| 7420032889 | keratin:
-type of protein
-structure
-stabilization
-2 other characteristices | -fibrous protein
-Amino acids form a helix, 2 alpha helices intertwine forming a coiled-coil. Then 2 coiled coils twist together to form a protofilament, and protofilaments combine to form protofibrils
-stabilized via disulfide bonds (high degree of cysteine residues)
-composed of many hydrophobic residues
-high tensile strength | | 0 |
| 7420032890 | hair perms and straightening is... | a reduction of disulfide bonds that make up keratin | | 1 |
| 7420032891 | collagen molecules/Gly-X-Y | collagen molecules are made of 3 interwound alpha helices (each alpha helix has 3 residues per turn and is therefore tighter than average)
the alpha helices are composed of repeating tripeptides of Gly-X-Y
gly=glycine
X=proline (proline contains kinks which provide stability and tightness to the helices)
Y=hyPro (hydroxylated proline) | | 2 |
| 7420032892 | collagen fibril | composed of many (triple helical) collagen molecules that are covalently bound via cross links (providing strength and stability)
via a post-translational modification, a cross link forms between 2 lysine residues of separate triple helical collagen molecules, one of which is hydroxylated | | 3 |
| 7420032893 | basis of rigid and brittle CT during aging | as you age, there is an increase in the amount of cross-linking in collagen fibrils, leading to rigid and brittle CT | | 4 |
| 7420032894 | why does one need vitamin C (ascorbic acid) for collagen? | -Prolyl 4-hydroxylase catalyzes 2 separate reactions, one of which hydroxylates Pro to form hyPro (Y of GlyXY; forces Pro into exo conformation to form tight turns of collagen triple helices) (this rxn occurs via oxidative decarboxylation of alpha ketoglutarate to form CO2 and succinate)
-Fe must be in its 2+ oxidation state on prolyl 4-hydroxylase in order for it to function properly
-prolyl 4-hydroxylase also catalyses a separate oxidative decarboxylation of alpha ketogluterate (not coupled to pro hydroxlation); this rxn requires ascorbate to keep Fe in prolyl 4-hydroxylase in Fe2+ oxidation state to restore the enzyme's activity
-without ascorbate, Fe becomes oxidized to Fe3+, therefore prolyl 4-hydroxylase cannot catalyze the hydroxylation of proline, and colllagen is therefore unable to form tight turns | | 5 |
| 7420032895 | fibrin structure | a fibrous protein that consists of layers of antiparallel beta sheets rich in Ala and Gly residues (which are small and hydrophobic)
-does not stretch b/c phi and psi angles in beta sheets are already fully extended
-flexible due to numerous weak interactions (such as hydrophobic and H bonds) | | 6 |
| 7420032896 | globular proteins: folding | -globular proteins contain segments of polypeptide chain folded back on each other, making globular proteins compact and complex
-this folding leads to the structural diversity necessary for proteins' wide array of functions | | 7 |
| 7420032897 | 3D/tertiary structure | assemblage of polypeptide segments in the alpha helical and beta conformations, linked by connecting segments: distinguish fibrous from globular proteins | | 8 |
| 7420032898 | difference b/t globular and fibrous proteins | differ mainly in their 3D structures
-fibrous proteins have simple repeating elements of secondary structure, are spacious, and serve mainly structural roles
-globular proteins' 3D structure is more complicated, often containing several types of secondary structure in the same polypeptide chain, have folding and are thus more compact and structurally diverse, and serve a variety of functions | | 9 |
| 7420032899 | free energy in proteins: what is it? what is biggest contributor? | protein stability is the difference in free energy b/t the folded and unfolded state of proteins (more free energy in folded state than unfolded)
-hydrophobic effect (burial of hydrophobic a.a.'s to exclude water) is the primary contributor to the free energy
-protein folding is hard to predict since folded protein is only marginally stable | | 10 |
| 7420032900 | forces that provide protein stability & how they contribute to free energy | -hydrophobic effect (primary source of free energy and thus stability)
