CHEM 313 Chapter 2 Notes
CHEM 313 Chapter 2 Notes CHEM
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This 5 page Class Notes was uploaded by ishoemak on Sunday April 10, 2016. The Class Notes belongs to CHEM at California Polytechnic State University San Luis Obispo taught by Dr. Anya Goodman in Spring 2016. Since its upload, it has received 46 views.
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Date Created: 04/10/16
California Polytechnic State University, San Luis Obispo; CHEM 313; Goodman; Spring 2016 CHEM 313-11 Survey of Biochemistry Chapter 2 Notes Highlight = Key Term Ch. 2 Water, Weak Bonds, and the Generation of Order Out of Chaos Intro - Molecules are stable mainly due to the covalent bonds they are made up of. - Cells are stabilized by weak interactions - The sheer number of weak interactions in a cell amounts to a massive stabilizing force - Weak bonds can easily be formed and broken allowing for dynamic interactions and the movement of energy and information around the cell - It is these transient interactions that form the basis of life. - Lipid membranes and proteins fold mainly because of their noncovalent interactions with water - Molecules interact noncovalently at a distance of about 4nm (4 Å) 2.1 Thermal Motions Power Biological Interactions - The movement of particles in a gas or liquid, Brownian motion, is the result of thermal noise - The rate at which water and gas molecules move around is determined entirely by temperature - Brownian motion is responsible for the initiation of most biochemical interactions - In cells, water serves as the medium for Brownian motion 2.2 Biochemical Interactions Take Place in an Aqueous Solution - The typical cell is about 70% water - Water is a good biosolvent because of its polarity - Oxygen is electronega tive and therefore exerts a stronger pull on the electrons in its covalent bond to hydrogen - Because of this unequal pull, the electrons spend more time near oxygen than hydrogen and give oxygen a negative partial charge(δ) and give hydrogen a positive partial charge(δ) - + - The δ on the oxygen of one water molecule can interact with the δ on the hydrogen of another water molecule in what is called a hydrogen bond - This water to water interaction makes water cohesive - Water’s polarity and H bonding ability makes it a good solvent for charged and polar molecules - These hydrogen bonds are not exclusive to water molecules and are transient interactions - Transpiration is the process by which tall vascular pl ants use evaporation from leaves and the cohesive power of water to transport water throughout its body - Water cannot dissolve nonpolar or hydrophobic molecules Ian Shoemaker firstname.lastname@example.org Spring 2016 California Polytechnic State University, San Luis Obispo; CHEM 313; Goodman; Spring 2016 - In water, these molecules aggregate by the hydrophobic effect - The hydrophobic effect is what allows cellular membranes to form 2.3 Weak Interactions Are Important Biochemical Properties - There are three fundamental noncovalent bonds that play roles in the flow of energy and information in the cell : - Ionic Bonds or Electrostatic Interactions - Hydrogen Bonds - Van der Waals Interactions Electrostatic Interactions Are Between Electrical Charges - The interactions between atoms bearing complete charges - The energy of an electrostatic interaction can be calculated using Coulomb’s Law E is the energy ????????▯ ▯ k is the proportionality constant ???? = q1and 2 are the charges on the atoms ???????? r is the distance between the atoms - The polar nature of water weakens electrostatic interactions - Water molecules destroy ionic bonds by binding to the individual ions Hydrogen Bonds Form Between an Electro negative Atom and Hydrogen - Hydrogen bonds can form on any hydrogen that is covalently bonded to an electronegative atom - Oxygen and Nitrogen are the two most common electronegative atoms that contribute to H bonds - H bonds are much weaker and longer than covalent bonds - H bonds between molecules are interrupted in water because water takes their place Van de Waals Interactions Depend on Transient Asymmetry in Electrical Charge - Molecules that are neither polar nor charged can still electrostatically interact with one another through Van der Waals interactions - The distribution of electrons around an atom is not constant nor is it equal. This results in transient δ and δ around every atom. These partial charges cause corresponding partial charges in neighboring atoms . - These partial charges attra ct atoms from other molecules with opposite charges - These attractions become stronger until the the two atoms reach a distance known as the Van der Waals contact distance at which the strength of the attraction decreases - Two molecules with complementary sh apes can be held together very tightly through numerous weak Van der Waals forces Weak Bonds Permit Repeated Interactions - An important feature of these weak noncovalent interactions is that they can be broken and reformed easily - In DNA hydrogen bonds hold complementary base pairs togethe r but can be broken to facilitate replication of the double helix Ian Shoemaker email@example.com Spring 2016 California Polytechnic State University, San Luis Obispo; CHEM 313; Goodman; Spring 2016 2.4 Hydrophobic Molecules Cluster Together - The second law of thermodynamics states that the entropy of a system always increases - Entropy is a measure of randomness - When a hydrophobic molecule is introduced to a polar/charged soluti on like water a cavity forms around the hydrophobic molecule because there is no way for the two types of molecules to interact. - The waters around the hydrophobic molecule must rearrange to make as many hydrogen bonds as possible . This results in more order than in the rest