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BIOSCI 101 BioChem Short Answers Flashcards

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1
Q

What are the 2 Laws of Thermodynamics?

A

Energy is conserved, the Universe is becoming more disordered.

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2
Q

Which Food Sources Release which amounts of Energy when Combusted?

A

Least to most: carbohydrates, proteins, alcohol, fat.

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3
Q

How many Kcal/g are in Carbohydrates, Proteins, Fats and Alcohol?

A

Carbohydrate: 4
Protein: 4
Fat: 9
Alcohol: 7

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4
Q

What is the Main Contributor to Useful Energy per Oxygen?

A

Access to C-C bonds.

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5
Q

Which Food Sources Give which amounts of Energy per Oxygen?

A

Least to most: fat, alcohol, protein, carbohydrate.

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6
Q

How does ATP Work?

A

Negative charges repel each other, making ATP unstable - making molecular spring to force reactions, shape/charge changes.

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7
Q

What is Unique about the Energy Released from ATP?

A

Energy released from the terminal phosphate of anhydride bond hydrolysis, is high.

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8
Q

What happens to the Free Energy of Formation of ATP?

A

IT is greater than the sum of the products of formation of ADP + Pi.

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9
Q

How do you Calculate G?

A

H - T S = G

Energy of reaction - Change in order = Change in energy for a given reaction

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10
Q

What is the 1st Law of Thermodynamics?

A 
H = q + w
Enthalpy = Heat + work done
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11
Q

What is the 2nd Law of Thermodynamics?

A

Systems will progress towards increased entropy.

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12
Q

What is Entropy?

A

Symbol S. Turning in - a measure of order.

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13
Q

What is G?

A

Gibbs free energy.

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14
Q

How does an Exothermic Reaction relate to H?

A

Has a negative H by convention - the enthalpy of the products is lower than the reactants.

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15
Q

How can we Understand Glycolysis Simply?

A

It is sugar splitting - glyco-lysis.

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16
Q

Which Bonds are Oxidised in Biology?

A

C-H bonds.

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17
Q

What are the 2 Main Reaction Types in Metabolism of Fuels?

A

Rearrangement/Preparation

Oxidation/Reduction

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18
Q

What are the 3 Types of Oxidation?

A

Alcohol to ketone, alkane to alkene, aldehyde to an acid.

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19
Q

Which Enzyme is Responsible for Biological Redox Reactions?

A

Dehydrogenases.

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20
Q

What is Involved in all Oxidation Reactions?

A

Hydrogen.

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21
Q

What is LEOGER?

A

LEO refers to the loss of an electron (oxidation), GER refers to the gain of an electron (reduction).

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22
Q

Why can only C-H Bonds be used in Oxidation?

A

Lipids in membranes; full of C-C bonds, oxidising these would metabolise our membranes, C-C bonds form backbones of sugars.

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23
Q

What are the 3 Stages of Cellular Respiration?

A

Glycolysis, citric acid cycle, oxidative phosphorylation.

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24
Q

What is Important to Remember about Km and Affinity?

A

Km is the reciprocal of affinity.

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25
Q

What Happens in the Trapping and Investment Stage of Glycolysis?

A

Glucose is trapped in the cell, phosphate charged and glucose not recognised by GLUT, Glucose-6-Phosphate tagged for other things.

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26
Q

What Happens in the 1st Rearrangement Stage in Glycolysis?

A

Phosphoglucoisomerase catalyses rearrangement of glucose-6-phosphate to fructose-6-phosphate.

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27
Q

What Happens in the Commitment and Investment Stage of Glycolysis?

A

Phosphofructokinase converts ATP to ADP, adding a phosphate to fructose-6-phosphate, forming fructose-6-biphosphate.

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28
Q

What Happens in the 2nd Rearrangement Stage in Glycolysis?

A

Aldolase splits fructose-6-biphosphate into dihydroxyacetonephosphate and glyceraldehyde-3-phosphate.

