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BM 210: Introduction to Biochemistry > Block B Part 1: Proteins and Enzyme Catalysts > Flashcards

Block B Part 1: Proteins and Enzyme Catalysts Flashcards

1
Q

State 5 functions of proteins.

A

Catalysts
Transport Molecules
Storage Molecules
Mechanical Support
Immune protection
Movement
Transmission of nerve impulses
Growth and differentiation
(Lecture 1, Slide 3)

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2
Q

How are amino acids chiral?

A

As 4 different groups are bonded to the tetrahedral α (alpha) carbon
(Lecture 1, Slide 5)

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3
Q

What are the two mirror image isomers of amino acids?

A

L isomer and D isomer
(Lecture 1, Slide 5)

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4
Q

Which isomer of amino acids is the only one found in proteins?

A

The L isomer (remember L for Life)
(Lecture 1, Slide 5)

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5
Q

Why do amino acids exist as dipolar ions at neutral pH?

A

As the amino group (NH3+) and the carboxyl group (COO-) are charged
(Lecture 1, Slide 6)

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6
Q

What changes the ionisation state of the amino acids?

A

The pH in solution
(Lecture 1, Slide 6)

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7
Q

What is the reaction that forms a peptide bond between amino acids and what does it release?

A

It is a condensation reaction which releases water
(Lecture 1, Slide 8)

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8
Q

What is the primary structure of a protein?

A

The sequence of the amino acids
(Lecture 1, Slide 9)

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9
Q

What termninal is taken as the beginning of a polypeptide chain?

A

The amino terminal end
(Lecture 1, Slide 10)

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10
Q

Why does the backbone of a polypeptide have hydrogen bonding potential?

A

Because of the carbonyl groups and the hydrogen atoms that are bonded to the nitrogen of the amine group (NHR1R2)
(Lecture 1, Slide 10)

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11
Q

What is a disulphide bridge?

A

A way to connect 2 proteins using 2 sulphur atoms from 2 cysteines
(Lecture 1, Slide 11)

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12
Q

How are disulphide bridges formed?

A

By the oxidation of 2 cysteines
(Lecture 1, Slide 11)

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13
Q

What are the cross-linked cysteines in a disulphide bridge called?

A

Cystine
(Lecture 1, Slide 11)

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14
Q

How is the peptide bond essentially planar?

A

As six atoms lie in a plane
(Lecture 1, Slide 12)

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15
Q

What is a plane in biochemistry?

A

A plane refers to a flat surface or geometrical arrangement
(Lecture 1, Slide 12)

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16
Q

How does the peptide bond have partial double bond character?

A

Due to resonance
(Lecture 1, Slide 12)

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17
Q

What does the partial double bond character of a peptide bond result in?

A

Prevention of rotation around the bond
(Lecture 1, Slide 12)

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18
Q

Why is the trans peptide bond strongly favoured over the cis peptide bond?

A

As steric (spatial) clashes that arise in the cis form between the R groups
(Lecture 1, Slide 12)

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19
Q

Why is rotation allowed around the phi and psi bonds despite rotation around the whole peptide bond not being allowed?

A

As these involve single bonds in the protein backbone and don’t have resonance
(Lecture 1, Slide 13)

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20
Q

What do the phi (Φ) and psi (ψ) bonds and angles refer to?

A

Phi refers to the N-Cα bond whereas psi refers to the Cα-Carbonyl bond
(Lecture 1, Slide 13)

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21
Q

What does rotation around the phi and psi angles allow?

A

Proteins to fold in many ways
(Lecture 1, Slide 13)

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22
Q

What 2 things makes protein folding possible?

A

Restrictions by the rigidity of the peptide bond due to resonance
A restricted set of allowed phi and psi angles due to steric hinderance
(Lecture 1, Slide 13)

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23
Q

What is the secondary structure of a protein?

A

The 3D structure formed by hydrogen bonds between NH and CO groups of amino acids near each other in the primary structure
(Lecture 1, Slide 15)

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24
Q

What 3 things are prominent examples of secondary protein structure?

A

α-helices
ß-strands
turns
(Lecture 1, Slide 15)

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25
Q

What is an α-helix in secondary structure of a protein?

A

A tightly-coiled rod-like structure with the R groups sticking out from the axis of the helix
(Lecture 1, Slide 16)

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26
Q

Which of the backbone CO and NH groups form hydrogen bonds in an α-helix?

