(P1) Amino Acid Degradation and Urea Cycle

Degradation of amino acids

This slide is breaking an amino acid into its three key parts and showing how they are handled during degradation (breakdown).

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1. Amino Group (–NH₂) → Nitrogen handling

• This part contains nitrogen (N)

• During degradation, it is removed (called deamination or transamination)

• The nitrogen is toxic if it accumulates → gets converted into urea in the liver → excreted

👉 Key idea:
Amino group = where nitrogen is removed and detoxified

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2. Side Chain (R group) → What makes each amino acid unique

• The “R” group is different for every amino acid

• During degradation, this part determines what the amino acid becomes

It can turn into:

• Glucose precursors (glucogenic amino acids)

• Ketone bodies (ketogenic amino acids)

• Intermediates like pyruvate, acetyl-CoA, or TCA cycle molecules

👉 Key idea:
R group = determines metabolic fate and energy use

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3. Carboxyl Group (–COOH) → Carbon backbone

• This part, along with the central carbon, becomes part of the carbon skeleton

• After nitrogen is removed, what remains is used for:

  • Energy (ATP production)

  • Glucose synthesis (gluconeogenesis)

  • Fat/ketone production

👉 Key idea:
Carboxyl group contributes to the carbon skeleton used for energy

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Putting it all together (big picture)

When your body breaks down amino acids:

1. Remove nitrogen (amino group) → send to urea cycle

2. Keep carbon skeleton (carboxyl + R) → convert into usable energy molecules

3. R group decides pathway → glucose vs ketones vs TCA intermediates

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Simple way to remember

• Amino group = Nitrogen → waste (urea)

• R group = Identity → determines pathway

• Carboxyl group = Carbon → energy production

Amino Acid Degradation Strategy

• The degradation of amino acids and synthesis of urea may be divided for discussion into four stages:
• Removal of amino groups mostly by transamination

This slide is outlining the overall strategy your body uses to break down amino acids and safely deal with their nitrogen.

Step 1 (shown on your slide): Removal of amino groups

“Removal of amino groups mostly by transamination”

What is happening?

• The amino group (–NH₂) is removed from the amino acid

• BUT instead of being released directly, it is transferred to another molecule

This process is called: Transamination

How it works (simple):

• Amino acid + α-ketoglutarate → new amino acid (glutamate) + new keto acid

So instead of free ammonia (toxic), nitrogen is safely carried as glutamate

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Why transamination is important

• Prevents buildup of toxic ammonia

• Collects nitrogen in one place (glutamate)

• Prepares nitrogen for the next step → urea cycle

This slide is expanding the full pathway of amino acid breakdown—basically showing how the body handles nitrogen and then uses what’s left for energy. Let’s go step by step in a clean, intuitive way.

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1. Dehydration of serine and threonine

👉 Special case for certain amino acids

• Serine and threonine can lose water (dehydration)

• This creates intermediates that can directly release ammonia (NH₃)

Why it matters:

• This is an alternative way to remove nitrogen (not just transamination)

• Produces:

  • Pyruvate (serine) → can go to glucose

  • α-ketobutyrate (threonine) → energy pathways

👉 Think: shortcut way to remove nitrogen

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2. Oxidative deamination of glutamate

👉 Main step where nitrogen is actually released

• Earlier, nitrogen was collected on glutamate

• Now glutamate is converted:

Glutamate → α-ketoglutarate + NH₃

• Enzyme: glutamate dehydrogenase

• Occurs mainly in the liver

Why it matters:

• This is where free ammonia is produced

• Links amino acid metabolism to the TCA cycle

👉 Think: this is the “release nitrogen” step

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3. Ammonia transport

👉 Moving toxic nitrogen safely through the body

Ammonia (NH₃) is toxic, so it’s not transported freely.

