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First year > Biochemistry semester 1 > Flashcards

Biochemistry semester 1 Flashcards

1
Q

What is Hunds Rule?

A

When 2 or more orbitals of equal energy and available electrons will be placed in turn into each orbital until they are both half filled.

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2
Q

What is hybridisation?

A

Combining of two pure atomic orbitals to make a new orbital which is more stable than pure atomic orbitals.

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3
Q

What does more s character in a bond correlate too?

A

More s character means that the bond is shorter, stronger and has a larger bond angle.

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4
Q

Do L and D isomers of amino acids have the same stability?

A

Yes, although all naturally occurring amino acids are L isomers.

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5
Q

What bond angles can rotate in a peptide bond?

A

Alpha Carbon - N and Alpha Carbon - C

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6
Q

Where are disulphide bonds normally found?

A

The extra cellular domains of proteins where they confer stability.

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7
Q

In the Anfinsen experiment what was the purpose of urea?

A

It weakened the covalent bonds

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8
Q

In the Anfinsen experiment what was the purpose of B - metcaptoethanol?

A

It reduces the disulphide bonds.

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9
Q

What is the Levinthal paradox?

A

The Levinthal parodic states that due to the large amount of degrees of freedom there are an astronomical amounts of possible conformations of a protein.

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10
Q

Where are ionic interactions strongest and why?

A

In the core of a protein due to the low dielectric constant.

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11
Q

What is the VDW contact distance?

A

r^-6

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12
Q

Do ionic forces or permenant dipoles greatly stabilise a protein?

A

Permenant dipoles although they are weaker.

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13
Q

What causes London Dispersion forces?

A

Non polar small dipoles at the VDW contact distance.

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14
Q

Are hydrogen bonds longer or shorter than covalent bonds?

A

Longer, so electronegative atoms are kept apart.

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15
Q

When are hydrogen bonds strongest?

A

When they are linear, for example in DNA. (The donor hydrogen will be along the acceptors lone pair orbital).

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16
Q

Are glutamate and aspatarte hydrogen donors or acceptors?

A

Acceptors.

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17
Q

Are lysine and arginine hydrogen donors or acceptors?

A

Donors.

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18
Q

Where are the most hydrogen bonds found in proteins?

A

Between two main chain atoms.

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19
Q

Why is water not a typical solvent?

A
  1. Has a high dielectric constant.
  2. Low compressibility.
  3. High specific heat capacity.
  4. High surface tension.
  5. High enthalpy of vaporisation.
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20
Q

Does water stabilise non polar substances?

A

No.

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21
Q

Why does S increase as the protein folds?

A

Water molecules in caged structures are released.

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22
Q

What drives protein folding?

A

Non covalent forces of attraction and repulsion.

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23
Q

What is the strongest non covalent interaction in aqueous medium?

A

Hydrogen bond.

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24
Q

In an alpha helix are all main chain CO and NH groups hydrogen bonded?

A

Yes.

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25
Q

In an alpha helix hydrogen bonds forms between the CO and the NH group ___ places in front.

A

4

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26
Q

How can longer alpha helices form?

A

Multiple helices can intertwine. Normally an alpha helix can not be more than 45A in length.

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27
Q

Are alpha helices left or right handed?

A

Right.

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28
Q

Do helices carry a macro dipole?

A

Yes, the amine end is positive.

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29
Q

How many residues are there per turn in an alpha helix?

A

3.6

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30
Q

What degree of rotation is there per turn in an alpha helix?

A

100

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31
Q

What is the rise in an alpha helix?

A

1.5A

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32
Q

Are helices amphiphilic?

A

Yes, but in a transmembrane protein it can also all be hydrophobic.

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33
Q

What angle are antiparallel beta sheets found at?

A

90 degrees.

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34
Q

What angle are parallel beta sheets found at?

A

Slightly offset.

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35
Q

Why do beta sheets sometimes adapt a twisted shape?

A

There can be steric repulsion in the backbone and side chain atoms.

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36
Q

How is a beta turn achieved?

A

A hydrogen bound between a CO and NH group which is 3 places ahead.

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37
Q

Why would a beta turn need to be achieved?

A

When a universal change in direction is required.

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38
Q

What is the Pauli Exclusion Principle?

A

That each orbital can hold two electrons with opposite spin

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39
Q

Name three examples of super secondary structure.

