Ch 13 Intro to Metabolism

Life needs what?

Energy

Living structures are built of what? (broad term)

Complex structures

How is building of complex structures that are low in entropy possible?

Energy is spent in the process

The ultimate source of energy that life on Earth uses is what?

Sunlight

In energy cycling what type of organisms directly use sunlight?

Photosynthetic autotrophs

What do photosynthetic autotrophs produce?

Oxygen (O2) and organic products such as glucose and other carbohydrates

What is metabolism?

The sum of all chemical reactions in a cell

A typical eukaryotic cell has the capacity to make approximately how many different proteins?

~30,000 different proteins

What two functions do proteins primarily have in a cell?

Structural and enzymes

Can metabolites be shared by more than one “pathway”?

Yes, most are shared

What do heterotrophs produce?

CO2, H2O, and ATP (energy)

There are thousands of different reactions that can occur in a cell how many metabolites can some of these “pathways” have?

Many hundreds

Catabolic pathways deliver what? In the form of what? How are these deliveries used?

Catabolic pathways deliver chemical energy in the form of ATP, NADH, NADPH, and FADH2. These energy carriers are used in anabolic pathways to convert small precursor molecules into cellular macromolecules.

Are anabolic pathways synthesizing or degrading?

Synthesizing

Are catabolic pathways synthesizing or degrading?

Degrading

Conversion from energy-containing nutrients such as carbohydrates, fats, and proteins, to energy-depleted products such is CO2, H2O, and NH3 coupled with the release of chemical energy is what type of process?

Catabolism

When electron carriers like NAD+, NADP+, and FAD go through a catabolic process are they oxidized or reduced?

Reduced to NADH, NADPH, and FADH2

The use of precursor molecules like amino acids, sugars, fatty acids, and nitrogenous bases to build cell macromolecules such as proteins, polysaccharides, lipids, and nucleic acids through the use of chemical energy is what type of process?

Anabolism

When electron carriers like NAD+, NADP+, and FAD go through a anabolic process are they oxidized or reduced?

Oxidized

A pathway that is dual-purpose that both generates energy (catabolic) and provides precursor molecules for biosynthesis (anabolic) is called what?

Amphibolic pathway (The citric acid cycle is an example of this type of pathway)

Enzymes are regulated by one mechanism or many?

Many

Can any gene directly make animo acids?

No, genes can make enzymes that produce amino acids which can be regulated up to down as needed.

What is the definition of of a metabolic pathway?

A series of consecutive enzymatic reactions that result in a product that is either used or excreted by the cell. MULTIPLE REACTIONS!

What are the 3 major forms in a metabolic pathway

Precursors → Intermediates (Metabolites) → Product

Do catabolic pathways converge or diverge?

Converge

Do anabolic pathways converge or diverge?

Diverge

What do catabolic pathways converge towards and anabolic pathways diverge from? What key central metabolite?

Acetate (acetyl-CoA)

Do chemical changes and energy transductions in living organisms follow the laws of thermodynamics?

Yes

Define the free-energy change in terms of ability to do work

When a chemical reaction occurs the free-energy change is the maximum energy made available to do work

When combining two reactions to yield a third reaction how is the overall free energy change calculated?

A sum of the two reactions free energy changes

Cells accomplish energy-requiring chemical work how?

By coupling an energy-releasing (exergonic) reaction, like cleavage of ATP, to an endergonic reaction (which requires energy input)

When describing the thousands of different chemical reactions that occur in the biosphere they can fall into a large or small set of reaction types?

Small

What is the universal energy currency in living organisms?

ATP

Why is ATP the universal energy currency?

Transfer of its phosphoryl group to a water molecule or metabolic intermediates provides the energetic push for muscle contraction, the pumping of solutes against concentration gradients, and the synthesis of complex molecules.

What type of reactions indirectly provide much of the energy needed to make ATP? And how?

