Introduction to Metabolism Flashcards
What are Metabolic pathways
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
What are the Two Major Purposes of Metabolism
- To obtain usable chemical energy from the environment. (Capturing solar energy (photosynthesis) and consuming and breaking down nutrient molecules)
- To make the specific molecules that cells need to live and grow.
What are anabolic pathways
Anabolic pathways use energy to build larger molecules and are generally reductive (electrons are used to make new bonds)
What are catabolic pathways
Catabolic pathways release energy (some of which is stored) and are generally oxidative (electrons are removed as bonds are broke).
What are amphibolic pathways
Amphibolic pathways operate in both catabolic and anabolic processes (depending on conditions).
What are the purposes of metabolism
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.
What are the dietary macromolecules
Nucleic acids (nucleotides), Proteins (amino acids), Polysaccharides and complex carbohydrates (monosaccharides and simple sugars) Triacylglycerols and fat (fatty acids)
What dietary macromolecules are not a significant fuel source
Nucleic acids
What dietary macromolecules are a significant fuel source
Polysaccharides and Triacylglycerols
What is the balance between storage and mobilization of fuel molecules
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
Where are excess fuels stored
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)
What is the biochemical standard state
pH = 7 [S] & [P] = 1 M Temperature = 25 degrees Celsius / 298 K Pressure = 1 atm [H2O] = 55 M
How would you describe the free energy in an exergonic equation.
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.
What happens when actual free energy is above 0
Reaction will not occur in a forward direction
What happens when actual free energy is below 0
Reaction will occur in a spontaneous fashion
What happens when the free energy is significantly below 0
The reaction may be considered “irreversible”
What happens when the free energy is approximately 0
Reaction is considered “reversible.” It is close to equilibrium
In irreversible steps are the enzymes regulated
Irreversible steps are usually regulated
In reversible steps are the enzymes regulated
Reversible steps are not usually regulated
What is the “Rate-Limiting Step”
In a pathway that is irreversible, regulated reaction that determines the overall rate of they pathway
What is product inhibition
An enzyme is inhibited by the product of its reaction
What is feedback inhibition
An enzyme is inhibited by a metabolite further down the pathway. Likely to be negative heteroallostery
What is activiation
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
What is reciprocal regulation
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
What are high-energy intermediates
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)
What are the three major types of high-energy intermediates
- Electron carriers (NADH, NADPH, FADH2, FMNH2)
- Nucleotide triphosphates (NTPs: ATP, UTP, GTP)
- Thioesters
What happens during catabolism
Catabolism is oxidative. Metabolites are oxidized (lose electrons). Cofacters are reduced (“oxidizing agents”). Typically, NAD+, FAD become reduced
What happens during anabolism
Anabolism is reductive. Metabolites are reduced (gain electrons). Cofactors are oxidized (“reducing agents”). Typically, NADPH becomes oxidized.
What nucleotides play another central role in metabolism, as electron carriers
NAD+ and FAD
What is the reduction of cofactors
- NAD+ can be reduced to NADH
- NADP+ can be reduced to NADPH
- FAD can be reduced to FADH2
What is a typical co-substrate
NAD+ and NADP+
What is a prosthetic group
FAD
How does FAD/FADH2 work as a prosthetic group
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.
Why is ATP a “high energy” molecule
Decreased electrostatic repulsion. Resonance stabilization and Solvation effects
How is ATP used
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)
What is the Coupling of Free Energies
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.
