Module 2 - very vconv PDF

Preview

Summary

very vconv...

Description

Module 2 Video 1 Molecular Interactions Water - Solvent of life - >70% of weight of most living systems - Non-covalent interactions occur between macromolecules, occur in aqueous, or water environment - Water has a higher melting point, boiling point, and heat of vaporization than most other solvents - Attractive forces between water molecules provide great internal cohesion for liquid water - Each hydrogen atom of water molecule shares an electron pair with central oxygen atom - Geometry of this molecule is in large dictated by shapes of the outer electron orbitals of the oxygen atom - Orbitals assume a rough tetrahedron with hydrogen atom at each end of the two corners and unshared electron pairs at the other 2 corners - Result of unequal electron sharing is two electric dipoles, one along each of the H-O bonds, each H baring partial positive charge, and oxygen atom baring partial negative charge equal in magnitude to sum of two partial positive charge - Result of unequal sharing of electrons in water molecule gives rise to the first of the noncovalent interactions - Electrostatic attraction between oxygen atom of one water molecule and the hydrogen atom another water molecule is called hydrogen bond Covalent vs. non-covalent interactions - Covalent: strong bond, requires a lot of energy break and therefore a very stable bond in macromolecules - Non-covalent bond: individually, a very weak bond that does not require a lot of energy to break apart Non-covalent interactions - Driving force of molecular interactions that occur within cells - Some examples: protein-protein, protein-nucleic acid, nucleic acid- nucleic acid interactions The hydrogen bond

to

-

-

-

Relatively weak, bond dissociation energy (energy required to break bond) in liquid water is 23 kJ/mol Covalent O-H bond in water sits around 470kJ/mol, covalent C-C bond sits around 348 kJ/mol Hydrogen bonds are not unique to water, form easily between electronegative atom and hydrogen atom covalently bonded to another electronegative atom in same molecule Hydrogen bond donor: atom where hydrogen atom is bonded to Hydrogen bond acceptor: atom with non-bonded electron

More electronegative the donor atom, more electron density it pulls away from hydrogen, allowing hydrogen to gain partial positive charge and becoming strongly attracted to electron pair of an acceptor Hydrogen bond is like charge-charge interaction and has electron sharing. Hydrogen bond is about 10% covalent, and 90% electrostatic Tetrahedral arrangement of orbitals around oxygen atom allows each water molecule to form hydrogen bonds with as many as 4 neighbouring water molecules Weak bond dissociation leads to being easily broken and formed Lifetime of each hydrogen bond is short lived (picoseconds) Hydrogen bonds are individually weak, but when large numbers of hydrogen bonds form, like in ice structure, it takes a lot of heat to break them apart

Electrostatic Interactions - Also called charge-charge interactions - Water readily dissolves most biomolecules which have charged or polar regions - Amphipathic compounds are said to have both hydrophilic and hydrophobic parts Coulomb’s law in a vacuum - Law of physics describing electrostatic interaction between electrically charged particles in a vacuum - States that like charges repel while opposite charges attract - Closer two charges are, the stronger the force between them will be, this is true for + and – charge but it is very weak force between two like charges as they are repelled - Coulomb’s law is quantitative, two charged objects are multiplied Coulomb’s law is an inverse square law - Larger the distance, smaller the force

Coulomb’s law in a cell - In the real cell the actual force is usually lower due to the screening effect inflicted by the crowded environment - The relative permittivity, also known as, dielectric constant epsilon - Permittivity: material property that expresses the force between two-point charges in the material - Relative permittivity is the factor by which electric field between charges is decreased relative to a vacuum - Epsilon is inversely proportional to force, higher the dielectric constant, the lower or weaker the force between two charges - Energy of interaction is the energy required to pull apart two charged particles - The resulting energy of two oppositely charged objects is always negative, signifying attraction, but energy approaches zero as distance separating two objects becomes large Non-polar compounds and water - Non-polar compounds do not dissolve in water - Interfere with hydrogen bonding of water molecules, which compensate or lost water-water hydrogen bonds by forming new solute-water interactions, non-polar compounds cannot form - Many compounds in our cells are also amphipathic, when placed in water, polar hydrophilic region interacts with water and tends to dissolve, but non-polar hydrophobic region will have none of this, does not interact with water - Non-polar regions will cluster together, and polar regions arrange, maximizing their interaction with the water solvent - The overall system achieves the greatest thermodynamic stability by minimizing number of ordered water molecules required to surround hydrophobic portions of solute molecules - This is known as the hydrophobic effect, one of the main driving forces for a lot of cellular activities, from cell membrane to driving protein folding Description of various non-covalent interactions

