Biochem Concepts and Bioenergetics Flashcards
What is the building block for a protein?
amino acid
What is the building block for DNA?
nucleic acid
What is the building block for a cell membrane?
phospholipids
Macromolecule
Large polymer made of monomers covalently bonded to each other
ex: lipids, proteins
Supramolecular structure
Large structure held together by strong interactions (noncovalently bonded)
ex: micelles, double helix of DNA
Stereoisomer
2 chemical structures w/ same chemical formula and connectivity but different spatial configuration
Why does stereoisomeric form matter?
Stereochem impacts how a molecule interacts w/ other biological structures, specificity (ex: substrate binding)
Different stereoisomer may result in different product
Catabolism
Taking bond energy from compounds, converting it to ATP and NADPH
- oxidation
- exergonic
- convergent (many different large compounds -> few small similar compounds)
Anabolism
Using ATP and NADPH generated from catabolism, used to perform biochemical work
- reduction
- endergonic
- divergent (few small similar compounds -> many different large compounds)
What properties of water make it important for biological chemistry?
- hydrogen bonding
- high specific heat: stores high energy, high heat of vaporization - maintains body temp
- high cohesion: transpiration in plants
- good reactant: hydrolysis, dehydration, photosynthesis
How does water affect how biological molecules behave?
Biological molecules usually behave actively in aqueous environments
Water can influence structural and functional properties
What is the role of water in spontaneous assembly of lipid or protein structures? How are energetics related to this?
Hydrogen bonds in water and disruption of the bonds drives self-assembly
Entropy-driven hydrophobic effect drives self-assembly into specific orientations, higher entropy = more favorable
Enthalpy
Sum of a system’s energy based on bonds in rxn (# and type)
- decr = favorable
Entropy
Order in a system (incr entropy = incr disorder)
- incr = favorable
What defines the “standard free energy change” of a chemical reaction? How is this related to enthalpy and entropy?
Amount of energy released in the conversion of reactants to products under standard conditions; ΔG° = ΔH° - TΔS° - energy change incr as enthalpy decr, entropy incr; energy change decr as enthalpy incr, entropy decr
ΔG
Difference in between reactants and products; changes b/c of changing conditions; spontaneity dependent on this
ΔG°
Difference in between reactants and products in standard conditions; doesn’t change
How is ΔG° related to Keq?
inversely related
Why does it make intuitive sense that a reaction with a high Keq value would have a low ΔG value?
High Keq = more conc of products than reactants
Low ΔG = reactants have more free energy than products
Reactants have more energy to spontaneously form lots of product
How does removal of products from a reaction affect ΔG?
Equilibrium shifts towards products to replace removed product, Keq incr and ΔG decr
ΔG formula
Under standard conditions
ΔG = ΔH - TΔS
Why does coupling ATP hydrolysis to reaction make that reaction favorable?
ATP hydrolysis highly favorable b/c breaking of phosphoanhydride bond releases lots of energy
Makes nonfavorable rxns favorable by forming unstable phosphorylated intermediate - allows rxn to take place in series of energetically favorable steps
What characteristics of ATP and its chemistry make this molecule so “energetic”?
Phosphate tail w/ 3 adjacent neg charges - makes ATP unstable, really wants to release phosphate groups, breaking bonds between groups releases lots of energy
ΔG for ATP hydrolysis (1 mol ATP)
-30.5 kJ/mol
How can an enzyme reaction have a ΔG° that differs from the ΔG of the same reaction in a cell?
Enzymes don’t affect ΔG° or ΔG; ΔG° only describes standard conditions while ΔG describes differing conditions and differing concentrations
How does the last enzymatic reaction in a series of coupled reactions affect the overall rate? The overall ΔG?
Last enzymatic rxn must have lower energy than the initial rxn, lowers overall ΔG, does not affect overall rate
Q
Reaction quotient, ratio of concentrations in nonstandard conditions (may not reach equilibrium)
When Q = Keq, ΔG = ΔG°
What happens to an enzymatic reaction when products build up or substrate levels decrease? How does this affect ΔG?
Product buildup -> decr enzymatic function
Decr substrate levels -> decr enzymatic function
Does not affect ΔG
How can changes in substrates and products of a series of coupled reactions affect the rate of each individual reaction? Of the overall rate of the series?
Changes in substrates and products may cause individual rxns to fail, products of previous rxns often used as reactants for next individual rxn
May slow down overall rate of series
If the last reaction in a series is highly favorable, how does this affect the preceding reactions?
Does not impact previous rxns, impacts overall rxn
Reduction potential (E)
Potential (in volts) for a compound to be reduced
High E = strong e- acceptor (oxidant)
Low E = strong e- donor (reductant)
Can the value of the overall reduction potential (ΔE) of a RedOx reaction predict whether the reaction is favorable in either direction?
More positive ΔE = to the right
More negative ΔE = to the left
In what direction do electrons flow? How does this impact ΔG?
e- flow in one direction in a half rxn
ΔG = neg, E = pos (proceeds forward)
ΔG = pos, E = neg (proceeds spontaneously backwards)
What makes a half reaction have a high or low reduction potential?
Depends on electronegativity of species in the rxn; more EN = higher E
How does reduction potential contribute to the direction of electron flow in the Electron Transport Chain?
Reduction potential incr as e- flow down the chain towards oxygen
Pyruvate kinase
Transfer of phosphate from high energy compound (phosphoenolpyruvate) to form a lower energy compound (ADP -> ATP)
Creatine kinase
Highly enriched in muscle and brain
Stores high energy phosphate donor to provide addnl source of ATP when ATP stores run low during muscle contraction (process that consumes ATP)
TCA/Krebs Cycle
Example of series of chemical oxidations coupled to NAD+ reductions
