1. The Citric Acid Cycle The tricarboxylic acid (TCA) cycle
三羧酸循环
roundabout            n.
旋转木马 (= merry - go - round)
（道路交叉处的）环行圈，环行岛
hub           
轮轴，轴心
（重要性、活动等的）中心
The Citric Acid Cycle
The tricarboxylic acid (TCA) cycle

3. The TCA Cycle—A Brief Summary
The entry of new carbon units into the cycle is through acetyl-CoA.
This entry metabolite can be formed either from pyruvate (from glycolysis) or from oxidation of fatty acids.
In the process, metabolic energy is captured in the form of ATP, NADH, and enzyme-bound FADH2 (symbolized as [FADH2]).
metabolite            n.
代谢物
symbolize           
vt.
用符号表示, 是...的符号; 象征, 代表

4. The citric acid cycle is the central metabolic hub of the cell.
It is the gateway to the aerobic metabolism of any molecule that can be transformed into an acetyl group or dicarboxylic acid.
The cycle is also an important source of precursors, not only for the storage forms of fuels, but also for the building blocks of many other molecules such as amino acids, nucleotide bases, cholesterol, and porphyrin (the organic component of heme).
porphyrin            n.
[生化]卟啉

5. aconitase            n.
[生化]顺乌头酸酶

6. The citric acid cycle is the final common pathway for the oxidation of fuel molecules—amino acids, fatty acids, and carbohydrates.
Most fuel molecules enter the cycle as acetyl coenzyme A.
citric acid cycle, also called the tricarboxylic acid (TCA) cycle or the Krebs cycle (after its discoverer, Hans Krebs).

7. Under aerobic conditions, the pyruvate generated from glucose is oxidatively decarboxylated to form acetyl CoA.
In eukaryotes, the reactions of the citric acid cycle take place inside mitochondria, in contrast with those of glycolysis, which take place in the cytosol.
cristae
词性及解释
【医】 嵴
invagination            内陷 入鞘 套入

8. moiety            n.
二分之一, 一部分, 半族

9. The Bridging Step: Oxidative Decarboxylation of Pyruvate
oxidative decarboxylation reaction

10. pyruvate dehydrogenase complex(PDC) a cluster of enzymes—multiple copies of each of three enzymes—located in the mitochondria of eukaryotic cells and in the cytosol of prokaryotes.
It contains three enzymes: pyruvate dehydrogenase (E1), dihydrolipoyl transacetylase 二氢硫辛酸转乙酰基酶(E2), and dihydrolipoyl dehydrogenase二氢硫辛酸脱氢酶 (E3)—each present in multiple copies.

12. The overall reaction involves a total of five coenzymes: thiamine pyrophosphate焦磷酸硫胺素, coenzyme A, lipoic acid硫辛酸, NAD, and FAD.
The fifth cofactor of the PDH complex, lipoate
(Fig. 16–4), has two thiol groups that can undergo
reversible oxidation to a disulfide bond (OSOSO),
similar to that between two Cys residues in a protein.
Because of its capacity to undergo oxidation-reduction
reactions, lipoate can serve both as an electron hydrogen
carrier and as an acyl carrier, as we shall see.

13. 硫辛酸同酶分子中Lys残基的ε-NH2以酰胺键共价结合

16. Flexible Linkages Allow Lipoamide to Move Between Different Active Sites

18. Thiamine-deficient
As one might predict, mutations in the genes for the subunits of the PDH complex, or a dietary thiamine deficiency, can have severe consequences.
Thiamine-deficient animals are unable to oxidize pyruvate normally. This is of particular importance to the brain, which usually obtains all its energy from the aerobic oxidation of glucose in a pathway that necessarily includes the oxidation of pyruvate.
Beriberi脚气病, a disease that results from thiamine deficiency, is characterized by loss of neural function. This disease occurs primarily in populations that rely on a diet consisting mainly of white (polished) rice, which lacks the hulls in which most of the thiamine of rice is found.
People who habitually consume large amounts of alcohol can also develop thiamine deficiency, because much of their dietary intake consists of the vitamin-free “empty calories” of distilled spirits.
An elevated level of pyruvate in the blood is often an indicator of defects in pyruvate oxidation due to one of these causes.
thiamine            n.
[生化]硫胺(维生素B1)

19. 硫辛酸 (Thioctic Acid, Lipoic Acid)
酵母和微生物等必需的生长因子，含硫的八碳酸，对于动物不能算是一个维生素，但是一个辅酶，通过氧化还原作用参与生物体的递氢和传递乙酰基的作用。
以硫辛酸（酰胺）为辅酶的酶有：硫辛酸转乙酰酶、二氢硫辛酸脱氢酶、丙酮酸脱氢酶、α-酮戊二酸脱氢酶，与糖代谢关系密切。

20. Entry into the Cycle: The Citrate Synthase Reaction

23. Synthases and Synthetases
Synthases合酶 catalyze condensation reactions in which no nucleoside triphosphate (ATP, GTP, and so forth) is required as an energy source.
Synthetases合成酶 catalyze condensations that do use ATP or another nucleoside triphosphate as a source of energy for the synthetic reaction.

