Metabolic Pathways
(general description and terminology)

1

Reactants

The reactants are the biochemicals that come together and interact at the beginning of the process such that they are converted into one or more different biochemicals - some or all of which may become intermediates (for the next step in the process) or common intermediates (if the next step in the metabolic pathway is a branching point).

2

Precursors

In chemistry generally, the word 'precursor' may be used in a similar way to the word "reactant" to refer to a chemical that participates as one of the starting chemicals in a chemical reaction that produces other substance(s).

However, in the context of biochemistry, 'precursor' is used more specifically to refer to a chemical compound preceding another in a metabolic pathway.

3a

Enzymes

Enzymes are types of proteins that play an important role in metabolism by catalyzing the individual reactions in metabolic pathways. As explained below, catalysts in general are specific to particular reactions, hence specific enzymes catalyze specific reactions.

Enzymes that catalyze the first reaction in a metabolic pathway are sometimes subject to allosteric control by the concentration of the end product of the metabolic pathway - see "end products" below.

3b

Catalysts

'Catalyst' is a word used in chemistry generally (not just biochemistry) to refer to chemicals that affect the rate (speed) of chemical reactions by participating in the reaction(s) but in such a way that the catalyst is not consumed by the reaction itself. So, the presence of a catalyst may be necessary for a reaction to occur to any meaningful extent under certain conditions. Although the catalyst takes part in the reaction the overall effect is as if it had not been there because the amount of catalyst is not reduced by the reaction - irrespective of how much (mass) of reactants are converted to how much (mass) of end products.

Because catalysts do take part (in interim steps) in the reactions they catalyze, any particular reaction can only be catalyzed by catalyst(s) for that particular reaction.

A catalyst that works well for one process may not work at all in another.

4

Intermediates

Intermediates are compounds that are neither the initial (starting) chemicals in a pathway or 'process', nor the end-products used directly or secreted by the cell, nor catalysts (that participate in but are not used-up by the reactions). Instead, intermediates are compounds that are formed as temporary 'steps' in the overall chemical process. After being formed by one reaction in the process, they are then changed into something else or several other substances - often due to the action of a different, subsequent enzyme acting as a catalyst for the next step in the process.

5

Common intermediates

Common intermediates are compounds that occur at branching points in metabolic pathways.

6

End products

The end products of metabolic pathways are compounds that are produced by metabolic reactions that do not go on to participate in a subsequent reaction in the methabolic pathway. Instead, these compounds can be used or secreted by the cell. However, such compounds must not accumulate excessively.

The concentration of the end products of a metabolic pathway often regulates the rate of the reaction that produces them, i.e. effectively a 'feedback loop' prevents over-production. There are two common mechanisms by which this occurs:

• allosteric control (also known as allosteric regulation) -
• end product inhibition -

7a

Branching points

Some branching points in metabolic pathways are sometimes called 'cross-over points'. Both of these terms refer to a stage in a metabolic pathway at which an intermediate (usually a molecule or part of a molecule), could proceed to change in more than one possible way, i.e. it could follow two or more possible '(metabolic) pathways'.

The 'pathway' followed (next change undergone) by the intermediate is usually the one of most immediate benefit to the cell, that 'decision' being determined by the activity of enzymes present around the intermediate.

Some 'branching points' are also 'key junctions' in metabolic pathways:

7b

Key junctions

In general, a 'junction' is a position at which at least two 'paths' intersect.
Examples of such 'paths' in everyday life include routes, roads, wires, cables and pipes. Depending on the direction of movement, a junction could be a position at which paths come together to form a single path, separate into multiple paths, or cross-over such that matter passing along the pathways approaching the junction may take any of at least two possible pathways after it. A junction is therefore another way to refer to branching point. However, a 'key junction' implies that the intersection is particularly important, i.e. one at which decisions taken about which on-going paths to follow from that point onwards may change depending on circumstances and have important consequences.

8

Metabolites

Metabolites are substances (usually compounds) that participate in metabolism processes and are either produced during metabolism reactions or are 'constituents of' i.e. parts that make-up, foods taken into the body - then broken-down via the digestive processes. Metabolites are therefore among the chemicals included in metabolic pathways. They are often intermediates between reactants and end-products.

9

Metabolic cycles

Metabolic cycles is the descriptive term used to refer to some metabolic pathways or parts of metabolic pathways that take the form of repeated 'cycles' in which product(s) of the individual metabolic reactions in the sequence become the reactants, i.e. the 'starting chemicals', for the next metabolic reaction in the sequence.

Examples of metabolic cycles in the human body:

• Krebs TCA cycle (also known as tricarboxylic acid cycle, TCA cycle, the Krebs cycle and citric acid cycle)
• Calvin cycle
• Urea cycle

10

Metabolic hubs

The term metabolic hub is not a key commonly used phrase with specific meaning in the context of biochemistry. However, as it is included in some textbooks, it is worth clarifying.

In general, a 'hub' is a point at which many 'pathways' meet. These could be routes, wires, lines of communication or similar e.g. as used in the context of air-travel or information technology. This can be compared with general use of the term 'cycle' in biology as a repeating sequence of events e.g. life cycle (of organisms), cell cycle, menstrual cycle, etc..

A metabolic hub can therefore be thought of as a location at which many metabolic processes occur, enabling substances such as molecules, e.g. reaction intermediates, to transfer between reaction processes on an as-needed basis.

Examples of metabolic hubs in the human body:

• Krebs TCA cycle - central metabolic hub of the cell
• The Liver - sometimes described as the 'Metabolic hub' of the body