BioChem Unit 3

1. Structure of glycogen

Glycogen is a highly branched homopolymer of glucose that serves as the major carbohydrate storage molecule in animals.

• The glucose residues in straight chains are connected by α(1→4) glycosidic bonds.

• Branch points are formed by α(1→6) glycosidic bonds.

• Glycogen is built around a central protein called glycogenin.

• The largest glycogen stores are in the liver and skeletal muscle.

Reducing and nonreducing ends

Why is branching important?

Branching creates numerous nonreducing ends, allowing multiple glycogen phosphorylase molecules to remove glucose residues simultaneously. This enables rapid glucose mobilization when energy is needed.

Liver versus muscle glycogen

Exam takeaway: The liver stores glycogen primarily for whole-body glucose homeostasis, whereas muscle stores glycogen primarily for its own energy needs.

2. The five main enzyme activities of glycogenolysis

OBJECTIVES 3 AND 7 | LECTURE SLIDES 10–25

Glycogenolysis is the process of breaking down glycogen to produce glucose-1-phosphate and a smaller amount of free glucose.

Enzyme 1: Glycogen phosphorylase

Function: Removes glucose residues from nonreducing ends by phosphorolysis.

Reaction:

\[ \text{Glycogen}_n+P_i \rightarrow \text{Glycogen}_{n-1}+\text{G1P} \]

Important details:

• Breaks α(1→4) glycosidic bonds.

• Uses inorganic phosphate (\(P_i\)), not water.

• Produces α-D-glucose-1-phosphate.

• Retains the α configuration at carbon 1.

• Cannot cleave α(1→6) bonds.

• Stops when four glucose residues remain before a branch point.

This remaining branched structure is called a limit dextrin.

Why does phosphorylase stop four residues away? Its glycogen-binding region requires several glucose residues to interact effectively with the substrate. Near the branch point, the structure prevents proper binding and catalysis.

Enzyme 2: Transferase

Also called 4-α-glucanotransferase.

Function: Transfers three glucose residues from a short branch to another nonreducing end.

Sequence:

1. Glycogen phosphorylase approaches a branch point and stops.

2. Four residues remain on the short branch.

3. Transferase moves the outer three residues to a nearby chain.

4. One glucose residue remains connected through an α(1→6) bond.

The transferred residues can subsequently be removed by glycogen phosphorylase.

Enzyme 3: α(1→6)-glucosidase

Function: Removes the remaining glucose residue at the branch point.

Reaction:

\[ \text{Branch glucose}+H_2O \rightarrow \text{Free glucose} \]

• Cleaves the α(1→6) glycosidic bond by hydrolysis.

• Releases free glucose rather than glucose-1-phosphate.

• Allows phosphorylase to resume degrading the now-linear chain.

Important distinction: Transferase and α(1→6)-glucosidase are two catalytic activities of the same glycogen debranching enzyme in mammals.

Enzyme 4: Phosphoglucomutase

Function: Converts glucose-1-phosphate into glucose-6-phosphate.

\[ \text{G1P}\rightleftharpoons\text{G6P} \]

Glucose-6-phosphate can enter glycolysis, the pentose phosphate pathway, or be converted into free glucose in the liver.

Enzyme 5: Glucose-6-phosphatase

Function: Removes the phosphate group from glucose-6-phosphate.

\[ \text{G6P}+H_2O \rightarrow \text{Glucose}+P_i \]

This enzyme is especially important in the liver because it allows glucose to be released into the bloodstream.

Enzyme summary table

Energy question likely to appear on an exam: Why is glucose released from an α(1→6) bond less energetically efficient for glycolysis than glucose released from an α(1→4) bond?

Glucose released through an α(1→4) bond is already phosphorylated as G1P and can become G6P without spending ATP. Glucose released through α(1→6) hydrolysis is free glucose and must use ATP through hexokinase to become G6P if it is to enter glycolysis.

3. Phosphoglucomutase mechanism and glucose-1,6-bisphosphate

OBJECTIVE 10 | LECTURE SLIDE 21

This mechanism explains why glucose-1,6-bisphosphate exists as a temporary intermediate.

Step 1: Glucose-1-phosphate

Phosphate attached to carbon 1

The enzyme's phosphorylated serine transfers phosphate to carbon 6.

Step 2: Glucose-1,6-bisphosphate

Phosphates on both C1 and C6

The phosphate on carbon 1 transfers back to the enzyme's serine.

Step 3: Glucose-6-phosphate

Phosphate remains on carbon 6

Why is glucose-1,6-bisphosphate formed?

