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Notes for Biochem Exam 1

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Notes for Biochem Exam 1 87222 - BCHM 3050 - 002

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These are all the notes for the first exam.
Essential Elements of Biochemistry
Srikripa Chandrasekaran
Study Guide
biochem, biochemistry, Clemson, amino acids, peptides, Proteins, Water, pH, bonds, exam
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This 21 page Study Guide was uploaded by America Seach on Wednesday January 27, 2016. The Study Guide belongs to 87222 - BCHM 3050 - 002 at Clemson University taught by Srikripa Chandrasekaran in Spring 2016. Since its upload, it has received 153 views. For similar materials see Essential Elements of Biochemistry in Biology at Clemson University.


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Date Created: 01/27/16
Chapter 3: 3.1: Molecular structure of water - Polar: there is an unbalance in electron distribution - dipoles: molecules, such as water, in which charge is separated - hydrogen bond: hydrogen is unequally shared by the two electronegative centers - electrostatic interaction: occurs between any two opposite partial charges (polar molecules) or full charges (ions or charged molecules) - covalent bonds: involve electron sharing with orbital overlap or mixing 3.2: Noncovalent bonding - noncovalent interactions are usually electrostatic meaning that they occur between the positive nucleus of one atom and the negative electron clouds of another nearby atom - in living organisms, the most important are ionic interactions, van der Waals interactions, and hydrogen bonds - Ionic interactions: occur between charged atoms or groups are nondirected- they are felt uniformly in space around the center of charge; opposite charges attract, similar charges repel; the attraction of positively and negatively charged amino acid side chain forms SALT BRIDGES - Hydrogen bonds: in water each molecule can form hydrogen bonds with four other water molecules; bond is partially covalent and causes the force of attraction to have directionality - Van der Waals forces: relatively weak electrostatic interactions; electronegative atoms with unshared pairs of electrons are easily polarized 1. Dipole-dipole: occur between molecules containing electronegative atoms causing them to connect from the negative and positive ends; hydrogen bonds are strong 2. Dipole-induced dipole: a permanent dipole induces a transient dipole in a nearby molecule by distorting its electron distribution; weaker than dipole-dipole 3. Induced dipole- induced dipole: the motion of electrons in nearby nonpolar molecules result in transient charge imbalance in adjacent molecules; often called London dispersion forces which are very weak - Noncovalent bonds (ionic interactions and van der Waals forces) are important in determining the physical and chemical properties of living systems - Hydrogen bonds, with both dipole/dipole and covalent character, play a critical role in the properties of water and its place in the structure and function of cells 3.3: Thermal Properties of Water - Water is liquid at room temperature, and its melting and boiling points are high - Hydrogen bonding is responsible for its unique characteristics - The maximum number of hydrogen bonds form when water has frozen into ice; energy is required to break these bonds - Ice is less dense than water in its liquid state - When ice is warmed to its melting point, approximately 15% of hydrogen bonds break - Hydrogen bonding is responsible for water’s unusually high freezing and boiling points - Because water has a high heat capacity, it can absorb and release heat slowly. Water plays an important role in regulating heat in living organisms 3.4: Solvent Properties of Water - Water is the ideal biological solvent and it easily dissolves a wide variety of the constituents of living organisms - Hydrophilic molecules, cell water structuring, and sol-gel transitions: o Salts are held together by ionic forces o Because water molecules are polar, they are attracted to charged ions (either positive or negative) o Shells of water are known as solvation sphere and they cluster around positive and negative ions o The capacity of a solvent to reduce the electrostatic attraction between charges is indicated by its dielectric constant o Water is sometimes referred to as the universal solvent because of the large variety of ionic and polar substances it can dissolve and its large dielectric constant o When ionic compounds such as NaCl is dissolved in water, its ions separate because the polar water molecules attract the ions more than the ions attract each other. In reality, the solvation sphere of Na+ has four times the volume of that Cl- because of the higher charge density of the sodium ion o Sol-gel transitions: a gel is a colloidal mixture (consisting of biopolymers with polar surfaces in association with absorbed water); the stability of a gel is very dependent on the length and cross-linking of the polymer and continuity of the adsorbed water; changes in temperature, matrix architecture, and inclusion of solutes can lead to a transition from the gel to a “sol” or liquid state; transitions from gel to sol contributes to cell functions- most notably cell movements; a cell moves forward because of the coordination of sol-gel transition in the cell cortex(ectoplasm) and the cytoplasm in the cell’s interior(endoplasm)- a contractile force in the rear of the cell squeezes the fluid endoplasm forward o Hydrophobic molecules and hydrophobic effect: hydrophobic-water hating- molecules, such as the hydrocarbons, are insoluble in water; the hydrophobic effect is