Chapter 1

Life: Foundations of Biochemistry

Instructor: Rashid Syed

Textbook: Biochemistry (4th Edition ) by Donald Voet Judith G. Voet

Cell: The Universal Building Block Living organisms are made of cells Simplest living organisms are single-celled Larger organisms consist of many cells with different functions Not all of the cells are the same

All cells share some common features

Three Distinct Domains of Life Defined by: Cellular and Molecular Differences

Bacterial Cell Structure

PresenterFIGURE 16 (part 1) Common structural features of bacterial cells. Because of differences in cell envelope structure, some bacteria (gram-positive bacteria) retain Grams stain (introduced by Hans Christian Gram in 1882), and others (gram-negative bacteria) do not. E. coli is gram-negative. Cyanobacteria are distinguished by their extensive internal membrane system, which is the site of photosynthetic pigments. Although the cell envelopes of archaea and gram-positive bacteria look similar under the electron microscope, the structures of the membrane lipids and the polysaccharides are distinctly different (see Fig. 1012).

Structure Composition Function

Cell wall Peptidoglycan Mechanical support Cell membrane Lipid + protein Permeability barrier Nucleoid DNA + protein Genetic information Ribosomes RNA + protein Protein synthesis Pili Protein Adhesion, conjugation Flagella Protein Motility Cytoplasm Aqueous solution Site of metabolism

Components of Bacterial Cell

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Eukaryote Cells: More Complex

Have nucleus by definition protection for DNA; site of DNA metabolism selective import and export via nuclear membrane pores some cells become anuclear (red blood cells)

Have membrane-enclosed organelles Mitochondria for energy in animals, plants, and fungi Chloroplasts for energy in plant Lysosome for digestion of un-needed molecules

Spatial separation of energy-yielding and energy- consuming reactions helps cells to maintain homeostasis and stay away from equilibrium

Bacterial, animal, and plant cells are different

PresenterFIGURE 17a Eukaryotic cell structure. Schematic illustrations of two major types of eukaryotic cell: (a) a representative animal cell, and (b) a representative plant cell. Plant cells are usually 10 to 100 m in diameterlarger than animal cells, which typically range from 5 to 30 m. Structures labeled in red are unique to either animal or plant cells. Eukaryotic microorganisms (such as protists and fungi) have structures similar to those in plant and animal cells, but many also contain specialized organelles not illustrated here.

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Bacterial, animal, and plant cells are different

PresenterFIGURE 17b Eukaryotic cell structure. Schematic illustrations of two major types of eukaryotic cell: (a) a representative animal cell, and (b) a representative plant cell. Plant cells are usually 10 to 100 m in diameterlarger than animal cells, which typically range from 5 to 30 m. Structures labeled in red are unique to either animal or plant cells. Eukaryotic microorganisms (such as protists and fungi) have structures similar to those in plant and animal cells, but many also contain specialized organelles not illustrated here.

Biochemistry: the Chemistry of Living Matter

The basis of all life is the chemical reactions that take place within the cell.

Chemistry allows for: A high degree of comlexity and organization Extraction, transformation, and systematic use of

energy to create and maintain structures and to do work

The interactions of individual components to be dynamic and coordinated.

The ability to sense and respond to changes in surrounding

A capacity for fairly precise self-replication while allowing enough change for evolution

Organisms Classification based on different energy and carbon sources

PresenterFIGURE 15 All organisms can be classified according to their source of energy (sunlight or oxidizable chemical compounds) and their source of carbon for the synthesis of cellular material.

Living systems extract energy

From sunlight plants green bacteria cyanobacteria

From fuels animals most bacteria

Energy input is needed in order to maintain life

The Molecular Logic of Life

We look at the chemistry that is behind: Accelerating reactions Organization of metabolism and signaling Storage and transfer of information

The ABCs of Life

PresenterFIGURE 1-10 The organic compounds from which most cellular materials are constructed: the ABCs of biochemistry. Shown here are (a) six of the 20 amino acids from which all proteins are built (the side chains are shaded pink); (b) the five nitrogenous bases, two five-carbon sugars, and phosphate ion from which all nucleic acids are built; (c) five components of membrane lipids; and (d) D-glucose, the simple sugar from which most carbohydrates are derived. Note that phosphate is a component of both nucleic acids and membrane lipids.

The Molecular Hierarchy of Structure

PresenterFIGURE 111 Structural hierarchy in the molecular organization of cells. The nucleus of this plant cell is an organelle containing several types of supramolecular complexes, including chromatin. Chromatin consists of two types of macromolecules, DNA and many different proteins, each made up of simple subunits.