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29
Q

What Happens in the Oxidation (Energy Harvest) Stage in Glycolysis?

A

There is an injection of Pi, using no ATP - a phosphate is added.

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30
Q

What Happens in the 2nd Energy Harvest Stage in Glycolysis?

A

Phosphoglycerokinase turns 2 ADP into 2 ATP, removing a P.

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31
Q

What Happens in the 3rd Rearrangement Stage in Glycolysis?

A

Phosphoclyceromutase moves a phosphate up to carbon chain.

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32
Q

What Happens in the 4th Rearrangement/Dehydration Stage in Glycolysis?

A

Enolase removes 2 H2O to form a pyruvate.

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33
Q

What Happens in the Final Energy Harvest Stage in Glycolysis?

A

Pyruvate kinase turns 2 ADP into 2 ATP, forming pyruvate.

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34
Q

What are the ATP Yields at each Phase of Glycolysis?

A

Investment - 2 ATP
Payoff - 4 ATP
Net gain of 2 ATP

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35
Q

How is ATP Captured in Glycolysis?

A

By substrate level phosphorylation.

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36
Q

What is Important to Remember about Glycolysis?

A

It is highly regulated and irreversible in vivo.

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37
Q

What are the 4 Regulators for PFK?

A

Inhibited by high ATP, AMP activates PFK, also inhibited by citrate from the CAC, proton numbers inhibit PFK.

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38
Q

What is NAD Reduced to?

A

NADH.

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39
Q

What Happens to Glycolysis if there is no Oxygen?

A

There is limited NAD in cells so it stops - must be regenerated by lactate.

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40
Q

Which 2 Factors Lead Kreb to Discover the CAC?

A

Citrate did not vanish, pyruvate had 1 too many carbons.

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41
Q

What Discovery did Kreb Make that Linked Glycolysis to Respiration?

A

There was a loss of C from pyruvate to make acetate, which leads to making citrate.

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42
Q

What does Glucose Produce in the Citric Acid Cycle?

A

6CO2, 8NADH + H, 2FADH2, 2GTP (or ATP).

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43
Q

What does Glucose Produce in Glycolysis?

A

2NADH and 2ATP.

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44
Q

How does Pyruvate Lead to Acetyl CoA?

A

Pyruvate is decarboxylated then oxidised and then CoA attached.

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45
Q

What Happens in Stage 1 of the Citric Acid Cycle?

A

Acetyl group adds 2C to oxaloacetate.

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46
Q

What is Unique about Aconitase?

A

It has an iron-sulphur complex; very sensitive to free radical superoxide and damaged in diseased states.

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47
Q

What Happens in Stage 2 of the Citric Acid Cycle?

A

H2O removed and re-added - rearrangement.

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48
Q

What is Isocitrate Dehydrogenase?

A

A regulator enzyme, increases activity with Ca and decrease with high ATP/ADP ratios.

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49
Q

What Happens in Stage 3 of the Citric Acid Cycle?

A

NAD is reduced to NADH and CO2 is removed.

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50
Q

What Happens in Stage 4 of the Citric Acid Cycle?

A

Another CO2 removed and another NAD reduction, and CoA-AH added (weak bond).

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51
Q

What Happens in Stage 5 of the Citric Acid Cycle?

A

CoA-SH released and substrate level phosphorylation, GTP formed and converted to ATP at no cost.

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52
Q

What Happens in Stage 6 of the Citric Acid Cycle?

A

2 H transferred to FAD (FADH2), succinate oxidised.

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53
Q

What is SDH?

A

Part of the electron transport system - in the inner mitochondrial membrane.

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54
Q

What is the Role of SDH?

A

Handles some very dangerous free radicals, but appears very robust.

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55
Q

What Happens in Stage 7 of the Citric Acid Cycle?

A

Water added to fumarate and rearrangement.

