scale – each unit represents a tenfold change in the concentration of H+ Neutral = 7 Acids = below 7 Bases = above 7 o A Buffer Helps Maintain a Solution at a Relatively Constant pH In most mammals (including humans) both the cytoplasm and the fluids that the cell resides in are nearly neutral – pH 7.3 to 7.4 Small increases or decreases in pH can lead to the death of cells or the entire organism Buffers found in living organisms control the H+ given off by the many chemical reactions that happen constantly A buffer is a compound that tends to maintain a solution at a constant pH by accepting or releasing H+ in response to small changes in H+ concentration. If the H+ concentration increases – buffers combine with H+ If the H+ concentration decreases – buffers release H+ Common buffers in living organisms include bicarbonate (HCO3-) and phosphate (H2PO4- and HPO42-) Both can accept or release H+ depending on the circumstance If blood becomes too acidic – bicarbonate accepts H+ to form carbonic acid: HCO3+ H+ ----> H2CO3 (bicarbonate) (hydrogen ion) (carbonic acid) If blood becomes too basic – carbonic acid combines with excess OH- to form water: H2CO3 + OH----> HCO3+ H2O (carbonic acid) (hydroxide ion) (bicarbonate) (water) o Water Moderates the Effects of Temperature Changes Your body and the bodies of other organisms can survive only within a limited temperature range High temperatures may damage enzymes that guide the chemical reactions essential to life Low temperatures slow enzymes action Water has important properties that moderate the effects of temperature changes Help keep the bodies of organisms within tolerable temperature limits Has moderate effects on climates of the nearby land of large lakes/oceans Temperature reflects the speed of molecules The higher the temperature – the greater their average speed 1 calorie of energy will raise the temperature of 1 gram of water by 1°C o 0.6 calorie will heat 1 gram of alcohol o 0.2 calorie will heat 1 gram of table salt o 0.02 calorie will heat 1 gram of rock such as granite or marble The energy required to heat a gram of a substance by 1C is called its specific heat o Water has a very high specific heat, therefore is able to moderate temperature changes. Water also moderates the effects of high temperature because it takes a great deal of heat to convert liquid water to water vapor (539 calories per gram) For a water molecule to evaporate, it must absorb sufficient energy to make it move quickly enough to break all the hydrogen bonds that hold it to nearby water molecules The heat required to vaporize water is called its heat of vaporization – water’s heat of vaporization is one of the highest known Water moderates the effects of low temperatures because an unusually large amount of energy must be removed from molecules of liquid water before they form the precise crystal arrangement of ice Water freezes more slowly than many other liquids at a given temperature and loses more heat to the environment in the process This property of a substance is called its heat of fusion – water’s heat of fusion is very high o Water Forms an Unusual Solid: Ice Water is become a solid after prolonged exposure to temperatures below its freezing point Solid water is unusual Ice is unique because it is less dense than liquid water The regular arrangement of water molecules in ice crystals keep them farther apart than they are in the liquid phase (more closely together) – thus ice is less dense than water In the environment, ice floats on top of liquid water – forming an insulating layer that delays the freezing of the rest of the water Allows fish, plants, and other organisms to survive in the liquid water below Why Is Carbon So Important in Biological Molecules? •Organic describes molecules that have a carbon skeleton and also contain some hydrogen atoms •Inorganic describes molecules that include carbon dioxide and all molecules without carbon – such as water. •Tremendous variety of organic molecules is possible because of the carbon atom. –Very versatile – able to form many bonds; become very stable by sharing electrons (covalent bonding) •Molecules with many carbon atoms can assume complex shapes – chains, branches, and rings – the basis for an amazing diversity of molecules. •Similarity among organic molecules from all forms of life are the consequence of 2 main features: –The use of the same set of functional groups –The “modular approach” of synthesizing large organic molecules How Are Organic Molecules Synthesized? •2 Ways to Manufacture a large complex molecule: –Combine atom after atom following an extremely detailed blueprint –Pre-assembling smaller molecules and hooking them together •“The Modular Approach” taken by life is found in the small organic molecules that are used as subunits that combine to synthesize longer molecules – like cars in a train: –The individual subunits are called monomers – one part –Long chains of monomers are called polymers – many parts Biological Molecules Are Joined Together or Broken Apart by Removing or Adding Water •Water also plays a central role in reactions that break down biological molecules to release the subunits that the body can use. •When complex molecules are synthesized in the body, water