Biochem Exam 3 Part 3

digestion

large molecules in food are broken down into smaller molecules (no useful energy yet)

What are two key molecules that many small molecules are processed into during metabolism?

1. acetyl CoA (fuel)

2. some ATP

What is significantly produced from the complete oxidation of acetyl CoA?

ATP

Describe this diagram.

this shows the stages of catabolism

Living organisms require a continual input of free energy for three major purposes. What are they?

1. performance of mechanical work in muscle contraction and cellular movements

2. active transport of molecules and ions

3. synthesis of macromolecules and other biomolecules from simple precursors

What are the six basic principles that govern energy manipulations in all cells?

1. molecules are degraded or synthesized stepwise in a series of reactions termed metabolic pathways

2. ATP is the energy currency of life

3. ATP can be formed by the oxidation of carbon fuels

4. although many reactions occur inside a cell, a limited number of reaction types that involve particular intermediates are common to all metabolic pathways

5. metabolic pathways are highly regulated

6. the enzymes involved in metabolism are organized into large complexes

Metabolism is a series of linked ____________ that convert a specific __________ into a specific ___________

reactions, reactant, product

What are the two types of metabolic pathways?

1. catabolic pathways

2. anabolic pathways

catabolic pathways

combust carbon fuels to synthesize ATP or ion gradients

Large molecules are broken down to smaller products, releasing energy and transferring electrons to acceptor molecules of various sorts. The overall process is one of oxidation.

anabolic pathways

use ATP and reducing power to synthesize large biomolecules

Small molecules react to give rise to larger ones; this process requires energy and involves acceptance of electrons from a variety of donors. The overall process is one of reduction.

Useful equations for metabolism

For A <=> B, describe how ΔG changes

• if ΔG is negative, A->B is favored

• if ΔG is positive, B-> A is favored

• if ΔG is 0, B-> A and A-> B are equally favored

• At ΔG = 0, the system is at equilibrium

What is the difference between ΔG and ∆G°’ (and the corresponding equation)?

Value of ΔG under a given set of conditions depends on the value of ΔG° and on the concentration of reactants and products

What are the two criteria that must be met in order to construct a metabolic pathway?

1. the individual reactions must be specific

2. the pathway in total must be thermodynamically favorable

How can a thermodynamically unfavorable reaction in a pathway be made to occur?

it can be made by coupling it to a more favorable reaction

What is energy derived from fuels or light converted into?

adenosine triphosphate (ATP), the cellular energy currency

If the reaction A → B has ΔG = +25 Joule/mol and the reaction B → C has ΔG = -15 Joule/mol, the overall energy change A → C will be

+10 Joule/mol

What do phosphoric anhydride linkages being high-energy bonds mean for the amount of energy that is released when those linkages are broken?

High-energy bonds mean that breaking these bonds releases a significant amount of energy and forming them costs that same amount of energy

Why is the hydrolysis of ATP exergonic?

because the triphosphate unit contains two phosphoanhydride bonds that are unstable

The energy released from what is used to power a host of cellular functions?

ATP hydrolysis

What are the structures, charges, and stability of ATP, ADP, and AMP, respectively?

• ATP has four negative charges, whereas ADP has three. AMP has two.

• ATP is less stable than ADP and AMP because of electrostatic repulsion.

• Energy must be expended to put on additional negative charge on ADP or AMP.

ATP hydrolysis drives what process by shifting the equilibrium of coupled reactions?

metabolism

Example of coupling reaction:

What is phosphoryl-transfer potential (the standard free energy of hydrolysis) used to measure?

means of comparing the tendency of organic molecules to transfer a phosphoryl group to an acceptor molecule

Is phosphoryl transfer from ATP endergonic or exergonic?

this is an energetically favorable, or exergonic, process

What are the four key factors that contribute to ATP having a high phosphoryl-transfer potential?

1. charge repulsion - four negative charges in close proximity

2. resonance stabilization - free Pi has greater resonance stabilization than do any of the phosphates in ATP

3. increase in entropy - entropy is increased when on molecule of ATP is converted into ADP and Pi

4. stabilization by hydration - ATP hydrolysis is more effectively stabilized by association with water than is ATP

When ATP is formed from ADP and Pi, what happens to the resonance-stabilized phosphate ion?

Free Inorganic phosphate can adopt multiple resonance structures.

When ATP is formed from ADP and Pi, there is a loss of the resonance-stabilized phosphate ion.

There are fewer resonance structures available to the __________________ of ATP than to _____________________________.

