biochem 2 final

Glucose 6-phosphate dehydrogenase

catalyzes the first step in the pentose phosphate pathway (glucose 6-phosphate to 6-phospho-glucono-δ-lactone

Glycogen phosphorylase

catalyzes the removal of glucose residues from glycogen to yield glucose 1-phosphate

Transferase

is necessary for the remodeling of a-1,6 branch points in glycogen

 

Adenylate cyclase

catalyzes the synthesis of cyclic AMP from ATP and is important for the activation of protein kinase A.

Protein phosphatase I (PPI)

PPI is a phosphatase that is activated in response to elevated glucose levels.  PPI is heavily regulated in both muscle and liver.

Acylcarnitine transferases (I and II)

these enzymes mediate the transfer of fatty acyl CoA into the mitochondrial matrix.  Acylcarnitine transferase I is inhibited by malonyl CoA.

Acyl CoA dehydrogenase

catalyzes the first oxidation step in fatty acid b-oxidation

 

Acetyl CoA carboxylase (ACC)

catalyzes the synthesis of malonyl CoA from acetyl CoA.  This is the major control point in fatty acid synthesis.

Aminotransferases/transaminases

catalyze the transfer of an amine group from an amino acid to a carbon skeleton to make a new amino acid

The nitrogenase (dinitrogenase) complex

catalyzes the fixation of nitrogen

Carbamoyl phosphate synthetase

catalyzes the conversion of ammonia and bicarbonate into carbamoyl phosphate in the urea cycle

Glutamate dehydrogenase

catalyzes the direct deamination of glutamate and the reverse reaction, the addition of an amine group to a-ketoglutarate to make glutamate.

Calvin cycle

1. Carbon fixation

2. Reduction

3. Regeneration

Converts CO₂ into carbohydrate precursors using ATP and NADPH from light reactions.

Carbon fixation (calvin cycle)

• rubisco catalyzes

• ribulose-1,5-bisphosphate (RuBP) + CO₂ + H₂O
  → 2 molecules of 3-phosphoglycerate (3-PGA)

reduction (calvin cycle)

3-phosphoglycerate is reduced by NADPH to form hexoses

regeneration (calvin cycle)

Ribulose 5-phosphate is regenerated and reenters to the Calvin cycle to fix more CO2

Pentose phosphate pathway

• NADPH production

• Ribose-5-phosphate production

NADPH production (Pentose phosphate pathway)

• Fatty acid synthesis

• Cholesterol synthesis

• Neurotransmitter synthesis

• Protection against oxidative stress via glutathione

Ribose-5-phosphate production (pentose phosphate pathway)

Used for nucleotide synthesis.

Oxidative phase (The pentose phosphate pathway)

Rate-limiting enzyme:

Glucose-6-phosphate dehydrogenase (G6PD)

G6P
→ 6-phosphoglucono-δ-lactone + NADPH

Nonoxidative phase (The pentose phosphate pathway)

Uses:

• Transketolase

• Transaldolase

Produces:

• Fructose-6-phosphate

• Glyceraldehyde-3-phosphate

Glycogen breakdown

Main enzyme

Glycogen phosphorylase

Glycogen + Pi
→ Glucose-1-phosphate

Breaks α-1,4 glycosidic bonds using phosphorolysis.

Branch removal

Transferase

Moves glucose residues near branch points.

α-1,6-glucosidase

Removes branch-point glucose.

liver

• Has glucose-6-phosphatase

• Releases glucose into blood

muscle

• Lacks glucose-6-phosphatase

• Uses glucose internally via glycolysis

Glycogen synthesis

Activated donor

UDP-glucose

G1P + UTP
→ UDP-glucose

UDP-glucose is used by glycogen synthase.

Glycogen Synthase

Active form:

• Glycogen synthase a

• Dephosphorylated

Inactive form:

• Glycogen synthase b

• Phosphorylated

Fatty acid oxidation (β-Oxidation)

1. oxidation (FADH2)

2. hydration

3. oxidation (NADH)

4. Thiolysis

oxidation (Fatty acid oxidation)

Acyl-CoA dehydrogenase

Produces:

• trans-Δ²-enoyl CoA

• FADH₂

hydration (fatty acid oxidation)

Adds water across double bond.

oxidation 2 (fatty acid oxidation)

Produces:

• β-ketoacyl CoA

• NADH

thiolysis (fatty acid oxidation)

Produces:

• Acetyl-CoA

• Fatty acyl CoA shortened by 2 carbons

Fatty acid synthesis

1. condensation

   1. Acetyl + malonyl units join

2. reduction

   1. uses NADPH

3. dehydration

4. reduction

   1. uses NADPH again

repeated until palmitate forms

Ubiquitin

Small protein attached to lysine residues of target proteins.

