Chapter 3: Proteins Flashcards
What do protein chaperones do? why do they need to do this?
encourage proper protein folding; allows for different conformations/independent from cytosolic concentrations
What are the two secondary structures of proteins?
alpha helices + beta sheets
How often do H bonds occur between amino acids in an alpha helix?
every <4 amino acids
About how far apart are beta sheets?
~0.7 nm
What level of protein structure do domains typically occur as?
tertiary
What is a typical domain size in AAs?
40-350 AA
This is a specific portion of a protein that has known functions (whether that be catalytic, spacing, etc.)
domain
This is a specific subset of domians that are considered to be “genetically mobile”; can be found in many other proteins performing the same function
modules
What function does the Kringle module complete?
protein-protein interactions
What function does the immunoglobulin module complete?
antigen OR other protein/moleucle recognition
What function does the fibronectin type 3 module complete?
cell-to-cell interactions
What is the common function of an SH2 domain?
recognizes P-Tyrosine
Why are non-covalent bonds much more common between protein-protein/polypeptide-polypeptide interactions?
allow protein conformational changes without being “irreversible” like covalent bonding
What regions are the complementary structure of proteins sourced from?
R-regions of amino acids
The bonds between many actin modules to form actin fibers are usually ___? why?
weaker; allow for dynamic growth/shrinkage
The bonds within a collagen fiber tend to be _____ than the bonds within actin fibers. why?
stronger; used as structural support/should not be easily altered
Why can’t disulfide bonds exist easily within the cell?
The cell environment is reductive; easily cleaved
What is critical for the correct folding of insulin?
connecting peptide
What are 2 defining characteristics of phosphates?
- very large
- very negatively charged
What are the two “pockets” found within the SH2 domain of a protein?
- specificity pocket
- p-Tyrosine pocket
What are 3 notable domains found in Src-type protein kinases?
- SH3
- SH2
- kinase domain
What are 3 notable domains found in Src-type protein kinases?
- SH3
- SH2
- kinase domain
what is the function of a kinase domain in a Src-type protein kinase
performs phosphorylating catalytic activity
What is the function of an SH3 domain in a Src-type protein kinase?
binds to the activating ligand with specificity
What is the function of an SH2 domain in a Src-type protein kinase?
recognizes p-Tyr molecules attached to other specific molecules
What happens to the kinase domain after SH3 binds to the activating ligand in Src-type kinase?
catalytic region of kinase domain becomes stabilized enough to self-phosphorylate –> activates kinase
what happens when Src kinase protein activity increases excessively?
summed apoptosis signals decrease –> induces tumorgenesis
What protein does the HIV virus produce inside an infected cell to influence SRC kinase?
NeF protein (negative regulatory factor protein)
What are the steps of what HIV does in a cell?
produces NeF –> NeF interacts w/ SH3 –> Src kinase hyperactivity –> decreased apoptosis signals –> cell reproduces virus longer
What do GTP binding proteins do after GTP hydrolysis takes place?
GDP removed –> replaced with new GTP
What does the addition of ATP to motor proteins (kinesin) do to their activity?
adds directionality to natural movement
What is the name of the SARS-Cov-2 spike protein?
Trimeric S protein
What is the trimeric S protein?
a homodimer that has up (active) and down (inactive) states
The up conformation of the trimeric S protein allows binding to which human receptor?
ACE2 PD domain
