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Biochem Exam 2 > objectives > Flashcards

objectives Flashcards

1
Q

catabolic pathway

A

combust carbon fuels to synthesize ATP

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2
Q

anabolic pathway

A

pathways that use ATP and reduce power to synthesize large biomolecules

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3
Q

amphibolic pathways

A

can function anabolically or catabolically

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4
Q

what is creatine phosphate?

A
  • can regenerate ATP from ADP (allowing a short burst of activity as in a sprint)
  • once creatine phosphate stores are depleted, ATP must be generated by metabolic pathways
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5
Q

why are phosphate and its esters prominent in biology for several reasons?

A

1) are thermodynamically unstable, yet kinetically stable
2) stable because the inherent negative charges resist hydrolysis
3) are ideal regulatory molecules, added to molecules by kinases and removed by phosphatases

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6
Q

oxidation reactions

A

loss of electrons

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7
Q

reduction reactions

A

gain of electrons

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8
Q

why are oxidation and reduction reactions coupled?

A
  • carbon atoms in fuels are oxidized to yield CO2, and the electrons are ultimately accepted by oxygen to form H2O
  • the more reduced an oxygen is, the more free energy is released upon oxidation
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9
Q

what are activated carriers?

A

exemplify the modular design and economy of metabolism

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10
Q

what are the 2 characteristics that are common to activated carriers?

A

1) kinetically stable in the absence of specific catalysts

2) metabolism of activated groups is accomplished with a small number of carriers

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11
Q

what is an example of an activated carrier?

A
  • ATP; it is an activated carrier of phosphoryl groups
  • Nicotinamide adenine dinucleotide (NAD+) & flavin adenine dinucleotide (FAD) carry activated electrons derived from the oxidation of fuels
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12
Q

what are 3 regulatory controls in metabolism?

A

1) amount of enzymes present (gene expression)
2) catalytic activity of enzymes (allosteric regulation, covalent modification)
3) accessibility of substrates

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13
Q

what is the summary of glycolysis?

A

converting one molecule of glucose to 2 molecules of pyruvate with the generation of 2 net molecules of ATP

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14
Q

what are the 2 stages of glycolysis?

A

stage 1 = traps glucose in the cell & modifies it so that it can be CLEAVED into a pair of phosphorylated 3-carbon compounds (high-phosphoryl-transfer potential)

stage 2 = oxidizes the 3-carbon compounds to pyruvate while generating 2 molecules of ATP

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15
Q

what does hexokinase do?

A
  • traps glucose in cell and begins glycolysis
  • requires Mg2+ OR Mn2+ as a cofactor
  • catalyzes the reaction
  • employs substrate-binding induced fit to minimize hydrolysis of ATP
  • increased specificity - decreases chance of becoming an indiscriminate ATPase
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16
Q

what are the enzymes that catalyze the 3 irreversible steps in glycolysis?

A
  • hexokinase
  • phosphofructokinase
  • pyruvate kinase
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17
Q

what is alcoholic fermentation?

A

conversion of glucose into 2 molecules of ethanol

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18
Q

what is lactic acid fermentation?

A

conversion of glucose into 2 molecules of lactate

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19
Q

how else can NADH be oxidized?

A

by converting pyruvate to lactate in a reaction catalyzed by lactate dehydrogenase

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20
Q

where can fructose come from?

A

table sugar or high-fructose corn syrup

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21
Q

where does galactose come from?

A

milk sugar

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22
Q

how is fructose metabolized in the liver?

A

by the fructose 1-phosphate pathway

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23
Q

how is fructose metabolized in adipose tissue?

A

it is directly phosphorylated by hexokinase

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24
Q

what are the key regulators of phosphofructokinase in the liver?

A
  • citrate

- fructose 2,6-bisphophate

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25
Q

where is GLUT1 located?

A

all mammalian tissues

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26
Q

where is GLUT2 located?

A

liver and pancreatic beta cells

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27
Q

where is GLUT3 located?

A

all mammalian tissues

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28
Q

where is GLUT4 located?

A

muscle and fat cells

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29
Q

where is GLUT5 located?

A

small intestine

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30
Q

what steps in glycolysis make ATP?

A
  • step 6 = phosphoglycerate kinase

- step 9 = pyruvate kinase

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31
Q

what steps in glycolysis change ATP to ADP?

A
  • step 1 = hexokinase

- step 3 = phosphofructokinase

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32
Q

which step in glycolysis oxidizes NAD+ to NADH?

A

step 5 = glyceraldehyde 3-phosphate dehydrogenase

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33
Q

what is gluconeogenesis?

A

synthesis of glucose from non-carbohydrate precursors

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34
Q

where does gluconeogenesis occur?

A

mainly in the liver, but can occur in the kidney

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35
Q

why is gluconeogenesis not a simple reversal of glycolysis?