-ionic interactions
-H bonds: important for conformation of protein (secondary structure) but do not contribute much free energy b/c an H bond formed within the protein is equivalent to one formed in water
-Van der Waals (difficult to quantify free energy difference b/t folded and unfolded state)
-disulfide bridges | | 11 |
| 7420032901 | Anfinsen's experiment | =denaturation/renaturation of ribonuclease
-didn't know structure of ribonuclease, but knew that it cleaves RNA
-purified and measured its activity: if the protein cut RNA he deduced that it was folded
-added mercaptoethanol to reduce disulfide bonds and urea to break hydrophobic interactions, thus unfolding ribonuclease; then measured its activity and it no longer diced RNA
-used dialysis (to remove mercaptoethanol and urea), and the ribonuclease worked again | | 12 |
| 7420032902 | Anfinsen's conclusion, and why is this not completely true today | amino acid sequence determines 3D structure (a.a. sequence contains all the info required to fold the chain into its native, 3D structure)
however, even though all proteins contain the info to fold into their native structure, most require more assistance (i.e. chaperone proteins) | | 13 |
| 7420032903 | proteostasis | Continual maintenance of the necessary set of active cellular proteins (proteome). Requires regulation of synthesis, folding, refolding, and degradation (of irreversibly unfolded proteins) (proteasome) | | 14 |
| 7420032904 | proteostasis processes | 1. proteins synthesized on the ribosome and must fold into their native conformations
2. multiple pathways contribute to protein folding, many of which require chaperones
--chaperones also contribute to refolding of proteins that are partially/transiently unfolded
3. proteins that are irreversibly unfolded are subject to sequesteration and degradation of several other pathways, with the aid of proteasomes |  | 15 |
| 7420032905 | proteasome | a supramolecular assembly of enzymatic complexes that function in the degredation of damaged or unneeded cellular proteins | | 16 |
| 7420032906 | proteome | the entire set of proteins expressed by a given cell or group of cells; maintained by proteostasis | | 17 |
| 7420032907 | motif (+ examples) | AKA fold or supersecondary structure
recognizable folding pattern involving 2 or more elements of secondary structure and the connections between them
examples include β α β loop and β barrel | | 18 |
| 7420032908 | protein aggregates | partially unfolded proteins and protein folding intermediates that escape the quality control activities of chaperones and degradative pathways may become sticky (due to exposed hydrophobic surfaces), forming both disordered aggregates and amyloid-like aggregates that contribute to diseases and aging | | 19 |
| 7420032909 | chaperone proteins | proteins that interact w/ partially folded or improperly folded polypeptides, facilitating the correct folding pathways or providing microenvironments in which folding can properly occur
2 types=Hsp and chaperonins | | 20 |
| 7420032910 | Hsp70 | bind to regions of unfolded polypeptides that are rich in hydrophobic residues, thus breaking up aggregates or preventing new ones from forming; bind to and release polypeptides in a cycle that uses energy from ATP hydrolysis and several other proteins | | 21 |
| 7420032911 | amyloidosis | set of diseases caused by *(normally soluble)* proteins that have been secreted by the cell in a *misfolded* state and converted into an *insoluble extracellular amyloid fibrils*
-examples: Huntington's, type 2 DM, Alz, some CA | | 22 |
| 7420032912 | formation of amyloid fibrils | proteins have a concentration of hydrophobic amino acids in a core region of beta sheets; core folds into a β sheet before the rest of the protein folds correctly; sheets from 2 or more incompletely folded proteins begin forming an amyloid fibril, which grows in the extracellular space; other parts of the protein then misfold, remaining on the outside of the β sheet core in the growing fibril |  | 23 |
| 7420032913 | prion diseases (+ examples) | (proteinaceous infection)
