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7.11: Why It Matters- Metabolic Pathways - Biology

7.11: Why It Matters- Metabolic Pathways - Biology


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Why explain the metabolic pathways involved in the capture and release of energy in cells?

Every time you move—or even breathe—you’re using energy. Two of these ways are photosynthesis and cellular respiration.

Plants (and other autotrophs) undergo photosynthesis to create energy. Humans (and other heterotrophs) on the other hand must consume something that has energy (like plants or other animals)—we take this energy and convert it into a form our body can use. This process is known as cellular respiration.

Watch this 5 minute video for an overview of why even small changes in the global climate have the potential for big impacts on our daily lives through our food sources.

A YouTube element has been excluded from this version of the text. You can view it online here: pb.libretexts.org/bionm1/?p=214

  • What role does farming play in giving us energy to use every day?
  • How do plants get energy to grow, and how do we then get our energy from them?

Ok, let’s see where we get all the energy to stay awake during biology class!


We discovered that whale and dolphin brains produce lots of heat. Why it matters

Paul Manger receives funding from the National Research Foundation of South Africa.

Partners

University of the Witwatersrand provides support as a hosting partner of The Conversation AFRICA.

The Conversation UK receives funding from these organisations

We have all heard the mantra that dolphins and whales (cetaceans) are highly intelligent animals. Some claim they’re on par with great apes and humans – maybe even smarter. But where does this concept come from?

There are two lines of thought. Firstly, a range of cetacean behaviours are interpreted as displays of notable intelligence. Second, cetaceans have very large brains several species have brains that weigh more than human brains. We have large brains, and it is the structure and activity within these large brains that determines our abilities to examine, analyse and manipulate the world in a very complex way. So it has been thought that any other animal that has a brain as large, or larger, must be using their brain for the same thing.

But this logic is based on a very specific assumption: that 1 gram of brain tissue has, on average, the same capacity to process information in the same way irrespective of the brain in which it is found. It is this assumption that I have questioned over the past 20 years and I have come to a very different conclusion.

In my most recent study, my colleagues and I have ascertained that the cetacean brain is indeed special. Not for intelligence, though: it is special because it produces a lot more heat than the brains of other mammals. Through our research we’ve concluded that the cetacean brain has a specialised thermogenic system. It helps the animal’s brain to produce enough heat to maintain a functional brain temperature, and we believe this will combat the loss of heat to the water. This is separate to the special way whales and dolphins keep their bodies warm.

Evidence suggests the neurothermogenic specialisation we describe evolved around 32 million years ago.

With this knowledge, scientists can better understand how important water temperature is to the survival of cetaceans. This, in turn, will allow us to understand what will happen to certain species of cetaceans during the inevitable rise in oceanic temperatures associated with anthropogenic-induced climate change.

It is quite possible that some species, such as those dependent on the polar ice, like narwhals and beluga whales, may become victims of global warming. This new understanding of cetaceans will allow us to direct our conservation efforts in the most appropriate way to secure the future of as many species of cetacean as possible.


Introduction

Prostate cancer is one of the most frequently diagnosed malignance in males worldwide, especially in developed countries 1 . It was ranked as the most commonly diagnosed cancer and second leading cause of lethal cancer in American males of year 2014 2 . The early detection of prostate carcinoma suffers from low specificity and sensitivity of PSA, reflected by unnegligible rate of PCa including high-grade PCa among individuals with a PSA level ≤4 ng/ml as well as relatively high rate of non-malignant cases among men with a 4–10 ng/ml PSA level determined by biopsy 3,4 . These pitfalls have led to PSA controversy in considering the cost of substantial over-diagnosis and overtreatment following PSA elevation 5 . Therefore it is critical to develop novel diagnostic biomarkers with greater accuracy.

Metabolic reprogramming, including that of lipid metabolism, represents an established signature of cancer biology 6,7 . Bioactive lipids and lipid-modified proteins participate in pathogenesis of multiple cancers via lipid signaling networks 8 . Lipidomics approach, which enables a precise characterization of lipid structures and compositions within given cells or organisms, has been widely applied in cancer research 9 . Facilitated by high-throughput lipidomics, the relevance of lipids to cancer pathogenesis in context of, for instance, oncogene MYC overexpression 10 , hypoxia and Ras activation 11 , have been investigated. Meanwhile, the lipid metabolic features associated with breast cancer aggressiveness and progression have been characterized by lipidomics 12 .

In-depth delineation of lipid metabolic atlas in PCa is expected to open new insights into cancer tumorigenesis and progression, and may provide potential biomarker candidates for better diagnosis and prognosis. Existing studies have demonstrated that alterations in lipid metabolic enzymes and pathways, including those of fatty acids 13,14 and cholesterol metabolism 15,16,17 , are closely associated with PCa. However, comprehensive elucidation of lipid metabolic events and its regulations in PCa remains largely unexplored, especially in context of system-level networks. By far, a panel of lipid metabolites, including (ether-linked) phosphatidylethanolamines, fatty acids, lysophospholipids and other phospholipids, have been proposed as potential PCa biomarkers in distinguishing PCa patients from healthy individuals 18,19,20 . Nevertheless, most of them failed to correlate with PCa metastasis, aggressivity and benign hyperplasia. Based on metabolic profiling sarcosine has been identified as a potential biomarker to distinguish benign, localized and metastatic PCa 21 . However, the utility of sarcosine remains controversial 22 .

Since the adaptive transformation of lipid metabolism is highly dynamic and involved with complex regulatory networks, a focus on lipids phenotype per se remains insufficient. Recently approaches by integrating multi-omics datasets, i.e., information on genome-, proteome-, metabolome-scale etc., have achieved unprecedented insights into complex biological systems. Lipogenic network has been identified associated with hepatocellular carcinoma progression by combined analysis of metabolite and gene expression profiles 23 . By similar approach, the reliance of highly proliferating cancer cells on amino acid glycine has been revealed 24 .

To broaden our understanding of the metabolic alterations of lipid-gene networks in PCa and to identify potential biomarkers, 76 PCa and 19 BPH patients were enrolled in this study (Table 1, supplementary Table S1). Integrated study of lipidomics and transcriptomics (gene and miRNA expression profiling) was performed in paired ANT-PCT tissues from 25 PCa patients (discovery set). The identified biomarker candidates were further externally validated in a cohort including 51 PCa patients and 19 BPH patients (validation set). The workflow of study design is provided in supplementary information (supplementary Fig. S1).


2. Mechanisms: The Basics

Biologists frequently appeal to mechanisms in their explanations and descriptions of biological phenomena. They discuss mechanisms of gene regulation, DNA synthesis, nerve firing, muscle contraction, visual processing, and so on. When they use the mechanism concept they often suggest that some biological phenomenon can be understood as a kind of machine or mechanical system—such as a car engine or clock—in the sense of having particular features. This machine analogy encourages thinking of biological phenomena as having component parts that are spatially organized and that causally interact to produce some behaviour of the system. A key feature of this explanatory pattern is that it involves explaining some outcome by appealing to its causal parts. The system-level behaviour serves as the effect or explanatory target, while the interacting mechanical parts are what explain this behaviour.

Three features of this mechanism concept should be highlighted. First, mechanisms are often characterized as having a constitutive makeup, in the sense of involving particular systems with higher-level behaviours that can be decomposed into lower-level causal parts. This feature is exploited in efforts to discover mechanisms through the common investigative strategies of ‘decomposition and localization’, which are considered the ‘central heuristics’ of mechanism discovery (Wimsatt [1974] Bechtel and Richardson [2010] Bechtel and Levy [2013]). These strategies involve a process where scientists identify a system and behaviour of interest and then ‘drill down’ to identify the system’s parts, their location, and how they interact to produce the behaviour in question. This process reveals the role of single effects or higher-level explanatory targets in the discovery and individuation of mechanisms. In particular, mechanisms are circumscribed on the basis of which parts causally interact to produce a particular effect. 7 Those causal factors that produce this behaviour make up the mechanism and those that are not involved in this production are not mechanism components. This supports a picture where mechanism boundaries are drawn on the basis of methodological and pragmatic considerations, as opposed to capturing fixed, natural divisions in the world (Craver [2009] Bechtel [2015]). 8 This contributes to our conception of mechanisms as discrete causal entities in the same way that we talk about particular car engines or clock mechanisms as single, distinct causal systems (Bechtel and Richardson [2010], p. 35). These causal systems have boundaries and they can be discussed as individual units that are distinct from other causal systems in the world (Andersen [2014a], p. 276).