Polyubiquitination signals degradation.

Proteasome

Structure:

• α₇β₇β₇α₇

β subunits contain protease activity.

Ubiquitin mediated protein degradation

Products

Protein
→ peptides
→ amino acids

Amino acids can be used for:

• glucose synthesis

• fatty acid synthesis

• cellular respiration

Amino acid degradation

Step 1: Transamination

Amino acid + α-ketoglutarate
→ α-keto acid + glutamate

Catalyzed by aminotransferases.

Step 2: Deamination

Glutamate
→ α-ketoglutarate + NH₄⁺

Catalyzed by glutamate dehydrogenase.

Step 3

Ammonium enters urea cycle.

The urea cycle

Purpose

Detoxifies NH₄⁺ by converting it to urea.

Steps

1. Carbamoyl phosphate synthetase

2. Ornithine transcarbamoylase

3. Argininosuccinate synthetase

4. Argininosuccinase

5. Arginase

Produces urea and regenerates ornithine.

First amino acids formed

Glutamate
Glutamine

These serve as nitrogen donors for synthesis of other amino acids.

Rubisco

catalyzes carbon fixation and the formation of 3-phosphoglycerate from ribulose 1,5-bisphosphate and CO₂.  most abundant enzyme in the biosphere

rubisco reaction and mechanism

Ribulose-1,5-bisphosphate (RuBP) + CO₂ + H₂O
→ 2 molecules of 3-phosphoglycerate (3-PGA)
Lys201 is carbamylated

1. Mg²⁺ binds active site

2. RuBP forms an enediol intermediate

3. CO₂ added to substrate

4. Unstable 6-carbon intermediate forms

5. Cleavage produces two 3-PGA molecules

Urea Cycle Defects

Hyperammonemia

Excess NH₄⁺ accumulates.
→ glutamine synthesis

Glutamine accumulates in neurons.

→ osmotic stress
→ brain swelling
→ neurological damage

Mutant Argininosuccinase

Argininosuccinate
❌→ Arginine + fumarate

Treatment:

• excess arginine

• reduced protein diet

Excess argininosuccinate is excreted and removes nitrogen from body.

Mutant Carbamoyl Phosphate Synthetase

Cannot form carbamoyl phosphate.

Treatment:

• benzoate

• phenylacetate

These remove nitrogen through alternative excretion pathways.

Toxic drug-induced necrosis

Cells rupture.

→ mitochondria released

→ GLDH elevated in blood

Used to distinguish types of liver injury.

Diagnostic enzyme for liver diseases

Glutamate dehydrogenase (GLDH)

Viral hepatitis

Mitochondria remain intact.

→ little GLDH released

Starvation and how this condition affects the urea cycle

Glucose-Alanine Cycle

During starvation:

Muscle protein
→ amino acids

Branched-chain amino acids degraded in muscle.

Amino groups transferred to pyruvate.

Pyruvate + NH₂
→ alanine

Alanine transported to liver.

In liver:

• amino group enters urea cycle

• carbon skeleton used for gluconeogenesis

Fatty acyl CoA

• Long hydrocarbon chain

• Thioester linkage

• Attached to coenzyme A

Phosphatidic acid

• Glycerol backbone

• Two fatty acids

• One phosphate group

Cytidine diphosphate choline

• Cytidine nucleotide

• Diphosphate

• Choline head group

Citrate

• 6-carbon TCA intermediate

• Three carboxyl groups

Malonyl CoA

• CoA attached

• Three-carbon dicarboxylic acid

Cells heavily dependent on PPP

Red blood cells

RBCs require NADPH to maintain reduced glutathione and protect against oxidative stress.

Evidence comes from G6PD deficiency causing RBC hemolysis.