Instead, the body uses carriers:

Main carriers:

• Glutamine

  • Transports ammonia from tissues → liver

• Alanine (glucose-alanine cycle)

  • Moves nitrogen from muscle → liver

Why it matters:

• Prevents ammonia toxicity (especially in brain)

👉 Think: package nitrogen safely for delivery

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4. Reactions of the urea cycle

👉 Detox step in the liver

• Ammonia → converted into urea

• Happens in liver (mitochondria + cytosol)

Urea cycle goal:

• Take 2 nitrogen atoms

• Turn them into urea (safe, water-soluble)

Then:
➡ Urea → blood → kidneys → urine

👉 Think: final disposal of nitrogen

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5. Fate of the carbon skeleton

👉 What happens after nitrogen is removed

Once NH₃ is gone, you’re left with the carbon backbone

This can become:

• Glucose (gluconeogenesis) → glucogenic amino acids

• Ketone bodies or fat → ketogenic amino acids

• TCA intermediates → energy (ATP)

Examples:

• Alanine → pyruvate → glucose

• Leucine → acetyl-CoA → ketones

👉 Think: use the leftover carbon for fuel

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Big picture (connect everything)

1. Remove nitrogen (transamination or dehydration)

2. Release ammonia (oxidative deamination)

3. Transport it safely (glutamine/alanine)

4. Detox it (urea cycle)

5. Use carbon skeleton (energy, glucose, or fat)

Transamination: transferring “trans” an amino group (–NH₂) “amination” from one molecule to another

Instead of releasing toxic ammonia directly, the body moves nitrogen safely between molecules.

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What your slide is showing Left side (generic reaction)

• Amino donor = an amino acid (has –NH₂)

• Amino acceptor = a keto acid (no –NH₂)

After the reaction:

• Donor loses NH₂ → becomes a keto acid (ketone byproduct)

• Acceptor gains NH₂ → becomes a new amino acid

So: Amino acid₁ + Keto acid₂ ⇄ Keto acid₁ + Amino acid₂

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Right side (same idea, more specific)

• (α-amino acid)₁ → becomes (α-keto acid)₁

• (α-keto acid)₂ → becomes (α-amino acid)₂

It’s reversible (can go both directions)

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Key enzyme for transamination: transaminase

• Called transaminase (aminotransferase)

• Examples:

  • ALT (alanine aminotransferase)

  • AST (aspartate aminotransferase)

• Requires vitamin B6 (PLP) as a cofactor

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Why this process is important

1. Prevents ammonia toxicity

• No free NH₃ released immediately

• Nitrogen is safely transferred instead

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2. Collects nitrogen onto glutamate

Most reactions funnel nitrogen to:

• α-ketoglutarate → becomes glutamate

Glutamate = central “nitrogen collector”

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3. Links amino acids to energy metabolism

• When amino acid loses NH₂ → becomes keto acid

• Keto acids enter:

  • TCA cycle

  • Gluconeogenesis

  • Ketone production

Example (high-yield)

Alanine + α-ketoglutarate ⇄ Pyruvate + Glutamate

• Alanine loses NH₂ → becomes pyruvate

• α-ketoglutarate gains NH₂ → becomes glutamate

This is one of the most important reactions (ALT)

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Big picture (connect to previous slides)

1. Transamination → move nitrogen

2. Glutamate holds nitrogen

3. Later → deamination releases NH₃

4. NH₃ → urea cycle

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Simple way to remember

“Swap the NH₂

• One molecule gives NH₂

• Another takes it

• No free ammonia yet

What this specific transamination reaction shows

This slide is a real example of transamination—not just the general idea.

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The reaction (what’s happening)

Aspartate + α-ketoglutarate ⇄ Oxaloacetate + Glutamate

• Aspartate = amino acid (has NH₃⁺ group)

• α-ketoglutarate = keto acid

After the reaction:

• Aspartate loses NH₂ → becomes oxaloacetate

• α-ketoglutarate gains NH₂ → becomes glutamate

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The enzyme for transamination: Glutamate-oxaloacetate transaminase (GOT)
Also called: AST (Aspartate Aminotransferase)

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Step-by-step (simple logic)

1. Aspartate donates its amino group

2. α-ketoglutarate accepts that amino group

3. Products form:

   • Oxaloacetate (carbon skeleton of aspartate)

   • Glutamate (now carrying the nitrogen)

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Why this reaction is important

1. Moves nitrogen safely

• No free ammonia released yet

• Nitrogen is now stored in glutamate

Glutamate = central nitrogen carrier

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2. Feeds into the urea cycle

• Aspartate is actually one of the nitrogen sources for urea

• This reaction helps shuttle nitrogen into the system

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3. Links to energy metabolism

• Oxaloacetate enters the TCA cycle

  • Can be used for:

    • ATP production

    • Glucose (gluconeogenesis)

So:

