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Molecules, Genes, and Cells > Metabolism and Localisation of Biochemical Pathways > Flashcards

Metabolism and Localisation of Biochemical Pathways Flashcards

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Organic Chemistry 101 flashcards
1
Q

What are the three major types of membrane lipids?

A

Phospholipids, glycolipids, cholesterol

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2
Q

What two alcohols can phospholipids be derived from?

A

Glycerol and sphingosine

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3
Q

What are phospholipids derived from glycerol called?

A

Phosphoglycerides

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4
Q

What are phosphoglycerides composed of?

A

Glycerol backbone, two fatty acid chains, and a phosphorylated alcohol

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5
Q

Do glycolipids contain sugar?

A

Yes

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6
Q

What functional group does cholesterol belong to?

A

Sterol

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7
Q

Is cholesterol more present in eukaryotes or prokaryotes?

A

Eukaryotes

-present in eukaryotes but not in most prokaryotes

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8
Q

Are plasma membranes or organelle membranes are rich in cholesterol?

A

Plasma membranes

-membranes of organelles typically have smaller amounts of cholesterol than the cholesterol rich plasma membrane

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9
Q

What technique is used to identify lipid components of membranes?

A

Thin layer chromatography (TLC)

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10
Q

What is the basic structure of a phospholipid?

A

Hydrophilic (polar group) head and hydrophobic (hydrocarbon) tail

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11
Q

What is the hydrophobic unit of phosphoglycerides?

A

2 fatty acid chains

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12
Q

What is the hydrophilic unit of phosphoglycerides?

A

Phosphorylated alcohol

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13
Q

What is the hydrophobic unit of sphingomyelin?

A

Fatty acid chain and hydrocarbon chain of sphingosine

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14
Q

What is the hydrophilic unit of sphingomyelin?

A

Phosphorylated choline

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15
Q

What is the hydrophobic unit of glycolipids?

A

Fatty acid chain and hydrocarbon chain sphingosine

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16
Q

What is the hydrophilic unit of glycolipids?

A

One or more sugar residues

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17
Q

What is the hydrophobic unit of cholesterol?

A

Entire molecule except for OH group

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18
Q

What is the hydrophilic unit of cholesterol?

A

OH group at carbon 3

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19
Q

What are the three potential arrangements for phospholipids in aqueous medium?

A

Micelle, liposome, lipid bilayer

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20
Q

Why are micelles difficult to form?

A

Fatty acid chains are too bulky to fit inside

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21
Q

What is the most common structure of phospholipids in aqueous medium?

A

Lipid bilayer

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22
Q

What stabilises a lipid bilayer?

A

Dispersion (London) forces and hydrophobic interactions between hydrocarbon chains and electrostatic & hydrogen bonding attractions between the polar head group and water

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23
Q

How do we know the arrangement of lipids in the membrane?

A

X-ray diffraction

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24
Q

What is membrane fluidity controlled by?

A

Fatty acid composition, cholesterol content

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25
Q

What are the two possible conformations of fatty acyl chains?

A

Trans (rigid) or gauche (more fluid)

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26
Q

How can cholesterol regulate membrane fluidity?

A

Increases fluidity by preventing crystallisation of fatty acyl chains and can decrease fluidity by sterically blocking larger motions of fatty acyl chains

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27
Q

What are integral membrane proteins?

A

Proteins which are embedded in and span the lipid bilayer

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28
Q

What are peripheral membrane proteins?

A

Proteins bound to the membrane by electrostatic and hydrogen-bond interactions

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29
Q

What type of membrane proteins are used for active transport?

A

ATP-powered pumps

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30
Q

What are the four classes of ATP-powered pumps?

A

P-class, V-class, F-class, ABC superfamily

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31
Q

What do P-class pumps transport?

A

Ions

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32
Q

Where are P-class pumps found?

A
  • Plasma membrane of plants, fungi, and bacteria (H+ pump)

- NA+/K+ pump of higher eukaryotes plasma membrane

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33
Q

What do V-class pumps transport?

A

Protons (across pH)

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34
Q

Where are V-class pumps found?