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56
Q

What Happens in Stage 8 of the Citric Acid Cycle?

A

Last oxidation and oxaloacetate reformed.

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57
Q

How how Stages of Oxidation are there in the Citric Acid Cycle?

A

4.

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58
Q

What is ESSENTIAL to Remember about the Citric Acid Cycle?

A

Glucose makes 2 pyruvates, so there are basically 2 CACs occuring simultaneously.

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59
Q

What are the 2 Regulators of Metabolism and the CAC?

A

ATP/ADP and NADH.

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60
Q

What Effect does High NADH Have?

A

A lot of reducing power.

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61
Q

Which Ratio is also Known as the Redox State?

A

NADH/NAD ratio.

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62
Q

How is IDH Activity Regulated?

A

ADP/ATP ratio:
10/2 goes faster
2/10 goes slower
Also Ca

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63
Q

What Impact do Large Quantities of Succinyl/Acetyl-CoA Have?

A

CoA becomes limiting and the CAC slows.

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64
Q

What are the 2 Benefits of Mitochondrial Fusion?

A

Enhanced ATP production, protects mitochondria from degradation.

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65
Q

What is the Redox Potential for NADH in ETS?

A

1.135V.

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66
Q

What is the Redox Potential for FADH2 in ETS?

A

0.815V.

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67
Q

How do Electrons Flow through Iron Sulphur Clusters?

A

The Fe atoms change oxidation state (Fe3 to Fe2), and act as a wire to ‘conduct’ electrons.

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68
Q

What is Ubiquinone?

A

Oxidised form of Coenzyme Q.

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69
Q

What is Semiquinone?

A

1/2 reduced/oxidised form of Coenzyme Q.

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70
Q

What is Ubiquinol?

A

Reduced form of Coenzyme Q - two alcohols.

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71
Q

Which Factors can Impact Complex 1?

A

Anaesthetics - rotenone, amytal.

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72
Q

Which Factors can Impact Complex 2?

A

Mythioxiol, antimycin a.

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73
Q

Which Factors can Impact Complex 4?

A

Cyanide, nitric oxide, CO, H2S.

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74
Q

How many Protons are Shifted for 1 NADH + H?

A

10 protons.

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75
Q

Which Complexes Transfer Protons in ETS?

A

Complexes 1, 3, 4.

76
Q

How many more Hydrogens does NADH move than FADH2?

A

4 more hydrogens.

77
Q

How are Oxidation and ATP Synthesis Coupled?

A

By transmembrane proton fluxes.

78
Q

What Happens to the Excess Protons from the Proton Fluxes?

A

A chemiosmotic gradient forms.

79
Q

What is Unique about the Gradients within Mitochondria?

A

There is a chemiosmotic gradient - both and electric potential and chemical gradient.

80
Q

What Addition enabled ATP Synthase to make ATP?

A

The addition of OH.

81
Q

What are the 2 Major ways to Stop ATP Synthesis?

A

Chemicals can uncouple the proton gradient or poison the electron flow.

82
Q

How do Proton Gradients Lead to Photosynthesis?

A

Electron flow drives proton pumps, protons accumulate in gradients, protons then drive ATP synthesis.

83
Q

What are the 2 Components of the Proton Motive Force?

A

Concentration gradient and an electric charge.

84
Q

What is the Average pH of the Mitochondrial Matrix and the Inter-membrane Space?

A

Matrix: 7.8
IMS: 7.6

85
Q

How is it Ensured that the Protons don’t diffuse Randomly in the Bulk Stage?

A

Phosphate heads of lipids are -vely charged and H is attracted to these heads, so flow along the membrane, separated by thin water layer.

86
Q

How is Cristae Shape Determined?

A

The dimerised ATP synthases fold the inner membrane to give their shape.

87
Q

Where is the Greatest Negative Charge on Cristae?

A

Inside surface tips.

