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Study Guide, Chapter 1-4 Biochemistry Organic chemistry study of compounds of carbon and hydrogen and derivatives biomolecules are part of the subject matter of organic chemistry o Functional Groups a type of classification method of organic molecules o Reactions of molecules based on reactions of respective functional groups o ATP molecule of energy in cell ester and anhydride with phosphate 1.1 The Beginnings of Biology: Origin of Life How and When did the Earth Come to be? o Big bang theory most universally accepted theory as for the origin of the universe o Particularly stable nuclei are in the most abundant isotopes of biologically important elements like carbon, oxygen, nitrogen, phosphorus and sulfur o Produced by nuclear reactions in first generation stars, the original stars produced after the beginning of the Universe o Early earth always had ultraviolet light from the sun because there was no ozone to block it chemical reactions that produced simple biomolecules took place Biomolecules: How Were Biomolecules Likely to have Formed on the Early Earth? o Simple compounds of the early atmosphere were found to act abiotically without life o Monomers small molecules, Polymers macromolecules made up of units of monomers o Proteins made from many amino acids o Nucleic Acids made from the monomers, nucleotides o Polysaccharides polymerizations of sugar monomers o Proteins and nucleic acids play a key role in life processes o Many amino acids and nucleotides can be distinguished easily o Genetic code lies in a sequence of monomeric nucleotides nucleic acids o All building blocks have a head and a tail end direction of monomer o Catalytic Activity proteins call enzymes that increase the rates of chemical reactions compared with uncatalyzed reactions o Catalysis important functions of proteins, specific sequence of amino acids determines properties of all y pes of proteins o DNA is the coding material for all cells o Genetic Code relationship between the nucleotide sequence in nucleic acids and the amino acid sequence in proteins Molecules to Cells: Which Came First—The Catalysts or the Hereditary Molecules? o RNA is thought to be the original coding material because it can code and preform catalysis o Polypeptides are much more efficient at catalysis than polynucleotides o Development of living cells is the formation of membranes that separate cells from their environment o Order of amino acids is artificially synthesize proteinoids is not random because order is preferred o A well established, unique amino acid sequence exists for each protein produced by present day cells o There are several theories to describe how life came to be on earth, DNA, RNA and DoubleOrigin Theory 1.2 The Biggest Biological Distinction—Prokaryotes and Eukaryotes Genome total DNA of a cell Genes individual units of heredity, controlling individual traits by coding for a function protein or RNA Prokaryotes earliest cells, very simple with minimum apparatus necessary for life processes, ex. bacteria and cyanobacteria What is the Difference Between a Prokaryote and a Eukaryote o Eukaryotes true nucleus, more complex organisms and can be multicellular or singled celled o A nucleus with a membrane is a distinguishing factor o Organelle a part of the cell that has a distinct different function and surrounded by its own membrane within the cell o Main difference is existence of organelles in the nucleus in eukaryotes o Plasma membranes is the only membrane that a prokaryotic cell has o In both eukaryotic and prokaryotic organisms, the cell membrane is a lipid bilayer o Mitochondria and Ern (endoplasmic reticulum) are common in all eukaryotic cells o Mitochondria power house of the cell, where energy yielding oxidation occurs o Ribosome bound to the ER, contain RNA and protein, the sight of protein synthesis in all living organisms o In prokaryotes, ribosomes are free floating the cytosol o Cytoplasm portion of cell outside the nucleus o Cytosol aqueous portion of cell that lies outside the membrane bounded organelles o Chloroplasts preform photosynthesis, only found in plant cells and green algae 1.3 Prokaryotic Cells How is Prokaryotic DNA Organized without a Nucleus? o Nuclear Region DNA of cell is concentrated in this region, directs workings of cell o Cell Membrane (plasma membrane) assemblage of lipid molecules and proteins o Cell Wall made up of polysaccharide material, in bacterial prokaryotic cells and eukaryotic plant cells 1.4 Eukaryotic Cells Most important organelles are nucleus, mitochondrion and chloroplast Each separated by a double membrane Nucleus contains DNA of the cell and site of RNA synthesis Chloroplasts and mitochondria have DNA that differ from DNA in nucleus What are the Most important Organelles? o Nucleus most important, surrounded by Nuclear double membrane o Nucleolus contains RNA, synthesized on DNA template ion nucleolus for export to cytoplasm, eventually going to ribosomes o Chromatin aggregate of DNA and protein o Chromosomes tightly coiled strands of chromatin o Cristae inner membrane of the mitochondria that has many folds o Matrix space within the inner membrane o Endoplasmic Reticulum (ER) part of continuous single membrane system throughout the cell o Rough ER has ribosomes studded all along it o Smooth ER there are no ribosomes o Grana found within plant cells and is found within the chloroplast as stacks of membranous bodies, preforms photosynthesis What are Some Other Important Components of Cells? o