γ-phosphate, free orthophosphate

ATP has a phosphoryl-transfer potential that is intermediate among the biologically important phosphorylated molecules. What does this intermediate position enable?

enables ATP to function efficiently as a carrier of phosphoryl groups

Describe this diagram.

This shows that ATP has a central position in phosphoryl-transfer reactions

What are the standard free energies of PEP, 1,3-BPG, creatine phosphate, and ATP (to ADP)

ATP falls in the middle of the compounds listed in Table 15.1. Why is this advantageous for energy coupling?

ATP can be regenerated by coupling with other reactions that release more free energy than -7.3kcal/mol. Thus ATP can act as an effective carrier, since it both accepts and donates phosphoryl groups.

ATP is the immediate _______ of free energy for biological activities.

donor

• However, the amount of ATP is limited.

• Consequently, ATP must be constantly recycled to provide energy to power the cell.

What is the fundamental biological role of ATP as an energy coupling compound?

to convert thermodynamically unfavorable processes into favorable ones

Calculate ∆G°’.

(61.9) + (-30.5) = 31.4

Calculate ∆G°’.

(31.4) + (-45.6) = -14.2

(-14.2) + (-19.2) = -33.5

Explain oxidation-reduction reactions in terms of coupling.

Oxidation reactions involve loss of electrons. Such reactions must be coupled with reactions that gain electrons (reduction).

What do the carbon atoms in fuels yield when oxidized? What is formed when the electrons are ultimately accepted by oxygen

CO2, H2O

What happens to free energy the more reduced a carbon atom is?

more free energy is released upon oxidation

Are fats or glucose a more efficient food source?

Fats because they are more reduced

Describe this diagram.

It shows the free energy of oxidation of single-carbon compounds

What is the essence of catabolism?

capturing the energy of carbon oxidation as ATP

What is the carbon in glucose and fats oxidized to? What is the energy released used to regenerate?

CO2, ATP from ADP and Pi

What may form from oxidation of the carbon atom in glucose and fats?

a compound with high phosphoryl-transfer potential compound which is then used to form ATP

What are the two characteristics common to activated carriers?

• the carriers are kinetically stable in the absence of specific catalysts

• the metabolism of activated groups is accomplished with a small number of carriers

ATP is an active carrier of ______________________________.

phosphoryl groups

(other activators common in biochem + derived from vitamins)

________________________________________ and _______________________________________ carry activated electrons derived from the oxidation of fuels

nicotinamide adenine dinucleotide (NAD+), flavin adenine dinucleotide (FAD)

Describe this diagram.

Structure of NAD+

A nicotinamide-derived electron carrier-

(A) Nicotinamide adenine dinucleotide (NAD+) is a prominent carrier of high-energy electrons derived from the vitamin niacin (nicotinamide) shown in red.

(B) NAD+ is reduced to NADH.

Describe this diagram.

Reaction of NAD+ being reduced to NADH

the nicotinamide ring accepts a hydrogen ion and two electrons, which are equivalent to a hydride ion

Describe this diagram

A redox dehydrogenation reaction.

NADH is an activated carrier molecule used as

• a cofactor for many enzymes that catalyze redox reactions.

• NADH also donates electrons to the electron- transport chain, which is essential for the production of ATP.

Describe this diagram.

This shows the structure of the oxidized form of Flavin Adenine Dinucleotide (FAD)

This electron carrier consists of the vitamin riboflavin (shown in blue) and an ADP unit (shown in black).

Describe this diagram.

These show the structures of the reactive parts of FAD and FADH2.

The electrons and protons are carried by the isoalloxazine ring component of FAD and FADH2.

Nicotinamide adenine dinucleotide phosphate (NADP+) is an active carrier of electrons for ______________________________.

reductive biosynthesis’

Activated Carriers Exemplify the Modular Design and Economy of Metabolism

Describe this diagram.

This shows the structure of nicotinamide adenine dinucleotide phosphate (NADP+)

NADP+ provides electrons for biosynthetic purposes. Notice that the reactive site is the same in NADP+ and NAD+

Coenzyme A (CoA or CoA-SH) is an activated carrier of ________________

acyl groups (such as acetyl group

Is the transfer of an acyl group endergonic or exergonic?

exergonic because the thioester is unstable

Thioesters are more unstable than oxygen esters because the electrons of the C=O bond cannot form resonance structures with the C-S. Thus thioester is not stabilized by resonance.

Describe this diagram.

This shows the structure of coenzyme A

What is this table showing?

These are some activated carriers in metabolism

Where are many activated carriers derived from?

vitamins

What do B vitamins function as?

coenzymes

Vitamins A, C, D, E, and K play a variety of roles but do not serve as coenzymes.

What is this table showing?