is often produced as a by-product •The subunits that make up large biological molecules almost always join together by means of a chemical reaction called dehydration synthesis – to form by removing water •In dehydration synthesis, a hydrogen ion (H+) is removed from one subunit and a hydroxyl group (OH-) is removed from a second subunit, creating openings in the outer electron shells of the two subunits. •These openings are filled when the subunits share electrons, creating a covalent bond that links them. •The free hydrogen and hydroxyl ions then combine to form a molecule of water (H2O) •The reverse reaction splits the molecule back into its original subunits, known as hydrolysis – to break apart with water. •Nearly all biological molecules fall into one of only 4 general categories: –Carbohydrates - Lipids •Glucose • Oils •Sucrose • Fats •Starch • Waxes •Glycogen •Cellulose –Proteins •Keratin •Silk •Hemoglobin - Nucleic Acids • DNA, RNA • ATP • cyclic AMP What Are Carbohydrates? •Carbohydrate molecules are composed of carbon, hydrogen, and oxygen in the approximate ratio of 1:2:1 •The origin of the name literally means “carbon plus water” •All carbohydrates are either small, water-soluble sugars or polymers of sugar – such as starch •If a carbohydrate consists of just one sugar molecule, it is called a monosaccharide – single sugar •When 2 monosaccharides are linked, they form a disaccharide – two sugars •A polymer of many monosaccharides is called a polysaccharide – many sugars •Carbohydrates are important energy sources for most organisms •Other carbohydrates, such as cellulose, provide structural support for individual cells or even for the entire bodies of organisms as diverse as plants, fungi, bacteria, and insects •Most small carbohydrates are soluble in water There Are Several Monosaccharides with Slightly Different Structures •Monosaccharides usually have a backbone of 3 to 7 carbon atoms •Most of these carbon atoms have both a H+ and OH- attached to them •When dissolved in water, such as in the cytoplasm of the cell, the carbon backbone of a sugar usually forms a ring –Sugars in ring form can link together to make disaccharides and polysaccharides •Fructose (corn sugar) •Galactose (milk sugar) •Glucose is the most common monosaccharide in living organisms and is a subunit of most polysaccharides •Glucose has six carbons, so its chemical formula is C6H12O6 •Other common monosaccharides have 5 carbons, such as ribose and deoxyribose •Ribose and deoxyribose are parts of the genetic molecules: –Deoxyribonucleic acid (DNA) that store the genetic code –Ribonucleic acid (RNA) that directs protein synthesis Disaccharides Consist of Two Single Sugars Linked by Dehydration Synthesis •Monosaccharides have a short life span in a cell •Most are either broken down to free their chemical energy for use in various cellular activities or are linked by dehydration synthesis to form disaccharides or polysaccharides •Disaccharides are often used for short-term energy storage, especially in plants, and are present in many foods we eat •Common disaccharides: –Sucrose (glucose + fructose) –Lactose (glucose + galactose) –Maltose (glucose + glucose) – forms in the digestive tract as you break down starch •When energy is required, the disaccharides are broken apart into their monosaccharide subunits by hydrolysis Polysaccharides Are Chains of Single Sugars •Monosaccharides (usually glucose) are joined together into polysaccharides to form starch (in plants) or glycogen (in animals) •Used for long-term energy •Starch is commonly formed in roots and seeds •Starch may occur as coiled, unbranched chains of up to 1000 glucose subunits –More commonly found as huge branched chains of up to 500,000 glucose monomers •Glycogen is stored as an energy source in the liver and muscles of animals –Generally much smaller than starch and branches every 10 to 12 glucose subunits •Makes is easier to split for quick energy release •Many organisms also use polysaccharides as structural materials. •One of the most important structural polysaccharides is cellulose •Makes up most of the cells walls of plants •98% of the fluffy white bolls of a cotton plant •About half the bulk of a tree trunk •There is probably more cellulose on Earth than all other organic molecules combined •Ecologists estimate that about 1 trillion tons of cellulose are synthesized each year •Cellulose, like starch, is a polymer of glucose •Only a few microbes – like those in the digestive tracts of cows or termites – can digest cellulose •The orientation of the bonds between subunits is different in the two polysaccharides •In cellulose, every other glucose is “upside down” •This bond orientation prevents animals’ digestive enzymes from attacking the bonds between glucose subunits •For most animals, cellulose is roughage or fiber, material that passes undigested through the digestive tract •While it is valuable in preventing constipation, we don’t derive any nutrients from it •The hard outer coverings (exoskeletons) of insects, crabs, and spiders are made of chitin, a polysaccharide in which the glucose subunits have been chemically modified by the addition of a nitrogen-containing functional group •Chitin also stiffens the cell walls of many