responsible for the generation of stable lipid membranes that contribute to the fidelity of protein folding o Amphipathic molecules: a large number of biomolecules ~amphipatic~ contain both polar and nonpolar groups; when they are mixed with water, they form structures called micelles in which the charged species (polar heads) have oriented themselves so they contact water and the hydrophobic tails are on the interior; allows for phospholipid bilayer to form o Water’s dipolar structure and its capacity to form hydrogen bonds enable water to dissolve many ionic and polar substances o Nonpolar molecules cannot form hydrogen bonds with water and are excluded via clathrate formation o Amphipathic molecules, such as fatty acid salts, spontaneous rearrange themselves in water to form micelles o Osmotic pressure:  Osmosis: the spontaneous passage of solvent molecules through a semipermeable membrane  Osmotic pressure: the pressure required to stop the net flow of water across a membrane; depends on the solute concentration; calculated by π= iMRT where π is osmotic pressure (atm), i is vant hoff factor, M is molarity (mol/L), R is the gas constant (0.082), and T is temperature in Kelvin  The concentration of a solute can be expressed in terms of osmolarity  Isotonic solution: the concentration of solute and water is the same on both sides of the selectively permeable membrane; there is no net movement in either direction  HypOtonic solution: when cells are placed into a solution with a lower concentration, water moves into the cell; this causes the cell to swell and rupture through a process called hemolysis; what plants typically exist in, rigid cell walls prevent the cells from bursting  HypErtonic solution: when cells are placed in solutions with higher solute concentrations, the cell shrivels because there is a net movement of water out of the cell; this process is called crenation; the cell membrane pulls away from the cell wall because of water loss and the plant wilts  Macromolecules have little direct effect on cellular osmolarity because their cellular molar concentration are relatively low  Membrane potential: the electrical gradient established because of asymmetry on the surface of cell membranes; it provides the means for electrical conduction, active transport and even passive transport o Osmosis is the movement of water across a semipermeable membrane from a dilute solution to a more concentrated solution o Osmotic pressure is the pressure exerted by water on a semipermeable membrane as a result of a difference in the concentration of solutes on either side of the membrane 3.5: Ionization of water - A solution that contains equal amounts of H+ and OH- is said to be neutral; when it has excess H+, it is acidic; when it has excess OH-, it is basic - Acids, Bases, and pH: o Strong acids and bases ionize almost completely in water; separate completely o Weak acids: organic acids (compounds with carboxyl groups) do not dissociate completely in water o Weak bases: organic bases have a small but measurable capacity to combine with hydrogen ions; many contain amino groups o Conjugate base: the deprotonated product of the dissociation reaction (will have a negative charge) o Strength of a weak acid (capacity to release hydrogen ions) can be determined by finding the Ka or dissociation constant----  Ka= [H+][A-] ÷ [HA]  The larger the Ka value, the stronger the acid  Use pKa=-log(Ka) to find it on a logarithmic scale; the smaller the value of the pKa, the stronger the acid o To find the pH using hydrogen ion concentration: pH= -log[H+] or [H+]= 10^(-pH) o pH 7 is neutral and has [H+] equal to 1x10^-7, below 7 is acidic and [H+] greater than 1x10^-7, above 7 is basic/alkaline - Buffers: help to maintain a relative constant hydrogen ion concentration; most common buffers consist of a weak acid and their conjugate base; resist changes to pH o Acidosis: a condition that occurs when human blood pH falls below 7.35; results from excessive production of acid in the tissues; the CNS becomes depressed and can cause a coma or death o Alkalosis: a condition that occurs when pH goes above 7.45; overexcites the CNS and muscles go into spasmatic attack; if not corrected, it can cause convulsions and respiratory arrest o Le Chatelier’s principle: states that if stress is applied to a reaction at equilibrium, the equilibrium will be displaced in the direction that relieves the stress o A buffers capacity to maintain a specific pH depends on 2 factors: 1. The molar concentration of the acid-conjugate base pair 2. The ratio of their concentrations o Henderson-Hasselbalch equation:  pH= pKa + log [A-]/[HA] - Liquid water molecules have a limited capacity to ionize to form H+ and OH- ions - The concentration of hydrogen ions is a crucial feature of biological systems primarily because of their effects on biochemical reaction rates and protein structure - Buffers, which consist of weak acids and their conjugate bases, prevent changes in pH (a measure of [H+]) - Weak Acids with more than ONE ionizable group: some acids can donate more than one hydrogen ion o use titration to show each single proton leaving o at a low pH, most molecules are fully protonated; as a strong base (NaOH) is added, protons are released in the order of decreasing acidity, with the least acidic proton (largest pKa value) ionizing last - Physiological buffers: three most important in the body are bicarbonate buffer, the phosphate buffer, and the protein buffer o Bicarbonate buffer: most important in the blood; has three components  Carbon dioxide reacts with water to form carbonic acid, Carbonic acid dissociates to form H+ and HCO3- ions (bicarbonate) o Phosphate buffer: consist of the weak acid-conjugate