Lecture 1: Review of biomolecules, thermodynamics, water and acid base (Biochemistry)
What is the pH of a solution of .01M HCL? .01M NaOH?
0.01M H⁺ and .01M OH⁻ because HCL and NaOH fully dissociate pH = -log (.01) = 2 pOH = -log(.01) = 2. 14-2 = pH = 12
Biological Importance of Buffers
1. Buffers resist change in pH 2. Buffers require weak acid systems 3. at pH = pKa there is 50:50 mixture of the acid and conjugate base of the compound
Common Features of Life
1. Cells: the basic structural and functional units of life 2. Macromolecules (proteins/DNA) and metabolites (glucose) are common to all living things, with minor variations 3. Key metabolic processes are common to many living organisms (glycolysis)
How is energy extracted and consumed in Living Cells?
1. From Sunlight - Plants - Green bacteria - Cyanobacteria 2. From fuels - Animals - Most bacteria
What are some characteristics of living organisms?
1. High degree of complexity 2. Extraction, transformation, and systematic use of energy to create and maintain structures and to do work 3. Ability to sense and respond to changes in surrounding 4. A capacity for fairly precise self-replication while allowing enough change for evolution
Two Types of Interactions in Biochemistry:
1. Intramolecular Interactions - Covalent Bonds - Ionic Bonds 2. Intermolecular Interactions (non-covalent "weak" forces) (strength in numbers) - Hydrogen Bonds - Ionic Interactions - Hydrophobic Interactions - Van der Waals Interactions
The Importance of Hydrogen Bonding
1. Source of unique properties of water. - H bonds allow for lattice structure of ice which causes the difference in density between ice and water which was critical for evolution of life on earth. 2. Structure and function of proteins - Folding (structure begets function) 3. Structure and function of DNA - Strong enough to hold together but can separate to copy 4. Structure and function of polysaccharides 5. Binding of substrates to enzymes 6. Binding of hormones to receptors
Why Carbon for life?
1. Tetravalence: Carbon can make 4 bonds - allows it to have bonding versatility 2. Catenation: ability of carbon to bond to itself - forming long chains Carbon counts for half of the dry weight of cells. No other element can form such diverse shapes and sizes
pH 2 units less than pKa then..
10² = 100 times as much acid form as CB form
pH 2 units greater than pKa then..
10² = 100 times more CB form than Acid form
How many more protons in stomach (pH=2) compared to pH of Saliva (6)
10⁴ (6-2 = 4 then 10 to that)
How much more acidic is 3 to 7?
10⁴ = 10,000 fold more acidic
What are we seeing in a Titration Curve
A graph of pH vs volume of titrant added. As we add OH to solution (base) it interacts with H+ to make water, taking away H+. - This messes with the equilibrium, so re-established by more acid dissociating. - Acid slowly decreases in concentration 1. Beginning = All Acid 2. pH = Pka. Equal amounts of Acid/ CB 3. End of Titration is when all acid is gone Horizontally flat area is a buffer region.
ATP is the Energy Currency of a Cell
ATP is the best energy coupler we have in our cells. It makes unfavorable processes happen.
Acids / Bases
Acids: Proton Donors Bases: Proton Acceptors Strong Acids and Bases: completely ionize in dilute aqueous solutions Weak Acids and Bases: not completely ionized when dissolved in water (acetic acid) Weak acids and bases are ubiquitous in biological systems. Strong acids are rarely found in biological systems. - Strong acids not present in cellular system because it would have neg. affects on system.
99% of us is made up of:
Amino Acids Nucleic Acids Lipids
Using what you know about thermodynamics, and the equation for delta G, explain why water and ice are in equilibrium at 0 degrees Celsius.
At equilibrium ∆G = 0 ∆G = ∆H - T∆S ∆H must have to = T∆S for ∆G = 0. 1. Going from liquid to solid, disorder is going to decrease. ∆S is going to be negative. 2. ∆H is going to be negative going from liquid to solid. (give off energy to get more stable) Kelvin matters, Lower temp causes ∆S to equal H When ∆H and ∆S are both negative. Temperature is the deciding factor. Temperature very high less likely to be in solid form, and ∆G is going to be more positive.