-

-

-

-

Many types of interactions can occur between molecules and ions Examples: o charge-charge o Charge-dipole o Dipole-dipole A molecule knows which types of interactions to make by the relative orientation of the dipole and distance Dipole interactions are shorter range interactions Dipole interactions need to be a lot closer for this interaction o occur, larger the distance, smaller energy of attraction A molecule that can be induced by a dipole moment by exposing to electric field can be polarizable Aromatic rings, like benzene, with conjugated electron systems are polarizable molecules Can create more interactions called induced dipole interactions Even if two molecules have no permanent dipole and no net charge can attract one another, but they have to be close in distance This can occur by the distribution of electronic charge, which is in a constant state of flux so it can be morphed and redistributed given the right conditions These types of interactions are individually quite weak, but collectively they play a huge role in stability of macromolecules

How close is too close? - When two uncharged atoms are brought very close together, their surrounding electron clouds influence each other, might create a transient electric dipole, inducing a transient opposite electric dipole in the nearby atom - Net result: the two dipoles, or induced dipoles. Attract one another very weakly bringing two nuclei together - These are called van der Waals interactions - Distance between these two nuclei must be perfect to allow for maximum net attraction between these two atoms before they repel one another - Can’t have two atoms overlapping to such an extent that their positive nuclei and negative electron orbitals come into close contact as they will repel one another

Video 2 Water as a solvent - Universal solvent - Solvent: a substance that dissolves a solute resulting in a solution Water - Water is amphiprotic, can act as an acid or base o Acids are proton donors, bases are proton acceptors Ionization of water - Degree of ionization of water into hydronium and hydroxide ions is very small - Keq: equilibrium constant of water which is a product of the concentration of hydrogen ion and hydroxide ion concentrations or molarities - Kw: new equilibrium constant of water, described as the ion product of water - Ion product of water is 1.0x10-14 - In pure water, concentrations of hydronium and hydroxide ions are equal and solution is at neutral pH - Therefore, in a sample of pure water, hydrogen ion concentration is 1x10-7 mol/L

-

As ion product of water is constant, when [H+] is greater than 1x10-7 mol/L, the [OH-] must be less than this number and vice versa

The pH scale “Power of

-

hydrogen” or “potential of the hydrogen ion” scale Converts all negative powers of 10 to much easier to digest numerical values Negative log of activity of hydrogen ion Kw of 1.0x10-14 is pKw of 14

pKa and pKb – the weak world - The larger the Ka, the stronger the acid, smaller the pKa - pKa + pKb = 14 The physiological pH range - blue portion indicates basic substances range from 7-14 - red portion indicates acidic substances range from 0-7 - pH affects the structure and activity of most macromolecules Weak acids and bases - strong acids and bases typically ionize fully in aqueous environments, but weak acids and bases are much more interesting, they play an important role in metabolism and regulation - reversible reaction, and each acid has its own characteristic tendency to lose its proton in aqueous solution - stronger the acid, the higher the tendency to lose its proton in an aqueous solution

Henderson Hasselbalch equation - the HH equation which describes a direct relationship between the pH of solution and ratio of concentrations of deprotonated form and protonated form of an ionizable group - can see how pH of solution changes as we add base to this solution, called a titration

