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Chapter 2 Cell Molecular Biology

by: Lauren Maddox

Chapter 2 Cell Molecular Biology Bio 214

Marketplace > James Madison University > Biology > Bio 214 > Chapter 2 Cell Molecular Biology
Lauren Maddox

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Textbook notes discussing chemical bonds
Molecular and Cell Biology
Dr. Doyle
Class Notes
Biology; Cell Molecular Biology; BIO 214
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This 9 page Class Notes was uploaded by Lauren Maddox on Saturday March 12, 2016. The Class Notes belongs to Bio 214 at James Madison University taught by Dr. Doyle in Fall 2015. Since its upload, it has received 15 views. For similar materials see Molecular and Cell Biology in Biology at James Madison University.


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Date Created: 03/12/16
Chapter 2 Bio 214 Chemical Bonds • Matter is made of combinations of elements • The smallest particle of an element is an atom • Each atom has a positive nucleus in its center, which is surrounded by a cloud of negatively charged electrons. They are held there by electrostatic attraction to the nucleus. • Two things in the nucleus- protons and neutrons • Neutrons contribute to the structural stability of the nucleus, if they have two few there can be radioactive decay. This allows them to be isotopes-different number of neutrons but the same number of protons. • The innermost electron shell can only hold 2 electrons. The second shell can hold 8. The third can hold 8 and the fourth can hold 18. • The arrangement of electrons in an atom is most stable when all the electons are in the most tightly bound states that are possible for them. • When they are all filled the atom is unreactive. • Ionic bonds- formed when electrons are donated by one atom to another • Covalent bonds formed when two atoms share a pair of electrons. • A molecule is a cluster of atoms held together by covalent bonds. • H2 for example, shares the electrons, forming a cloud of negative charge. The electron density helps to hold the nuclei together by opposing the negative repulsion between their positive charges that would otherwise force them apart. The attractive and repulsive forces are in balance when the nuclei are separated by a characteristic distance called bond length • Sharing of two electrons- each donate one-single bond • Four electrons being shared- each donate 2- double bond • Covalent bonds in which the electrons are shared unequally are known as polar covalent bonds. • A polar structure is one in which the positive charge is concentrated toward one end of the molecule and the negative is concentrated toward the other. • Bond strength is measured by the amount of energy that must be supplied to break the bond. • Covalent bonds are resistant to being broken by heat. • In living organisms, they are typically only broken during chemical reactions that are carefully controlled by enzymes. • Ionic bonds are formed between atoms that can attain a completely filled outer shell most easily by donating electrons, or accepting electrons • When an electron jumps from one element to another, they both become electrically charged ions. • Losing electrons (+) • Ions held by ionic bonds are called salts • Positive ions are called cations, and negative ions are called anions • In water, ionic bonds are much weaker than covalent. • Noncovalent bond- electrostatic attraction are strongest when the atoms involved are fully charged • Hydrogen bonds are much weaker covalent bonds- can be disrupted easily. • Hydrophilic- love water- sugars, DNA, RNA, and majority of proteins • Hydrophobic-hate water, uncharged and form few or no hydrogen bonds. • Hydrocarbons- hydrophobic- H is covalently linked to C atoms by nonpolar bonds. H has almost no net positive charge so no hydrogen bonds • This is tough for cells because their membranes are made from lipid molecules with hydrocarbon tails- lipids don’t dissolve in water. • When a molecule possessing a highly polar covalent bond between a H and another atom dissolves in water. The H atom gives up its electron almost entirely to the companion atom, so it is an almost naked positively charged hydrogen nucleus, called a proton (H+). When the polar molecule becomes surrounded by water molecules, the proton will be attracted to the partial negative charge on the oxygen atom of the water molecule, forming H3O+ hydronium ion. • These substances are called acids. • These is the concentration of H+, also expressed as the pH scale. • Strong acids lose their protons easily. • Acids, especially weak acids, will give up their protons is H+ is low • A base is a molecule that accepts a proton