Biological Polymers (Macromolecules)

Biochemistry: Unique Role of Carbon

PresenterFigure 1-14 Versatility of carbon bonding. Carbon can form covalent single, double, and triple bonds (all bonds in red), particularly with other carbon atoms. Triple bonds are rare in biomolecules.

30 Elements Essential for Life Other than carbon, elements H, O, N, P, S are also common Metal ions (e.g., K+, Na+, Ca++, Mg++, Zn++, Fe++) play important roles

in metabolism

PresenterFIGURE 113 Elements essential to animal life and health. Bulk elements (shaded orange) are structural components of cells and tissues and are required in the diet in gram quantities daily. For trace elements (shaded bright yellow), the requirements are much smaller: for humans, a few milligrams per day of Fe, Cu, and Zn, even less of the others. The elemental requirements for plants and microorganisms are similar to those shown here; the ways in which they acquire these elements vary.

Common Functional Groups of Biological Molecules

PresenterFigure 1-16 Some common functional groups of biomolecules. Functional groups are screened with a color typically used to represent the elelment that characterizes the group: gray for C, red for O, blue for N, yellow for S, and orange for P. In this figure and throughout the book, we use R to represent any substituent. It may be as simple as a hydrogen atom, but typically it is a carbon-containing group. When two or more substituents are shown in a molecule, we designate them R1, R2, and so forth.

Biological molecules typically have several functional groups

PresenterFIGURE 117 Several common functional groups in a single biomolecule. Acetyl-coenzyme A (often abbreviated as acetyl-CoA) is a carrier of acetyl groups in some enzymatic reactions. The functional groups are screened in the structural formula. As we will see in Chapter 2, several of these functional groups can exist in protonated or unprotonated forms, depending on the pH. In the space-filling model, N is blue, C is black, P is orange, O is red, and H is white. The yellow atom at the left is the sulfur of the critical thioester bond between the acetyl moiety and coenzyme A.

Stereoisomers: molecules with the same chemical bonds and chemical formula but different configuration (the fixed spatial arrangement of atoms) Geometric Isomers (cis vs. trans)

have different physical and chemical properties Enantiomers (mirror images)

have identical physical properties (except with regard to polarized light) and react identically with achiral reagents

Diastereomers have different physical and chemical properties

The function of molecules strongly depends on three-dimensional structure

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Cis vs. Trans

PresenterFIGURE 119a Configurations of geometric isomers. (a) Isomers such as maleic acid (maleate at pH 7) and fumaric acid (fumarate) cannot be interconverted without breaking covalent bonds, which requires the input of much more energy than the average kinetic energy of molecules at physiological temperatures.

Cis vs. Trans

PresenterFIGURE 119b Configurations of geometric isomers. (b) In the vertebrate retina, the initial event in light detection is the absorption of visible light by 11-cis-retinal. The energy of the absorbed light (about 250 kJ/mol) converts 11-cis-retinal to all-trans-retinal, triggering electrical changes in the retinal cell that lead to a nerve impulse. (Note that the hydrogen atoms are omitted from the ball-and-stick models of the retinals.)

Enantiomers and Diastereomers

PresenterFIGURE 121 Enantiomers and Diastereomers. There are four different stereoisomers of 2,3-disubstituted butane (n = 2 asymmetric carbons, hence 2n = 4 stereoisomers). Each is shown in a box as a perspective formula and a ball-and-stick model, which has been rotated to allow the reader to view all the groups. Two pairs of stereoisomers are mirror images of each other, or enantiomers. All other possible pairs are not mirror images and so are diastereomers.

Enantiomers and Diastereomers

PresenterFIGURE 124a Stereoisomers have different effects in humans. (a) Two stereoisomers of carvone: (R)-carvone (isolated from spearmint oil) has the characteristic fragrance of spearmint; (S)-carvone (from caraway seed oil) smells like caraway.

Interactions between biomolecules are specific

Macromolecules have unique binding pockets

Only certain molecules fit in well and can bind

Binding of chiral biomolecules is stereospecific

Interactions between biomolecules are specific

PresenterFIGURE 123 Complementary fit between a macromolecule and a small molecule. A glucose molecule fits into a pocket on the surface of the enzyme hexokinase (PDB ID 3B8A), and is held in this orientation by several noncovalent interactions between the protein and the sugar. This representation of the hexokinase molecule is produced with software that can calculate the shape of the outer surface of a macromolecule, defined either by the van der Waals radii of all the atoms in the molecule or by the solvent exclusion volume, the volume a water molecule cannot penetrate.