A second feature of the mechanism concept is that it is used to refer to causal systems that are described in significant amounts of causal detail as opposed to systems that abstract from such information. Consider the ‘mechanism of enzyme catalysis’ where an enzyme catalyses (or speeds up) the chemical conversion of an upstream substrate into a downstream product. Scientists refer to these enzymes as ‘molecular machines’ because they perform these conversions in multi-subunit complexes that have many causally interacting parts (Spirin [2002], p. 153). These parts and their interactions are represented in ‘reaction mechanism’ diagrams. These diagrams include components such as the enzyme itself, its substrate, and various cofactors and regulators that alter its functionality. Scientists expect complete descriptions of these mechanisms to contain large amounts of causal information. Consider the following:

An understanding of the complete mechanism of action of a purified enzyme requires identification of all substrates, cofactors, products, and regulators. Moreover, it requires a knowledge of (1) the temporal sequence in which enzyme-bound reaction intermediates form, (2) the structure of each intermediate and each transition state, (3) the rates of interconversion between intermediates, (4) the structural relationship of the enzymes to each intermediate, and (5) the energy contributed by all reacting and interacting groups to intermediate complexes and transition states. As yet, there is probably no enzyme for which we have an understanding that meets all these requirements. (Lehninger and Cox [2008], p. 205)

A third feature of the mechanism concept is that it often involves an emphasis on the ‘force’, ‘action’, and ‘motion’ involved in causal relationships. This emphasis is evident in how we discuss machines in ordinary life. Machines have parts such as pulleys, levers, hammers, and gears that actively do things. We do not simply say that these parts ‘cause’ various outcomes in each system, we say that they ‘push’, ‘pull’, ‘bend’, and ‘compress’ some downstream component. Mechanism descriptions in biology involve a similar emphasis. Scientists say that a cofactor ‘activates’ an enzyme, which then ‘binds’ to a substrate, before ‘splicing’ off a chemical moiety, and ‘attaching’ it to another molecule. The fact that the mechanism concept has this feature should be somewhat unsurprising, because the term ‘mechanism’ literally draws on mechanics or the branch of science and mathematics concerned with ‘motion and the forces producing motion’ (Soanes [2012], p. 449). What is the significance of this feature? Emphasizing the force or action of causal relationships serves several functions in biological (and other) contexts. First, it helps to satisfy our interest in understanding ‘how’ a mechanism works—adding force or motion terms adds something more than just saying that X causes Y. Second, these terms also function to fill in space between cause and effect variables, which can suggest closer physical proximity and satisfy our interest in getting more detail about the mechanism of interest. Causal terms involving force and motion appear to fill in black boxes and suggest that we know more about some causal process than merely saying ‘that’ X causes Y.

In the biological sciences, ‘mechanism’ is often used to refer to causal systems that have a constitutive character, that are represented in significant, fine-grained detail, and that contain an emphasis on the ‘force’, ‘action’, or ‘motion’ of causal relations. This concept is associated with the causal investigative strategies of decomposition and localization and it is involved in an explanatory pattern where some outcome is explained by appealing to the causal components that produce it.


5 Major Metabolic Pathways in Organisms| Microbiology

The following points highlight the five major pathways in organisms. The pathways are: 1. Glycolysis 2. Pentose Phosphate Pathway 3. Entner-Doudoroff Pathway 4. Tricarboxylic Acid Cycle 5. Glyoxylate Cycle.

Metabolic Pathway # 1. Glycolysis:

Glycolysis (glyco-sugar of sweet, lysis-breakdown) is the initial phase of metabolism during which the organic molecule glucose and other sugar are partially oxidized to smaller molecules e.g. pyruvate usually with the generation of some ATP and reduced coenzymes. Microorganisms employ several metabolic pathways to catabolize glucose and other sugars.

There are three important routes of glucose conversion to pyruvate such as glycolysis or Embden-Myerhof pathway (BMP) pathway, pentose phosphate pathway, and Entner-Doudroff pathway. Glycolysis is the most important type of mechanism by which organisms obtain energy from organic compounds in absence of molecular oxygen. As it occurs in the absence of oxygen, therefore, it is also called anaerobic fermentation.

Since living organisms arose in the environment lacking oxygen, anaerobic fermentation was the only method to obtain energy. However, glycolysis or anaerobic fermentation is present in both aerobic and anaerobic organisms.

Most higher organisms have retained the glycolytic pathway of degradation i.e. glucose to pyruvic acid as a preparatory pathway for complete aerobic catabolism of glucose. Glycolysis also serves as an emergency mechanism in anaerobic organisms to produce energy in the absence of oxygen.

(i) EMP Pathways:

In case of aerobic catabolic carbohydrate metabolism (aerobic respira­tion), some bacteria such as E. coli, Azotobacter spp., Bacillus eutrophus, etc. exhibit EMP pathway whereas, ED pathway (phosphorylated) is followed by the species of Alcaligenes, Rhizobium, Xanthomonas, etc. The non-phosphorylated ED pathway occurs in archaea (Pyrococcus spp., Thermoplasma spp, etc.). It is interesting to note that no archaeobacteria uses EMP pathway.

EMP pathway in bacteria initiates by using the phosphoenol pyruvate phosphotransferase system (PEP: PTS) that converts glucose to glucose 6-phosphate during nutrient transport across the cell membrane.

The glucose 6-phosphate is then isomerized to fructose 6-phosphate which is further converted to fructose 1, 6-bi-phosphate. This conversion requires ATP as a source of energy and an enzyme called phosphofructokinase.

It is essentially the reversal of glycolysis, which fulfills a similar anaplerotic role. It is particularly important during growth on pyruvate related C3 compounds and C2 units. The several class of flow of carbon from pyruvate maintains a supply of hexoses. These are required for cell wall and its component synthesis.

The complete pathway of glycolysis from glucose to pyruvate (Fig. 12.4) were elucidated by Gustav Embden (who gave the manner of cleavage of fructose 1, 6-diphosphate and pattern of subsequent steps) and Otto Meyerhof (who confirmed Embden’s work and studied the energetics of glycolysis), in late 1953s. Therefore the sequence reaction from glucose to pyruvate is also called Embden-Meyerhof pathway or glycolysis (EMP).

The overall balance sheet of glycolysis is given below:

Glucose + 2ADP + 2Pi + 2NAD + → Pyruvate + 2ATP + 2NADH + 2H +

In anaerobic organisms pyruvate is further converted to lactate or other organic compounds like alcohol, etc., after using NADH and H + formed during glycolysis:

Pyruvate + NADH + H+ ↔ Lactate + NAD +

In aerobes the pyruvate is converted to acetyl CoA as a preparatory step for entrance into tricarboxylic acid cycle, for complete oxidation of glucose.

Pyruvate + NAD + + CoA → Acetyl CoA + NADH + H + + CO2

Glycolysis is carried out by the help of ten enzymes for ten reactions of the glycolytic pathway. These enzymes are present in the soluble portion of the cytoplasm. All the mtermediates of the glycolytic pathway are phosphorylated compounds. The most important use of phosphate groups is in the production of ATP from ADP and phosphate.

The complete reactions of glycolytic pathway can be divided into two stages. In the first stage, ATP is utilized and glucose is converted into two molecules of three carbon compounds, glyceraldehyde 3-phosphate and dihydroxy acetone phosphate. The glyceraldehyde 3-phosphate is converted into pyruvic acid resulting in a net synthesis of two molecules of ATP.