Golgi apparatus series of membranous stacks, involved in secretion of proteins from the cells, allows sugars to be linked to other cellular components o Lysosomes membraneenclosed sacs containing hydrolytic enzymes that break down target molecules from outsides sources and processes the nutrients o Peroxisomes similar to lysosomes, contain enzymes involved in the metabolism of hydrogen peroxide, also contains enzyme catalase o Cytoskeleton located in cytosol, connects all organelles o Vacuoles sacs in the cytoplasm surrounded by a single membrane, isolate water substances that are toxic to plant 1.5 Five Kingdoms, Three Domains How do Scientists Classify Living Organisms Today? o Five kingdom system allows for differences between prokaryotes and eukaryotes o Monera only has prokaryotic organisms o Protista unicellular organisms, algae is a multicellular Protista o Fungi yeasts, molds, mushrooms o Other two kingdoms are Plantae and Animalia o Archaebacteria found in extreme environments, extremophiles o Eubacteria true bacteria 1.6 Common Ground for All Cells Did Symbiosis Play a Role in the Development of Eukaryotes? o Endosymbosis larger host cell has many smaller organisms o Theory that mitochondria origin based on endosymbiosis o Fact that both mitochondria and chloroplasts have own DNA is a clue that supports the idea that the development of the mitochondria beginning from bacteria and evolving to what it is today o Genetic code in mitochondria differs from nucleus supports idea of independent origin 1.7 Biochemical Energetics What Source of Energy in Life Processes? o Cells require energy for many things o Sun is the ultimate source of energy for all life o Plants trap the light energy and use it to convert carbon dioxide to and water to carbs and water through reduction o Animals use carbs as energy sources by breaking them down through oxidation o Oxidation is the loss of electrons and reduction is the gain of electrons How do we Measure Energy Changes in Biochemistry? o Themordynamics branch of science that deals with how the energy changes in favor of a certain process 1.8 Energy and Change What Kinds of Energy Changes Take Place in Living Cells? o Many forms of energy o Formation and breakdown of biomolecules involve changes in chemical energy o Spontaneous any process that will actually take place with no outside intervention, does not mean fast o Laws of thermodynamics can predict change involving transformation of energy 1.9 Spontaneity in Biochemical Reactions How can We Predict What Reactions Will Happen in Living Cells o Free Energy, G indicates predicting of spontaneity o Value of the change in free energy gives information about the spontaneity of the process under consideration o When delta G is negative exergonic energy is released o Change in free energy is positive, process is nonspontaneous, Endergonic energy is absorbed o Equilibrium no net change in either direction, change in free energy= 0 1.10 Life and Thermodynamics Is Life Thermodynamically Possible? o Laws of thermodynamics can be stated many ways o 1 law it is impossible to convert energy from one form to another at greater that 100% efficiency (law of the conservation of energy) o Two laws of thermodynamics are combined to get: ∆G=∆H−T ∆S o G free energy, H Enthalpy, Sentropy o Increase in entropy of a system represents an increase in the number of possible arrangements of objects o In any spontaneous process, the entropy of the universe increase, delta S is greater than 0 o Entropy changes are particularly important in determining the energetics of protein folding 2.1 Water and Polarity Electronegativity tendency of an atom to attract electrons to itself in a chemical bond What is Polarity? o Atoms with same electronegativity form a bond electrons shared equally between two atoms o Differing electronegativity causes electrons to be shared unequally with one atom having more of a negative charge o Polar bonds difference in electronegativity between oxygen and hydrogen gives rise to a partial positive and negative charge o Nonpolar bond sharing of electrons in the bond is very nearly equal o Having polar bonds doesn’t make it a polar molecule o Dipoles bonds with positive and negative ends Solvent Properties of Water o Why do some chemicals dissolve in water while others do not? Polarity of water determines solvent properties Iondipole and dipoledipole interactions are responsible for attractions between water molecules Interactions between nonpolar molecules and water are very weak Hydrophobic don’t like water, Hydrophilic water loving Hydrophobic interactions interactions between nonpolar molecules o Why do oil and water mixed together separate into layers? Amphipathic having both polar and nonpolar portions Interactions between nonpolar molecules are very weak depend on short lived temporary dipoles Temporary dipole can induce another dipole in a neighboring molecule, similar to a permanent dipole Van der waals interaction low interaction energy because of short lived association with a dipole 2.2 Hydrogen Bonds Hydrogen bonding electrostatic origin and can be considered a special case of dipole dipole interaction Group with electronegative atom that is covalently bonded to hydrogen hydrogen bond donor Why does water have such interesting and unique properties? o Each water has 4 hydrogen bonds with donor and acceptor having 2 o In liquid water, hydrogen bonds are constantly breaking and forming new ones o Hydrogen bonds weaker than covalent bonds o Melting point and boiling point