A

B-A-B unit
B hairpin
A-A motif

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40
Q

How long does an amino acid chain need to be to form domains?

A

At least 200 residues.

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41
Q

What occupies the cleft between domains?

A

Binding sites

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42
Q

How many layers of structure are found in domains and why?

A

2+ to bury hydrophobic residues.

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43
Q

What is the immunoglobulin fold held together by?

A

Disulphide bridges.

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44
Q

What is the immunoglobulin fold compromised off?

A

Antiparallel beta sheets surrounding a hydrophobic core.

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45
Q

What makes up the quaternary structure?

A

More than one polypeptide chain associated non covalently.

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46
Q

What type of tetramer is heamoglobin?

A

2a2b

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47
Q

What is an Oligomer?

A

A monomer whose molecules consist of relatively few repeating units.

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48
Q

What is an allosteric interaction?

A

When the binding of a ligand to one unit can affect the affinity of the ligand to the other unit.

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49
Q

What are post translational modifications?

A

Covalent modification of amino acid side cabins.

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50
Q

What type of group is

Phosphorylated?

A

Hydroxyl groups

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51
Q

Is phosphorylation reversible?

A

Yes

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52
Q

Glycosalation acts on which molecules?

A

Proteins that have been secreted.

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53
Q

What amino acid is often involved in glycosalation?

A

Asparagine

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54
Q

What does glycosalation allow?

A

An increase in hydrophilicity.

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55
Q

What is the post translational modification of proline called and what is it’s purpose?

A

Hydroxyproline

It strengthens newly formed collagen fibres, also preventing scurvy.

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56
Q

Y- Carboxyglutamate acts on residues in which molecule?

A

Prothrombin

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57
Q

Lack of which vitamin results in insufficient carboxylation of glutamate molecules?

A

Vitamin A

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58
Q

Protein families have similar amino acid sequences and structure, but different what?

A

Substrate affinity.

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59
Q

What is the serine protease family made up off?

A

Chymotrypsin, trypsin and elastase. All of these have an almost identical 3D structure.

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60
Q

What can give a protein extra function?

A

Tightly bound molecules.

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61
Q

What is the definition of a supersecondary structure?

A

The packaging of secondary structure elements into local modules.

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62
Q

What is the definition of a domain?

A

The assembly of part of a polypeptide chain into a compact globular structure, often with a specific function.

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63
Q

What is a nucleophile?

A

An electron donor.

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64
Q

What is an electrophile?

A

An electron acceptor.

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65
Q

What effect does nucleophilic substitution have on a molecule?

A

It inverts chirality.

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66
Q

What does glutamate dehydrogenase allow?

A

The oxidative deamination of glutamate into alpha- ketoglutamate.

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67
Q

How many subunits does glutamate dehydrogenase have?

A

6 - it is a hexamer.

Each subunit has 2 domains and a cleft between these to bind NAD+.

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68
Q

What stabalises the pyro phosphate group on NAD+?

A

A helix dipole.

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69
Q

Why do the two domains move closer together during the reaction in glutamate dehydrogenase?

A

To exclude bulk water from the active site.

70
Q

What is brought closer together when the two domains move closer together in the reaction involving glutamate dehydrogenase?

A

The alpha carbon on glutamate and the nictinamide ring in NAD+.

71
Q

In Glutamate dehydrogenase, which amino acid abstracts a proton from the glutamate amine group?

A

ASP165.

This allows hydride transfer from CA to C4 on the nicinamide ring.

72
Q

What two amino acids stabilise the glutamate side chains on the enzyme surface in glutamate dehydrogenase?

A

SER380 and LYS89.

73
Q

What is the purpose of LYS113 in glutamate dehydrogenase?

A

It stabilises the carbonyl group on the glutamate.

74
Q

What is the purpose of LYS125 and GLN in glutamate dehydrogenase?

A

They trap the water molecule.

75
Q

Why do the two domains open at the end of the reaction with glutamate dehydrogenase?

A

So LYS and ASP can become deprontated again.

76
Q

When the domains come together in glutamate dehydrogenase does the reaction have to occur?

A

No.

77
Q

Why can aspartate not fit into the active site of glutamate dehydrogenase?

A

It is shorted by CH2.