A

there are 3 irreversible steps in glycolysis that must be bypassed in gluconeogenesis:

  • hexokinase
  • phosphofructokinase
  • pyruvate kinase
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36
Q

how much energy is expended, or spent, in the synthesis of glucose?

A

2 molecules of ATP

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37
Q

the fasting state uses which process?

A

gluconeogenesis

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38
Q

the fed state uses which process?

A

glycolysis

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39
Q

what are the negative regulators in gluconeogenesis?

A
  • F-2,6-BP
  • AMP
  • ADP x2
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40
Q

what are the negative regulators in glycolysis?

A
  • ATP x2
  • Citrate
  • H+
  • Alanine (increased in skeletal muscle breakdown)
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41
Q

what are the positive regulators in glucogenesis?

A
  • Citrate

- Acetyl CoA

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42
Q

what are the positive regulators in glycolysis?

A
  • F-2,6-BP
  • AMP
  • F-1,6-BP
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43
Q

what is the role of phosphofructokinase 2 (PFK2)?

A

kinase that synthesizes fructose-2,6-bisphosphate

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44
Q

what is the role of fructose bisphosphate 2 (FBPase2)?

A

phosphatase that hydrolyzes fructose-2,6-bisphosphate

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45
Q

what happens to gluconeogenesis in patients suffering from Type 2 diabetes?

A
  • in type 2, insulin fails to act (aka insulin resistance)

- causing levels of enzymes to be high, leading to abnormally high levels of blood glucose

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46
Q

what is the Cori cycle?

A

series of reactions that occur in the muscle and liver that display inter-organ cooperation

  • lactate is produced by muscle during CONTRACTION
  • lactate released into blood
  • liver receives blood and removes the lactate to convert into glucose
  • glucose then released into the blood
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47
Q

where does the citric acid cycle take place?

A

under aerobic conditions, the MITOCHONDRIA

- pyruvate enters the mitochondria to be converted into acetyl CoA

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48
Q

what are the 2 parts of converting pyruvate to acetyl CoA?

A

1) citric acid cycle: carbon fuels are completely oxidized with the concomitant generation of high-transfer-potential electrons
2) oxidative phosphorylation: the movement of the high-transfer-potential electrons to oxygen to produce water (redox reactions)

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49
Q

what are the 2 principle fates for acetyl CoA?

A

1) metabolism by the citric acid cycle

2) incorporation into fatty acids

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50
Q

how is the pyruvate dehydrogenase complex regulated?

A

by energy charge

  • ATP, acetyl CoA, and NADH inhibit the complex
  • ADP and pyruvate stimulate the complex
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51
Q

what is lactic acidosis?

A

the process of pyruvate being processed into lactate, due to the inhibition of the pyruvate dehydrogenase complex
- production of lactate in the presence of oxygen is a characteristic of cancer cells

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52
Q

what are the clinical symptoms of Beriberi?

A

inhibited complex activity to the brain, leading to strange behavior
- neuromuscular pathologies

53
Q

what causes Beriberi?

A

insufficient pyruvate dehydrogenase activity due to thiamine deficiency (aka vitamin deficiency)

54
Q

what is the overall function of the citric acid cycle? (CAC)

A

harvests high-energy electrons from carbon fuels - oxidizing the acetyl fragment of acetyl CoA to CO2

55
Q

which steps in the CAC that produce NADH?

A
  • step 3 = isocitrate to alpha-ketoglutarate
  • step 4 = alpha-ketoglutarate to succinyl CoA
  • step 8 = Malate to oxaloacetate
56
Q

which step(s) in the CAC produce FADH2?

A

step 6 = succinate to fumarate

57
Q

which step(s) in the CAC produce ATP?

A

step 5 = succinyl CoA to succinate

58
Q

how many ATP are generated from the electrons of NADH?

A

2.5 ATP

59
Q

how many ATP are generated from the electrons from FADH2?

A

1.5 ATP

60
Q

what is an anaplerotic reaction?

A

a replenishing reaction, if/when the energy status of the cells changes

61
Q

explain an anaplerotic reaction in terms of oxaloacetate and pyruvate carboxylase

A

pyruvate carboxylase is a biotin-dependent enzyme that catalyzes the carboxylation of pyruvate into oxaloacetate

62
Q

what is the outer mitochondrial membrane permeable to?

A
  • most small ions and molecules (due to the channel protein, PORIN)
63
Q

what channel allows for passage of small molecules and ions in the outer mitochondrial membrane?

A

the voltage dependent anion channel (VDAC)

64
Q

what does the structure of the inner mitochondrial membrane look like?

A

it is folded into ridges called CRISTAE

65
Q

what is the permeability of the inner mitochondrial membrane?

A

it’s impermeable to most molecules

66
Q

what is the inner mitochondrial membrane a site for?

