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AMS Semester 1 > PM-150 > Flashcards

PM-150 Flashcards

1
Q

What is the Aufbau Principle?

A

Electrons fill orbitals of increasingly higher energy.

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2
Q

What is the Pauli Exclusion Principle?

A

An orbital contains no more than two electrons.

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3
Q

What is Hund’s Rule?

A

Degenerate orbitals are partially filled until an orbital is completely filled.

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4
Q

What are valence electrons and what do they define?

A

The outermost shell electrons. Chemical reactivity.

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5
Q

What do ionic substances tend to form?

A

Crystalline lattices.

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6
Q

What do covalent bonds form?

A

Individual molecules.

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7
Q

What is a polar covalent bond?

A

A covalent bond with greater electron density around one of the two atoms.

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8
Q

What do double bonds contain?

A

A pi bond and a sigma bond.

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9
Q

What do triple bonds contain?

A

2 pi bonds and a sigma bond.

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10
Q

What is a dative (coordinate) bond?

A

1 pair of shared electrons between two atoms.

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11
Q

What is a conjugated bond system?

A

System of connected p orbitals with delocalised electrons in a molecule, which lowers the overall energy of the molecule and increases stability.

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12
Q

What is a polyatomic compound?

A

A compound containing both ionic and covalent bonds. e.g CaCO3

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13
Q

Define electronegativity.

A

Ability of an atom to attract electrons to itself in a chemical bond (which results in polar bonds). Measured in chi.

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14
Q

What are the most and least electronegative elements?

A

Fluorine is most. Francium is least.

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15
Q

When does ionic bonding occur?

A

When 2 elements have different chi (>1.7).

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16
Q

When does covalent bonding occur?

A

When 2 elements have similar chi.

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17
Q

What is the trend in atomic radius in the periodic table?

A

Increases down group and decreases across periods.

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18
Q

What is the trend in ionisation energy in the periodic table?

A

Decreases down the group and increases across periods.

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19
Q

What is the trend in electron affinity in the periodic table?

A

Decreases down the group and increases across periods.

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20
Q

What do intramolecular forces cause?

A

Protein folding.

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21
Q

What do intermolecular forces cause?

A

DNA hydrogen bonding.

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22
Q

What are properties of non-covalent forces?

A

Generally electrostatic in nature.
Requires close proximity.
Non-polar nature of bonds and electronegativity.

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23
Q

What are the types of non-covalent forces?

A 
Dispersion forces (Induced dipole)
Hydrophobic forces.
Permanent dipole forces.
Hydrogen bonds.
Ionic interactions.
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24
Q

What are dispersion forces?

A

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.

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25
Q

What are the properties of dispersion forces?

A

Temporarily present.
Very weak.
Any molecule can exhibit them.
Can occur between 2 non-polar molecules.

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26
Q

What are hydrophobic forces and what do they create?

A

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.

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27
Q

What are permanent dipole interactions and their properties?

A

Dipole-dipole. Attractions between partial charges in polar covalent bonds.
Long-lasting.
Requires permanent dipole.

28
Q

What is hydrogen bonding?

A

Type of dipole-dipole interaction in which a H is bonded to an F, O or N by electrostatic interaction. Strong bond.

29
Q

What are ionic interactions and their properties?

A

Attraction between ionic species formed as a result of a permanent transfer of electrons. Long lasting.

30
Q

What are Van Der Waals forces and what do they define?

A

Non covalent interactions. Define boiling point. Hydrogen = strong. Permanent dipole = medium. Induced dipole (dispersion) = weak.

31
Q

How do non covalent interactions define boiling point?

A

Compounds with more non covalent interactions have a higher boiling point.

32
Q

What is Avogadro’s Constant?

A

Number of atoms in 12g of Carbon-12. 6.022x10^23 moles.

33
Q

Equation for moles.

A

Moles=Mass/Mr

34
Q

Define molarity.

A

Number of moles of a compound dissolved in a litre of liquid.

