1A: Acids, Bases, Buffers, Oh My!

Areas of Biochemistry: Structural & Functional: Chemical structures and 3D arrangements of molecules Bioenergetics: The flow of energy in living organisms and how it is transferred from one process to another Key Definitions: Intermolecular Forces: hold molecules together inside of the cell Dipole: separation of charge Ka: how much acid has dissociated; indicates acid's strength (ie. the larger the number, the more product that's produced, the more dissociation that has taken place, the stronger the acid) pKa: pH where 50% of the protons have come off pH: -log[H+] ; free [H+] Hypercapnia: too much CO2 in lungs Hypoventilation: too little CO2 being expelled (breathed out) HA: acid, a proton and its conjugate base H+: proton released when acid dissociates in water (also H3O) A-: the conjugate base General Notes Relationships between processes are key. Might be a good idea to go through and find relationships as we are taught more processes We won't be covering Nucleic Acid stuff Amides- Sp2 HYBRIDIZED b/c resonance Resonance limits rotation, and in this case prevents it entirely ---> makes shape important Higher bp/mp means that the forces are harder to pull apart and are thus stronger Higher bp/ lower mp means that the forces are easier to pull apart and are thus weaker

4 Major Classes of Biomolecules: Macromolecule Monomer Linkage Protein Amino acid Peptide (amide) Polysaccharide Monosaccharide Glycoside (acetal) Lipids Fatty acids Ester Nucleic Acids Nucleotide Phosphodiester Intermolecular Forces: Ion Interactions Ion- dipole: between an ion and a molecule with a dipole Hydrogen bond: (FON) Dipole-dipole/ ion-ion: between two dipolar molecules or two ions Dipole-induced dipole: the dipole of one molecule induces a dipole in a non-polar molecule Dispersion forces: in every molecule

Acids and Bases: pKa Ka Smaller pKa--> stronger acid Larger pKa--> weaker acid (stronger conj. Base) pKa= -log(ka) Large Ka--> strong acid This means the substance has been mostly dissociated into H+ and base (A-), and that there is not much HA left This occurs when numerator is large, and denominator is small Reaction will shift to side with weaker acids/bases So this means the reaction will shift to the side with the bigger pKa Buffers: Best buffers have equal concentration of acid and conj. Base If more H+ is added… Equilibrium shifts to the side the acid is on Why? Because the added H+ will react with the conj. Base and make more acid When you add acid, you'll make more acid If base is added… Equilibrium shifts to the side the base is on Why? Because the added base will react with the conj. Acid and make more base When you add base, you make more base The [H+] doesn't change very much, but the ratio does The Henderson-Hasselbalch equation explains how buffers work Add acid that will react with A- to make more HA Add base that will react with HA to make more A- Three Major Physiological Buffer Systems: Protein Buffer System: helps regulate pH in ECF and ICF; interacts extensively with other buffer systems Carbonic Acid Bicarbonate Buffer System: most important in ECF Phosphate Buffer System: buffers pH of ICF and urine The Carbonic Acid Bicarbonate : Carbonic Acid: H2CO3 Bicarbonate: HCO3- Used because you can regulate it HOW????? Carbonic Anhydride catalyzes dissociation of Carbonic Acid into H+ and HCO3- You can remove CO2 from blood (breathing) to increase pH (more basic) You can remove HCO3- from blood (vomiting, urinating) to lower the pH (more acidic) This can result in two conditions if taken too far… What happens if your body strays from its happy pH?? Acidosis Alkalosis Blood pH decreases Becomes acidic [H+] increases Too much CO2 Blood pH increases Becomes basic [H+] decreases Not enough CO2 Respiratory Acidosis: Cause: body can't get rid of CO2 Signs: low plasma pH from hypercapnia [CO2] increases, equilibrium shifts to opposite side of CO2 (side with Bicarbonate) and pH goes down (acidic) Metabolic Acidosis: Cause: production of large numbers of fixed or organic acids (lactic acidosis from anaerobic cell respiration); Ketoacidosis (excess ketone bodies from starvation, untreated diabetes); too much alcohol; excessive loss of bicarbonate ions; impaired kidney function Bicarbonate concentration drops, equilibrium shifts toward bicarbonate Respiratory Alkalosis Cause: hyperventilation Signs: elevated pH due to hypocapnia [CO2] decreases, equilibrium shifts toward side with depleted CO2, conc. of H+ decreases, pH goes up (basic) Metabolic Alkalosis: Cause: gain [HCO3-] or loss H+ Add bicarb Loss of fluids with low bicarb Loss of hydrogen Loss of 1 H = addition of 1 bicarb Bicarb concentration increases, system shifts to make more CO2, H+ conc decreases, pH rises (basic) Hemoglobin Buffer System Hemoglobin buffers CO2 and H+ CO2 diffuses across RBC membrane from tissue 20% CO2 binds directly with hemoglobin and is released into lungs 70% of CO2…. Reacts with water and forms carbonic acid Inside of the RBC, carbonic acid dissociates into bicarbonate Bicarb ions diffuse into plasma as Cl- ions diffuse from plasma into RBC H+ then can bind to hemoglobin and be released in the RBCs in lungs to combine with bicarb CO2 reformed for exhalation in lungs Buffers in Kidneys Only kidneys can get rid of metabolic acids Ie) H+ and bicarb Help us to eliminate large amounts of H+ in a normal volume Acidotic conditions: kidneys excrete H+ and retain bicarb Alkalotic conditions: kidneys retain H+ and excrete bicarb Slower process than breathing, but more powerful because it lasts longer Buffers in Urine Carbonic Acid-Bicarbonate Buffer System Phosphate Buffer System: H2PO4 (weak acid) and HPO4 (conj. Base) Ammonia Buffer System: bicarb is reabsorbed along with Na+