Proteins Flashcards
What 6 elements are key structural components of cells?
C N O H (these make up 99% of cell)
P, S, Cl, K, Ca, Na, Mg (0.9%)
What are the 4 main classes of macromolecules of cells (monomer and polymer)? Name their different structural types if they have any.
sugar… polysaccharide… can be linear or branched
amino acids… proteins… 1 stucture
Nucleotide… nucleic acids… 2 structural types
Lipid.. NO POLYMER… many structural types
How many amino acids in an oligopeptide? What are some examples and what is their general function? Are these considered proteins?
2-20 AA
NOT A PROTEIN
neuropeptides (opiate peptides, substance P, vasopressin)
How many amino acids in a polypeptide? Are these considered proteins?
greater than or equal to 30, usually several hundred though
Considered proteins
Are proteins folded or unfolded when they are newly synthesized?
unfolded
In order to be funcitonal, proteins must be?
Folded PROPERLY
if misfolded they may not function or have abnormal function
What are the three traits that all proteins share?
- all have a stable 3D shape, known as a conformation.
- all proteins bind to at least one molecular target
- all proteins perform at least one cellular function
Describe the general structure of an amino acid, there are 4 things.
- Amino terminus
- Core alpha carbon
- Carboxy terminus
- side group (Confers properties of amino acids)
Where do the peptide bonds form between two amino acids?
Between the carboxy group of one and the amino group of another.
What are the elements of a protein backbone? What does this leave out?
H, N, C, O
This leaves out the diverse side groups
What chemical reaction forms a peptide bond? Briefly describe it.
Dehydration
By taking 1 O from the carboxy group and 2 H from the amino group the two amino acids form a peptide bond and H2O is a byproduct.
What are the 5 different classes of amino acids? Describe them.
- Aliphatic: nonpolar carbon chain
- Aromatic: Carbon RINGS
- Polar side groups: not chaged
- Positively charged
- Negatively charged
How many amino acids do humans use?
20
How many levels of protein structure are there? Very briefly describe these.
PRIMARY - the sequence of amino acids linked by peptide bonds
SECONDARY - H-bonds between either amino acids in same backbone (alpha helix), align amino acid chains (pleated sheet), and 3rd type is a random coil
TERTIARY - Side group interactions, described as either local or global.
QUANTERNARY - Proteins made up of more than 1 polypeptide chain.
In regards to the TERTIARY STRUCTURE, what is meany by local (3A) vs global (3B: overall) structure? What is a motif? What is a domain? What are the 4 we cover?
Local: This is the combination of multiple individual secondary structures into “motifs”. A domain is made up of a larger arrangement of these motifs in sections of the protein.
Overall: This is the shape of the entire protein, can be shown in ribbon form (shows secondary structure as well as tertiary motifs) or in space-filling form which just shows the overall shape.
What are amyloid fibers created from? Where and with what disease have these fibers been found in humans?
These are when proteins misfold in a way where many beta sheets are stacked on each other.
These have been found in the brains of people with alzheimers and other neurodegenerative diseases.
What are the two types of 3B structures we cover in class?
- globular - not necessarily a sphere, but roughly that shape
- fibrous - long and rod-shaped. Made from parallel cross-linked polypeptide chains
Describe the QUATERNARY protein structure. What is an example?
- present in multimeric proteins, or proteins with multiple polypeptide subunits.
- about the spatial arrangement of each subunit in the protein.
- Interactions between the polypeptide subunits are the same interactions involved in the secondary and tertiary structures. There are covalent (disulfide) and weaker noncovalent bonding present.
- antibodies are an example of a protein with a quaternary structure. They have 2 light chain and 2 heavy chain polypeptides. On the ends of each chain they have a variable regions to form the antigen binding site.
Describe the 5 different large protein assemblies that can form in the quaternary structure,
- Dimer - two polypeptide subunits linked together.
- helix - coil shaped
- ring
- Spherical shell
- hollow tube
What is the only covalent bond that occurs in protein folding?
DISULFIDE
What are the 4 noncovalent bonds involved in protein folding?
- H-bond
- electrostatic interactions (ionic bonds) - when they occur on interior they neutralize and charged residues to keep interior hydrophobic.
- Hydrophobic interactions on interior that leave polar residue at surface to interact with water
- Van der waals at very short distances.
How does a protein switch conformation?
Through reorganization of a few of its non-cavalent bonds.
Describe the Anfinsen experiment for protein folding. What does the result of this experiment tell us?
- Ribonuclease A contains strong disulfide bonds between their cysteine AA.
- Harsh chemical added (2-mercaptoethanol and urea) the disulfide bonds are broken and the protein unfolds.
- Remove the chemical and expose protein to air, observed the protein return to its native conformation including restoration of disulfide bonds.
This tells us that all necessary information for proper protein folding is contained in its primary level structure.
What are some caveats to the invitro denatured protein experiment? Why do proteins renature?
- Most proteins cant refold to their active conformation.
- If they can, it is a much slower process than what happens in the cell.
- they renature due to that conformation being their lowest energy state.
