BIOCH 200: Slide 7 Intro Metabolism (Purpose, concepts + High E molecules)

What are the 2 Major Purposes of Metabolism?

1. Obtain usable chemical energy (from environment)

2. Make specific molecules needed to grow

What are the 2 major ways organisms obtain energy from the enviornment?

1. Solar E (Photosynthesis)

2. Consuming + breaking down nutrient molecules

Where does all E ultimately come from?

the sun

Anabolism vs Catabolism definition

Anabolism: Building larger molecules

Catabolism: Break down + Release energy

Anabolism vs. catabolism. Which is generally reductive and which is generally oxidative?

Reductive = Anabolism (electrons used to make new bonds)

Oxidative = Catabolism (electrons = removed as bonds broken)

Amphibolic pathway?

Operate in both catabolic and anabolic processes (depends on conditions)

Overall scheme/ purpose/ flow of metabolism?

Food — catabolism —> Metabolites + E —Anabolism —> Cellular constituents + E

What are the 4 dietary Macros?

1. Nucleic acids

   • Nucleotides

2. Proteins

   • A.A

3. Polysaccharides

   • Monosacch.

4. Triacylglycerol (fat)

   • F.A

Which of the 4 macros are the most significant fuel sources and which are the least?

Most = Triacylglycerol + Polysaccharides

Least = Nucleic acids

Which term best describes pathway that both consumes high energy molecules and convers monomers to polymers?

• Amphibolic

• Anabolic

• Catabolic

• Metabolic

Anabolic

What is the storage form of carbs? and what is it made of?

Glycogen: polymer of glucose

Where is glycogen stored in the body? (2 locations)

Liver (hepatocytes) = store for other tissues to use + Skeletal muscle (myocytes) = store for self to use

What are F.A. stored as? + where?

Fat (Triacylglycerol) in adipose tissue

Most oxidized vs. Least oxidized

Most = CO2 (Far right)

Least = CH4 (Far left)

True or false: Fats + F.A.s are MORE REDUCED Than carbs and will generally need less oxidation steps to oxidize them?

False

• Fats + FAs are more reduced

• Need MORE oxidations steps to oxidize

  • They have a lot more electrons (and thus more E)

During catabolism what happens to the oxidation state of metabolites?

They becomes more OXIDIZED

What is typically the end product of oxidation of carbon atoms?

CO2

Anapleurotic definition

Processes that FORM/RESTORE METABOLIC INTERMEDIATES

• Crucial for preserving the Equilibrium of metabolism

Compare + Contrast

Delta G = Actual energy change (tells if rxn will occur or not)

Delta G Naught = E change under Standard conditions (1 M (pH = 0), 1 atm + 25 degrees)

Delta G Prime = Under physiological pH = 7

Delta G Naught Prime = Under physiological + Standard conditions (1 M, 1 atm, 25 degrees + pH = 7)

True or False: A rxn will only proceed in the forward direction when the associated value of Delta G prime = negative (exergonic)

True

What does “spontaneous” means, when describing a biochemical reaction.

Can occur without energy input because Delta G prime = negative

Will the rxn proceed is Delta G prime if Greater than 0?

Rxn will not occur (in regards to the fwd rxn)

Will the rxn proceed if Delta G prime is less than 0?

Rxn will occur (spontaneous)

What direction will the rxn proceed is Delta G prime is MUCH LESS than 0? ( G «« 0)?

Fwd + IRREVERSIBLE

What direction will the rxn proceed is Delta G prime is EQUAL to 0?

BOTH WAYS (REVERSIBLE)

Why reactions with a delta G of approx. 0 are reversible?

System = close to equilibrium

• any change in concentration of product or substrate may change direction of the rxn (chateliers)

The standard free energy change (DG°´) for the hydrolysis of ATP to ADP and P_i is about -30 kJ/mol but in red blood cells the actual free energy change is about -52 kJ/mol. This means…

B

• net energy is now more negative than the standard state, this means the product of the concentrations of reactants must be greater than the concentration of products (as this makes the ratio less than zero, making the second term in the equation negative

Metabolic pathway definition?

Series of ENZYME-CATALYSED chemical rxns

• each individual rxn must obey thermodynamic laws

• Overall rxn must also obey

Metabolic pathways exist in a “steady state” What does this mean?

“water” flowing in = “water” flowing out + the pool stays at a CONSTANT level

• The [metabolic intermediate] do not change significantly once the pathway operates

Enzyme regulation in metabolic pathways: Of Reversible vs Irreversible which rxns are typically regulated and which are not?

Irreversible = regulated

Reversible = typically not

What is the “Rate limiting step” in a metabolic pathway?

the IRREVERSIBLE regulated rxn that determines the overall rate of the pathway

3 types of regulation that can occur?

1. Inhibition

2. Activation

3. Reciprocal regulation

2 types of Inhibition?

1. Product inhibition

2. Feedback inhibition

What is product inhibition?

Enzyme = inhibited by the product of its reaction (immediate product)

What is feedback inhibition?