Genetic Information

Genetic information is contained in DNA. Double helical DNA molecule contains

information for its own replication and repair. This ensures genetic identity and continuity.

The complete human genome is sequenced. Need to identify the functions of each gene. Which genetic errors cause disease ? Gene expression during development. Genetic changes during evolution.

Flow of Information

Genetic information flows from DNADNARNAProteinFunction

DNA is the Blue print RNA is the Messenger (RNA also has structural and adapter roles) Protein is the Performer/Effector DNA and RNA sequences are made up of

only 4 bases each Protein sequences contain 20 amino acids.

Formation of Macromolecules

Both DNA and protein are linear polymers The sequence of amino acids in a protein is determined

by the sequence of the DNA encoding it. The linear sequence of aa in a protein leads to its folding

into a unique 3-D structure. The folded structure confers affinity for other

macromolecules or small ligands. Two or more components with high affinity for each

other self-assemble into supramolecular complexes. The overall structure of a complex is key to its function.

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Assembly of Supramolecular

Complexes

Structure-Function Relationship

Underlying principle throughout Biochemistry: Structure determines function.

The structure (sequence) and therefore, the function, of each gene is unique.

In the double helix, A-T and G-C pairing is based on chemical structure of A, T, G, and C.

In proteins, not only the sequence of amino acids, but also the 3D folding patterns and oligomeric composition affect function.

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Chapter 3

Thermodynamics Principles: A Review

Instructor: Rashid Syed

Textbook: Biochemistry (4th Edition ) by Donald Voet Judith G. Voet

Organisms perform energy transductions to accomplish work to stay alive

PresenterFIGURE 125 Some energy transformations in living organims. As metabolic energy is spent to do cellular work, the randomness of the system plus surroundings (expressed quantitatively as entropy) increases as the potential energy of complex nutrient molecules decreases. (a) Living organisms extract energy from their surroundings; (b) convert some of it into useful forms of energy to produce work; (c) return some energy to the surroundings as heat; and (d) release end-product molecules that are less well organized than the starting fuel, increasing the entropy of the universe. One effect of all these transformations is (e) increased order (decreased randomness) in the system in the form of complex macromolecules. We return to a quantitative treatment of entropy in Chapter 13.

ATP: Chemical Currency of Energy

PresenterFIGURE 126 Adenosine triphosphate (ATP) provides energy. Here, each P represents a phosphoryl group. The removal of the terminal phosphoryl group (shaded pink) of ATP, by breakage of a phosphoanhydride bond to generate adenosine diphosphate (ADP) and inorganic phosphate ion (HPO42), is highly exergonic, and this reaction is coupled to many endergonic reactions in the cell (as in the example in Fig. 126b). ATP also provides energy for many cellular processes by undergoing cleavage that releases the two terminal phosphates as inorganic pyrophosphate (H2P2O72 ), often abbreviated PPi.

How to speed reactions up Higher temperatures Stability of macromolecules is limiting Higher concentration of reactants Costly as more valuable starting material is needed Change the reaction by coupling to a fast one Universally used by living organisms Lower activation barrier by catalysis Universally used by living organisms

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Unfavorable and Favorable Reactions

Synthesis of complex molecules and many other metabolic reactions requires energy (endergonic) A reaction might be thermodynamically unfavorable (G > 0)

Creating order requires work and energy Metabolic reaction might have too high energy barrier (G > 0)

Metabolite is kinetically stable

Breakdown of some metabolites releases significant amount of energy (exergonic) Such metabolites (ATP, NADH, NADPH) can be synthesized using the

energy from sunlight and fuels Their cellular concentration is far higher than their equilibrium

concentration

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Energy Coupling

Chemical coupling of exergonic and endergonic reactions allows otherwise unfavorable reactions

The high-energy molecule (ATP) reacts directly

with the metabolite that needs activation

PresenterFIGURE 127b Energy coupling in mechanical and chemical processes. (b) In reaction 1, the formation of glucose 6-phosphate from glucose and inorganic phosphate (Pi) yields a product of higher energy than the two reactants. For this endergonic reaction, G is positive. In reaction 2, the exergonic breakdown of adenosine triphosphate (ATP) has a large, negative free-energy change (G2). The third reaction is the sum of reactions 1 and 2, and the free-energy change, G3, is the arithmetic sum of G1 and G2. Because G3 is negative, the overall reaction is exergonic and proceeds spontaneously.

