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Biochemistry > Semester 2 > Flashcards

Semester 2 Flashcards

1
Q

High / Low Affinity Binding Curve:

What does the release of the FIRST oxygen do?

A

It causes a conformational change in the other 3 subunits.
It converts them from a relaxed state to a more tense state. (Back to a lower affinity!)
So we have EASIER release of the 2nd oxygen, which makes it even more tense!
And then the same process with the 3rd and 4th oxygen…

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2
Q

High / Low affinity binding curve:

Why is this type of curve NOT seen in Myoglobin?

A

Due to its structure: It only has 1 subunit and therefore NO cooperative activity.

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3
Q

Identify the correct characteristic of Hydroxyproline + Hydroxylysine

A

They are required for proper functioning of Collagen.

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4
Q

The protein capsid of a virus has what structure?

A

Primary, secondary, tertiary AND quaternary structure!

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5
Q

Which compound is an inhibitor of Nitric Oxide Synthase?

A

N-Methylarginine

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6
Q

Methyllysine has the following important roles…

A

Epigenetics + Myosin function

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7
Q

Food Pickling affects protein structure by disrupting…

A

Electrostatic Interactions

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8
Q

Which amino acid is commonly found in Beta Turns?

A

Cis- Proline

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9
Q

Which of the following cofactors is required for the formation of Gamma- Carboxyglutamate?

A

Vitamin K

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10
Q

The effect of pH on the binding of O2 to Haemoglobin is known as the…

A

Bohr Effect

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11
Q

The following type of Alpha-Helix is commonly found in membranes to form Pores…

A

Amphipathic

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12
Q

An elite athlete trains for 4 weeks at 4,500m. What is the efficiency of O2 transport from the lungs to the tissues?
(Graph)

A

37%

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13
Q

What molecule provides proteins with ‘Elastic’ properties?

A

Desmosine

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14
Q

What amino acid is a ‘classic’ disruptor of Alpha- Helices?

A

Proline

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15
Q

What is an INCORRECT characteristic for protein alpha- helices?

A

A channel is formed down the centre of the alpha helix.

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16
Q

Phosphoserine, phosphothreonine and phosphotyrosine are formed by…

A

Kinases

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17
Q

What methods can be used to determine the 3D structure of proteins?

A

X-Ray Crystallography or Nuclear Magnetic Resonance (NMR)

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18
Q

What roles do metals perform in Restriction Enzymes?

A

They help ALIGN the Scissile bond correctly in the active site and they REDUCE electrostatic repulsion.

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19
Q

The Aconitase enzyme converts Citrate to Isocitrate through…

A

Sequential processes of Dehydration/ Hydration

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20
Q

What roles does Mg2+ play in the functioning of Hexokinases?

A

It REDUCES electrostatic repulsion and correctly orientates the SUBSTRATES of the hexokinase reaction.

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21
Q

Why is Vitamin D currently a ‘hot topic’?

A

It is thought to reduce infection by the Covid-19 virus.

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22
Q

How can UV-visible Spectroscopy be used to detect oxygen levels in the blood?

A

By measuring the RATIO of the Soret band absorbance at 414nm and 429nm.

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23
Q

What is the biochemical role of Glutathione Peroxidase?

A

It converts Hydrogen Peroxide to water, utilising GSH as a reductant!

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24
Q

What is the biochemical / physiological function of Carbonic Anhydrase?

A

It is an enzyme that REVERSIBLY converts C02 to carbonic acid OR carbonic acid to C02.

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25
Q

What are the functions of the Cytochrome P450 enzymes?

A

Vitamin D Synthesis
Testosterone and Oestrogen Synthesis
Bile Salt Synthesis
Drug Metabolism

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26
Q

What is the function of bile salts?

A

They act as Biological Detergents in the small intestine and facilitate excretion of EXCESS Cholesterol.

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27
Q

What amino acid binds to the Iron-Sulfur centre of Aconitase?

A

Cysteine

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28
Q

An enzyme has a Km of 0.5mM while the substrate concentration is 10mM.
At what % of Vmax is the enzyme catalysing the conversion of substrate to product?

A

V0 = Vmax x [S] divided by KM + [S]
(Michaelis - Menten Equation)

For KM = 0.5mM
and
[S] = 10mM

( If it’s a percentage of Vmax then assume the Vmax is always 100%!)

