Nucleic Acids to Protein Structure Flashcards
Lecture 4
How is the number of molecules present related to the cell’s size?
Proportionally; As the cell increases in size, the number of molecules also increases, leaving the number of molecules at the same concentration.
About how many protein molecules are there per cell?
10^6 - 10^10 protein molecules per cell
What does a copy number indicate?
how many identical matches there are to one molecule
How many copies of each protein molecule do yeast cells have on average?
50-1000s of copies
How many copies of each protein molecule do mammalian cells have on average?
10^5 - 10^6 of copies
What is the average concentration for each protein in a cell?
10nM - 1 uM
Is the copy number of one type of protein constant among individual cell types?
No, the copy number can be very strictly regulated or can vary between generations. Among cells of the same type, the level of a given protein can vary severalfold.
What can happen if the copy number of a protein changes within a cell?
The concentration of proteins can change as well.
What is a proteome?
the complete inventory of all the proteins a cell can have
Which is larger, the number of different proteins or the number of genes?
the number of proteins
Does the cell contain its entire proteome at any one time?
No, only has a subset of the total inventory.
How many proteins are expressed within a mammalian cell at any given moment?
17000 (less than a fifth of the proteome)
How many proteins can 20,000 cells generate?
Over 100,000
Where are polypeptides synthesized?
on a ribosome
Is protein folding co- or post-translational?
Can be both
Is protein modification co- or post-translational?
Can be both
Is protein targeting/sorting co- or post-translational?
Can be both
Is protein degradation co- or post-translational?
post-translational
Describe the principle for self-assembly.
Neither energy nor extrinsic steric information is required for folding. Denaturing or renaturing depends on the environment.
Where does protein folding and targeting occur?
the cytoplasm, not the nucleus
What joins amino acids together?
covalent peptide bonds
What is the primary amino acid level of peptide organization?
sequence of amino acids that specifies 3d structure
Describe the hydrophobic effect.
Water molecules interact with each other near nonpolar molecules, forming a cagelike structure around hydrophobic molecules.
What causes the hydrophobic effect?
Water molecules’ inability to form hydrogen bonds with nonpolar molecules.
What impact does hydrophobic aggregation have?
Individual hydrophobic molecules surrounded by water molecules are at a state of low entropy and high order. When they aggregate (combining multiple hydrophobic molecules inside the same cagelike structure), it creates a thermodynamically favorable state of low order and high entropy.
Describe the protein folding process.
- A growing polypeptide chain begins on a ribosome.
- The N terminal domain begins folding.
- The C terminal domain begins folding.
- The folding completes after release from the ribosome.
When does the hydrophobic effect begin?
Co-translationally, before the polypeptide comes off the ribosome.
Which terminal domain begins folding first?
The N terminal domain folds first.
What kind of noncovalent bonds can be present in peptides?
Ionic bonds between charged side chains, van der Waals interactions between atoms, and hydrogen bonds.
What allows proteins to transverse Levinthal’s Paradox? Why is it possible?
Proteins do not move through every conformational possibility. That would require them to move to states of higher free energy, which is thermodynamically unfavorable. They only move through a portion of the free energy landscape.
What are the three potential outcomes non-covalent bonds can cause monomers to have?
No interaction
Kiss n go
Stable quaternary structure
Describe the kiss n’ go outcome.
This occurs when the non-covalent bonds have a weak interaction, leading to two peptides to come together briefly, but fall apart later.
What does Hsp-70 prevent?
- It prevents the polypeptide from folding until the C-terminus is created. This can prevent the formation of an improper tertiary structure.
- It also prevents the polypeptide from interacting with other surfaces and aggregating, which prevents precipitation reactions.
- It prevents the preventative degradation of a polypeptide.
How do chaperonins work?
A misfolded protein enters the chaperonin (barrel), a lid goes on the barrel, and 1-15 seconds later, the lid comes off, and a (hopefully) properly folded polypeptide is released.