A
  • Vacuolar membranes of plants, yeast, and other fungi

- Endosomal and lysosomal membranes in animal cells

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35
Q

What do F-class pumps transport?

A

Protons

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36
Q

Where are F-class protons found?

A
  • Bacterial plasma membranes

- Inner mitochondrial membrane

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37
Q

What does the ABC superfamily transport?

A

Small molecules

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38
Q

Where are ABC superfamily pumps found?

A
  • Bacterial plasma membranes

- Mammalian plasma membranes

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39
Q

Which class of ATP-powered pumps is cystic fibrosis linked to?

A

ABC superfamily

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40
Q

What are ABC superfamily transporters made up of?

A

Transmembrane domains and two cytosolic ATP binding sites

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41
Q

Which ions can be transported down concentration gradients by their specific ion channels?

A

NA+, K+, Ca2+, Cl-

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42
Q

Is the potential difference negative inside or outside the cell?

A

Inside

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43
Q

What is the difference between gated and non-gated ion channels?

A

Gated change state in response to membrane potential signalling but non-gated have no response

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44
Q

What is resting membrane potential?

A

The potential difference between the inside and outside of the cell

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45
Q

What is the typical range fo resting membrane potential?

A

30 to -100 mV

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46
Q

What are the three reasons for the existence of the resting membrane potential?

A
  • semi-permeable cell membrane means unequal ion distribution inside and outside of cell
  • presence of ion pumps
  • presence of ion channels
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47
Q

What is a uni-porter?

A

Transport only one type of species substrate

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48
Q

What is co-transport?

A

Happens against the conc. gradient and is where a molecule and ion are coupled and must move together

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49
Q

What is symport?

A

When coupled molecule/ion move in the same direction

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50
Q

What is antiport?

A

When coupled molecule/ion move in opposite directions

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51
Q

A mutation in which transport protein contributes towards epilepsy?

A

Brain Na+ channels

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52
Q

A mutation in which transport protein contributes towards cystic fibrosis?

A

CFTR

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53
Q

A mutation in which transport protein contributes towards cancer drug resistance?

A

MDR-1

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54
Q

Which channel is inhibited to treat stomach ulcers?

A

Gastric H+/K+ ATPase

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55
Q

Which biomolecules are the most abundant on Earth?

A

Carbohydrates

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56
Q

Name 6 structural and protective elements contributed to by carbohydrates

A
  • cell walls of bacteria and plants
  • connective tissues of animals and lubrication of skeletal joints
  • adhesion between cells
  • exoskeletons
  • essential to protein function
  • central to cell survival and cell-to-cell communication
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57
Q

What are carbohydrates made from?

A

Monosaccharides

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58
Q

What functional groups are the monosaccharides that make up carbohydrates?

A

Aldehydes or ketones:

- aldoses/ketoses

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59
Q

Are carbohydrate chiral?

A

Yes

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60
Q

What is the definition of chirality?

A

Non-superimposable on its mirror image

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61
Q

Which isomers are the most naturally occurring monosaccharides?

A

D-isomers

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62
Q

What is the predominant form of saccharides with 5 or more carbons?

A

Cyclic

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63
Q

How does cyclisation of D-glucose occur?

A

Nucleophilic attack of the C5 hydroxyl on the C1 aldehyde/ketone to form the hemiacetal/hemiketal

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64
Q

How many saccharide units in oligosaccharides?

A

Two to ten

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65
Q

In what form are polysaccharides stored in plants?

A

Starch

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66
Q

What are the two types of glucose polymer in starch?

A

Amylose and amylopectin

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67
Q

Describe amylose

A

Long, unbranched chains of D-glucose, alpha 1,4 linkages

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68
Q

Describe amylopectin

A

Highly branched, alpha 1,4 and 1,6 linkages

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69
Q

In what form are polysaccharides stored in animal cells?

A

Glycogen

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70
Q

In which tissues is glycogen most abundant?