diseases that infect animal populations and spread through exposure to misfolded proteins; once exposed, the misfolded proteins recruit other proteins to become misfolded, forming plaques in the brain and eventually death
ex: scrapie (in sheep), mad cow disease | | 24 |
| 7420032914 | 2 ways to determine protein structure: advantageous and disadvantages | X-ray crystallography: allows you to see the density of atoms, thus determining their spatial arrangement (limitation is the protein must be crystallized first, which can cause slight changes in their 3D shape)
2D NMR: protein does not have to be crystallized first, but this method does not have as good of resolution | | 25 |
| 7420032915 | Ka and Kd: equations and what do they tell you? | *low Kd/high Ka means the ligand has a high affinity for/binds well to the protein*
P+L⇌PL: Ka=[PL]/[P][L], is the association constant and Kd=1/Ka, is the dissociation constant
these are measures of the affinity of a ligand for a protein/how well a ligand binds to a protein | | 26 |
| 7420032916 | what is θ? what is its relationship to [L]? | θ=a fraction of how much ligand is bound to the protein (value ranges from 0 to one)=binding sites on a protein occupied divided by total # of binding sites
θ is a hyperbolic function of [L], meaning that as [L] increases, the fraction of ligand binding sites occupied approaches saturation | | 27 |
| 7420032917 | relationship of Kd to θ and [L]: binding of a ligand to a protein | Kd is the concentration of ligand at which half of the ligand binding sites on a protein are occupied ([L] when θ=1/2) |  | 28 |
| 7420032918 | heme: definition | a prosthetic group that is covalently attached to myoglobin and hemoglobin; contains iron in order for myoglobin and hemoglobin to perform their oxygen binding functions | | 29 |
| 7420032919 | heme: structure | central Fe2+ atom which has 6 coordination bonds: 4 of which are bonded to the 4 N atoms that are part of the flat protoporphyrin IX ring, and 2 that are perpendicular to protoporphyrin IX, which bind the proximal His and O2 |  | 30 |
| 7420032920 | proximal His: what is it's purpose? | in order to keep heme's central iron in its Fe2+ state (and not Fe3+), one of its coordination bonds is bound to the N of a histidine residue on the protein heme is bound to |  | 31 |
| 7420032921 | myoglobin | A globular protein that has the ability to bind oxygen and functions as oxygen storage. Myoglobin is found in the muscle tissues and helps to store oxygen in the muscle for use in aerobic respiration | | 32 |
| 7420032922 | heme bound to myoglobin (or Hb) | Fe2+ of heme is bound to the proximal His on myoglobin (or Hb); also bound to O2, which is bound to the distal His on myoglobin (or Hb)
O2 is bound at a 120 degree angle to heme and is stabilized via a H bond to the distal His
heme is found deep w/i a pocket of Mb or Hb |  | 33 |
| 7420032923 | binding of O2 vs CO to heme | CO binds better to free heme b/c it binds with the CO axis perpendicular to the plane of the porphyrin ring while O2 binds to heme with the O2 axis at a 120 deg angle; however, this angle is favored by heme bound to myoglobin b/c of the distal His
when CO binds to heme in myoglobin it is forced to adopt a slight angle b/c of sterics; this weakens the binding of CO to heme myoglobin
CO still binds better, but b/c there is such little concentration of CO in our bodies compared to O2, this is not an issue | | 34 |
| 7420032924 | O2 binding curve for Mb | -fraction of O2 bound to myoglobin as a function of concentration of O2 (partial pressure of O2)
-is a hyperbolic function: O2 binds very rapidly and reaches saturation quickly
-Kd is extremely small, therefore O2 has a very high affinity for Mb |  | 35 |
| 7420032925 | why is Mb a good storer of O2 but a poor transporter of O2 | -Kd is very small for O2: O2 has a high affinity for Mb; it rapidly binds and quickly saturates Mb binding sites
-concentration of O2 in lungs is 13 kPa and in tissues it is 4 kPa; using equation, we find that the saturation of Mb in the lungs would be 98% and in the tissues it would be 94%