when dissolved in water. They raise the concentration of OH- ions by removing a proton from a molecule. • Strong bases dissociate readily. NaOH is an example. • An increase in OH- concentration causes an decrease in H+ concentration. Water, having a pH of 7, is neutral, has equal amounts of both. • The interior of a cell is kept close to neutral by the presence of buffers- mixtures of weak acids and bases that can adjust proton concentrations around pH 7. Small molecules in cells • The small and large carbon compounds made by cells are called organic compounds • All other compounds are said to be inorganic. • Small organic compounds can be used as monomers to construct macromolecules- proteins, nucleic acids, and large polysaccharides. • Some are energy sources or subunits for macromolecules • All organic compounds are synthesized from and broken down into the same set of simple compounds. • Compounds in a cell are chemically related and can be classified into small number of distinct families. • Four major families of small organic molecules- sugars, fatty acids, amino acids, and nucleotides. • Simplest sugars- monosaccharides- have the formula (CH2O)n. • They are also called carbohydrates. • Sets of molecules with the same chemical formula but different structures are called isomers and the mirror-image pairs of such molecules are called optical isomers. • Monosaccharides can be linked by covalent bonds- glycosidic bonds- to form larger carbohydrates • Sugars are formed- a bond is formed between an OH group on one sugar and an OH group on another by condensation, in which a molecule of water is expelled as the bond is formed. The bonds created can also be broken by hydrolysis- water molecule is consumed. • Each monosaccharide has free OH groups that can form a link to another monosaccharide, sugar polymers can be branched, so it is difficult to determine the arrangement of sugars in a complex polysaccharide. • Glucose is broken down to smaller molecules releasing energy that the cell can harness to do useful work • Cells use polysaccharides composed only of glucose units- animals (glycogen) and plants (starch), as long term stores of glucose. • Sugars are used for mechanical supports. For example cellulose- forms plant cell walls- polysachharide of glucose. Chitin is another example • Oligosaccharides can covalently linked to proteins to form glycoproteins or to lipids called glycolipids. The sugar side chains attached to them in the plasma membrane are thought to help protect the cell surface and help cells adhere to one another. • A fatty acid molecule has a long hydrocarbon chain- hydrophobic and not reactive chemically, and they have a carboxyl group, which behaves like an acid. In an aqueous solution it is ionized, hydrophilic and chemically reactive. • Fatty acid molecule is covalently bonded to other molecules by their carboxylic acid group. • When things are both hydrophobic and hydrophilic-amphipathic. • If the hydrocarbon tail has no double bonds between its carbon bonds and contains the max number of hydrogens- saturated • One or more double bonds- unsaturated • Double bonds create kinks in the tails, inferring with their ability to pack together • Tails are found in the cell membrane, tightness of packing affects the fluidity of the membrane • Fatty acids serve as a concentrated food reserve in cells- broken down into energy. They are stored in the cytoplasm, in the form of fat droplets composed of triacylglycerol molecules • Triacylglycerol is a compound made of 3 fatty acid chains covalently joined to a glycerol molecule. They are the fats found in meat, butter and cream, and plant oils. When a cell needs energy, the fatty acid chains can be released from triacylglycerols and broken down into 2 carbon units. • Fatty acids and their deriatives are lipids. Molecules that are insoluble in water but soluble in fat and organic solvents. • They have the lipid bilayer- composed of phospholipids. • The glycerol is joined to 2 fatty acid chains. The OH group is linked to a hydrophilic phosphate group, which is attached to a small hydrophilic compound. They have two hydrophobic fatty acid tails and a hydrophilic head. • The cell membranes also contain one of more sugars instead of a phosphate group. They form membranes in water. They spread over the surface of water to form a monolayer • Amino acids all possess a carboxylic acid group and an amino group, both linked to their alpha carbon atom. They also have a side chain, attached to its alpha carbon. The side chain is what distinguishes one amino acid from another. • Amino acids build proteins- joined head to tail in a long chain that folds up into a 3d structure. • Amino acids are held