A

All of them, except those at the end of the helix
(Lecture 1, Slide 16)

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27
Q

What is the α-helix stabilised by?

A

Intrachain (same chain) hydrogen bonds
(Lecture 1, Slide 16)

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28
Q

Are α-helices primarily right or left handed?

A

Right handed
(Lecture 1, Slide 16)

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29
Q

What are ß-sheets formed by?

A

Adjacent ß-strands
(Lecture 1, Slide 17)

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30
Q

What is a ß-strand?

A

A linear, or nearly linear stretch of a polypeptide that is stretched out and extended
(Lecture 1, Slide 17)

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31
Q

How are ß-sheets stabilised?

A

Hydrogen bonds between strands
(Lecture 1, Slide 18)

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32
Q

Are the strands of a ß-sheet parallel or antiparallel?

A

They can be parallel, antiparallel or mixed
(Lecture 1, Slide 18)

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33
Q

What 2 conformations can ß-sheets have?

A

Flat or twisted
(Lecture 1, Slide 18)

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34
Q

What 2 ways can proteins change directions?

A

ß-turns (hairpin turns) and Omega (Ω) loops
(Lecture 1, Slide 19)

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35
Q

What does the tertiary structure of a protein refer to?

A

The spatial arrangement of amino acids that are far apart in the primary structure, and the pattern of disulphide bridges
(Lecture 1, Slide 20)

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36
Q

What is the location of polar and non-polar (hydrophobic) amino acids in globular proteins ?

A

The interior contains mainly non-polar amino acids whereas the exterior contain mainly polar amino acids
(Lecture 1, Slide 21)

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37
Q

What is the location of polar and non-polar (hydrophobic) amino acids in membrane proteins?

A

The interior contains mainly polar amino acids whereas the interior contains mainly non-polar amino acids
(Lecture 1, Slide 22)

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38
Q

What are motifs (supersecondary structures)?

A

Combinations of secondary structures that are found in many proteins
(Lecture 1, Slide 23)

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39
Q

What do some proteins have that can be called (modular) domains?

A

Two or more similar or identical compact structures
(Lecture 1, Slide 23)

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40
Q

What is the role of ß-mercaptoethanol?

A

It reduces disulphide bonds and is itself oxidised forming dimers
(Lecture 1, Slide 25)

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41
Q

What proteins are said to display quaternary structure?

A

Proteins composed of multiple polypeptide chains (known as subunits)
(Lecture 1, Slide 26)

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42
Q

What determines the folding of a protein into its 3D structure?

A

The amino acid sequence
(Lecture 1, Slide 28)

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43
Q

What is post-translational modification in a protein?

A

After synthesis (translation), many proteins undergo further modification determining their fate in the cell
(Lecture 1, Slide 31)

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44
Q

What are 2 types of post-translational modification?

A

Converting a proprotein (precursor protein) into a mature protein by proteolytic cleavage
Addition of various chemical groups modifying either the N-terminal amino group, the C-terminal carboxyl group or the side chains of the amino acids throughout the length of the protein
(Lecture 1, Slide 31)

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45
Q

What can lack of appropriate post-translational protein modification lead to?

A

Pathological conditions
(Lecture 1, Slide 31)

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46
Q

What does a catalyst do to the activation energy of a reaction?

A

It lowers it
(Lecture 2, Slide 5)

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47
Q

What does a catalyst do to the rate of a reaction?

A

It increases it
(Lecture 2, Slide 5)

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48
Q

Is a catalyst consumed in a reaction?

A

No, it remains chemically unchanged
(Lecture 2, Slide 5)

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49
Q

Do catalysts affect the equilibrium?

A

No
(Lecture 2, Slide 5)

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50
Q

How is an enzymes active site formed?

A

Folding of a protein brings side-chains of various amino acids that may be far apart in the primary sequence into close proximity, forming an active site
(Lecture 2, Slide 6)

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51
Q

What are the 5 stages of an enzyme catalysed reaction?

A
  1. Substrates enter active site
  2. Substrates are held in place by weak interactions
  3. Substrates are converted into products
  4. Products are released
  5. Active site is now available for new substrates
    (Lecture 2, Slide 7)
52
Q

How does the active site position the substrate(s)?

A

In the most favourable relative orientation for the reaction to occur
(Lecture 2, Slide 8)

53
Q

Is the active site complementary to the transition state?

