Question

Energy cost of macro molecular synthesis In this problem you will determine the bio synthetic cost of generating the amino acid serine from glucose used as food. The bio synthetic costs of all the amino acids are given in Table \(5.1,\) and now you will get a first-hand sense of how to obtain those values, Visit the website "ecocyc.org" and find the metabolic pathways for serine synthesis and glycolysis. The starting molecule of the ser. Ine synthesis pathway is an intermediate in glycolysis. How many molecules of glucose must be taken up to provide the carbon skeleton used to make serine? Draw the biochemical pathway starting with glucose and ending in serine, labeling the energy-requiring and energy Eenerating steps. How many molecules of ATP are consumed and created along the way? How many reducing equivalents of NADH and NADPH are consumed or created along the way? In order to answer this question com pletely you may need to consider a few other pathways as well. For example, it is likely that the displayed glycolysis pathway does not actually start with glucose. To get glucose- 6 -phosphate from glucose requires 1 ATP. One of the steps in the serine synthesis pathway is coupled to a conversion of \(L\) -glutamate to 2 -ketoglutarate. You will have to look up the "glutamate biosynthesis III" pathway to determine the cost of regenerating \(L\) -glutamate from 2-ketoglutarate. Assuming that each NADH or NADPH is equivalent to 2 ATP, which is a reasonable conversion fac tor for bacteria, what is the net energy cost to synthesize one molecule of serine in units of \(\mathrm{ATP}\) and units of \(k_{B} T ?\)

Short answer

The short answer lies in the calculation of all biochemical pathways from the beginning to the ending of serine synthesis which consumes one glucose molecule. Label all involved steps, and then add up the total energy consumption through ATP, NADH, and NADPH (convert into ATP equivalent).

Step-by-step solution

Calculate the glucose molecules uptake

To synthesize serine, you need to start from the intermediate compound 3-phosphoglycerate which is derived from glucose during glycolysis, so one molecule of glucose is used in this process.

Analyze the serine synthesis pathway

Analyze the entire serine synthesis pathway, which starts from 3-phosphoglycerate (an intermediate of glycolysis) and ends at serine. Label the energy-requiring and energy-generating steps involved.

Determine the ATP involvement

Calculate the number of ATP molecules consumed and created during this process. Remember to consider both the synthesis of serine and the pathway to get glucose-6-phosphate from glucose, which involves both the production and use of ATP after glycolysis.

Determine the NADH and NADPH involvement

Determine the consumption or creation of NADH and NADPH reducing equivalents during these pathways. These molecules play an essential role in the biochemical energy generation/storage.

Analyze the 'glutamate biosynthesis III' pathway

Analyze the 'glutamate biosynthesis III' pathway as it's significant during the conversion of L-glutamate to 2-ketoglutarate. Calculate the cost of regenerating L-glutamate from 2-ketoglutarate.

Convert NADH or NADPH to ATP

Each NADH or NADPH is equivalent to 2 ATPs in bacteria. Convert the NADH/NADPH units to ATP units to find the total energy cost.

Determine the energy cost for synthesizing one serine molecule

Add up the energy costs obtained from each step (calculated in units of ATP), which would give the net energy cost for synthesizing one serine molecule.

Key concepts

Metabolic Pathways

Metabolic pathways are essentially a series of chemical reactions occurring within a cell that lead to the conversion of one substance to another. In the context of biology, these pathways are crucial for maintaining life as they allow organisms to perform essential functions such as energy production, growth, and cellular repair. Different pathways interact and intersect, forming an intricate network that ensures cells can adapt to their nutritional environment and energy demands.

For synthesizing complex molecules like serine, which is derived from glucose, cells utilize specific pathways. Each step in these pathways might involve the consumption or generation of energy in the form of ATP. Enzymes play the role of catalysts, speeding up the reactions while ensuring the cell's energy is used efficiently. Understanding these pathways gives scientists insights into how life sustains itself and how conditions like diabetes or genetic mutations can affect cellular metabolism.

Glycolysis

Glycolysis is a key metabolic pathway for cellular respiration, in which glucose is broken down to pyruvate, yielding small amounts of ATP and NADH in the process. It occurs in the cytoplasm and can function with or without oxygen, which is why it is considered an anaerobic process when oxygen is absent. During this ten-step reaction, enzymes aid in conversion processes like the phosphorylation of glucose, splitting of the sugar backbone, and finally, the production of pyruvate.

This pathway not only provides quick bursts of energy but also creates intermediates that serve as starting points for other metabolic pathways, like the synthesis of amino acids, including serine. By studying glycolysis, we gain a foundation for understanding how cells generate ATP and how intermediate products are utilized for synthesizing complex biomolecules.

ATP Consumption and Creation

The creation and consumption of ATP (adenosine triphosphate) is vital for life, often likened to a cellular currency. ATP stores energy in the bonds between its phosphate groups, and when the cell needs energy, ATP is hydrolyzed into ADP (adenosine diphosphate), releasing energy.

During glycolysis, ATP is initially consumed to help convert glucose into a form that can be broken down further. However, as the pathway progresses, more ATP is generated than consumed. In cellular respiration, for instance, the overall process results in a net production of ATP. Similarly, other metabolic pathways, including serine synthesis, require ATP to drive unfavorable reactions. The balance between ATP consumption and the creation is finely regulated, enabling the cell to function optimally and respond to energy demands.

NADH and NADPH in Biochemistry

NADH and NADPH are coenzymes that act as electron carriers in metabolic reactions. NADH is mainly involved in catabolic reactions where it plays a central role in transferring electrons gathered from the breakdown of food molecules during processes like glycolysis and the citric acid cycle. It eventually donates these electrons to the electron transport chain, a series of reactions that lead to the production of a significant amount of ATP.

NADPH, on the other hand, is typically involved in anabolic reactions, such as fatty acid and nucleotide synthesis. It provides the reducing power necessary to synthesize these complex molecules. Both NADH and NADPH are crucial for maintaining the redox balance within the cell and are often interconverted through various metabolic pathways, depending on the cell's needs.