V0 = 100% x 10 divided by (0.5 + 10)

V0 = 95% of Vmax!

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29
Q

An enzyme has a Km of 0.5mM, a Vmax of 100 mmoles of product formed per minute and the substrate concentration is 10mM.
Calculate V0.

A

V0 = Vmax x [S] divided by KM + [S]
(Michaelis - Menten Equation)

KM = 0.5
Vmax = 100mmoles product per min
[S] = 10mM

V0 = 100 x 10 divided by 0.5 + 10

V0 = 95 mmoles product formed per min!
(V0 is ALWAYS IN THE SAME UNIT as Vmax!)

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30
Q

The reaction catalysed by Hexokinase is as follows: Glucose +ATP > Glucose-6-phosphate + ADP
What is the role of ATP in this reaction?

A

Provide energy to drive the reaction forward AND to donate a phosphate (Pi)

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31
Q

What parameters are affected by doubling enzyme concentration?

A

Vmax and Vi

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32
Q

What compound binds PERMANENTLY to a protein?

A

Prosthetic Group

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33
Q

What molecule is NOT an enzyme cofactor?

A

Glutamate

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34
Q

Enzymes are biological catalysts that…

A

INCREASE the rate of reaction by REDUCING the Transition State Energy Barrier

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35
Q

The affinity of an enzyme for a substrate is indicated by the…

A

Km

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36
Q

The Km of a reaction is 5mM, Vmax is 20nmoles / minute and substrate concentration is 5nM.
What is the rate of reaction Vi? (Interchangeable with V0)

A

V0 = vmax x [S] divided by km + [S]

V0 = 20 x 5 divided by 5 + 5

V0 = 10 nmoles / min (SAME UNITS AS VMAX!)

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37
Q

What mechanims of Rate Enhancement are used by Chymotrypsin?

A

Acid base catalysis
Covalent catalysis
Electrostatic catalysis / environment
Proximity + orientation effects

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38
Q

B with a lone pair of electrons in covalent and base catalysis is a…

A

Base Catalyst

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39
Q

NADPH donates … electrons to Cytochrome P450 Reductase, which donates… electrons to Cytochrome P450

A

2

1

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40
Q

In the catalytic mechanism of Chymotrypsin, His 57 acts as a…

A

BOTH base and acid catalyst

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41
Q

What rate enhancement mechanism is NOT used by Chymotrypsin?

A

Metal Ion Catalysis

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42
Q

Base Catalysis is defined as…

A

Temporary proton abstraction

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43
Q

In Elastase, the catalytic triad consists of…

A

Asp-102, Ser-195 and His-57

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44
Q

The substrate specificity of Trypsin is defined by a binding pocket that contains…

A

A negatively charged Aspartate residue

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45
Q

The catalytic mechanism of chymotrypsin, trysin and elastase is a…

A

2 substrate ping pong mechanism

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46
Q

What is INCORRECT regarding covalent catalysis?

A

Cannot take place with hydroxyl groups

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47
Q

The first step in catalysis by Chymotrypsin is…

A

Substrate binding

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48
Q

Rate Enhancement strain and distortion takes place in…

A

Lysozyme and Endonucleases

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49
Q

If you add 200ul of your 6M ethanol to the reaction, what is the FINAL concentration in the cuvette during the reaction? Final volume = 2.4 ml.

A

Vi x Ci = Vf x Cf

Vi = 200ul
Vf = 2400ul (CONVERT UNITS)
Ci = 6000mM (as answer was in mM, if theres a M and an mM value, convert to mM!)

Cf = 200 x 6000 / 2400
= 500mM

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50
Q

In the alcohol dehydrogenase practical (ADH), you measured the initial rates (Vi) of the following reaction:
C2H5OH + NAD+ > CH3CHO + NADH + H+
Which component is DIRECTLY measured?

A 
NADH increase
 (you are measuring the change in absorbance at 340nm ie. the conversion of NAD+ to NADH)
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51
Q

In the ADH practical you measured the initial rate over … seconds

A

30

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52
Q

You are using a P200 pipette set at 050. What volume will this measure?