The enzyme temporarily adds a second phosphate before removing the original phosphate. This two-step phosphate transfer allows the enzyme to move the phosphate group from C1 to C6 while regenerating its phosphorylated serine residue.

No net ATP consumption is required for the phosphoglucomutase reaction.

4. Regulation of glycogen phosphorylase: a, b, T, and R states

OBJECTIVE 4 | LECTURE SLIDES 27–28

Glycogen phosphorylase is the major regulatory enzyme controlling glycogen breakdown.

There are two different ways to describe its state.

• a versus b: Describes phosphorylation state.

• R versus T: Describes protein conformation and catalytic activity.

R = Relaxed = Active

T = Tense = Less active

Phosphorylation of serine 14 favors the R conformation because the added negatively charged phosphate forms favorable ionic interactions with positively charged arginine residues, promoting a structural rearrangement that makes the active site more accessible.

Important exam distinction

Phosphorylation does not mean an enzyme must always be active, and dephosphorylation does not mean it must always be inactive.

For example, muscle phosphorylase b can become active when AMP binds and shifts its conformation toward the R state.

This is an example of allosteric regulation.

5. Allosteric regulation in muscle and liver

OBJECTIVE 5 | LECTURE SLIDES 29–32

Muscle glycogen phosphorylase

Muscle glycogen breakdown responds to the energy needs of muscle contraction.

AMP stabilizes the R state, whereas ATP and G6P favor the T state.

Example: During intense exercise, ATP consumption increases AMP levels. AMP activates muscle glycogen phosphorylase b, increasing glycogen breakdown to supply glycolysis.

Liver glycogen phosphorylase

The liver is primarily concerned with maintaining blood glucose concentration.

• Glucose is an important negative allosteric effector of liver phosphorylase a.

• When blood glucose is high, glucose binding favors the T state, decreasing glycogen breakdown.

• Liver phosphorylase is much less responsive to ATP than muscle phosphorylase.

• The liver is especially sensitive to glucagon signaling during fasting.

Muscle versus liver comparison

Memorize: Muscle asks, Do I need energy? Liver asks, Does the blood need glucose?

6. Hormonal regulation: glucagon and epinephrine

OBJECTIVES 6 AND 9 | LECTURE SLIDES 34–40

Hormones and their roles

Receptor distribution

The glucagon and β-adrenergic pathways activate Gs proteins and increase cAMP. In the liver, α₁-adrenergic signaling can also activate the phosphoinositide/Ca²⁺ pathway.

Step-by-step cAMP signaling pathway

1. Glucagon or epinephrine binds its GPCR

2. Receptor activates Gs protein

3. Gα exchanges GDP for GTP

4. Gα-GTP activates adenylyl cyclase

5. ATP is converted into cAMP

6. cAMP activates protein kinase A (PKA)

7. PKA phosphorylates phosphorylase kinase

8. Phosphorylase kinase phosphorylates glycogen phosphorylase b → a

9. Phosphorylase a increases glycogen breakdown

Signal amplification

A single activated receptor can activate multiple G proteins, leading to production of many cAMP molecules. Each activated kinase can phosphorylate multiple downstream targets.

Therefore, a small amount of hormone can produce a large glycogenolytic response.

How does signaling stop?

Your professor identifies three important mechanisms:

1. Gα hydrolyzes GTP to GDP, stopping activation of adenylyl cyclase.

2. Phosphodiesterase breaks down cAMP into AMP.

3. Protein phosphatases remove activating phosphate groups from phosphorylase kinase and glycogen phosphorylase.

7. Phosphorylase kinase regulation

OBJECTIVE 8 | LECTURE SLIDE 39

Phosphorylase kinase is controlled by two main factors.

Either factor can partially activate phosphorylase kinase, while both together produce stronger activation.

Why does this make physiological sense?

During muscle contraction, calcium is released to initiate contraction. The same calcium signal activates phosphorylase kinase, helping mobilize glycogen to meet increased ATP demand.

Meanwhile, epinephrine signaling promotes phosphorylation of phosphorylase kinase, coordinating the body's energy supply with stress or physical activity.

This means muscle contraction and hormonal signaling work together to promote glycogen breakdown.

8. Glucose-6-phosphatase and tissue distribution

OBJECTIVE 11 | LECTURE SLIDES 22–23

Glucose-6-phosphatase converts glucose-6-phosphate into free glucose.

\[ \text{G6P}+H_2O\rightarrow\text{Glucose}+P_i \]

Tissue distribution

• Liver: High activity, supporting blood glucose homeostasis.