-the ability to transfer O2 from lungs to tissues is proportional to the difference in binding b/t 2 locations, meaning O2 would be a poor transporter of O2 b/c it binds too tightly
-tissues would be starved for O2 | | 36 |
| 7420032926 | % saturation of Hb in arterial blood vs venous blood | in arterial blood, Hb is 96% saturated vs in venous blood it is 64% saturated, meaning Hb releases app 30% O2 in tissues | | 37 |
| 7420032927 | similarities between myoglobin and hemoglobin structures | each subunit of Hb is similar to Mb: similar 3D structures, similar alpha helices, similar binding for heme w/ the proximal and distal His | | 38 |
| 7420032928 | interactions stabilizing the 4 subunits of Hb | hydrophobic interactions stabilize everywhere, H bonds, and ion pairs (salt bridges)
more ionic interactions stabilizing α1β1 (and α2β2) along the horizontal axis than α1β2 (α2β1) along the vertical axis
if Hb is subjected to mild conditions, α1β1 (and α2β2) remain intact while α1β2 (α2β1) break: this led to the discovery of the T and R states of Hb |  | 39 |
| 7420032929 | difference in structures b/t Hb T and R states and what occurs during transition | T state is stabilized by more ionic interactions, esp along the α1β1 (α2β2) axes compared to the R state
T-->R:
when O2 binds to heme (in a subunit of Hb) in the T state, it pulls on the alpha helices of heme (shifting position of proximal His), causing it to assume a slightly more planar conformation; these changes lead to adjustments in the ion pairs at the α1β2/(α2β1) interface, causing these subunits to slide past each other and rotate | | 40 |
| 7420032930 | Hb O2 binding curve: how does it make Hb a good transporter of O2? | Hb exhibits allostery in which there is communication b/t the 4 subunits of the heterotetramer: as soon as 1 O2 molecule binds to a subunit of Hb, it begins transition to the R state, thus increasing Hb's affinity for O2 (each molecule of O2 binds with more affinity)
this results in the sigmoidal curve, as Hb transitions from T state to R state in the presence of increasing [O2], allowing for Hb to release 30% O2 in the tissues and pick up O2 in the lungs |  | 41 |
| 7420032931 | how does the difference in O2 binding curves b/t Hb and Mb result in Hb's better ability to transport O2 | the allosteric property of Hb allows its affinity for O2 increase as O2 binds: the first molecule binds with the majority of Hb in the T state (w/ a low affinity for O2), which begins the transition to the R state; R state has higher affinity for O2, so as Hb transitions to R state, the affinity increases
-the [O2] in the lungs is high, at which point Hb is almost all in the R state which has a very high affinity for O2, so Hb picks up O2 in the lungs
-the [O2] in the tissues is low, where Hb population is mostly in the T state w/ a low affinity for O2, so it releases O2 in the tissues
the hyperbolic curve of Mb demonstrates that Mb has a high affinity for O2 that does not change, so it would not release O2 in the tissues even though the [O2] at the tissues is low | | 42 |
| 7420032932 | allosteric protein | a protein w/ multiple ligand binding sites in which the binding of a ligand to one site affects the binding properties of another site on the same protein
-ex=Hb and O2 | | 43 |
| 7420032933 | Hill's coefficient | the slope of a Hill plot which is a measure of the degree of cooperativity exhibited by a protein
-if Hill's coefficient (slope)=1 ligand binding is not cooperative
if Hill's coefficient is greater than 1, the ligand binding to the protein exhibits positive cooperativity
if Hill's coefficient is less than one, the protein has negative cooperativity in which the binding of one molecule impedes the binding of others | | 44 |
| 7420032934 | Hill plot and Hill equation | tells you the degree of cooperativity of a protein
Hill equation: log(θ/(1/θ))=nlog[L]-logKd
Hill plot: log(θ/(1/θ)) vs log[L] | | 45 |
| 7420032935 | Bohr effect | low pH and high [CO2] (in the tissues) stabilize the T state of Hb, decreasing the affinity of Hb for O2; therefore in the tissues, H+ and CO2 (byproducts of cellular respiration) are bound to Hb and O2 is released