The complete reaction with respective enzyme is shown in Fig. 12.4:

Apart from glucose, other types of sugar (monosaccharides, disaccharides, polysaccharides) can also enter the glycolytic pathway.

(а) Polysaccharides e.g. Glycogen:

Glucose-6-phosphate Glucose 6 – phosphate can enter as an intermediate of glycolysis.

(b) Disaccharides e.g. Sucrose:

The three key regulatory enzymes, hexokinase, phosphofructokinase and pyruvate kinase act irreversibly and rest of the steps are reversible.

(c) Homo-saccharides: e.g. Fructose:

Fructose can enter the glycolysis by changing to glyceraldehyde 3-phosphate.

Dihydroxyacetone phosphate can enter the glycolysis after enzymatically converting to dihydroxyacetone phosphate.

(ii) Alternate EMP Pathway-Methyl Glyoxal Pathway:

The methyl glyoxal pathway is an alternate of the EMP pathway. It Operates in the presence of low concentration of phosphate to the bacteria, E. coli, Clostridium spp., Pseudomonas spp. etc. In this pathway, dihydroxyacetone so formed converted to methyl glyoxal which later on gives rise to pyruvate.

Hence, there is complete absence of the phosphorylation step in which glyceraldehyde 3-phosphate forms 1, 3-bis-phospho- glycerate. The methyl glyoxal pathway consumes O2 and ATP and no ATP is generated in this pathway (Fig. 12.5).

Metabolic Pathway # 2. Pentose Phosphate Pathway (PPP):

Pentose phosphate pathway is an alternative of glucose degradation. This pathway, also called hexose monophosphate shunt (HMP) or phosphogluconate pathway is not the major pathway, but is a multipurpose pathway. Its main function is to generate reducing power in the extra-mitochondrial cytoplasm in the form of NADH. Its second function is to convert hexoses into pentoses, required in synthesis of nucleic acids.

Its third function is complete oxidative degradation of pentose. The reactions of phosphogluconate pathway take place in the soluble portion of extra-mitochondrial cytoplasm of cells.

The bacteria which show PPP are Bacillus subtilis, E. coli. Streptococcus faecalis and Leuconostoc mesenteroides. Apart from microorganisms the prominent tissues which show PPP are liver, mammary gland and adrenal cortex. The complete PPP is given in Fig 12.6.

There are three enzymes involved in PPP i.e. transketolase, transaldolase and ribulosephosphate 3-epimerase. Ribulose phosphate 3-epimerase catalyzes the conversion of ribulose 5-phosphate into the epimer xylulose 5-phosphate. Transketolase transfers the glycoaldehyde group (CH, OH—CO—) from xylulose 5-phosphate to ribose 5-phosphate to yield sedoheptulose 7-phosphate and glyceraldehyde-3-phosphate.

Transketolase also catalyzes the transfer of glycoaldehyde group from a number of 2-keto sugar phosphate to carbon atom one of a number of different aldose phosphate. Transaldolase acts on the products of transketolase and transfer dihydroxyacetone group to form fructose 6-phosphate and erythrose 4-phosphate (Fig. 12.6).

Fig. 12.6 : The Pentose phosphate pathway.

Pentose phosphate pathway thus functions according to the needs of the cell. If the requirement of reducing power is more then it proceeds towards the formation of NADPH but if pentoses are required it functions in the direction of formation of pentose. But if the cell requires instant energy the PPP stops and glycolysis and TCA proceed.

(a) To anabolic reactions that require electron donors

(b) To Calvin-Benson Cycle (dark reactions of photosynthesis)

(c) To synthesis of nucleotides and nucleic acids

(d) To step e of glycolysis

(e) To glucose 6-phosphate which can enter the pentose phosphate pathway or glycolysis

(f) To synthesis of several amino acids.

Metabolic Pathway # 3. Entner-Doudoroff Pathway:

Apart from glycolysis, Entner-Doudoroff pathway is another pathway for oxidation of glucose to pyruvic acid. This pathway is found in some Gram-negative bacteria like Rhizobium, Agrobacterium and Pseudomonas and is absent in Gram-positive bacteria. In this pathway each molecule of glucose, forms two molecules of NADPH and one molecule of ATP. The complete pathway is shown in the Fig. 12.7.

In this pathway glucose 6-phosphate is oxidized to 6-phosphogluconate, then converted to 2- keto-3-deoxy-6-phosphoglucose (kDPG) cleaved using enzyme to give rise glyceraldehyde’s 3- phosphate and pyruvate directly without generation of ATP. The catabolism of glucose results in production of only one ATP molecule whereas in EMP pathway, two ATP molecules are produced. This seems that EMP pathway more efficient than that of ED pathway.

Further, difference between ED pathway and PP pathway is the generation of reduced NADPH from NADP in the former. It is interesting to note that coenzyme NADP+ and NADPH are used in anabolic reactions. Thus, the ED pathway provides an important mechanism for producing NADPH and the 3-carbon building blocks used in biosynthetic reactions etc.

Partially non-phosphorylated ED pathway is involved in some bacteria such as Clostridium spp. Achromobacter spp., Alcaligens spp. and Archaea (Halobacterium spp.) In this case, intermediate product formed prior to kDPG is non-phosphorylated, and phosphogluconate is dehydrated to give rise kDPG, which gives to pyruvate.

In later steps, the reactions of ED pathway are followed. This pathway is also found in other bacteria such as Pseudomonas aeruginosa, Azotobacter, and Enterococcus faecalis, and an anaerobic bacterium Zymomonas mobilis.

Metabolic Pathway # 4. Tricarboxylic Acid Cycle:

The tricarboxylic acid cycle was first given by H.A. Krebs in 1937. H.A. Krebs then gave the name citric acid cycle. Because of citric acid is the first product of Krebs cycle, is also known as TCA cycle due to presence of three carboxylic groups in a molecule of citric acid.

The cycle is of universal occurrence in all the aerobic organisms and leads to complete oxidation of glucose to CO2 and H2O while glycolysis leads to incomplete oxidation of glucose to pyruvate.

Tri-carboxyhc acid cycle completely oxidises it to release large amount of energy in the form of NADH + H + mainly and GTP. NADH + H + enter the respiratory chain where each NADH + H + produces three ATP molecules. GTP is converted to ATP by substrate level oxidation. Another form of energy is in the form of substrate of FADH 2 , which also enters the respiratory chain to form two molecules of ATP.

All the reactions of tricarboxylic acid cycle take place in the inner compartment of mitochondrion. Some of these enzymes occur in the matrix of inner compartment, while rest of them occur on the inner mitochondrial membrane. For the start of the cycle, the pyruvate formed in the glycolysis is first converted to acetyl Co-A by preparatory reaction.

Pyruvate + NAD + + CoA → acetyl CoA + NADH + H+ + CO2

The reaction is irreversible and is not itself a part of the tricarboxylic acid cycle. It is carried out with the help of the enzyme pyruvate dehydrogenase. Acetyl CoA then enters the cycle after combining with oxaloacetate to form citrate, after which a cycle of reactions occurs (Fig. 12.8) leading to the formation of six CO2, eight NADH + H + , one FADH2 and one molecule of glucose.

There are few key steps in the tricarboxylic acid cycle which control the cycle as per need of the cell. The first of these controls is the preparatory reaction. The activity of pyruvate dehydrogenase is reduced in the presence of excess ATP and again increases in the absence of ATP.

There are two more steps which can control the cycle. These are the isocitrate dehydrogenase reaction (which requires ADP as positive regulation), and succinate dehydrogenase reaction (promoted by succinate, phosphate and ATP). However, the key control of the cycle is the reaction carried out by citrate synthase. This is the primary control of the cycle.

Metabolic Pathway # 5. Glyoxylate Cycle:

It is anaplerotic reaction in which oxaloacetate is taken from TCA cycle to meet out the demand of carbon requirement for amino acid biosynthesis. Hence, these intermediates have to be replenished via an alternate route, called anaplerotic pathway i.e. glyoxylate pathway. This cycle operates for glucoiieogenesis. Glyoxylate cycle was given first by Krebs and H.R. Kornberg.

