BIOL 304 Chapter 15 Metabolism, Basic Themes and Concepts

What is energy required for?

mechanical work (muscle contraction/cell movement), active transport, and biosynthesis

What are phototrophs?

capture energy from sunlight (ex. plants)

What are chemotrophs?

capture energy through the oxidation of chemicals (all animals)

What is metabolism?

highly integrated network of chemical reactions that carry out energy extraction and synthesis of new material; generally of in the direction of favorable

What is a metabolic pathway?

a series of linked reactions by which fuels are degraded and large molecules are constructed

What is one example of common theme of all metabolic reactions?

adenosine triphosphate (ATP) is used as an energy currency to link energy-releasing (exergonic) and energy-requiring (endergonic) pathways

What is another example of common theme of all metabolic reactions?

either sunlight or the oxidation of chemical fuels powers ATP formation

Why are metabolic reactions highly regulated?

metabolic pathways are interdependent, meaning that these reactions are connected, and the reactions require another reaction one way or another (dependent on each other); also regulated in order to keep the body in homeostasis

What is the first reason why many enzymes involved in metabolism are organized into large complexes?

it increases speed and efficiency

What is the second reason why many enzymes involved in metabolism are organized into large complexes?

allows efficient processing of unstable or toxic intermediates; immediately moving intermediates to the next step prevent intermediates from becoming toxic; this is why it's so important that metabolic reactions are continuous

What is catabolism?

reactions that break down complex molecules into simpler ones to capture energy in useful forms >:)

What molecules are broken down in catabolism?

carbohydrates or fats

Why is catabolism important?

produces useful energy, which is crucial for anabolism to take place

What is anabolism?

reactions that construct a more complex molecule from simpler molecules by using energy

What are amphibolic pathways?

pathways that can be either anabolic or catabolic depending on cellular energy conditions

What is the first criteria that a metabolic pathway must meet?

individual reactions need to be specific

What is the second criteria that a metabolic pathway must meet?

each of the reactions in the pathway must be thermodynamically favored under real conditions

When is a metabolic reaction able to occur spontaneously?

only if delta G, the change in free energy, is negative

True or False: overall free-energy change for a chemically coupled series of reactions equals the sum of the free-energy changes of the individual steps

True! this allows for the coupling of thermodynamically unfavorable and favorable reactions in enzyme active sites

How is free energy created?

from the oxidation of food and from light, this free energy is then transformed into ATP

True or False: ATP acts as the free-energy acceptor in most energy-requiring processes

False! it is the free-energy donor

What is ATP?

a nucleotide consisting of adenine, a ribose, and a triphosphate unit; active in complex with Mg2+ and Mn2+

True or False: ATP hydrolysis is exergonic

True! ATP is energy-rich because its triphosphate unit contains two phosphonanhydride linkages; a lot of energy is released when ATP is hydrolyzed for this reason

What causes the release free energy in ATP hydrolysis?

the formation of new covalent bonds or formation of noncovalent interactions with water

Does ATP hydrolysis cause an increase or decrease in entropy?

increase in entropy

The delta G for ATP hydrolysis is around -50 kJ mol, why is this important?

this is a decent amount of negative free energy, which can be used to power other reactions

What other molecules can drive reactions aside from ATP?

GTP, UTP, and CTP

What are nucleoside monophosphate kinases?

enzymes that phosphorylate nucleoside monophosphates (transfers a phosphate to nucleoside)

What are nucleoside diphosphate kinases?

enzymes that phosphorylate nucleoside diphosphates (transfers 2 phosphates to nucleosides)

What are the derivates of ATP?

the electron carriers NAD+ and FAD, acyl group carriers, and coenzyme A

How does ATP hydrolysis drive metabolism?

by shifting the equilibrium of coupled reactions; by coupling these reactions under the standard conditions of ATP hydrolysis, the equilibrium ration can be shifted from one molecule to another

What is phosphoryl-transfer potential?

the tendency of organic molecules to transfer its phosphoryl group of water

Why does ATP have a high phosphoryl-transfer potential?

due to its structure

What structural feature of ATP that give it high phosphoryl transfer potential?