of water are higher than predicted o Ice has lower density than liquid water o Polar solute acting as donor or acceptor of hydrogen bonds when dissolved in water Other Biologically important Hydrogen Bonds o Hydrogen bonding in proteins creates alpha helix and beta pleated sheets 2.3 Acids, Bases and pH What are acids and bases? o Acid molecule that acts as a proton donor o Base molecule that acts as a proton acceptor o Acid strength amount of hydrogen ion released when a given amount of acid is dissolved in water What is pH? o K , won product constant for water concentration of water has been added to value, 55.5+ o pH=log[H ] o pH values of some aqueous samples can be determined by that calculation o pH of 7 is neutral, acidic is less than 7, basic is greater than 7 Why do we want to know the pH? o It can be important to control the pH of a solution for optimum reaction conditions o Bad things can happen when there is pH fluctuations in the body o Henderson Hasselbalch equation the relationship between pH and pK : a A−¿ ¿ ¿ pH=pKa+log¿ o Equation contains equal concentrations of weak acid and its conjugate base, pH of that solution equals the pa value of the weak acid 2.4 Titration Curves Titration experiment in which measured amounts of base are added to a measured amount of acid Equivalence point point in titration at which the acid is exactly neutralized Near the inflection point, pH changes very little when more base is added Monoprotic, diprotic number of hydrogens released When pH of a solution is less than pK aof an acid, pronated form predominates, pH is greater then deprontonated forms predominates 2.5 Buffers Buffer something that resists change Buffer solution resists change in pH when small to moderate amounts of a strong acid or strong base are added How do Buffers work? o Increase in hydroxide ions shows that hydrogen ion concentration has decreased and that pH increases o Many reactions wont take place unless pH remains within some limits o Buffers are very important in laboratory conditions How do we choose a buffer? o pH of a sample being titrated changes very little around inflection point o pH at inflection point is based on pK a o buffer solution can maintain pH at a relatively constant value because of presence of appreciable amounts of both the acid and conjugate base o buffer solution with low concentrations of both acid and base forms have low buffering capacity How do we make buffers in laboratory? o Making it starts with conjugate acid and added NaOH until have correct pH o Based on relationship between pH and pK a base might be easier to use a Are naturally occurring pH buffers present in living organisms? o Buffer systems in living organisms are based on many types of compounds o In living organisms, pH must stay very close to 7 o Carbon dioxide can dissolve in water to form carbonic acid which then precipitates o pH of blood and pressure of carbon dioxide in lungs is extremely importanT 3.1 Amino Acids Exist in a Three dimensional World Why is it important to specify the three dimensional structure of amino acids? o Amino acids have amino group and carboxyl group bonded to alpha carbon o Alpha carbon bonded to a hydrogen and the side chain group (R) o Sterochemistry twodimensional formula only partially conveys common structure of amino acids because one of the most important properties of these compounds is their three dimensional shape o Chiral nonsuperimposable mirror images o Achiral has symmetry o Stereoisomers alpha carbon with four different groups bonded to it giving rise to two nonsuperimosable o Possible stereoisomers of a chiral compound are L and Dglyceraldehyde 3.2 Individual Amino Acids: Their Structures and Properties Why are amino acid side chains so important? o R groups individual amino acids classified according to polarity of side chain and the presence of acidic or basic group on side chain o Side chain of glycine a hydrogen atom o Side chain carbon atoms are designated with letters of the greek alphabet starting at the alpha carbon o Terminal carbon is referred to as the wcarbon (last letter of greek alphabet) Which amino acids have nonpolar side chains? (group 1) o One group of amino acids have nonpolar side chains o Glycine, alanine, valine, leucine, isoleucine, proline, phenylalanine, tryptophan, and methionine o Alanine, valine, lucine, and isoleucine side chains is an aliphatic(lacking of benzene ring) hydrocarbon group o Amino groups of other common amino acids are amines o Phenylalanine hydrocarbon group is aromatic (has cyclic group like benzene ring) o Tryptophan side chain has indole ring aromatic o Methionine side chances has sulfur atom and aliphatic hydrocarbon groups Which Amino Acids have Electrically neutral polar side chains? (group 2) o Tyrosine hydroxyl group is bonded to aromatic hydrocarbon loses a proton at higher pH o Cysteine polar side chain is a thiol group (SH), reacts with other cysteine thiol group to form disulfide bridges of proteins o Glutamine and asparagine deretives of group 3 amino acids, glutamic acids and aspartic acids have carboxyl groups on side chains Which Amino Acids have carboxyl groups in their side chains? (group 3) o Glutamic acid and aspartic acid have carboxyl groups o Carboxyl group can lose proton forming carboxylate anion o Both are negatively charged at neutral pH Which Amino acids have basic side chains? (group 4) o Lysine side chaing amino gropu attached to aliphatic hydrocarbon tail o Arginine side chain basic group (guanidine group) more complex in structure