88
Q

How do Cristae Enable ATP Synthase to be Driven?

A

Protons gathered around inside surface tips lower local pH to 6.

89
Q

What does Organisation of OXPHOS Achieve?

A

Enhances proton flow, concentrates the effort.

90
Q

What is Important to Remember about the Internal Rod in the ATP Synthase Machine?

A

It isn’t straight.

91
Q

What Happens to the ATP Synthase Rotor if ATP is added?

A

It can spin backwards and act as a proton pump.

92
Q

How many ATP are Made for Each Rotation of the Internal Rod in ATP Synthase?

A

3 ATP.

93
Q

How can we Judge the Number of ATP Made based on C Ring Size?

A

The bigger the C ring, the less ATP is made per proton.

94
Q

What are the 2 Ways of Using the NADH Formed in Glycolysis?

A

Malate Aspartate shuttle, G3PDH shuttle.

95
Q

Why is the Yield of ATP Vague?

A

Membranes leak when hot, NADH from glycolysis has 2 fates.

96
Q

Which Shuttle Produces More ATP - Malate Aspartate or G3PDH?

A

Malate Aspartate.

97
Q

Which Complex is Most Impacted by Damage?

A

Complex 1: oxidative stress, heart attack etc.

98
Q

What Happens if Inner Mitochondrial Membranes become Damaged?

A

Uncoupling proteins are activated (ACPs), increasing leakiness.

99
Q

Which 2 Tissues Release Glucose?

A

Liver and kidneys.

100
Q

How does Glycogen Protect Osmotic Pressure of a Cell?

A

Small glucose molecule attracts water, large polymers do not.

101
Q

What is Glycogen?

A

Storage of glucose in the cytosol.

102
Q

Why can Muscle hold Less Glycogen than the Liver?

A

Space limits.

103
Q

Which Bond in Glycogen is Branching?

A

Alpha 6.

104
Q

What is Glycogenesis?

A

Glycogen birth.

105
Q

How is Glucose Trapped in the Hepatocyte?

A

Phosphorylation - charge is changed.

106
Q

What does Glucose Pass Through to Enter the Hepatocyte?

A

A GLUT.

107
Q

How is UDPG Formed?

A

G1P + UTP - energy has been invested.

108
Q

Where is Glucose Added?

A

Non-reducing ends.

109
Q

How can we Remember the Difference Between Alpha 4 and Alpha 6 Bonds?

A

Alpha 6 branch off - like workers to the pub at 6.

110
Q

How is Glycogen made Dense?

A

Branching enzyme creates new branches towards the core.

111
Q

What is Glycogenolysis?

A

Glycogen cutting/breakdown.

112
Q

Where is Glycogen Broken Down?

A

From the non-reducing ends - other end is buried in glycogen mass.

113
Q

How does Glycogenolysis Work?

A

G1P is released - working to leave 4 glycosyl residues.

114
Q

Why is Hydrolysis not Used to Break Down Glycogen?

A

Hydrolysis leaves an unphosphorylated glucose, released glucose is chraged and trapped in cells, saves an ATP as Pi is used.

115
Q

Where is G6Pase Found?

A

Only in the liver and kidneys.

116
Q

What does Coordinated Control of Glycogen Metabolism Ensure?

A

Glycogen is not being made as it is broken down.

117
Q

What is von Gierke’s Disease?

A

Mutation in G6P, can’t release glucose from liver.

118
Q

What is Mc Ardle’s Disease?

A

Lack of glucose release, so little glycogen phosphorylase activity in muscles (cramp).

119
Q

What is Gluconeogenesis?

A

Making glucose.

120
Q

What are the Building Blocks of Gluconeogenesis?

A

Lactate, amino acids, glycerol, TCA intermediates.

121
Q

Which 3 Reactants of Gluconeogenesis are Important to Remember?

A

4ATP, 2GTP, 2NADH.

122
Q

When are Glycolysis Reactions Reversible?