Titrating a weak acid with a strong base - titration is the slow addition of one solution of a known concentration (titrant) to known volume of another solution of unknown concentration (analyte) until reaction reaches neutralization, indicated by colour change - reaction between a weak acid and a strong base involves the transfer of hydrogen ion from formic acid to hydroxide ion of the strong base to create conjugated base and water Titration curve of 1.0M formic acid with NaOH - x-axis depicts amount of Oh ions added and yaxis depicts pH of solution - titrate 1M formic acid with sodium hydroxide, pKa formic acid is 3.75 Titration curve actual data - area around pKa, addition of strong base does not seem to affect pH at all - this is principle of buffering solutions

Buffer solutions - resists change in pH

Molecules with multiple ionizing groups - glycine is an ampholyte, it has 2 pKas due to its two ionizable groups - amino group is a great proton acceptor and carbonyl group is a proton donor - if glycine is in a solution of pH 1, it will have lots of free hydrogen ions so any group that can be protonated will be protonated - glycine molecule will look like this and have net positive charge - both molecules are protonated and the net charge on glycine is +1

Video 3 Second law of thermodynamics: any spontaneous process increases the disorder or randomness of the universe - Spontaneous: not requiring outside energy from universe Entropy: measure of molecular randomness or disorder - helps make chemical reactions possible and predict useful work - a state function - can calculate change in entropy: products-reactants

Gibbs Free Energy: amount of energy in a system that is available or free to do work -

matters on entropy change (disorder) and enthalpy change (heat)

-

Large change in enthalpy can determine the direction of a free energy change even if entropy changes in opposite direction If absolute value of change in enthalpy is greater than absolute value of product of temperature and change in entropy, it is said reaction is enthalpy-driven o Means flow of thermal energy provides most of free energy in reaction

-

If absolute value of TdeltaS is greater than absolute value of enthalpy change, reaction is entropy driven, o Meaning increased disorder provides most of the reaction’s free energy

-

Tells us whether reaction is spontaneous or not

2.1 Weak interactions in aqueous systems textbook Interaction  Hydrogen bonds between water molecules provide the cohesive forces that make water a liquid at room temperature and a crystalline solid (ice) with a highly ordered arrangement of molecules at cold temperatures.



Hydrogen bonds and ionic, hydrophobic, and van der Waals interactions are individually weak, but collectively they have a very significant influence on the three-dimensional structures of proteins, nucleic acids, polysaccharides, and membrane lipids.

Hydrogen Bonding Gives Water Its Unusual Properties  The bond angle is 104.5 , slightly less than the 109.5 of a perfect tetrahedron because of crowding by the nonbonding orbitals of the oxygen atom. o



o

Extended networks of hydrogen-bonded water molecules also form bridges between solutes (proteins and nucleic acids, for example) that allow the larger molecules to interact with each other over distances of several nanometers without physically touching.





In liquid water at room temperature, water molecules are disorganized and in continuous motion, so that each molecule forms hydrogen bonds with an average of only 3.4 other molecules. In ice, each water molecule is fixed in space and forms hydrogen bonds with a full complement of four other water molecules to yield a regular lattice structure



Hydrogen bonds account for the high melting point of water, because much thermal energy is required to break sufficient hydrogen bonds to destabilize the crystal lattice of ice. When ice melts or water evaporates, heat is taken up by the system:



During melting or evaporation, the entropy increases.



At room temperature, both the melting of ice and the evaporation of water occur spontaneously; the tendency of the water molecules to associate through hydrogen bonds is outweighed by the energetic push toward randomness. Free-energy change (ΔG) must have a negative value for a process to occur spontaneously: o ΔG = ΔH − TΔS, where ΔG represents the driving force, ΔH the enthalpy change, and ΔS the change in randomness. o Because ΔH is positive for melting and evaporation, it is clearly the increase in entropy (ΔS) that makes ΔG negative and drives these changes.





Water Form Hydrogen Bonds with Polar Solutes  Hydrogen atoms covalently bonded to carbon atoms do not participate in hydrogen bonding, because carbon is only slightly more electronegative than hydrogen and thus the bond is only very weakly polar.  Hydrogen atoms participate in HB when covalently bonded to electronegative atoms (usually O or N).  The distinction explains why butane CH3(CH2)2CH3 has a boiling point of only -0.5 C, whereas butanol CH3(CH2)2CH2OH has a relatively high boiling point of 117 C. O

O



Alcohols, aldehydes, ketones, and compounds containing bonds all form hydrogen bonds with water molecules, and tend to be soluble in water.