bonded to aliphatic hydrocarbon tail ; o Free histidine side change imidazole group has high pK a o pK values of amino acids depend on environment o properties of may proteins depend on individual histidine residues Uncommon Amino acids: Which Amino acids are found less commonly in proteins o Derived from common amino acids and produced by modification of parent amino acid after protein is synthesize by organism – posttranslational modification o Hydroxyproline and hydroxylysine have hydroxyl group son side chains, only found in few connective tissue proteins o Thyroxine has extra iodine containing aromatic group on side chain produced only in thyroid glad 3.3 Amino Acids can act as Both acids and bases? Free amino acid carboxyl group and amino group are charged at neutral pH Zwitterion has equal positive and negative charge in solution What happens when we titrate an amino acid? o Titration curve shows reaction of each functional group with hydrogen ion o Can react as a mono, di or triprotic acid o Titratable groups of each of the amino acids have characteristic pKa values of alpha carboxyl groups are fairly low o Amino acids, peptides and proteins have different pKa values different changes at pH o Electrophoresis common method for separating molecules in an electric field o Isoelectric pH isoelectric point molecule will not mirage in an electric field 3.4 The Peptide Bond Which Groups on Amino Acids React to form the peptide bond o Individual amino acids linked to by covalent bonds o Formed between alpha carboxyl groups of one acids and the alpha amino group of the next one o Residues the linked of amino acids after water is eliminated o Peptide bond bonded formed by eliminating water from the amino acids o Peptides compounds formed by linking small numbers of amino acids, ranging from two to several dozen o Many amino acids linked by a peptide bond polypeptide chain o Resonance structure differ from one another in only the position of the electrons o Resonance structures contribute to the bonding situation as a whole o Important implications of thee 3D conformations of peptides and proteins o Free rotations around bonds between the alpha carbon of given amino acid residue and the amino nitrogen and carbonyl carbon 3.5 Small Peptides with Physiological Activity What are Some biological functions of small peptides? o Dipeptide simplest possible covalently bonded combination of amino acids o Nterminal one has free amino group other residues are given as they occur in sequence o Cterminal has free carboxyl group o Amino group is bonded to the third or beta carbon of the alanine o Glutathione occurring tripeptide considerable physiological importance because it is a scavenger for oxidizing agents o Disulfide bond responsible for cyclic structure 4.1 Protein Structure and Function Proteins are polymers consisting of amino acids linked by covalent peptide bond Native conformations structures with biological activity Frequently described as having large segments of random structure Random same nonrepeating structure is found in the native conformation of all molecules of a given protein and this conformation is needed for its proper function Proteins are complex, defined in terms of four levels of structures Why are the Levels of Protein structure? o Primary structure order in which the amino acids are covalently linked together o Primary structure is one dimensional first step o Secondary structure arrangement in space of the atoms in the peptide back bone, alpha helix and beta pleated sheet arrangements o Have repetitive interactions resulting from hydrogen bonding between amine groups o Domains, or super secondary structure folding of parts of the chain that occur independently of the folding of other parts o Tertiary structure 3d arrangement of all the atoms in a protein o Prosthetic groups groups of atoms other than amino acids 4.2 Primary Structure of Proteins Why is it Important to Know the Primary Structure? o Sicklecell anemia consequence from a change in one amino acid residue in the sequence of the primary structure o Conformation of altered protein be determined by sequence 4.3 Secondary Structure of Proteins Hydrogen bonded arrangement of back bone of protein Bond between the alpha carbon and the amino nitrogen of that residue and the bond between the alpha carbon and the carboxyl carbon of that residue determine shape Alpha Helix and beta pleated sheets hydrogen bonded structures Periodic Structure in Protein Backbones o Periodic structures o Features at regular intervals o Alpha helix is rod like and involves only one polypeptide chain o Beta pleated sheet structure gave two dimensional array and has one or more polypeptide chain Why is the Alpha Helix so Prevalent? o Stabilized by hydrogen bonds parallel to the helix o Four residues away from covalently bonded sequence o Helical conformation allowed linear arrangement of atoms o Proteins have varying amounts of alpha helical structures How is the Beta sheet different from the Alpha helix? o Peptide backbone in beta pleated sheets is extended o Hydrogen bonds formed between different parts of single chain o Peptide chains run in same direction o Alternating chains run in opposite directions o Hydrogen bonding between peptide chains in beta pleated sheets o Hydrogen bones are perpendicular to direction of protein chain, not parallel to alpha helix Irregularities in Regular Structures o Helical structures found in proteins found in shorter stretches than alpha helix o Occur between normal beta structure