24. The Isomerization of Citrate by Aconitase乌头酸酶
aconitate hydratase乌头酸水合酶

25. The active site of aconitase
The active site of aconitase. The iron-sulfur cluster (red) is coordinated by cysteines (yellow) and isocitrate (white).

27. Fluoroacetate氟乙酸 Blocks the TCA Cycle
trojan horse inhibitor.
Citrate synthase converts fluoroacetate to inhibitory fluorocitrate for its TCA cycle partner, aconitase, blocking the cycle.
Trojan horse (神话)特洛伊木马(特洛伊战争时希腊人做的木马, 希腊兵藏在木马腹中, 混入特洛伊城); [喻]内部的破坏集团

28. Isocitrate Dehydrogenase—The First Oxidation in the Cycle

29. There are two different forms of isocitrate dehydrogenase in all cells, one requiring NAD as electron acceptor and the other requiring NADP.
In eukaryotic cells, the NAD-dependent enzyme occurs in the mitochondrial matrix and serves in the citric acid cycle.
The main function of the NADP-dependent enzyme, found in both the mitochondrial matrix and the cytosol, may be the generation of NADPH, which is essential for reductive anabolic reactions.

30. Citrate: A Symmetrical Molecule That Reacts Asymmetrically2

32. α-Ketoglutarate Dehydrogenase— A Second Decarboxylation

33. Like the pyruvate dehydrogenase complex, α-ketoglutarate dehydrogenase is a multienzyme complex—consisting of α-ketoglutarate dehydrogenase, dihydrolipoyl transsuccinylase, and dihydrolipoyl dehydrogenase—that employs five different coenzymes.

34. Succinyl-CoA Synthetase—A Substrate- Level Phosphorylation

35. Succinyl-CoA is itself a high-energy intermediate and is utilized in this step of the TCA cycle to drive the phosphorylation of GDP to GTP (in mammals) or ADP to ATP (in plants and bacteria).
The reaction is catalyzed by succinyl-CoA synthetase, sometimes called succinate Thiokinase琥珀酸硫激酶.

37. Succinate Dehydrogenase—An Oxidation Involving FAD

38. The oxidation of succinate to fumarate is carried out by succinate dehydrogenase, a membrane-bound enzyme that is located in the inner-membrane of mitochondrial .
It is actually part of the electron transport chain.

39. methylene            n.
亚甲基

40. Succinate dehydrogenase, like aconitase, is an iron–sulfur protein铁硫蛋白.
Indeed, succinate dehydrogenase contains three different kinds of iron–sulfur clusters, 2Fe-2S (two iron atoms bonded to two inorganic sulfides), 3Fe-4S, and 4Fe-4S.

41. Fumarase Catalyzes Trans-Hydration of Fumarate

43. This enzyme is highly stereospecific; it catalyzes hydration of the trans double bond of fumarate but not the cis double bond of maleate (the cis isomer of fumarate).
In the reverse direction (from L-malate to fumarate), fumarase is equally stereospecific: D-malate is not a substrate.
马来酸

44. Malate Dehydrogenase—Completing the Cycle

45. Binding of NAD causes a conformational change in the 20-residue segment that connects the D and E βstrands of the β-sheet.
The change is triggered by an interaction between the adenosine phosphate moiety of NAD and an arginine residue in this loop region.

46. A Summary of the Cycle

47. The Fate of the Carbon Atoms of Acetyl-CoA in the TCA Cycle

50. The TCA Cycle Provides Intermediates for Biosynthetic Pathways
In aerobic organisms, the citric acid cycle is an amphibolic pathway, one that serves in both catabolic and anabolic processes.
Besides its role in the oxidative catabolism of carbohydrates, fatty acids, and amino acids,
the cycle provides precursors for many biosynthetic pathways.

51. 异戊烯焦磷酸(isopentenyl pyrophosphate，IPP ）
ketoadipic acid 酮己二酸
aminolevulinate
词性及解释
【医】氨基酮戊酸盐(酯、根)
diamine            n.
[化]二(元)胺
pimelate           
庚二酸盐[酯]

52. malic enzyme
Finally, citrate can be exported from the mitochondria and then broken
down by ATP-citrate lyase to yield oxaloacetate and acetyl-CoA, a precursor of
fatty acids (Figure 20.23). Oxaloacetate produced in this reaction is rapidly
reduced to malate, which can then be processed in either of two ways: it may
be transported into mitochondria, where it is reoxidized to oxaloacetate, or it
may be oxidatively decarboxylated to pyruvate by malic enzyme, with subse-quent mitochondrial uptake of pyruvate. This cycle permits citrate to provide
acetyl-CoA for biosynthetic processes, with return of the malate and pyruvate
by-products to the mitochondria.

