CHEMISTRY

2021-2022
 Chemistry First Semester program
Lectures: 3 h/week
• General chemistry and organic chemistry - 7 lectures
• Structural biochemistry -7 lectures
Seminary: 1 h/week (2 h every even week)
Practicals: 1 h/week (2 h every odd week)

Bibliography:
• Books of Chemistry and Biochemistry (choice)
• Lecture notes, presentations (slides)

Exam:
• Written/Oral test (compulsory) – January/February 2021
• Midterm (partial) examination (written test, optional,
minimum score 6 out of 10 for each section)
 Bibliography
• Peter N. Campbell, Anthony D. Smith, Illustrated Biochemistry,
2000
• Lehninger,A.L., Biochemistry, 2000, 2005
• Pamela C.Champe, Harvey R., Biochemistry, Lippincott’s
Illustrated Reviews. 1987
• Murray, R.K., Granner, D.K., Mayes, P.A., Rodwell, V.W.,
Harper’s Illustrated Biochemistry, 2003, McGraw-Hill
• Adela Pintea, Structural Biochemistry, Academic Pres, 2009
• Dumitrița Ruginǎ, Adela Pintea, Chemistry and Structural
Biochemistry – Short course for veterinary students, Editura
Academic Pres, Cluj-Napoca, 2020
• Sanda Andrei, Adela Pintea, Constantin Bele, Veterinary
biochemistry, - practical works, Editura Academic Pres, Cluj-
Napoca, 2012
 What is biochemistry?
• Biochemistry is the study of life on the
molecular level
• It deals with the structure, function and
transformation of biomolecules
• Biomolecules are molecules which can be
found in living organisms
• Biomolecules are build from bioelements
• Structural biochemistry – study the
structure, occurrence, properties and
function of biomolecules
• Dinamic biochemistry (metabolism) –
study the biosynthesis (anabolism) and
the degradation (catabolism) of
biomolecules
 BIOMOLECULES
• Proteins
• Nucleic acids
• Carbohydrates (saccharides, sugars)
• Lipids

• Vitamins
• Enzymes
• Hormones
Hierarchical organization of living material
Building blocks of Macromolecules (monomeric units)

• Amino Acids

• Nucleotides

• Carbohydrates

• Lipids
Bioelements
 Element % of dry weight
C 61,7
N 11,0
O 9,3
H 5,7
P 3,3
S 1,0
Ca 5,0
K 1,3
Cl 0,7
Na 0,7
Mg 0,3
B, F, Si, V, Cr, Mn, Fe, Co,
traces
Cu, Zn, Se, Mo, Sn, I
 Atom models
- Rutherford – planetary model
- Bohr – an electron could only orbit the nucleus
in particular circular orbits
- Modern model – based on duality of electrons
(wave and particle); describes the positions of
electrons in an atom in terms of probabilities
(atomic orbitals)
The location of an electron: quantum
numbers (n, l, ml, ms)

• n principal quantum number (integer values n ≥1) indicates the shell or energy
level in which the electron is found (K, L, M, N, O.. (radius and energy)
• l orbital angular momentum quantum number (0 ≤ l ≤ n-1) indicates the subshell
s, p, d, f, g… and the shape of the atomic orbital
• ml magnetic quantum number represents the orbitals of a given subshell
(-l ≤ ml ≤ +l)
• ms spin magnetic quantum number (can only have a value of either +1/2 or -1/2
(spin orientation, rotation)
For one value of n, correspond 2n electronic states
Atomic Orbital - the regions of space around the nucleus of the
atom, where the electron has a high probability of being found
Each orbital can be occupied by two
electrons of opposite spin

total number of
subshell number of orbitals possible electrons in
each orbital
s 1 2
p 3 (px, py, pz) 6
d 5 (dx2-y2, dz2, dxy, dxz, dyz) 10
7 (fz3, fxz2, fxyz, fx(x2-3y2),
f 14
fyz2, fz(x2-y2), fy(3x2-y2)
 Electron configuration