An enzyme is inhibited by a metabolite FUTHER downstream

What is Feed forward activation?

Enzyme = activated by metabolite up stream

What does feed forward activation do in terms of maintaining flow/ steady state

Ensure pathway = functioning properly + in concert

• prevent buildup of intermediates

What is reciprocal regulation?

OPPOSING pathways are regulated in opposite ways, so that ONLY ONE is active at a time

What purpose does reciprocal regulation achieve?

Ensure that both do not operate simultaneously (one = ON other must be OFF)

• prevent making a molecule just to break it down again (prevent wasting E)

Which of the following is true in regards to reversible metabolic rxns?

C

What are High E Intermediates?

Compounds which contain usable chemical energy

What are the 3 major types of high E intermediates?

1. Electron carriers

2. NTP (ATP, GTP etc..)

3. Thioesters

Catabolism vs Anabolism: Which is oxidative which is reductive?

Catabolism = oxidative

Anabolism = Reductive

In catabolism what is oxidized and what is reduced?

Metabolites = oxidized

Cofactors (oxidizing agents) = Reduced

• Cofactors = NAD+ and FAD

In Anabolism what is oxidized and what is reduced?

Metabolites = Reduced

Cofactors (reducing agents) = Oxidized

• Cofactors = NADPH

What are the 4 electron carriers?

NADH, NADPH, FADH2 + FMNH2

Which of the cofactors typically act as cofactors?

NAD+ (NADH), FAD+ (FADH2) and NADPH

True or False: Nucleotides are important electron acceptors/carriers in metabolism

True

• NAD (nicotinamide adenine dinucleotide)

• FAD (Flavin adenine dinucleotide)

What portion of these dinucleotides (NAD, NADP + FAD) enable them to undergo reversible reduction rxns?

the NITOGEN BASE

What part of the Dinucleotides (NADH and NADPH) confers the high E? and how does it work?

What is a cosubstrate?

Bind, converted, oxidized/reduced + released

What is a prosthetic group

Converted in place, does not disassociate. Need to reconvert in the enzyme active site where it resides

NAD+

• oxidizes ethanol to aldehyde

Of the 3 high E cofactors which are cosubstrate and which are prosthetic groups

Cosubstrate = NAD+ and NADP+

Prosthetic group = FAD

How is FADH2 as a prosthetic group reoxidized back to FAD? (CAC)

Coenzyme Q

What is the function of an electron carrier?

“carry” high E electrons from one part of a rxn to another

What is the reduction of the 3 cofactors

Why is ATP a high E molecule?

Phosphoanhydride bonds

What is a Phosphoanhydride bond?

Connection of 2 phosphates

Which of the following are generally true for anabolic pathways?

E: all of the above

The reaction A + B ® C has a ∆G'° of –20 kJ/mol at 25°C.  Starting under standard conditions, one can predict that:

C: As the reaction has a large negative values of deltaG, the reaction will proceed towards the formation of significant amounts of product

3 Reasons why ATP = High E molecule

1. 3 negative charges = squished together = Electrostatic repulsion (when phosphate comes off = release tension = favorable)

2. Inorganic phosphate = more resonance stabilized (when ATP = broken —> stable molecule Pi = favorable)

   1. Solvation: after ATP = broken = water can more easily surround + stabilize ADP + P)

What is a thioester?

Which of the following = High E molecule

D

• Both GTP and GDP have Phosphoanhydride bonds

What are 2 ways the ATP = generated by catabolism?

1. Substrate level phosphorylation (DIRECTLY)

   1. Oxidative phosphorylation (Via Reoxidation of NADH + FADH2)

What are 3 uses of ATP?

1. Driving unfavorable rxns (coupling)

2. Movement (muscles flagella)

3. Primary Active transport (ion pumps)

Define coupling of free energies

Free energy changes = ADDITIVE

• Unfavorable rxn = can occur when it occurs in concert with a favorable rxn

State the 2 conditions that must be satisfied for reactions to be coupled.

1. Share a common intermediate

   • product of one reaction is also a reactant in the next.

2. Overall Delta G must be negative

Define phosphate transfer potential

Free E of hydrolysis for phosphate containing compounds

some examples of phosphate transfer potential and their ranking

C

• One reaction must be reversed, and that would be reaction 1 as it has the lower magnitude free energy change. As for rxns to be coupled they must have a negative delta g. The net free energy change is then -32 + 9 kJ/mol, or -23 kJ/mol.

What is the Delta G naught prime?

-11 kj/mol

What is the role of phosphocreatine in muscle?

Emergency energy reserve to make ATP really fast when you suddenly need energy

• short term supply

Which of the following statements concerning ATP = false?

C is false (Phosphate groups in ATP have less resonance, making them higher energy)

Metabolic pathways operate in steady states. Which of the following does not contribute to this?

C. While the statement is true, it does not relate to the concept of steady state.

Which of the following about this structure is true?

D. This is not a dinucleotide (only one base is shown here).

D

Rxn equation of phosphocreatine use?

Phosphocreatine + ADP —> Creatine + ATP