Metabolism Flashcards
State two major purposes of metabolism
- To obtain usable chemical energy from the environment
- To make the specific molecules that cells need to live and grow
Identify the two major ways in which organisms obtain energy from the environment
- phoyosynthesis
- consuming and breaking down nutrient molecules
List 3 features that distinguish catabolic and anabolic pathways
anabolic: (build)
- use energy
- builds larger molecules
- reductive (something else is getting oxidized, electrons are used to make new bonds)
- NAD+, FAD
catabolic: (break)
- release energy (some of which is stored)
- breaking down of molecules
- oxidative (electrons are removed as bonds are broken)
- NADPH, FADH
define 1) amphibolic and 2) anapleurotic
- Operate in both catabolic and anabolic processes, can both break down and build molecules
- A reaction that replenishes the intermediates of
a metabolic pathway
how are carbohydrates and fatty acids stored?
- as glycogen (a polymer of glucose molecules) in the liver (hepatocytes) and in skeletal muscle (myocytes)
- fatty acids are stored as fat (triacylglycerols) in adipocytes (fat cells)
Carbon oxidation
- during catabolism, carbon molecules generally become more oxidized
hydoxyls→carbonyls→carboxylates→carbon dioxide
- fats are more reduced than carbs and will generally need more oxidation steps to be oxidized
- CO2 is typically the end product for carbon atoms coming in as fuel molecules after catabolism
State the relationship between the magnitutde of the free energy change of a reaction and the direction in which that reaction will proceed
- if free energy is negative, rxn is exergonic and occurs spontaneously
- if free energy is positive, rxn is endergonic and does not occur without the input of energy
explain what the term “spontaneous” means, when describing a biochemical reaction
- thermodynamic process that can occur without the input of energy
- net decrease in free energy
Explain why reactions with a ΔG of approx. 0 are reversible
- if free energy = 0, reaction is in equilibrium
- no change in energy is observed meaning forward and reverse reactions occur simutaneaously
- a change in concentration of R/P may change the direction of the reaction ~Le Chatelier’s Principle~
Compare and contrast ΔG, ΔG’ and ΔG° and ΔG°’
ΔG - represents FEC under non-standard conditions, indicating whether or not the reaction is spontaneous
ΔG’ - represents the FEC for a reaction under biological standard conditions, providing a reference point for comparing the favourability of biochemical reactions
ΔG° - represents FEC for a reaction under standard conditions, providing a reference point for comparing the favourability of reactions under different conditions
ΔG°’ - represents FEC for a biochemical reaction under standard conditions with all R and P at their standard concentrations, useful for comparing the favourability of biochemical reactions involving proton transfers
FEC - free energy change
Biochemical Standard State
- pH = 7
- substrate and product concentration = 1M
- temperature = 25℃
- pressure = 1 atm
- concentration of water = 55M
equation describing the actual free energy change depending on the concentration of substances in system
ΔGreaction = ΔG°’ + RTIn (products/reactants)
Enzyme regulation in metabolism
- irreversible steps are usually regulated
- reversible steps are not usually regulated
examples of inhibition and activation
inhibition:
1. product inhibition - enzyme is inhibited by the product of it’s reaction (allosteric regulatory process)
2. feedback inhibition - enzyme is inhibited by a metabolite further down the pathway (downstream)
activation:
- feed forward activation: enzyme may be activated by a metabolite upstream (positive homoallostery)
net flux of pathway will increase if irreversible reactions are increased
State the function of electron carriers
- high energy intermediate that shuttles electrons around during important chemical reactions in cells
- contain useable chemical energy that can be recovered or used (reaction associated with large FEC)
- helps generate energy that cells can use
Identify three electron carriers that function as cofactors in enzymes which catalyze redox reactions
- NADH
- NADPH
- FADH₂
the nitrogen base portion of these dinucleotides enables them to undergo a reversible reduction reaction
Explain the terms 1) “high-energy” intermediate and 2) “energy currency”
- molecule possessing an unstable arrangement of atoms or chemical bonds, which makes it capable of releasing a significant amount of energy when it undergoes a specific chemical reaction. Carriers/donors of energy in a pathway
- molecule that serves as a universal carrier of chemical energy within a cell. can store energy in a readily accessible form and release it when needed to drive various cellular processes. (eg. ATP)
Identify three types of substances which can act as “high-energy” intermediates
- Electron carriers (NADH, FADH₂)
- Nucleoside triphosphates (ATP, GTP - contain phosphoanhydride bonds)
- Thioesters
Explain why the free energy change of hydrolysis of ATP is large and negative
the high-energy phosphate bonds between its phosphate groups are relatively unstable and have a high potential energy because there are 4 negative charges in close proximity due to the phosphate group
the LFEC is due to:
- decreased electrostatic repulsion between phosphate groups
- resonance stabilization and lower energy state of the molecules: terminal phsphoryl has 3 RS, inorganic phosphate has 4
- solvation effects: it becomes easier to from H bonds
ATP hydrolysis - ΔG’° ~32kJ/mol
RS - resonance structures
How is ATP generated? (2)
- directly by catabolism: substrate-level phosphorylation
- reoxidation of NADH/FADH₂: oxidative phosphorylation
List three energy-requiring processes “driven” by ATP
- unfavourable reactions (coupling)
- cellular movement (muscle, flagella)
- primary active transport (ion pumping)
State the conditions that must be satisfied for reactions to be coupled
free energy changes for reactions are additive
- the combined reactions must have an overall/net ΔG < 0 to be spontaneous
-
What is phosphate transfer potential
the free energies of hydrolysis for phosphate-containing compounds
**Use the formation of glucose-6-phosphate as an example to illustrate “coupling”
Outline the role of phosphocreatine in muscle and explain how it fulfills this role
- Phosphocreatine (PCr) serves as a reservoir of high-energy phosphate bonds in muscle cells. When ATP is used up during intense muscle contractions, PCr steps in as a rapid source of energy.
phosphocreatine hydrolysis coupled to formation of ATP:
phosphocreatine + ADP ⇋ creatine + ATP
ΔG = -11kJ
hydrolysis of phosphocreatine ΔG = -43kJ/mol
Define the terms 1) rate-limiting step and 2) reciprocal regulation, as they apply to metabolic pathways
- the irreversible, regulated reaction that determines the overall rate of the pathway
- when opposing pathways catalyze the “reverse” of another pathway, irreversible reactions must be replaced or bypassed, ensures that both do not operate at the same time
identify a phosphoanhydride bond
two phosphate groups connected together by a shared oxygen atom
state what is meant when nucleoside triphosphates are described as being “high energy” molecules
eg. ATP: contains unstable phosphate anhydride bonds containing negative charges that repel each other - hydrolysis = large release in free energy
- high energy means that these molecules are able to serve readily as a source of energy
Explain why the hydrolysis of phosphoanhydride bonds is a highly favourable reaction
It leads to a lower energy product - more resonance stabilization, more solvation
phosphoanhydride bonds are very high energy due to low stability
recognize NADP+, NAD+ and FAD as dinucleotides
- the nitrogen base portion enables them to undergo a reversible reduction reaction
- ## NAD+: 2 bases, 2 sugars, 2 phosphates
what are the equations to describe the reduction of NAD+, NADP+ and FAD
NAD⁺ + 2H⁺ + 2e- ⇌ NADH + H⁺
NADP⁺ + 2H⁺ + 2e- ⇌ NADPH + H⁺
FAD + 2H⁺ + 2e- ⇌ FADH₂