This cycle is a modified form of tricarboxylic acid cycle found in plants and those microorganisms which utilize fatty acids as the source of energy in the form of acetyl Co A.

In this cycle the CO2 evolving steps of tricarboxylic acid cycle were by-passed and instead a second molecule of acetyl CoA is utilized (which condenses with glyoxylate to form malate). Succinate is a by product, used for biosynthesis, particularly in gluconeogenesis.

The overall reaction of glyoxylate cycle is given below:

2 Acetyl Co-A + NAD + + 2H2O → Succinate + 2CoA + NADH + H +

The two key enzymes, isocitrate lyase and malate synthase of glyoxylate cycle are localised in cytoplasmic organelles called glyoxysomes. Glyoxylate cycle goes on simultaneously with the tricarboxylic acid cycle, while tricarboxylic acid provides energy glyoxylate cycle provides succinate for the formation of new carbohydrate from fats as shown in Fig. 12.9.


Critical Thinking Questions

Which statement best explains how electrons are transferred and the role of each species. Remember that R represents a hydrocarbon molecule and RH represents the same molecule with a particular hydrogen identified.

  1. ext acts as a reducing agent and donates its electrons to the oxidizing agent ext^ <+>, forming ext and ext .
  2. ext^ <+>, the oxidizing agent, donates its electrons to the reducing agent ext , forming ext and ext .
  3. ext acts as an oxidizing agent and donates electrons to the reducing agent ext^ <+>, producing ext and ext .
  4. ext^ <+>, the reducing agent, accepts electrons from the oxidizing agent ext , producing ext and ext .
  1. The presence of glycolysis in nearly all organisms indicates that it is an advanced and recently evolved pathway that has been widely used due to the benefits it provides.
  2. Glycolysis is absent in a few higher organisms, which contradicts the assertion that it is one of the oldest metabolic pathways.
  3. Glycolysis is present in some organisms and absent in others. This inconsistency fails to support the assertion that it is one of the oldest metabolic pathways.
  4. To be present in so many different organisms, glycolysis was probably present in a common ancestor rather than evolved many separate times.
  1. Cells need energy to perform cell division. Blocking glycolysis in RBCs interrupts the process of mitosis, leading to nondisjunction.
  2. Cells require energy to perform certain basic functions. Blocking glycolysis in RBCs causes imbalance in the membrane potential, leading to cell death.
  3. Cells maintain the influx and efflux of organic substances using energy. Blocking glycolysis stops the binding of CO2 to the RBCs, causing cell death.
  4. Cells require energy to recognize attacking pathogens. Blocking glycolysis inhibits the process of that recognition, causing invasion of the RBCs by a pathogen.
  1. The reactant and the product are the same in a circular pathway but different in a linear pathway.
  2. The circular pathway components get exhausted whereas those of the linear pathway do not and are continually regenerated.
  3. Circular pathways are not suited for amphibolic pathways whereas linear pathways are.
  4. Circular pathways contain a single chemical reaction that is repeated while linear pathways have multiple events.
  1. Removal of a carboxyl group from pyruvate releases carbon dioxide. The pyruvate dehydrogenase complex comes into play.
  2. Removal of an acetyl group from pyruvate releases carbon dioxide. The pyruvate decarboxylase complex comes into play.
  3. Removal of a carbonyl group from pyruvate releases carbon dioxide. The pyruvate dehydrogenase complex comes into play.
  4. Removal of coenzyme A from pyruvate releases carbon dioxide. The pyruvate dehydrogenase complex comes into play.
  1. Pyruvate dehydrogenase removes a carboxyl group from pyruvate, producing carbon dioxide. Dihydrolipoyl transacetylase oxidizes a hydroxyethyl group to an acetyl group, producing NADH. Lastly, an enzyme-bound acetyl group is transferred to CoA, producing a molecule of acetyl-CoA.
  2. Pyruvate dehydrogenase oxidizes hydroxyethyl group to an acetyl group, producing NADH. It further removes a carboxyl group from pyruvate, producing carbon dioxide. Lastly, dihydrolipoyl transacetylase transfers enzyme-bound acetyl group to CoA, forming an acetyl-CoA molecule.
  3. Pyruvate dehydrogenase transfers enzyme-bound acetyl group to CoA, forming an acetyl CoA molecule. It then oxidizes a hydroxyethyl group to an acetyl group, producing NADH. Dihydrolipoyl transacetylase removes a carboxyl group from pyruvate, producing carbon dioxide.
  4. Pyruvate dehydrogenase removes carboxyl group from pyruvate, producing carbon dioxide. Dihydrolipoyl dehydrogenase transfers enzyme-bound acetyl groups to CoA, forming an acetyl-CoA molecule. Lastly, a hydroxyethyl group is oxidized to an acetyl group, producing NADH.
  1. CoQ and cytochrome c covalently bind electrons, while NADH dehydrogenase and succinate dehydrogenase are bound to the inner mitochondrial membrane.
  2. CoQ and cytochrome c are bound to the inner mitochondrial membrane, while NADH dehydrogenase and succinate dehydrogenase are mobile electron carriers.
  3. CoQ and cytochrome c covalently bind electrons, while NADH dehydrogenase and succinate dehydrogenase are mobile electron carriers.
  4. CoQ and cytochrome c are mobile electron carriers, while NADH dehydrogenase and succinate dehydrogenase are bound to the inner mitochondrial membrane.
  1. The ATPs produced are immediately utilized in the anaplerotic reactions that are used for the replenishment of the intermediates.
  2. Most of the ATPs produced are rapidly used for the phosphorylation of certain compounds found in plants.
  3. Transport of NADH from cytosol to mitochondria is an active process that decreases the number of ATPs produced.
  4. A large number of ATP molecules are used in the detoxification of xenobiotic compounds produced during cellular respiration.
  1. Complex IV consists of an oxygen molecule held between the cytochrome and copper ions. The electrons flowing finally reach the oxygen, producing water.
  2. Complex IV contains a molecule of flavin mononucleotide and iron-sulfur clusters. The electrons from NADH are transported here to coenzyme Q.
  3. Complex IV contains cytochrome b, c, and Fe-S. Here, the proton motive Q cycle takes place.
  4. Complex IV contains a membrane-bound enzyme that accepts electrons from FADH2 to make FAD. This electron is then transferred to ubiquinone.
  1. Fermentation uses glycolysis, the citric acid cycle, and the ETC but finally gives electrons to an inorganic molecule, whereas anaerobic respiration sues only glycolysis and its electron acceptor is an organic molecule.
  2. Fermentation uses only glycolysis and its final electron acceptor is an organic molecule, whereas anaerobic respiration uses glycolysis, the citric acid cycle, and the ETC but finally gives electrons to an inorganic molecule other than O2.
  3. Fermentation uses glycolysis, the citric acid cycle, and the ETC but finally gives electrons to an organic molecule, whereas anaerobic respiration uses only glycolysis and its final electron acceptor is an inorganic molecule.
  4. Fermentation uses glycolysis and its final electron acceptor is an inorganic molecule, whereas anaerobic respiration uses glycolysis, the citric acid cycle, and the ETC but finally gives electrons to an organic molecule.

What type of cellular respiration is represented in the following equation, and why?

