chapter 2 physical chemistry

bioenergetics

energy conversion processes in biological systems, including transformation of solar energy into chemical energy and interconversion of chemical energy through oxidation and reduction of organic molecules

chemical energy is used by organisms to

perform work, which is necessary for cells to survive

three types of work in living systems

• osmotic work (maintaining differential solute concentrations across biological membranes)

• chemical work (biosynthesis and degradation of organic molecules)

• mechanical work (protein conformational changes required for muscle)

homeostasis

the use of energy to maintain a dynamic steady state of an organism that can adjust to changing environmental conditions

living organisms maintain homeostasis to avoid

equilibrium with their environment

for living organisms, equilibrium with the environment means

death of the organism

solar energy provides all the energy required for

photosynthetic autotrophs and heterotrophs to inhabit earth

photosynthetic autotrophs use

solar energy to oxidize water and produce oxygen which generates chemical energy in the form of glucose

aerobic respiration

a set of metabolic processes that uses oxygen and glucose to generate ATP

heterotrophs

an organism that cannot directly convert solar energy to chemical energy but must depend on nutrients obtained from autotrophs and other heterotrophs as a source of energy

carbon fixation

the conversion of carbon dioxide to organic compounds

photosynthesis and aerobic respiration interconvert energy using a series of

linked oxidation-reduction reactions (redox reactions)

redox reactions transfer

electrons from one compound to another in sequential fashion

chemical work can be preformed using the energy made available by

electron transfer

oxidation

loss of electrons (increase in number of bonds to oxygen, decrease in number of bonds to hydrogen)

reduction

gain of electrons (increase in number bonds to hydrogen, decrease in number of bonds to oxygen)

biological processes and physical processes follow the same

universal laws and thermodynamic principles

system

a collection of matter in a defined space

surroundings

everything but the system

open system

matter and energy are freely exchanged with the surroundings

closed system

energy is exchanged with the surroundings but matter is not

isolated system

neither matter nor energy is exchanged with the surroundings

biological systems are

open systems

the first law of thermodynamics

energy can neither be created nor destroyed, only transformed

the second law of thermodynamics

in the absence of an energy input, entropy of the universe is always increasing

all biological energy conversion processes are less than 100% efficient because

some of the converted energy is lost as heat rather than used for work

energy change in a system is equal to

the difference between the final and initial energy states

under biological conditions

pressure and volume do not change and no work is done, so the change in enthalpy is a function of the change in energy which is a measure of heat

exothermic reactions

• release energy (heat) to the surroundings

• has a negative change in enthalpy

endothermic reactions

• system absorbs energy (heat)

• has a positive change in enthalpy

the change in entropy is a measure of

the spreading of energy

entropy increases when there is more

dispersal of energy in a system

the entropy of the universe is always

increasing and is equal to the entropy of the system plus the entropy of its surroundings

gibbs free energy

measures the spontaneity of a reaction and is the difference between the enthalpy and the entropy of a system at a given temperature

at equilibrium gibbs free energy is

zero (bc Keq is 1)

exergonic reaction

• gibbs free energy is less than zero

• reaction is overall favorable and spontaneous

endergonic reaction

• gibbs free energy is greater than zero

• reaction is overall unfavorable and nonspontaneous

the standard gibbs free energy is directly related to the equilibrium constant through the equation

Keq

• Keq < 1 = the reactants are favored

• Keq > 1 = the products are favored

• Keq = 1 = equilibrium

the standard gibbs free energy change is used to

compare chemical reactions under a defined set of conditions (1 atm, 298 K, 1 M)

biochemical standard free energy change

the amount of energy needed to go from the biochemical standard condition (standard conditions and pH =7, concentration of water = 55.5 M, Mg2+ = 1 mM) where all reactants and products are present initially at 1 M, to the condition at which all reactants and products have reached equilibrium concentrations

when reactants and products are not at 1 M initial concentrations we use the

reaction quotient

exergonic and endergonic reactions are

coupled in metabolism (catabolic and anabolic)

ATP hydrolysis is a common in a

coupling reaction to make an overall reaction favorable

the overall free energy of a coupled reaction must be?

negative

ATP contains two

phosphoanhydride bonds

glutamine synthesis

• first step: γ-phosphoryl group of ATP is transferred to glutamate forming a glutamyl phosphate intermediate and ADP is released

• second step: ammonium reacts with glutamyl phosphate to generate glutamine and the release of inorganic phosphate

ATP will always try to break it’s phosphoanhydride bonds because

• there is electrostatic repulsion between the charged phosphoryl groups which destabilizes ATP; the repulsion is reduced when ATP is hydrolyzed

• the released phosphate ion has more resonance structures (it is entropically favored) than when bonded to adenylate

• the phosphate ion and ADP have a greater degree of solvation than ATP (they form hydration layers and are more stable than ATP)

adenylate system

a group of several phosphoryl transfer reactions that interconvert ATP, ADP, and AMP

the adenylate system manages

short term energy needs

energy charge (EC)

a measure of the energy state of a cell in terms of ATP, ADP, and AMP ratios

most cells have an EC value in the range of

0.7-0.9

a cell maintains the desired EC range by

regulating metabolic flux via pathways that generate and consume ATP

EC related to the values of ATP, ADP, and AMP

• when EC is near 0.7, ATP levels are relatively low and ADP levels are near maximum

• when EC is at 0.9, ATP levels are near maximum and AMP levels are very low

catabolic pathways

• a metabolic pathway that converts energy-rich compounds into energy-depleted compounds which releases energy for the cell