1. Pauli-exclusion principle: each electron can be

described with a unique set of four quantum
numbers. (each shell can be occupied by
maximum 2n² electrons, n is the number of shell)
2. The Aufbau principle (Madeling, Klechowsky) -
electrons occupy orbitals in order of increasing
energy. The order of occupation is as follows:
1s<2s<2p<3s<3p<4s<3d<4p<5s<4d<5p<6s<4f<5d<
6p<7s<5f<6d<7p
3. Hund's Rule: when electrons occupy degenerate
orbitals (i.e. same n and l quantum numbers), they
must first occupy the empty orbitals before double
occupying them.
Periodic system - blocks
 Chemical Bonds and Forces

• Covalent bonds ~ 80 kcal/mole

• Coordinative bond
• Ionic interactions (charge-charge) ~10 -20
kcal/mole
• Hydrogen bonds 3-5 kcal/mole
• Van derWaals:
dipole-dipole <1kcal/mole; London <0.1 kcal,
• Hydrophobic interactions (forces)
Pauling – Electronegativity scale
 Ionic bonds (interactions)

• Ionic bonds are formed by the transfer of one or

more valence electrons from one atom to another
• Between 2 atomes with high difference in
electronegativity (ΔEn > 1.7)
• Atom that gives up the electron(s) becomes
positively charged – cations
• Atom that receives electron(s) becomes negatively
charged - anions
Ionic interaction (electrostatic attraction)
Ionic interaction
 Covalent bond
• A covalent bond involves the mutual sharing
of one or more electron pairs between atoms

• The shared electron pair is called a covalent

bond, because it bonds or links the atoms
together
 Covalent bond
- Simple
- Double
- Triple
 sp3 Hybridization

s + 3 p

sp3

-The carbon atom is sp3 hybridized to obtain

tetrahedral geometry
-All bond angles are equal at 109.50
sp2 Hybridization
The carbon atom is sp2 hybridized to obtain trigonal planar geometry

s + 2p
There is one p orbital left over,
and it would be along the z
axis.

3 sp2 orbitals
sp Hybridization 180o
acetylene

s + p = sp + sp

Two sp orbitals

• there are two p orbitals

leftover and these would be
located on the y and z axes
 Covalent bond
- Nonpolar - between atoms with similar electronegativity
(ΔE = 0 ÷ 0.4)
- Polar – between atoms with different electronegativity
(ΔE = 0.4 ÷ 1.7)

Polar covalent bond

Nonpolar covalent bond
(partial charge)
C-H; ΔEn = 0.35
C-Cl; ΔEn = 0.61
Strenghts of covalent bonds
Coordinate covalent bond (coordinative bond)

Is a special type of a
covalent bond between +
two atoms in which both
electrons shared in the
bond come from the same
atom.
+
 Hydrogen bond
• Formed between a hydrogen atom linked to one electronegative
atom and another electronegative atom (nitrogen, oxygen,
fluoride)
• Hydrogen donors: hydroxyl, amino, carboxyl groups
• Hydrogen acceptors: heteroatoms (nitrogen, oxygen, fluoride)
having
• Stronger than Van der Waals forces
Hydrogen bonds
 Van der Waal’s interactions
Nonspecific attractive or repulsive forces between molecules
(when they are closed):

- Permanent dipole - Permanent dipole (Keesom forces)

- Permanent dipole - Induced dipole (Debye forces)
- Instantaneous induced dipole – Induced dipole (London
forces)
- Very weak forces but important for the structure of
biomolecules (proteins)
 Hydrophobic interactions
Water is Polar

• Molecules devoid of charged groups or atoms capable of forming

hydrogen bonds are termed hydrophobic substances
• If a hydrophobic molecule enters the network of hydrogen bonds
of water, it will break them locally. This network will be
replenished by separating hydrophobic molecules which
themselves will tend to leak water to form a separate phase; it is
hydrophobic interaction
• Despite the non polarity of hydrophobic molecules, the electron
cloud of two neighboring molecules interact so that it partial
charges of opposite sign appear
• Attraction between these transition dipoles (constituted by
electron of an atom and the nucleus of another atom) are called
dispersion forces London and they are the essence of the
Hydrophobic interactions
Hydrophobic interactions

