cell chemistry and bioenergetics

living creatures as chemical systems

• life depends on chemical reactions that take place in aqueous solution

• most carbons present are incorporated into macromolecules, allowing cells to grow and function

• interlinking networks of chemical reactions

types of chemical interactions

• covalent

• non-covalent

properties of chemical bonds

• bond strength is the amount of energy needed to break it

• covalent bonds are stronger and are only broken by biologically catalyzed chemical reactions

• non-covalent bonds allow molecules to recognize each other and reversibly associate

abundant chemical groups in cells

• methyl

• hydroxyl

• carboxyl

• carbonyl

• phosphate

• sulfhydryl

• amino

biological preference for carbon

• carbon atoms can form four covalent bonds with other atoms (high ability to form macromolecules)

• C-C stable bonds form chains and rings (generating large and complex molecules)

organic compounds

• carbon-based compounds made by cells

• found in free solution

major families of organic compounds

• sugars

• amino acids

• fatty acids

• nucleotides

uses of organic compounds

• monomer subunits to construct polymeric macromolecules

• energy sources, broken down and transformed into other small molecules

macromolecules

• most abundant carbon-containing molecules

• principal building and functional blocks of cells

• made by covalently linked organic molecules in chains

proteins

• versatile and perform thousands of functions

• enzymes catalyze formation and breaking of covalent bonds

assembly of macromolecules

• subunits are added in a precise order, following a sequence

• covalent bonds allow rotation about the bond, giving flexibility and allowing for several conformations

• non-covalent bonds allow assembly of macromolecules and constrain the shape to one conformation

chemical bond strengths

• covalent bonds are strongest, independent of environment

• ionic bonds are weaker, stronger in vacuum than in water

• hydrogen bonds are even weaker, stronger in vacuum than in water

• van der Waals interactions are weakest, independent of environment

anabolic catalytic pathway

• condensation / building larger molecules

• energetically unfavourable (requires a lot of energy)

catabolic catalytic pathway

• hydrolysis / breaker up molecules

• energetically favourable

second law of thermodynamics

• in any isolated system, the degree of disorder always increases

• the most probable arrangement is the most disordered

entropy (S)

amount of disorder in a system (greater the disorder, greater the entropy)

cell heat

originates from catabolic pathways, is released unless needed to create more order in the cell

first law of thermodynamics

energy can be converted from one form to another, but cannot be created or destroyed

enthalpy (H)

energy that can be released from chemical bonds

energetically favourable reaction

• negative free Gibbs energy

• reduction of order (increase in S)

• loss of free energy

enzymes

• catalyze reactions by lowering the activation energy required for a reaction to take place

• cannot force energetically unfavourable reactions to occur

coupling of chemical reactions

energetically unfavourable reaction is driven by the energetically favourable reaction because the net free-energy change for the pair of reactions is less than zero

ATP hydrolysis

involves coupled reactions that drive synthesis of biological polymers

equilibrium

• molecules A → B = molecules B → A

• no net change between the number of reactants and products

oxidation

removal of electrons from an atom (partially positive charge)

reduction

addition of electrons to an atom (partially negative charge)

hydrogenation

molecule picks up a hydrogen along with an electron

reduction

number of C-H bonds in a molecules increases

group carried in high-energy linkage of ATP

phosphate

group carried in high-energy linkage of NADH, NADPH, FADH₂

electrons and hydrogens

group carried in high-energy linkage of acetyl CoA

acetyl group

group carried in high-energy linkage of carboxylated biotin

carboxyl group

group carried in high-energy linkage of S-adenosylmethionine

methyl group

group carried in high-energy linkage of uridine diphosphate glucose

glucose

free Gibbs energy

change in enthalpy - temperature (kelvin) x change in entropy