Cell and Molecular Biology

• Atom


  The smallest unit of matter that still retains the properties of an element
• Dalton


  The same as the atomic mass unit, neutrons and protons have masses close to 1
• Atomic number


  Number of protons
• Atomic mass number


  Proton + neutron
• Neutrons


  Atomic mass-atomic number
• Bohr model


  • Protons and neutrons in the nucleus with electrons around it
• Schrodinger model


  • Nucleons in the nucleus and a cloud of electrons
• Electron arrangement


  • Arranged in shells, 2 in the first shell and maximum of 8 in other shells. If a shell is unfilled, it is more reactive
• Element


  Any substance that cannot be broken down to any other substances by chemical reactions which can form compounds
• Compound


  A substance consisting of two or more different elements combined in a fixed ratio
• Isotopes


  Atoms with the same number of protons but a different number of neutrons
• Radioactive isotopes


  Where the nucleus decays spontaneously, giving off particles and energy
• When the radioactive decay leads to a change in the number of protons, it transforms the atom to an atom of a different element.
• Alpha decay: the nucleus loses two protons.

  Beta decay: the nucleus either loses or gains a proton

  Gamma decay: no change in proton number occurs, so the atom does not become a different element
• Radioactive isotopes are often used as diagnostic tools in medicine.

  The radioactive isotopes are incorporated into biologically active molecules, which are then used as tracers to track atoms during metabolism, the chemical processes of an organism.
• Valence: The bonding capacity of a given atom; the number of covalent bonds that an atom can form, which usually equals the number of unpaired electrons in its outermost (valence) shell.
• Valence electron: An electron in the outermost electron shell.
• Valence shell: The outermost energy shell of an atom, containing the valence electrons involved in the chemical reactions of that atom.
• An electron’s energy level is correlated with its average distance from the nucleus.
• The chemical behaviour of an atom depends mostly on the number of electrons in its outermost shell.
• Covalent bond - A type of strong chemical bond in which two atoms share one or more pairs of valence electrons.

  o   Eg. H2, O2, H2O, CH4
• Ionic bonds – A chemical bond resulting from the attraction between oppositely charged ions.

  o   Ions: An atom or group of atoms that has gained or lost one or more electrons, thus acquiring a charge.

  o   Cation: A positively charged ion.

  o   Anion: A negatively charged ion.
• Electronegativity: The attraction of a given atom for the electrons of a covalent bond.
• Non-polar covalent bond: A type of covalent bond in which electrons are shared equally between two atoms of similar electronegativity.
• Hydrogen Bonding: Weak electrostatic interactions between hydrogen atoms bound to highly electronegative elements (N, F, O) and other nearby electronegative atoms.
• Polar covalent bond: A covalent bond between atoms that differ in electronegativity. The shared electrons are pulled closer to the more electronegative atom, making it slightly negative and the other atom slightly positive.

  Eg. Water (S+, S-)
• Van der Waals interactions - are dipole-dipole interactions, which commonly exist in gases, liquids, and solids.
• Dipoles - set of separated charges within an atom/molecule.
•  

  There are three types of Van der Waals forces:

  1.     Dipole-dipole interactions

  o   Attractive/repulsive forces that exist between two polar molecules. Strongest.

  2.     Dipole-induced dipole interactions

  o   Attractive/ repulsive forces between a polar molecule and an atom/molecule with an induced dipole

  3.     London dispersion forces

  o   Attractive/ repulsive forces between a nonpolar molecule with an instantaneous dipole and a non-polar atom/molecule with an induced dipole.
• The four classes of hydrocarbons are alkane, alkene, alkyne and arene.
• Alkanes are saturated hydrocarbons. Each carbon is bonded to 4 other atoms. CNH2N+2
• Alkenes are unsaturated hydrocarbons, 1/+ double or triple bonds between carbon atoms. CNH2N
• Alkynes: CnH2n-2 for non-cyclic compounds
• Amino acids have carboxyl and amine groups. As well as a variable R group. And 1 H
• Two Sulfhydryl groups can cross link and stabilise protein structure
• Methyl groups are hydrophobic and non polar.
• DNA methylation

  -       Change activity of DNA segment without changing sequence

  -       methyl groups are added to the DNA molecule.
• Isomers are equal numbers of atoms of the same element that have the same molecular formula but different arrangement of atoms. Different structures and properties
• Chain isomerism – different arrangement of chain backbone.
• Position isomerism – different position of functional group