Exam 1: Ch 3 Flashcards
conformation
closely related 3-D shape a protein folds into
what determines a protein’s function
its conformation combined with the chemical properties of its aa side chains
structural protein
determine the shapes of cells and their extracellular environments
guide wires or rails to direct intracellular movement of molecules or organelles
how are structural proteins formed
assembly of multiple protein subunits into large structures
scaffold proteins
bring other proteins together in ordered arrays to perform specific functions
enzymes
proteins that catalyze chemical reactions without being altered or consumed
membrane transport proteins
permit the flow of ions & molecules across the cell’s membrane
called integrated membrane proteins (channels/pumps)
regulatory proteins
act as signals, sensors and switches to control activities of cells by altering the functions of other proteins and genes
regulatory proteins include _______ proteins
signaling
signaling proteins
hormones and cell-surface receptors that transmit extracellular signals to the cell interior
motor proteins
move other proteins, organelles, cells, or even whole organisms
protenome
entire protein complement of an organism
humans have 20,000-23,000 genes that code for proteins
what is a protein’s 3-D structure determined by
aa sequence (primary structure) and intramolecular noncovalent interactions
peptide bond
planar bond formed between the amino group of one aa and the carboxyl group of another
dehydration rxn to form
hydrolysis to break
protein
a polypeptide that has a well-defined 3D structure and function
how is size of a protein expressed
daltons (1 AMU) or MW
random coil
a type of secondary structure that is highly flexible and has no fixed 3D structure
tertiary structure
overall conformation of a polypeptide chain
the 3D arrangement of aa residues stabilized by hydrophobic interactions and h-bonds
disulfide bonds
formed by cysteine residues
covalently link regions of proteins reducing flexibility
globular protein
water soluble, compact spheroidal structures made of a mix of secondary structures
fibrous proteins
large, elongated and stiff molecules with repeat units
usually play a structural role or participate in cellular movements
ex. collagen
structural motif
combination of 2 or more 2ndary structures that form a distinct 3D structure with a specific function
ex. coiled coil (heptad repeat) - transcription factor
leucine zipper
a structural motif that looks like a zipper made of leucine
protein domains
distinct regions of protein structure
structural, functional, or topological
functional domain
region of a protein that exhibits a particular activity characteristic
ex. some region of a protein is specifically responsible for its catalytic activity
protease
enzyme that cleaves peptide bonds
structural domain
a region ~40 aa or more that represents a single, stable and distinct structure
usually has one or more 2ndary structures that can fold independently from rest of protein
topological domain
region of protein defined by its location in the protein
ex. integrated membrane proteins have an extracellular domain, membrane spanning domain, and cytoplasmic domain
protein homolog
proteins that have a common ancestor
determined by sequence similarity
native state
most stable folded form of the protein that permits normal function
conformation with lowest delta G
denaturation
process by which a protein’s structure is disrupted
chaperones
a set of protein that facilitate proper folding of proteins
use ATP binding, hydrolysis, and exchange of ATP for ADP to induce conformational changes to assist protein folding
ATP also enhances binding of protein substrates
functions of chaperones
fold newly proteins into functional conformations
refold misfolded or unfolded proteins
disassemble toxic protein aggregates
assemble or dismantle large multiprotein complexes
molecular chaperone
bind to a short segment of protein substrate and stabilize unfolded or partly folded states
prevents these proteins from aggregating and being degraded
chaperonins
form small folding chambers where all or part of an unfolded protein is gathered, giving it time and the appropriate environment to fold correctly
alzheimers
aggregation of improperly folded proteins into plaques in the brain
affinity
tightness or strength of a protein binding its ligand
expressed by Kd (dissociation constant)
higher affinity = lower Kd
how does a catalyst work
lowers Ea by lowering energy of the transition state (stabilizes it)
active site regions
substrate-binding site: recognizes (specificity) and binds substrate
catalytic site: carries out chemical reaction
michaelis menten kinetics
rate (kinetics) of enzyme is proportional to substrate concentration at low [ ]s, but reaches Vmax