• Nitrogen → goes to disposal

• Carbon → goes to energy

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High-yield connections

• This is one of the two major transaminases:

  • AST (this reaction)

  • ALT (alanine ↔ pyruvate)

• Clinically:

  • AST levels ↑ in liver damage

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Simple way to remember

👉 Aspartate gives NH₂ → becomes oxaloacetate
👉 α-ketoglutarate takes NH₂ → becomes glutamate

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Big picture

This is just one example of the general rule:

👉 All amino acids transfer their nitrogen to α-ketoglutarate → forming glutamate

Then later:

• Glutamate → releases NH₃ → urea cycle

What this slide is showing (in plain terms)

This is a specific example of transamination—the process where one molecule hands off an amino group (–NH₂) to another.

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The reaction

Aspartate + α-ketoglutarate ⇄ Oxaloacetate + Glutamate

Read it like a swap:

• Aspartate loses NH₂ → becomes oxaloacetate

• α-ketoglutarate gains NH₂ → becomes glutamate

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Step-by-step logic

1. Aspartate (amino acid) has a nitrogen

2. It donates that nitrogen

3. α-ketoglutarate accepts it

4. Products form:

   • Oxaloacetate (no nitrogen now)

   • Glutamate (now carrying nitrogen)

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The enzyme

Glutamate–oxaloacetate transaminase (GOT)
Also called: AST (Aspartate Aminotransferase)

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Why this reaction matters

1. Safely moves nitrogen

• No free ammonia yet (important because NH₃ is toxic)

• Nitrogen is stored in glutamate

Think: glutamate = nitrogen shuttle

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2. Connects to the urea cycle

• Aspartate is one of the nitrogen sources for urea

• This reaction helps route nitrogen into disposal pathways

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3. Feeds energy metabolism

• Oxaloacetate goes into:

  • TCA cycle (Krebs cycle) → ATP

  • Gluconeogenesis → glucose

So:

• Nitrogen → disposal (urea cycle)

• Carbon → energy

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High-yield connections

• One of the two major transaminases:

  • AST (this reaction)

  • ALT (alanine ↔ pyruvate)

• Clinically:

  • ↑ AST = liver damage or muscle injury

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Simple way to remember

👉 “Aspartate → Oxaloacetate (loses NH₂)”
👉 “α-ketoglutarate → Glutamate (gains NH₂)”

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Big picture takeaway

This reaction is part of a larger strategy:

Collect nitrogen onto glutamate → later release it → convert to urea

This is the key step where nitrogen is finally released as ammonia.

in the previous reaction of transamination (where aspartate becomes OAA, and alpha ketoglutarate becomes glutamate)

in this step, nitrogen, from glutamate, is being released as ammonia (NH3).

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The reaction: Glutamate + H₂O + NAD⁺ ⇄ α-ketoglutarate + NH₄⁺ + NADH + H⁺

In words:

• Glutamate loses its amino group

• That nitrogen becomes ammonium (NH₄⁺)

• The carbon skeleton becomes α-ketoglutarate

• NAD⁺ is reduced → NADH

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What kind of reaction is this? Oxidative deamination

• Deamination = removing NH₂

• Oxidative = electrons transferred to NAD⁺ → NADH (this is reduction, however, we are naming it based on the glutamate losing molecules, which is oxidation).

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Step-by-step logic

1. Glutamate (holding nitrogen) enters

2. Enzyme removes NH₂

3. Nitrogen → released as NH₄⁺ (ammonia form)

4. Remaining molecule → α-ketoglutarate

5. NAD⁺ → becomes NADH (energy carrier)

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The enzyme: Glutamate dehydrogenase (GDH)

• Located in mitochondria in the liver.

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Why this step is VERY important

1. This is where ammonia is actually released

• All earlier steps (transamination) just moved nitrogen

• This step frees it

First time NH₃/NH₄⁺ appears

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2. NH4+ feeds directly into the urea cycle

• NH₄⁺ → enters urea cycle → becomes urea → excreted

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3. Links amino acids to energy metabolism

• Product = α-ketoglutarate

• This enters the TCA cycle

So:

• Nitrogen → waste

• Carbon → energy

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4. Produces NADH

• NADH → goes to electron transport chain

• Generates ATP

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Big picture connection

You can now see the flow:

1. Transamination → collect nitrogen on glutamate

2. Glutamate dehydrogenase (this step) → release NH₄⁺

3. Urea cycle → detoxify NH₄⁺

4. Carbon skeleton (α-ketoglutarate) → energy

This slide is showing how nitrogen is safely moved FROM muscle TO liver and disposed of, while also recycling carbon for energy. It combines three key ideas:

1. The big picture (what’s the goal?)

When muscle breaks down amino acids:

• You get toxic nitrogen (NH₃ / NH₄⁺)

• You also get carbon skeletons for energy

Problem: ammonia is toxic
Solution: package it (ammonia) as alanine → send to liver → convert to urea

2. Glucose–Alanine Cycle (top diagram)

In muscle:

1. Glucose → Pyruvate (glycolysis)

2. Amino acids lose nitrogen → becomes NH₄⁺

3. That nitrogen is transferred to pyruvate

   • via alanine aminotransferase

4. Pyruvate + NH₃ → Alanine

Alanine = safe nitrogen carrier

In blood: Alanine travels to the liver

In liver:

1. Alanine → Pyruvate + NH₃

2. Pyruvate → Glucose (gluconeogenesis)

3. NH₃ → Urea (detoxified)

Glucose (from gluconeogenesis) goes back to muscle → cycle repeats

3. The nitrogen flow (bottom diagram)

This is the core chemistry behind it all:

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Step 1: Transamination : Moves nitrogen between molecules (no free ammonia yet)

Key reaction:

• Amino acid + α-ketoglutarate ⇌ α-keto acid + glutamate

Glutamate = nitrogen collector

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Step 2: Oxidative deamination

• Now nitrogen is actually released

• Glutamate → α-ketoglutarate + NH₃

This is where your earlier question comes in:

• NAD⁺ → NADH

• So:

  • Glutamate is oxidized

  • NAD⁺ is reduced

✔ That’s why it’s called oxidative deamination

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Step 3: Urea cycle

• NH₃ + CO₂ → Urea

• Urea is excreted safely

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4. How everything connects

Think of it like a logistics system:

• Muscle

  • Packs nitrogen → alanine (safe transport)

• Blood

  • Delivers alanine

• Liver

  • Unpacks nitrogen → ammonia

  • Converts → urea (safe disposal)

  • Sends glucose back

Non-oxidative deamination = removing NH₃ without using NAD⁺/NADH

No redox
No electron transfer
Just rearranging + breaking bonds

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What’s special here?

Most amino acids: Transfer Nitrogen → glutamate → oxidative deamination

BUT

Serine & threonine can skip that (Serine and threonine can skip transamination because their side chains contain an –OH group that enables a dehydration reaction.) → they directly release NH₃

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Mechanism (this is the key)

Step 1: PLP grabs the amino acid

• Enzyme: serine dehydratase

• Cofactor: PLP (vitamin B6)

PLP stabilizes the amino group and makes the molecule reactive

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Step 2: Dehydration (this is the weird part)

• H₂O is removed

  • OH from side chain

  • H from adjacent carbon

👉 This creates a double bond intermediate

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Step 3: Rearrangement → unstable intermediate

• Forms an imine-like structure (C=NH)

This is key: now the nitrogen is easier to remove

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Step 4: NH₃ leaves: The amino group is released as NH₃

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Step 5: Final product forms

• Remaining carbon skeleton becomes: Pyruvate

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Net reaction (super important)

Serine → Pyruvate + NH₃

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⚖ Compare to oxidative deamination

Feature	Oxidative	Non-oxidative
Uses NAD⁺?	✅ Yes	❌ No
Uses glutamate?	✅ Yes	❌ No
Direct NH₃ release?	❌ No	✅ Yes
Amino acids	Most	Serine, Threonine

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Intuition (easy way to remember)

• Serine has –OH group
  → That allows dehydration (loss of H₂O)

• Once water leaves:
  Structure becomes unstable
  NH₃ can leave easily

Big idea

When amino acids are degraded:

• Nitrogen → urea (waste)

• Carbon skeleton → used for energy or glucose

This slide focuses on the carbon part

🔥 What “gluconeogenic” means

Gluconeogenic amino acids = can be converted into glucose (amino acids that are able to make glucose “gluconeogenic)

👉 The carbon FROM AMINO ACIDS ends up as molecules that can:

• enter the TCA cycle

• then become oxaloacetate → glucose

The 5 key entry points

These are the molecules your slide lists — they are all TCA cycle intermediates or closely related