Catalysis

A catalyst is a compound that increases the rate of a chemical reaction

Catalysts lower the activation free energy G Catalysts does not alter G Enzymatic catalysis offers:

acceleration under mild conditions high specificity possibility for regulation

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Enzymes lower the activation energy to increase the reaction rate

PresenterFIGURE 1-28 Energy changes during a chemical reaction. An activation barrier, representing the transition state (see Chapter 6), must be overcome in the conversion of reactants (A) into products (B), even though the products are more stable than the reactants, as indicated by a large, negative free-energy change (G). The energy required to overcome the activation barrier is the activation energy (G). Enzymes catalyze reactions by lowering the activation barrier. They bind the transition-state intermediates tightly, and the binding energy of this interaction effectively reduces the activation energy from G uncat (blue curve) to G cat (red curve). (Note that activation energy is not related to free-energy change, G.)

Metabolic Pathway produces energy or valuable materials

Signal Transduction Pathway

transmits information

Series of related enzymatically catalyzed reactions forms a pathway

Example of a negative regulation: Product of enzyme 5 inhibits enzyme 1

Pathways are controlled in order to regulate levels of metabolites

Chapter 2

Aqueous Solutions

Instructor: Rashid Syed

Textbook: Biochemistry (4th Edition ) by Donald Voet Judith G. Voet

Water, pH, and Buffers

Structure of water Hydrogen bond Interactions of water with biomolecules Weak acids and bases Buffers pH and pKa: The Henderson-Hasselbalch

equation

Water Most biochemical reactions occur in an aqueous

environment. There is a significant difference in electronegativity

between H (2.1) and O (3.5). There is a partial positive charge (+) on H and partial negative charge (-) on O.

The presence of two lone pairs of electrons on O leads to a bond angle of 104.5o instead of 109.5o .

Because of its bent shape, and the partial charges on H and O, water is a highly polar molecule.

Water is highly cohesive because of inter-molecular hydrogen bonding. This results in its higher MP, BP and heat of vaporization than other common solvents.

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Structure and H-bonding of Water Molecules

PresenterFIGURE 2-1a Structure of the water molecule. (a) The dipolar nature of the H2O molecule is shown in a ball-and-stick model; the dashed lines represent the nonbonding orbitals. There is a nearly tetrahedral arrangement of the outer-shell electron pairs around the oxygen atom; the two hydrogen atoms have localized partial positive charges (+) and the oxygen atom has a partial negative charge (). FIGURE 2-1b Structure of the water molecule. (b) Two H2O molecules joined by a hydrogen bond (designated here, and throughout this book, by three blue lines) between the oxygen atom of the upper molecule and a hydrogen atom of the lower one. Hydrogen bonds are longer and weaker than covalent OH bonds.

Hydrogen Bond

The attractive force between a partially negatively charged electronegative atom and a partially positively charged H atom is called a Hydrogen Bond.

H-bonds are considerably weaker than covalent bonds. Bond energy for covalent HO bond = 420 kJ/mol Bond energy for H-bond = 20 kJ /mol Non-covalent bonds such as H-bonds, van der waals

interactions and hydrophobic interactions are individually weak, but collectively they greatly stabilize the conformation of biomolecules.

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PresenterFIGURE 2-3 Common hydrogen bonds in biological systems. The hydrogen acceptor is usually oxygen or nitrogen; the hydrogen donor is another electronegative atom.

Biologically Important H-Bonds

PresenterFIGURE 2-4 Some biologically important hydrogen bonds.

PresenterFIGURE 2-5 Directionality of the hydrogen bond. The attraction between the partial electric charges (see Figure 2-1) is greatest when the three atoms involved in the bond (in this case O, H, and O) lie in a straight line. When the hydrogen-bonded moieties are structurally constrained (when they are parts of a single protein molecule, for example), this ideal geometry may not be possible and the resulting hydrogen bond is weaker.

Interactions of water with Biomolecules

Biomolecules may be polar, non-polar or amphipathic. Water is a polar solvent; it dissolves most polar or

charged compounds (including high molecular weight proteins and DNA/RNA) by hydration.

Hydration involves formation of H-bonds between water and charged ions or polar groups of solutes, thus neutralizing electrostatic interactions amongst solute molecules.

Hydrophobic molecules align surrounding water molecules into highly ordered H-bonded cages.

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Water Dissolves Polar Solutes by Hydration

PresenterFIGURE 2-6 Water as solvent. Water dissolves many crystalline salts by hydrating their component ions. The NaCl crystal lattice is disrupted as water molecules cluster about the C and Na+ ions. The ionic charges are partially neutralized, and the electrostatic attractions necessary for lattice formation are weakened.