(in lungs, CO2 is excreted and pH rises, affinity for O2 increases and Hb binds more O2)
lower pH's shift O2 Hb saturation curve to the right | | 46 |
| 7420032936 | how are high [CO2] and low pH related | CO2 and H+ are byproducts of cellular respiration, which occurs at the tissues
CO2 is hydrated to form bicarbonate, which H+ is a byproduct of (CO2 + H2O⇌H2CO3⇌H+ + HCO3-), resulting in an increase in H+ concentration
these stabilize the T state of Hb, decreasing O2 saturation | | 47 |
| 7420032937 | factors that stabilize the T conformation of Hb, thus reducing its affinity for O2: how do each of these stabilize the T state? | increase in CO2: combines w/ N terminus of Hb and other blood proteins to form carbamates (further increasing H+)
decrease pH (increase in [H+]): H+ helps to stabilize ion pairs, stabilizing the T state
increase BPG: binds to positively charged residues between beta subunits in the T state; the transition to R state narrows this cavity and eliminates BPG binding site | | 48 |
| 7420032938 | how are CO2 and H+ transported in Hb | they stabilize the T state, CO2 is mostly transported as HCO3-, but CO2 can also combine w/ the N terminus of Hb and other blood protein to form carbamates
H+ is transported bound to several side chains on Hb whose pKa's are altered by the transition from T to R (high pKa in the T state b/c H+ stabilizes ion pairs) | | 49 |
| 7420032939 | Hb action in lungs vs tissues picture | |  | 50 |
| 7420032940 | how does your body compensate for the lack of oxygen at high altitudes | increases BPG, shifting O2-Hb saturation curve to the right, so that your tissues can get the O2 they need | | 51 |
| 7420032941 | how does sickle cell anemia work | HbSxHbS causes a point mutation in which the 6th a.a. on the beta subunit of Hb is changed from glu to val, thus changing it from negative a.a. to neutral a.a
causes hydrophobic effect in RBCs, crystallizing Hb in RBCs | | 52 |
| 7420032942 | myosin structure | 6 subunit: 2 heavy chains and 4 light chains
heavy chains start as globular heads and then twist into 2 supercoiled alpha helices | | 53 |
| 7420032943 | F vs G actin | G actin=globular actin
G actin is the monomer that spirals around each other to make up F (filamentous) actin | | 54 |
| 7420032944 | 4 repeated steps of a muscle contraction | myosin heads move an array of actin closer the center (M line) thus shortening the sarcomere (bringing Z disks closer together) |  | 55 |
| 7420032945 | how are muscle contractions regulated by troponin and tropomyosin | in the absence of Ca., tropomyosin (bound to troponin I) blocks the binding site on actin, but when an AP initiates the release of Ca from the SR, Ca binds to trop C, which causes tropomyosin to expose the active site on actin | | 56 |
| 7420032946 | cofactor | An inorganic ion that binds to an enzyme, enabling a substrate to fit into an enzyme's active site | | 57 |
| 7420032947 | coenzyme | An organic or metalloorganic molecules that binds to an enzyme, enabling a substrate to fit into an enzyme's active site | | 58 |
| 7420032948 | prosthetic group | A cofactor or coenzyme that is covalently bonded to a protein to permit its function
-ex: heme | | 59 |
| 7420032949 | holoenzyme | a complete enzyme w/ cofactors &/or coenzymes bound | | 60 |
| 7420032950 | apoenzyme | an enzyme w/o cofactors &/or coenzymes bound | | 61 |
| 7420032951 | enzymes affect______ not______
b/c of what equations? | rxn rates; equilibria
b/c *equilibrium* of a rxn is linked to ΔG°' where ΔG°'=-RTlnK(eq)'
whereas the *rate* of a rxn is linked to ΔG(transition) which includes Ea in its equation | | 62 |
| 7420032952 | events that need to occur in order for a rxn to take place (i.e. "causes" of Ea); how does an enzyme overcome these? (x4) | *1. reduction of entropy (i.e. reactants must find each other)*
-binding energy holds the substrate in proper orientation to react with the enzyme
*2. removal of water solvation shell*
-enzyme-substrate interactions replace most/all H bonds b/t substrate and water
*3. distortion of substrates (i.e. change bond angles or conformation)*
