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.
Which terminal domain begins folding last?
The C terminal domain begins folding last.
Is the folding of the N and C terminals dependent on each other?
No, they occur independently.
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 creates secondary and tertiary structure?
Hydrogen bonding among main chain carbons.
Not interactions between side chains or the formation of covalent bonds.
Describe secondary protein structure.
local folding caused by hydrogen bonding along the main chain of carbons; beta sheets or alpha helices
Describe tertiary structure.
Long-range folding mediated by side chains of amino acids, hydrogen bonding, and ionic bonding
Describe quarternary structure.
Multimers - combination of multiple polypeptides
What forms when quaternary structures come together?
Supramolecular structures
Can quaternary structures have multiple different kinds of polypeptides joined together or do they all have to be the same kind?
Can have multiple kinds.
At which level in the protein structure hierarchy is the hydrophobic effect most important?
tertiary structure
Describe Levinthal’s Paradox.
It would take 4 billion years to fold a polypeptide that only had 100 amino acids if the amino acids only had two conformational possibilities and the polypeptide had to test each one.
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.
Why can each structural domain have different functions?
Because each folds independently of other domains; function is informed by structure.
What are disulfide bonds? What do disulfide bonds do?
Disulfide bonds are covalent bonds formed between the sulfur atoms of two cysteine amino acid residues that stabilize quaternary structures (extracellular proteins).
What environment does a disulfide bond need to form? Where do they generally form?
Disulfide bonds form in oxidative environments. They usually form outside the cell because the inside of a cell is generally reducing.
What environment breaks a disulfide bond? Where do they generally form?
Reducing environments break a disulfide bond; they usually form extracellularly in oxidative environments.
Do proteins need to have anything more than a primary structure to be functional?
No.
What constitutes the antigen binding site?
heavy and light chains (2 polypeptides)
What is beneficial about having multiple non-covalent bonds within a polypeptide?
Multiple non-covalent bonds promote higher order. They are more likely to form stable quaternary structures that survive for the duration of the proteins’ lifetimes.
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 is necessary for a stable quaternary structure?
multiple non-covalent bonds
What is the N-terminus?
The side of a polypeptide with an amino group; the first amino acid; is created before the C-terminus
What is the C-terminus?
The side of a polypeptide with a carboxy group; the last amino acid; is created last when creating a peptide
Do all proteins have structural domains?
No.
What determines topology?
Position of a polypeptide’s domain relative to another domain.
Are all functional domains made up of one structural domain?
No. For example, the antigen bonding site is comprised of two structural domains, light and heavy chains.
Are disulfide bonds interchain or intrachain?
Can be both.
What are heat shock proteins and when are they expressed?
Heat shock proteins were originally thought to only be expressed at higher temperatures to protect proteins from denaturing. However, researchers realized that they’re also expressed to stabilize peptides folding.
Why are proteins unstable while being created?
The N-terminus cannot interact with the C-terminus because it has not been created yet.
Interacting with a surface or molecule may cause a nascent polypeptide to…
- Aggregate/precipitate
- Degrade
- Form a non-functional tertiary structure
Do heat shock proteins impart steric information?
No.
Do heat shock proteins provide a template?
No.
Is Hsp-70 a chaperone or a chaperonin?
chaperone
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 does the Hsp-70 behave?
It binds to ATP, leading to the release of inorganic phosphate and the Hsp preventing the protein from folding. When ADP is released and new ATP is present, the Hsp-70 comes off the nascent polypeptide chain.
Do chaperones act co- or post-translationally?
co-translationally
Do chaperonins act co- or post-translationally?
post-translationally
Describe the structure of chaperonins.
Chaperonins are large protein complexes that form a barrel-like structure.
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.
What happens to a misfolded polypeptide inside of a chaperonin? Why?
It is turned inside-out due to the hydrophobic amino acids in their side-chains inside of the chaperonin, then rapidly refolds after leaving.
What level of protein hierarchical organization are alpha-helices and beta sheets?
secondary
Does a protein need a tertiary structure to function?
No. Disordered proteins lack a fixed 3D structure.
