Chapter 6.1 and 6.2 Flashcards
what are the 5 major protein classes?
- enzymes
- structural
- cell signalling
- genomic caretaker
- transport
what do enzymes do?
catalyze biochemical reactions
how do enzymes catalyze biochemical reactions? (3)
- lower activation energy
- increase rate of product formation
- involved in energy conversion pathways
do enzymes alter the equilibrium concentration of products and reactants?
HELL NO
how do enzymes work?
mostly as complexes of 2-60 subunits
what are eznymes responsible for?
the synthesis and degradation of macromolecules as they convert one to another
where are enzymes found?
often found in the cytoplasm
give an example of an enzyme
malate dehydrogenase
what do structure proteins do?
maintain cell structure and shape
what do structural proteins provide?
a framework for cells, tissue, and organs
what are the most abundant type of proteins?
structural proteins
what do structural protein often form?
polymers (often fibrous)
where are structural proteins found
through membranes
what is a type of structural protein responsible for cell shape, cell migration, and cell signaling?
cytoskeletal proteins
give 3 examples of cytoskeletal proteins
- actin
- tubulin
- collagen
where is actin abundant?
in animal cells
where is actin found?
in muscle
what do actin subunits form?
self-assemble from actin monomers to form long polymers called thin filaments
what are the 2 forms of actin?
- g-actin
- f-actin
describe g-actin
the inactive, globular, monomer form of actin
describe f-actin
the active, filament, polymer form of actin
where is tubulin abundant?
in animal cells
what do tubulin monomers form?
seld-assemble to form polymers called microtubules
what do microtubules do?
act as roads for movement of organelles and chromosomes during cell division
what is the major structural protein in animals?
collagen
what is collagen a primary component of?
connective tissue
what does collagen do? (3)
- provides skin elasticity
- bolsters joint health
- promotes bone health
describe collagen structure (4)
- every 3rd residue is glycine
- contains many proline and hydroxyprolines
- repetitive motif
- special left-handed helix secondary structure
describe the repetitive motif of collagen
either Gly-Pro-X or Gly-X-Hyp (X is any other amino acid)
what do 3 collagen chains form?
a triple helix structure
where are the glycine side chains in the triple helix structure and why?
in the middel! they have no side chain therefore no hinderance in any way (steric or electrical)
what would happen if you replaced glycine in collagen with any other amino acid?
the triple helix would break
how are the triple helices of collagen stabilized?
through hydrogen bonding between the backbone N on glycine hydrogen bonding to the backbone carbonyls of the adjacent residues
what do cell signaling proteins do?
transmit extracellular and intracellular signals
what do signaling protein exist as?
molecular switches, with one “on” active conformation and one “off” inactive conformation
what are the 3 types of cell signaling proteins and where are they found?
- membrane receptors in membranes
- intracellular signaling proteins in the cytoplasm
- nuclear receptors in the nucleus
give 3 examples of membrane receptos cell signaling proteins
- g-couple protein receptors
- receptor tyrosine kinases
- growth hormone receptors
describe the general structure of a cell signaling protein (3)
- extracellular component receives signal
- transmembrane/membrane component transmits the signal
- intracellular component does the thing with the signal
how do intracellular proteins exist?
as molecular switches; change conformation in response to incoming signals
what is receptor activation for intracellular proteins?
when they change conformation in response to incoming signals, since they exist as molecular switches
what are 2 examples of intracellular signaling proteins?
- adenylate cyclase
- protein kinases
what do protein kinases do? how ? (2)
reversibly phosphorylate proteins at Ser and Thr
1. use ATP
2. activate downstream target proteins in response to upstream receptor activation
what do nuclear receptors function as?
transcription factors
what do nuclear receptors, acting as transcription factors, do?
regulate gene expression in response to ligand binding
where are nuclear receptor proteins found?
in the nucleus
give an example of a nuclear receptor protein
thryoid receptor
what is the implication of most ligands for nuclear receptors being hormones?
they are susceptible to imbalances and disorders
what do genomic caretaker proteins do?
maintain the integrity and accessibility of genomic info
where are genomic caretaker proteins found?
in the nucleus
give 4 specific functions of genomic caretaker proteins
- DNA replication
- DNA repair
- DNA recombination
- gene expression
give 4 examples of genomic caretaker proteins and then say generally what they make up
- DNA polymerase
- DNA ligase
- DNA helicase
- topoisomerase
make up the replication fork
what do transport proteins do?
facilitate movement of molecules within and between cells
where are transport proteins abundant?
in the plasma membrane
what do transport proteins allow?
permit polar and charged molecules to enter and exit the cell
what are the 2 membrane-bound transport protein classes?