-weak interactions formed only during rxn transition state compensate for any distortion the substrate must undergo to react (primarily e- distribution)
*4. alignment of functional groups*
-enzyme undergoes a change in conformation when substrate binds (induced fit), bringing key functional groups into proper position | | 63 |
| 7420032953 | specificity | ability of an enzyme to discriminate b/t a substrate and a competing molecule | | 64 |
| 7420032954 | enzyme interacts/covalently bonds to/is complementary with the substrate during which part of the rxn | transition state b/c if the enzyme was complementary w/ the substrate as it is, the substrate would be happy at the enzyme's active site and not undergo a rxn | | 65 |
| 7420032955 | general acid base catalysis | an example of a mechanism in which once an ES complex is formed, properly positioned catalytic fxl groups aid in the cleavage and formation of bonds; in acid base catalysis, the enzyme donates a proton from one of its amino acids: | | 66 |
| 7420032956 | pre-steady state kinetics: definition, picture, advantage and disadvantages | Branch of enzyme kinetics investigating parameters that govern reaction rates prior to the formation of the steady state (rapidly changing)
-best method to determine rxn mechanisms, but requires expensive instrumentation & vast knowledge of kinetics |  | 67 |
| 7420032957 | steady state kinetics | -enzyme-substrate concentration appears constant overtime Linear plot where enzyme is saturated
-the sum of the rate of formation of [ES] and the rate of loss of [ES] approaches zero
-Michaelis-Menten kinetics assumes this |  | 68 |
| 7420032958 | steady state kinetics: determines what 4 parameters? advantages over pre-steady state kinetics? | Vmax, km, kcat, enzyme efficiency to compare enzymes
-is easy to measure, requires inexpensive instrumentation, and only a knowledge of M-M kinetics | | 69 |
| 7420032959 | how to measure V0 | need to measure the progress of a rxn (disappearance of substrate or appearance of product) over time | | 70 |
| 7420032960 | experiment (PNPP-->PNP, catalyzed by AP) to determine V0 | -set up assay of 7 rxns of PNPP (substrate) with AP (enzyme): use 1 micromolar alkaline phosphatase with increasing concentration of PNPP (starting at 0)
-measure appearance of PNP by measuring absorbance at 410 nm (this is possible b/c PNPP and PNP absorb light differently)
-plot absorbance as a function of concentration of PNPP, the substrate
-use Beers Law to get the velocity (A=eLc) to get epsilon, which is a function of how well a substance absorbs light: then slope of graph divided by epsilon gives the velocity
then get michaelis menten plot ([substrate] vs V0) | | 71 |
| 7420032961 | MIchaelis Menten plot
equation of this plot | for an enzyme-catalyzed rxn, this is a graph of V0 (initial velocity) as a function of substrate concentration: is a hyperbola
V0=(Vmax)[S]/([S]+Km) |  | 72 |
| 7420032962 | Vmax | maximal velocity of an enzyme: reached when enzyme is completely saturated by a substrate (in the equation E+S⇌ES, most exists in ES)
at this point, further increases in substrate concentration will have no effect on rate |  | 73 |
| 7420032963 | Km | Michaelis constant=concentration of substrate necessary to reach half of the maximal velocity
[S] at which half of the enzyme's active sites are full (the [S] at 1/2 Vmax), measure of the affinity of the enzyme for the substrate | | 74 |
| 7420032964 | 2 assumptions of M-M kinetics | 1. assumption of equilibrium
--rate equation: : Δ[ES]/Δt=K1[E][S]-K-1[ES]-K2[ES] (E+S⇌ES⇌E+P)
2. assumption of steady state as measuring initial velocity, [ES] does not change (Δ[ES]/Δt=0) | | 75 |
| 7420032965 | Kcat | this is K2, which equals Vmax/total enzyme
equal to the number of substrate molecules converted to product in a given time (when the enzyme is saturated)
AKA turnover number | | 76 |
| 7420032966 | enzyme efficiency | =specificity constant, the turnover number normalized to Km
divide Kcat/Km; this is the best way to compare enzymes | | 77 |
| 7420032967 | double reciprocal plot (Lineweaver-Burke) | an easier way to find Vmax; plot 1/V0 as a function of 1/[S] | | 78 |
