chapter 3 Flashcards
what is the sequence of protein structure
primary –> secondary –> tertiary –> quaternary –> function or supramolecule (large scale assembly)
what are some of the functions that a quaternary protein can perform
regulation (giving signal to turn on/off), structure, movement (in/out of the cell+chromosome separation), catalysis, transport, signaling
where does peptide bond formation happen
in the cytoplasm
how is a peptide bond formed
amino acid + amino acid = peptide bond + water (water is released in the process)
what is the primary structure of a protein
the linear sequence of amino acids linked together by peptide bonds (methionine is always first but it is VERY often cleaved)
what are the two common secondary structures that proteins adopt
alpha helix and beta sheets
what is the backbone of an alpha helix made out of
polypeptides (CCN - peptide bond - CCN, etc)
how does an alpha helix form
the polypeptide backbone is folded into a spiral that is held in place by hydrogen bonds between BACKBONE oxygen and hydrogen atoms
in alpha helix, R groups determine what
HOW spiral takes place (hydrophobic/hydrophilic quality) but they are NOT actively involved in the structure (bonds between R groups do not occur/do not form the helix)
how does a beta sheet form
hydrogen bonds form between the carbonyl oxygen atoms of each residue(amino acid) in one B strand and the amide hydrogen atom of a residue(amino acid) in a separate, BUT ADJACENT, B strand
what are the two structures of beta sheets
anti-parallel and parallel
what is the structure of a beta sheet turn
four residues (amino acids) reverse the direction of the chain
what are the two common amino acids in beta sheet turns
glycine, proline
what is the oil drop effect in protein folding
proteins will fold so hydrophilic side chains will be outwards to cell (bc the cell is an aqueous environment) and hydrophobic side chains will go to the core away from the cell
NOTE: membrane proteins and channel proteins will be vice versa bc the inside of these are hydrophobic so the hydrophobic side chains will be outwards
what is the hand in glove fit in the quaternary structure of a protein
molecular complementarity between the molecule in question and the site to which it binds (epitope)
how are the light chains and heavy chains of an antibody linked together
by disulfide bonds
what are structural motifs of secondary structure
regular combinations of secondary structures usually with a specific type of function
NOTE: can be encoded by a highly conserved sequence motif
what are three common motifs
coiled-coil motif, EFhand/helix-loop motif, Zinc-finger motif
what is a motif (for dummies)
a combination of secondary structures (alpha helix, beta sheets) that is regularly observed and used by the cell when making proteins that is associated with a particular function
proteins will take on certain motifs when being created because the motifs are associated with a certain function
basic: small regions of protein sequences that are shared between different proteins
NOTE: secondary structure only
what is a domain (for dummies)
domains are distinct functional and/or structural units in a protein
usually they are responsible for a particular function or interaction, contributing to the overall role of a protein
NOTE: domains can be made up of motifs
what is EGF
a small, soluble peptide hormone that binds to cells and promotes their cell division
EGF domains
EGF precursor: epidermal growth factor precursor - generated by cleavage and generates multiple EFGs
Neu: EGF domain + other domains
TPA: tissue plasminogen activator - EGF domain + other domains
NOTE: ~75% of eukaryotic proteins have multiple structural domains
what are supramolecule complexes
can contain tens ot hundreds of polypeptide chains and sometimes other biopolymers such as nucleic acids
what is an example of a supramolecule
transcription initiation complex
what are the two things that assist in protein folding
- molecular chaperone
- chaperonins
what is molecular chaperone-mediated protein folding
molecular chaperones bind to a short segment of a protein substrate and stabilize unfolded or partly folded proteins, preventing aggregation or degradation
what is chaperonin-mediated protein folding
chaperonins are folding chambers into which all or part of an unfolded protein can be found in an appropriate environment, giving it time to fold properly
what is molecular chaperone-mediated protein folding common
during stress and mitochondrial functions
commonly functioning during normal processes