A

50 ul

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53
Q

In order to measure the REDUCTION of NAD+ to NADH your spectrophotometer wavelength will be set to…

A

340 nm

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54
Q

In the ADH practical, the spectrophotometer should be ‘blanked’ by…

A

Checking the correct wavelength has been set, inserting a cuvette containing 2.5ml water OR buffer, then pressing ‘measure blank’

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55
Q

In order to measure the OXIDATION of NADH to NAD+ your spectrophotometer wavelength will be set to…

A

340nm

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56
Q

You have measured the absorbance of 1nM solution of pure compound Y at 340nm.
The pathlength of the cuvette is 1cm. If the measured absorbance is 0.05, what is the extinction coefficient of compound Y?

A

Beere-Lambert equation: Abs =ecl

E = Abs/ cl
= 0.05 / (1mM x1cm )

= 50 mM -1 cm -1

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57
Q

Which component of the enzyme reaction is added immediately before oressing ‘measure sample’ on spectrophotometer?

A

Enzyme

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58
Q

What is NOT a common function of carbohydrates?

A

Catalysing reactions in cells

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59
Q

Which carbon atom in a glucose ring can have a hydroxyl group bound in an ‘Up’ or ‘Down’ orientation?

A

Anomeric carbon

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60
Q

Which bond links glucose monomers in Maltose?

A

Alpha 1-4 glycosidic bonds

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61
Q

Which is NOT a storage carbohydrate in plants?

A

Glycogen

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62
Q

What is FALSE about cellulose?

A

Coils are stabilised by hydrogen bonds

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63
Q

Mushroom cell walls are made from…

A

Chitin

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64
Q

Which enzyme is most likely to hydrolyse a Beta 1-4 glycosidic bond?

A

Endochitinase

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65
Q

What property of cellulose makes it HARD for most mammals to digest?

A

The anomeric state of its monomers!

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66
Q

What is the name of the monomers that make up Chitin?

A

N - acetylglucosamine

67
Q

When Chitin is converted to Chitosan, which group is LOST from its structure?

A

Acetyl

68
Q

The shells of molluscs are made from chitin.

True or false?

A

FALSE

Shells are made from calcium carbonate, beaks and teeth are made from chitin

69
Q

What is NOT a common function of carbohydrates?

A

Catalysing reactions in cells

70
Q

Which carbon atom in the pyranose form of glucose can have a hydroxyl group bound in an ‘UP’ or ‘down’ orientation?

A

Anomeric carbon

71
Q

What type of bond links glucose monomers in a molecule of maltose?

A

Alpha 1-4 glycosidic bond

72
Q

What is a branched homopolysaccaride?

A

Glycogen

73
Q

Which polysaccharide has alpha 1-6 glycosidic bonds every 24-30 residues?

A

Amylopectin

74
Q

What polysaccharide does NOT contain an N- acetyl group?

A

Heparin

75
Q

What is the best description of a proteoglycan?

A

A Core protein with an attached glycosaminoglycan.

76
Q

What is NOT a major component of the Extracellular Matrix?

A

Actin filaments

77
Q

Are GAGs heteropolysaccharides or homopolysaccharides?

A

heteropolysaccharides

78
Q

Which GAG has the longest chain length?

A

Hyaluronan

79
Q

Which GAG forms ‘dead horny’ structures?

A

Keratan sulfate

80
Q

One monomer in the repeated disaccharide that makes up a GAG is ALWAYS…

A

N-acetylglucosamine OR N-acetylgalactosamine

81
Q

Which GAG is NOT most commonly found bound to proteins?

A

Hyaluronan

82
Q

What is

A
83
Q

According to a recent paper, which type of molecule helps coronavirus bind to cells?

A

Heparan sulfate proteoglycan

84
Q

Which molecules determine human blood types?

A

Glycolipids

85
Q

N-linked glycoproteins have carbohydrates attached to which amino acid?

A

Asparagine

86
Q

What is the best description of a proteoglycan?

A

Core protein with attached GAG

87
Q

Which atom is NOT involved in linking oligosaccharides to glycoproteins?

A

Oxygen in the R group of asparagine

88
Q

What best describes a glycoprotein?

A

Large protein with small CHOs attached

89
Q

The time course of the alcohol dehydrogenase graph shows different final absorbances depending on the ethanol concentration.
This is due to…

A

The reactions reaching an equilibrium (reaction is reversible)

90
Q

The absorbance for alcohol dehydrogenase was measured at 340nm because…

A

NAD+ was being reduced to NADH

91
Q

What would the x axis label be for the Michaelis Menten alcohol dehydrogenase plot?