at Vmax the rate is directly proportional to how much enzyme is present in rxn mixture (all enzyme sites occupied)
michaelis constant Km
Km = substrate concentration required for the reaction to occur at 1/2 Vmax
Low km means higher affinity b/c less substrate needed to get enzyme to 1/2 vmax
turnover number
max number of substrate molecules converted to product at a single enzyme active site per second
metabolic coupling
enzymes participating in a common metabolic pathway are sometimes physically associated with each other
products of one rxn are passed to next enzyme without leaving the complex
3 ways proteins can be regulated
cells inc or dec steady-state level of the protein by altering its rate of synthesis, degradation or both
cells change the intrinsic activity distinctly from the amount of the protein
change in location or [ ] within the cell of the protein itself, the protein’s substrate, or a molecule required for the protein’s activity
rate of protein synthesis determined by…
rate of transcription, steady state of mRNA in the cell, rate of translation
protein degredation
chaperones
lysosomes
cytoplasmic
proteasomes
large protein degrading macromolecular machines
influence cell cycle, transcription, DNA repair, apoptosis, recognition and response to foreign organisms, removal of misfolded proteins
proteasome structure
30,000 in a mammalian cell
~50 protein subunits
cylindrical barrel like core with caps
partial proteasome inhibition for short intervals has been introduced as an approach to…
cancer chemotherapy
cells die by apoptosis, can target cancer cells and not normal cells in multiple myeloma
how do cells mark proteins that should be degraded?
covalently attaching them to multiple copies of the 76 residue polypeptide ubiquitin
3 steps of ubiquitination
activation of ubiquitin activating enzyme by adding ubiquitin (uses ATP)
transfer of ubiquitin molecule to cysteine in ubiquitin-conjugating enzyme
form covalent bond btw lysine of target protein and glycine 76 of ubiquitin by ubiquitin-protein ligase
overall picture of ubiquitination
target protein gets 4 ubiquitins attached, which signals degradation in a proteasome
Dubs
enzymes that deubiquitinate targeted proteins in the proteasome
cyclins
proteins that control the cell cycle
after phosphorylation, become targets of ubiquitination
allostery
any change to a protein’s tertiary or quaternary structure that is induced by noncovalent binding of a ligand
do allosteric proteins have more than one binding site?
yes
at least 1 for the allosteric effector
at least 1 for the other molecules the protein interacts with
what happens when a ligand binds an allosteric protein?
conformation change, which affects the activity of a different binding site
allosteric effector
the ligand that induces a conformational change in an allosteric protein
is allosteric change in activity positive or negative?
it can be either
negative allostery
often found in biochemical pathways
when end product builds up, it reduces the activity of the enzyme to prevent excess buildup of product (feedback inhibition)
cooperativity
influence that ligand binding has on the other subunits of the protein
amplifies sensitivity of a system to [ ] changes in its ligands (imparts a selective evolutionary advantage)
ex. hemoglobin
do michaelis menten proteins exhibit cooperativity?
no
importance of Ca2+
concentration in cell’s cytosol is low, extracellular higher
cytosolic [ ] can increase 100 fold by channels, which is sensed by binding proteins
binding proteins alter cellular behavior by switching other proteins on or off
calmodulin
Ca2+ binding EF hand protein (monomeric or multimeric)
binding Ca2+ causes a conformational change that turns activity of other proteins on or off (switch protein)
GTPase superfamily
group of intracellular switch proteins that hydrolyze GTP to GDP
ex. Ras or G alpha
functions of GTPase superfamily
bind to cell membrane for cell signaling
cell proliferation & differentiation
protein synthesis, transport
2 forms of GTPases
1) active when bound to GTP
2) inactive when bound to GDP
covalent modification
phosphorylation (kinase) and dephosphorylation (phosphatase)
changes a protein’s charge, which can induce conformational change
proteolytic cleavage activation/deactivation
irreversible mechanism for protein regulation
zymogen
inactive precursor enzyme
cleaved via proteolytic cleavage to become active
ex. trypsinogen cleaved to trypsin, which can activate other zymogens
ex. clotting cascade
protein self-splicing
rate form of proteolytic processing in bacteria and some eukaryotes
middle portion of polypeptide removed, and ends rejoined
ex. hedgehog: membrane bound signal that does this
compartmentation
separation allows competing rxns to take place simultaneously in different parts of the cell
allows control of substrate delivery and product exiting
