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Proteins and Membranes

Lecture 2: Covalent bonds and non-covalent interactions

Atomic Interactions and Molecular Interactions
Strong (50=200kcal/mol) Weak (1=5 kcal/mol)
Holds atoms together Determine the 3D shape of macromolecules
3-5 Covalent Phosphodiester bonds between nucleotides Hydrogen bonds between the bases
Covalent peptide bonds between amino acids in a DNA The 3D polypeptide/protein structure in the double helix is
strand a result of these interactions

Atomic Structure; electrons, orbitals and bonds

- An atom is composed of a dense nucleus: protons (+) and neutrons ( )
- The Atomic Number of an atom is the number of protons
- The Atomic Mass of an atom is the number of protons and neutrons
- The nucleus is surrounded by a cloud of negatively charged electrons located in areas called shells
- within each shell there are sub shells or atomic orbitals which vary in shape and orientation
- The number of electrons in the outer shell indicates which group the atom is in.
- The number of valence electrons indicates how many bonds it can form
- Eg. Oxygen has 6 valence electrons, thus can form 2 bonds

Covalent bonds
- The sharing of electrons to create a full outer shell.
- Covalent bonds are directional
- The shape of a molecule is determined by the mutual repulsion of the atoms.

No. of e- pairs Type of pairs Shape Bond angles

2 2 BP Linear 180o
3 3 BP Trigonal Planar 120o
3 2 BP, 1 LP Bent 119o
4 4 BP Tetrahedral 109.50
4 3 BP, 1 LP Trigonal pyramidal 1070
4 2 BP, 2 LP Angular 104.5o
5 5 BP Trigonal bipyramidal 90o, 120o
5 4 BP, 1 LP Sawhorse <900, <1200
,5 3 BP, 2 LP T-shaped 90o
5 2 BP, 3 LP Linear 1800
6 6 BP Octahedral 90o
6 5 BP, 1 LP Square pyramidal ~900
6 4 BP, 2 LP Square planar 90o
6 3 BP, 3 LP T-shaped 900
6 4 BP, 2 LP Linear 180o
Strength of Covalent Bonds

Bond Energy (unit kj/mol)

Single bond ~ 90 C-N 70
C-C 83
C-O 84
C-H 99
O-H 110
Double bond ~160 C=C 146
C=O 170
Triple bond ~200 CC 195

- The power of an atom to attract electrons to itself

* Remember the ones in bold *

Element Electronegativity (Pauling units)

Fluorine 4.0
Oxygen 3.5
Chlorine 3.0
Nitrogen 3.0
Sulfur 2.5
Carbon 2.5
Hydrogen 2.1
Sodium 0.9
Potassium 0.8

Polar and Nonpolar covalent bonds

- In a nonpolar covalent bond, electrons are shared equally between two atoms. Which possess similar electronegativities
- In a polar covalent bond, electrons are shared unequally between two atoms of different electronegativities (>0.5)
the shared electrons are closer to one atom than the other
one atom is slightly negatively charged (-) and the other is slightly positively charged (+)
there is a dipole effect, expressing the magnitude of the polarity

Types of Non-covalent bonds

- Ionic (transfer of electrons)
- Electrostatic interactions (charges and dipoles)
- Van der Waals interactions (transient dipoles)
- Hydrogen bonds (hydrogen and polar covalent bond)
- Hydrophobic interactions (attraction and repulsion)

Ionic bonds
- The two atoms have very different electronegativities.
- Bonding electrons are not shared between two atoms.
- The electrons are transferred from one atom to the other.
- Ionic bonds (collectively)in crystal lattice are strong (~120 kcal/mol).
Electrostatic interactions
There are three types of electrostatic interactions
- charge to charge
- dipole to charge
- dipole to dipole

Van der Waals interactions

- Non-specific attraction between adjacent atoms.
- Owing to transient asymmetry of electrons
- Electron distribution around ALL atoms changes with time
- At any instant, the charge distribution is not symmetrical.
- This generates a transient dipole moment which can induce an asymmetrical electron distribution in adjacent atoms
- This causes ATTRACTION

Hydrogen bonds
- Form when two atoms interact with a hydrogen atom.
- The hydrogen is covalently bonded to one of them the Donor.
- The hydrogen is attracted to the other the Acceptor.
- Both Donor and Acceptor groups need to have polar covalent bonds.
- The + of the hydrogen is attracted to the - of the Acceptor.
- Nitrogen and oxygen can act as Donors and Acceptors.
- Donors include -N-H and -O-H (when they are covalently bound to H)
- Acceptors when they are covalently bonded to something else which is more
electronegative. They will be attracted to the + H.
- C-H = a nonpolar covalent bond and so do not form H-bonds.

- Water is a polar molecule
- Electronegativity of oxygen is 3.5.
- Electronegativity of hydrogen is 2.1
- Has a permanent polar bond
- Water is highly cohesive
- Every water molecule has a H-bond donor and acceptor
- O-H groups are H-bond donors
- O atoms are H-bond acceptors

Hydrophobic interactions
- NONPOLAR molecules (or parts of them) are HYDROPHOBIC.
- They cannot participate in H-bonding and so tend to associate with each other when in water.
= This is the Hydrophobic effect
- Nonpolar groups tend to be hidden away from water and therefore found on the inside of macromolecules.
- C-C and C-H bonds (hydrocarbons) are nonpolar and therefore hydrophobic.
- Attractions and repulsions are equally important in determining structure.