base pair H2PO4- and HPO4^(2-)  Does not have a major effect in the blood  Important in extracellular fluids o Protein buffer: composed of amino acids linked together by peptide bonds, proteins contain several types of ionizable groups in side chains that can donate or accept protons; since protein molecules are highly present in living organisms, they are powerful buffers; hemoglobin and blood pH Biochem Notes  Chapter 5: Amino Acids, Peptides, and Proteins  proteins can be distinguished based on their  number of amino acids (amino acid  residues), their overall amino acyl composition, and their amino acyl sequence  Polypeptides: molecules with molecular weights ranging from several thousand  to several million daltons  peptides: low molecular weight, consisting of fewer than 50 amino acids  protein: describes molecules with more than 50 amino acids, used  interchangeably with polypeptide 5.1: Amino Acids  there are 20 standard amino acids; they contain a central carbon atom (alpha  carbon) to which an amino group, a carboxylate group, a hydrogen group, and an R group (side chain) are attached   nonstandard amino acids consist of amino acid residue s that have been  chemically modified after incorporation into a polypeptide or amino acids that  occur in living organisms but are not found in proteins  At pH of 7, the carboxyl group of an amino acid is in its conjugate base form  (COO­) and the amino group is in its conjugate acid form (NH3+)  amphoteric: can act as an acid or a base  Zwitterions: molecules that have a negative and a positive charge on different  atoms  Amino acid classes: o Nonpolar: contain mostly hydrocarbon R groups that do not bear a  positive or negative charge; interact poorly with water (hydrophobic); two  types of hydrocarbon side chains­ aromatic (contain cyclic structures that  constitute a class of unsaturated hydrocarbons) and aliphatic (non  aromatic hydrocarbons such as methane and cyclohexane);  Phenylalanine, tryptophan, glycine, alanine, valine, leucine, isoleucine,  proline, and cystine o polar: have functional groups capable of hydrogen bonding; hydrophilic  and easily interact with water; serine, threonine, tyrosine, asparagine,  glutamine o acidic: have a sidechain with carboxylate groups; are negatively charged  at physiological pH; Aspartate and glutamate o basic: have positive charges at physiological pH; lysine, arginine, and  histidine o amino acids are classified according to their capacity to interact with  water; this criterion may be used to distinguish the four classes o Biologically Active Amino Acids: 1. Neurotransmitters: several alpha­amino acids or their derivatives act as  chemical messengers; Hormones: chemical signal molecules produced in  one cell that regulates the function of other cells 2. amino acids are precursors of a variety of complex nitrogen­containing  molecules; includes components of nucleotides and nucleic acids, heme  (iron­containing organic group required for the biological activity of several  important proteins), and chlorophyll  3. Several standard and nonstandard amino acids act as metabolic  intermediates  Modified Amino Acids in Proteins: several proteins contain amino acid derivatives that are formed after a polypeptide chain has been synthesized  Amino Acid Stereoisomers: because the alpha­carbon of 19 out of the 20 amino  acids have four different groups attached, they are known as asymmetric, or  chiral, carbons; molecules with chiral carbons can exist as stereoisomers  (molecules that differ only in the spatial arrangement of their atoms); two isomers that are mirror images of each other are enantiomers; optical isomers are when  the light waves of a plane­polarized light vibrate in only one place  molecules with asymmetric or chiral carbon atoms differ only in the spatial  arrangement of the atoms attached to the carbon  the mirror­image forms of a molecule are called enantiomers  most asymmetric molecules in living organisms occur in only one stereoisometric form  Titration of amino acids: because amino acids contain ionizable groups, the  predominant ionic form of these molecules in solution depends on the pH;  Isoelectric point (pI): is the pH at which the carboxyl group has lost its proton and has no net charge, electrically neutral­ can be calculated by pI= (pK1 + pK2) 2;  as titration continues, the ammonium group loses its proton leaving an  uncharged amino group giving the molecule a negative charge  When amino acids are incorporated in polypeptides, the ­aminoand  ­carboxylgroup lose their charges; consequently, except for the N­ and the C­ terminal residues, all the ionizable groups of proteins are the side chain groups of seven amino acids: histidine, lysine, arginine, aspartate, glutamate, cysteine,  tyrosine  Amino Acid Reactions:  o Peptide bond formation: peptide bonds are amide linkages formed when  the unshared electron pair of the alpha­amino nitrogen atom of one amino acid attacks the a­carboxyl carbon of another in a nucleophilic acyl  substitution reaction o have an amino acid sequence: the order in which the amino acids are  linked together  o Cysteine Oxidation: the sulfahydryl group of cysteine is highly reactive;  oxidation of two molecules of cysteine form cystine, a molecule with a  disulfide bond; when two cysteine residues form such a bond, it is  referred to as a disulfide bridge that help stabilize polypeptides and  proteins o Schiff Base Formation: molecules that possess primary amine groups can reversibly react with carbonyl groups; the imine products are known as  Schiff bases; the most important examples of Schiff base formation in  biochem occur in amino acid metabolism­ aldimines formed by the  reversible reaction of an amino