Hydrogen bonds are strongest when the bonded molecules are oriented to maximize electrostatic interaction → hydrogen atom and the two atoms that share it are in a straight line. Arrangement puts the positive charge of hydrogen ion directly between two partial negative charges.



Water Interacts Electrostatically with Charged Solutes  Water dissolves charged and polar molecules.



Ionic interactions between dissolved ions are much stronger in less polar environments, because there is less screening of charges by the nonpolar solvent.

Nonpolar Gases are Poorly Soluble in Water  The biologically important gases CO , O , and are nonpolar molecules.  The movement of molecules from the disordered gas phase into aqueous solution constrains their motion, therefore represents a decrease in entropy - not favourable.  The nonpolar nature of these gases and the decrease in entropy make them very poorly soluble in water. 2

2



Some organisms have water-soluble “carrier proteins” (hemoglobin and myoglobin) that facilitate the transport of O . Carbon dioxide forms carbonic acid in aqueous solution and is transported as the (bicarbonate) ion, either free—bicarbonate is very soluble in water —or bound to hemoglobin. Three other gases, NH , NO, and H S, also have biological roles; polar and dissolve readily in water. 2





3

2

Nonpolar Compounds Force Energetically Unfavorable Changes in the Structure of Water  The net change in enthalpy (ΔH) for dissolving polar or charged solutes is generally small.  Hydrophobic solutes may result in a small gain of enthalpy and decrease in entropy. o The free-energy change for dissolving a nonpolar solute in water is thus unfavorable: ΔG = ΔH − TΔS, where ΔH has a positive value, ΔS has a negative value, and ΔG is positive.



Disruption of ordered water molecules is part of the driving force for binding of a polar substrate to the complementary polar surface of an enzyme: entropy increases as the enzyme displaces ordered water from the substrate and as the substrate displaces ordered water from the enzyme surface

Weak Interactions Are Crucial to Macromolecular Structure and Function  Van der Waals interactions are much weaker than covalent interactions.

 

Hydrophobic effects are also much weaker than covalent bonds, although they are substantially strengthened by a highly polar solvent. Ionic interactions and hydrogen bonds are variable in strength, depending on the polarity of the solvent and the alignment of the hydrogen-bonded atoms, but they are always significantly weaker than covalent bonds.



In aqueous solvent at 25 C o The available thermal energy can be of the same order of magnitude as the strength of these weak interactions o The interaction between solute and solvent (water) molecules is nearly as favorable as solute-solute interactions. o Consequently, hydrogen bonds and ionic, hydrophobic, and van der Waals interactions are continually forming and breaking.



For macromolecules, the most stable structure is usually that in which these weak interactions are maximized (cumulative effect of many such interactions can be very significant). o The folding of a single polypeptide or polynucleotide chain into its three-dimensional shape is determined by this principle. o The binding of an antigen to a specific antibody depends on the cumulative effects of many weak interactions. o The energy released when an enzyme binds noncovalently to its substrate is the main source of the enzyme’s catalytic power. o The binding of a hormone or a neurotransmitter to its cellular receptor protein is the result of multiple weak interactions. o One consequence of the large size of enzymes and receptors (relative to their substrates or ligands) is that their extensive surfaces provide many opportunities for weak interactions.



Water molecules are often found to be bound so tightly to hemoglobin protein that they are part of the crystal structure; the same is true for water in crystals of RNA or DNA.

o

Concentrated Solutes Produce Osmotic Pressure  Solutes of all kinds alter certain physical properties of the solvent, water: its vapor pressure, its boiling point, its melting point (freezing point), and its osmotic pressure. o These properties are called colligative properties o The effect of solute concentration on the colligative properties of water is independent of the chemical properties or mass of the solute; it depends only on the number of solute particles.





When two different aqueous solutions are separated by a semipermeable membrane (one that allows the passage of water but not solute molecules), water molecules diffusing from the region of higher water co...