Section 2 Chemical and Biologic Foundations of Biochemistry

Section 2 Chemical and Biologic Foundations of Biochemistry • Chapt. 4. Basics of Biochemistry • Student Learning Outcomes: • Describe the importance of water - solvent of life • Explain the pH of a solution, and the reason maintenance of pH, and hydration is so critical • Describe some strong acids and bases and their dissociation in water • Describe some key metabolic acids and bases • Describe typical buffers in biological systems • (much more later in Physiology)

4. Homeostasis and maintenance of body pH • Maintenance of body pH is critical: • 13-22 mol/day of acid produced • from normal metabolism • Buffers maintain neutral pH • CO2 is expired through lungs • NH4+ and ions are excreted • through kidneys Fig. 4.1

Water • Water is solvent of life: • ~ 60% of body is water • bathes cells • transports compounds in blood • separates charged molecules • dissapates heat • participates in chemical reactions Fig. 4.2 Fluid compartments in typical 70-kg man

Hydrogen bonds in water Fig. 4.4: A. H bonds B. Hydration shells around ions • Hydrogen bonds: • Dipolar nature makes H2O good solvent; unequal sharing of e- • H bonds are weak (5% of covalent) • Dynamic lattice; thermoregulation (Sweat cools) Fig. 4.3

Electrolytes • Table 4.1 Ions in Body Fluids • ECF mmol/L ICF mmol/L • Cations • Na+ 145 12 • K+ 4 150 • Anions • Cl- 105 5 • HCO3- 25 12 • inorganic phosphate 2 100 • Energy-requiring transporter (Na+/K+ ATPase) • maintains the Na+/K+ gradient

Osmolality and water movement • Water distributes between compartments • Acccording to osmolality • (concentration of dissolved molecules mOsm/kg H2O) • Cell membrane semi-permeable • H2O moves from its high conc to its low • (or from low solute -> high) • Ex. Water from blood to urine • to balance excretion of ions • Ex. Hyperglycemia: • high sugar in blood • pulls water from cells

II. Acids and bases • Review Acids and Bases: • Acids donate H+ (proton) • Bases (like OH-) accept H+ • pH = -log [H+]; acidic < pH 7; basic > pH 7 • in pure H2O, [H+] = 10-7 mol/L = pH of 7 • Kd = [H+] [OH-]/ [H2O]; but [H2O] ~ constant • Kw = [H+] [OH-] = 1 x 10-14 • increase [H+] -> decrease [OH-], & vice versa Fig. 4.5

Table 4 Acids in blood of person • Acid anion pKa source • Sulfuric (H2SO4) SO42- completely • dissociated dietary aa • Carbonic acid • (R-COOH) R-COO- 3.8 CO2 from TCA • Acetic acid • (R-COOH) R-COO- 4.76 ethanol metab • Acetoacetic acid • (R-COOH) R-COO- 3.62 fatty acid oxid ketone bodies • Ammonium ion • (NH4+) NH3 9.25 diet N-containing

Acids • Strong acids dissociate completely; • Weak acids dissociate partially – depends on pH Fig. 4.6: HA <-> A- + H+ Acid ends in -ic, Conjugate base ends in -ate Ketone bodies are weak acids

Henderson-Hasselbalch equation • Ka, equilibrium constant for dissociation of weak acid: • describes tendency of HA to donate H+ • HA <-> A- + H+ Ka = [H+] [A-] / [HA] • Higher Ka = greater tendency to donate: • acetic acid Ka = 1.74 x 10-5 • NH4+ = 5.6 x 10-10

Henderson-Hasselbalch equation • Henderson-Hasselbalch equation describes relationship between pH of a solution, Ka of acid and extent of its dissociation • pKa = negative log of Ka • For weak acid HA: pH = pKa + log [A-]/[HA] • a weak acid is 50% dissociated at pH = pKa • [HA] = [A-] • Acids with pKa of 2 are stronger than those pKa of 5: • much more is dissociated at any pH

Buffers resist changes in pH • Buffers resist changes in pH • within ~ 1 pH unit of pKa • Acetic acid: • pH = pKa = 4.76; • 50% dissociated: • [A]: [HA] = 1:1 • pH 3.76: [A-]: [HA] = 1:10 • (not much A- left to • receive more H+) Fig. 4.7

Metabolic buffers • Buffers maintain body pH in narrow ranges: • despite huge amounts of acid produced/ day • Blood: pH 7.36-7.44 • Intracellular: pH 6.9-7.4 • Beating heart: pH 6.8-7.8 • Major acid is CO2 from TCA cycle • Metabolic buffers: Bicarbonate-carbonic acid (ECF) • Hemoglobin (rbc), proteins (cells and plasma) • Phosphate in all cell types