group with an aldehyde are the  intermediates o Polypeptides are polymers composed of amino acids linked by peptide  bonds; the order of the amino acids in the polypeptide is called amino  acid sequence o disulfide bridges, formed by the oxidation of cysteine residues, are an  important structural element in polypeptides and proteins o schiff bases are imines that form when amine groups react reversibly with carbonyl groups 5.2 PEPTIDES  the tripeptide glutathione contains an unusual y­amide bond; found in almost all  organisms, it is involved in protein and DNA synthesis, drug and environmental  toxin metabolism, amino acid transport and other biological processes; an  important intracellular antioxidant  homeostasis: process to maintain a stable internal environment  vasopressin: antidiuretic hormone; affects blood volume; contains nine amino  acid residues; synthesized in the hypothalamus; released in response to low  blood pressure or high Na+ in the blood  oxytocin: stimulates the ejection of milk by the mammary glands  atrial natriuretic factor (ANF): peptide produced by the heart in response to  stretching; also stimulates the production of dilute urine (opposite of vasopressin)  Although small in comparison to larger protein molecules, peptides have  significant biological activity; they are involved in a variety of signal transduction  processes 5.3 PROTEINS  have the most diverse functions: 1. catalysis: enzymes are proteins that accelerate chemical reactions; the can  perform under mild conditions of pH and temperature because they can  induce or stabilize strained reaction intermediates 2. structure: provide structural support; have specialized properties (EX:  collagen, fibroin have mechanical strength; elastin is in the muscles that have to be elastic to function) 3. movement: proteins are involved in all cell movements 4. defense: keratin (found in skin cells) protects the organism against  mechanical and chemical injury; antibodies; blood clotting proteins prevent  bleeding out 5. regulation: control different functions such as regulating blood glucose levels 6. transport: function as carriers of molecules or ions across membranes or  between cells 7. storage: serve as a reservoir of essential nutrients 8. stress response: the capacity of living organisms to survive a variety of  stresses is mediated by certain proteins; excessively high temperatures and  other stresses such as the synthesis of a class of proteins called heat shock  proteins (hsps) that promote the correct refolding of damaged proteins­ if  such proteins are severely damaged, hsps degrades it  multifuntion proteins (moonlighting proteins): examples are GAPD (catalyzes  the oxidation of glyceraldehyde­3­phosphate; has roles in DNA replication and  repair) and crystallin  crystallin must prevent the scattering of visible light; have to appear genetically  “recruited” from metabolic enzymes, but still retained old functions  Protein families: composed of protein molecules that are related by amino acid  sequence similarity; have common ancestry  superfamilies: proteins that are more distinctly related  proteins are often classified based on shape and composition:  o fibrous proteins: long rod shaped molecules; insoluble in water and tough; have structural and protective functions EX. keratin o globular proteins: compact, spherical; usually water soluble; dynamic  functions o conjugated protein: a simple protein combined with a nonprotein  component known as a prosthetic group  glycoproteins: contain a carbohydrate component  lipoproteins: contain a lipid molecule  metalloproteins: contain metal ions  phosphoproteins: contain a phosphate group  hemoproteins: have heme groups  Protein structure: several levels of structural organization of proteins  Primary: polypeptides that have similar amino acid sequences and have arisen from the same ancestral gene are homologous; the  amino acid residues that are identical in all homologues of a  protein are known as invariant and are essential for the protein’s  function  primary structure, evolution, and molecular diseases: a significant  number of primary sequence changes do not affect the function;  some substitutions are known as conservative; if it is variable, it  has a nonspecific role for the polypeptide’s function  conservative and variable sites have been used to track  evolutionary relationships (the longer they’ve been  diverged, the more differences the polypeptides structure  will have)  molecular diseases: mutations can be lethal, but not all of  them all immediately EX­ sickle cell   the primary structure of a polypeptide is its amino acid sequence,  the amino acids are connected by peptide bonds  Amino acid residues that are essential for the molecule’s function  are referred to as invariant  proteins with similar amino acid sequences and functions and a  common origin are said to be homologous  Secondary: consists of several repeating patterns; most common  types are the alpha­helix and the beta­pleated sheets­ both are  stabilized by localized hydrogen bonding between the carbonyl  and N­­­H groups in the polypeptide’s backbone; they occur when  all the phi (Φ) angles (from the alpha carbon­­­­N) and the psi(ψ)  angles (from the alpha carbon­­­­C) are equal  beta­pleated sheets can be antiparallel (chains are  arranged in opposite directions) or parallel (hydrogen  bonds in the chains are arranged in the same direction)  many globular proteins contain combinations of alpha­helix and B­pleated sheet secondary structures; known as  supersecondary structure or motifs  Tertiary: refers to the unique 3D conformations that  globular proteins assume as they fold into their native structures  protein folding is unorganized  