of the solution - This increased order causes a decrease in entropy which is not favored - When multiple hydrophobic molecules are introduced to a polar/charged solution like water the hydrophobic molecules coalesce into one larger molecule - This does not happen because there is any attraction between the molecules t hemselves but because the surface area of the combined molecules is smaller than that of both individual molecules. - Less surface area between the water and hydro phobic molecules results in less water molecules that have to order themselves - Fewer ordered water molecules results in less order and more entropy - This whole process is called the hydrophobic effect - The interactions that result from the hydrophobic eff ect are called hydrophobic interactions Membrane Formation Is Powered by the Hydrophobic Effect - Molecules that have hydrophobic and hydrophilic areas are known as amphipathic or amphiphilic - When exposed to water these molecules will orient th emselves so that their hydrophobic parts only interact with one another while their hydrophilic parts only interact with water - This process results in membrane formation if exposed to specific conditions Protein Folding Is Powered by the Hydrophobic Effect - Proteins are capable of forming complicated three-dimensional structures that can perform multiple types of interactions with oth er molecules - The second law of thermodynamics still applies and even though the amino acid chains are folding into specific conformations, it is the increased entropy of water molecules caused by the decreased surface area due to non polar amino acid interactions that abides by this law - Hydrophobic interactions power the folding of a protein but H bonding and Van der Waals forces replace the interactions with water to allow for increased entropy Functional Groups Have Specific Chemical Properties - Functional groups are found in all biomolecules - There are eight common functional groups which impart chemical properties onto the molecules they are bound to - Every functional group can either hydrogen bond or form ionic bonds or both except for the hydrophobic groups which can only interact with other hydrophobic groups through Van der Waals interactions Ian Shoemaker firstname.lastname@example.org Spring 2016 California Polytechnic State University, San Luis Obispo; CHEM 313; Goodman; Spring 2016 2.5 pH Is an Important Parameter of Biochemical Systems - The release or binding of a hydrogen ion (H ), also called a proton, is a very important example of a reversible reaction - pH is the measure of hydrogen ion concentration in solution with values ranging from + 0-14 (low values implying high con centrations of H and an acidic solution and high values implying low concentrations of H +and a basic environment) - A fairly small change in the pH of a biological environment can be deadly because of its effect on weak bonds Water Ionizes to a Small Extent - Water dissociates into H and OH ions - The equilibrium constant of a solution (K ) equals the concentration of the dissociated ions into the numerator and the concentration of the original molecule into the denominator + - H [ OH] ????▯▯ = [H 0] 2 + - To find the pH of a solution we take the negative log of the H ion concentration pH = -log ▯▯ ] ▯ - The pH and the pOH must add up to 14 An Acid Is a Proton Donor, whereas a Base Is a Proton Acceptor - Organic acids will ionize into a proton and a base Acid ⇌ H + base - An acid is ionized into its conjugate base while a base is protonated into its conjugate acid - Strong acids dissociate completely while weak acids only disso ciate to an equilibrium point Strong Weak ▯ ▯ ▯ ▯ HA → H + A HA ⇌ H + A - The larger the K ahe stronger the acid ▯▯ [▯ ] ????▯= [▯▯] Acids Have Differing Tendencies to Ionize - The Henderson-Hasselbalch equation tells us how dissociated a weak acid is at a particular pH A▯ pH = pK + ▯og ▯▯ HA - When the ratio of weak acid to conjugate base is equal the pH will equal the pK a Buffers Resist Change in pH - Acid-base conjugate pairs resist changes in pH and are called buffers - The graph of the change in pH as base is added to a buffer solution is called a titration curve - The inflection point of the curve is called the half equivalence point and is where the pH = pK aad half of the acid has dissociated - At this point the solution can take lots of acid or base and will maintain a pH within 1 pH unit of the pK bafore its buffering abilities are depleted. Buffers Are Crucial in Biological Systems - Biological systems are very sensitive to pH and therefore use buffers frequently Ian Shoemaker email@example.com Spring 2016 California Polytechnic State University, San Luis Obispo; CHEM 313; Goodman; Spring 2016 - When CO is2produced as a byproduct of cellular respiration it reacts with water to form a weak acid called Carbonic acid ???????? ▯ ???? ????▯⇌ ???? ???????? ▯ ▯ - This weak acid quickly dissociates into a proton and the bicarbonate ion ▯ ▯ ????▯???????? ▯⇌ ???? + ???????????? ▯ - This Carbonic acid-bicarbonate conjugate pair acts as a biological buffer - This blood-pH control mechanism is called compensatory respiratory alkalosis REMEMBER: 1. Work to understand organismal and cellular processes at the molecular level 2. Use the concepts of energy, equilibrium, kinetics, and binding specificity to describe the structure and behavior of molecules 3. Molecular structure is determined by covalent bonds and weak interactions between atoms and determines the function of the molecule 4. Genes and the environment interact to determine the traits and phenotypes of an organism 5. The life processes of an organism are regulated in order to maintain homeostasis Ian Shoemaker firstname.lastname@example.org Spring 2016
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