- passive transporters
- active transporters
what do passive transport proteins do?
allow molecules to move across a membrane DOWN a concentration gradient
describe passive transport proteins’ energy relationship
energy independent
give two examples of passive transport proteins
- porins
- ion channels
what are porins?
specific holes; allow easy access but only for desired molecules
describe active transport proteins’ energy relationship
require energy
why do active transport proteins require energy?
the energy causes a conformational change that opens or closes the channel
what do active transport proteins do?
pump small molecules UP a concentration gradient
describe where the energy for pirmary and secondary active transport proteins comes from
- primary active transport proteins do ATP hydrolysis (ATP dependent)
- secondary active transport proteins couple with primary and utilize the ionic gradient formed by the primary proteins
give 2 examples of globular transport proteins
- myoglobin
- hemoglobin
is myoglobin a monomer or a polymer?
monomer
describe the size of myoglobin
small and compact; 153 amino acids
where is myoglobin found?
in muscle tissue
what is the function of myoglobin?
oxygen storage; reversibly binds O2
what is myoglobin composed of, secondary structurally?
8 alpha helices (A-H)
what does myoglobin contain?
a prosthetic heme group (added after translation, like a prosthetic limb added after birth)
describe the structure of heme
porphyrin ring system
where is the heme group in myoglobin?
placed in a hydrophobic pocket between helices E and F
what is at the center of the heme group?
an iron atom
what is the role of the iron atom at the center of the heme group?
coordinate covalent bonds with electronegative atoms
what are the 2 forms of the iron atom at the center of the heme group? which one do you want and why?
can be Fe2+ (ferrous) or Fe3+ (ferric); want Fe2+ because only ferrous REVERSIBLY binds O2 (Fe3+ irreversibly binds=bad news bears)
how many coordination sites does Fe2+ at center of heme group have? what goes there?
6
4 bonds to pyrrole N’s
1 goes to the proximal histidine (His F8)
1 binds to O2
what does the distal histidine of the heme group binds to? (this is His E7)
O2
contrast the distal and proximal histidines of the heme group of myoglobin and how they bind to iron
proximal histidine directly binds to iron
distal histidine binds to the O2 bound to the iron (indirect)
what does the heme-O2-heme complex do?
oxidized Fe2+ to Fe3+ and causes nonreversible O2 binding
what does the proximal histidine do for the heme?
keeps the heme coordinated to the protein
what does the distal histidine do for the the heme? how?
prevents other hemes from binding Fe2+ to O2 becuase its steric hindrance disallows a second heme from entering the O2 binding site
what is the equation for the binding of any ligan (L) to any protein (P)?
P + L double arrow PL
what is Kd?
the dissociation constant of ligands and proteins
give the equation for Kd
[P]][L]/[PL]
what are the units of Kd?
Molarity
what is Ka?
the association constant of proteins and ligands
give the equation for Ka
[PL]/[P][L]
how is Ka related to binding affinity?
Ka is directly related to binding affinity
what does a higher or lower Ka mean?
higher Ka means stronger binding, lower Ka means weaker binding
how is Kd related to binding affinity?
Kd is inversely related to binding affinity
what does a higher or lower Kd mean?
higher Kd means weaker binding and lower Kd means stronger binding
how is fraction saturation (theta) related to Kd?
fractional saturation is inversely related to Kd
what is the equation for fractional saturation?
[L]/[L]+Kd
how is ligand concentration related to fractional saturation?
the higher concentration of ligand [L], the higher the fractional saturation because there are more ligands to bind (saturate)
what is the standard value of fractional saturation used to compare binding affinities between proteins? why?
0.5; past that it’s hard to measure anything about the protein
what will a stronger binding curve look like? describe L and Kd
will curve left, with a lower Kd and less [L] needed to reach half saturation
what will a weaker binding curve look like? describe L and Kd
will curve right with a higher Kd and with more [L] needed to reach half saturation
how do you calculate fractional saturation in terms of proteins and ligands
occupied binding sites/ total binding sites, so [PL]/[PL]+[P]
for the equation Mb + O2 double arrow MbO2, how would you calculate fractional saturation?