Physics of Noncovalent Interactions

Ionic (Coulombic) Interactions Electrostatic interactions between permanently charged species,

or between the ion and a permanent dipole Dipole Interactions

Electrostatic interactions between uncharged, but polar molecules

van der Waals Interactions Weak interactions between all atoms, regardless of polarity Attractive (dispersion) and repulsive (steric) component

Hydrophobic Effect Complex phenomenon associated with the ordering of water

molecules around nonpolar substances

Noncovalent interactions do not involve sharing a pair of electrons. Based on their physical origin, one can distinguish between:

Examples of Noncovalent Interactions

Non-polar regions cluster together Exposure of hydrophobic region is minimized

Hydrophobic Interactions

Ionization of Water

Weak ionization of water: H2O H+ + OH- Free protons do not exist in solution; they get hydrated H2O + H2O H3O+ and OH- The equilibrium constant for the dissociation of water

Keq = [H+] [OH-] / [H2O] Keq [H2O] = [H+][OH-] The concentration of water is constant at 55.5 M Keq[H2O] is a constant referred to as Kw = [H+][OH-] Keq = 1.8 x 10-16 M by electrical conductivity measurements Kw = 1 x 10-14 M2 = [H+][OH-]

Acids and Bases, pH

For pure water [H+] = [OH-] = 10-7 M The ion ratios change in the presence of an acid or base. An acid is defined as a proton donor AH = A- + H+ AH is the acid and A- is its conjugate base. Base is defined as a proton acceptor B + H2O = BH+ + OH- B is the base and BH+ is its conjugate acid pH = -log [H+] pOH = -log [OH-] ([H+] and [OH-] in M) [H+] x [OH-] = 1 x 10-14 M2. Therefore, pH + pOH = 14

The pH scale An acidic solution is one in which [H+] > [OH-]

In an acidic solution: [H+] > 10-7, pH < 7.

A basic solution is when [OH-] > [H+].

In a basic solution: [OH-] > 10-7, pOH < 7, and pH >7.

When the pH = 7, the solution is neutral.

Physiological pH range is 6.5 to 8.0

pH scale is logarithmic: 1 unit = 10-fold

Weak Acids and pKa The strength of an acid is determined by its dissociation

constant, Ka. Dissociation of an acid: HA = H+ + A- the dissociation constant Ka = [H+][A-] / [HA] Acids that do not dissociate significantly in water are weak

acids. When Ka < 1, [HA] > [H+][A-] and HA is not significantly

dissociated. Thus, HA is a weak acid when Ka < 1. The lesser the value of Ka, the weaker the acid. The value of Ka is represented by pKa: pKa = -log Ka. The larger the pKa, the weaker the acid. pKa is a constant for each conjugate acid and its conjugate base

pair. Most biological compounds are weak acids or weak bases.

pKa Values of Conjugate Acid-Base Pairs

Polyprotic Acids

Some acids are polyprotic acids; they can lose more than one protons.

In this case, the conjugate base is also a weak acid. For example: Carbonic acid (H2CO3) can lose two

protons sequentially. Each dissociation has a unique Ka and pKa value. Ka1 = [H+][HCO3-] / [H2CO3] Ka2 = [H+][CO3-2] / [HCO3-] Note: (The difference between a weak acid and its

conjugate base is one hydrogen)

Weak Acids and their Conjugate Bases

Titration of a weak acid with a strong base

Normally, a weak acid is mostly in its conjugate acid form

When strong base is added, it removes protons from the solution (acid is neutralized), Equilibrium shifts to the right and acid is converted to its conjugate base. The pH increases.

The pH can be determined by using a pH meter or indicator dye.

A titration curve of pH vs moles of OH-/moles of initial HA is drawn.

When x-axis value is 0.5, the amount of OH- added is exactly half of the initial acid. The weak acid and its conjugate base are in equal amounts.

At this point the pH = pKa. (pKa is the pH at which [WA]=[CB])

If more base is added, the conjugate base form predominates till the equivalance point when all acid is in conjugate base form.