B vitamins

What is homeostasis, a stable biochemical environment, maintained by?

careful regulation of biochemical processes

What three regulatory controls are especially prominent in homeostasis?

1. the amount of enzymes present

2. the catalytic activity of enzymes

3. the accessibility of substates

The quantity of enzyme present can be regulated what level?

gene transcription

What are the two ways in which catalytic activity can be regulated?

• allosterically

• reversible covalent modification

How do hormones coordinate metabolic activity?

Often by instigating the covalent modification of allosteric enzymes

The energy status of the cell is often an important _____________ of
enzyme activity.

regulator

What are two common mean used to assess energy status?

• energy charge

• phosphorylation potential

Describe this diagram.

This shows how energy charge regulates metabolism.

High concentrations of ATP inhibit the relative rates of a typical ATP-generating (catabolic) pathway and stimulate the typical ATP-utilizing (anabolic) pathway.

____________ reactions such as fatty acid synthesis and degradation may occur in ____________ cellular compartments.

opposing, different

Regulating the flux of substrates between compartments is used to regulate ______________.

metabolism

Metabolism can be subdivided into ____________ and ________________ .

catabolism, anabolism

The useful forms of energy that are produced in ______ are employed in _____ to generate complex structures from simple ones or energy-rich states from energy-poor ones.

catabolism, anabolism

Organisms always need energy. Where does this energy come from?

the Sun

The currency of energy is generally high-energy phosphate-containing molecule. ATP is the best- known and most abundant. However, the following molecules are also important energy sources.

• GTP- energy source for protein synthesis

• CTP – for synthesis of glycerophospholipids

• UTP – for synthesis of glycogen and other sugar compounds

In each case, the energy is in the form of _____________ stored in the multiple-phosphate bonds. ___________ those bonds releases the energy in them.

potential chemical energy, hydrolyzing

ATP is made by what three distinct types of phosphorylation?

• Substrate level phosphorylation (in enzymatically catalyzed reaction – glycolysis and the citric acid cycle)

• Oxidative phosphorylation in mitochondria – most ATP is produced in this process.

• Photophosphorylation in chloroplasts of plants and algae

What values are included in the chemical standard state?

• Pure solids and liquids - Pure substance itself

• Gases - Pressure of 1.00 atmosphere of the respective gas

• Solutes - 1.00 molar concentration

ΔG ͦ ’ – the change in Standard Gibbs Free Energy

the change in energy that occurs when all of the products and reactants are at standard conditions and the pH is 7.0 (physical constant for given reaction)

EX. if the ΔG ͦ ’ for the reaction is – 0.5 kJ/mol, meaning that if this reaction starts with equal concentrations of reactants and products, AT EQUILIBRIUM, there will be a small excess of products.

The standard free energy change ΔG ͦ ’ for ATP hydrolysis is -30.5kJ/mol. ATP, ADP, and Pi are mixed together at initial concentrations of 1 M of each, then left until the reaction has come to equilibrium. Will the concentration of each will be equal to 1M, less than 1M, or larger than 1 M?

ATP < 1M, ADP > 1M, Pi > 1 M

The value of ΔG under a given set of conditions depends on the value of ΔG° and the concentration of reactants and products. Please remember that ΔG is variable

Consider the reaction A+B→C+D, If the equilibrium constant for this reaction is a LARGE number, what do you know about the standard free energy change for this reaction?

If Keq is a large number, the term -RTlnKeq has a relatively large negative number. ΔG ͦ ‘ is negative.

Consider this reaction: Glucose –1 phosphate → Glucose 6- phosphate. A 0.1M solution of glucose 1 phosphate is incubated until equilibrium is reached. At equilibrium, the concentration of glucose 1 phosphate is 4.5X 10-3 M and that of glucose 6 phosphate is 8.6X 10- 2 M. What is Keq’ and ΔG ͦ ‘?

Keq’ = [Glucose 6- phosphate]/ [Glucose 1- phosphate] = 0.086M/0.045M =19

ΔG ͦ ‘ = -7.3kJ/mol

In the cell, the hydrolysis of an ATP molecule in a coupled reaction changes the equilibrium ratio of products to reactants by a very large factor; thus, a thermodynamically unfavorable reaction sequence can be converted into a favorable one by coupling it to the hydrolysis of ___________ molecules in a new reaction.

ATP

The hydrolysis of ATP has a large negative ΔG ͦ ‘; nevertheless, it is stable in solution due to

a) Ionization of phosphate

b) Resonance stabilization

c) The hydrolysis reaction being endergonic

d) The hydrolysis reaction having a large activation energy

d) The hydrolysis reaction having a large activation energy