hydrogen bonds and involves two residues on one strand and one on the other o Protein folding needs peptide backbones, secondary structures able to change directions Secondary Structures and Domains o Alpha and beta strands produces super secondary structures in proteins o Motif repetitive super secondary structure o Helixturnhelix antiparallel alpha helices o Protein sequences that allow beta meander to be arranged into a beta barrel in tertiary structure o Proteins have same type of function as similar protein sequences o Domains have been identified with three different types of domains by which proteins bind to DNA The Collagen Triple Helix o Collagen component of bone and connective tissue o Organized in water insoluble fibers of great strength o Has three polypeptide chains wrapped around each other like ropelike twists Two types of Protein Conformations: Fibrous and Globular o fibrous proteins amino acids which collagen, fibroin, keratin are composed determine which conformation they adopt o proteins and backbone fold back on itself producing more or less spherical shape o globular proteinshelical and pleated sheet arranged bringing ends of sequence close to each other in three dimensions 4.4 Tertiary Structure of Proteins protein three dimensional arrangement of atoms in a molecule globular proteins more information needed, interactions between side chains play important role in folding of proteins Forces involved in tertiary structures o Forces are covalent but not usually o Usually protein order of amino acids in polypeptide chain o Higher order levels of structure depend on noncovalent interactions o Protein has many subunits depend on noncovalent interactions o Hydrogen bonding can occur o Backbone hydrogen major determinant of secondary structure o Electrostatic attraction between oppositely charged groups o Disulfide bonds form covalent links between side chains o Complete covalent structure of protein determined by order of amino acids Myoglobin: an Example of Protein Structure o Classic example of globular protein o First protein which complete tertiary structure was determined o Heme group is main group in hemoglobin o Has alpha helical regions and no beta pleated sheets Why does oxygen have imperfect binding to the heme group? o Guards against possibility that traces of carbon monoxide produced during metabolism o Remember our metabolism requires hemoglobin and myoglobin bind to oxygen o Combination of heme and protein is needed to bind oxygen for oxygen storage Denaturing and Refolding o Noncovalent interactions maintain three dimensional structure are weak and easily disrupted o Denaturation unfolding of protein o Reduction of disulfide bonds lead to extensive unraveling of tertiary structure o Proteins denature by heat, extreme pH, detergents 4.5 Quaternary Structure of Proteins Number of chains range from 2 to more Dimers, trimers, tetramers define amount of polypeptide chains Chains interact with one another noncovalently with electrostatic attractions Allosteric proteins that cause drastic changes in properties at a distant site Hemoglobin o Tetramer has four polypeptide chains, two alpha or two beta o Alpha chains hemoglobin are identical are two beta chains o Positive cooperativity one oxygen molecule is bound, becomes easier for next to bind o Cooperative binding binding of first oxygen with allows second to bond easier and etc. How does Hemoglobin work? o Different types of behavior related to functions of proteins o Structural changes during binding of small molecules will show allosteric proteins o Changes marked with that hemoglobin has different crystal structures Conformational Changes that Accompany hemoglobin function o Many ligands involved o Oxygen binding ability of myoglobin not affected by presence of hydrogen or carbon dioxide o Increase concentration of hydrogen reduced oxygen affinity o Changes of quaternary structure of hemoglobin modulate buffering of blood through hemoglobin molecule o Large amounts of hydrogen and carbon dioxide release oxygen 4.6 Protein Folding Dynamics Can we predict the tertiary structure of a protein if we know its amino acid sequence? o Homology similarity of two or more sequences o Fold recognition allows comparison with known folding motifs common to many secondary structures Hydrophobic interactions: case study in thermodynamics o Bilayers are less complex than folded protein o Interactions lead to formation o Liposomes bilayers that form 3d structures o Interactions between bilayers are embedded proteins o Hydrophobic interaction play crucial role in protein folding o Major factor in folding of proteins because they are enzymes, oxygen carriers or structural elements What Makes hydrophobic interactions favorable? o Hydrophobic interactions are spontaneous processes o Formation of mixed solution is nonspontaneous o Nonpolar substances do not dissolve in water The Important of Correct folding o Primary structures conveys necessary information to produce the correct tertiary structure o Proteins need to remain unfolded long enough to be transported across membrane o Correctly folded proteins are usually soluble Protein Folding Chaperones o Aid in correct and timely folding of many proteins o Exit in organisms from prokaryotes though humans Chapter 15: metabolism 439445, 448453 15.1 Standard States for Free Energy Changes Lowering energy dispersal on molecular level is spontaneous What are Standard States? o Standard conditions choice is arbitrary all substances involved in the reaction are in