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Titration Curve for Acetic Acid

Buffers Definition: A buffer is a solution that resists a significant

change in pH upon addition of an acid or a base. Chemically: A buffer is a mixture of a weak acid and its

conjugate base Example: Bicarbonate buffer is a mixture of carbonic acid

(the weak acid) and the bicarbonate ion (the conjugate base): H2CO3 + HCO3-

All OH- or H+ ions added to a buffer are consumed and the overall [H+] or pH is not altered

H2CO3 + HCO3- + H+ 2H2CO3 H2CO3 + HCO3- + OH- 2HCO3- + H2O For any weak acid / conjugate base pair, the buffering

range is when pH = pKa +1.

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Mechanism by which Buffers Operate

Example: CH3COOH + CH3COO- + OH- = 2CH3COO- + H2O (you get more conjugate base)

CH3COOH + CH3COO- + H+ = 2CH3COOH (you get more weak acid)

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Antacids

Alka-seltzer contains NaHCO3 which is a salt of HCO3- a conjugate base of H2CO3

TUMS: contains CaCO3, which is a salt of CO3-2, the conjugate base of HCO3-.

Antacids neutralize excess H+ by forming the weak acid. The weak acid remains mostly undissociated.

The conjugate base (antacid) and the weak acid formed together form a buffer and resist change in pH.

Buffering range for weak acids

Initially, [WA] >>> [CB]

When [WA]=[CB], pH=pKa

The central region of the curve (pH+1) is quite flat because:

When [CB]/[WA] = 10, pH = pKa +1;

When [CB]/[WA] = 0.1, pH = pKa - 1

Titration curve is reversible, if we start adding acid, [WA] increases

The Henderson-Hasselbalch equation

Dissociation of a weak acid is mathematically described by the Henderson-Hasselbalch equation

Ka = [H+][A-] / [HA] or Ka = [H+] x [A-] / [HA] logKa = log[H+] + log {[A-] / [HA]} -log[H+] = -logKa + log {[A-] / [HA]} pH = pKa + log {[A-] / [HA]} So, if CB = conjugate base and WA = weak acid, then: pH = pKa + log {[CB] / [WA]} This is the Henderson-Hasselbalch equation Note: pH = pKa when [CB] = [WA] When pH > pKa, [CB] > [WA]

Biological Buffers

Biological systems use buffers to maintain pH in the physiologic range.

Intracellular buffers: proteins, biomolecules with ionizable functional groups, phosphate.

Extracellular buffers: bicarbonate, phosphate H2PO4- HPO4-2 + H+ pKa = 6.86 H2CO3 HCO3- + H+ pKa = 6.37 H2CO3 is CO2 dissolved in H2O; the amount of CO2

dissolved depends on the partial pressure of CO2. The equilibrium of each of these reactions is shifted to

maintain the plasma pH at ~ 7.4

The Bicarbonate Buffer System

Slide Number 1Cell: The Universal Building Block Three Distinct Domains of Life Defined by: Cellular and Molecular DifferencesSlide Number 4Components of Bacterial CellSlide Number 6Eukaryote Cells: More ComplexSlide Number 8Slide Number 9Slide Number 10Biochemistry: the Chemistry of Living MatterOrganisms Classification based on different energy and carbon sourcesLiving systems extract energyThe Molecular Logic of LifeSlide Number 15Slide Number 16Slide Number 17Slide Number 18Biochemistry: Unique Role of CarbonSlide Number 20Common Functional Groups of Biological MoleculesBiological molecules typically have several functional groupsSlide Number 23Slide Number 24Slide Number 25Slide Number 26Slide Number 27Interactions between biomolecules are specificSlide Number 29Genetic InformationFlow of InformationFormation of MacromoleculesSlide Number 33Structure-Function RelationshipSlide Number 35Slide Number 36Slide Number 37Slide Number 38Slide Number 39Slide Number 40Slide Number 41Slide Number 42Slide Number 43How to speed reactions upUnfavorable and Favorable ReactionsEnergy CouplingSlide Number 47CatalysisSlide Number 49Series of related enzymatically catalyzed reactions forms a pathwayPathways are controlled in order to regulate levels of metabolitesSlide Number 52Water, pH, and BuffersWaterSlide Number 55Slide Number 56Hydrogen BondSlide Number 58Slide Number 59Slide Number 60Interactions of water with BiomoleculesSlide Number 62Slide Number 63Physics of Noncovalent InteractionsExamples of Noncovalent InteractionsSlide Number 66Ionization of WaterAcids and Bases, pHSlide Number 69Slide Number 70Weak Acids and pKaSlide Number 72Polyprotic AcidsSlide Number 74Titration of a weak acid with a strong baseSlide Number 76Buffers Slide Number 78AntacidsSlide Number 80The Henderson-Hasselbalch equation Biological BuffersSlide Number 83