fungi •Bacterial cell walls contain other types of modified polysaccharides –As well as the lubricating fluids in out joints and the transparent corneas of our eyes •Many other molecules – including mucus, some hormones, and many molecules in the plasma membrane that surrounds each cell – consist partially of carbohydrate What Are Lipids? •Lipids form a diverse group of molecules with 2 important features: –Contain large regions composed almost entirely of hydrogen and carbon, with nonpolar carboncarbon or carbon-hydrogen bonds –These nonpolar regions make lipids hydrophobic and insoluble in water •Serve a wide variety of functions –Some are energy-storage molecules –Some form waterproof coverings on plant or animal bodies –Some make up the bulk of all the membranes of a cell –Others are hormones •Lipids are classified into 3 major groups: –Oils, fats, and waxes –Phospholipids –The “fused-ring” of Steroids Oils, Fats, and Waxes Are Lipids Containing Only Carbon, Hydrogen, and Oxygen •Oils, fats, and waxes are related in 3 ways: –Contain only carbon, hydrogen, and oxygen –Contain one or more fatty acid subunits – long chains of carbon and hydrogen with a carboxyl group (-COOH) at one end –Usually do not have ring structures •Fats and oils are formed by dehydration synthesis from three fatty acid subunits and one molecule of glycerol – a short, three-carbon molecule with one hydroxyl group (-OH) per carbon –This structure gives fats and oils their chemical name, triglycerides. •Fats and oils possess a high concentration of chemical energy •Fats and oils are used for long-term energy storage in both plants and animals. •Because fats store the same energy with less weight than do carbohydrates, fat is an efficient way for animals to store energy •The difference between a fat (such as beef fat) – which is solid at room temperature – and an oil (such as corn oil used to fry food) lies in their fatty acids •Fats have fatty acids with all single bonds in their carbon chains. –Hydrogens occupy all the other bond positions on the carbons –The resulting fatty acid is said to be saturated – because it is saturated with hydrogens •The saturated fatty acids of fats nestle closely together – forming solid lumps at room temperature •Most of the common saturated fat in the human diet – including butter, bacon fat, and fat on steak – comes from animals •If there are double bonds between some of the carbons, and consequently fewer hydrogens, the fatty acid is said to be unsaturated –Oils have mostly unsaturated fatty acids –We get most of our unsaturated oils from seeds of plants •Corn oil, peanut oil, and canola oil are all examples –The double bonds produce kinks in the fatty acid chains •The kinks keep oil molecules apart – as a result, oil is liquid at room temperature. •Trans fats – double and single bond configuration where the carbon chain bends in a zig-zag shape – allows them to assemble into a solid –Artificial – very rare naturally •Although waxes are chemically similar to fats, they are not a food source –We and most other animals do not have the appropriate enzymes to break them down –Waxes are highly saturated and therefore solid at normal outdoor temperatures –Waxes form a waterproof coating over the leaves and stems of land plants –Animals synthesize waxes as waterproofing for mammalian fur and insect exoskeletons –In a few cases – to build elaborate structures such as beehives Phospholipids Have Water-Soluble “Heads” and Water-Insoluble “Tails” •Phospholipids are similar to an oil – except that one of the three fatty acids is replaced by a phosphate group with a short, polar functional group (typically containing nitrogen) attached to the end. •Unlike the two fatty acid “tails” that are insoluble in water – the phosphate-nitrogen “head” is polar – so is water soluble –A hydrophillic head attached to hydrophobic tails –This dual nature of phospholipids is crucial to the structure and function of the plasma membrane Steroids Consist of Four Carbon Rings Fused Together •Steroids are structurally different from all other lipids •All steroids are composed of four rings of carbon fused together with various functional groups protruding from them •One type of steroid is cholesterol –Cholesterol is a vital component of the membranes of animal cells and is also used by cells to synthesize other steroids: •Male and female sex hormones •Hormones that regulate salt levels •Bile that assists in fat digestion What Are Proteins? •Proteins are molecules composed of one or more chains of amino acids •Perform many functions •Enzymes are important proteins that guide almost all chemical reactions that occur inside cells –Because each enzyme assists only one or a few specific reactions – most cells contain hundreds of different enzymes •Other types of proteins are used for structural purposes: •Elastin – gives skin its elasticity •Keratin – the principal protein of hair, horns, nails, scales, and feathers •Silk – spider webs and silk moth cocoons •Other proteins provide a source of amino acids for developing young animals: •Albumin – protein in egg white •Casein – protein in milk •The protein hemoglobin transports oxygen in the blood •Contractile proteins – found in muscle – allow for cell movement •Some hormones are proteins: •Insulin and growth hormones •Antibodies – fight disease and infection •Many poisons produced by animals – rattlesnake venom Proteins Are Formed from Chains of Amino Acids •Proteins are polymers of amino acids. •All amino acids have the same fundamental structure – a central carbon bonded to 4 different functional groups: –A nitrogen-containing amino group (-NH2) –A carboxyl or carboxylic acid group (-COOH) –A hydrogen –A variable group called the R group •The R group differs among amino acids and gives each its distinctive properties variable group R H amino group C O N H C C carboxylic acid group C O H H hydrogen •20 amino acids are commonly found in the proteins of organisms –Some are hydrophillic – their R group are polar and soluble in water –Some are hydrophobic – with nonpolar R groups and insoluble in water •Cysteine – R group contains sulfur and can form covalent bonds with other cysteines, also called disulfide bridges –These bridges give proteins the ability to bend and fold their polypeptide chain •Amino acids differ in their chemical and physical properties – size, water solubility, electrical charge – because of the R group differences –The exact sequence of amino acids dictates specific properties: •The function of each protein •Whether it is water-soluble •Whether is an enzyme, hormone, or a structural protein Amino Acids Are Joined to Form Chains by Dehydration Synthesis •Proteins are formed by dehydration synthesis •The nitrogen in the amino group of one amino acid is joined to the carbon in the carboxyl group of another amino acid by a single covalent bond – called a peptide bond •The resulting chain of two amino acids is called a peptide •Amino acid chains in living cells vary in length from 3 to thousands of amino acids –Protein or polypeptide describe long chains ( 50 or more amino acids) –Peptide describes shorter chains A Protein Can Have Up to Four Levels of Structure •Proteins are highly organized molecules that come in a variety of shapes •4 levels of organization: –Primary structure – the sequence of amino acids linked by peptide bonds –Secondary structure – hydrogen bonds between parts of amino acids; many form a helix shape or pleated sheet –Tertiary structure – 3-dimensional; determines the final configuration of the polypeptide –Quaternary structure – individual polypeptides linked together by hydrogen bonds or disulfide bridges Tertiary Structure Primary Structure Quaternary Structure Secondary Structure •Hemoglobin exhibits all four levels The Functions of Proteins Are Linked to Their Three-Dimensional Structures •Within a protein, the exact type, position, and number of amino acids with specific R groups determine both the structure and biological function •In any given protein, some amino acids are more important than others •For an amino acid to be in the proper location within a protein, it must be in the proper sequence •The protein must have the correct secondary and tertiary structures so the amino acid is correctly positioned within the protein. –When these structures are altered – the protein is said to be denatured and will no longer be able to function What Are Nucleic Acids? •Nucleic acids are long chains of similar but not identical subunits called nucleotides. •All nucleotides have a 3-part structure: –A five-carbon sugar (ribose or deoxyribose) –A phosphate group –A nitrogen-containing base (differs among nucleotides) •2 Types of nucleotides: –Ribose nucleotides (contains sugar ribose) •Bond to 4 types of nitrogen-containing bases: –Adenine - Guanine –Cytosine - Uracil –Deoxyribose nucleotides (contains sugar deoxyribose) •Bond to 4 types of nitrogen-containing bases: –Adenine - Guanine –Cytosine - Thymine •Nucleotides may be strung together in long chains forming nucleic acids with a phosphate group of one nucleotide covalently bonded to the sugar of another •2 Types of nucleic acids: –Deoxyribonucleic acid (DNA) –Ribonucleic acid (RNA) DNA and RNA, the Molecules of Heredity, Are Nucleic Acids •Deoxyribose nucleotides form chains millions of units long called DNA. •DNA is found in the chromosomes of all living things. •Its sequence spells out the genetic information needed to construct the proteins of each organism. •Chains of ribose nucleotides called RNA, are copied from the central repository of DNA in the nucleus of each cell. •The RNA carries DNA’s genetic code into the cell’s cytoplasm and directs the synthesis of proteins. Other Nucleotides Act as Intracellular Messengers, Energy Carriers, or Coenzymes •Not all nucleotides are part of nucleic acids. •Some exist singly in the cell or occur as parts of other molecules. •Cyclic nucleotides – such as cyclic AMP – are intracellular messengers that carry chemical signals from the plasma membrane to other molecules in the cell. •ATP – a triphosphate nucleotide – are unstable molecules that carry energy, stored in bonds between the phosphate groups from place to place within a cell. •They capture energy where it is produced and release it to drive energy-demanding reactions elsewhere. •Coenzymes – nucleotides that assist enzymes in their role of promoting and guiding chemical reactions. •Most coenzymes consist of a nucleotide combined with a vitamin.