As shown in the diagram above, NAD+ is reduced and becomes NADH by gaining two electrons
Now, where did the hydrogen come from?
In the diagram, pyruvate has 3 hydrogen, but it still has 3 hydrogen in acetyl CoA.
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$\begingroup$ @Astrolamb has given you a good answer here. In general, be aware that counting atoms will often result in a headache in biochemistry. There are large parts of key molecules that are often not represented. $\endgroup$ – De Novo Jul 22 '18 at 19:23
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$\begingroup$ @DeNovo is absolutely right; when looking at biochemical systems, if something doesn't seem to make sense, try to find a diagram that includes ALL the puzzle pieces. $\endgroup$ – Astrolamb Jul 22 '18 at 19:29
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The Wikepedia page has a really good diagram of the reactions involved. The Pyruvate Dehydrogenase Complex facilitates the removal of CO2, and the addition of two hydrogen atoms to the overall reaction come from the FADH2/FAD molecule.
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1$\begingroup$ This is an example of how, in biochemistry, the rules for writing a reaction equation are much more flexible, and generally based on convention. NAD+, for example, has a negative charge at physiologic pH. We write it as NAD+ to emphasize the active moeity in the oxidation/reduction reaction. H+s, in particular, are often poorly accounted for in our short hand. $\endgroup$ – De Novo Jul 22 '18 at 19:24