Oxidation-reduction reactions. Reduced substrates like glucose are oxidized in several steps, with the energy of oxidation steps conserved in the form of a reduced cofactor, NADH. Energy stored in NADH is used to drive the synthesis of ATP.

What are two major mechanisms by which cells regulate enzymes?

1. Change the number of enzyme molecules

2. Change the catalytic activity of preexisting enzyme molecules

What 3 statements about living organisms use of energy is universally and thermodynamically always true?

• Living organisms cannot create energy from nothing

• Living organisms cannot destroy energy into nothing

• Living organisms may transform energy from one form to another

In the process of transforming energy living organisms must increase or decrease the entropy of the universe

Increase

In order to maintain organization within themselves, living systems must be able to do what?

Extract usable energy from their surroundings and release useless energy (heat) back to their surroundings

Is delta G positive or negative if Keq is > 1.0. Is the reaction spontaneous?

Negative. Yes a spontaneous reaction.

Is delta G positive or negative if Keq is < 1.0. Is the reaction spontaneous?

Positive. Reaction is non-spontaneous.

What is the relationship between Keq and delta G?

Exponential

What is Keq?

[Products] / [Reactants]

Hydrolysis of one ATP can generate ~30kJ of energy which can increase product formation of a reaction by how much?

10^6 or an increase of 1,000,000x

When Keq is 1.0 what is delta G equal to? What does this mean about the reaction?

Zero. The reaction is at equilibrium.

What is the standard free energy change assumption regarding concentration of components?

All components start at 1M

The ACTUAL free-energy change of a reaction in the cell depends on what?

• The standard free energy change

• Actual concentrations of products and reactants

Standard free energy changes in a pathway way are totaled how?

Additive

How can thermodynamically unfavorable (endergonic) reactions be driven in the forward directions?

By coupling to a highly exergonic (energetically favorable) reaction. Often ATP hydrolysis.

Approximately how much free energy is released from hydrolysis of ATP under standard conditions?

-30.5 kJ/mol

How does ATP hydrolysis drive metabolism?

Shifts the equilibrium of coupled reactions

How are Keq (equilibrium constants) for coupled reactions associated together?

Multiplicative

How are delta G for coupled reactions associated together?

Additive

What does a positive Keq mean? More product or more reactant?

More product than reactant

What does a negative Keq mean? More product or more reactant?

More reactant than product

Why is hydrolysis of ATP highly favorable under standard conditions? (3 major reasons)

• Electrostatic repulsion

  • Removal of phosphate group takes away a negative repulsive charge, more stable product

• Resonance stabilization

  • ADP and Pi, have a greater resonance stabilization than ATP. Electrons are shared better.

• Stabilization due to hydration (cells are aq. environments)

  • More water can bind more effectively to ADP or Pi, than ATP, thereby stabilizing ADP and Pi

At pH 7.0 what charge does ATP carry?

-4

The Delta G of ATP hydrolysis is dependent on what? How does it regulate ATP hydrolysis?

ATP hydrolysis is Mg++ dependent. ATP in a cell always has Mg++ bound which prevents spontaneous hydrolysis by partially shielding negative charges and influencing the conformation of phosphate groups.

Mg++ from where binds to ATP and ADP?

The cytosol

Enzymes which participate in phosphate transfers and have an affinity for Mg are known as what?

Kinases

What is the true substrate in most enzymatic reactions involving ATP?

MgATP

When ATP is involved in a reaction how does it affect the product?

It phosphorylates the product

What is phosphorylation potential (delta Gp)?

The actual free energy of hydrolysis of ATP under intracellular conditions which varies from cell to cell and over time based on available concentrations

In vivo (in the cell), the energy release by ATP is greater or less than the standard free-energy change?

Greater

Are there biosynthetic reactions that use NTPs other than ATP such as UTP, GTP, and CTP? How much energy does hydrolysis of these NTPs release under standard conditions?

Yes other NTPs are required. They release a very similar amount of energy as ATP, -30.5kJ/M

Are the concentrations of ATP, ADP, and Pi every actually all 1M?