53. Why Is the Oxidation of Acetate So Complicated?
The eight-step cyclic process for oxidation of simple twocarbon
acetyl groups to CO2 may seem unnecessarily
cumbersome 讨厌的, 麻烦的, 笨重的
and not in keeping with the biological principle
of maximum economy. The role of the citric acid
cycle is not confined to the oxidation of acetate, however.
This pathway is the hub of intermediary metabolism.
Four- and five-carbon end products of many catabolic
processes feed into the cycle to serve as fuels. Oxaloacetate
and -ketoglutarate, for example, are produced from
aspartate and glutamate, respectively, when proteins are
degraded. Under some metabolic circumstances, intermediates
are drawn out of the cycle to be used as precursors
in a variety of biosynthetic pathways.
The citric acid cycle, like all other metabolic pathways,
is the product of evolution, and much of this evolution
occurred before the advent of aerobic organisms.
It does not necessarily represent the shortest pathway
from acetate to CO2, but it is the pathway that has, over
time, conferred the greatest selective advantage. Early
anaerobes most probably used some of the reactions of
the citric acid cycle in linear biosynthetic processes. In
fact, some modern anaerobic microorganisms use an incomplete
citric acid cycle as a source of, not energy, but
biosynthetic precursors (Fig. 16–14). These organisms
use the first three reactions of the cycle to make -
ketoglutarate but, lacking -ketoglutarate dehydrogenase,
they cannot carry out the complete set of citric
acid cycle reactions. They do have the four enzymes that
catalyze the reversible conversion of oxaloacetate to
succinyl-CoA and can produce malate, fumarate, succinate,
and succinyl-CoA from oxaloacetate in a reversal
of the “normal” (oxidative) direction of flow through the
cycle. This pathway is a fermentation, with the NADH
produced by isocitrate oxidation recycled to NAD by
reduction of oxaloacetate to succinate.
With the evolution of cyanobacteria蓝绿菌 that produced
O2 from water, the earth’s atmosphere became aerobic
and organisms were under selective pressure to develop
aerobic metabolism, which, as we have seen, is much
more efficient than anaerobic fermentation.
advent            n.
(尤指不寻常的人或事)出现, 到来

54. Anaplerotic Reactions Pathway 回补途径
As intermediates of the citric acid cycle are removed to serve as biosynthetic precursors, they are replenished by anaplerotic reactions.

55. Pyruvate carboxylase exists in the mitochondria of animal cells but not in plants.
PEP carboxylase occurs in yeast, bacteria, and higher plants, but not in animals.
Malic enzyme苹果酸酶 is found in the cytosol or mitochondria of many animal and plant cells.

57. The pyruvate carboxylase reaction requires the vitamin biotin生物素 , which is the prosthetic group of the enzyme.
Biotin plays a key role in many carboxylation reactions. It is a specialized carrier of one-carbon groups in their most oxidized form: CO2.

58. enolate           
烯醇化物

59. tether            n.
(拴牛马等的)绳; 系链
(知识、力量、财源、权限等的)限度, 范围

60. Regulation of the Citric Acid Cycle
acetate            n.
醋酸盐
combustion            燃烧
（有机体内营养料的）氧化

61. Regulation of the Citric Acid Cycle
The flow of carbon atoms from pyruvate into and through the citric acid cycle is under tight regulation at four sites:
The conversion of pyruvate to acetyl-CoA, the starting material for the cycle (the pyruvate dehydrogenase complex reaction).
The entry of acetyl-CoA into the cycle (the citrate synthase reaction).
The isocitrate dehydrogenase reaction.
α-ketoglutarate dehydrogenase reactions.

63. Regulation of Pyruvate Dehydrogenase Complex
Pyruvate Dehydrogenase Complex is allosterically inhibited by ATP and by acetyl-CoA and NADH.
The allosteric inhibition of pyruvate oxidation is greatly enhanced when long-chain fatty acids are available.
AMP, CoA, and NAD+ allosterically activate the Pyruvate Dehydrogenase Complex(PDC).

64. Acetyl-CoA specifically blocks dihydrolipoyl transacetylase, and NADH acts on dihydrolipoyl dehydrogenase.

65. Mg2+ is needed
The mammalian pyruvate dehydrogenase is also regulated by covalent modifications.

67. Hans Krebs and the Discovery of the TCA Cycle
1932 Krebs was studying the rates of oxidation of succinate, fumarate, acetate, malate, and citrate by kidney and liver tissue.

