Study Guide, Midterm 1
Study Guide, Midterm 1 BCH 110
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This 15 page Study Guide was uploaded by Cassidy Zirko on Tuesday February 23, 2016. The Study Guide belongs to BCH 110 at University of Montana taught by Scott Samuels in Spring 2016. Since its upload, it has received 141 views. For similar materials see Intro Biology for Biochemist in Biology at University of Montana.
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Date Created: 02/23/16
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 Can a Chemist Make Molecules of Life in a Lab? o Functional Groups a type of classification method of organic molecules o Reactions of molecules based on reactions of respective functional groups What Makes Biomolecules Special? o Many functional groups (contain nitrogen and organic) o Most polar in nature reactivity 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 o The earliest known rocks are 3.8 billion years old and are carbonates o Any ammonia that was present dissolved in the oceans and the left over nitrogen gas created proteins and nucleic acids 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 All cells contain DNA 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 all prokaryotes are single celled organism, but can form colonies 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 o Chomatophores found in prokaryotes, extension of plasma membrane and preform photosynthesis 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 DNA is pretty simple o Only a single, closed, circular molecules of DNA in prokaryotes o Ribosomes allow a slightly grainy appearance because of how they float within the cytosol 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 o Cell wall also serves as protection for cell 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 Glyoxysomes only in plant cells, contains enzymes that catalyze the glyoxylate cycle (pathway that convers lipids into carbs using glyoxylic acid) 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 Is there a Simpler Basis for Classifying Organisms? o Three domains bacteria (eubacteria) , archaea (archaebacterial) and eukarya (eukaryotes) 1.6 Common Ground for All Cells Did Eukaryotes Develop from Prokaryotes? o Symbiosis plays major roll in most current theories o Mutualism benefits both parties involved o Parasitic symbiosis only one party benefits at the other parts expense 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 Heat of reaction at constant pressure (delta H), easy to measure o Enthalpy y changes all the time o Entropy changes are important in biochemistry 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 Partial positive charge when bonded with oxygen or nitrogen because of polar bond Partial positive charge interacts with unshared pairs of electrons Group with electronegative atom that is covalently bonded to hydrogen hydrogen bond donor Hydrogen bond acceptor electronegative atom that contributes the unshared pair of electrons to the interaction 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 A−¿ ¿ o Acid dissociation constant, K a [ ] K a¿ o No naked protons in a solution, (free hydrogen ions) What is pH? o K , ion product constant for water concentration of water has been added to w 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 half of acid originally presented has ben converted to conjugate base 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 baae might be easier to use 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 o zwitterions compounds that have both a positive charge and a negative charge 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 o L left, DRight o L and D amino acids stereoisomers of each amino acids on basis of similarity to the glyceraldehyde standard o Position of amino group on the left or right side of alpha carbon determines L or D designation 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 Proline aliphatic cyclic structure, nitrogen bonded to two carbon groups 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 groupls Which Amino Acids have Electrically neutral polar side chains? (group 2) o Serine and thernin polar group is a hydroxyl bonded to aliphatic hydrocarbon 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 histidine found in protonated or unprotanted form in proteins 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 o Amino acids have only two pka values0 equation used to ejaculate the pI 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 Peptide bond is also stronger than an ordinary stronger bond because of resonance stabilization 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 o Some peptides cyclic structure is formed by the peptide bonds ‘ 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 Amino acid sequence of protein determines the 3d structure Correct 3d structure is needed for correct functioning 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 o Proline has bend in backbone because of cyclic structure o Cant have alpha helix because rotation around bond between nitrogen and alpha carbon is restricted and proline alpha amino group cant participate in intrachain hydrogen bonding o Crowding caused by proximity of several side chains o Alpha carbon outside helix, crowding can occur 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 Beta bulge no repetitive irregularity found in antiparallel beta sheets 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 o Revers turns polypeptide chain changes direction 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 o Three chains has within limits repeating sequences of three amino acid residues o Triple helix is arranged so that every third residue on each chain is inside helix 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 o 3D of protein result from interplay of stabilizing forces o Segments of proteins bends at polypeptide chain and in other portions of the protein not involved in helical or pleated sheet structures called random 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 o Polar residues are on exterior molecule o Interior has protein contains exclusively nonpolar amino acids Why does oxygen have imperfect binding to the heme group? o Has affinity to free 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 Final level of protein structure have more than one polypeptide chain 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 Sequence of amino acids determines 3D structure of protein Can we predict the tertiary structure of a protein if we know its amino acid sequence? o Bioinformatics encounter of biochemistry and computing o Prediction of protein structure o All we need to know is the nucleotide 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 Large arrays of molecules take on definite structures because of hydrophobic interactions 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 Water molecules surrounding nonpolar molecules can hydrogen bond with each others o Required entropy to decrease large for processes to take place 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
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