The biggest thing is to not be intimidated by them! Instead, after looking at the “start” and the “end” of a pathway as written (which are both usually really just intermediates of other pathways!), and, with your eye on the big picture, home in on that “start”. Then follow the arrows step-by-step.
As you go along, some key things to focus on are:
- Reversibility: is there a one-directional arrow for an enzyme (indicating irreversible) or arrows going both directions for a single enzyme (indicating reversible)?
- What’s coming & going other than the main intermediates? (ATP, NAD+, etc.). Look to the little curvy arrows above and/or below the main arrows to see these.
- Are carbons being gained or lost? (keep an eye out for CO2)
- Where do you use energy stored in the form of ATP (or other NTP)?
- Where do you generate energy stored in the form of ATP (or other NTP)?
- Where do you use and where do you generate reducing equivalents, and which ones (NADH or NADPH or FADH2)?
- Where are there branch points with multiple enzymes that can take you off in different ways? Using your above answers, think about when you might want to go which way.
- Regulation – when indicated, look at what stimulates enzymes (often indicated by a green triangle, arrow, plus sign, etc.) & what inhibits them (often indicated by a red X, minus sign, capped line, stop sign, etc.).
- Given your above answer, why do these regulators make sense?
- Look for examples of feedback inhibition, feedforward stimulation, inter-pathway cross-regulation, & hormonal regulation
- Also keep in mind that for the reversible steps especially, concentrations of intermediates and even cofactors are going to matter greatly
And, finally, revel in the beauty of the complexity! Realizing it’s really not as scary as it seems. The logic is consistent and logical and the arrows help you follow it all!
Here’s a link to the metabolic chart. Feel free to use, but please cite the bumbling biochemist if you do. Thank you and happy learning! PDF: http://tinyurl.com/4v3a5xsx
more on all sorts of metabolic stuff: https://bit.ly/bbmetabolism