A

Yes
(Lecture 2, Slide 8)

54
Q

What stabilises the electron distribution of the transition site during an enzyme catalysed reaction?

A

Amino acid side chains of the active site
(Lecture 2, Slide 8)

55
Q

Why is the substrate strained on binding to the active site?

A

As it lowers the activation energy and increases the reaction rate
(Lecture 2, Slide 8)

56
Q

How are products released from the enzyme?

A

As the products bind less tightly to the enzyme and are released
(Lecture 2, Slide 8)

57
Q

What are 3 ways that reactive groups at the active site surface catalyse the reaction?

A

Donating or withdrawing electrons
Stabilising or generating free radical intermediates
Forming temporary covalent bonds (a transition state intermediate)
(Lecture 2, Slide 10)

58
Q

What are non-proteins molecules in an enzyme called?

A

Cofactors
(Lecture 2, Slide 12)

59
Q

What are 3 types of cofactors found in enzymes?

A

Metal group
Prosthetic group
Coenzyme
(Lecture 2, Slide 12)

60
Q

What is a prosthetic group cofactor?

A

A covalently bound organic molecule
(Lecture 2, Slide 12)

61
Q

What is a coenzyme cofactor?

A

A tightly but not covalently bound organic molecule
(Lecture 2, Slide 12)

62
Q

What is an enzyme with a prosthetic group / coenzyme called and is it catalytically active?

A

It’s called a halo-enzyme and it is catalytically active
(Lecture 2, Slide 12)

63
Q

What is an enzyme without a prosthetic group / coenzyme called and is it catalytically active?

A

It’s called an apoenzyme and it is catalytically inactive
(Lecture 2, Slide 12)

64
Q

What are the 6 types of enzymes?

A

Hydrolases
Oxidoreductases
Transferases
Lyases
Isomerases
Synthetases
(Remember HOTLIS)
(Lecture 2, Slide 14)

65
Q

What reactions do oxidoreductases cover?

A

Oxidation and reduction reactions
(Lecture 2, Slide 14)

66
Q

What do transferases do?

A

Transfer a chemical group from one substrate to another
(Lecture 2, Slide 14)

67
Q

What do hydrolases do?

A

hydrolysis (water splits the bond) of C-O, C-N, C-S and O-P bonds
(Lecture 2, Slide 14)

68
Q

What do lyases do?

A

Addition reaction across a double bond
(Lecture 2, Slide 14)

69
Q

What do isomerases do?

A

Intramolecular arrangements
(Lecture 2, Slide 14)

70
Q

What do synthetases do?

A

Form bonds between two substrates
(Lecture 2, Slide 14)

71
Q

What is 1 enzyme unit (EU) equal to and what does it measure?

A

An enzyme unit measures enzyme activity with 1 enzyme unit being equal to 1 μmol min-1
(Lecture 2, Slide 15)

72
Q

What is the specific activity of an enzyme and what does this give a measurement of?

A

Activity of an enzyme per mg of total protein in the enzyme preparation (expressed in μmol mil-1 mg-1)
this gives a measurement of the purity of the enzyme
(Lecture 2, Slide 16)

73
Q

What is the reaction rate?

A

Generation of the reaction product with time
(Lecture 2, Slide 17)

74
Q

What 3 things needs to be fixed in order to measure an accurate reaction time?

A

Enzyme concentration
Temperature
pH
(Lecture 2, Slide 17)

75
Q

What are 3 reasons why the rate of a reaction graph is hyperbolic?

A

Accumulation of product
Depletion of substrate
Denaturation of enzyme
(Lecture 2, Slide 17)

76
Q

What needs to measured to ensure a meaningful quantitative assay of enzyme activity?

A

Initial velocities (V0; reaction rates)
(Lecture 2, Slide 18)

77
Q

What are 5 factors affecting enzyme activity?

A

pH
Temperature
Concentration of enzyme
Concentration of substrate
Covalent modification of enzyme
(Lecture 2, Slide 21)

78
Q

State 2 reasons why chemical reactions proceed faster at higher temperatures.

A

Molecules move faster, giving them a greater chance to collide
Electrons gain activation energy easier
(Lecture 2, Slide 25)

79
Q

Why does too high of a temperature denature an enzyme?

A

As it leads to a loss of hydrogen bonding holding the enzyme together, resulting in it changing shape and no longer fitting the substrate
(Lecture 2, Slide 25)

80
Q

What does the temperature optimum depend on?