F= Q1Q2 / εr2
Attractive Force between two charged ions. ε = depends on polarity of solvent The more polar the larger, so force decreases the more polar. - add NaCl in water, very polar, F decreases dramatically
Elements of life
Carbon, Hydrogen, Nitrogen, Oxygen Phosphorus, Sulfur, Chlorine, Sodium, Potassium, Calcium 12 Trace Elements (including iodine important in thyroid hormones)
First Law of Thermodynamics***
Energy can be transferred and transformed, but it cannot be created or destroyed. Living organisms are simply transducers of energy
Energy Coupling
Energy released by one reaction (exogonic) will be absorbed by another (endogonic) Example: Glucose + pi → Glucose-6-phosphate (G=13kj/mol) - Every cell does this all the time, how does it do this? Energy Coupling I t is coupled with exergonic reaction ATP → ADP + Pi (-30kj/mol) ∆G = ∆G1 + ∆G2 -17= 13 + -30 Glucose + ATP → glucose 6-phosphate + ADP (spontaneous)
Hydrophobic Interactions Promote Receptor-Ligand Binding
Enzymes often have hydrophobic active sites and the substrate is also hydrophobic. Hydrophobic things like to cluster together (have an affinity for each other) in water environments
Series of Enzymatically Catalyzed Reactions.. (2 Main Types)
Form an Enzymatic Pathway. Two main types: 1. Metabolic Pathway: Consumes or Produces energy or useful biomolecules. - Glycolysis, TCH cycle 2. Signal Transduction Pathway: Transmits Information - kinase cascade
Which acid will be more dissociated at pH = 5 Formic Acid pKa = 3.75 Acetic Acid pKa = 4.76
Formic Acid pH = pka 50/50 pH < pKa = more acid pH > pKa = more dissociation 5 > 3.75
Gibbs Free Energy
Free energy change: ∆G = ∆H - T∆S ∆H is negative for a reaction that releases heat ∆S is positive for a reaction that increases randomness -∆G Exergonic: Process occurs spontaneously (favorable) ∆G Endergonic: Process is non-spontaneous (unfavorable) What does it mean if ∆G=0?
Explain why ethanol (CH3CH2OH) is more soluble in water than is ethane (CH3CH3).
Hydrogen bonds on the O-H in ethanol create polarity from a dipole moment being created allowing water to pull it apart from its partial poles created by its O-H bond. Ethane has no dipole moment and is not charged or polar
Hydrophilicity vs. Hydrophobicity
Hydrophilic (Water Loving): Water is a good solvent for charged and polar substances - Amino Acids and Peptides - Small Alcohols - Carbohydrates Hydrophobic (Water Fearing): Water is a poor solvent for non-polar substances - Nonpolar gases - Aromatic Groups - Aliphatic Chains Amphipathic Compounds contain regions that are polar and regions that are non polar - Phospholipids - Bile Salts
So why given the second law of thermodynamics do we have ordered molecules?
In order to overcome the tendency of the universe towards increasing disorder, you must supply free energy.
Ionic Interactions in proteins
Intermolecular Ionic Interactions (not bond) Stabilize the structure of proteins - Structure begets function, so this is very important Would these interactions be stronger in hydrophilic or hydrophobic pocket of protein? - Hydrophobic because in Polar solvent. We generally find ionic interactions happening in hydrophobic pockets of proteins.
What is stronger a covalent bond or an ionic bond?
It depends specifically if you are in water or not. Most bonds between Carbon-Carbon are weaker than NaCl, but in water NaCl becomes super week. In life we are dealing with an aqueous solution of ourselves ionic bonds are much weaker than covalent, but outside this is opposite.
The delta G under standard conditions for the above reaction is -30.5KJ/mole. Is this reaction spontaneous under standard conditions?
It is Spontaneous because ∆G is negative.
Smaller Pka means
Larger Ka, Stronger Acid Ka = dissociation products / acid reactant More dissociation, more products, less acid left
pH = pKa + log([A-]/[HA]). What do ratio of A to HA tell us?
Log (fraction) = negative number so pH will be smaller than pKa meaning more acid Log (whole) = positive number so pH will be greater than pKa meaning more dissociation.
If a cell needs more products (but in general unfavorable process G): X - Y
More products needed, so cell may keep the concentration of reactants very high ∆G = ∆G₀ + RTln [products]/[reactants] ln (fraction less than 1) = negative number
Lower the pH the ___ H+
More.
Can Enzymes affect ∆G?
No!, but they can change the Activation Energy and therefore the rate of reaction. They do not affect free energy.
Polar vs. Non Polar Bonds
Polar Bonds: Charged or Hydrogen bonds possible Hydrophilic Non-Polar Bonds: No Hydrogen Bonds, Hydrophobic
What does it mean if ∆G=0?
Rxn is at Equilibrium Gibbs free energy is a measure of how much "potential" a reaction has left to do a net "something." So if the free energy is zero, then the reaction is at equilibrium, an no more work can be done.
Single Most Important Concept in this class:
Small Structural changes can create enormous functional change
Does ∆G tell us about the rate of reaction?
Spontaneity of a Reaction DOES NOT tell us anything about its Rate. Activation Barrier (Rate determining Step) Determine the rate of reaction, not the ∆G.