has several features: 1. many polypeptides fold in such a fashion that amino acid  residues that are distant from each other in the primary  structure come into close proximity  2. globular proteins are compact because of efficient packing as it  folds 3. large globular proteins often contain several compact units  called domains (structurally independent segments that have  specific functions); the core 3D structure of a domain is a fold 4. modular and mosaic proteins contain duplicate or imperfect  copies of one or more domains that are linked in series  Types of interaction to stabilize tertiary structure: 1. hydrophobic interactions: hydrophobic R groups are brought in close  proximity because they are excluded from water 2. Electrostatic interactions: strongest interaction in proteins occurs between  ionic groups of opposite charge­ known as salt bridges­ are noncovalent  bonds which excludes water because of the energy required to remove water  molecules 3. Hydrogen bonds: form within the protein’s interior and on its surface;  presence of water precludes the formation of hydrogen bonds 4. covalent bonds: created by chemical reactions that alter a polypeptides  structure during or after synthesis­ most prominent in tertiary structure are  disulfide bridges  5. Hydration: structured water is an important stabilizing feature of protein  structure  free energy equation: ΔG =ΔH ­ TΔS o  Quaternary: multisubunit proteins in which some or all subunits are identical are  oligomers, which are made up of protomers; A large number of oligomeric proteins contain  two or four subunits are referred to as dimers and tetramers o several reasons for common occurrence of multisubunit proteins:  synthesis of separate subunits may be more efficient than substantially  increasing the length of a single polypeptide chain, in supramolecular complexes  such as collagen fibers, replacement of smaller worn out or damaged  components can be managed more effectively; the complex interactions of  multiple subunits help regulate a protein’s biological function o allostery­ the control of protein function through ligand bind o allosteric transitions­ ligand­induced conformational changes in a protein o effector/modulator­ ligands that trigger the proteins o unstructured protein: some proteins are completely or partially  unstructured  IUPs: intrinsically unstructured proteins  natively unfolded proteins: complete lack of ordered structure  many involved in the regulation of signal transduction,  transcription, translation, and cell proliferation  Loss of protein structure: denaturation is the disruption of the  structure which may include protein unfolding but doesn’t have to;  Christian Anfinsen dealt with reversible denaturation of  Bovine pancreatic ribonuclease that is denatured by β­mercaptoethanol and 8M  urea; during this process, ribonuclease (composed of a single polypeptide and 4  disulfide bridges) completely unfolds and loses all biological activity; can be  reversed by removing the denaturing agents with dialysis  Denaturing conditions include: 1. strong acids or bases: changes in pH alters hydrogen bonding and salt  bridge patterns; as it approaches its isoelectric point, it becomes less  soluble and may precipitate from solution 2. organic solvents: water­soluble organic solvents interfere with  hydrophobic interactions; so do nonpolar solvents 3. detergents: disrupt hydrophobic interactions and proteins unfold into  extended polypeptide chains; they are amphipathic because they have  hydrophobic and hydrophilic components 4. reducing agents: in the presence of urea (or other reagents) reducing  agents convert disulfide bridges to sulfhydryl groups; disrupts hydrogen  and hydrophobic interactions 5. salt concentration: water molecules that interact with the proteins  ionizable groups get distracted by/attracted to salt when concentration is  high; when its high enough, solvation sphere is removed and protein  molecules collect together and precipitate­ called salting out 6. heavy metal ions: may disrupt salt bridges, protein structure and function;  EX. Anemia  7. temperature changes: temperature increases, increasing molecular  vibration; after time, the weaker bonds break and cause the protein to  unfold 8. mechanical stress: stirring and grinding can disrupt the forces holding the  protein together  biochemists distinguish four levels of the structural organization of proteins  in primary structure, the amino acid residues are connected by peptide bonds  the secondary structure of polypeptides is stabilized by hydrogen bonds.  Prominent examples are alpha helices and beta pleated sheets  tertiary structure is the unique 3D conformation that a protein assumes  because of the interactions between amino acid side chains; several types of  interaction stabilize tertiary structures  proteins that consist of several separate polypeptide subunits exhibit  quaternary structure  both noncovalent and covalent bonds hold the subunits together; some  proteins are partially or completely unstructured  The Folding Problem: due to Anfinsens’s experiment, scientist suggested that  they could predict the 3D structure of any protein if the physical and chemical  properties of the amino acids and the forces that drive the folding process  were understood; Site­directed mutagenesis (a recombinant DNA technique in which specific sequence changes can be introduced into a predetermined  position in cloned genes)­ showed that depending on where the hydrophobic  interaction occurred and between which amino acids could cause either no  effects to the structure (amino acids on the surface) or serious structural  changes (core amino acids)  o problems with the model: 1. time