Few questions about homemade IrDA module

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Gorstak
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First of all, I'm not an electrician, I'm a medical student who occasionally grab a soldering iron for some fun. So if I'm asking something really stupid, I'm sorry.
I found scheme forIR transciever on http://www.hardwaresecrets.com/article/86/2 and I'm plannig to build it. I was wondering is it ok to rearrange circuit (attached picture, left side) in order to bring photodiode and LED physically close and to reduce wiring, and is there a "wrong and right" way to connect photodiode and LED (I mean does polarity matters and how can I distiguish anode from cathode)
Thanks everyone
 

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Welcome to PF Gorstak.

Electronic schematics show the electrical connections between components in a easy to read format, not the physical locations of the components relative to each other on the board.

Yes, there is a polarity for semiconductor devices such a LEDs and photo diodes. See the flat area next to the cathode terminal of this LED.
200px-LED%2C_5mm%2C_green_%28en%29.svg.png