A

Muscle and liver

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71
Q

Describe glycogen

A

Succesive D-glucose molecules, alpha 1,4 linkage, alpha 1,6 branch points, more extensively branched than amylopectin

72
Q

Where are alpha-amylases and glycosidases secreted?

A

Salivary glands and pancreas

73
Q

What is the role of alpha-amylases and glycosidases?

A

Break alpha 1,4 glycosidic bonds between glucose units during digestion allowing ingested starch and glycogen to serve as sources of D-glucose for aerobic respiration

74
Q

Describe cellulose

A

Tough, fibrous, water insoluble, found in plant cell wall, polymer of D-glucose, unbranched, homopolysaccharide, beta D-glucose, 1,4 linkage

75
Q

How many enzyme catalysed reactions are there in glycolysis?

A

10

76
Q

What are the two phases of glycolysis?

A

Preparatory and payoff

77
Q

What happens overall in the preparatory phase?

A

ATP consumption

78
Q

What happens overall in the payoff phase?

A

ATP production

79
Q

Describe the first reaction of glycolysis

A 
Reactant: Glucose
Product: Glucose-6-phosphate
Enzyme: Hexokinase
Reversible?: No
Produces ADP from ATP
80
Q

Describe the second reaction of glycolysis

A

Reactant: Glucose-6-phosphate
Product: Fructose 6-phosphate
Enzyme: Phosphoglucose isomerase
Reversible?: Yes

81
Q

Describe the third reaction of glycolysis

A 
Reactant: Fructose 6-phosphate
Product: Fructose 1,6-biphosphate
Enzyme: Phosphofructokinase
Reversible?: No
Produces ADP from ATP
82
Q

Describe the fourth reaction of glycolysis

A

Reactant: Fructose 1,6 biphosphate
Product: Glyceraldehyde 3-phosphate (GAP) and dihydroxyacetone phosphate
Enzyme: Aldolase
Reversible?: Yes

83
Q

Describe the fifth reaction of glycolysis

A

Reactant: Dihydroxyacetone phosphate
Product: Glyceraldehyde 3-phosphate (GAP)
Enzyme: Triose phosphate isomerase
Reversible?: Yes

84
Q

Describe the sixth reaction of glycolysis

A

Reactant: Glyceraldehyde 3-phosphate (GAP)
Product: 1,3-biphosphoglycerate
Enzyme: Glyceraldehyde 3-phosphate dehydrogenase
Reversible?: Yes
Produces NADH from Pi and NAD+

85
Q

Describe the seventh reaction of glycolysis

A 
Reactant: 1,3-biphosphoglycerate
Product: 3-phosphoglycerate
Enzyme: Phosphoglycerate kinase
Reversible?: Yes
Produces ATP from ADP
86
Q

Describe the eighth reaction of glycolysis

A

Reactant: 3-phosphoglycerate
Product: 2-phosphoglycerate
Enzyme: Phosphoglycerate mutase
Reversible?: Yes

87
Q

Describe the ninth reaction of glycolysis

A 
Reactant: 2-phosphoglycerate
Product: Phosphoenolpyruvate
Enzyme: Enolase
Reversible?: Yes
Produces water
88
Q

Describe the tenth reaction of glycolysis

A 
Reactant: Phosphoenolpyruvate
Product: Pyruvate
Enzyme: Pyruvate kinase
Reversible?: No
Produces ATP from ADP
89
Q

Which reactions of glycolysis make up the preparatory phase?

A

1-5

90
Q

Which reactions of glycolysis make up the payoff phase?

A

6-10

91
Q

How many molecules of GAP are produced in the preparatory phase?

A

Two

92
Q

List the ten enzyme used in glycolysis

A
  1. Hexokinase
  2. Phosphoglucose isomerase
  3. Phosphofructokinase
  4. Aldolase
  5. Triose phosphate isomerase
  6. Glyceraldehyde 3-phosphate dehydrogenase
  7. Phosphoglycerate kinase
  8. Phosphoglycerate mutase
  9. Enolase
  10. Pyruvate kinase
93
Q

What is the pyruvate dehydrogenase complex?