A

site of electron transport and ATP synthesis

67
Q

where does the citric acid cycle and fatty acid oxidation occur?

A

in the mitochondrial matrix

68
Q

what is the reduction potential, or redox potential?

A

measure of molecule’s tendency to donate OR accept electrons

69
Q

what is a strong reducing agent?

A

readily DONATES electrons and has a NEGATIVE E0′

70
Q

what is a strong oxidizing agent?

A

readily ACCEPTS electrons and has a POSITIVE E0′

71
Q

how many protein complexes is the electron transport chain composed of?

A

4 large protein complexes

72
Q

why are the electrons carried by FADH2 not as energy rich as those carried by NADH? what is the consequence of this?

A

the electrons in FADH2 have a lower reduction potential

- thus, the electrons pump fewer protons and yield fewer molecules of ATP

73
Q

what are the roles of superoxide dismutase?

A

scavenges superoxide radicals by catalyzing the conversion of two of these radicals into hydrogen peroxide and molecular oxygen

74
Q

what is catalase and what is its role in the cell?

A

it is an ubiquitous heme protein that catalyzes the dismutation of hydrogen peroxide into water and molecular oxygen

75
Q

what are the steps in glycolysis where ADP is formed?

A
  • step 1: glucose -> glucose-6-phosphate (hexokinase)

- step 3: fructose 6-phosphate -> fructose 1,6-bisphosphate (phosphofructokinase)

76
Q

which steps in glycolysis generate ATP?

A
  • step 6: 1,3-bisphosphoglycerate -> 3-phosphoglycerate (phosphoglycerate kinase)
  • step 9: phosphoenolpyruvate -> pyruvate (pyruvate kinase)
77
Q

which step in glycolysis generates NADH?

A

step 5: glyceraldehyde 3-phosphate -> 1,3-bisphosphoglycerate (glyceraldehyde 3-phosphate dehydrogenase)

78
Q

what is the proton-motive force and how does it produce ATP?

A

it is the proton gradient generated by the oxidation of NADH and FADH2
- this force powers the synthesis of ATP

79
Q

what is the chemiosmotic hypothesis?

A

proposed that electron transport and ATP synthesis are coupled by a proton gradient across the inner mitochondrial membrane (the coupled pair being oxidation and phosphorylation)

80
Q

what is the purpose and process of the “glycerol 3-phosphate shuttle”?

A
  • introduces NADH into the electron-transport chain
  • reduces dihydroxyacetone phosphate to glycerol 3-phosphate
  • electron transfer to FAD prosthetic group in membrane-bound glycerol 3-phosphate dehydrogenase reoxidizes glycerol 3-phosphate
  • subsequent electron transfer to Q to form QH2 allows these electrons to enter the electron-transport chain
81
Q

what is the purpose and process of “malate-aspartate shuttle”?

A
  • brings electrons from cytoplasmic NADH into the mitochondria in the HEART & LIVER
  • consists of 2 membrane transporters and 4 enzymes
82
Q

what does the “ATP-ADP translocase” do?

A
  • enables the exchange of cytoplasmic ADP for mitochondrial ATP
83
Q

what happens when the electron transport is uncoupled from ATP synthesis? what is this called?

A

heat is generated; it is called non-shivering thermogenesis

84
Q

how is uncoupling facilitated?

A

in a regulated fashion by uncoupling protein 1 (UCP-1) AKA thermogenin

85
Q

where does rotenone and amytal block in the electron-transport chain?

A

when NADH-Q oxidoreductase would be converted into QH2

86
Q

which step does antimycin A block in the electron-transport chain?

A

blocks the reaction where Q-cytochrome c oxidoreductase would be converted to cytochrome c

87
Q

which step does cyanide, azide, and carbon monoxide block in the electron-transport chain?

A

block the reaction where cytochrome c oxidase would be converted into O2

88
Q

why was 2,4-dinitrophenol (DNP) used as a weight loss drug?

A
  • DNP inhibits ATP synthesis
  • causes increased oxygen consumption and energy is released as heat
  • increase in metabolic rate & body temp
  • can lead to organ failure
89
Q

what is a reducing sugar?

A

sugars that react with oxidizing agents; they donate electrons

90
Q

what is an O-glycosidic bond?

A

bond formed between the anomeric carbon of a glucose and a hydroxyl group of an alcohol (oxygen bond)

91
Q

what is a N-glycosidic bond?

A

bond formed between an anomeric carbon atom of a glucose and the nitrogen from an amine (nitrogen bond)

92
Q

what is an oligosaccharide?

A

molecule that contains 2 or more monosaccharides linked by O-glycosidic bonds (max is 10 before it’s considered technically a polysaccharide)

93
Q

what does glycosyltransferases do?

A

they are a class of enzymes that catalyze the formation of glycosidic bonds (take sugar and transfer it)

94
Q

what are the different forms of glycoproteins?

