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python -c "import pdfplumber; p='/tmp/workspace/attachments/c2ab5e24-9767-4874-8c47-8e4625f382ea/DOC-20261001-WA0006.pdf'; pdf=pdfplumber.open(p); print('PAGES',len(pdf.pages)); [print('\\n--- PAGE',i+1,'---\\n',page.extract_text() or '[NO EXTRACTABLE TEXT]') for i,page in enumerate(pdf.pages)]"

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shikimate pathway

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shikimate pathway mevalonate pathway plant secondary metabolites overview

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mkdir -p "/tmp/workspace/pdf-explanation/rendered" && python -c "import fitz, os; p='/tmp/workspace/attachments/c2ab5e24-9767-4874-8c47-8e4625f382ea/DOC-20261001-WA0006.pdf'; d=fitz.open(p); out='/tmp/workspace/pdf-explanation/rendered'; [page.get_pixmap(matrix=fitz.Matrix(1.2,1.2), alpha=False).save(os.path.join(out, f'page_{i+1:02}.png')) for i,page in enumerate(d)]; print(len(d),'pages rendered')"

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python -c "from pypdf import PdfReader; from pathlib import Path; p=Path('/tmp/workspace/attachments/c2ab5e24-9767-4874-8c47-8e4625f382ea/DOC-20261001-WA0006.pdf'); out=Path('/tmp/workspace/pdf-explanation/rendered'); out.mkdir(parents=True,exist_ok=True); r=PdfReader(str(p)); n=0 for k,page in enumerate(r.pages): for j,img in enumerate(page.images): data=img.data f=out/f'p{k+1:02}_i{j+1}.{img.name.split(chr(46))[-1]}' f.write_bytes(data); print(f.name,len(data)); n+=1 print('extracted',n)"

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This PDF explains how plants make important natural chemicals, especially compounds used as medicines, flavors, fragrances, and pigments.

Main idea

Plants take simple substances from food-making processes and convert them into more complex chemicals. These chemicals are called plant metabolites.
There are two major routes in this presentation:
  1. Acetate-mevalonate pathway
  2. Shikimic acid pathway
Think of them as two different factory assembly lines inside a plant.

1. Acetate-mevalonate pathway

This pathway starts with a small molecule called acetyl-CoA.

In simple words

Acetyl-CoA molecules join together step by step:
Acetyl-CoA → Mevalonic acid → small isoprene units → bigger plant chemicals
The small isoprene units act like building blocks. Plants combine many of them to make substances such as:
  • Essential oils
  • Terpenes
  • Steroids
  • Carotenoids
  • Rubber-like compounds

Easy example

The smell of peppermint, eucalyptus, and many aromatic plants comes from chemicals made using this type of pathway.
So, the acetate-mevalonate pathway mainly helps plants produce oils, scents, and terpene-type compounds.

2. Shikimic acid pathway

This pathway helps plants make aromatic amino acids.
“Aromatic” here does not only mean fragrant. In chemistry, it means that the molecule has a special ring-shaped structure.

It produces three important amino acids

  • Phenylalanine
  • Tyrosine
  • Tryptophan
These amino acids can later be converted into many plant chemicals, including:
  • Flavonoids
  • Tannins
  • Lignin
  • Alkaloids
  • Coumarins
  • Cinnamon-related compounds
The shikimate pathway is an important connection between a plant's basic metabolism and its specialized natural products. A recent review describes it as the source of phenylalanine, tyrosine, and tryptophan, as noted in this 2024 pathway review.

Easy example

Phenylalanine can be changed into substances involved in:
  • Plant color
  • Plant smell
  • Plant defense against insects and microbes
  • The hard woody material in stems

Amino acids explained simply

Amino acids are the small building blocks used to make proteins.

Essential amino acids

Humans cannot make enough of these, so we need to get them from food.
The PDF lists 9:
  • Histidine
  • Isoleucine
  • Leucine
  • Lysine
  • Methionine
  • Phenylalanine
  • Threonine
  • Tryptophan
  • Valine

Non-essential amino acids

Our body can usually make these by itself, such as alanine, glycine, serine, glutamate, and others.
Plants are different. They can make all 20 standard amino acids. This is one reason plants are able to produce such a wide variety of natural compounds. See PDF p. 21.

Cinnamaldehyde formation

Cinnamaldehyde is the main chemical responsible for cinnamon's characteristic smell and flavor.
The last slide explains how a plant makes it:

Step 1: Phenylalanine becomes cinnamic acid

An enzyme called phenylalanine ammonia lyase (PAL) removes an ammonia group from phenylalanine.
Phenylalanine → Cinnamic acid

Step 2: Cinnamic acid becomes cinnamoyl-CoA

Another enzyme, 4-coumarate-CoA ligase (4CL), activates cinnamic acid by attaching CoA.
Cinnamic acid → Cinnamoyl-CoA
ATP provides the energy needed for this step.

Step 3: Cinnamoyl-CoA becomes cinnamaldehyde

An enzyme called cinnamoyl-CoA reductase (CCR) uses NADPH and reduces cinnamoyl-CoA.
Cinnamoyl-CoA → Cinnamaldehyde

Very short flowchart

Phenylalanine
     ↓ PAL
Cinnamic acid
     ↓ 4CL + ATP
Cinnamoyl-CoA
     ↓ CCR + NADPH
Cinnamaldehyde
This is part of the shikimic acid pathway-related metabolism, because it begins with phenylalanine. See PDF p. 28.

One-line summary

  • Acetate-mevalonate pathway: makes terpene and oil-like plant compounds.
  • Shikimic acid pathway: makes aromatic amino acids and compounds such as cinnamon-related chemicals.
  • Cinnamaldehyde: is made from phenylalanine through cinnamic acid and cinnamoyl-CoA.
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