Proteins Flashcards
(27 cards)
Which amino acids are in the “greasy”, hydrophobic family?
- Valine (Val, V)
- Leucine (Leu, L)
- Isoleucine (Ile, I)
- Methionine (Met, M)
Which amino acids are in the aromatic family?
- Phenylalanine (Phe, F)
- Tyrosine (Tyr, Y)
- Tryptophan (Trp, W)
Which amino acids are charged (basic)?
- Lysine (Lys, K)
- Arginine (Arg, R)
- Histidine (His, H) – not usually charged in neutral pH
What makes cysteine (Cys, C) special?
Contains a sulfhydryl (SH) group at the end of its side chain.
-SH group can form disulfide bridges between 2 cysteines to create tertiary structure.
Which amino acids have polar side chains?
- Aspargine (Asn, N)
2. Glutamine (Gln, Q)
Which amino acids have side chains ending in hydroxyl (OH) groups?
- Serine (Ser, S)
2. Threonine (Thr, T)
What do hydroxyl groups on amino acids allow?
Attaching of a phosphate group to the OH by protein kinases (enzymes).
Which amino acid has cyclic structure?
Proline (Pro, P)
Which amino acids have side chains of carboxylic acids (negatively charged)?
- Aspartate (Asp, D)
2. Glutamate (Glu, E)
How is a peptide bond formed?
Linking of amino acids to form polypeptide chain requires formation of a covalent bond between the amino group of one amino acid and the carboxyl group of another amino acid.
In the cell, formation of the bond is carried out by the ribosome
Water must be removed to form the bond and added to cleave it.
What is special about a peptide bond?
Bond has semi-planar characteristics because resonance (sharing) of electrons occurs across the peptide bond. Gives partial double bond character and prevents free rotation of the bond from occurring.
What are the 3 protein secondary structures?
Helix (alpha is most common): coiled polypeptide chain
Beta sheet (parallel and anti-parallel): extended polypeptide chain
Beta turn
What bonds form the alpha helix?
hydrogen bonds from peptide backbone (NOT from R-groups) between the CO group and the NH group.
N is always the bond donor; O is always the acceptor.
How far apart are the residues that form the bonds of the helix?
4 amino acids apart
What function do alpha helices play in the lipid bilayer?
Form parts of proteins that pass through plasma membrane.
What is a beta turn?
turns the polypeptide chain 180 degrees; a minimum of 2 amino acids are involved in the turn.
Properties of beta turns
- Occur on surfaces of proteins
- Often sites of glycolysation: where sugars are attached
- Important sites of immunological recognition (to tell if something is foreign)
- Antibodies like to look at beta turns - Somewhat predictable from the amino acid sequence
What are some protein misfolding diseases?
- Transmissible spongiform encephalopathies (Cruezfeldt-Jakob, mad cow disease, scrapie) where misfolded proteins called PRIONS are the infectious agent
- Alzheimer’s disease
Why are prions so dangerous?
Can convert additional molecules of the normal protein into prions. Prion versions of the protein also form aggregates (amyloid); amyloid aggregates disrupt normal cellular function and cause disease.
What is a protein domain?
Unit of a protein’s 3D structure that folds autonomously, is formed from secondary structural elements connected by loops, has its own hydrophobic core, and has an independent functional or structural property.
What are protein motifs?
Functional/structural units which occur within domains
What are crosslinks?
Disulfide bonds S-S; on amino acids, these require CYSTEINES.
Most common covalent cross-link in proteins b/c very hard to break, so suitable for harsher conditions outside the cell.
What does X-ray crystallography do?
Determines protein’s 3D structure.
What are the steps of X-ray crystallography?
- Must make a uniformly repeated lattice of molecules out of the protein to be studied (i.e. crystals)
- Hit crystal w/ x-rays from various angles
- Obtain a diffraction pattern
- Fourier transformation of this pattern reveals an electron density map that can be converted to an atomic map.
