Summary Learning objectives Molecular Biology

Chapter 2
1. Describe the build of atoms and name concepts like atoms, mass and atom number
- Atoms
o Protons (positive charge)  Mass of 1 Dalton (Da)
o Neutrons (neutral charge)  Mass of 1 Da
o Electrons (negative charge)  Mass is negligible
o Protons and neutrons in the atom nucleus
o Electrons in a cloud around the nucleus
o Mass number: protons + neutrons  Upper left corner of the element ( 12C)
o Atomic number: number of protons  Bottom left corner of the element (6C)
 Atoms with the same atom number have the same chemical characteristics
and are the same element
 Determines which the kind of element
o Example: an element with atom number 19 and mass number 39 has 19 protons, 19
electrons and 20 neutrons

2. Know the difference between two isotopes of an element
- Isotopes and radioactive decay
o Isotopes are atoms with the same number of protons but a different number of
neutrons
 Different mass number but same atomic number
 Example: there are three types of carbon:
 Carbon-12 has 6 protons and 6 neutrons
 Carbon-13 has 6 protons and 7 neutrons
 Carbon-14 has 6 protons and 8 neutrons
o Radioactive isotopes  unstable isotopes
 Carbon-14 decays into nitrong-14
 Carbon-14 (β-decay) nitrogen-14 + electron + antineutrino
 Decay rate expressed in half-life  Varies per isotope
 Applications
 Radioactive tracers
 Radiometric dating

3. Determine which type of binding is plausible from the distribution of electrons in shells.
And divide the electrons in shell 1 and 2 over different orbitals
- Electron distribution
o Chemical characteristics of an atom is determined by the distribution of electrons
 Elements with the same distribution means same characteristics
o Valence electrons  electrons in the outermost shell (valence shell)
o Atoms try to fill up their outermost shell
 Making them inert (less reactive)
o Orbitals (cloud of electrons)
 Every shell contains a specific number of orbitals
 Every orbital contains two electrons
o Shell 1  1 orbital (1s)  2 electrons
o Shell 2  4 orbitals (2s and three 2p; 2px, 2py, 2pz)  8 electrons

,4. Distinguish between the different types of binding (covalent and noncovalent) and
determine the type of binding, polar or nonpolar, by using the concept of electron-
negativity




- Bonds
o Covalent: electron pair sharing
 Interaction between atoms

,  Hydrogen has a valence of 1  two hydrogen atoms can share their
electrons making H2
 Oxygen has a valence of 2  two hydrogen atoms and one oxygen
atom can share their electrons making H 2O
 Single covalent bond  sharing one electron pair
 Double covalent bond  sharing two electron pairs
 Triple covalent bond  sharing three electron pairs
 Display of molecules
 Molecular formulas (H2)
 Lewis Dot structure (H:H)
 Structure formulas (H – H, single bond) (O=O, double bond)
 Space-Filling model (represent the actual shape of the molecule)
 Not always an equal distribution
 Electron negativity of the atom
o Depends on the number of protons and the distance from
the shell to the nucleus
o Determines the type of bond
 Nonpolar covalent bond (H2)
 Electrons distributed equally
 Electron negativity difference of less than 0,5
 Polar covalent bond
 Electrons are closer to one of the atoms
 Electron negativity difference of 0,5 to 1,6
 Causes partial charge of the molecule
 For example, H2O has hydrogen and oxygen share a polar covalent
bond because oxygen is one of the most electronegative elements
o The oxygen atom has a partial negative charge  δ-
o The hydrogen atom has a partial positive charge  δ+
o Ion: electron transmission
 Atoms take over the electrons of their binding partner atom
 Both atoms are charged after transmission
o Charged atom/molecule = ion
 Cation is positive
 Anion is negative
o NaCl  Na+ + Cl-
 Chemical ion bond  salts
 Create crystal structure

5. Distinguish between the strength of different kinds of binding
- Weak chemical interactions
o Hydrogen bonds
 Hydrogen atom
 Covalently linked to a strong electronegative atom
 Attracted to other electronegative atoms
o Van der Waals forces
 Coincidental unequal distribution of electrons over a molecule
 Attraction between molecules that are in close proximity
o Cause big biological molecules to stay intact
o Interaction is reversible

, Chapter 3
6. Explain the four important characteristics of water
- Polarity of water
o Polar covalent bond
o Water is a polar molecule
 Charges are unequally distributed
o Water molecules form hydrogen bonds
 Weak
 Short lived
 Changing contacts
- Cohesion characteristics
o Hydrogen bonds keep water molecules together  cohesion
o Attraction between different compounds (water and glass)  adhesion
o The surface tension of water is very high by cohesion of water molecules
- Temperature and thermal energy
o Thermal energy is kinetic energy of the molecules
 Random movements of molecules and atoms
o When two objects come into contact
 Thermal energy of warm objects to colder objects
o Water can absorb high amounts of energy
 High specific warmth
 1 calory = energy needed to warm one gram of water
 Water works as a buffer in the world  sea
 Heat absorption  H-bond breaks
 Heat release  H-bond forms
 High heat of evaporation
 Energy needed to evaporate one gram liquid to gas
 Evaporation = when some molecules move fast enough to leave the
liquid
 Evaporation also takes place at lower temperatures but faster at
higher temperatures
 Evaporative cooling liquids evaporate, remaining liquid cools down
o sweat
- Expansion by freezing
o In ice water forms a crystal structure
 Hydrogen bonds are not broken anymore
 Water molecules are further apart
o The density of ice is lower than water
 Making ice float above the water
- Solvent
o A solution is a liquid with a homogeneous mix of compounds
 Solvent and solute
o Water is an excellent solvent
o Hydrophilic  high affinity for water
o Hydrophobic  low to no affinity for water
 Oil, most nonpolar covalent bindings
 Membranes consist partly of hydrophobic molecules
 Micelles