No

Are the free concentrations of ATP the same as the actual concentrations of ATP?

No, ATP can be found bound to several proteins.

What is an essential form of cellular energy transformation?

Phosphoryl transfer potential

What 3 molecules have a higher phosphoryl transfer potential (free energy change due to hydrolysis) than ATP?

• 1,3-Bisphosphoglycerate

• Phosphoenolpyruvate

• Phosphocreatine

Acetyl-Coenzyme A has what type of high energy bond?

Thioesters

Are thioesters more or less stable than oxygen esters? Why?

Less. Oxygen is stabilized by resonance.

How does ATP provide energy?

Group transfers

What are the two major steps by which ATP provides energy?

1. Transfer part of ATP molecule to substrate or amino acid residue activating it

2. Displacement of the phosphate-containing moiety generating Pi, PPi, or AMP as the leaving group

Most reactions in biochemistry are what type of process? Heterolytic or homolytic?

Heterolytic

Nucleophiles react with what?

Electrophiles

Heterolytic bond breakage often gives rise to what?

Transferable groups, such as protons

Oxidation of reduced fuels often occurs via what type of process?

Transfer of electrons and protons to a dedicated redox cofactor

Are nucleophiles electron rich or poor? What type of charge do they react with?

Electron rich and react with positive charges

Are electrophiles electron rich or poor? What type of charge do they react with?

Electron poor (positively charged) and react with negative charges

What 6 reaction categories do most reactions fall into? If applicable what mechanisms do they use?

1. Cleavage and formation of C-C bonds

   1. Homolytic cleavage (very rare)

   2. Heterolytic cleavage (most common)

2. Cleavage and formation of polar bonds

   1. Nucleophilic substitution mechanism

   2. Addition-elimination mechanism

      1. Hydrolysis

      2. Condensation reactions

3. Internal rearrangements

4. Eliminations (without cleavage)

5. Group transfers (H+, CH3+, PO3²-)

6. Oxidation-reductions (e- transfers)

Define homolytic cleavage

Cleavage of C-C or C-H bond where each atom keeps one of the bonding electrons, resulting in the formation of carbon radicals or uncharged hydrogen atoms. Equal distribution of electrons.

Define heterolytic cleavage

Clevage of a C-C or C-H bond where one of the atoms retains both of the bonding electrons. Leads to formation of carbon ions which are highly unstable.

Carbon ions are so unstable that they are unable to be captured by what?

Enzymes

What are three functional groups that can help to stabilize carbon ions and facilitate their formation as intermediates?

1. Carbonyl group - electrophilic

2. Imine group - electrophilic

3. Carbonyl groups augmented by a metal ion or general acid (HA)

What are 3 reaction types that are an example of nucleophilic C-C bond formation reaction?

1. Aldol condensation - carbanion serves as nucleophile and carbon of carbonyl serves as electrophile

2. Claisen ester condensation - carbanion stabilized by carbonyl of an adjacent thioester

3. Decarboxylation of a Beta-keto acid - carbanion forms as the CO2 leaves

In each case of nucleophilic C-C bond formation the carbanion is stabilized by what?

Carbonyl at the adjoining carbon

In internal rearrangement, isomerization and elimination is there a change in the oxidation state?

No change in oxidation state

What enzyme is involved in changing Glucose 6-phosphate to Fructose 6-phosphate? What type of intermediate is involved in this process?

Phosphohexose isomerase and an enediol intermediate

(aldose → ketose)

What are the 5 steps in changing Glucose 6-phosphate to Fructose 6-phosphate

1. B1 abstracts a proton (acts as a base)

2. Formation of C=C

3. e- from carbonyl form O-H w/ H donated by B2

4. B2 abstracts proton, allowing formation of C=O bond

5. e- pair is displaced from C=C bond to form C-H bond w/ proton donated by B1

(Step 4 & 5 occur in enediol intermediate)

(B1 and B2 are ionizable groups on the enzyme)