Directionality of Hydrogen Bonds
Stronger hydrogen bonds have O-H-O lined up directly Important in regards to protein folding
If the ATP-binding site of an enzyme is buried in the interior of the enzyme, in a hydrophobic environment, is the ionic interaction between enzyme and substrate stronger or weaker than that same interaction would be on the surface of the enzyme, exposed to water? Why?
Stronger, because the more polar the solvent the weaker the ionic interaction due to: F= Q₁Q₂ / Er² E is greater for more polar substances making the attractive force between them weaker. - In a hydrophobic environment the Force would be greater so the interaction would be stronger.
Second law of Thermodynamics***
The tendency in nature towards increasing disorder - The total entropy (∆S) of the universe is continually increasing
Self-ionization of water
Water has a slight tendency to Ionize: 2 water molecules produce a hydronium ion and a hydroxide ion by transfer of a proton Concentration of [H+] and [OH-] = 1*10⁻¹⁴ [H+] = 10⁻⁷ = [OH-] pH = 7 = pOH In Pure Water
The interactions between biomolecules are often stabilized by weak interactions such as hydrogen bonds. How might this be an advantage to the organism?
Weak interactions are advantageous because they allow for biomolecules to come off/on whenever the cell needs them to.
Hydrophobic Interactions and the Lipid Bilayer
What conformation is more thermodynamically favorable? Tendency to cluster together because hydrophobic like each other more than water. This is what forms the bilayer of the cell membrane How does this organization not violate the principle of entropy? - together they are actually more disordered. (lipids are more ordered, but water is now less ordered because before ordered water was around each lipid)
pH is higher than the pKa
You would expect to have more CB form. A lot of OH taking H out of solution, so reaction being pushed to right.
pH is lower than pKa
You would expect to have more of the Acid form. Not a lot of OH taking H out of solution, so reaction not being pushed to the right.
Ka / pKa
[HA] ⇌ [H+] + [A-] Acid Dissociation Constant: Each acid has a characteristic tendency to lose its proton in aqueous solution Ka = [H⁺][A⁻]/[HA] (equilibrium dissociation point for strength of acid) - Tells us how strong acid is. High Ka = strong acid, Low Ka = weak acid
Ln of a fraction is..
a negative number
Calculate the pH of a solution prepared by diluting 3.0 mL of 2.5M HCl to a final volume of 100 mL with H2O.
fully dissociates so you know 2.5 (mols/ 1 L) x .003L = .0075 mols / .1 L = 0.75M pH = - log (.75M) = 1.12
pH of Water
pH = 7 = [H] = 10⁻⁷ pOH = 7 = [OH] = 10⁻⁷ In Pure Water
Buffer Region
pH = pKa = (50/50) or equal amounts of [Weak acid] and its [Conjugate Base] The region of a titration curve in which the concentration of a conjugate acid is approximately equal to that of the corresponding base. The pH remains relatively constant when small amounts of H+ or OH- are added because of the combination of these ions with the buffer species already in solution.
Characteristics of pKa's of Monoprotic, Diprotic, and Triprotic Acids
pKa of an ionizable group. Acetic acid can only lose one proton so one pKa Some amino acids can lose more than one proton so they have multiple pKa's Diprotic = 2 H's Triprotic = 3 H's
Larger pKa means
smaller Ka, weaker acid Ka = dissociation products / acid reactant Less dissociation, more of the acid left
Suppose we have a reaction that is very endergonic under standard conditions. Under what circumstances would that reaction become spontaneous?
∆G = ∆G₀ + RT ln ([products]/[reactants]) It could increase reactants or decrease products, which makes the ln (smaller), making that = larger neg. number So it needs to push the reaction to the left. - It does this by getting rid of products very quickly making concentration very low. It also could import reactants quickly.
In living cells it is experimentally determined that the [ATP] = 2.25mM, [ADP]= 0.25mM , and [Pi]= 1.65mM Is this reaction spontaneous in living cells? What is the change in free energy between standard conditions and what is found in living cells.
∆G = ∆G₀ + RT ln([products]/[reactants] ∆G = ∆G₀ + (8.3)(Body Temp) * ln (0.25x1.65)/(2.25)
∆G = ∆G₀ + RTln [products]/[reactants]
∆G = ∆G₀ + RTln [products]/[reactants] The cell can control the spontaneity of any reaction by controlling the concentration of products and reactions ∆G₀ = standard conditions (cell cannot control this) Cell CAN control the concentration of products and reactants for any reaction.
∆G Products / Reactants
∆G represents the difference in Free Energy between the products and reactants. ∆G = Gproducts - Greactants If G of products is less than G reactants then spontaneous Exergonic: ∆G < 0, Rxn is spontaneous G (reactants) > G (products) Endergonic: ∆G > 0, Rxn is not spontaneous G (products) > G (reactants)