ATP has an orthophosphate (Pi) that has greater resonance stabilization than any of the other ATP phosphoryl groups

What is another reason why ATP has a high phosphoryl-transfer potential?

it has a high delta G value; this high value is produced when the orthophosphate (Pi) is removed

How are ADP and Pi stabilized?

through hydration

Which molecules have a higher phosphoryl-transfer potential than ATP?

phosphoenolpyruvate (PEP), 1,3-bisphosphoglycerate (1,3-BPG), and creatine phosphate

What special function does phosphoenolpyruvate (PEP), 1,3-bisphosphoglycerate (1,3-BPG), and creatine phosphate have?

they can transfer their phosphoryl group to ADP to form ATP

Why can PEP, 1,3-BPG, and creatine phosphate be used to form ATP from ADP?

components with high phosphoryl-transfer potentials are able to do this, all of these compounds have high potentials

Does PEP, 1,3-BPG, and creatine phosphate have a more or less negative free energy value than ATP?

has a more negative value

What is creatine kinase?

catalyzes the regeneration of ATP from creatine phosphate and ADP

Why is creatine phosphate important?

serves as a reservoir of high potential phosphoryl groups that can be used to produce more ATP when needed by muscle cells

If exercise only occurs for a few seconds, which source of energy is most likely to be used?

ATP is used

If exercise only occurs for a few minutes, which source of energy is most likely to be used?

creatine phosphate

If exercise occurs for more than few minutes, which source of energy is most likely to be used?

anaerobic metabolism will occur

If exercise occurs for a long period of time, which source of energy is most likely to be used?

aerobic metabolism will occur

Why is oxidation an important source of cellular energy?

ATP is limited and must be constantly generated from ADP, oxidation helps form ATP from ADP

What happens when carbon atoms are oxidized?

they yield CO2

What happens to free energy as a carbon atom becomes more reduced?

the more reduced a carbon atom is, the more free energy it releases upon oxidation

Why are fats more effective fuel sources than carbohydrates?

the carbon in fats are more reduced; carbon resides on the end of the molecule, making it easily accessible, while the carbon in glucose is more hindered, making it a little more difficult to break down

What happens when compounds with high phosphoryl-transfer potential couple withe carbon oxidation reactions?

ATP synthesis occurs

What is glyceraldehyde 3-phosphate?

a metabolite of glucose formed during glucose oxidation

What happens when glyceraldehyde 3-phosphate is oxidized?

3-phoshoglyceric acid is formed, however, this oxidation does not occur directly

How is glyceraldehyde 3-phosphate able to generate 3-phosphoglyceric acid if it cannot be oxidized directly?

carbon oxidation generates 1,3-bisphosphoglycerate (1,3-BPG) from glyceraldehyde 3-phosphate, and the electrons released are captured by NAD+ to form NADH

Why is it important that 1,3-BPG is generated during glyceraldehyde 3-phosphate oxidation?

1,3-BPG has high phosphoryl-transfer potential, and its hydrolysis can be coupled to the synthesis of ATP , which can now be used to generate 3-phosphoglyceric acid

What does the oxidation of fuel molecules produce?

electrochemical potentials of ion gradients across membranes

Why are the electrochemical potentials produced from oxidation important?

serve as a means of coupling thermodynamically unfavorable and favorable reactions

What is oxidative phosphorylation?

the process of generating ATP through the coupling of energy of a protein gradient and an ATP synthesis reaction; these protein gradients can power ATP synthesis

Why are phosphate esters thermodynamically unstable yet kinetically stable in water?

stability is caused by the negative charges that resist hydrolysis in the absence of enzymes

How can phosphate esters release energy?

through manipulation by enzymes

What does the addition of a phosphate group do?

changes molecule conformation and behavior

Why are phosphates unique?

no other ions have the chemical characteristics of phosphates; this makes them play a prominent role in biochemical processes

What is the first metabolic stage in the extraction of energy from food?

large molecules in food are broken down into smaller units

What is the second metabolic stage in the extraction of energy from food?

small molecules are degraded to a few simple units that play a central role in metabolism

What is the third metabolic stage in the extraction of energy from food?