• Kidney: Also expresses glucose-6-phosphatase and contributes to glucose production.

• Intestine: Can express glucose-6-phosphatase and contribute to glucose release.

• Skeletal muscle: Lacks significant glucose-6-phosphatase activity.

Your lecture particularly emphasizes the liver-versus-muscle distinction.

Why must glucose be dephosphorylated before release?

Glucose-6-phosphate cannot be transported out of cells by ordinary glucose transporters. Removing the phosphate group allows free glucose to leave the liver and enter the bloodstream.

In skeletal muscle, G6P remains inside the cell and is primarily used for energy production.

9. High-yield concepts to memorize

These are the main facts that connect multiple learning objectives.

1. Glycogen phosphorylase requires vitamin B6

Glycogen phosphorylase uses pyridoxal 5′-phosphate (PLP), a cofactor derived from vitamin B6.

PLP helps facilitate the phosphorolysis reaction. Its phosphate group participates in acid–base catalysis, helping inorganic phosphate cleave the glycosidic bond and produce glucose-1-phosphate.

If PLP-dependent catalysis is disrupted: Glycogen phosphorylase activity decreases, limiting the production of glucose-1-phosphate from glycogen.

2. Glucose inhibits liver phosphorylase through two connected mechanisms

Your lecture explains that glucose stabilizes the inactive T state of liver phosphorylase a.

The additional reference explains another important consequence: glucose binding promotes dephosphorylation by protein phosphatase 1 (PP1).

The sequence is:

Glucose increases → glucose binds liver phosphorylase a → T state becomes favored → PP1-mediated dephosphorylation is facilitated → glycogen breakdown decreases.

If PP1 is inhibited: Phosphorylase a may remain phosphorylated longer, making it harder to shut down glycogen breakdown.

3. Calcium connects muscle contraction to glycogen breakdown

During muscle contraction, calcium released from the sarcoplasmic reticulum binds calmodulin, a regulatory component of phosphorylase kinase.

This activates phosphorylase kinase even without the complete epinephrine–cAMP signaling pathway.

If calcium cannot activate phosphorylase kinase: The muscle loses an important mechanism for rapidly increasing glycogen breakdown during contraction.

4. Glycogen degradation has clinical consequences

One relevant example is glycogen storage disease type VI (Hers disease), caused by deficient liver glycogen phosphorylase activity.

Because the liver cannot efficiently mobilize glycogen, affected individuals can experience fasting hypoglycemia and liver glycogen accumulation.

1. Energetics of glycogen synthesis

OBJECTIVE 1 | LECTURE SLIDES 3–8

Glycogen synthesis is an anabolic pathway. Building a larger polymer from individual glucose molecules requires an energy input and an activated glucose donor.

The activated glucose donor is UDP-glucose (uridine diphosphate glucose).

Formation of UDP-glucose

The enzyme is UDP-glucose pyrophosphorylase, called UDP-glucose phosphorylase in your lecture.

The product PPi is inorganic pyrophosphate, consisting of two linked phosphate groups.

PPi is then hydrolyzed by inorganic pyrophosphatase:

Your professor's slide 8 gives approximately −19.2 kJ/mol for PPi hydrolysis under the stated conditions.

Why does PPi hydrolysis favor glycogen synthesis?

UDP-glucose formation is reversible on its own. However, rapid hydrolysis of PPi removes one of its products, pulling the reaction toward UDP-glucose formation.

This is an example of reaction coupling and the thermodynamic effect of product removal.

Energy cost

For glucose entering from the bloodstream, there are two important energy-consuming steps:

1. Glucose phosphorylation consumes one ATP.

2. UDP-glucose formation consumes one UTP, equivalent to one ATP in energetic cost.

Thus, incorporation of one free glucose residue into glycogen costs approximately two high-energy phosphate equivalents.

If glucose is already present as G6P, the initial ATP cost has already been paid.

Predicting disruptions

Exam takeaway: PPi hydrolysis helps make UDP-glucose formation thermodynamically favorable, while UDP-glucose supplies the activated glucosyl group for polymer elongation.

2. Enzymes involved in glycogen synthesis

OBJECTIVES 2–3 | LECTURE SLIDES 9–15

Your professor emphasizes four core synthesis enzymes or activities: UDP-glucose pyrophosphorylase, glycogenin, glycogen synthase, and branching enzyme. Hexokinase and phosphoglucomutase are also needed when starting from free glucose.

Complete pathway

A. Hexokinase / glucokinase

B. Phosphoglucomutase

G6P ←> G1P

The enzyme transfers the phosphate group between carbon 6 and carbon 1 through a glucose-1,6-bisphosphate intermediate.