A

When the reactants and products are in equilibrium.

123
Q

Which 3 Bypasses are required for the Kinases?

A

Bypass 1, 2 and 3.

124
Q

Which Enzymes are Used in Bypass 1?

A

Pyruvate carboxylase, PEPCK.

125
Q

Which Enzymes are Used in Bypass 2?

A

Fructose 1,6-biphosphatase.

126
Q

Where does Bypass 1 Take Place?

A

Cytosol and mitochondria.

127
Q

Where does Bypass 2 Take Place?

A

ER, cytosol.

128
Q

Which Enzyme is Used in Bypass 3?

A

Glucose 6-phosphatase.

129
Q

What is the Balance of ATP Between Gluconeogenesis and Glycolysis that Proves they Shouldn’t Run Together?

A

Gluconeogenesis consumes 12 ATP, glycolysis makes 2 ATP, mis-match of -10 ATP.

130
Q

Which Endocrine Organ Maintains Glucose Levels?

A

The pancreas.

131
Q

What do the Endocrine Islets of Langerhans do?

A

Secrete hormones.

132
Q

What do Exocrine Glands in the Pancreas do?

A

Secretes digestive enzymes.

133
Q

When do Alpha Cells Produce Glucagon?

A

When there is low blood glucose.

134
Q

How does Glucagon Raise Blood Glucose Levels?

A

Stimulates glycogen breakdown, signals liver cells to turn glycogen into glucose for the blood.

135
Q

When do Beta Cells Produce Insulin?

A

When there is high blood glucose levels.

136
Q

How does Insulin Lower Blood Glucose Levels?

A

Stimulates all body cells to take up glucose (except brain).

137
Q

What are the 2 Other Effects of Insulin?

A

Stimulates glycogen synthesis, promotes storage of fuel.

138
Q

What does Insulin do?

A

Drives glucose uptake in tissues, importantly the skeletal muscle and the liver.

139
Q

Which Broad Hormone Family is Insulin Part of?

A

Anabolic.

140
Q

Which 3 Things can Insulin Promote?

A

Fat deposition, glycogen storage, growth.

141
Q

What are the Normal Levels of Blood Glucose?

A

4.5 - 5 mM.

142
Q

What Happens to the Heart with Cardiomyopathy?

A

Heart muscle becomes enlarged.

143
Q

What Happens to the Kidney due to Nephropathy?

A

Granular surface, decreased function, smaller size, high urine protein.

144
Q

What is Diabetes?

A

Typically hyperglycaemic - excess glucose in blood appears in urine.

145
Q

What are the Characteristics of Type 1 Diabetes?

A

Autoimmune disorder, usually appears in childhood - cannot produce insulin.

146
Q

What is the Treatment for Type 1 Diabetes?

A

Insuline injections.

147
Q

What are the Characteristics of Type 2 Diabetes?

A

Target cells have decreased responsiveness to insulin, 90% of Diabetes cases.

148
Q

What Happens on the Cellular Level as a Result of Type 2 Diabetes?

A

Cells desensitised, beta cells work harder to supply large body mass and fail, uptake and disposal of glucose impaired.

149
Q

What Happens when there is too much Fuel?

A

Too few mitochondria, they produce free radicals, cell protects itself by decreasing GLUTs, blood glucose rises.

150
Q

What can Improve and Eradicate Type 2 Diabetes?

A

Exercise.

151
Q

What Fuel Switch Occurs due to Starvation?

A

Glucose to ketone bodies used in the brain.

152
Q

Where is Acetone Expired?

A

In the breath.

153
Q

How does Ketone Used in the Brain Change due to Starvation?

A

3 days starvation - 30% ketones, 40 days - 70% ketones.

154
Q

What is Ketoacidosis?

A

Where the pH of the blood drops due to use of ketone bodies rather than glucose.

155
Q

How is ATP Replaced during Muscle Use?