78
Q

When the a-ketoglutarate packs against the proteins surface it can only be attacked by the ammonia on one side, what does this result in?

A

Only L isomers of glutamate are formed.

79
Q

What would not occur if bulk water was not excluded in glutamate dehydrogenase?

A

Hydride transfer to NAD+.

80
Q

What does pKa equal?

A

-log(ka).

81
Q

Water is a weak ___?

A

Nucleophile.

82
Q

What does a molecules ionisation state depend on?

A

The pKa of it’s functional groups.

83
Q

What can greatly influence side chain pKa?

A

The environment.

84
Q

Why can amino acids be used as buffers?

A

They are polyprotic.

85
Q

When is a molecule deprotonated?

A

pH > pI

86
Q

When does histidine become protonated?

A

pH of around 6.

87
Q

What is the Henderson- Hasselbach equation?

A

pH= pKa + log (A-/HA)

88
Q

Enzymes enhance reactions by ______ and ______ effects.

A

Orientation, Proximity.

89
Q

What speed do enzymes increase the reaction rate too?

A

10^8 to 10^12.

90
Q

What do enzymes prefer to bind?

A

Translation states?

91
Q

What does binding to transition states to an enzyme do to the energy barrier?

A

It reduces it.

92
Q

Can transition states be isolated?

A

No.

93
Q

Do enzymes bind tightly?

A

No.

94
Q

Can enzymes undergo conformational change?

A

Yes.

95
Q

The induced fit theory is:

Substrate ______ to enzyme ______

A

Stressed, strained.

96
Q

What is a metalloenzyme?

A

When a metal is tightly associated to an enzyme.

Includes Fe, Cu, Zn

97
Q

What does it mean if an enzyme is metal activated?

A

A metal is loosely associated with the enzyme.

Eg
Ca, Mg

98
Q

What 4 things can metal ions participate in enzyme based reactions?

A
  1. They can stabilise transition state charge without effecting pH.
  2. They can generate nucleophilic species.
  3. They can increase binding interactions, such as Mg 2+ with ATP.
  4. Metal oxidation state changes can facilitate catalyst.
99
Q

What is an Apoenyzme?

A

An enzyme with no cofactor bound.

100
Q

What is a haloenzyme?

A

An enzyme with a bound cofactor:

101
Q

In NAD where does hydride transfer occur?

A

The nicinamide ring, which has a positive charge despite the whole charge being negative.

102
Q

What are oxidoreductase enzymes also known as?

A

Dehydrogenase.

103
Q

What process do transferase enzymes assist with?

A

Nucleophilic substitution reactions.

104
Q

Hydrolyses are a sub group of which other enzyme?

A

Transferases.

105
Q

Lysases/ synthases do what?

A

Add or remove groups to form a double bond.

106
Q

What is the purpose of isomerases?

A

Allow interconversion of isomeric forms of compounds.

107
Q

Do ligases require chemical energy?

A

Yes.

108
Q

What are ligases also known as?

A

Synthetases.

109
Q

How many domains are in the IG fold?

A

12

8 in heavy
4 in light

110
Q

How many heavy and light chains are there in the IG fold?

A

2 of each.

111
Q

What is an isoprenoid?

A

Steroid cholesterol and lipid vitamins.

112
Q

What effects the physical properties of a fatty acid?

A

Chain length and presence of double bonds.

113
Q

What defines the phospholipid type?

A

The alcohol attached to the phosphate group.

114
Q

Glycerol is a _____ _____ molecule.

A

Small, central.

115
Q

What type of linkage do plasmalogens use?

A

Vinyl - ether.

116
Q

What is a shingolipid?

A

An amide bond to another fatty acid.

117
Q

What allows self sealing of a membrane?

A

Diffusion along the plane?

118
Q

How much slower is diffusion across the membrane compared to diffusion along the plane of the membrane?

A

10^9

119
Q

How is cholesterol distributed in the membrane?

A

Evenly.

120
Q

What influences membrane curvature?

A

Phospholipid head size and the segregation of lipids.

121
Q

What shape are phosphatidyl chlorines?

A

Fairly flat.

122
Q

What shape are phosphatidyl ethanol amines?

A

Curved or cone shaped.

123
Q

What determines membrane fluidity?

A

Fatty acid and cholesterol content.

124
Q

How do bacteria regulate membrane fluidity?

