Essential chemistry in

Biochemistry
Cristina Malagelada, PhD.
Unit of Biochemistry and Molecular Biology
Faculty of Medicine University of Barcelona

SOURCES:
Jonsson AL, Roberts MAJ, Kiappes JL, Scott KA. Essential chemistry for biochemists Essays Biochem. 2017 Oct
31;61(4):401-427.
http://www.chemsimplified.com

BIOCHEMICAL REACTIONS
CATABOLISM: breaking molecules to generate energy

BIOCHEMICAL REACTIONS
ANABOLISM: building blocks to produce complex molecules

ENZYMES
↓∆G
↑V reaction

traces

Most abundant in humans

PCHON: building blocks of organic

biomolecules
Ca: bones and teeth, signaling
P : bones and teeth, signaling, DNA, adenosine
triphosphate ATP
BIOCHEMICAL REACTIONS: WHY DO THEY HAPPEN???
THERMODYNAMICS: ∆G: Gibbs free energy
∆H : Entalpy or heat of a system
∆G= ∆H - T∆S T: Temperature in kelvins
∆S: Entropy or disorder

∆H + : system absorbes heat à endothermic reaction

∆S universe = _ ∆G ∆H - : system gives out heat à exothermic reaction
T ∆S + : the disorder increases

∆G<0 à spontaneous process = the reaction will be thermodynamically allowed

∆G◦ = The standard free energy change for a chemical reaction is the change in free energy for reactants
combined in molar stoichiometric amounts according to a balanced chemical equation if the reactants were
converted completely into products.

BIOCHEMICAL REACTIONS: WHY DO THEY HAPPEN???

CHEMICAL EQUILIBRIUM

R is the molar gas constant: 8.314 J mol K−1

If ∆G◦ is large and negative, K will be a large positive number
T is the temperature in Kelvin,
ln is the natural logarithm. A+B àC+D
BIOCHEMICAL REACTIONS: WHY DO THEY HAPPEN???
IN LIVING SYSTEMS: COUPLED REACTIONS
A THERMODINAMICALLY NON-FAVORABLE REACTION CAN BE ACHIEVED
IF IT IS COUPLED TO A THERMODYNAMICALLY FAVORABLE REACTION

ATP hydrolysis

BIOCHEMICAL REACTIONS: WHY DO THEY HAPPEN???

KINETICS

ENZYMES: are very efficient catalysts which ensure that the chemical reactions involved in metabolism
proceed at a useful rate
ATOMIC STRUCTURE AND BONDING
ELECTRONS: ORGANIZED IN SHELLS WITH SUCCESSIVE HIGHER ENERGIES/GREATER DISTANCE FROM THE NUCLEUS

SHELLS: Identified by principal quantum number 1à7

s SUBSHELL à 1 orbital : 2e-
SUBSHELLS: spdf p SUBSHELL à 3 orbitals : 6e-
d SUBSHELLà 5 orbitals : up to 10e-

ORBITALS : regions of space occupied by 1 or 2 electrons

energy and shape predicted by the “wave function” or probability to find an e- in a particular position around
the nucleus

SHELL FILLING: first Shell , the lowest principal quantum number

outer Shell higher principal quantum number

FULL OUTER SHELL (VALENCE SHELL) IS MORE FAVOURABLE THAN PARTIALLY FILLED SHELL
FULL OUTER SHELL: NOBLE GASES

BOND FORMATION: Movement of e- between atoms to achieve

a full outer shell, like in noble gases

# OF BONDS PER ELEMENT

# OF BONDS PER ELEMENT

BONDS
- COVALENT BONDS: e- are shared between atoms but they atract the e-
BOND differently: different electronegativityà dipoles
TYPES
- IONIC BONDS: e- are transferred from one atom to another resulting in
one + charged species and one - charged species

THE NUMBER OF e- in the OUTER OR VALENCE SHELL à # of bonds an atom will need to fullfill the outer shell

BOND FORMATION: THE ENERGY OF THE e- IN THE BOND HAS TO BE LOWER THAN THE ENERGY OF
THOSE e- IN THE ISOLATED ATOM

DELOCALIZATION OF e- : ressonance mostly in double bonds i.e. Benzene

NON-COVALENT INTERACTIONS
• ELECTROSTATIC INTERACTIONS WITHOUT SHARING E- BETWEEN MOLECULES
OR ATOMS
• MUCH WEAKER THAT COVALENT BONDS
• VERY FREQUENT AND IMPORTANT IN DNA PROTEIN STRUCTURE LIPID
BILAYERS AND MOLECULAR RECOGNITION
• TYPES: A) VAN DER WAALS
B) HYDROGEN BONDS
C) IONIC INTERACTIONS
• “HYDROPHOBYC” EFFECT

Donat el caràcter i la finalitat exclusivament docent i eminentment il·lustrativa

de les explicacions a classe d'aquesta presentació, l’autor s’acull a l’article
32 de la Llei de propietat intel·lectual vigent respecte de l'ús parcial d'obres
alienes com ara imatges, gràfics o altre material contingudes en les diferents
diapositives

Cristina Malagelada Setembre 2019

FUNCTIONAL GROUPS
• http://www.chemsimplified.com/explore-functional-groups/