1. Pyruvate

• Direct precursor to glucose

• Can become: Oxaloacetate → glucose

👉 Example amino acids:

• Alanine

• Serine

2. Oxaloacetate (OAA)

• Already a gluconeogenesis starting point

👉 Goes straight to: PEP → glucose

👉 Example: Aspartate

3. α-Ketoglutarate

• Enters TCA cycle

• Eventually becomes oxaloacetate

👉 Example: Glutamate

4. Succinyl-CoA

• TCA intermediate → oxaloacetate

Example:

• Methionine

• Valine

5. Fumarate

• TCA intermediate → oxaloacetate

Example:

• Phenylalanine

• Tyrosine

The unifying logic

All of these:
👉 Feed into the TCA cycle
👉 Become oxaloacetate (Goes straight to: PEP → glucose)
👉 Then → glucose (via gluconeogenesis)

KEY EXAM TRAP

Not all amino acids can make glucose.

👉 Only gluconeogenic ones do this

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Contrast:

• Glucogenic → glucose

• Ketogenic → ketone bodies (NOT glucose)

Ketogenic (important!):

• Leucine

• Lysine

Leucine and lysine are ketogenic because their carbon skeletons become acetyl-CoA (or acetoacetate), NOT TCA intermediates that can make glucose.

Why that matters

To make glucose (gluconeogenesis), you need:
👉 Oxaloacetate (OAA)

But:

👉 Acetyl-CoA cannot be converted into oxaloacetate in humans (Glycolysis → pyruvate, Pyruvate → acetyl-CoA (via pyruvate dehydrogenase) This is called the link reaction (not a cycle)

Clean mental model

Think: Amino acids → remove nitrogen → carbon skeleton → plug into TCA → become glucose

TCA cycle for reference of oxaloacetate

Position of oxaloacetate in the TCA cycle

Oxaloacetate (OAA) is both:

• the last product of the cycle

• and the starting molecule for the next turn

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🔄 Order at the end of the TCA cycle

The final steps are:

1. Malate → Oxaloacetate

2. Oxaloacetate + Acetyl-CoA → Citrate (cycle restarts)

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So:

• Malate = second-to-last

• Oxaloacetate = last

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🔁 Why it’s confusing

Because OAA is:

• immediately used up to form citrate
  👉 it feels like it’s not the end

But chemically:
👉 it is the final product regenerated each cycle

This slide is about what the carbon skeletons of amino acids become after you remove nitrogen (via transamination/deamination).

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Big idea

Once the amino group (NH₃) is removed, the leftover carbon skeleton:

• either helps make glucose → “gluconeogenic”

• or helps make ketone bodies / fat → “ketogenic”

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1. Gluconeogenic vs Ketogenic (core distinction) Gluconeogenic amino acids

Become intermediates like:

• pyruvate

• oxaloacetate

• α-ketoglutarate

• succinyl-CoA

These can go → gluconeogenesis → glucose

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Ketogenic amino acids

Become:

• acetyl-CoA

• acetoacetate

These go → ketone bodies or fatty acids, NOT glucose

Why not glucose?
Because acetyl-CoA carbons are lost as CO₂ in the TCA cycle, so there’s no net glucose production.

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2. Aromatic amino acids (Phe, Tyr, Trp)

These are both gluconeogenic AND ketogenic.

👉 Why?

Because when they break down, they produce two types of products:

• Some carbons → TCA intermediates → glucose

• Some carbons → acetyl-CoA / acetoacetate → ketones

So they “split” into both pathways.

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3. Lysine & Leucine (special case)

Purely ketogenic

They break down ONLY into:

• acetyl-CoA

• acetoacetate

❗ They cannot form glucose at all.