their standard states, also said to be at unit activity o Pure solids and liquids standard states is the pure substance o Pure gases standard state is take as pressure at 1 atm of gas o Solutes standard state is at 1M concentration What do Standard States have to do with Free Energy Change? o Can write any equation relating free energy change for reaction under any conditions C cD d ∆ G=∆G +RTln [ ] [ ] o [A] [B]b , brackets show molar concentrations, R, gas constant, T is absolute temperate o Equation holds under all circumstances reaction doesn’t have to be at equilibrium o Free energy under a given set of conditions depends on value of the standard free energy and concentration of reactants and products ° o When reaction is at equilibrium, ∆ G =−RTlnK eq with the equilibrium constant used in the equation rather than the concentrations 15.2 A Modified Standard State for Biomedical Applications Why do we need a Modified Standard State for Biochemical Applications o Free energy changes includes stipulation that all substances be in standard states o pH is zero if the hydrogen ion concentration is 1M o living cell pH is normally neutral standard state in biochemical practice one that differs from the original standard state only by the change in the hydrogen ion concentrations o free energy changes calculated on basis of modified standard state 15.3 The Nature of Metabolism What is Metabolism? o Metabolism the biochemical basis of all life processes o Molecules of carbs, fats and proteins are processes in a variety of ways to extract energy o Catabolism breakdown of larger molecules to smaller ones o Small molecules are used as a starting point of reactions to produce larger more complex molecules proteins and nucleic acids (Anabolism) o Catabolism and anabolism separate pathways, not just reverse of each other o Catabolism oxidative process that releases energy o Anabolism reductive process that requires energy 15.4 The Role of Oxidation and Reduction in Metabolism How are Oxidation and Reduction Involved in Metabolism? o Oxidationreduction reactions redox reactions those in which electrons are transferred from donor to an acceptor o Oxidation loss of elections o Reduction gain of elections o Reducing agent substance that loses electrons (electron donor, one being oxidized) o Oxidizing agent substance gains electrons (electron acceptor, one being reduced) o Both oxidizing agent and reducing agent are necessary for transfer of elections o Example: strip of metallic zine placed in solution with copper ions o Zinc metal disappears and zinc ions go into solution copper ions removed from solution and copper metal is deposited o Zinc lost two electrons becoming positively charged, was oxidized o Copper gained two elections becoming stable, was reduced o Half reaction separate equation from original that is written as part of the overall reaction o When the half reactions are combined you get the full reaction o Biological redox reactions oxidation state of carbon atom changes 15.6 Coupling of Production and Use of Energy Energy cant be used directly need to be shunted into an easily accessible form of chemical energy Coupling of energy producing reactions and energy requiring reactions is central feature in metabolism How do Energy Producing Reactions allow Energy Requiring Reactions to take Place? o Phosphorylation of ADP to produce ATP requires energy supplied by oxidation of nutrients o Hydrolysis of ATP to create ADP releases energy o Energy must be expended to put an additional negatively charged phosphate group on ADP by forming a covalent bond to phosphate group o Entropy loss when ADP is phosphorylated because there are fewer molecules than before o Decrease in electrostatic repulsion on phosphorylation of ADP to ATP o Bond is hydrolyzed when reaction takes place high energy bond reaction in which hydrolysis of specific bond releases a useful amount of energy o Free energy of hydrolysis of organophosphates is higher than that of ATO and able to drive phosphorylation of ADP to ATP o Phosphoenolypyruvate molecule involved in glycolysis high energy compound because of resonance stabilization of liberated phosphate when hydrolyzed o Energy of hydrolysis of ATP not stored energy, electric current doesn’t represent stored energy o Cycling of ATP and ADP is metabolic processes getting energy from production to its uses when it is needed o Oxidation takes place when organisms need energy that is generated by hydrolysis of ATP o Chemical energy is stored form of fats and carbs metabolized as needed o Energy supplied for endergonic reactions comes from hydrolysis of ATP and indirectly from oxidation of nutrients o When we add two chemical reactions to obtain an equation for overall reaction can also add free energy changes to find overall free energy change o Free energy is a state function only depends on beginning and ending values o Exergonic reactions provides energy drive endergonic processes o Coupling percentage of released energy that is used to phosphorylate ADP is the efficiency of energy used in anaerobic metabolism o Break down of glucose goes further under aerobic conditions end products of aerobic oxidation 6 molecules of carbon dioxide and water for every molecule of glucose o Added two reactions and free energies got overall equation and overall free energy change o More ATP produced by coupling process in aerobic oxidation of glucose Chapter 16: Carbohydrates 16.3 Some Important Oligosaccharides Oligomers of sugars disaccharides formed by linking two