  1. Anaerobic respiration, because the final electron acceptor is inorganic.
  2. Aerobic respiration, because oxygen is the final electron acceptor.
  3. Anaerobic respiration, because NADH donates its electrons to a methane molecule.
  4. Aerobic respiration, because water is being produced as a product.
  1. Metabolic pathways are wasteful, as they perform uncoordinated catabolic and anabolic reactions that waste some of the energy that is stored.
  2. Metabolic pathways are economical due to the presence of anaplerotic reactions that replenish the intermediates.
  3. Metabolic pathways are economical due to feedback inhibition. Also, intermediates from one pathway can be utilized by other pathways.
  4. Metabolic pathways are wasteful, as most of the energy produced is utilized in maintaining the reduced environment of the cytosol.
  1. Glucagon and glycogen can be converted to 3-phosphoglyceraldehyde that is an intermediate of glycolysis.
  2. Chylomicrons and fatty acids get converted to 1,3-bisphosphoglycerate that continues in glycolysis, forming pyruvate.
  3. Sphingolipids and triglycerides form glucagon that can be fed into glycolysis.
  4. Cholesterol and triglycerides can be converted to glycerol-3-phosphate that continues through glycolysis.
  1. Citrate and ATP are negative regulators of hexokinase.
  2. Citrate and ATP are negative regulators of phosphofructokinase-1.
  3. Citrate and ATP are positive regulators of phosphofructokinase-1.
  4. Citrate and ATP are positive regulators of hexokinase.
  1. Negative feedback mechanisms maintain homeostasis whereas positive feedback drives the system away from equilibrium.
  2. Positive feedback mechanisms maintain a balanced amount of substances whereas negative feedback restricts them.
  3. Negative feedback turns the system off, making it deficient of certain substances. Positive feedback balances out these deficits.
  4. Positive feedback brings substance amounts back to equilibrium while negative feedback produces excess amounts of the substance.

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    • Book title: Biology for AP® Courses
    • Publication date: Mar 8, 2018
    • Location: Houston, Texas
    • Book URL: https://openstax.org/books/biology-ap-courses/pages/1-introduction
    • Section URL: https://openstax.org/books/biology-ap-courses/pages/7-critical-thinking-questions

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    Module six - metabolic pathways: biology 1308 (textbook)

    Plants (and other autotrophs) undergo photosynthesis to create energy. Humans (and other heterotrophs) on the other hand must consume something that has energy (like plants or other animals)—we take this energy and convert it into a form our body can use. This process is known as cellular respiration.

    P). This is illustrated by the following generic reaction:

    A + enzyme + ATP → [A − enzyme −

    P] → B + enzyme + ADP + phosphate ion

    The energy that is harnessed from photosynthesis enters the ecosystems of our planet continuously and is transferred from one organism to another. Therefore, directly or indirectly, the process of photosynthesis provides most of the energy required by living things on earth.

    Heterotrophs are organisms incapable of photosynthesis that must therefore obtain energy and carbon from food by consuming other organisms. The Greek roots of the word heterotroph mean "other" (hetero) "feeder" (troph), meaning that their food comes from other organisms. Even if the food organism is another animal, this food traces its origins back to autotrophs and the process of photosynthesis. Humans are heterotrophs, as are all animals. Heterotrophs depend on autotrophs, either directly or indirectly. Deer and wolves are heterotrophs. A deer obtains energy by eating plants. A wolf eating a deer obtains energy that originally came from the plants eaten by that deer. The energy in the plant came from photosynthesis, and therefore it is the only autotroph in this example. Using this reasoning, all food eaten by humans also links back to autotrophs that carry out photosynthesis.

    Photosynthesis is a multi-step process that requires sunlight, carbon dioxide (which is low in energy), and water as substrates. After the process is complete, it releases oxygen and produces glyceraldehyde-3-phosphate (GA3P), simple carbohydrate molecules (which are high in energy) that can subsequently be converted into glucose, sucrose, or any of dozens of other sugar molecules. These sugar molecules contain energy and the energized carbon that all living things need to survive.

    Although the equation looks simple, the many steps that take place during photosynthesis are actually quite complex. Before learning the details of how photoautotrophs turn sunlight into food, it is important to become familiar with the structures involved.

    In plants, photosynthesis generally takes place in leaves, which consist of several layers of cells. The process of photosynthesis occurs in a middle layer called the mesophyll. The gas exchange of carbon dioxide and oxygen occurs through small, regulated openings called stomata (singular: stoma), which also play roles in the regulation of gas exchange and water balance. The stomata are typically located on the underside of the leaf, which helps to minimize water loss. Each stoma is flanked by guard cells that regulate the opening and closing of the stomata by swelling or shrinking in response to osmotic changes.

    Visible light constitutes only one of many types of electromagnetic radiation emitted from the sun. The electromagnetic spectrum is the range of all possible wavelengths of radiation. Each wavelength corresponds to a different amount of energy carried.

    Each type of electromagnetic radiation has a characteristic range of wavelengths. The longer the wavelength (or the more stretched out it appears), the less energy is carried. Short, tight waves carry the most energy. This may seem illogical, but think of it in terms of a piece of moving rope. It takes little effort by a person to move a rope in long, wide waves. To make a rope move in short, tight waves, a person would need to apply significantly more energy.

    All photosynthetic organisms contain a pigment called chlorophyll a, which humans see as the common green color associated with plants. Chlorophyll a absorbs wavelengths from either end of the visible spectrum (blue and red), but not from green. Because green is reflected, chlorophyll appears green.

    Other pigment types include chlorophyll b (which absorbs blue and red-orange light) and the carotenoids. Each type of pigment can be identified by the specific pattern of wavelengths it absorbs from visible light, which is its absorption spectrum.

    The light-dependent reactions begin in a grouping of pigment molecules and proteins called a photosystem. Photosystems exist in the membranes of thylakoids. A pigment molecule in the photosystem absorbs one photon, a quantity or "packet" of light energy, at a time.

    A photon of light energy travels until it reaches a molecule of chlorophyll. The photon causes an electron in the chlorophyll to become "excited." The energy given to the electron allows it to break free from an atom of the chlorophyll molecule. Chlorophyll is therefore said to "donate" an electron.

    To replace the electron in the chlorophyll, a molecule of water is split. This splitting releases an electron and results in the formation of oxygen (O2) and hydrogen ions (H+) in the thylakoid space. Technically, each breaking of a water molecule releases a pair of electrons, and therefore can replace two donated electrons.

    The replacing of the electron enables chlorophyll to respond to another photon. The oxygen molecules produced as byproducts find their way to the surrounding environment. The hydrogen ions play critical roles in the remainder of the light-dependent reactions.

    Keep in mind that the purpose of the light-dependent reactions is to convert solar energy into chemical carriers that will be used in the Calvin cycle. In eukaryotes, two photosystems exist, the first is called photosystem II, which is named for the order of its discovery rather than for the order of function.

    The buildup of hydrogen ions in the thylakoid space forms an electrochemical gradient because of the difference in the concentration of protons (H+) and the difference in the charge across the membrane that they create. This potential energy is harvested and stored as chemical energy in ATP through chemiosmosis, the movement of hydrogen ions down their electrochemical gradient through the transmembrane enzyme ATP synthase, just as in the mitochondrion.

    The Calvin cycle reactions can be organized into three basic stages: fixation, reduction, and regeneration. In the stroma, in addition to CO2, two other chemicals are present to initiate the Calvin cycle: an enzyme abbreviated RuBisCO, and the molecule ribulose bisphosphate (RuBP). RuBP has five atoms of carbon and a phosphate group on each end.

    RuBisCO catalyzes a reaction between CO2 and RuBP, which forms a six-carbon compound that is immediately converted into two three-carbon compounds. This process is called carbon fixation, because CO2 is "fixed" from its inorganic form into organic molecules.

    ATP and NADPH use their stored energy to convert the three-carbon compound, 3-PGA, into another three-carbon compound called G3P. This type of reaction is called a reduction reaction, because it involves the gain of electrons. A reduction is the gain of an electron by an atom or molecule. The molecules of ADP and NAD+, resulting from the reduction reaction, return to the light-dependent reactions to be re-energized.

    One of the G3P molecules leaves the Calvin cycle to contribute to the formation of the carbohydrate molecule, which is commonly glucose (C6H12O6). Because the carbohydrate molecule has six carbon atoms, it takes six turns of the Calvin cycle to make one carbohydrate molecule (one for each carbon dioxide molecule fixed). The remaining G3P molecules regenerate RuBP, which enables the system to prepare for the carbon-fixation step. ATP is also used in the regeneration of RuBP.

    is the reverse of the overall reaction for cellular respiration:

    Photosynthesis produces oxygen as a byproduct, and respiration produces carbon dioxide as a byproduct.