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Easy way to remember

• “LL = only fat”
  👉 Lysine & Leucine = strictly ketogenic

• Aromatic trio (Phe, Tyr, Trp)
  👉 both (they’re versatile)

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🧬 Why this matters (clinically + MCAT)

• During fasting/starvation:

  • gluconeogenic AAs → maintain blood glucose

  • ketogenic AAs → fuel brain (via ketones)

• Test favorite:
  “Which amino acids are purely ketogenic?”
  ✔ Leucine & Lysine

Big idea

After deamination, the carbon skeleton enters metabolism at specific points:

All of these products can make glucose → gluconeogenic

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The “carbon-count rule” 3-carbon amino acids → Pyruvate

• End up as pyruvate (3C) (because pyruvate has 3 carbons)

Pyruvate can:

• go → glucose (gluconeogenesis)

• go → acetyl-CoA (energy, enters into the Krebs cycle)

Think: small = pyruvate

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4-carbon amino acids → Oxaloacetate (OAA)

• End up as oxaloacetate (4C) (because OAA has 4 carbons)

Oxaloacetate is:

• a direct gluconeogenesis substrate

• part of the TCA cycle

Very efficient for making glucose

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5-carbon amino acids → α-Ketoglutarate

• End up as α-ketoglutarate (5C) (because alpha-ketoglutarate has 5 carbons)

➡ This enters the TCA cycle, then can become:

• oxaloacetate → glucose

according to the figure for a-ketoglutarate, it’s already a substrate for the Kreb’s Cycle

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🔄 Why this works (connect the dots)

All three products:

1. Pyruvate (end of glycolysis)

2. Oxaloacetate (end of TCA and also start of TCA)

3. α-Ketoglutarate (middle of TCA)

are either:

• already gluconeogenesis substrates

• or can become one through the TCA cycle

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Contrast with ketogenic (important)

These DO NOT follow this rule:

• Leucine & Lysine → acetyl-CoA only → NO glucose

Because: acetyl-CoA carbons are lost as CO₂

• no net glucose production

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Easy memory shortcut

• 3C→ Pyruvate

• 4C → OAA

• 5C → α-KG

count every carbon in the molecule.

All = gluconeogenic pathway

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🧬 Why this matters (test logic)

If you see:

• amino acid → pyruvate / OAA / α-KG
  ✔ Answer = gluconeogenic

If you see:

• amino acid → acetyl-CoA
  ✔ Answer = ketogenic

This slide is showing how serine, glycine, and cysteine are metabolized, and how their carbons end up as pyruvate (→ gluconeogenesis) while also linking to nitrogen metabolism and one-carbon metabolism.

Let’s break it cleanly 👇

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LEFT SIDE: Serine ↔ Glycine (One-Carbon Metabolism)

Key reaction: Serine ⇄ Glycine

Enzyme: serine hydroxymethyltransferase

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What’s happening?

• Serine (3C) loses one carbon

• That carbon is transferred to THF (tetrahydrofolate)

Forms:

• Glycine (2C)

• 5,10-methylene-THF

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🔑 Why this matters:

• THF carries 1-carbon units

• Used for:

  • DNA synthesis

  • nucleotide production

👉 This is part of folate metabolism (VERY high-yield)

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🔥 ALSO: Serine → Pyruvate

Enzyme: serine dehydratase

Reaction:

• Removes NH₄⁺ (ammonia)

• Leaves behind pyruvate

👉 This shows:
✔ Serine is gluconeogenic

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🧠 RIGHT SIDE: Cysteine → Pyruvate

Step-by-step: 1. Cysteine oxidation

• Cysteine + O₂ → oxidized form (adds oxygen to sulfur)

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2. Transamination

• Uses α-ketoglutarate (α-KG)

• Produces:

  • L-glutamate (L-Glu)

  • modified cysteine intermediate

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3. Sulfur removal

• Releases SO₃²⁻ (sulfite)

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4. Final product:

👉 Pyruvate

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🔑 Big picture (connect everything)

All three amino acids:

Amino Acid	Final Carbon Product
Serine	Pyruvate
Glycine	→ Serine → Pyruvate
Cysteine	Pyruvate

👉 Therefore:
✔ All are gluconeogenic

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⚠ Important insights 1. These AAs can release free NH₄⁺ directly

Unlike most AAs:

• they don’t always need glutamate first

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2. Link between pathways

This slide connects:

• Amino acid metabolism

• Folate (1-carbon) metabolism

• TCA cycle (via pyruvate)

• Nitrogen disposal

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🔥 Easy way to remember

👉 “Serine family → pyruvate”

• Serine → pyruvate

• Glycine → serine → pyruvate

• Cysteine → pyruvate

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🧬 Why this is high-yield

• Folate cycle questions (THF!!)

• Which AAs → pyruvate

• Direct NH₃ release (serine, threonine similar idea)

• Gluconeogenesis during fasting