A

By creatine phosphate almost immediately.

156
Q

What Happens if ATP Stores Decline?

A

Cells die by necrosis.

157
Q

Why do we Use Anaerobic Pathways?

A

Creatine phosphate and glycogen are self contained within cells, oxygen pathways have to wait for oxygen transport.

158
Q

Where are Light Reactions Carried out?

A

In the thylakoid membranes.

159
Q

What are the 2 Outcomes of Light Reactions?

A

Convert light to chemical energy of ATP and NADH, split H2O and release O2.

160
Q

Where is the Lack of Absorbance of Chlorophyll?

A

Wavelength of 500 - 600 nm.

161
Q

What is the Chemical Equation of Photosynthesis?

A

H2O + CO2 = (CH2O) + O2

162
Q

What are Chloroplast Antennae Used for?

A

To acquire more electrons (100 photons per second).

163
Q

How does Photosystem 2 Harvest Light?

A

Light hits PS2, electron jumps up, transferred to Q, goes to cytochrome complex, oxidises Q through Q cycle.

164
Q

How does Photosystem 1 Harvest Light?

A

Light hits PS1, electron jumps up, 2 fates; electrons can move down string, NAD can be reduced to NADH.

165
Q

Which Photosystem Comes First in the Chain of Linear Electron Flow?

A

Photosystem 2 - photosystem 1 was just discovered first.

166
Q

How does the Cytochrome Complex Make ATP?

A

Indirectly - transferring 4 H+ - these drive ATP synthesis as in mitochondria.

167
Q

What are the 2 Ways a Proton Gradient is Formed?

A

Splitting of water, cytochrome complex transfers 4 H+ to in thylakoid space.

168
Q

How do C-Ring Subunits Compare between Plants and Mammals?

A

Plants have 14, mammals have 8.

169
Q

What are the Differences between the Gradients of Mitochondria and Chloroplasts?

A

Mitochondria - uses proton gradient and electrical charge

Chloroplast - Proton gradient only

170
Q

What are the Differences in Reduction between Mitochondria and Chloroplasts?

A

Mitochondria: es reduce oxygen
Chloroplasts: es reduce NADP

171
Q

Why Have Cyclic Electron Flow?

A

Produces only ATP, some bacteria only have PS1.

172
Q

What is the Cyclic Electron Flow?

A

Where the electrons take an alternate path - using PS1 but not PS2.

173
Q

What is Pq in the Light Reactions?

A

Plastoquinone/ol.

174
Q

What is Pc in the Light Reactions?

A

Plastocyanin.

175
Q

Where does the Calvin Cycle Take Place?

A

The stroma.

176
Q

What are the 3 Phases of the Calvin Cycle?

A

CO2 fixation, reduction, regeneration.

177
Q

What is RuBisCo?

A

The most abundant protein on Earth.

178
Q

What Happens to Carbon Numbers during Carbon Fixation in the Calvin Cycle?

A

3 x 5C becomes 6 x 3C.

179
Q

How many Calvin Cycles are Required to make 1 Glucose?

A

2, with 1 G3P being removed each cycle.

180
Q

What are the 2 Ways the Calvin Cycle is Regulated by Light?

A

pH, antioxidant enzyme.

181
Q

How does pH Regulate the Calvin Cycle?

A

More alkaline the stroma, the faster the cycle works.

182
Q

How does an Antioxidant Enzyme Regulate the Calvin Cycle?

A

Reduces RuBisCo.

183
Q

Why is RuBisCo Useful?

A

Many plants shut down photosynthesis at midday - C4 plants store CO2 to survive hot climates.

184
Q

What is the Purpose of the C4 Pathway?

A

C3 is wasteful, C4 concentrates CO2 so less O2 is present for photorespiration.

185
Q

How does the C4 Pathway Accomodate for more ATP being Used?

A

Uses the cyclic electron flow.

Biology (15 decks)

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