A

Ethanol concentration - mM

92
Q

What would the y axis label be for the Michaelis Menten alcohol dehydrogenase plot?

A

Initial velocity - Change in Abs at 340nm min-1

93
Q

What is the best definition of vmax?

A

Vmax is the maximum rate of reaction under specific conditions used

94
Q

How can you use Michaelis Menten plot to estimate vmax?

A

Find the y axis value where the plot plateaus off at an infinite substrate concentration

95
Q

What is the best definition of Km?

A

Km is the Michaelis constant, a measure of enzyme- substrate affinity

96
Q

How can you use Michaelis Menten plot to estimate Km?

A

Find the x axis value where rate = 1/2 of vmax

97
Q

What is the shortest length of hydrocarbons in a fatty acid?

A

4

because subunit that produces fatty acids can only add 2 carbons at a time

98
Q

What is the longest length of hydrocarbons in a fatty acid chain?

A

36

99
Q

What do triglycerides include?

A

3 fatty acids, 3 ester bonds and 1 glycerol

100
Q

How many calories per gram of fat?

A

9

101
Q

Sphingolipids can be classed as?

A

Phospholipid and a glycolipid

102
Q

How many non- polar tails do sphingolipids, finger lipids and galactolipids have?

A

2

103
Q

A lipid wrapped in a cell membrane contains cholesterol and…

A

Sphingolipids

104
Q

Eicosanoids are derived from…

A

Arachidonic acid

105
Q

What cannot passively cross the cell membrane?

A

Cholesterol

106
Q

Which vitamin is NOT found in eggs?

A

Vitamin C

107
Q

What levels of protein structure only apply to 1 polypeptide chain?

A

Secondary structure
Tertiary structure
Primary structure

108
Q

What are the control points of glycolysis?

A

Pyruvate kinase
Hexokinase
Phosphofructokinase

109
Q

Stage 1 of respiration takes place in the…

A

Cytosol

110
Q

Where does glycolysis take place in the cell?

A

Cytosol

111
Q

What is the benefit of lactate fermentation in humans?

A

Continued supply of NAD+

112
Q

What enzymes are found in the mitochondrial matrix?

A

Malate dehydrogenase
Fumarase
Succinyl CoA synthetase

113
Q

The end product of glycolysis is…

A

Pyruvate

114
Q

What inhibits the formation of Acetyl CoA from pyruvate?

A

Acetyl CoA

115
Q

The role of ATP in the reaction catalysed by Hexokinase is to…

A

Provide energy to drive reaction forward

Donate a phosphate

116
Q

In glycolysis, ATP is utilised by the following enzymes…

A

Phosphofructokinase-1
Hexokinase
Phosphofructokinase-2

117
Q

Fructose 1-6 bisphosphate is formed during glycolysis because…

A

It can be broken down into 2,3 carbon sugar phosphates

It is symmetrical

118
Q

Glucose 6 phosphate is produced during the first reaction in glycolysis. Why?

A

Because glucose 6 phosphate does NOT affect concentration gradient of glucose, allowing continued glucose uptake

Because glucose 6 phosphate is NOT a ligand for glucose transporters

119
Q

What intermediate is unique to glycolysis in Erthrocytes?

A

2,3-bisphosphoglycerate

120
Q

In the FULL oxidation of a 16-carbon fatty acid during respiration, the NET yield of ATP per fatty acid is approx…

A

108 ATP

121
Q

Is you were asked to measure a volume of 15ul what pipettes should you use?

A

P20

122
Q

What is the main energy source of Erythrocytes?

A

Glucose

123
Q

In the alcohol dehydrogenase practical, you calculated the extinction coefficient for NADH.
You calculated value was lower than the expected value, why?

A

The assumption that ALL NAD+ is converted to NADH is incorrect.
It is a reversible reaction, thus equilibrium has been reached!

124
Q

Synthesis of FAs by fatty acid synthase:

Most 2 carbon units are provided by the substrate…

A

Malonyl CoA

Acetyl CoA is only for the very first 2C units

125
Q

Identify the component that does NOT form part of glycerophospholipids

A

Sphingomyelin

126
Q

Mammals can’t introduce double bonds to FA chains between which carbon and terminal end?

A

C10

Can readily introduce at C9

127
Q

The reaction catalysed by which enzyme is the rate limiting step of FA biosynthesis?