A

The time of incubation
(Lecture 2, Slide 25)

81
Q

How does increasing enzyme concentration effect the relative activity normally?

A

Predictable linear increase in product formation
(Lecture 2, Slide 26)

82
Q

How does increasing enzyme concentration effect the relative activity when the enzyme dimer is active and the enzyme monomer is inactive or has low activity and why?

A

Starts of with less activity than normal as active dimer dissociates at low concentration, but then increases more rapidly than usual
(Lecture 2, Slide 27)

83
Q

How does increasing enzyme concentration effect the relative activity when the enzyme monomer is active and why?

A

It increases more rapidly than normal at first but then increases slower than normal as the enzyme associates to less active dimer at high concentrations
(Lecture 2, Slide 28)

84
Q

What is Km (the Michaelis constant)?

A

The concentration of substrate required to achieve half the maximum rate of the reaction
(Lecture 2, Slide 29)

85
Q

What does the Michaelis-Menten equation describe?

A

The dependence of the rate of reaction on concentration of substrate at a steady state and vast molar excess of substrate over enzyme
(Lecture 2, Slide 30)

86
Q

What is the equation of the Michaelis-Menten equation?

A

v = Vmax[S] / Km + [S]
v = rate of reaction
Vmax = max rate of reaction
[S] = concentration of substrate
Km = Michaelis constant
(Lecture 2, Slide 30)

87
Q

What does high Km correspond to?

A

Low affinity
(Lecture 2, Slide 31)

88
Q

Do enzymes with a low Km compared to the concentration of the substrate act at their maximum or minimum rate?

A

Maximum
(Lecture 2, Slide 31)

89
Q

Is the rate of reaction of enzymes with a low Km compared to the concentration of the substrate affected by minor changes in the substrate concentration?

A

No
(Lecture 2, Slide 31)

90
Q

Does the rate of reaction of enzymes with a high Km change a small or large amount with minor changes in the concentration of the substrate?

A

Large
(Lecture 2, Slide 31)

91
Q

Why can an enzyme with high Km (low affinity) eventually outperform an enzyme with low Km (high affinity)?

A

The Km number only refers to the amount of substrate required for the enzyme to operate at half of their maximum velocity (Vmax/2) and isn’t related to the actual vMax value. At high substrate concentrations where both enzymes may be operating at, or close to, vMax the Km of the enzyme starts to matter less and less
(Lecture 2, Slide 32)

92
Q

State 2 ways to experimentally determine Km and Vmax.

A
  1. Incubation of enzyme under optimal conditions for a short time (assumes no change in concentration of substrate or product)
  2. Using a range of concentrations of substrates
  3. Plotting the double reciprocal (Lineweaver-Burk) plot.
  4. Extrapolating back from the experimental points to determine the intercepts
    (Lecture 2, Slide 33)
93
Q

What is the Lineweaver-Burk double reciprocal plot?

A

It is a graphical representation of the Michaelis-Menten equation where 1/v is on the Y axis and is plotted against 1/s on the X axis
(Lecture 2, Slide 34)

94
Q

What is the slope and intercept in a Lineweaver-Burk plot?

A

The slope is Km/Vmax and the intercept is 1/Vmax
(Lecture 2, Slide 34)

95
Q

What is a sequential reaction in the context of enzymes with two substrates?

A

Each substrate binds in turn
(A + Enz <> A-Enz
A-Enz + B <> A-Enz-B <> C-Enz-D <> C-Enz + D
C-Enz <> Enz + C)
(Lecture 2, Slide 35)

96
Q

What is a ternary complex?

A

A complex containing 3 different molecules
(Lecture 2, Slide 35)

97
Q

What is a Ping-pong reaction in the context of enzymes with two substrates?

A

One substrate reacts and modifies the enzyme, then the second substrate reactions with the modified enzyme
(A + Enz <> A-Enz <> C-Enz* <> C + Enz*
B + Enz* <> B-Enz* <> D-Enz <> D + Enz)
(Lecture 2, Slide 37)

98
Q

What is an allosteric enzyme?

A

An enzyme containing binding sites other than substrate binding sites
(Lecture 2, Slide 38)

99
Q

Where are allosteric enzymes often found?

A

Often in a multi-subunit complex, with more than one active site in the complex
(Lecture 2, Slide 38)

100
Q

How do allosteric enzymes bind more than one substrate?