Cells using large amounts of NADPH

• Adipose tissue

• Lipid-synthesizing tissues

PPP mode 3 is specifically for high NADPH demand.

Cells that rely less heavily on PPP

Cells primarily interested in ATP production rather than NADPH generally rely more on glycolysis than PPP.

Glucagon

Released during fasting.

Effects:

• glycogen breakdown ↑

• glycogen synthesis ↓

Epinephrine

Released during stress/exercise.

Effects:

• glycogen breakdown ↑

• lipolysis ↑

Insulin

Released in fed state.

Effects:

• glycogen synthesis ↑

• glycogen breakdown ↓

PKA

Glucagon/Epinephrine
→ Adenylate cyclase
→ cAMP
→ PKA

PKA

Activates

Phosphorylase kinase
→ Glycogen phosphorylase

Inhibits

Glycogen synthase

PP1

Opposite of PKA.

PP1 dephosphorylates:

• glycogen synthase

• phosphorylase kinase

• glycogen phosphorylase

Result:

• glycogen synthesis ON

• glycogen breakdown OFF

Muscle phosphorylase

Activated:

• AMP

Inhibited:

• ATP

• G6P

Liver phosphorylase

Inhibited:

• glucose

PLP (Pyridoxal Phosphate)

Active form of vitamin B6.

Used by:

• aminotransferases

• glycogen phosphorylase

Functions in amino acid metabolism.

ACP (Acyl Carrier Protein)

Used by:

Fatty acid synthase.

Function:

Carries growing fatty acid chain during synthesis.

FeMo Cofactor

Used by:

Nitrogenase.

Function:

Nitrogen fixation.

N₂ → NH₄⁺

Regulatory steps in Fatty acid oxidation

Rate-limiting control:

CPT-I

Inhibited by:

Malonyl-CoA

Prevents newly synthesized fatty acids from being degraded.

Regulatory steps in Fatty acid synthesis

Rate-limiting enzyme:

ACC

Acetyl-CoA
→ Malonyl-CoA

Activated by

• citrate

Inhibited by

• palmitoyl-CoA

• AMPK phosphorylation

ketone bodies

Water-soluble fuels produced in liver mitochondria from excess acetyl-CoA.
acetoacetate, acetone, D-3-Hydroxybutyrate

Extrahepatic tissues convert ____ back into acetyl-CoA for energy production.

When are ketone bodies produced?

• Starvation

• Fasting

• Type 1 diabetes

When OAA is diverted toward gluconeogenesis and acetyl-CoA accumulates.

Carbamoyl Phosphate Synthetase (CPS I)

Reaction

NH₄⁺ + HCO₃⁻ + 2 ATP
→ Carbamoyl phosphate

Location

Mitochondrial matrix

Important

• First step

• First nitrogen enters cycle

Ornithine Transcarbamoylase (OTC)

Reaction

Ornithine + Carbamoyl phosphate
→ Citrulline

Location

Mitochondria

Important

Citrulline leaves mitochondria and enters cytoplasm.

Argininosuccinate Synthetase

Reaction

Citrulline + Aspartate
→ Argininosuccinate

Important

Aspartate contributes the second nitrogen of urea.

Argininosuccinase

Reaction

Argininosuccinate
→ Arginine + Fumarate

Fumarate
→ Malate
→ Oxaloacetate

Links urea cycle to central metabolism.

Arginase

Reaction

Arginine
→ Ornithine + Urea

Products:

Urea:

• excreted

Ornithine:

• reenters cycle

Ketogenic amino acids

Produce:

• Acetyl-CoA

• Acetoacetyl-CoA

Examples:

• Leucine

• Lysine

glucogenic amino acids

Produce:

• Pyruvate

• OAA

• α-ketoglutarate

• Succinyl-CoA

• Fumarate

Can contribute to gluconeogenesis.

Nitrogen fixation

Conversion of atmospheric nitrogen:

N₂
→ NH₄⁺

• cyanobacteria

• soil bacteria

• also lightning (extreme heat)

can perform it.

Glutamine synthetase

Heavily regulated.

Inhibited by:

• Glycine

• Alanine

• Multiple nitrogen-containing end products synthesized from glutamine

Covalent regulation (glutamine)

When glutamine is abundant:

Glutamine synthetase becomes adenylylated

→ activity decreases