Micelle Lipid double layer Liposome (unilamelar)

 Water

• Water molecule is Polar

• Oxygen atom draws electrons away from the hydrogen
nuclei which become positively charged
• Flickering structure
• Water plays an important role for the formation of three
dimensional structure and function of macromolecules
Water is highly cohesive

• Water molecules interact

strongly with one other through
hydrogen bonds
• Water has a very high boiling
point (100°C) and an unusually
high dielectric constant (twice
than of methanol and 40 times
that of hexane)
• Is an excellent solvent for polar
molecules
• Gives shape, structure, allows
transport, acts as chemical
reagent (hydrolysis, addition).
Water/Ice density
Due to the network of H-bonded protons 'jump' from one
water molecule to another
 Ionization of water

- pH measure the acidity (alkalinity of a_ solution)

pH = ‑lg[H+] pOH = ‑lg[OH ]

pH + pOH = 14
Ke = 1.8x10-16
[H2O] = 55.6
Acids

• According to Brönsted – acids are proton

(H+) donors
• According to Lewis – acids are electron pair
acceptors
 Acids

• Inorganic acids (HCl, H2SO4, HNO3)

• Organic acids (CH3COOH, HCOOH, C6H5COOH)
 Acids
• Strong acids (HCl, HBr, HI, HClO4, H2SO4, HNO3) -
completely dissociated
HCl + H2O → H3O+ + Cl-

HCl → H+ + Cl-
• Weak acids (CH3COOH, H2CO3, fatty acids, etc.)
– partially dissociated
CH3COOH + H2O ↔ H3O+ + CH3COO-

CH3COOH ↔ H+ + CH3COO-
Strong acids Weak acids
- Weak acids – most of the acids found in living organisms
- Weak acids are characterized by the acidity constant

HA(aq) + H2O ⇌ H3O+(aq) + A-(aq)

pKa = - lgKa

Ka = acidity constant

Higher is the Ka, stronger is the acid !!!

Higher is the pKa, weaker is the acid !!!
Henderson-Hasselbalch equation
 Acid KA pKA

Formic Acid HCOOH 1,78 x 10‑4 3,75

Acetic Acid CH3COOH 1,75 x 10‑5 4,76

Lactic Acid CH3‑CH(OH)‑COOH 1,38 x 10‑4 3,86

Oxalic Acid 5,37 x 10‑2 1,27 (pK1)

Oxalate ‑ 5,37 x 10 ‑5 4,27 (pK2)

Succinic Acid 6,17 x 10‑5 4,21 (pK1)

Succinate ‑ 2,29 x 10‑6 5,64 (pK2)

Phosphoric Acid H3PO4 7,25 x 10‑3 2,14

H2PO4‑ 1,38 x 10‑7 6,86

HPO42‑ 3,98 x 10‑13 12,4

Carbonic Acid H2CO3 1,70 x 10‑4 3,77

Bicarbonate HCO3‑ 6,31 x 10‑11 10,2

Acids
• Monoprotic (HCl, CH3COOH)
• Diprotic (H2SO4, H2CO3)
• Polyprotic (H3PO4)
Base (alkali)

• According to Brönsted - substances that can

accept protons (release hydroxide ions)
• According to Lewis – electron pairs donors

• Strong base – KOH, NaOH, Ba(OH)2

• Weak base - NH4+, amines
Base

Strong base:
NaOH → Na+ + OH−

Weak base:
NH3 + H2O ↔ NH4+ + OH−
Weak base are characterized by the
basicity constant
 SALTS = products of the neutralization
reaction
acid + base = salt + water

• Strong acid + strong base: NaCl, K2SO4, NaNO3

• Strong acid + weak base: NH4Cl, (NH4)2SO4
• Weak acid + strong base: Na2CO3, CH3COONa
• Weak acid + weak base: (NH4)2CO3, CH3COONH4.
Protein structure and activity is sensitive to pH