This is the same enzyme discussed in Chapter 24, but it operates in the opposite direction during glycogen synthesis.

C. UDP-glucose pyrophosphorylase

It creates the activated glucose donor required for glycogen synthesis.

D. Glycogenin

Glycogen synthase cannot efficiently start a glycogen molecule from a single free glucose residue. It requires a preexisting short glucose chain.

Glycogenin solves this problem.

• Glycogenin is a glycosyltransferase.

• It forms a homodimer.

• It covalently attaches glucose to a tyrosine residue.

• It extends the primer to approximately eight glucose residues using UDP-glucose.

• Glycogen synthase then takes over chain elongation.

This process is called autoglycosylation.

If glycogenin is defective: Formation of new glycogen particles is impaired because normal primer formation is disrupted.

E. Glycogen synthase

Glycogen synthase is the main regulatory enzyme of glycogenesis.

It:

• Adds glucose to nonreducing ends.

• Forms α(1→4) glycosidic bonds.

• Releases UDP.

• Requires an existing primer.

If glycogen synthase is defective: Glycogen elongation decreases, resulting in reduced glycogen stores.

F. Branching enzyme

The branching enzyme creates α(1→6) linkages.

Your lecture describes three major requirements:

• The donor chain must contain at least 11 glucose residues.

• A terminal block of approximately seven residues is transferred.

• The new branch must be at least four residues away from an existing branch point.

Branching improves glycogen solubility and creates more nonreducing ends for rapid synthesis and degradation.

If the branching enzyme is deficient: Glycogen becomes abnormally structured, with longer outer chains and fewer branches. This can cause insoluble, poorly branched glycogen-like material to accumulate.

3. Phosphorylation and the activity of regulatory enzymes

OBJECTIVE 4 | LECTURE SLIDES 17–30

This is one of the most important parts of Chapter 25 because it connects glycogen synthesis to glycogen degradation.

The central rule

During fasting or exercise, phosphorylation generally promotes glycogen breakdown and suppresses glycogen synthesis.

During the fed state, dephosphorylation promotes glycogen synthesis and suppresses glycogen breakdown.

However, not every kinase is activated by phosphorylation, and PKA has a different activation mechanism.

Supplementary clarification: GSK3 has multiple phosphorylation sites; phosphorylation is not universally inhibitory. The inhibitory effect here specifically refers to Akt-mediated phosphorylation.

Why is reciprocal regulation important?

If glycogen synthase and glycogen phosphorylase were simultaneously highly active, glucose residues could be repeatedly added to and removed from glycogen.

This would waste energy through a futile cycle.

Reciprocal regulation minimizes this waste.

Fasting / exercise:

PKA signaling ↑

Phosphorylase activity ↑

Synthase activity ↓

Glycogen breakdown favored

Fed / resting:

Insulin signaling ↑Inhibited

Synthase activity ↑

Phosphorylase activity ↓

Glycogen storage favored

Important allosteric exception: G6P

Glucose-6-phosphate can allosterically activate glycogen synthase, especially its phosphorylated, less-active form.

This makes metabolic sense: abundant G6P indicates that glucose is available for storage.

Prediction: If G6P rises while glycogen synthase remains phosphorylated, synthase activity may increase through allosteric activation, although phosphorylation still limits its activity.

4. Protein phosphatase 1: GM and GL regulatory subunits

OBJECTIVE 5 | LECTURE SLIDES 28–38

Protein phosphatase 1 (PP1) removes phosphate groups from proteins.

In glycogen metabolism, PP1 helps reverse the effects of phosphorylation-dependent regulation.

PP1 performs three important reactions:

1. Dephosphorylates phosphorylase kinase, decreasing its activity.

2. Dephosphorylates glycogen phosphorylase a, converting it to b.

3. Dephosphorylates glycogen synthase b, converting it to the more-active a form.

Therefore, PP1 generally promotes glycogen synthesis.

GM regulatory subunit in muscle

GM is a glycogen-targeting regulatory subunit that helps localize PP1 to glycogen particles.

During epinephrine signaling:

• PKA phosphorylates GM at a regulatory site.

• PP1 association with the glycogen particle can decrease.

• PKA also promotes PP1 inhibition through inhibitor-1.

• This reduces PP1-mediated reversal of the glycogenolytic response.

The net result is greater glycogen breakdown and less glycogen synthesis.

If GM cannot respond normally to phosphorylation: Hormonal control of glycogen-associated PP1 may become impaired, disrupting the balance between glycogen synthesis and degradation.

