Introduction to Metabolism

Question 1

What are Metabolic pathways

Answer 1

Series of enzyme-catalyzed reactions. Metabolites or metabolic intermediates are the chemical intermediates. Many pathways are shared between organisms and cell types. Many pathways differ between cells. Different organisms (plants vs. animals; eukaryotes vs. procaryotes). Different tissues (liver vs. skeletal muscle). All pathways share the same fundamental chemical and thermodynamic principles

Question 2

What are the Two Major Purposes of Metabolism

Answer 2

1. To obtain usable chemical energy from the environment. (Capturing solar energy (photosynthesis) and consuming and breaking down nutrient molecules)
2. To make the specific molecules that cells need to live and grow.

Question 3

What are anabolic pathways

Answer 3

Anabolic pathways use energy to build larger molecules and are generally reductive (electrons are used to make new bonds)

Question 4

What are catabolic pathways

Answer 4

Catabolic pathways release energy (some of which is stored) and are generally oxidative (electrons are removed as bonds are broke).

Question 5

What are amphibolic pathways

Answer 5

Amphibolic pathways operate in both catabolic and anabolic processes (depending on conditions).

Question 6

What are the purposes of metabolism

Answer 6

CO2 + H20 are produced through oxidized carbon atoms. Catabolism is taking food and making metabolic intermediates. Electrons are reduced cofactors. Anabolism is taking metabolic intermediates, electrons and any other intermediates and creating cellular constituents.

Question 7

What are the dietary macromolecules

Answer 7

Nucleic acids (nucleotides), Proteins (amino acids), Polysaccharides and complex carbohydrates (monosaccharides and simple sugars) Triacylglycerols and fat (fatty acids)

Question 8

What dietary macromolecules are not a significant fuel source

Answer 8

Nucleic acids

Question 9

What dietary macromolecules are a significant fuel source

Answer 9

Polysaccharides and Triacylglycerols

Question 10

What is the balance between storage and mobilization of fuel molecules

Answer 10

When we eat, we then digest food which turns into fuel molecules, this then will create energy. Fuel molecules when not needed are stored in fuel stores. When fuel stores are needed they are mobilized into fuel molecules to create energy

Question 11

Where are excess fuels stored

Answer 11

Carbohydrates are stored as glycogen – a polymer of glucose molecules – in the liver (hepatocytes) and in the skeletal muscles (myocytes)
Fatty acids are stores as fat (triacylglycerols) in adipocytes (fat cells)

Question 12

What is the biochemical standard state

Answer 12

pH = 7
[S] & [P] = 1 M
Temperature = 25 degrees Celsius / 298 K
Pressure = 1 atm
[H2O] = 55 M

Question 13

How would you describe the free energy in an exergonic equation.

Answer 13

A reaction will only proceed in the forward direction when the associated value of the delta G reaction (actual free energy change) is negative (<0). This would be described as spontaneous, will proceed, etc.

Question 14

What happens when actual free energy is above 0

Answer 14

Reaction will not occur in a forward direction

Question 15

What happens when actual free energy is below 0

Answer 15

Reaction will occur in a spontaneous fashion

Question 16

What happens when the free energy is significantly below 0

Answer 16

The reaction may be considered “irreversible”

Question 17

What happens when the free energy is approximately 0

Answer 17

Reaction is considered “reversible.” It is close to equilibrium

Question 18

In irreversible steps are the enzymes regulated

Answer 18

Irreversible steps are usually regulated

Question 19

In reversible steps are the enzymes regulated

Answer 19

Reversible steps are not usually regulated

Question 20

What is the “Rate-Limiting Step”

Answer 20

In a pathway that is irreversible, regulated reaction that determines the overall rate of they pathway

Question 21

What is product inhibition

Answer 21

An enzyme is inhibited by the product of its reaction

Question 22

What is feedback inhibition

Answer 22

An enzyme is inhibited by a metabolite further down the pathway. Likely to be negative heteroallostery

Question 23

What is activiation

Answer 23

An enzyme may be activated by a metabolite “upstream.” Ensures the pathway is function in concert (otherwise intermediates may accumulate). Likely to be positive heteroallostery

Question 24

What is reciprocal regulation

Answer 24

Opposing pathways catalyze the “reverse” of another pathway. The irreversible reactions must be replaced or be bypassed. Pathways are regulated to ensure that both do not operate simultaneously

Question 25

What are high-energy intermediates

Answer 25

Compounds with contain “usable” chemical energy. Energy can be recovered or used. Simple reaction associated with a large delta G (usually larger than 20 kJ/mol that are released)

Question 26

What are the three major types of high-energy intermediates

Answer 26

1. Electron carriers (NADH, NADPH, FADH2, FMNH2)
2. Nucleotide triphosphates (NTPs: ATP, UTP, GTP)
3. Thioesters

Question 27

What happens during catabolism

Answer 27

Catabolism is oxidative. Metabolites are oxidized (lose electrons). Cofacters are reduced (“oxidizing agents”). Typically, NAD+, FAD become reduced

Question 28

What happens during anabolism

Answer 28

Anabolism is reductive. Metabolites are reduced (gain electrons). Cofactors are oxidized (“reducing agents”). Typically, NADPH becomes oxidized.

Question 29

What nucleotides play another central role in metabolism, as electron carriers

Answer 29

NAD+ and FAD

Question 30

What is the reduction of cofactors

Answer 30

1. NAD+ can be reduced to NADH
2. NADP+ can be reduced to NADPH
3. FAD can be reduced to FADH2

Question 31

What is a typical co-substrate

Answer 31

NAD+ and NADP+

Question 32

What is a prosthetic group

Answer 32

FAD

Question 33

How does FAD/FADH2 work as a prosthetic group

Answer 33

As a prosthetic group, FADH2 must be re-oxidized back to FAD for the next enzyme cycle to occur. In the citric acid cycle, coenzyme Q is used to carry out this re-oxidization.

Question 34

Why is ATP a “high energy” molecule

Answer 34

Decreased electrostatic repulsion. Resonance stabilization and Solvation effects

Question 35

How is ATP used

Answer 35

Energy currency: Common in multiple systems. Phosphoanhydrige bond makes it “high-energy.”
Generated by catabolism: Directly by “Substrate-level phosphorylation.” Via reoxidation of NADH/FADH2 “Oxidative phosphorylation”
Used in: Driving unfavourable reactions (coupling), Movement (muscle, flagella) and Primary active transport (ion pumping)

Question 36

What is the Coupling of Free Energies

Answer 36

Free energy changes for reactions are additive. A reaction with an overall unfavourable free energy change (>0) can occur when another favourable reaction (<0) occurs in concert. The combined reactions must have an overall free energy change greater than 0 to be spontaneous.