constraints 2. complexity  recent advances have been made in protein folding research using  imaginative combinations of technologies: Circular Dichroism is a type of  spectroscopy in which the relationship between motion and structure is  probed with electromagnetic radiation, and NMR is an imaging technique  that measures the absorption of electromagnetic radiation by atomic  nuclei in the presence of a strong magnetic field; these two techniques  have shown that proteins do not have one pathway of folding, and  depending on the size of the polypeptide it could have intermediates as  well; molten globule is a partially organized globular state of a folding  polypeptide that resembles the molecule’s native state and within the  interior of molten globules the tertiary interaction have not yet stabilized;  molecular chaperones: aid living cells during their folding process  Molecular chaperones: assist unfolded proteins in two ways: first­ proteins  must be protected during inappropriate protein­protein interactions; second­  proteins must fold rapidly and precisely into their correct conformations; there  are two major classes of chaperones: 1. Hsp70s: family that bind to and stabilize proteins during the early  stages of proteins 2. Hsp60s: once an unfolded polypeptide has been released by hsp70,  they are sent to these chaperones that mediate protein folding  all the information required for each newly synthesized polypeptide to fold into its  new biologically active conformation is encoded in the molecules primary  sequence  some relatively simple polypeptides fold spontaneously into their native  conformations  other larger molecules require the assistance of proteins called molecular  chaperones to ensure correct folding  Fibrous proteins: typically contain high proportions of regular secondary  structures such as alpha helices and beta pleated sheet; have structural rather  than dynamic roles o Collagen: composed of three left­handed polypeptide helices that are  twisted around each other to form a right handed triple helix; type I  collagen molecules (in teeth, bone, skin, and tendons) make up 90% of  the collagen found in the human body; consists of large numbers of  repeating triplets with the sequence Gly­­X­­Y normally with x and y being proline and hydroxyproline o Globular proteins: functions involve the precise bind of small ligands or  large macromolecules such as nucleic acids or other proteins; well researched  examples are myoglobin and hemoglobin  myoglobin: found in high concentrations in skeletal and cardiac  muscle; gives tissue their red color­ if they have extremely high  concentrations then the muscles will appear brown; composed of globin,  which is a single polypeptide chain that has 8 segments of alpha­ helix;  have heme binding unit  hemoglobin: spherical molecule found in red blood cells and  transport oxygen from the lungs to the tissues of the body; there are  different forms of hemoglobin molecules but each has two alpha­chains  and two beta­chains  amino acid sequences of myoglobin and hemoglobin are very  different although their 3D configurations are very similar  cooperative binding: as the first O2 binds to hemoglobin the  binding of another hemoglobin to the same molecule is enhanced; results  from changes in hemoglobin’s 3D structure that are initiated when the first O2 binds  hemoglobin’s dissociation curve has a sigmoidal shape and  myoglobin’s dissociation curve is hyperbolic  Bohr effect: the dissociation of oxygen from hemoglobin is  enhanced if pH increases; causes oxygen to be delivered to cells in  proportion to their needs  Globular protein function usually involves bind to small ligands or  to other macromolecules  the oxygen­binding properties of myoglobin and hemoglobin are  determined in part by the number of subunits they contain Biochem Chapter 6: Enzymes 6.1: Properties of Enzymes - activation energy: the minimum amount of energy a molecule must possess in order for a chemical reaction to occur; also known as free energy of activation - enzymes are catalysts that have several remarkable properties: 1. the rates of enzymatically catalyzed reactions are extremely high 2. enzymes are highly specific to the reactions they catalyze and side products are rarely formed 3. because they are large and complex, they can be regulated - catalyst: a substance that enhances the rate of a chemical reaction but it is not permanent - transition state: occurs at the apex of both reaction pathways - substrate: a reactant - ΔGŧ : the free energy of activation; amount of energy required to convert 1 moles of substrate molecules from the ground state to the transition state - Active site: the unique binding surface of an enzyme molecule - The shape and charge distribution of an enzyme’s active site constrains the motions and allowed conformations of the substrate, forcing it to adopt a conformation more like the transition state- the structure of the active site is used to position the substrate correctly - The ratio of the forward and reverse constants is the equilibrium constant: K eq= [B] ÷ [A] N - The equilibrium is not changed due to the addition of a catalyst - Cofactors: may be ions or complex organic molecules (coenzymes) - Apoenzyme: the protein component of an enzyme that lacks an essential cofactor - Holoenzymes: intact enzymes with their bound cofactors - Enzymes are catalysts - Catalysts modify the rate of a reaction because they provide an alternative reaction pathway that requires less activation energy than the uncatalyzed reaction - Most enzymes are proteins 6.2: Classification of Enzymes - Typically named by adding the suffix –ase to the name of the substrate - The six major enzyme categories: 