ATP is produced from the complete oxidation of the acetyl unit of acetyl CoA

What are activated carriers?

small molecules to which a chemical group or electrons have been added, which can then be donated to another molecule

What role do activated carriers usually have?

usually act as coenzymes or cosubstrates

What is an example of an activated carrier?

ATP, acts as a carrier for phosphate groups

What role do fuel molecules play in electron transfer?

transfer electrons to carriers, which then transfer their high-potential electrons to O2

What is nicotinamide adenine dinucleotide (NAD+)?

transfer electron carrier that accepts a proton and two electrons in the oxidation of a substrate to form NADH

What is the reactive part of NAD+?

nicotinamide ring

What is flavin adenine dinucleotide (FAD)?

transfer electron carrier that accepts two protons and two electrons in the oxidation of a substrate to form FADH2

What is the reactive part of FAD?

isoalloxazine ring

Where is the isoalloxazine ring in FAD derived from?

vitamin riboflavin

What role does NADPH play?

serves as an electron donor in most reductive biosynthesis

What is coenzyme A (CoA)?

a carrier of acyl groups that is derived from vitamin B5 (pantothenate)

What parts of coenzyme A (CoA) are reactive?

its terminal sulfhydryl group

How are acyl groups linked to coenzyme A?

linked to CoA by thioester bonds to form acyl CoA

What is acetyl CoA?

acetyl linked to CoA

Why is the transfer of an acyl group exergonic?

due to the thioester bonds being thermodynamically unstable, this is why the hydrolysis of acetyl CoA has a large, negative delta G value

Why are thioester bonds considered unstable?

electron in the C=O bond of thioester cannot form resonance structures with C-S bind that are stable; not stabilized by resonance structures

What does kinetic stability allow?

allows for enzymatic control over the flow of energy

What happens to NADH, NADPH, and FADH2 in the absence of a catalyst?

these carriers react slowly with O2

What happens to ATP and acetyl CoA in the absence of a catalyst?

these compounds are hydrolyzed slower

Where are many activated carriers derived from?

vitamins; activated carriers act as coenzymes that are derived from vitamins

What are vitamins?

organic molecules that are needed in small amounts in the diets of some higher animals

True or False: vitamins need to be modified to serve a function

True!

What is an oxidation-reduction reaction?

reaction that results in electron transfer

What is a group transfer reaction?

reaction that transfers a functional group from one molecule to another

What is a hydrolytic reaction?

a reaction that results in the cleavage of bonds by the addition of water

What is a carbon bond cleavage reaction (one that occurs without hydrolysis or oxidation)?

two substrates yielding one product or vice verse; when H2O and CO2 are a product, a double bond is formed

What is an isomerization reaction?

reaction that results in the rearrangement of atoms to form isomers

What is a ligation requiring ATP cleavage reaction?

reaction that results in the formation of covalent bonds (ex. carbon-carbon bonds)

Why are oxidation-reduction reactions important?

they allow energy to pass from one molecule to another; produce useful energy that can be used for other reactions (ex. oxidation-reduction reactions of the citric acid cycle)

Why are group-transfer reactions important?

used to synthesize ATP and in signaling pathways, among others (ex. phosphoryl group transfer)

Why are hydrolytic reactions important?

used to degrade large molecules (ex. hydrolytic cleave of proteins)

What is an example of an carbon bond cleavage reaction?

the conversion of the six-carbon molecule fructose 1,6-bisphosphate into two three-carbon fragments during glycolysis

Why are isomerization reactions important?

prepare a molecule for a subsequent reaction (ex. conversion of citrate to isocitrate)

What is the first mechanism used to regulate metabolic pathways?

altering the amount of enzymes present

What is the second mechanism used to regulate metabolic pathways?

restricting the accessibility of substrates