GL regulatory subunit in liver

GL is the liver glycogen-targeting regulatory subunit of PP1.

Your professor's slides 35–38 show an important regulatory sequence.

1. Glucose concentration increases.

2. Glucose binds liver glycogen phosphorylase a.

3. Phosphorylase shifts from the R state toward the T state.

4. Its interaction with the GL-associated PP1 complex changes.

5. PP1 becomes more available to dephosphorylate phosphorylase a.

6. PP1 also dephosphorylates glycogen synthase.

7. Glycogen degradation decreases while synthesis increases.

Muscle versus liver PP1

Exam takeaway: GM and GL do not perform the phosphatase reaction themselves. They regulate PP1 localization, substrate access, and responses to cellular signals.

5. Insulin versus glucagon and epinephrine signaling

OBJECTIVE 6 | LECTURE SLIDES 19–32

The most important distinction is the receptor type.

Insulin uses a receptor tyrosine kinase (RTK). Glucagon and epinephrine use G-protein-coupled receptors (GPCRs).

Insulin signaling pathway

Insulin is secreted by pancreatic β cells when blood glucose increases.

Its pathway promotes glucose uptake and glycogen synthesis.

The detailed PI3K–Akt–GSK3 pathway supplements your lecture's abbreviated IRS/protein-kinase diagram. It is also documented in an accessible biochemistry teaching reference.

In skeletal muscle, insulin also promotes GLUT4 translocation to the plasma membrane, increasing glucose uptake.

Glucagon and epinephrine pathway

The overall effect is increased glycogen breakdown and decreased glycogen synthesis.

Receptor comparison

What happens when signaling components are disrupted?

6. Hormone levels during different physiological conditions

OBJECTIVE 7

The body changes hormone secretion according to glucose availability and energy demand.

These are qualitative trends, not fixed hormone concentrations. Responses vary with exercise intensity, duration, nutrition, and other physiological conditions.

Important: During exercise, skeletal muscle can increase glycogen breakdown through calcium and AMP signaling even before a large hormonal response develops.

7. Reciprocal regulation: putting everything together

OBJECTIVE 8 | LECTURE SLIDES 17–38

This objective combines hormonal signaling, protein phosphorylation, PP1, and the GM/GL regulatory subunits.

During fasting or exercise

Glucagon in the liver or epinephrine in liver and muscle activates cAMP/PKA signaling.

• Phosphorylase kinase becomes more active.

• Glycogen phosphorylase becomes more active.

• Glycogen synthase becomes less active.

• PP1 action on relevant glycogen-associated targets is reduced or opposed by kinase activity.

Net effect: Glycogenolysis ON, glycogenesis OFF.

After a meal

Insulin signaling increases, while glucagon signaling generally decreases.

• Akt inhibits GSK3.

• Glycogen synthase phosphorylation decreases.

• PP1 promotes activation of glycogen synthase.

• PP1 helps inactivate phosphorylase kinase and glycogen phosphorylase.

• Increased glucose availability supports glycogen formation.

Net effect: Glycogenesis ON, glycogenolysis OFF.

Why is the liver's response to glucose especially important?

The liver responds to elevated glucose through both hormonal and direct metabolic mechanisms.

Glucose binding to liver phosphorylase a favors its less-active T state and promotes its dephosphorylation. This helps shift the liver from glucose production toward glucose storage.

Your professor illustrates this particularly clearly in slides 34–38.

8. Enzyme deficiencies and metabolic consequences

OBJECTIVE 9 | SUPPLEMENTARY CLINICAL APPLICATIONS

The final objective asks you to predict what happens when an enzyme is deficient.

A useful strategy is to ask three questions: What substrate accumulates? What product decreases? How does glycogen quantity or structure change?

Clinical example: Glycogen storage disease type IV

This disease, also called Andersen disease, results from glycogen branching enzyme deficiency.

Because the enzyme cannot form normal branches, abnormal glycogen-like material accumulates in affected tissues, particularly the liver and sometimes muscle.

Possible consequences include liver enlargement, progressive liver disease, and muscle or cardiac involvement depending on the disease form.

Clinical example: Glycogen storage disease type 0

Glycogen synthase deficiency can produce very low hepatic glycogen stores.

The liver therefore has difficulty maintaining blood glucose through glycogenolysis during fasting, which can contribute to fasting hypoglycemia.

Exam reasoning: Branching enzyme deficiency changes glycogen structure; glycogen synthase deficiency primarily reduces the amount of glycogen produced.