Few questions about homemade IrDA module

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SUMMARY

The discussion centers on building a homemade Infrared Data Association (IrDA) module using a transceiver circuit found on Hardware Secrets. The user seeks advice on rearranging the circuit to minimize wiring by placing the photodiode and LED closer together. It is confirmed that polarity is crucial for semiconductor devices like LEDs and photodiodes, with the anode being the longer lead and the cathode identifiable by a flat area on the LED casing.

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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
 
LEDs are also supplied with the anode (+) lead longer than the cathode (-) lead.