[MbO2]/[MbO2]+[Mb]
what is the shape of the myoglobin binding curve?
hyperbolic
what is Kd on the myoglobin saturation curve? why?
the concentration of O2 when half of Mb bind to O2, but is hard to measure the concentration of gases, so we use partial pressure instead (on all gases!), so Kd=P50
where is hemoglobin found?
in red blood cells
describe the structure of hemoglobin
- a heterotetramer
- secondary and tertiary structures similar to myoglobin
- quarternary structure is 2 alpha chains and 2 beta chains
- each subunit has a heme group
describe the O2 capacity of hemoglobin compared to myoglobin and why?
hemoglobin has 4x the O2 capacity of myglobin because it has 4 subunits instead of 1
describe the shape of hemoglobin’s binding curve
sigmoidal
what does a sigmoidal binding shape indicate? describe
cooperative binding: binding of one ligan to one site increase binding affinity for another ligand at another site; also works in reverse as release of one ligand at one site decreases binding affinity for another ligand at another site
why doesn’t myoglobin have cooperative binding?
it only has one binding site, no one to cooperate with
why does hemoglobin have a lower fractional saturation in tissues than myoglobin?
so that it is able to drop its O2 off easier thaan myoglobin
what is the Hill coefficient?
a measure of cooperativity, n
what do the signs of the Hill coefficient, n, mean?
n=1: no cooperativity
n>1: positive cooperativity (easier for next ligand to bindor dissociate)
n<1: negative cooperativity (harder for next)
what are the 2 states of hemoglobin?
- deoxygenated
- oxygenated
what does the proximal histidine do to the Fe of hemoglobin when it is deoxygenated?
pulls Fe up and out of plane of the rest of the ring, resulting in a domed/puckered conformation
what does the bound oxygen to the Fe do to the shape of hemoglobin when it is oxygenated?
pulls the ring back to planar conformation
describe dexoygenated hemoglobin (3)
- No bound O2
- heme ring is not planar, in T or Tense conformation
- Fe lies approx 0.6A out of plane
describe oxygenated hemoglobin (3)
- O2 is bound
- heme ring is planar
- in R or Relaxed conformation
describe the conformational switch between deoxygenated and oxygenated hemoglobin
- O2 binding pulls Fe into plane of heme
- His F8 is pulled with Fe
- entire F helix moves toward the heme
what is the concept of allostery?
conformational switches underlie cooperativity
what does allostery do?
transmits changes in one subunit across the interface to the next subunit
what are the 2 models to explain allostery?
- concerted
- sequential
describe the concerted model to explain allostery (3)
- protein found in either ALL T or ALL R conformations
- binding to a single subunit helps stabilize the R state
- the whole molecule is affected at the same time at different levels of probability
describe the sequential model to explain allostery (3)
- protein found in a mix of T and R
- binding doesn’t convert the entire complex to the R state, just alters the affinity of ADJACENT subunits
- each neighbor is affected by the previous switch
describe positive allosteric effectors for hemoglobin (2)
increase Hb affinity for O2, shift equilibrium to the R state
what is the positive allosteric effector?
O2
describe negative allosteric effectors for hemoglobin (2)
decrease Hb affinity for O2, shift equilibrium toward the T state
what are the 3 negative allosteric effectors for hemoglobin?
- 2,3-BPG
- H+ (protons/lower pH)
- CO2
what does BPG stand for?
bisphosphoglycerate
how does 2,3-BPG work as a negative allosteric effector for Hb?
binds deoxygenated hemoglobin (T state) and stabilizes that T state
what would happen without 2,3-BPG?
Hb would bind O2 too tightly and not drop it off in tissues
describe fetal Hb binding affinity for BPG
fetal Hb binds BPG poorly, so fetal Hb binds O2 super strong to make sure gets O2 from mom
describe the Bohr effect decreasing binding affinity of Hb for O2
as pH drops, the binding affinity of Hb for O2 also drops because H+ and CO2 weaking binding affinit
describe how H+ and CO2 weaked Hb binding affinity
- residues on Hb can be protonated, which causes conformational changes to stabilize the T state
- increased CO2 increase H+ via carbonic anhydrase
- CO2 bunds to Hb at the N terminus, which stabilize the T state and produces H+