    In nature, there is no such thing as waste. Every single atom of matter is conserved, recycling indefinitely. Substances change form or move from one type of molecule to another, but never disappear.

    6CO2+6H2O→C6H12O6+6O2
    Because this process involves synthesizing an energy-storing molecule, it requires energy input to proceed. During the light reactions of photosynthesis, energy is provided by a molecule called adenosine triphosphate (ATP), which is the primary energy currency of all cells. Just as the dollar is used as currency to buy goods, cells use molecules of ATP as energy currency to perform immediate work. In contrast, energy-storage molecules such as glucose are consumed only to be broken down to use their energy. The reaction that harvests the energy of a sugar molecule in cells requiring oxygen to survive can be summarized by the reverse reaction to photosynthesis. In this reaction, oxygen is consumed and carbon dioxide is released as a waste product. The reaction is summarized as:

    C6H12O6+6O2→6H2O+6CO2
    Both of these reactions involve many steps.

    The processes of making and breaking down sugar molecules illustrate two examples of metabolic pathways. A metabolic pathway is a series of chemical reactions that takes a starting molecule and modifies it, step-by-step, through a series of metabolic intermediates, eventually yielding a final product. In the example of sugar metabolism, the first metabolic pathway synthesized sugar from smaller molecules, and the other pathway broke sugar down into smaller molecules. These two opposite processes—the first requiring energy and the second producing energy—are referred to as anabolic pathways (building polymers) and catabolic pathways (breaking down polymers into their monomers), respectively. Consequently, metabolism is composed of synthesis (anabolism) and degradation (catabolism).

    Biological organisms are open systems. Energy is exchanged between them and their surroundings as they use energy from the sun to perform photosynthesis or consume energy-storing molecules and release energy to the environment by doing work and releasing heat. Like all things in the physical world, energy is subject to physical laws. The laws of thermodynamics govern the transfer of energy in and among all systems in the universe.

    A living cell's primary tasks of obtaining, transforming, and using energy to do work may seem simple. However, the second law of thermodynamics explains why these tasks are harder than they appear. All energy transfers and transformations are never completely efficient. In every energy transfer, some amount of energy is lost in a form that is unusable. In most cases, this form is heat energy. Thermodynamically, heat energy is defined as the energy transferred from one system to another that is not work. For example, when a light bulb is turned on, some of the energy being converted from electrical energy into light energy is lost as heat energy. Likewise, some energy is lost as heat energy during cellular metabolic reactions.

    An important concept in physical systems is that of order and disorder. The more energy that is lost by a system to its surroundings, the less ordered and more random the system is. Scientists refer to the measure of randomness or disorder within a system as entropy. High entropy means high disorder and low energy. Molecules and chemical reactions have varying entropy as well. For example, entropy increases as molecules at a high concentration in one place diffuse and spread out. The second law of thermodynamics says that energy will always be lost as heat in energy transfers or transformations.

    Now what if that same motionless wrecking ball is lifted two stories above ground with a crane? If the suspended wrecking ball is unmoving, is there energy associated with it? The answer is yes. The energy that was required to lift the wrecking ball did not disappear, but is now stored in the wrecking ball by virtue of its position and the force of gravity acting on it. This type of energy is called potential energy. If the ball were to fall, the potential energy would be transformed into kinetic energy until all of the potential energy was exhausted when the ball rested on the ground. Wrecking balls also swing like a pendulum through the swing, there is a constant change of potential energy (highest at the top of the swing) to kinetic energy (highest at the bottom of the swing). Other examples of potential energy include the energy of water held behind a dam or a person about to skydive out of an airplane.

    If energy is released during a chemical reaction, then the change in free energy, signified as ∆G (delta G) will be a negative number. A negative change in free energy also means that the products of the reaction have less free energy than the reactants, because they release some free energy during the reaction. Reactions that have a negative change in free energy and consequently release free energy are called exergonic reactions. Think: exergonic means energy is exiting the system. These reactions are also referred to as spontaneous reactions, and their products have less stored energy than the reactants. An important distinction must be drawn between the term spontaneous and the idea of a chemical reaction occurring immediately. Contrary to the everyday use of the term, a spontaneous reaction is not one that suddenly or quickly occurs. The rusting of iron is an example of a spontaneous reaction that occurs slowly, little by little, over time.

    If a chemical reaction absorbs energy rather than releases energy on balance, then the ∆G for that reaction will be a positive value. In this case, the products have more free energy than the reactants. Thus, the products of these reactions can be thought of as energy-storing molecules. These chemical reactions are called endergonic reactions and they are non-spontaneous. An endergonic reaction will not take place on its own without the addition of free energy.

    The chemical reactants to which an enzyme binds are called the enzyme's substrates. There may be one or more substrates, depending on the particular chemical reaction. In some reactions, a single reactant substrate is broken down into multiple products. In others, two substrates may come together to create one larger molecule. Two reactants might also enter a reaction and both become modified, but they leave the reaction as two products. The location within the enzyme where the substrate binds is called the enzyme's active site. The active site is where the "action" happens. Since enzymes are proteins, there is a unique combination of amino acid side chains within the active site. Each side chain is characterized by different properties. They can be large or small, weakly acidic or basic, hydrophilic or hydrophobic, positively or negatively charged, or neutral. The unique combination of side chains creates a very specific chemical environment within the active site. This specific environment is suited to bind to one specific chemical substrate (or substrates).

    Active sites are subject to influences of the local environment. Increasing the environmental temperature generally increases reaction rates, enzyme-catalyzed or otherwise. However, temperatures outside of an optimal range reduce the rate at which an enzyme catalyzes a reaction. Hot temperatures will eventually cause enzymes to denature, an irreversible change in the three-dimensional shape and therefore the function of the enzyme. Enzymes are also suited to function best within a certain pH and salt concentration range, and, as with temperature, extreme pH, and salt concentrations can cause enzymes to denature.

    For many years, scientists thought that enzyme-substrate binding took place in a simple "lock and key" fashion. This model asserted that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a model called induced fit. The induced-fit model expands on the lock-and-key model by describing a more dynamic binding between enzyme and substrate. As the enzyme and substrate come together, their interaction causes a mild shift in the enzyme's structure that forms an ideal binding arrangement between enzyme and substrate.

    When an enzyme binds its substrate, an enzyme-substrate complex is formed. This complex lowers the activation energy of the reaction and promotes its rapid progression in one of multiple possible ways. On a basic level, enzymes promote chemical reactions that involve more than one substrate by bringing the substrates together in an optimal orientation for reaction. Another way in which enzymes promote the reaction of their substrates is by creating an optimal environment within the active site for the reaction to occur. The chemical properties that emerge from the particular arrangement of amino acid R groups within an active site create the perfect environment for an enzyme's specific substrates to react.

    The enzyme-substrate complex can also lower activation energy by compromising the bond structure so that it is easier to break. Finally, enzymes can also lower activation energies by taking part in the chemical reaction itself. In these cases, it is important to remember that the enzyme will always return to its original state by the completion of the reaction. One of the hallmark properties of enzymes is that they remain ultimately unchanged by the reactions they catalyze. After an enzyme has catalyzed a reaction, it releases its product(s) and can catalyze a new reaction.

    It would seem ideal to have a scenario in which all of an organism's enzymes existed in abundant supply and functioned optimally under all cellular conditions, in all cells, at all times. However, a variety of mechanisms ensures that this does not happen. Cellular needs and conditions constantly vary from cell to cell, and change within individual cells over time. The required enzymes of stomach cells differ from those of fat storage cells, skin cells, blood cells, and nerve cells. Furthermore, a digestive organ cell works much harder to process and break down nutrients during the time that closely follows a meal compared with many hours after a meal. As these cellular demands and conditions vary, so must the amounts and functionality of different enzymes.