68. In 1935 in Hungary, Albert Szent-Györgyi was studying the oxidation of similar organic substrates by pigeon breast muscle.
he observed that addition of any of three four-carbon dicarboxylic acids—fumarate, succinate, or malate—caused the consumption of much more oxygen than was required for the oxidation of the added substance itself.
Hungary            n.
匈牙利[欧洲]

69. Carl Martius and Franz Knoop found that citric acid could be converted to isocitrate and then to α-ketoglutarate.
This finding was significant because it was already known that α-ketoglutarate could be enzymatically oxidized to succinate.

70. In 1937 Krebs found that citrate could be formed in muscle suspensions if oxaloacetate and either pyruvate or acetate were added.
It is a cycle.

71. congestion            n.
拥塞, 充血

72. Steric Preferences in NAD-Dependent Dehydrogenases
ethanol            n.
乙醇, 酒精
acetaldehyde           
[化]乙醛, 醋醛

73. spinach            n. 菠菜
dihydroorotate
词性及解释
【医】二氢乳清酸
diaphorase           
[生化]心肌黄酶,黄递酶,硫辛酰胺脱氢酶
hydroxybutyric acid           
[化]羟基丁酸

75. Fool’s Gold and the Reductive Citric Acid Cycle—The First Metabolic Pathway?
How did life arise on the planet Earth? It was once supposed that a reducing atmosphere, together with random synthesis of organic compounds, gave rise to a prebiotic “soup,” in which the first living things appeared. However, certain key compounds, such as arginine, lysine, and histidine, the straight-chain fatty acids, porphyrins, and essential coenzymes, have not been convincingly synthesized under simulated prebiotic conditions.
This and other problems have led researchers to consider other models for the evolution of life.
prebiotic           
adj.
生命起源以前的

76. One of these alternate models, postulated by Günter Wächtershäuser, involves an archaic version of the TCA cycle running in the reverse (reductive) direction.
Reversal of the TCA cycle results in assimilation of CO2 and fixation of carbon as shown.
For each turn of the reversed cycle, two carbons are fixed in the formation of isocitrate and two more are fixed in the reductive transformation of acetyl-CoA to oxaloacetate. Thus, for every succinate that enters the reversed cycle, two succinates are returned, making the cycle highly autocatalytic.
Because TCA cycle intermediates are involved in many biosynthetic pathways, a reversed TCA cycle would be a bountifuland broad source of metabolic substrates.
archaic           
adj.
古老的, 古代的, 陈旧的
bountifuland丰富多样

78. A reversed, reductive TCA cycle would require energy input to drive it
A reversed, reductive TCA cycle would require energy input to drive it. What might have been the thermodynamic driving force for such a cycle? Wächtershäuser hypothesizes that the anaerobic reaction of FeS and H2S to form insoluble FeS2 (pyrite黄铁矿,also known as fool’s gold) in the prebiotic milieu could have been the driving reaction:
anaerobic           
adj.
[微]没有空气而能生活的, 厌氧性的
milieu            n.
周围, 环境

79. Substrate Channeling through Multienzyme Complexes May Occur in the Citric Acid Cycle
Although the enzymes of the citric acid cycle are usually described as soluble components of the mitochondrial matrix (except for succinate dehydrogenase, which is membrane-bound), growing evidence suggests that within the mitochondrion these enzymes exist as multienzyme complexes.
Although the enzymes of the citric acid cycle are usually
described as soluble components of the mitochondrial
matrix (except for succinate dehydrogenase, which
is membrane-bound), growing evidence suggests that
within the mitochondrion these enzymes exist as multienzyme
complexes. The classic approach of enzymology—
purification of individual proteins from extracts of
broken cells—was applied with great success to the citric
acid cycle enzymes. However, the first casualty of cell
breakage is higher-level organization within the cell—the
noncovalent, reversible interaction of one protein with
another, or of an enzyme with some structural component
such as a membrane, microtubule [生]微管
or microfilament.
When cells are broken open, their contents, including
enzymes, are diluted 100- or 1,000-fold (Fig. 16–19).
Several types of evidence suggest that, in cells, multienzyme
complexes ensure efficient passage of the product
of one enzyme reaction to the next enzyme in the
pathway. Such complexes are called metabolons蜕变中间物质 . Certain
enzymes of the citric acid cycle have been isolated
together as supramolecular超分子的 aggregates, or have been
found associated with the inner mitochondrial membrane,
or have been shown to diffuse in the mitochondrial
matrix more slowly than expected for the individual
protein in solution. There is strong evidence for
substrate channeling through multienzyme complexes in
other metabolic pathways, and many enzymes thought
of as “soluble” probably function in the cell as highly organized
complexes that channel intermediates. We will
encounter other examples of channeling when we discuss
the biosynthesis of amino acids and nucleotides in
Chapter 22.