A

A complex of 3 enzymes and 5 coenzymes that convert pyruvate into acetal-coA by pyruvate decarboxylation

94
Q

What is E1?

A

Pyruvate dehydrogenase

95
Q

Which cofactors accompany E1?

A

Thiamine pyrophosphate (TPP)

96
Q

What is E2?

A

Dihydrolipoyl transacetylase

97
Q

Which cofactors accompany E2?

A

Lipoic acid and coA-SH (coenzyme A)

98
Q

What is E3?

A

Dihydrolipoyl dehydrogenase

99
Q

Which cofactors accompany E3?

A

NAD+ and FAD

100
Q

What are the 5 cofactors in the pyruvate dehydrogenase complex?

A

TPP, lipoid acid, coA-SH, NAD+, FAD

101
Q

What is the fuel for the citric acid cycle?

A

Acetyl-CoA

102
Q

How many enzyme catalysed reactions are there in the citric acid cycle?

A

8

103
Q

Describe the first reaction in the citric acid cycle

A

Enzyme: Citrate synthase
Intermediate: Citrate
Converts acetyl-CoA into CoA-SH

104
Q

Describe the second reaction in the citric acid cycle

A

Enzyme: Aconitase
Intermediate: Isocitrate

105
Q

Describe the third reaction in the citric acid cycle

A

Enzyme: Isocitrate dehydrogenase
Intermediate: alpha-Ketoglutarate
Carbon dioxide produced
NADH produced from NAD+

106
Q

Describe the fourth reaction in the citric acid cycle

A

Enzyme: alpha-Ketoglutarate dehydrogenase
Intermediate: Succinyl-CoA
Carbon dioxide produced
NADH produced from NAD+

107
Q

Describe the fifth reaction in the citric acid cycle

A

Enzyme: Succinyl-CoA synthetase
Intermediate: Succinate
CoA-SH produced
ATP produced from ADP and Pi

108
Q

Describe the sixth reaction in the citric acid cycle

A

Enzyme: Succinate dehydrogenase
Intermediate: Fumarate
FADH2 produced by FAD

109
Q

Describe the seventh reaction in the citric acid cycle

A

Enzyme: Fumarase
Intermediate: Malate

110
Q

Describe the eighth reaction in the citric acid cycle

A

Enzyme: Malate dehydrogenase
Intermediate: Oxaloacetate
NADH produced by NAD+

111
Q

How many times must the citric acid cycle be completed before 1 glucose molecule is completely oxidised?

A

Twice

112
Q

Which intermediate is a source for fatty acids and sterols?

A

Citrate

113
Q

Which intermediate is a source for glutamate?

A

alpha-Ketoglutarate

114
Q

Which intermediate is a source for porphyrins, heme, and chlorophyll?

A

Succinyl-CoA

115
Q

Which intermediate is a source for aspartate and glucose?

A

Oxaloacetate

116
Q

What regulates the citric acid cycle?

A

Concentrations of ATP and NADH

117
Q

How does most recycling of ADP back to ATP take place?

A

Oxidative phosphorylation

118
Q

Is ubiquinone (UQ) hydrophilic or hydrophobic?

A

Very hydrophobic

119
Q

Where UQ found?

A

Inner mitochondrial membrane

120
Q

Where does oxidative phosphorylation take place?

A

Inner mitochondrial membrane

121
Q

What moves electrons through proteins in the electron transfer chain?

A

Cofactors with metal centres

122
Q

Describe the reactions that occur in complex I of the ETC

A
  • NADH is converted into NAD+
  • one electron from previous reaction is donated to the following reaction
  • 2H+, UQ, and the donated e- are converted into UQH2
123
Q

Describe the reactions that occur in complex II of the ETC

A
  • FADH2 (succinate) is converted into FADH
  • one electron from previous reaction is donated to the following reaction
  • 2H+, UQ, and the donated e- are converted into UQH2
124
Q

Describe the reactions that occur in complex III of the ETC

A
  • 2H+ go into the complex from the matrix
  • UQ is converted to UQH2
  • each UQH2 from complex I and complex II is converted into 2UQ
  • Fe3+ is converted into Fe2+
  • 4H+ leave the complex into the intermembrane space
125
Q

Describe the reactions that occur in complex IV of the ETC

A
  • 1/2 O2 and 2H+ are converted to H2O

- the Fe2+ from complex III is converted to Fe3+

126
Q

Compare the concentration of protons, pH, and relative charge of the matrix with the intermembrane space

A 
The matrix:
- lower conc. of proteins
- more alkaline
- more negative charge
than the inter membrane space
127
Q

What are the two types of reactions in photosynthesis?

