PM-150 Flashcards
What is the Aufbau Principle?
Electrons fill orbitals of increasingly higher energy.
What is the Pauli Exclusion Principle?
An orbital contains no more than two electrons.
What is Hund’s Rule?
Degenerate orbitals are partially filled until an orbital is completely filled.
What are valence electrons and what do they define?
The outermost shell electrons. Chemical reactivity.
What do ionic substances tend to form?
Crystalline lattices.
What do covalent bonds form?
Individual molecules.
What is a polar covalent bond?
A covalent bond with greater electron density around one of the two atoms.
What do double bonds contain?
A pi bond and a sigma bond.
What do triple bonds contain?
2 pi bonds and a sigma bond.
What is a dative (coordinate) bond?
1 pair of shared electrons between two atoms.
What is a conjugated bond system?
System of connected p orbitals with delocalised electrons in a molecule, which lowers the overall energy of the molecule and increases stability.
What is a polyatomic compound?
A compound containing both ionic and covalent bonds. e.g CaCO3
Define electronegativity.
Ability of an atom to attract electrons to itself in a chemical bond (which results in polar bonds). Measured in chi.
What are the most and least electronegative elements?
Fluorine is most. Francium is least.
When does ionic bonding occur?
When 2 elements have different chi (>1.7).
When does covalent bonding occur?
When 2 elements have similar chi.
What is the trend in atomic radius in the periodic table?
Increases down group and decreases across periods.
What is the trend in ionisation energy in the periodic table?
Decreases down the group and increases across periods.
What is the trend in electron affinity in the periodic table?
Decreases down the group and increases across periods.
What do intramolecular forces cause?
Protein folding.
What do intermolecular forces cause?
DNA hydrogen bonding.
What are properties of non-covalent forces?
Generally electrostatic in nature.
Requires close proximity.
Non-polar nature of bonds and electronegativity.
What are the types of non-covalent forces?
Dispersion forces (Induced dipole) Hydrophobic forces. Permanent dipole forces. Hydrogen bonds. Ionic interactions.
What are dispersion forces?
Electrons move within their orbitals. An uneven distribution causes electrical charge in the molecule. A negative area caused can attract a positive area = INDUCED DIPOLE.
What are the properties of dispersion forces?
Temporarily present.
Very weak.
Any molecule can exhibit them.
Can occur between 2 non-polar molecules.
What are hydrophobic forces and what do they create?
Hydrophobic regions orientate themselves to ‘hide’ inside the protein. Tend to be non-polar.
Creates MICELLES. All hydrophobic groups are sequestered for water; ordered shell of water molecules is minimised. ENTROPY INCREASES.
What are permanent dipole interactions and their properties?
Dipole-dipole. Attractions between partial charges in polar covalent bonds.
Long-lasting.
Requires permanent dipole.
What is hydrogen bonding?
Type of dipole-dipole interaction in which a H is bonded to an F, O or N by electrostatic interaction. Strong bond.
What are ionic interactions and their properties?
Attraction between ionic species formed as a result of a permanent transfer of electrons. Long lasting.
What are Van Der Waals forces and what do they define?
Non covalent interactions. Define boiling point. Hydrogen = strong. Permanent dipole = medium. Induced dipole (dispersion) = weak.
How do non covalent interactions define boiling point?
Compounds with more non covalent interactions have a higher boiling point.
What is Avogadro’s Constant?
Number of atoms in 12g of Carbon-12. 6.022x10^23 moles.
Equation for moles.
Moles=Mass/Mr
Define molarity.
Number of moles of a compound dissolved in a litre of liquid.
What is Beer’s Law?
The higher the concentration, the higher the absorbance.
What is Lambert’s Law?
The greater the thickness, the greater the absorption.
What is Beer-Lambert Law?
A=ECl A= absorbance at given wavelength (AU) E= molar absorption coefficient (Lmol^-1cm^-1) c= concentration of solution mol L^-1 l= path length (usually 1cm)
What are the three classifications of proteins? Give examples.
Structural = Keratin, Collagen Binding = Haemoglobin, Immunoglobulins Catalytic = DNA polymerase, Alcohol dehydrogenase
What is general formula for amino acids?
RCH(NH2)COOH
What amino acid isomers exist and which are found in proteins?
They are chiral molecules. L- or D- isomers. ONLY L-ISOMERS FOUND IN PROTEINS
How is a peptide bond formed?
Amino and carboxyl groups from 2 amino acids join together to form an amide or peptide bond, with the ELIMINATION of a WATER molecule.
What are the different ends of a polypeptide chain?
-NH3+ & -COO-
Chain as definite direction.
What direction does a polypeptide chain have?
N to C, 5’ to 3’
What is the simplest amino acid?
Glycine. Single hydrogen atom on side chain and no chiral centre.
What is the equation for pH?
pH= -log10[H+]
OR
pH= log10(1/[H+])
Concentration in moldm^-3
What is the equilibrium constant (K) for dissociation?
K= ([H+][OH-]/[H2O]
How many solutions are needed to calibrate a pH meter?
2 standardised solutions. The temperature should be recorded to obtain an accurate reading.
Equation for concentration.
Conc= amount/volume
Define an acid.
Substance which releases protons. PROTON DONOR.
A strong acid completely dissociates.
Define a base.
Substance which binds to protons. PROTON ACCEPTOR.
A strong base completely associates.
Equation for pH involving pKa.
Henderson-Hasselbach equation.
pH= pKa + log10([A-]/[HA])
Equation for pKa.
pKa= -log10Ka
What happens to acids when the pKa is lowered?
The lower the pKa = stronger acid.
The more easily protons are released, the higher the Ka value.
What happens to bases when the pKa increases?
Higher the pKa= stronger the base.
What do pKa values depend on?
Temperature, ionic strength and microenvironment of the ionisable group.
What is the isoelectric point?
At the mid point, the opposite charges exactly balance. The point where there is no net charge on the molecule.
What is a zwitterion?
A molecule or ion which contains separately positively and negatively charged groups.
What is a buffer?
A solution that resists change in pH on addition of an acid or alkali.
What happens when acid is added to an equilibrium mixture?
More HA forms.
What happens when base is added to the equilibrium mixture?
HA dissociates producing are protons.
When is a buffer most effective?
When it is maintaining a pH close to the pKa of the buffer compound itself. Within about 1 pH unit either side of its pKa.
How are nucleotides linked?
Via phosphodiester bonds to the phosphate groups in a linear sequence.
How are antiparallel strands of DNA held together?
Hydrogen bonds.
What is genetic code and how is it read?
Degenerate. Read in triplet codons.
64 triplet codons for 20 amino acids + stop codon.
What is the first codon in mRNA?
Met (AUG)
What are the practical consequences of changing a sequence of DNA?
Solubility
Surface charge density
Size (Mr) and shape
Specific binding to other molecules
What are physical/ chemical protein purification methods?
Precipitation
Ion exchange chromatography and electrophoresis
Dialysis, ultrafiltration & size/moleculare exclusion chromatography (gel filtration)
Affinity chromatography (biospecificity)