1. Oxidoreductases: catalyze oxidation-reduction reactions; involve one or two electron transfer reactions 2. Transferases: enzymes that transfer molecular groups from a donor molecule to an acceptor molecule; common names have trans in the beginning 3. Hydrolases: catalyze reactions in which cleavage bonds are accomplished by the addition of WATER 4. Lyases: catalyze reactions in which groups are removed by elimination to form a double bond or are added to a double bond 5. Isomerases: catalyze several types of intramolecular arrangements 6. Ligases: catalyze bond formation between two substrate molecules; synthetase; combining two things completely 6.3: Enzyme Kinetics - Velocity of a biochemical reaction is defined as the change in the concentration of a reactant or product per unit - Enzyme kinetics: the quantitative study of enzyme catalysis; provides information about reaction rates; measure affinity of enzymes for substrates and inhibitors - Order of a reaction: the sum of the exponents of the reactants; can be zero, first, pseudo-first, or second o First order: the exponent is 1, only depends on a single -1 reactant; units are s o Second Order: when exponents of the reactants total to the value of 2; units are M s1 -1 o Pseudo-first: when water is a reactant, but water is not included in the calculation of the order; looks like 2 but is really 1 o Zero order: when the addition of a reactant does not alter the reaction rate; exponent is 0 - Kinetics studies measure reaction rates and the affinity of enzymes for substrates and inhibitors - Kinetics provides insight into reaction mechanics - Molecularity: defined as the number of colliding molecules of a single-step reaction; unimolecular has molecularity of one and bimolecular has a molecularity of two - The Michaelis-Menten kinetic model explains several aspects of the behavior of many enzymes - Each enzyme has a characteristic Km for a particular substrate under specified conditions - Sequential reactions: cannot proceed until all substrates have been bound in the enzyme’s active site; can be ordered or random - Double-displacement reactions: the first product is released before the second substrate binds; enzyme is altered by the first phase of the reaction and restored during the second phase - Enzyme Inhibition: o Inhibitors: molecules that reduce enzyme’s activity- includes drugs, antibiotics, food preservatives, and poisons o Reversible inhibition: occurs when the inhibitory effect of a compound can be counteracted by increasing substrate levels or removing the inhibitor compound while the enzyme remains intact; will be competitive if the inhibitor binds to the free enzyme and competes with the substrate for occupation of the active site; noncompetitive if the inhibitor binds to both the free enzyme and the enzyme- substrate complex o Irreversible inhibition: occurs when inhibitor binding permanently impairs the enzyme, usually though a covalent reaction that chemically modifies the enzyme - Competitive inhibitors: bind reversibly to free enzymes to form an enzyme-inhibitor (EI) complex- binds to the active site; Vmax stays constant and K inmreases - Noncompetitive inhibitors: an inhibitor can bind to both the enzyme and the enzyme-substrate complex- doesn’t bind to the active site; Vmax decreases and K stams constant - Uncompetitive inhibitors: considered a noncompetitive inhibitor; the inhibitor binds only to the enzyme substrate complex, not the free enzyme; is ineffective at low concentration - Irreversible inhibition: usually bind covalently to the enzyme - Reversible inhibition of enzymes can be competitive, noncompetitive, or uncompetitive - Competitive inhibitors reversibly compete with substrate for the same site on free enzymes - Noncompetitive inhibitors can bind to both the enzyme and the enzyme-substrate complex - Uncompetitive inhibitors bind only to the enzyme-substrate complex, not the free enzyme - Macromolecular crowding: a phenomenon that occurs when the crowded interior of cells is highly heterogeneous and filled with macromolecules, membranes, cytoskeletal components, and other obstacles that impede molecular movement 6.4: Catalysis - Organic Reactions and the Transition State: o Reaction mechanism: step-by-step description of a reaction o Intermediate: species that exists for a limited amount of time then is transformed into a product o Carbocation: contains an electron-deficient, positively charged carbon atom o Free radicals: highly reactive species with at least one unpaired electron - Catalytic mechanisms: o Most important factors that contribute to this mechanism: proximity and side effects, electrostatic effects, acid-base catalysis, covalent catalysis, and quantum tunneling o Proximity and side effects: must be close to catalytic functional group within the active site; strain helps to bring the enzyme-substrate complex into the transition state o Electrostatic effects: weak electrostatic interactions contribute to catalysis o Acid-base catalysis: hydrolysis takes place more rapidly if the pH is raised; o Covalent catalysis: nucleophilic side chain group forms an unstable covalent bond with an electrophilic group on the substrate o Quantum tunneling: when hydrogen is transferred in the form of hydrogen atoms, which is a process in which a particle passes through an energy barrier instead of over it; possible only for light particles such as electrons and hydrogen atoms because a particle’s wavelength is inversely proportional to the square root of the particle’s mass - The Roles of Amino Acids in Enzyme Catalysis: the active sites of enzymes are lined with amino acid side chains that together creates a microenvironment that is conductive to catalysis o Catalytic: residues directly participate in the catalytic mechanism o Noncatalytic: residues have support functions o Only amino acids with polar and charged side chains participate in catalysis o Require precise positioning of one or more catalytic units that are composed of either two or three amino acid side chains called diads or triads - The Role of Cofactors in Enzyme Catalysis o Metals: alkali and alkaline earth metals have structural roles, and the transition metals have key roles in catalysis;  Transition metals: they have high concentration of positive charge that is useful to bind small molecules; act as Lewis acids and are effective electrophiles; can interact with two or more ligands; have two or more valence states, they can mediate oxidation-reduction reactions by gaining or losing electrons o Coenzymes: a group of organic molecules that provide enzymes with chemical versatility because they either possess reactive groups not found on amino acid side chains or can act as carriers for substrate molecules; most are derived from vitamins  Vitamins: nutrients required in small amounts for the human diet; divided into water soluble and lipid soluble  Coenzymes can be classified based on function: electron transfer, group transfer, and high-energy transfer potential - The amino acid side chains in the active site of enzymes catalyze proton transfers and nucleophilic substitutions, other reactions require nonprotein cofactors- metal cations and the coenzymes - Metal ions are effective electrophiles, and they help orient the substrate within the active site; in addition, certain metal cations mediate redox reactions - Coenzymes are organic molecules that have a variety of functions in enzyme catalysis - Effects of Temperature and pH on Enzyme-Catalyzed Reaction: o Temperature: all chemical reactions are affect by temperature; the higher the temp, the higher the reaction rate(more collisions); reaction velocity increases; an enzyme’s optimum temperature is the temp at which it operates at maximum efficiency- determined in the lab under specified conditions of pH, ionic strength, and solute concentrations; no single optimal temp for enzymes in living organisms o pH: hydrogen ion concentration; changes in pH can affect the ionization of active site groups; becomes so alkaline that the group loses a proton and enzyme activity depresses; substrate may be affected; drastic changes in pH often lead to denaturation; the pH at which an enzyme’s activity is maximal is called the pH optimum  pH optima of enzymes varies considerably - Detailed mechanism of enzyme catalysis: o Chymotrypsin o Alcohol dehydrogenase o - Each enzyme has a unique structure, substrate specificity, and reaction mechanism - Each mechanism is affected by catalysis- promoting factors that are determined by the structure of the substrate and the enzyme’s active site 6.5: Enzyme Regulation - Regulation is essential for several reasons 1. Maintenance of an ordered state: regulation of each pathway results in the production of the substances required to maintain cell structure and function in a timely fashion and without wasting resources 2. Conservation of energy: cells ensure that they consume just enough nutrients to meet their energy requirements by constantly controlling energy-generating reactions 3. Responsiveness to environmental change: cells can make relatively rapid adjustments to changes in temperature, pH, ionic strength, and nutrient concentrations because they can increase or decrease the rates of specific reations - Control is accomplished by genetic control, covalent modifications, allosteric regulation, and compartmentation - Genetic control: o Enzyme induction: the synthesis of enzymes in response to changing metabolic needs; allows cells to respond efficiently to changes in the environment o Repression: the synthesis of certain enzymes may also be specifically inhibited - Covalent Modification: some enzymes are regulated by the reversible interconversion between their active and inactive forms; in a process controlled by hormones, the inactive form is converted to the active form by adding a phosphate group to specific serine residue; proenzymes/zymogens- enzymes are produced and stored as inactive precursors- they can be converted to active enzymes by irreversible cleavage of one or more peptide bonds - Allosteric Regulation: the binding of ligands to allosteric sites on such an enzyme (one whose catalytic activity can be increased or decreased) triggers rapid conformation changes that can increase or decrease its rate of substrate binding; if the ligand is the same as the substrate it is homotropic, if it is different it is heterotropic; o Concerted model: it accounts for positive cooperativity- the first ligand increases subsequent ligand binding; but doesn’t account for negative cooperativity- the first ligand reduces the affinity of the enzyme for similar ligands - Compartmentation: created by cellular infrastructure; it solves several interrelated problems: 1. Divide and control- physical separation allows for coordinated regulation 2. Diffusion barriers- diffusion is possibly a limiting factor for reaction rates; cells create microenvironments in which enzymes and their substrates are concentrated 3. Specialized reaction condition- certain reactions require an environment with unique properties 4. Damage control- the segregation of potentially toxic reaction products protects other cellular components - All biochemical pathways are regulated to maintain the ordered state of living cells - Regulation is accomplished by genetic control, covalent modification of enzymes, allosteric regulation, and cell compartmentation


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