A

Light reactions and carbon-assimilation reactions

128
Q

What energy-transforming machinery do chloroplast thylakoid membranes contain?

A
  • light-harvesting proteins
  • reaction centres
  • electron transport chains
  • ATP synthase
129
Q

What is the structure of chlorophyll?

A

Cyclic tetrapyrrole

130
Q

Where does the Mg ion bind in chlorophyll?

A

At the centre of the structure

131
Q

What is photosystem II (PS II)?

A
  • large transmembrane assembly of over 20 subunits
  • catalyses light-driven transfer of e- from H2O to plastoquinone
  • drives reaction to a higher energy by harvesting solar energy
132
Q

What is plastiquinone?

A

An electron acceptor

133
Q

Describe the process that occurs in PS II

A
  1. P680 absorbs light at 680nm
  2. on excitation, P680 transfers an electron to a nearby pheophytin
  3. the e- is transferred to a tightly bound plastoquinone
  4. it is then transferred to a mobile plastoquinone
134
Q

Describe the process that occurs in photosystem I (PS I)

A
  1. P700 absorbs light at 700 nm
  2. the e- travels from P700, via a chlorophyll and a quinone, to a set of 4 Fe-4S clusters
  3. the e- is transferred to Ferredoxin and then to NADP+
135
Q

What is gluconeogenesis?

A

The synthesis of glucose from non-carbohydrate precursors

136
Q

Are tumour cells more regularly aerobic or anaerobic?

A

Anaerobic

137
Q

Do tumour cells consume ATP?

A

Yes (lots)

138
Q

Describe the four pathways of the metabolism of glucose?

A
  • Glycogen/starch/sucrose: storage
  • Pyruvate: Oxidation via glycolysis/gluconeogenesis
  • Ribose 5-phosphate: Oxidation via pentose phosphate pathway
  • Extracellular matrix and cell wall polysaccharides: structural polymer synthesis
139
Q

What are the 3 main precursors that can be used in gluconeogenesis?

A
  • lactate
  • amino acids
  • (not in animal cells) glycerol
140
Q

What are non-carbohydrates converted into to enter the pathway?

A

Pyruvate or enter the pathway at a later stage as an intermediate

141
Q

Which 2 molecules can the gluconeogenesis pathway start from?

A

Pyruvate or oxaloacetate

142
Q

Where does gluconeogenesis take place?

A

Mostly in the liver and some in the kidney

143
Q

Is glycolysis anabolic or catabolic?

A

Catabolic

144
Q

Is gluconeogenesis anabolic or catabolic?

A

Anabolic

145
Q

What regulates enzymes to prevent glycolysis and gluconeogenesis happening at the same time?

A

Allosteric mechanisms

146
Q

Why do glycolysis and gluconeogenesis not occur at the same time?

A

They are both high energy processes

147
Q

Give four reasons why the pentose phosphate pathway important?

A
  • source of NADPH
  • protects against oxidative stress
  • major product is pentose 5-phosphate which is used to make RNA, DNA, and coenzymes
  • important for rapidly dividing cells
148
Q

What are the two phases of the pentose phosphate pathway?

A
  • Oxidative generation of NADPH from NADP+

- Nonoxidative interconversion of sugars

149
Q

What is the initial reactant of the oxidative pentose phosphate pathway?

A

Glucose 6-phosphate

150
Q

What is ribose 5-phosphate a precursor for?

A

Nucleotide and nucleic acid synthesis

151
Q

What are fatty acids a source of?