    Since the rates of biochemical reactions are controlled by activation energy, and enzymes lower and determine activation energies for chemical reactions, the relative amounts and functioning of the variety of enzymes within a cell ultimately determine which reactions will proceed and at what rates. This determination is tightly controlled in cells. In certain cellular environments, enzyme activity is partly controlled by environmental factors like pH, temperature, salt concentration, and, in some cases, cofactors or coenzymes.

    Enzymes can also be regulated in ways that either promote or reduce enzyme activity. There are many kinds of molecules that inhibit or promote enzyme function, and various mechanisms by which they do so. In some cases of enzyme inhibition, an inhibitor molecule is similar enough to a substrate that it can bind to the active site and simply block the substrate from binding. When this happens, the enzyme is inhibited through competitive inhibition, because an inhibitor molecule competes with the substrate for binding to the active site.


    Results

    Extraction of Proteomics and Flux Data for L. lactis, Yeast, and Arabidopsis.

    Calculating CCR values for the enzymes in a cell or tissue requires 1) “proteome-wide” protein turnover data, 2) protein abundance data, and 3) measured or estimated flux rates through the enzyme reactions in operation under the conditions used to measure protein turnover (33). By matching published enzyme protein turnover and abundance data for L. lactis, yeast, and Arabidopsis leaves with estimates of the corresponding metabolite fluxes, we were able to extract all three of the values needed to calculate CCRs for 97 L. lactis enzymes, 182 yeast enzymes, and 123 Arabidopsis enzymes. All were enzymes of primary metabolism 14 were present in all three datasets ( Fig. 2A ). This fairly low commonality is attributable to inherent metabolic differences between the organisms, differences in growth conditions, and gaps in the datasets.

    Summary of primary data from which CCR values for 97 L. lactis, 182 yeast, and 123 Arabidopsis enzymes were calculated. (A) Venn diagram showing how many enzymes having the same EC number are shared between the datasets. There are fewer EC numbers than enzymes in each dataset because each organism had several enzymes (isoforms) with the same EC number. (BD) Cumulative distribution plots of enzyme protein turnover rates (per hour) (B), log10 enzyme protein abundances (copies per gram dry weight) (C), and log10 kapp, the estimated net in vivo metabolic flux for each enzyme (moles substrate processed per mole enzyme per second) (D). Median values are boxed.

    The protein turnover rate (Kd) data were for L. lactis grown anaerobically (22), for yeast grown aerobically (23), and for leaves of Arabidopsis grown in 16-h days in moderate light (24) (Datasets S1, S2, and S3). The protein abundance data for L. lactis and yeast came from the same sources as the turnover data the abundance data for Arabidopsis were from PaxDb (36). As for other data, we used cumulative probability plots to display the distributions of enzyme turnover rates ( Fig. 2B ) and abundances ( Fig. 2C ) for each organism. The median turnover rates ( Fig. 2B ) correspond to half-lives of 0.7 h in L. lactis, 2.7 h in yeast, and 5.8 d in Arabidopsis, which are in the typical ranges for these organisms (22, 23, 35). The sets of enzymes studied were thus representative in this respect. Enzyme abundances expressed per unit dry weight ( Fig. 2C ) were likewise as expected, the Arabidopsis median value being the lowest due to the high proportion of structural carbohydrates in leaf biomass (25).

    Metabolic fluxes for L. lactis and yeast were estimated using genome-scale flux balance analysis models (37, 38), which were constrained by the growth rates, media compositions, and incubation conditions of the cells used to measure protein turnover and abundance (22, 23). For L. lactis, the faster of the two reported growth rates (0.5 h 𢄡 ) was selected. Flux modeling details are given in Materials and Methods. Arabidopsis leaf fluxes were estimated from biomass composition (Dataset S3), Kyoto Encyclopedia of Genes and Genomes (KEGG) biosynthetic pathways (39), and the growth rate (0.1 d 𢄡 ) of the plants used to measure protein turnover (35). When expressed on a fresh weight basis, a subset of the estimated Arabidopsis fluxes agreed well (r 2 = 0.91) with a corresponding set of 11 measured photosynthetic and photorespiratory fluxes (40), allowing for experimental differences in light intensity and other conditions (Dataset S4). The flux through each enzyme reaction was divided by enzyme abundance from proteomics to give the apparent catalytic rate in vivo (kapp, per second) (41, 42) ( Fig. 2D ). All flux estimates for reversible reactions were for the net forward direction and are consequently minimum values.

    To cross-check the kapp estimates, we compared them with kcat values extracted from the BRENDA database (43) and original publications for L. lactis, yeast, and Arabidopsis if possible and for related organisms if not (Dataset S5). In this way we obtained kcat values for 78%, 30%, and 61%, respectively, of the L. lactis, yeast, and Arabidopsis enzymes with kapp values. Plotting the data for all three organisms as a log–log scatter diagram ( Fig. 3A ) confirmed that most (91%) of the data points fell below the 1:1 line, i.e., that, as expected, the in vivo fluxes through enzymes were generally below their maximum in vitro capacity. Plotting the data as cumulative probability distributions ( Fig. 3B ) further showed that the median kapp/kcat value was 30% in L. lactis but only 2.2% in Arabidopsis, with yeast between them at 7.4%. Similar values (38%, 1.8%, and 12%, respectively) can be estimated for an 𠇊verage enzyme” in each organism by linear regression analysis of the scatter plots shown in Fig. 3A , based on the Bar-Even et al. (44) observation that an average enzyme has a kcat ∼ 10 s 𢄡 . These percentages are consistent with the literature on microbes (42, 45) and Arabidopsis (46), including the finding that central metabolic enzymes in Arabidopsis operate further from saturation than their prokaryotic counterparts. The cross-check thus basically validated our kapp values.

    Relationships between estimated kapp values (in vivo fluxes) and published kcat values for 76 enzymes from L. lactis or other bacteria, 55 from yeast or other fungi, and 75 from Arabidopsis or other plants. (A) Scatter plot (log10 scale) of kapp vs. kcat for the enzymes from each organism. Note that most points fall below the 1:1 line. Linear regression analysis indicated that an 𠇊verage” enzyme (kcat ∼ 10 s 𢄡 ) operates in vivo at 38% of maximum velocity in L. lactis, at 12% in yeast, and at 1.8% in Arabidopsis. (B) Cumulative distribution plots of the kapp/kcat ratio (expressed as a percentage) for the enzymes from each organism. Values 𾄀% were scored as 100%. Median values are boxed and marked by vertical dashed lines.

    CCR Values in L. lactis, Yeast, and Arabidopsis Span at Least Five Orders of Magnitude.

    Pairing the above proteomics and flux data enabled the calculation of CCR values for the listed enzymes in each organism (Dataset S6). The values were distributed over a similarly wide range in each organism, from 㰐 3 to 㸐 7 ( Fig. 4A ), but the distributions had significantly different median values: 3𠄴 × 10 4 for L. lactis and yeast versus 4 × 10 5 for Arabidopsis ( Fig. 4A ). The distributions of the CCRs for the 14 enzymes common to all three datasets showed the same pattern, i.e., the L. lactis and yeast distributions differed significantly from Arabidopsis and had much lower median values (SI Appendix, Fig. S1). The agreement between the common enzymes and the whole datasets makes it reasonable to compare the whole datasets with each other even though they consist mostly of different enzymes. These findings supported the idea (33) that CCRs, like ex vivo total turnover numbers (14), vary greatly between enzymes and organisms and prompted investigation of the variation’s mechanistic basis.

    Distributions of CCR values for L. lactis, yeast, and Arabidopsis enzymes and their relationship to the chemistry of the reaction catalyzed. (A) Distribution of CCR values for each organism. The Arabidopsis distribution is significantly different from those of L. lactis and yeast with P values of 㰐 𢄦 (Kolmogorov–Smirnov test) and 㰐 𢄤 (Mann–Whitney U test). (BD) Distributions of CCR values for enzymes in each organism scored as being at no, low, and medium or high risk of damage from the reaction catalyzed. In each organism, the distributions of medium- plus high-risk and no-risk enzymes are significantly different with values of P < 0.005, and the distributions of medium- plus high-risk and pooled no-risk plus low-risk enzymes are significantly different with values of P < 0.01 (Kolmogorov–Smirnov test and Mann–Whitney U test). Numbers of enzymes are in parentheses. Median values are boxed and marked by dashed lines.