A

Binding of substrate to the active site of the first subunit leads to change in the conformations facilitating binding of substrates to other active sites
(Lecture 2, Slide 38)

101
Q

As opposed to a Michaelis-Menten-type enzyme forming a hyperbolic curve, what graph does an allosteric enzyme form on a graph plotting the rate of the reactions vs the substrate concentration?

A

Sigmoidal (S - shaped curve)
(Lecture 2, Slide 38)

102
Q

How do reversible inhibitors bind to enzymes?

A

Non-covalently
(Lecture 2, Slide 44)

103
Q

Are reversible inhibitors specific or non-specific?

A

Relatively unspecific
(Lecture 2, Slide 44)

104
Q

What is the mechanism of reversible inhibitors?

A

Block substrate binding or hindering catalytic steps
(Lecture 2, Slide 44)

105
Q

What are irreversible inhibitors also known as?

A

“Inactivators”
(Lecture 2, Slide 44)

106
Q

How do irreversible inhibitors bind to the enzyme?

A

Covalently (“suicide inhibitors”)
(Lecture 2, Slide 44)

107
Q

What is the main type of irreversible inhibitors?

A

Substrate analogues
(Lecture 2, Slide 44)

108
Q

What are substrate analogues?

A

Chemical compounds with a similar chemical structure to the substrate molecule
(Lecture 2, Slide 44)

109
Q

Do irreversible inhibitors take part in the reaction?

A

Yes
(Lecture 2, Slide 44)

110
Q

Is a competitive inhibitor reversible?

A

Yes
(Lecture 2, Slide 44)

111
Q

How does a competitive inhibitor inhibit an enzyme?

A

It competes with the substrate for binding at the active site
(Lecture 2, Slide 45)

112
Q

What 2 factors affect the effectiveness of a competitive inhibitor?

A

The relative affinities of the substrate and inhibitor for binding the enzyme
The relative concentrations of the substrate and inhibitor
(Lecture 2, Slide 45)

113
Q

How does a competitive inhibitor change Vmax and Km?

A

Vmax is unchanged, Km is increased
(Lecture 2, Slide 46)

114
Q

How is a competitive inhibitor overcame?

A

By adding enough of the substrate to outcompete the inhibitor for binding
(Lecture 2, Slide 46)

115
Q

Do mixed inhibitors bind to the enzymes active site?

A

No
(Lecture 2, Slide 47)

116
Q

Does a mixed inhibitor bind prior to the substrate binding or to the enzyme substrate complex?

A

It can bind in either scenario
(Lecture 2, Slide 47)

117
Q

What do mixed inhibitors do to the substrate binding site?

A

They distort it
(Lecture 2, Slide 47)

118
Q

What 2 things does a mixed inhibitor distorting an active site affect?

A

Apparent substrate affinity
Catalytic turn-over (the limiting number of chemical conversions of substrate molecules per second that a single active site will execute for a given enzyme concentration) which slows down catalysts
(Lecture 2, Slide 47)

119
Q

How does a mixed inhibitor change Km and Vmax?

A

They can either increase or decrease Km and they decrease Vmax
(Lecture 2, Slide 47)

120
Q

Does a non-competitive inhibitor bind to the enzyme’s active site?

A

No
(Lecture 2, Slide 49)

121
Q

How does a non-competitive inhibitor affect substrate affinity and rate of reaction?

A

The substrate affinity remains unchanged, but the rate of the reaction is slowed
(Lecture 2, Slide 49)

122
Q

How does a non-competitive inhibitor affect Km and Vmax?

A

Km is unchanged, Vmax is decreased
(Lecture 2, Slide 50)

123
Q

Does adding more substrate during non-competitive inhibition change the rate of reaction?

A

No
(Lecture 2, Slide 50)

124
Q

Is non-competitive inhibition reversible?

A

Yes
(Lecture 2, Slide 50)

125
Q

What effect do allosteric inhibitors have on the Km and substrate affinity?

A

They increase Km and therefore lower the apparent affinity of the enzyme for it’s substrate (see Lecture 2, Slide 31)
(Lecture 2 , Slide 52)

126
Q

What does a decrease in substrate affinity due to allosteric inhibitors lead to?

A

A decrease in enzyme activity
(Lecture 2, Slide 52)

BM 210: Introduction to Biochemistry (12 decks)

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