monosaccharides units by glyosidic bonds What makes Sucrose an Important Compound? o Sucrose able sugar from sugarcane and sugar beets o Monosaccharide units alpha D glucose and betaDfructose o Alpha C1 carbon of galucose is linked to beta C2 carbon of fructose in a glyosidic linkage o Sucrose is not reducing sugar because both anomeric groups are involved in glycosidic linkages o Free glucose is reducing sugar free fructose can give positive test (ketone rather than aldehyde in opening chain form) o When sucrose is consumed hydrolyzed to glucose and fructose degraded by metabolic processes to provide energy o Some artificial sweeteners derived from sucrose, less dangerous o Sucralose is not metabolize by bond does not provide calories safe sugar substitute Are any other Disaccharides important to us? o Lactose disaccharide with betadglucose o Galactose is C4 epimer of glucose only difference from glucose is C4 configuration is inverted o Anomeric carbon of glucose not involved in glycosidic linkage o 2 anomeric forms of lactose designated by glucose residue o Lactose is reducing sugar because the group at the anomeric carbon of glucose portion is not involved in a glyosidic linkage free to react with oxidizing agents o Maltose disaccharide from hydrolysis of starch Had two residues of Dglucose in a alpha (14) linkage Differences from cellobiose by glycosidic linkage Mammals can digest maltose but not cellobiose Maltose is used in milk and beer 16.4 Structures and Functions of Polysaccharides Polysaccharide many monosaccharides are linked together Occur in organisms that are compose of very few types of monosaccharide compontes Homopolysaccharide only one type of monomer Heteropolysaccharide more than one type of monomer Glucose is most common monomer Polysaccharides include specification of which monomers are present and sequence of monomers Requires type of glycosidic linkage Cellulose and chitin polysaccharides with beta glycosidic linkages structural materials Starch and glycogen polysaccharides with alpha glycosidic linkages serve as carbs storage polymers in plants and animals How Do Cellulose and Starch differ From Each other? o Cellulose is major structural component in plants o Linear homopholysaccharide of betaDglucose, all residues are linked in a beta 14 glycosidic bond o Individual chains are hydrogen bonded together o Animals cant hydrolyze cellulose o Cellulases hydrolyze cellulose by attacking the alpha and beta linkages between glucose Is there more than one form of starch? o Importance of carbs as energy sources is that there are uses for some polysaccharides in metabolism o Starches polymers of alphadglucose that occurs in plant cells o Types of starches can be distinguished from one another by chain branching o Starches are storage molecules mechanism for releasing glucose from starch when organism needs energy o Alpha and beta amylase attack alpha 14 linkages o Amylose can be completely degraded to glucose and maltose How is Glycogen related to starch? o Glycogen branched chain polymer of alphadglucose o Has chain of alpha 14 linkages with alpha 16 linkages at branch points o Main difference is that glycogen is more highly branched o Every glycogen molecule there is a protein called glycogenin o Number of branch points is important more branched polysaccharide more water soluble What is Chitin? o Polysaccharide that is similar to cellulose in both structure and function, also has linear homopolysaccharide with all the residues linked in beta 14 linkages o Differs from cellulose because of monosaccharide unit o Has Nacetylbetadglucosamine o Plays structural role and has mechanical strength because of how the individual strands are held together by hydrogen bonds o Component of exoskeletons of invertebrates, occurs in cell walls What roles do Polysaccharides play in structure of cell walls? o Heteropolysaccharides are major components of bacterial cell walls o Distinguishing feature polysaccharides are cross linked by peptides o Cross links of bacterial cell walls have small peptides o Tetrapeptides are cross linked by another small peptide and have five amino acids o Occurrence of d amino acids and nactylmuramic acid shows a biochemical and structural difference between prokaryotes and eukaryotes o Extensive cross linking produces three dimensional network of mechanical strength o Peptidoglycan formed by cross linking of polysaccharides by peptides o Pectin polymer made up of dgalacturonic acid derivative of galactose o Extracted from plants because of commercial importance o Lignin polymer of coniferyl alcohol tough and durable material 16.5 Glycoproteins Have carb residue and polypeptide chain Antibodies bind to and immobilize antigens Carbs are important in antigenic determinants portions of an antigenic molecule that antibodies recognize and to which they bind How are Carbs important in the immune response? o Super important in determinates of blood groups o A,B, AB, O blood groups o All blood types oligosaccharides contains sugar Lfuctose o Type A has NAcetylglactosamine on the nonreducing end of oligosaccharide o Type B alphadGlactose o Type O has neither terminal residues present o AB has both terminal residues Enzymes activation energy energy input required to initiate a reaction, higher for an uncatalyzed reaction activation energy and relationship to free energy change essentially a discussion of catalysts activation energy directly affects the rate of reaction more catalyst faster reaction transition state necessary amount of energy and correct