A

Energy

152
Q

What is produced during oxidation of fatty acids?

A

Acetyl-CoA

153
Q

What is the process of converting fatty acids to acetyl-CoA called?

A

β-oxidation

154
Q

What are the 7 steps of processing dietary lipids?

A
  1. Bile salts emulsify dietary fats in the small intestine, forming mixed micelles
  2. Intestinal lipases degrade triacylglycerols
  3. Fatty acids and other products are taken up by the intestinal mucosa and converted into triacylglycerols
  4. Triacylglycerols are incorporated into chylomicrons
  5. Chylomicrons move through the lymphatic system and bloodstream to tissues
  6. Lipoprotein lipase converts triacylglycerols to fatty acids and glycerol
  7. Fatty acids are oxidised as fuel or re-esterified for storage
155
Q

How are lipids often stored in cells?

A

Triacylglycerols

156
Q

How are triacylglycerols mobilised from adipose tissue?

A
  1. low levels of glucose in blood trigger glucagon release
  2. glucagon binds to its hormone receptor
  3. free fatty acids leave the adipocyte and are carried through the blood to provide energy to various cells
157
Q

What are the 3 stages of fatty acid oxidation?

A
  1. Long-chain fatty acid oxidised to give acetyl-CoA (β-oxidation)
  2. Acetyl groups oxidised to CO2 via citric acid cycle
  3. Electrons from stages 1 and 2 pass to O2 via respiratory chain, generating ATP
158
Q

How many steps are involved in β-oxidation?

A

4

159
Q

When are additional enzyme required in β-oxidation?

A

If the fatty acid:

  • is unsaturated
  • has odd number of carbons
160
Q

How many additional enzymes are required if the fatty acid is unsaturated?

A

2

161
Q

How many additional enzymes are required if the fatty acid has an odd number of carbons?

A

3

162
Q

In what 3 circumstances does oxidative degeneration of amino acids occur in animals?

A
  • during synthesis and degradation of cellular proteins
  • when amino acids cannot be stored, due to protein-rich diet provided excess amino acids than needed
  • during starvation/uncontrolled diabetes, when carbohydrates are unavailable or improperly used
163
Q

Where are amino acid groups catabolised?

A

Liver

164
Q

What happens if a muscle catabolises amino acids?

A

Nitrogen is transferred to alanine and released in the bloodstream

165
Q

What happens to alanine taken up in the liver?

A

Converted into pyruvate for the synthesis of glucose

166
Q

What happens to excess nitrogen?

A

Excreted via the urea cycle

167
Q

What is the principal form of stored energy in. most organisms?

A

Lipids

168
Q

Give the 7 examples of what specialised lipids serve as

A
  • pigments e.g. retinol, carotene
  • cofactors e.g. vitamin K
  • detergents e.g. bile salts
  • transporters e.g. dolichols
  • hormones e.g. vitamin D derivatives, sex hormones
  • extra- and intracellular messengers e.g. eicosanoids, phosphoinositols
  • anchors for membrane proteins e.g. prenyl groups
169
Q

Which hormones act faster: peptide and amine hormones or steroid and thyroid?

A

Peptide and amine hormones

170
Q

What is metabolism?

A

A series of activities that provide cells with the molecules and energy they need to function, grow, and divide

171
Q

Is the net ΔG of a metabolic pathway positive or negative under physiological conditions?

A

Negative

172
Q

Why must transport of ammonia be carefully regulated?

A

It is toxic (mainly due to effects on the brain)

173
Q

How is excess NH4+ (ammonium) excreted?

A

As ammonia, urea, or uric acid

174
Q

Define ureotelic

A

Excrete amino acids as urea

175
Q

What is energy coupling?

A

Mechanism to couple unfavourable reactions with strongly exergonic processes

176
Q

What is intermediary (central) metabolism?

A

Combined activities of all pathways that interconvert precursors and molecules of low molecular weight

177
Q

What are allosteric mechanisms?

A

The regulation of an enzyme by binding an effector molecule at a site other than the enzyme’s active site

Molecules, Genes, and Cells (4 decks)

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