• occurs when EC levels decrease due to sustained flux through anabolic pathways

• generates ATP and reduced coenzymes, NADH, NADPH, and FADH2 using stored fuel (carbs or lipids)

anabolic pathways

• a metabolic pathway for the biosynthesis of biomolecules from smaller precursors

• occurs when EC levels are high

• uses the generated ATP and reduced coenzymes to regenerate metabolic fuel

catabolic and anabolic balanced flux

two primary mechanisms of enzyme regulation in the context of metabolic control

• bioavailability (compartmentation within the cell and altered rates of protein synthesis and degradation)

• control of catalytic efficiency through protein modification (covalent modifications: phosphorylation, adenylation, acetylation; and noncovalent binding of regulatory molecules: interactions with molecules that cause conformational change in protein structure)

what is responsible for the unique properties of water?

hydrogen bonding

three unique properties of water that make it essential for life

1. water is less dense as a solid than as a liquid, which allows ice to float (allows oceans to remain unfrozen, and sustains life under the ice)

2. water is liquid over a wide range of temperatures, especially the temps found on earth (critical to aquatic life aka the photosynthetic algae which fuels our oxygen content)

3. water is an excellent solvent due to its hydrogen bonding abilities and polarity

bond angles in water

104.5

hydrogen bonds

a weak noncovalent bond in which hydrogen is shared between two electronegative atoms (N, O, F); strength of bond depends on the angle and the distance between the atoms

each water molecule can make up to

four hydrogen bonds (accept 2 and donate 2)

the accumulation of four hydrogen bonds leads

• higher viscosity

• higher boiling point

• higher melting point

(compared to other molecules of similar molecular mass)

the lifetime of a hydrogen bond is extremely

short (bonds break and reform with other water molecules every 1-10 picoseconds) (called flickering clusters)

proton hopping/ water wire

a series of hydrogen bond exchanges between adjacent water molecules leading to the transient formation of hydronium ions; through this exchange, the proton seems to move along a water wire to form a hydronium ion at the end (very fast process)

ice floats because of

the unusual geometry of hydrogen bonds between water molecules in an ice crystal; the water molecules in ice crystals all have four hydrogen bonds which creates a regular tetrahedral open-lattice structure (the cause of the lower density)

solubility

the ability of a solute to dissolve to homogeneity in a solvent such as water

water’s role in biomolecule solubility

when ionic compounds dissolve in water, water molecules create a hydration layer around each ion preventing the ions from rejoining its original crystal lattice structure

biochemical reactions rely on

weak interactions characterized by noncovalent bonds which are responsible for large-scale intramolecular and intermolecular structures

importance of noncovalent bonds in nature

permit unstable structures to exist for short periods of time, during which biochemical reactions can take place

three basic types of weak noncovalent interactions

1. hydrogen bonds

2. ionic interactions

3. van der waals interactions

ionic interactions

• bonds between oppositely charged atoms

• electrostatic interactions

• strength of bond depends on distance between ions and the environment between them

• strongest in hydrophobic environments

• ionic interactions in proteins are sometimes called salt bridges

van der waals interaction

a weak interaction between the dipoles of nearby electrically neutral molecules (caused by fluctuations in electron cloud) that depends on the distance between two atoms

van der waals interactions are most favorable when

the atoms are at a distance slightly greatly than when they are covalently bonded

van der waals radius

characteristic of each atom which is used to calculate the approximate volume occupied by an atom and to approximate when atoms are within van der waals contact distance

hydrophobic effect

the tendency of hydrophobic molecules to pack close together away from water (not true molecular attraction, not a noncovalent interaction)

the hydrophobic effect offsets the

decrease in entropy caused by the formation of cage-like structures of water molecules around uncharged nonpolar complexes in solution by reducing the amount of surface area of nonpolar molecules exposed to water molecules

hydrophobic effects between nonpolar amino acids in proteins play a

major role in the proper folding of newly synthesized proteins

the formation of many types of protein complexes, multi-subunit enzymes, and protein oligomers is often the result of

weak noncovalent interactions

weak noncovalent interactions play a major role in

the structure and function of biomolecules

certain protein-protein interactions use a combination of weak noncovalent interactions so

the complex can quickly dissociate if there are chemical changes in the environment or modifications to the molecules

osmosis

the diffusion of solvent molecules (water) from a region of lower solute concentration to higher solute concentration through a semipermeable membrane (plasma membrane)

the effects of solutes on colligative properties of a solution only depend on

the number of solute particles in the solute, not the chemical properties or molecular masses of the solute particles

osmotic pressure

a difference in pressure across a semipermeable membrane caused by osmosis across the membrane

osmotic pressure is proportional to

solute concentration

in living systems, osmotic pressure is controlled by

the plasma membrane

hypotonic solution

lower solute concentration outside of cell (cell swells)

hypertonic solution

higher solute concentration outside cell (cell shrinks)

isotonic solution

solution outside of cell is in equilibrium with solution inside cell

ionization constant of water (Kw)

only at 25 degrees cel

pH is the

negative log of the hydronium concentration

acidic solutions have a pH below

6.5

basic solutions have a pH above

7.5

pKa

the negative log of the Ka

weak acids have a (pKa/ Ka)

high pKa (low Ka)

strong acids have a (pKa/ Ka)

low pKa (high Ka)

henderson-hasselbalch equation

at the midpoint of a titration

pH = pKa (concentration of base is equal to concentration of acid)

buffer range

one pH unit above and below the pKa