A

Altering number of double bonds and fe length of the fatty acyl chain.

125
Q

What helps with membrane straightening?

A

Cholesterol.

126
Q

What are liposomes used for?

A

Experimental tools and delivery systems.

127
Q

What is the percentage composition of membranes?

A

10% carbohydrate
25-50% lipid
50-75% protein

Varies between membranes.

128
Q

What is the purpose of a FRAP experiment?

A

Quantifies lateral movement of membranes.

129
Q

What are intristix membrane proteins also known as?

A

Integral.

130
Q

What are extrinsic membrane proteins also known as?

A

Peripheral.

131
Q

How can you remove an integral membrane protein from a membrane?

A

Detergents.

132
Q

How embedded is an integral membrane protein?

A

Can be partially or fully embedded.

133
Q

What do peripheral membrane proteins associate with?

A

Integral proteins or associated with the lipid head group.

134
Q

How can you dissociate a peripheral membrane protein from the membrane?

A

Detergent or a salt wash.

135
Q

How do you remove anchored membrane proteins?

A

You have to remove the anchor.

136
Q

What type of tails to anchored membrane proteins have?

A

Greasy with ester or amide linkages. The side chains give it this property.

137
Q

What is a GPI protein?

A

Anchored protein with a bigger and bulkier group and the hydrophobic tail in the membrane. The c terminus is linked.

138
Q

What do transmembrane proteins often use to span the membrane?

A

Alpha helices.

139
Q

What does a low value on a hydropathy plot show?

A

Wants to be in a hydrophilic environment.

140
Q

What does a high value on a hydropathy plot show?

A

What’s to be in an hydrophobic environment.

141
Q

Where in channels are hydrophobic residues found?

A

The middle.

142
Q

What do pores transport across the membrane?

A

Ions.

143
Q

What is an example of a primary energy source?

A

ATP

144
Q

What is an example of a secondary energy source?

A

Coupling to a proton gradient.

145
Q

What is the energy an object has due to it’s position called?

A

Potential energy.

146
Q

What is the equation for work done?

A

Force applied x distance moved.

147
Q

Objects will move to ________ potential energy.

A

Decrease.

148
Q

What most the total kinetic energy and potential energy be?

A

The same.

149
Q

What is the formula for kinetic energy?

A

1/2 x mass x speed^2

150
Q

What does the Boltzmann distribution show?

A

That when the potential energy is low there is a high likelihood of the molecule being in that position.

151
Q

Most energy transferred by collisions is equal too?

A

KbT

152
Q

What happens to the potential energy as a protein unfolds?

A

It increases.

153
Q

Why is protein unfolding unlikely?

A

It requires a lot of unfavourable conditions.

154
Q

What does lots of ‘u’ states of a protein means…

A

There is high entropy.

155
Q

What are ‘F’ and ‘U’ ?

A

Macrostates.

156
Q

What does free energy take into account?

A

The number of microstates and the likelihood of microstates.

157
Q

What is the equation for ‘S’?

A

Kb x loge(N)

158
Q

What do all mixed microstates have?

A

An equal likelihood.

159
Q

When there is a high concentration of molecules in one place is the entropy low or high?

A

Low.

160
Q

In a mixed and separated mixture what is the pe?

A

The same.

161
Q

Na x Kb = ?

A

R.

162
Q

Delta G : A -> B (one mole) =?

A

RTloge(b/a).

If b/a is less than one will be spontaneous.

163
Q

What does mass action ratio represent?

A

Concentrations when equilibrium is not met.

164
Q

In a dead cell do all processes end up in equilibrium?

A

Yes.

165
Q

Is entropy independent of concentration?

A

Yes, can have intermolecular configurational entropy.

166
Q

If the number of products does not equal the number of reactants what unit must delta G be in?

A

Molar.

167
Q

What does deltaG equal when not at equilibrium?

A

DeltaG0 +RTln( P1P2 / R1R2)

OR

RTln( mass action ratio/ K)

168
Q

What does delta G equal at equilibrium?

A

0

169
Q

Why are H+ ions pushed through the channel?

A

It will be repelled by H+ and pulled though by anions.

170
Q

What is pe proportional too?

A

The charge of the object moved.

171
Q

What is the equation for energy change (joules)?

A

Charge on object (columbs) x PD (volts)

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