chapter 3 Flashcards
what specifies protein structure
amino acid sequence
how are amino acids connected
peptide bonds
repeating seq of atoms along core of polypeptide chain
polypeptide backbone
what is attached to polypeptide backbone
side chains
limit possible bond angles in polypeptide chain
constraints
do constraints limit protein folding completely
no, long flexible chain can still fold a lot of ways
folding of protein chain determined by what
many sets of non covalent bonds
what kinds of interactions determine protein folding
h bonds, electrostatic interaction, vander waals
non polar molecules tend to cluster where in protein
inside/core
polar molecules will try to do what in protein folding
form H bonds with water
protein fold into conformation w what
Lowest energy
assist in protein folding
molecular chaperones
a single conformation is always dynamic due to what
thermal energy
temporarily exposed hydrophobic region associating with each other
protein aggregates
what prevents protein aggregates in cytoplasm
chaperones
alpha helix originally found where
alpha keratin
beta sheet originally found where
fibroin
cores of many proteins contain extensive regions of what
beta sheets
regions of alpha helix common in where
cell membranes
2 alpha helix have most of non polar chains on one side Calld what
coiled coil
wehre do bonpolar SC face in coiled coil
facing inward
structural unit that folds independently
domain
how many aa make up domain
40-350
modular unit from which larger protein constructed
domain
present in many different protein in eukaryotic cells, responds to cell signals to cause certain protein molecules to bind to each other, altering cell behavior
SH2 domain
tertiary structure of SH2 domain made of what
2 alpha helix, 1 antiparallel beta sheet
different domains often associate with different…
functions
important for cell signaling and regulation
intrinsically disordered region
what kind of protein is unlikely to help survival of a cell
unpredictable variable structure and biochemical activity
what does it take to change function of a protein completely
change of just a few atoms
large family of protein cleaving enzymes, include chymotropsin, trypsin, elastase
serien proteases
2 protein with more than 25% identity in AA seq usually share same
overall structure
humans have how many protein coding genes
20000
what techniques do we use to know about proteins struct, func
X-ray crystallography, NMR, cry-electron microscopy
what is estimated # of ways proteins fold in nature
2000
relates structures often imply what
related function
large protein have evolved through joining of pre existing domains in new combos
domain shuffling
subset of protein domains that are especially mobile
protein modules
examples of protein modules
SH2, immunoglobin, fibronectin type 3, Kringle module
each of the protein modules has what
stable core made of beta sheets
loops ideally fit for what
binding sites with other molecules
why do modules have genetic success
convenient framework for generation of new binding sites of ligands
SH2, Kringle are what
plug in type, n term and c term close together
duplicated domains with inline arrangement can be
readily linked in serious to form external structures
domain shuffling during vertebrae evolution gives rise to
many. combos of domains
human proteins and mustard weed are different how
human proteins are more complex
weak non covalent bonds allow protein to…
bind to each other to produce larger structure in cell
any region of protein surface that can interact with another molecule through sets of non covalent bonds
binding site
larger protein molecule made of 2 proteins connected by polypeptide chains
protein subunit
protein subunits together make what
quaternary structure
2 identical folded polypeptide chains form symmetrical complex of 2 protein SU
dimer
polypeptide chain folds up like ball with irregular surface
globular protein
enzymes tend to be what kind of protein
globular
simple elongated 3d structure
fibrous protein
large family of fibrous protein
alpha keratin
dimer wit long alpha helixes of each subunit forming a coiled coil
alpha keratin
kind of protein abundant outside of cell
fibrous protein
main component of ECM
fibrous protein
collagen main comp is what
3 long polypeptide chains, glycine every 3rd position
stabilize extracellular protein
covalent cross linkages
either tie together 2 amino acid in same protein or join together many polypeptide chains in large protein complex
covalent cross linkages
most common covalent cross linkage
disulfide bonds
disulfide bonds fail to form where
in cytosol
large structure built from one or a few repeating small subunits only needs what
small amount of genetic info
formation of closed structures does what
increases stability
many structures in cell are capable of what kind of assembly
self assembly
aid formation of complex structures
assembly factors
utilized for some cell func, can contribute to disease when not controlled
amyloid fibrils
amyloid fibrils made of what
self propagating beta sheets
beta strands in amyloid fibrils stacked how
fibril axis
accumulation of amyloid fibrils can do what
kill cells, damage tissue
where is especially susceptable to amyloid fibril accumulation
brain
most severe thing amyloid fibrils known to cause
neurodegenerative disease
special type of pathology, can readily spread form 1 organism to another
prion disease
useful purpose of amyloid fibrils
can be used to treat infections
attach to viruses or bacteria to mark them for destruction
antibodies
substance bound by protein
ligand
ability of protein to bind selectively based on what
non covalent bonds
region or protein associated with ligand
binding site
ligand will do what if water Is not present
form stronger H bonds
Identifying sites in protein domain that are most crucial to domains function
evolutionary tracing
what sites are most likely to be conserved
those that bind to other molecules
portion of surface of 1 protein contacts etended loop of polypeptide chain on a second protein
surface string
two rigid surface, can be very tight
surface-surface
feature of surface surface
large # of weak bonds
protein produced by immune system in response to foreign molecules
antibodies
target of antibody
antigen
y shaped molecule with 2 binding sites
antibody
enzymes that catalyze hydrolytic cleavage rxn
hydrolyses
break down nucleic acids by hydrolyzing bonds between nucleotides
nucleases
break down proteins
proteases
synthesize molecules by condensing 2 smaller molecules together
synthases
join together 2 molecules in e dependent process
ligase
catalyze rearrangement of bonds
isomerase
phosphate group addition
kinase
removal of phos group
phosphatase
first step in enzyme catalysis
substrate binding
vmax/enzyme conc
turnover number
conc of substrates that allows ten to proceed at half its max rate
km
catalyzes cutting of polysaccharide chains in cell walls
lysozyme
small organic molecules that help enzymes perform functions that are hard/impossible
coenzymes
binding of ligand on one unit can cause allosteric change on the other to help it better bind the same ligand
symmetrical protein assemblies
phosphorylation can attract what
positive ions
phosphorylation can form the part of the structure that what recognizes
binding sites of other proteins recognize
phosphorylation can disrupt what
protein protein interaction
enzyme catalyzed transfer of the terminal phosphate group of an ATP to hydroxyl group on serine, threonine, tyrosine
protein phosphorylation
what amino acids can be phosphorylated
hydroxyl group of serine, threonine, tyrosine
catalyzes reverse of protein phosphorylation
protein phosphatase
phosphate groups on proteins are continuously doing what
turning over
why do phosphate groups turn over
allows rapid switch from one state to another
first tyrosine kinase to be discovered
SRC protein
Short N term of SRC protein becomes what
covalently linked to hydrophobic fatty acid
how many peptide binding domains in SRC
2
how to turn on SRC
remove c term phosphate, bind sh3 domain
Regulatory GTP binding proteins switched on and off by what
gain and loss of phos group
monomeric GTPase, plays important role in cell signaling
ras