together by peptide chains. Chain of amino acids is called a polypeptide chain. • Peptide bonds are formed by condensation reactions that link one amino acid to the next. • A polypeptide always has a NH2 group at one end, and it carboxyl group at the other. Gives it a structural polarity. • All amino acids exist as optical isomers in p-forms and l-forms. L forms are found in proteins. • Nucleotides make RNA and DNA. • Nucleosides are made of nitrogen containing ring (bases), linked to a five carbon sugar. • Nucleotides are nucleosides that contain one or more phosphate groups attached to the sugar. Can either be RNA or DNA. • Pyrimidines- cytosine, thymine, and uracil. Purines- guanine and adenine • Nucleotides can be short term carriers of chemical energy- ATP- partipates in the transfer of energy in hundreds of metabolic reactions. • ATP is formed through reactions that are driven by the energy released by the breakdown of foodstuffs. 3 phosphates are linked by two phosphoanhydride bonds. The rupture of these bonds releases lots of energy. • Nucleotides have role in the storage and retrieval of biological information. They serve as building blocks for nucleic acids. • Nucleic acids- polymers with nucleotide subunits that are linked by covalent phosphodiester bonds between the phosphate group attached to the sugar on one nucleotide and a hydroxyl group on the sugar of the next nucleotide. These chains are synthesized by a condensation reaction that releases inorganic pyrophosphate during phosphodiester bond formation. • RNA contains A, G, C and U. DNA contains A, G, C, and T. • RNA is single stranded and DNA is a double strand. • DNA is two polynucleotide chains that run in opposite directions and held together by hydrogen bonds between bases of the two chains. • DNA is more stable, with hydrogen bonded helices, is a long term repository for hereditary information. RNA is a more transient carrier of molecular instructions. Macromolecules in cells • Macromolecules are most abundant and most principle in cells. They are constructed by covalently linking organic monomers into polymers. • Each polymer grows by the addition of a monomer onto one end of the polymer chain via a condensation reaction. The reactions are catalyzed by specific enzymes. • Most macromolecules are made from a set of monomers that are slightly different from one another, the subunits are added in a particular order. • Most of the single covalent bonds that link together the subunits in a macromolecule allow rotation of the atoms they join- this allows a single- chain macromolecule to adopt an almost unlimited number of shapes- conformations. • Weak interactions—noncovalent—make the protein choose a shape • The noncovalent bonds important for the structure and function- electrostatic attractions and hydrogen bonds. • Electrostatic- enzyme that binds a positively charged substrate will often use a negatively charge amino acid side chain to guide its substrate into the proper position. • Hydrogen bonds-important in the folding of a polypeptide chain and in holding together the strands of a double stranded DNA molecule. • Van der waals attraction- noncovalent, a form of electrical attraction caused by fluctuating electric charges that arise whenever two atoms come within a very short distance of each other. Play role in the attraction between macromolecules with complementary shapes. • 3d shape of water- forces together the hydrophobic portions of dissolved molecules in order to minimize their disruptive effect on the hydrogen bonded network of water molecules. • Hydrophobic interaction- hold together phospholipid molecules in cell membranes, and in folding of protein molecules into a compact globular shape. • This binding makes proteins to functions as enzymes possible CHAPTER 3 • Living things create and maintain order in a universe that is tending always toward greater disorder • Enzyme- catalyzed reactions use connect in a series, so the product of one reaction becomes the starting material for the next. The linear reaction pathways, or metabolic pathways, that result are in turn linked to one another. • Catalysis allows cells to control its metabolism. • Metabolism- the total of all the chemical reactions it needs to carry out to survive, grow, and reproduce. • Two opposing streams of chemical reactions- catabolic pathways and anabolic pathways • Catabolic pathways- break down foodstuffs into smaller molecules- generating a useful form of energy for the cell and some of the small molecules that the cell needs as building blocks. • Anabolic- use the energy harnessed by catabolism to drive the synthesis of the many molecules that form the cell. • Living things generate order at every