What is the Difference Between Matrix and Stroma

The main difference between matrix and stroma is that matrix occurs in mitochondria while stroma occurs in chloroplasts.

Matrix and stroma are two components of organelles. They fill the space between the organelles.      

Key Areas Covered

1. What is Matrix
– Definition, Features, Function
2. What is Stroma
– Definition, Features, Function
3. Similarities Between Matrix and Stroma
– Outline of Common Features
4. Difference Between Matrix and Stroma
– Comparison of Key Differences

Key Terms 

Matrix, Stroma

Difference Between Matrix and Stroma - Comparison Summary

What is Matrix

Matrix is the internal space of mitochondria. It is a gel-like substance enclosed by the inner membrane of mitochondria. The matrix of mitochondria contains mitochondrial DNA, ribosomes, enzymes, small organic molecules, inorganic ions, and nucleotide cofactors. Importantly, the enzymes within the matrix of mitochondria are responsible for various metabolic reactions, including oxidative phosphorylation, citric acid cycle, beta-oxidation of fatty acids, and pyruvate oxidation. Here, oxidative phosphorylation is the oxidation of nutrients to produce ATP. Almost all organisms that are aerobic undergo oxidative phosphorylation. The citric acid cycle is responsible for releasing the energy stored in acetyl-CoA. Acetyl-CoA is derived from carbohydrates, proteins, and fats.

Compare Matrix and Stroma

Figure 1: Mitochondrial Matrix

Furthermore, beta-oxidation is a catabolic reaction that breaks down fatty acids into acetyl-CoA. On the other hand, pyruvate is a simple alpha-keto acid that serves as an intermediate for metabolic reactions. It is produced in glycolysis and converted back into carbohydrates in gluconeogenesis. Reaction with acetyl-CoA converts pyruvate into fatty acids. 

What is Stroma

Stroma is the colorless fluid surrounding the grana, the stacks of thylakoids. Generally, the main function of the stroma is to undergo the dark reaction of photosynthesis. However, photosynthesis converts light energy into chemical energy through cellular respiration. Furthermore, the two steps of photosynthesis are the light reaction and the dark reaction.

Matrix vs Stroma

Figure 2: Chloroplast Stroma

Moreover, the dark reaction of photosynthesis requires enzymes. These enzymes occur in the stroma of the chloroplast. The dark reaction uses carbon dioxide and water to produce simple carbohydrates. Additionally, it uses NADPH and ATP produced in the light reaction on the thylakoid membranes. 

The dark reaction occurs in two reaction mechanisms: the C3 and C4 cycles. The C3 cycle is called the Calvin cycle, whereas the C4 cycle is called the Hatch-Stack cycle. Calvin’s cycle occurs in three steps. During the first step, carbon dioxide is fixed into ribulose 1,5-bisphosphate, forming an unstable six-carbon compound, which is then hydrolyzed into a three-carbon compound, 3-phosphoglycerate. The enzyme involved in the process is rubisco. Due to the catabolic imperfection of rubisco, photorespiration occurs in the presence of low carbon dioxide concentrations. During the second step, some of the 3-phosphoglycerates are reduced to produce hexose phosphates. The remaining 3-phosphoglycerates are used in the recycling of ribulose 1,5-phosphate. 

Similarities Between Matrix and Stroma

  • Matrix and stroma are two components of organelles.
  • They fill the space inside organelles.
  • They contain DNA and various enzymes for metabolic reactions. 

Difference Between Matrix and Stroma


Matrix refers to the space inside mitochondria, containing the mitochondrial DNA, ribosomes, soluble enzymes, small organic molecules, nucleotide cofactors, and inorganic ions, while stroma refers to the fluid-filled internal space of the chloroplasts which encircle the grana and the thylakoids. 


Matrix occurs in mitochondria, while stroma occurs in chloroplast. 


The citric acid cycle occurs in the mitochondrial matrix, while the dark reaction of photosynthesis occurs in the stroma.


In brief, matrix and stroma are two spaces that occur in organelles. They contain DNA and various enzymes responsible for metabolic reactions. Matrix is the space inside mitochondria containing mitochondrial DNA and various metabolic enzymes. The citric acid cycle occurs in the matrix of mitochondria. In comparison, the stroma is the space inside chloroplasts that encircle the grana and thylakoids. The dark reaction of photosynthesis occurs in the stroma of chloroplasts. Therefore, the main difference between matrix and stroma is their function.

  1. Mitochondrial Matrix: Overview, Parts & Function. Study.com | Take Online Courses. Earn College Credit. Research Schools, Degrees & Careers. (n.d.). 
  2. Wikimedia Foundation. (2023j, May 27). Stroma (fluid). Wikipedia. 
Image Courtesy:
  1. Mitochondrion mini..” By Kelvinsong – Own work (CC0) via Commons Wikimedia
  2. Chloroplast mini.” By Kelvinsong – Own Work (CC BY 3.0) via Commons Wikimedia

About the Author: Lakna

Lakna, a graduate in Molecular Biology & Biochemistry, is a Molecular Biologist and has a broad and keen interest in the discovery of nature related things

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