6 core biochem principles
Which principle BEST explains why proteins fold into specific 3D shapes?
Structure determines function
The amino acid sequence dictates the final 3D structure, which determines the protein’s function.
What does spontaneous protein folding tell you about thermodynamics?
Negative ΔG (free energy decreases)
The folded state is more thermodynamically stable than the unfolded state.
Why is the final structure of a protein determined by amino acid sequence, not by the chaperone?
Structure determines function
The amino acid sequence contains all the information necessary to specify the final 3D structure.
Which type of interaction causes inappropriate clumping of misfolded proteins?
Hydrophobic interactions
Exposed hydrophobic regions from misfolded proteins stick together, causing aggregation.
What would happen if a hydrophobic amino acid in the protein’s interior was changed to a charged amino acid?
- Thermodynamically unstable in the hydrophobic core
- Protein might misfold
- Possible aggregation
- Reduced melting temperature
- Likely loss of function
This is a common disease-causing mechanism.
Which principle is MOST relevant to understanding how cells maintain high ATP levels?
Energy drives processes
ATP synthesis is thermodynamically unfavorable and requires energy input.
How does coupling an unfavorable reaction to a favorable reaction solve the thermodynamic problem?
- Free energy changes are additive
- ATP synthesis: ΔG = +30.5 kJ/mol (unfavorable)
- Electron transport: ΔG = -220 kJ/mol (favorable)
- Combined: ΔG = -189.5 kJ/mol (favorable overall)
Coupling is the fundamental strategy cells use to drive unfavorable reactions.
Complete the thermodynamics table:
Condition | ΔG | Spontaneous? | Example
Products more stable than reactants | Negative | Yes | ATP hydrolysis
Reactants more stable than products | Positive | No | ATP synthesis (alone)
At equilibrium | Zero | No net change | Reversible rxn at equilibrium
This table summarizes the relationship between stability and spontaneity.
How does high [ATP]/[ADP] ratio affect the actual ΔG of ATP hydrolysis?
Makes it more negative (more favorable)
The actual ΔG of ATP hydrolysis can be about -50 to -54 kJ/mol.
Why is ATP called ‘energy currency’ rather than ‘energy storage’?
- Constantly spent and regenerated
- Facilitates energy transfer
- Not a good long-term storage molecule
For long-term energy storage, cells use fats and carbohydrates.
Which principle does the central dogma represent?
Information flow controls activities
The central dogma describes how genetic information is stored, transmitted, and expressed.
Draw normal information flow and name the processes:
DNA → RNA → Protein
- DNA → RNA: TRANSCRIPTION
- RNA → Protein: TRANSLATION
This illustrates the flow of genetic information.
Why doesn’t reverse transcription violate the central dogma?
It involves nucleic acid → nucleic acid transfer
The central dogma allows for this possibility, but not for protein to nucleic acid transfer.
Why can’t cells make DNA directly from protein?
- DNA/RNA: 4 nucleotides encode information
- Proteins: 20 amino acids, no reverse code
- Multiple codons can code for same amino acid
Information content is fundamentally different.
Predict the cascade of effects from a DNA mutation.
- DNA mutation → mRNA change → Protein change → Function change
Effects depend on mutation type: silent, missense, nonsense, or frameshift.
Which principle BEST explains spontaneous bilayer formation?
Self-assembly creates organization
Bilayer formation is a classic example of self-assembly.
What drives phospholipids to form bilayers?
- Hydrophobic effect
- Hydrogen bonding
- Entropy increase of water molecules
The hydrophobic effect is the primary driver of bilayer formation.
Is bilayer formation thermodynamically favorable?
YES, it is spontaneous/favorable
ΔG is negative due to entropy increase and head group-water interactions.
Would protein regions INSIDE the bilayer be polar or nonpolar?
Nonpolar
Nonpolar amino acids are required for stability in the hydrophobic membrane interior.
Transmembrane protein amino acid distribution:
- Nonpolar amino acids in the MEMBRANE-SPANNING region
- Polar amino acids on the EXTRACELLULAR and CYTOPLASMIC regions
This arrangement allows for favorable interactions with both the membrane and aqueous environments.
Which TWO principles are MOST relevant to the Extremophile Puzzle?
- Structure determines function
- Evolution shapes mechanisms
These principles explain how thermophilic proteins are adapted to survive extreme conditions.
How do more ionic interactions and disulfide bonds help proteins survive high temperatures?
- Ionic interactions are stronger than H-bonds
- Disulfide bonds act as ‘staples’
These interactions maintain protein structure despite the loss of weak interactions.
Would a thermophilic protein function well at room temperature (25°C)?
No, it would be TOO stable
Thermophilic proteins are too rigid at lower temperatures, reducing catalytic efficiency.
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