level because of molecular mechanisms that extract energy from the environment and convert it into the energy stored in chemical bonds. • 2 law of thermodynamics- tendency of things to become disordered— systems will change spontaneously toward those arrangements that have the greatest probability. • Movement toward disorder is a spontaneous process • Entropy of the system- the measure of a systems disorder, greater the disorder the greater the entropy. • Systems will change spontaneously toward arrangements with greater entropy. • Cells take energy from the environment, and then uses it to generate order within itself, forging new chemical bonds and building large macromolecules. • When performing the chemical reactions, some energy is lost in the form of heat. • Heat is energy in its most disordered form. The heat energy that its reactions generate is quickly dispersed into the cell’s surroundings, the heat increases the intensity of the thermal motions of nearby molecules, increasing the entropy of the environment. • Increased order generated inside the cell is more than compensated for by • the increased disorder genereated in the environment- 2 law is satisfied. • The total amount of energy must always be the same-energy cant be created nor destroyed. • By directly linking the burning of food molecules to the generation of biological order, cells are able to create and maintain an island of order in a universe tending toward chaos. • All animals live on energy stored in the chemical bonds of organic molecules- food • Solar energy enters the living world through photosynthesis- converting electromagnetic energy in sunlight into chemical-bond energy in cells • Plants use the energy from sunlight to synthesize small chemical building blocks such as sugars, amino acids, nucleotides, and fatty acids. These are then turned into macromolecules. • Two stages of photosynthesis- energy from sunlight is captured and stored as chemical-bond energy in molecules called activated carriers. In the second stage- the activated carriers are used to help drive a carbon-fixation process in which sugars are manufactured from carbon dioxide. • To get the stored energy, organisms use a process called gradual oxidation or controlled burning. • A cell can obtain energy by allowing carbon and hydrogen atoms in these molecules to combine with oxygen-oxidized, to produce CO2 and H2O- cellular respiration • Oxidation occurs in any reaction in which electrons are transferred from one atom to another—removes the electrons. • Reduction- adds electrons • When a molecule picks up an electron, it often picks up a proton too (H+) • Hydrogenation reactions- reductions • Dehydrogenation reactions- oxidation • Reduction occurs when the C-H bonds increase • Burning of paper- heat is dispersed into chaotic random thermal motions of molecules, atoms and molecules of the paper become dispersed and disordered. There has been a release of free energy- energy can be harnessed to do work or drive chemical reactions. • Chemical reactions proceed only in the direction that leads to a loss of free energy • A molecule requires a boost over an energy barrier before it can undergo a chemical reaction that moves it to a lower energy state—activation energy • Inside cells, the push over the energy barrier is aided by specialized proteins called enzymes. They bind tightly to one or two molecules called substrates- holds them in a way that reduces the activation energy needed • Catalyst- substance that lowers the activation energy of a reaction, increase the rate of chemical reactions because they allow a much larger proportion of the random collisions with surrounding molecules to kick the substrates over the energy barrier • Enzymes are highly selective- they only speed up one particular reaction out of the several possible reactions, they direct each of the many different molecules in a cell along specific reaction pathways. • Enzyme molecules remain unchanged. • Free is also G- free- energy change • Delta G measures the amount of disorder created in the universe when a reaction involving these molecules takes place. Energetically favorable reactions- those that create disorder by decreasing the free energy of the system to which they belong- negative delta G. • Chemical reactions will proceed until they reach equilibrium. The rates of the forward and reverse reactions are equal, there is no further net change in the concentrations of substrate or product. • Living cells avoid reaching a state of equilibrium because they are constantly exchanging materials with their environment. Many of the individual reactions in the cells complex metabolic network also exist in disequilibrium because the products