    Low CCR Correlates with High Risk of Chemical Damage from the Reaction Catalyzed.

    To investigate mechanism, we first inspected Enzyme Commission (EC) numbers (Dataset S6) for links between CCR and enzyme class but found no consistent effects across all the three species. We therefore next looked for associations between CCR and the chemical reactivity hazards of the reaction catalyzed, the rationale being that 1) reactive metabolites attack protein side chains (47, 48) 2) many enzymes are known to be inactivated during catalysis (14, 49) and 3) enzymes at risk for active-site damage may be short-lived (14, 31) (SI Appendix, Table S1).

    While other reports have qualitatively assembled lists of risks (e.g., ref. 14), we could find no precedent for quantifying degrees of hazard to enzymes’ active sites. To approach quantification, we therefore defined six nonoverlapping risk factors based on the mechanism of the enzyme reaction and the chemical properties of each substrate, product, and cofactor ( Table 1 ). We gave each factor one, two, or four “risk points” based on the likely severity of the risk, e.g., a suicide reaction mechanism (certain inactivation) scored four points, a radical mechanism scored two, and a reactive carbonyl substrate (possible attack on a nucleophilic side chain) scored one ( Table 1 ). Each enzyme’s risk factors were scored and the points were summed on the basis that each risk could act independently, and thus additively, to inactivate an enzyme molecule. The most frequent risk factors were a reactive or unstable substrate, product, or reaction intermediate, and the least frequent were suicide and radical mechanisms ( Table 1 ).

    Table 1.

    Chemical risk factors assigned to enzymes based on their reaction mechanism, substrates, products, and cofactors

    Risk factor * Risk pointsNo. of enzymes
    L. lactisYeastArabidopsis
    1. Suicide mechanism4001
    2. Radical mechanism2221
    3. Photoreactive substrate/product/cofactor171013
    4. Carbonyl substrate/product † 1245237
    5. Reactive or unstable cofactor ‡ 1193619
    6. Reactive or unstable substrate § /product § /intermediate1 or 2 ¶ 418349

    We then grouped enzymes into three risk classes—no risk (0 points), low risk (1 point), and combined medium risk (2 points) plus high risk (𢙓 points)𠅊nd compared the cumulative distributions of their CCRs on a log scale ( Fig. 4 BD ). Note that “no risk” is a convenient label that does not imply absolute absence of risk, and that medium and high risk were combined due to the small number (�) of high-risk enzymes in each organism. In all three organisms, the distributions of medium- plus high-risk and no-risk enzymes were significantly different (P < 0.005) by both Kolmogorov–Smirnov and Mann–Whitney U tests. So also were the distributions of medium- plus high-risk enzymes and the pooled no-risk plus low-risk enzymes (P < 0.01), confirming that the medium- plus high-risk enzymes remain robustly distinct even when compared to all other enzymes rather than to just the no-risk enzymes. This was also still nearly always the case when we performed a sensitivity analysis in which the risk factors ( Table 1 ) were dropped out one-by-one (SI Appendix, Fig. S2) this outcome indicates that the various risk factors contribute similarly to CCR. The median CCR for the medium- plus high-risk class was always roughly one to two orders of magnitude below that of the no-risk class, with the median CCR of the low-risk class in an intermediate position in L. lactis and yeast ( Fig. 4 B and C ) and slightly above the no-risk class median in Arabidopsis ( Fig. 4D ). The log-transformed means for no-risk and medium- plus high-risk classes likewise always differed by one to two orders of magnitude (P < 0.001) and nearly all enzymes with CCRs ρ,000 were from the medium- plus high-risk class. Of note, the CCR variances of the risk classes in L. lactis and yeast were similar to each other and to the pooled no-risk plus low-risk class variance in Arabidopsis, but the Arabidopsis medium- plus high-risk class variance was much greater (P < 0.0001 SI Appendix, Table S2). We discuss below what this difference may imply. Collectively, these observations for 𾐀 enzymes show a robust, cross-kingdom correlation between degrees of hazardous reaction chemistry and a short working life span. We therefore explored the basis of this correlation.

    High-Risk Enzymes Carry Lower Metabolic Fluxes and Are More Abundant.

    Because CCR depends on three variables—metabolite flux rate and enzyme abundance (whose ratio is kapp), and enzyme turnover rate Kd—we examined how risk class impacts each variable. To simplify the analysis and increase statistical power, the medium- plus high-risk class was compared with pooled data from the no-risk plus low-risk classes. For all three organisms, the kapp distribution for the medium- plus high-risk class differed significantly from the pooled no-risk plus low-risk class, having a median value about 10-fold lower ( Fig. 5 AC ). In all cases, the difference was due to the medium- plus high-risk class having both lower metabolic fluxes and higher protein abundances. In contrast, the Kd value distributions for the two classes did not differ significantly ( Fig. 5 AC ). The differences in CCR between these grouped classes are thus determined predominantly by the numerator (kapp) in the CCR term and not by the denominator (Kd). One outcome of this analysis was to confirm that our simple scoring system for chemical risk ( Table 1 ) corresponds to in vivo enzyme characteristics, i.e., to biological reality. Other implications are discussed below.

    Relationships between enzyme risk class and each of the variables on which CCR values depend. Cumulative distributions (log scale) are plotted for L. lactis (A), yeast (B), and Arabidopsis (C) enzymes assigned to the medium- plus high-risk class (red lines) or to the pooled no-risk plus low-risk class (blue lines). The kapp units are per second. Flux units are millimoles per second per gram dry weight, enzyme abundances are molecules per gram dry weight, and Kd values are per hour. P values for Kolmogorov–Smirnov (KS) and Mann–Whitney U (MW) tests for significant differences between the distributions are shown in each frame.


    Figure 2

    Figure 2. Transport of reporter mRNA to the distal ends of microtubules in HeLa cells. (a) Schematic overview of KIF5-mediated mRNA transport. Microtubules are represented as black solid arrows pointing from their (+) to (−) ends. (b) Transport of FLuc mRNA to the cell periphery by KIF5-FRB and the PUF construct FFGPP. Hoechst, nuclear stain. White solid lines, cell outlines. Quantified areas: C, cytoplasm (light blue dashed lines) P, periphery (yellow dashed lines). PUF-BS, PUF-binding sites. Enriched spots indicated with arrows. Scale bar: 20 μm. (c) Quantitation of mRNA translocation to the cell periphery. RNA-FISH intensity at the region coinciding with the brightest fluorescent region of KIF5 immunofluorescence was normalized to an adjacent proximal region of the same area. n = 20 cells in 3 biological replicates. ***P < 0.001. Mean ± SEM.


    Metabolic Pathways in the Human Body

    Tsugikazu Komoda , Toshiyuki Matsunaga , in Biochemistry for Medical Professionals , 2015

    Abstract

    Major metabolic pathways for several biological materials are described, including carbohydrate and energy metabolism by electron transfer systems, lipids, lipoproteins, amino acids, nucleic acid and protein biosynthesis. Metabolic syndrome is caused by disruption of metabolic pathways or their regulation. Disorders in anaerobic sugar metabolism and glycogen metabolism can cause diabetes mellitus. Alzheimer and Parkinson disease are examples of disorders of electron transfer systems. Concerning the nature of sugar chains, certain blood group substances are useful as tumor markers. Dysfunction of the glycosylphosphatidylinositol moiety binding to asparagine-linked sugar chains causes paroxysmal nocturnal hemoglobinuria. Lipid metabolism is an important indicator of lipoprotein and fatty acids both cholesterol and lipid metabolism have relevance to disease. Disorders of amino acid metabolism and nucleic acid metabolism and the resulting diseases are illustrated. An overview of protein synthesis is provided.


    Watch the video: Metabolic Processes, Energy, and Enzymes. Biology (September 2022).


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