Bicarbonate buffer • Bicarbonate is metabolic buffer; • Acidderived from CO2 produced by fuel oxidation in TCA cycle • Reacts to form H2CO3 • Weak acid, dissociates to HCO3- • Respiration rate can be adjusted to modify/ in response to pH of blood • pH blood = 6.1 + log[HCO3-]/ 0.03 PaCO2 • where HCO3- = mEq/ml; • PaCO2 partial pressure arterial blood (mm Hg) • (much more later in Physiology) Fig. 4.8

Biological buffers maintain pH • Buffering systems in body: • Bicarbonate and H+ from dissolved CO2 in rbc • H+ buffered by Hemoglobin (Hb) and PO4-2 • HCO3- in blood buffers H+ from metabolic acids • Other proteins (Pr) also buffer; e.g., albumin in blood Fig. 4.9

Urinary hydrogen, ammonium and phosphate • Nonvolatile acid is excreted in urine: • H+ is often excreted as an undissociated acid • Urine has pH 5.5 to 7 • Inorganic acids include phosphate, NH4+, • Organic acids are citric, uric • Sulfuric acid from S in proteins, other compounds • NH3 is major buffer (NH3 + H+ <-> NH4+) NH3 is toxic to neurons; NH4+ is generated in kidney

Homeostasis requires fluid balance • Fluid balance is critical for homeostasis: • Dehydration if salt and water intake < combined rates of renal and extrarenal loss • Even if fasting, urinary water dilutes solutes and ions; expired air loses water. • Hormones help monitor blood volumes, osmolarity

Key concepts • Key concepts: • Water is the basis of life – 60% of body – H bonds • Intracellular and extracellular (interstitial, blood, lymph) • Compounds dissolved in water act as acids, bases • Acids release H+, bases accept H+ • Homeostasis requires neutral pH ([H+]), proper amount of body water • Buffers resist changes of pH if H+ or OH- added: • Physiological buffers: bicarbonate, phosphate • Normal metabolism generates acids and CO2 • CO2 + water -> carbonic acid -> bicarbonate and H+

Clinical comments • Di Abetes: type I diabetes (IDDM) – autoimmune destruction of b-cells of pancreas • ketoacidosis from blood ketoacids, lowers pH • respiration increases to compensate somewhat • increase urine to dilute blood glucose; • Hyperventilate can give alkalosis in normal person;

Chapt 4. Review questions • Chapter 4 Review questions: • 2. Which of the following is a universal property of buffers? • a. buffers are composed of mixture of strong acids and strong bases • b. buffers work best at pH at which they are completely dissociated • c. buffers work best at the pH at which they are 50% dissociated • d. buffers work best at one pH unit lower than the pKa • e. buffers work equally well at all concentrations.

Chapt. 5 Major compounds of the Body • Chapt. 5 Structures of Major Compounds • Student Learning Outcomes: • Describe structures, functions of major biological compounds: • Carbohydrates have C, H, O • Lipids have fatty acids and glycerol (triglycerides) • Other lipids are phosphoacyglycerols, cholesterol • Nitrogen compounds include amino acids, purines and pyrimidines, nucleosides

Biological compounds • Organic molecules of body have C, H, O, N, S, P: • Carbon is the basis: • Can do 4 covalent bonds • Aliphatic • Aromatic • Naming for number of C, • type of linkage Fig. 5.1

Functional groups • Functional groups dictate reactivities of molecules – especially C-O, C-N, C-S bonds • (C- H and C-C less reactive); oxidation state of C important Fig. 5.2

Reduced vs. oxidized • Reduced and oxidized state of carbon: • Number of electrons around C: • In Reduction, molecule gains e- and H+; • In Oxidized state, loses H or gains O Reduced  oxidized CH4 most reduced

Acidic and amino groups Fig. 5.3 • Functional groups include: • Acidic release H+ -> -O- • Amine gain H+ -> -NH3+ • unequal sharing • polar Fig. 5.4 Fig. 5.5

Reactivities of functional groups • Carboxyl C d+ is very reactive, attracts d-: • Acid + alcohol = ester • Acid + amine = amide (like peptide bond) • Phosphate + alcohol = phosphoester, • (phosphodiester) Fig. 5.7

Carbohydrates • Carbohydrates: (C H2 O)n • Nomenclature for C • Aldehyde vs. ketone • Polar molecules • Very soluble in water • Phosphate makes • more polar, keeps in cell Fig. 5.8 Fig. 5.9 Fig. 5.6

