17 - Introduction to Metabolism

Question 1

What is the definition of metabolism?

Answer 1

The set of chemical processes occurring within a living cell or organism that are necessary for the maintenance of life

Question 2

What are xenobiotics?

Answer 2

Chemicals that are found in organisms but are not produced in them. Often referred to as pollutants and that sort of thing. A role of metabolism is to break these down.

Question 3

What happens to energy in an endergonic metabolic pathway?

Answer 3

Energy is usually stored, in ATP or other ways

Question 4

What are the two exergonic processes for making ATP?

Answer 4

Oxidative phosphorylation

Glycolysis

Question 5

What can happen with metabolic intermediates?

Answer 5

There can be spin off reactions where metabolic intermediates begin their own reactions.

Question 6

True or false? Enzymes can only work in one direction.

Answer 6

False. Enzymes can often work in the forward and reverse reaction, this is to cut down on the number of enzymes that need be made.

Question 7

What is the committed step in a metabolic pathway?

Answer 7

The first step where there is no branching off. Usually highly exergonic and point of regulation. One road going to product.

Question 8

What type of fat provides energy?

Answer 8

Triacylglycerides

Question 9

What type of bonds exist between the phosphate groups of ATP? What type of bonds exist between the phosphate and the adenosine?

Answer 9

There are phosphoanhydride bonds between the phosphates and phosphoester bonds between the phosphate and adenosine.

Question 10

Is ATP exchanged among cells?

Answer 10

No

Question 11

Larger molecules contain more energy. Rank the four functions of energy in these molecules from most energy release to least amount (catabolism to anabolism)

Answer 11

Energy storage (eg. glycogen, triacylglycerides, proteins etc.)

Energy transport (eg. glucose, fatty acids, glycerol and amino acids)

Energy release (eg. through breakdown of macromolecules, catabolism)

Energy storage (anabolic pathways through synthesis of macromolecules)

Question 12

What type of redox reactions are usually with anabolism? Is it endergonic or exergonic?

Answer 12

Reductive and endergonic

Question 13

What type of redox reactions are coupled with catabolism of nutrients? Is this exergonic or endergonic?

Answer 13

Oxidative, exergonic

Question 14

After nutrients are uptaken and catabolized, what are they broken down to?

Answer 14

Acetyl CoA and finally to CO2 and H20

Coupled to ATP production

Question 15

What is a metabolome?

Answer 15

A snapshot of the steady-state in an organism

Question 16

What are phosphorylation and dephosphorylations doing? What is the speed of this?

Answer 16

Making covalent modifications, this is usually slow.

Question 17

In anabolism, what is being oxidized and what is being reduced? What is usually required to provide energy for this?

Answer 17

NADPH is usually being oxidized to NADP+ so that small metabolites can be reduced to complex metabolites. ATP is usually required.

Question 18

Generating a product with a higher level of free energy is a form of what? What law of thermodynamics is this?

Answer 18

Energy storage. By the first law of thermodynamics energy cannot be destroyed, but only converted.

Question 19

What are group transfer reactions?

Answer 19

Adding groups to molecules, common reactions in metabolic network. Includes acylation, phosphorylation, glycosylation

Question 20

What molecules are often involved in redox reactions? Are redox reactions always coupled?

Answer 20

Redox reactions often involve NAD+/NADH,, NADP+/NADPH as redox partners and are ALWAYS coupled.

Question 21

Dehydration formation of double bonds are possible examples of what types of chemical reactions (3 answers)

Answer 21

Eliminations
Isomerizations
Rearrangements

Question 22

What is product inhibition?

Answer 22

Negative feedback loop where product inhibits its own enzyme.

Question 23

Can you predict if phosphorylation will inactive or activate a protein?

Answer 23

No, example is kinase, which can do both

Question 24

What is feedforward activation?

Answer 24

Can make sure that a reaction goes to completion or that there is not an accumulation of a certain intermediate. Product or intermediate spurs on reaction.

Question 25

Of keto, aldehyde, thiol, hydroxy and carboxyl groups, rank them in terms of oxidation state

Answer 25

Carboxy > aldehyde, keto > hydroxy, thiol

Question 26

What is a metbabolic pathway usually describing?

Answer 26

A sequence of reactions, each catalyzed by an enzyme or enzyme complex

Question 27

What are the five metabolic principles?

Answer 27

A metabolic pathway describes a sequence of reactions, each catalyzed by an enzyme or enzyme complex. Catabolic and anablic pathways must differ to avoid a 'futile cycle' All metabolic pathways must be regulated in rate and direction Every metabolic pathway has a committed step Compartmentation in eukaryotic cells

Question 28

What is the free energy of reversible reactions like? How many enzymes involved?

Answer 28

Usually small. Only one enzyme for forward and reverse direction (meaning similar rate in both direction). Ratio of product to substrate usually determines direction of reaction.

Question 29

What is the free energy of irreversible reactions like? How many enzymes involved? What effects are there from changes in the activity of the enzyme?

Answer 29

There is a large free energy. Two different enzymes for catalysis of forward and reverse reaction. Forward rate higher than reverse rate. Changes in levels of reactants have little effect, but changes in the activity of the enzyme has large effect on the rate of reaction from substrate to product.

Question 30

What are the advantages of reversible reactions?

Answer 30

Fewer enzymes needed. SImpler and faster pathways. Changes in metabolite levels are quickly communicated through the network.

Question 31

What s the committed step?

Answer 31

A highly exergonic reaction early in a pathway that commits the intermediate it produces to the pathway. The substrate of the committed step can only enter one pathway (no more branches)

Question 32

What would happen to a cell if free energy was at equilibrium? (DeltaG = 0)

Answer 32

Cell death, nothing happening. There must be ongoing input and output. The flux through the pathway is regulated to maintain homeostasis and to balance supply and demand.

Question 33

Do steady state levels give information about the flux?

Answer 33

No, steady state does not change when flux increases or decreases. Flux is simply increasing production of something outside of steady state..

Question 34

What are metabolomics?

Answer 34

Measurement of metabolites at steady state. Read from genotype to phenotype. More powerful than measurement of one metabolite, but no direct information about flux.

Question 35

What is the order from genotype to phenotype in metabolomics? Eg. genome to transcriptome to (3 more)

Answer 35

``` Genome Transcriptome Proteome Substrates (metabolome) Metabolites ```

Question 36

What is the RATE limiting step?

Answer 36

Tje slowest step, this is the flux generating step that determines speed of reaction at its fastest. Under different conditions different steps can be rate-limiting, when they are they are usually a regulatory point.

Question 37

What is flux?

Answer 37

Usually by allosteric control, metabolites from the same or different pathways can change the enzyme activity of the regulatory steps of a pathway. Leads to coordination of the regulation of different pathways generating the same product.

Question 38

What is a long term regulatory mechanism in metabolism?

Answer 38

Enzyme synthesis and degradation. Often under hormonal control. Changes take longer to set in and ast longer (long-term changes)

Question 39

What are three ways that feedforward and feedback control can be achieved?

Answer 39

Allosteric regulators Enzyme modification Regulation of enzyme levels