A

1) proteoglycans

2) mucins/mucoproteins

95
Q

what is a N-linkage?

A

the bond that forms between a carb and the nitrogen atom in the side chain of asparagine

96
Q

what is an O-linkage?

A

the bond that forms between a carb and the oxygen on the side chains of either serine OR threonine

97
Q

how does blood type A come about?

A

N-acetylgalactosamine is added to the O antigen by a specific glycosyltransferase

98
Q

how does blood type B come about?

A

the addition of galactose to the O antigen

99
Q

what are the 5 classes of lipids?

A

1) free fatty acids
2) triacylglycerol
3) phospholipids
4) glycolipids
5) steroids

100
Q

what is the function of free fatty acids?

A

common fuel

101
Q

what is the function of triacylglycerols?

A

storage form of fatty lipids

102
Q

what is the function of phospholipids?

A

membrane lipids

103
Q

what is the function of glycolipids?

A

membrane lipids composed in part of carbohydrates

104
Q

what is the function of steroids?

A

polycyclic hydrocarbons with a variety of functions

105
Q

what is meant by the “melting temperature” of fatty acids?

A

the fluidity

106
Q

what does more unsaturation mean?

A

greater fluidity, shorter chain, more double bonds

107
Q

why are omega-3 fatty acids important for human health?

A

offer protection from coronary heart disease, and helps with brain health

108
Q

what is a triacylglycerol?

A

3 fatty acids esterified to one (1) molecule of glycerol

109
Q

between anhydrous fat stores and hydrated glycogen, which one lasts longer, energy-wise, and by how much?

A

a gram of anhydrous fat stores last more than 6x than a gram of hydrated glycogen

110
Q

where is triacylglycerol stored?

A

in adipose tissue

111
Q

what are the common types of membrane lipids?

A

1) phospholipids
2) glycolipids
3) cholesterol

112
Q

what role does cholesterol play in the cell?

A
  • maintains membrane fluidity

- precursor to steroid hormone

113
Q

what is the cause of “Hutchinson-Gilford progeria syndrome”?

A

inappropriate famesylation; the failure to remove a farnesyl group from the nuclear protein

114
Q

what are peripheral membrane proteins?

A

bound to the POLAR head groups of membrane lipids OR to exposed surfaces of integral membrane proteins

115
Q

how do COX inhibitors work?

A

they are dependent on a channel connecting the active site to the membrane interior

116
Q

what are the factors involved in transporting small molecules across a membrane?

A

1) concentration of the molecule is higher on one side of the membrane
2) molecule is lipophilic or soluble in nonpolar solutions

117
Q

what’s the difference between lipophilic and hydrophilic (polar) molecules?

A

lipophilic means the molecules are soluble in nonpolar solutions
- hydrophilic (or polar) means they are soluble in polar and/or water solutions

118
Q

what is a membrane channel?

A

particular protein that assists polar molecules diffusing across a membrane down their concentration gradient

119
Q

what is facilitated diffusion (aka passive transport)?

A

it is when molecules move down their concentration gradient to diffuse across a membrane

120
Q

how is the sodium gradient established across the membrane of a cell?

A

Na+ - K+ pump uses energy of ATP hydrolysis to simultaneously pump 3 Na+ ions out of the cell and 2 K+ ions into the cell against their concentration gradient

121
Q

describe the mechanism of a symporter

A

it powers the transport of a molecule against its concentration gradient by coupling the movement with the movement of another molecule down its concentration gradient, with both molecules moving in SAME direction

122
Q

describe the mechanism of an antiporter

A

use one concentration gradient to power the formation of another, but the molecules move in OPPOSITE directions

123
Q

what is digitalis, and how does it work?

A

it is a cardiotonic steroid that inhibits the Na+ - K+ pump by blocking its dephosphorylation
- it strengthens heart contractions and is used to treat heart disease

124
Q

what are the 2 types of ion channels?

A
  • voltage-activated

- ligand-activated

125
Q

what is a voltage-activated channel?

A

a channel that is activated by changes in the voltage across a membrane

126
Q

what is a ligand-activated channel?

A

a channel that can be activated by the binding of specific molecules to the channel

127
Q

what is a signal transduction cascade?

A

(1) releases a primary message as a response to a physiological circumstance
(2) reception of the primary message by a receptor
(3) relays the detection of the primary message to the cell interior by the generation of an intracellular second message
(4) activation of effector molecules by the second messenger that results in a physiological response
(5) termination of signal cascade

128
Q

what are the 3 major classes of membrane receptors?

A

(1) 7 transmembrane receptors associated w/ heterotrimeric G-proteins
(2) dimeric membrane receptors that RECRUIT protein kinases
(3) dimeric protein receptors that ARE protein kinases

Biochem Exam 2 (1 decks)

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