35
Q

What is Beer’s Law?

A

The higher the concentration, the higher the absorbance.

36
Q

What is Lambert’s Law?

A

The greater the thickness, the greater the absorption.

37
Q

What is Beer-Lambert Law?

A 
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)
38
Q

What are the three classifications of proteins? Give examples.

A 
Structural = Keratin, Collagen
Binding = Haemoglobin, Immunoglobulins
Catalytic = DNA polymerase, Alcohol dehydrogenase
39
Q

What is general formula for amino acids?

A

RCH(NH2)COOH

40
Q

What amino acid isomers exist and which are found in proteins?

A

They are chiral molecules. L- or D- isomers. ONLY L-ISOMERS FOUND IN PROTEINS

41
Q

How is a peptide bond formed?

A

Amino and carboxyl groups from 2 amino acids join together to form an amide or peptide bond, with the ELIMINATION of a WATER molecule.

42
Q

What are the different ends of a polypeptide chain?

A

-NH3+ & -COO-

Chain as definite direction.

43
Q

What direction does a polypeptide chain have?

A

N to C, 5’ to 3’

44
Q

What is the simplest amino acid?

A

Glycine. Single hydrogen atom on side chain and no chiral centre.

45
Q

What is the equation for pH?

A

pH= -log10[H+]
OR
pH= log10(1/[H+])
Concentration in moldm^-3

46
Q

What is the equilibrium constant (K) for dissociation?

A

K= ([H+][OH-]/[H2O]

47
Q

How many solutions are needed to calibrate a pH meter?

A

2 standardised solutions. The temperature should be recorded to obtain an accurate reading.

48
Q

Equation for concentration.

A

Conc= amount/volume

49
Q

Define an acid.

A

Substance which releases protons. PROTON DONOR.

A strong acid completely dissociates.

50
Q

Define a base.

A

Substance which binds to protons. PROTON ACCEPTOR.

A strong base completely associates.

51
Q

Equation for pH involving pKa.

Henderson-Hasselbach equation.

A

pH= pKa + log10([A-]/[HA])

52
Q

Equation for pKa.

A

pKa= -log10Ka

53
Q

What happens to acids when the pKa is lowered?

A

The lower the pKa = stronger acid.

The more easily protons are released, the higher the Ka value.

54
Q

What happens to bases when the pKa increases?

A

Higher the pKa= stronger the base.

55
Q

What do pKa values depend on?

A

Temperature, ionic strength and microenvironment of the ionisable group.

56
Q

What is the isoelectric point?

A

At the mid point, the opposite charges exactly balance. The point where there is no net charge on the molecule.

57
Q

What is a zwitterion?

A

A molecule or ion which contains separately positively and negatively charged groups.

58
Q

What is a buffer?

A

A solution that resists change in pH on addition of an acid or alkali.

59
Q

What happens when acid is added to an equilibrium mixture?

A

More HA forms.

60
Q

What happens when base is added to the equilibrium mixture?

A

HA dissociates producing are protons.

61
Q

When is a buffer most effective?

A

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.

62
Q

How are nucleotides linked?

A

Via phosphodiester bonds to the phosphate groups in a linear sequence.

63
Q

How are antiparallel strands of DNA held together?

A

Hydrogen bonds.

64
Q

What is genetic code and how is it read?

A

Degenerate. Read in triplet codons.

64 triplet codons for 20 amino acids + stop codon.

65
Q

What is the first codon in mRNA?

A

Met (AUG)

66
Q

What are the practical consequences of changing a sequence of DNA?

A

Solubility
Surface charge density
Size (Mr) and shape
Specific binding to other molecules

67
Q

What are physical/ chemical protein purification methods?

A

Precipitation
Ion exchange chromatography and electrophoresis
Dialysis, ultrafiltration & size/moleculare exclusion chromatography (gel filtration)
Affinity chromatography (biospecificity)

AMS Semester 1 (2 decks)

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