A

Acetyl- CoA carboxylase

Production of manyl CoA from Acetyl CoA

128
Q

Where does FA synthesis take place?

A

Cytosol

129
Q

In TOTAL one 16 carbon fatty acid can produce how many molecules of ATP?

A

108 ATP

130
Q

Which enzyme is the rate limiting step for B oxidation?

A

Carnitine acyl- transferase 1

131
Q

What following compounds are classified as hydrophobic vitamins…

A

Vitamins A, D, E and K

132
Q

What molecule triggers the release of fatty acids from adipocytes?

A

Glucagon

133
Q

Which additional enzyme is required for B oxidation when catabolising an UNsaturated FA?

A

Enoyl-CoA isomerase (making an isomer, cis-trans)

134
Q

The utilisation of a proton gradient to generate heat rather than ATP is due to the presence of… in the inner mitochondrial membrane

A

Uncoupling Protein 1

135
Q

What metabolite is NOT an intermediate of the Citric Acid Cycle?

A

Acetyl-CoA

136
Q

In the reaction of Succinyl CoA to Succinate, the conversion of GDP + Pi > GTP is an example of…

A

Substrate level phosphorylation

137
Q

The transport of ADP into the mitochondrial matrix requires…

A

Adenine Nucleotide Translocase (antiporter)

138
Q

In the electron transport chain ETC, FADH2 donates electrons directly to…

A

Complex 2

139
Q

The transportation of hydrogen ions by the ETC generates which force?

A

Proton motive force

140
Q

During oxidative phosphorylation, how many protons are required for the generation of 1 ATP from ADP + Pi?

A

4

141
Q

Entry of Acetyl-CoA into the citric acid cycle is DECREASED when…

A

The ratio of [ATP] to [ADP] is HIGH

142
Q

In the mitochondrial ATP synthase complex, the following functional unit is integrated into the inner mitochondrial membrane…

A

F0

143
Q

In mitochondria, the following compartment has a Low pH…

A

Inter-membrane space

144
Q

Compound X is a competitive inhibitor of succinate dehydrogenase enzyme of the citric acid cycle.
What compound would you expect to DECREASE in concentration?

A

Fumarate

145
Q

In the mitochondria, succinate dehydrogenase has the following functions…

A

Producing fumarate

Donating electrons to complex 2 of the electron transport chain

146
Q

The proton motive force links electron transport across mitochondrial inner membrane and creates an electrochemical proton gradient. The proton gradient is formed by…

A

Proteins actively transporting protons across inner mitochondrial membrane to the inter membrane space

Transfer of protons from mitochondrial matrix to inter-membrane space

Releasing protons from inter-membrane space into mitochondrial matrix

147
Q

In the mitochondrial ETC the transfer to electrons to Cytochrome C is via…

A

Complex 3

148
Q

Allosteric Regulators of the citric acid cycle include…

A 
ATP
ADP
NAD+
NADH
Ca2+
Succinyl CoA
149
Q

The mitochondrial ETC does NOT contain…

A

ATP Synthase

150
Q

What is true about the Xylose extracted from wood?

A

Always a D enantiomer

151
Q

What type of sugar is xylose?

A

Aldopentose

152
Q

What makes a carbon chiral?

A

It has 4 different groups attached

153
Q

How do we know something is a D enantiomer?

A

Almost ALL sugars commonly found in nature are D enantiomers

154
Q

What is meant by the term an anomer?

A

Either the a or B form produced when the sugar forms a ring

155
Q

What are the rules for numbering the carbon in glucose?

A

Clockwise from the oxygen in the ring

156
Q

What is the anomeric carbon in glucose?

A

Carbon 1

157
Q

What best describes the structure of glycogen?

A

A branched homopolysaccharide

158
Q

Why is cellulose difficult for many organisms to digest?

A

It contains B 1-4 glycosidic bonds

159
Q

True or false:

Heteropolysaccharides usually store energy

A

FALSE

160
Q

Which chemical group is NOT commonly found in glycosaminoglycans?

A

NH3+ (amino)

161
Q

What best describes a glycoprotein?

A

A relatively large protein with small carbohydrates attached

162
Q

Which atom is NOT involved in linking an oligosaccharide to a glycoprotein?

A

The O in the R group of asparagine

163
Q

How many chiral carbons does xylose have?

A

3

Biochemistry (9 decks)

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