of one reaction are being taken to become substrates in a different reaction. • K= [y]/[x] K=equilibrium constant • K becomes larger as the binding energy- energy released in the binding interaction, increases. • The larger K is, the greater the drop in free energy between the dissociated and associated states, and the more tightly the two molecules will bind. • To get the delta g’s of equations to be favorable (-), activated carriers can shuttle energy from one reaction site to another. • Rapid binding is possible because molecular motions are fast- heat energy makes molecules go in constant motion and they will explore the cytosolic space very efficiently by wandering randomly through it-diffusion. Every molecule in the cytosol collides with a huge number of other molecules each second. • The random encounters between an enzyme and its substrate often lead to the formation of an enzyme-substrate enzyme. Weak bonds between the substrate and the enzyme-holding it together. They persist until random thermal motion causes the molecules to dissociate again. • When the enzyme and substrate are well matched, they form many weak interactions, to keep them together long enough for a covalent bond in the substrate molecule to be formed or broken. • Finding rates of enzyme performance—substrate is introduced in increasing concentrations to a solution containing a fixed concentration of enzyme. It will rise in direct proportion to substrate concentration. This rate increases tapers off, until at a very high concentration of substrate it reaches a max value- Vmax. At this point, the active sites of all enzyme molecules in the sample are fully occupied by substrate, and the rate of product formation depends only on how rapidly the substrate molecule can undergo a reaction to form the product. • Michaelis constant- km, the concentration of substrate at which the enzyme works at half its max speed. • Small Km= substrate binding very tightly • Activated carriers are small organic molecules that contain one or more energy-rich covalent bonds- they diffuse rapidly and carry their bond energy from the sites of energy generation to the sites where energy is used for biosynthesis. • Activated carriers store energy in an easily exchangeable form, ATP, NADH, and NADPH. • Energy capture is achieved by means of a coupled reaction, in which an energetically favorable reaction is used to drive an energetically unfavorable one that produces an activated carrier • ATP is synthesized in a phosphorylation reaction, phosphate group is added to ADP. The regenerated ADP is then available for another round of phosphorylation reaction that forms ATP. • NADH and NADPH carry energy in the form of 2 high energy electrons plus a proton(H+), which form a hydride ion (H-), they pass their energy to a donor molecule and become oxidized to form NAD+ and NADP+ • A hydride ion is removed from the substrate molecule and added to NADP+ to form NADPH- substrate is oxidized and NADP+ is reduced. • The hydride ion carried by NADPH is given up because the ring can achieve more stable arrangement of electrons without it. • NADPH oxidizes and substrate is reduced, forming NADP+. • NADPH transfers phosphate because it is accompanied by a large negative free-energy charge. • NADPH operates enzymes that catalyze anabolic reactions, supplying the high-energy electrons needed to synthesize energy-rich biological molecules • NADH- role as an intermediate in the catabolic system of reactions that generate ATP through the oxidation of food molecules. • In cells, NADP+ to NADPH is kept low, and NAD+ to NADH is kept high. It provides NAD+ to act as an oxidizing agent and NADPH to act as a reducing agent. • FADH2 carries hydrogen and high-energy electrons • Acetyl CoA can add two carbon units in the biosynthesis of the hydrocarbon tails of fatty acids. • In activated carriers, the transferable group makes up only a small part, there is the organic portion that is the handle- facilitating the recognition of the carrier molecule by specific enzymes. Contains a nucleotide. • Activated carriers are ususally generated in reactions coupled to ATP hydrolysis- the energy that enables their groups to be used for biosynthesis comes from ATP. • For each macromolecule, an enzyme pathway exists—the OH group is removed in the condensation reaction is activated by forming a high energy linkage to a second molecule. Some mechanisms for linking ATP hydrolysis to the synthesis of proteins and polysaccharides are more complex than that for glutamine synthesis. A series of high-energy intermediates generates the final high-energy bond that is broken during the condensation step.


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