Stereoisomers • Asymmetric Carbon: • defines D and L sugars • Stereoisomers of monosaccharides C6H12O6 Fig. 5.10, 11

Ring forms of sugars in aqueous solution • Sugars form ring structures in aqueous solution: C=O reacts with other -OH • Can convert a -> b forms • Enzymes specific for each form Fig. 5.12, 13

Substituted sugars Figs. 14, 15 • Sugars can have substitutions: • -NH2, -PO4, • Oxidized has COO- • Reduced has H, or only OH

Glycosidic bonds join sugars • Sugars join in glycosidic bonds: • N- or O-linked • a or b –OH of C1 Fig. 5.16

Polysaccharides (Cooper cell biol) Glycogen: storage in animal cells Starch: storage in plant cells Cellulose plant cell wall. glucose, β configuration. β(1→4) linkagesform-> long chains that pack to form fibers

Lipids Lipids have 3 main roles: Energy storage Major components of cell membranes Important in cell signaling: steroid hormones, messenger molecules

Fatty acids Fatty acidsare simplest lipids: long hydrocarbon chains (16 or 20 C) with (COO−) at one end. Hydrocarbon chain is hydrophobic Saturated fatty acids: no double bonds. Unsaturated fatty acids: one or more double bonds (kink structure) Fig. 5.1 Cooper Cell Biology

Fatty acids • Fatty acids are saturated (solid) or unsaturated (fluid) • Nomenclature: • Cis- (natural) vs trans- from artificial hydrogenation of polyunsat f.a. Fig. 5.17

Fats – acyglycerols • Fats = triacylglycerols = triglycerides: 3 fatty acids, glycerol • Phosphoacylglycerols = • 2 fatty acids, glycerol, PO4- Fig. 5.18 Fig. 5.19

sphingolipids • Sphingolipids = serine + 2 fatty acids • Sphingosine = serine + palmitate • Ceramide = fatty acid + sphingosine • Gangliosides = sugar + sphingolipid Sphingomyelin: component of cell membranes, myelin sheath Fig. 5.20

Steroids cholesterol • Steroids have 4 ring structure: • Not very water soluble • Cholesterol is precursor for others: • Sex hormones • Bile salt cholic acid is soluble Fig. 5.21

Amino acids • Amino acids have –NH2 -COOH • Humans only La-aa in proteins (Fig. 5.22) • (Bacteria have D-aa in cell walls) Fig. 5.22 neurotransmitter

Nitrogen bases • Nitrogen-containing ring structures • (heterocyclic rings, nitrogenous bases): • N on ring can form H bonds with other molecules • Purines: A and G • Pyrimidines: T, C and U • Pyridines: - vitamins nicotinic acid (niacin) • pyridoxine (vitamin B6) Fig. 5.23

nucleosides • Bases are linked to sugars form nucleosides. • DNA has sugar 2′-deoxyribose, RNA has ribose. • Nucleotides have one or more phosphate groups linked to 5′ carbon of sugars. Cooper Cell Biology

The Molecules of Cells Important nucleotides: adenosine 5′-triphosphate (ATP), principal form of chemical energy Some (e.g., cyclic AMP) act as signaling molecules within cells. ATP Compare dATP to ATP cAMP

Tautomers • Tautomers in N-containing rings are alternate forms, can have different properties, reactivities: • Ex. Uric acid forms Na-urate crystals in gout • Acidic urine can precipitate uric acid (kidney stone) Fig. 5.24

Key concepts • Key concepts: • Carbohydrates [sugars, (CH2O)n]; • asymmetric carbon, carbonyl, linkages of sugars • Lipids are not very water soluble (hydrophobic): • triacylglcerol, phosphoacylglycerol, cholesterol • Nitrogen-containing compounds: • amino acids, purines, pyrimidines, pyridines • nucleosides, nucleotides • Glycoproteins and proteoglycans - sugars and proteins

Clinical comments • Lotta Topaigne – gouty arthritis: • urate from breakdown of G and A, precipitates with Na+ • phagocytosed by white blood cells; inflammatory reaction • Di Abietes – diabetic detoacidosis (DKA) • measure blood glucose, ketone bodies

Figure 2.33 A protein interaction map of Drosophila melanogaster Review questions: • Diagram the structure of a phospholipid and a fat • What are the major functions of fats and phospholipids in cells? • Diagram the structure of D-glucose, ribose and dexoyribose in ring form • Diagram the structure of a disaccharide

Section 2 Chemical and Biologic Foundations of Biochemistry