arrangement of atoms to produce products lower transition state with a catalyst standard free energy change remains constant for a reaction with or without a catalyst rate of a chemical reaction will increase with an increase in temperature substrate binds to enzyme forming complex active site location on enzyme where substrate binds o has certain amino acids that are important for enzyme activity induced fit model substrate and enzyme change shape slightly to fit each other at transition state substrate bound with reacting atoms o substrate has proper orientation o old bonds broken, new bonds form o product of enzyme catalyze reaction with substrate to create more product binding to active site is reversible, noncovalent interactions phosphorylation controls enzymes o side chain hydroxyl groups, serine, threonine and tyrosine form phosphate esters sodium potassium pump: potassium in, sodium up protein for pump from phosphorylation of ATP o ATP hydrolyzes ADP formed releasing energy Protein kinases: proteins that catalyze phosphorylation o Kinase enzymes that catalyzes transfer of phosphate group from ATP to substrate Glycogen phosphorylase allosteric regulation and covalent modification Coenzymes cofactors nonprotien substances that take part in enzymatic reactions that are regenerated for further reactions o Metal ions and coenzymes are 2 classes of cofactors metal ions act as lewis acids many coenzymes involved in redox reactions provide energy + NAD nicotinamide adenine dinucleotide coenzyme in redox reactions Lipids 3/9/16 Lipids o Heterogeneous group of compounds that are insoluble in water but soluble in nonpolar organize solvents o Open chain fatty acids, tryclycerols and others o Cyclic forms cholesterol, steroid hormones, bile acids Hydrophobic interactions weak interactions between nonpolar groups Hydrophobic interactions are driven by entropy want to get ride of water Lipid function o Fats store energy (long term) o Steroids cholesterol (biomembrane fluidity), hormones o Phospholipids biomembranes structure Fatty acid o Amphipathic compound with a polar head and nonpolar tail o Polar head carboxylic acid o Nonpolar tale hydrocarbon chain o 2 main parts o Carboxylic head charged under neutral conditions o Amphipathic structures drive membrane structure o Saturated fatty acid all single bonds o Unsaturated: Carbon, carbon double bond 1 double bond monounsaturated More than 1 double bond polyunsaturated Double bond on the same side create bend in molecule Trans molecules aren’t bent Trans fatty acids are very bad for you o Saturated vs. unsaturated only considering double bonds or not o Bend or straight structures determine fluidity Melting point o Depends on the number of double bonds and length o Longer chains mean higher melting point o Amount of double bonds creates a longer chain lower melting point Triaglclycerols o Ester of glycerol with there fatty acids o Stores excess energy o Oxidation of fat releases twice as much energy and oxidation of carbs Phospholipids o One alcohol group of glycerol is esterified to phosphoric acid o Major lipid component of most biological membranes many types base on R groups Membrane o Hydrophilic groups face both interior and outside of cell o Interior is hydrophobic parts Glycolipids o Carb bound to hydroxyl group of lipid o Sugar is glucose or galactose o Involved in cell and tissue recognition, like ABO blood type o Involved in antigens Steroids 3/11/16 Steroids o Group of lipids with fused ring structure of three six membraned rings and 1 5 membraned right o Basis of cholesterol Polar components is one hydroxyl and is highly hydrophobic Important in maintaining animal cell membrane fluidity Acts amphipathic o Sex hormones are steroids Androgen: Male sex hormone Estrogens: Female sex hormones Control of menstrual cycle Biological Membranes Cellular membranes o All cells have plasma membrane separates inside from outside o Controls transport of substances in and out o Eukaryotic cells membrane enclosed organelles Lipid bilayer structure o Polar head contact with aqueous environment o Nonpolar tails buried within bilayer o Major force driving formation of a lipid bilayer hydrophobic interactions o Fluidity of bilayer interior depends on types of fatty acids and temperature Double bonds in nonpolar tails increase fluidity Lipid bilayer asymmetry o Lipid composes inner and outer of leaf let lipid bilayers be different o Bulker heads group in outer shell o Smaller heads on interior, creates curvature o Hydroxyl group of cholesterol face either interior or exterior of cell o Cholesterol is very stiff Cholesterol buffers fluidity o Reduces fluidity by stabilizing extended chain conformations of the hydrophobic tails o Increases fluidity by preventing interactions between hydrophobic tails Lipids and Membrane Fluidity o Interactions between hydrophobic tails decreased fluidity o Shorter tails have fewer interactions o Unsaturated fatty acids kincked decrease interactions Membrane proteins o Integral embedded in phospholipid bilayer o Peripheral weakly bond to membrane o Lipid linked covalently attached to lipid o Lipid linked used by bacteria Integral membrane proteins Tightly bound to membranes by hydrophobic interactions o Can separate from membrane only by reactions that disrupt membranes Peripheral membrane proteins Attached to membrane by binding at surface usually to integral membrane lipid linkedcovalently linked to a lipid that anchors protein to the membrane
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