science

NDH-2

NDH-2 is a science topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand NDH-2 rather than just read about it. In short: NDH-2, also known as type II NADH:quinone oxidoreductase or alternative NADH dehydrogenase, is an enzyme (EC: 1.6.99.3) which catalyzes the electron transfer from NADH (electron donor) to a quinone (electron acceptor), being part of the electron transport chain. NDH-2 are peripheral membrane protein, functioning as dimers in vivo, with approximately 45 KDa per subunit and a single FAD as their cofactor.

Key takeaways

NDH-2 belongs to science; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect NDH-2 to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of NDH-2 from memory before moving on to harder problems.

Reference excerpt

NDH-2, also known as type II NADH:quinone oxidoreductase or alternative NADH dehydrogenase, is an enzyme (EC: 1.6.99.3) which catalyzes the electron transfer from NADH (electron donor) to a quinone (electron acceptor), being part of the electron transport chain. NDH-2 are peripheral membrane protein, functioning as dimers in vivo, with approximately 45 KDa per subunit and a single FAD as their cofactor. NDH-2 are the only enzymes with NADH dehydrogenase activity expressed in the respiratory chain of some pathogenic organisms (e.g. Staphylococcus aureus), and for that they have been proposed as new targets for rational drug design.

Structure

The structure/fold from these proteins may be divided into three domains: first dinucleotide binding domain (green in the figure), second dinucleotide binding domain (orange in the figure) and C-terminal domain (blue in the figure). The first domain is responsible for the noncovalent binding of FAD, while the second dinucleotide binding domain binds NADH. Both these domain are structurally organized in Rossmann folds, with the characteristic GxGxxG motif present. The third domain, C-terminal, is responsible for the protein-membrane interaction. Upon expression of a C-terminal truncated version of NDH-2, it was observed an intracellular delocalization from the membrane to the cytoplasm. The third domain, together with part of the first domain, is also partially responsible for the binding of the electron acceptor (quinone). There are currently crystallographic structures for NDH-2 from four different organisms:

Staphylococcus aureus (PDB ID:5NA4) Caldalkalibacillus thermarum (PDB ID:4NWZ) Saccharomyces cerevisiae (PDB ID:4G73) Plasmodium falciparum (PDB ID: 5JWB)

Reaction

The enzymatic oxidoreduction reaction catalyzed by NDH-2 may be described as follows: NADH + Q + H+ -----> NAD+ + QH2 (Q - quinone; QH2 - quinol) In this case, the electron donor is NADH and the electron acceptor is the quinone. Depending on the organism, the reduced quinone changes between menaquinone, ubiquinone or plastoquinone. The mechanism of the reaction may be divided in two half-reactions: 1stHR and 2ndHR. In the 1stHR, 2 electrons and 1 proton from NADH are transferred (simultaneously with an additional proton from the bulk) to the prosthetic group (FAD), giving rise to its protonated form FADH2. In this phase, an Enzyme-Substrate complex is established, characterized by the appearance of a "Charge-transfer complex". Na 2stHR, the quinone binds and the 2 electrons and one of the FAD protons are transferred for this second substrate (again, with an additional proton from the bulk), forming the product quinol. It is now accepted that the overall mechanism occurs by a ternary complex (simultaneous binding of both substrates to the enzyme), instead of the previously proposed ping-pong mechanism.

Phylogenetic distribution The presence of NDH-2 in organisms which genome as already been fully sequenced was studied by Bioinformatics. In this study, NDH-2 were identified in 83% of Eukaryotes, 60% of bacteria and 32% of Archaeas. It was also observed the absence of NDH-2 in phyla composed of anaerobic organisms. Despite being considered absent (hence being considered as drug targets), in this same study, the presence of a gene coding for a NDH-2 homolog was observed in the human genome.

References

Illustrations

Worked examples

Example 1 — a first encounter with NDH-2

Start with the simplest possible case. Write down what NDH-2 claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In science, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to NDH-2 before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about NDH-2 ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of NDH-2

In research: NDH-2 appears in science research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses NDH-2 in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: NDH-2 is common in secondary-school and first-year university syllabi. It links to neighbouring topics Enzymes, so understanding it makes those chapters shorter.
In everyday life: Look for NDH-2 outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study NDH-2 in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what NDH-2 means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain NDH-2 out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is NDH-2 in simple terms?

Why does NDH-2 matter?

Because it connects several science ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study NDH-2?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on NDH-2.