exam 2 biochem practice questions Flashcards

(107 cards)

1
Q

what is the major themes in chapter 4

A

primary sequence to 3-D structure

structure = function

each protein has a unique structure (is also not static but dynamic)

non-covalent forces are very important

many structures have common patterns that are given a name (like domain and motif….I think)

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2
Q

what is different about protein compared to other organic polymers

what does the conformation of a protein allow the protein to do

A

has a specific 3-D conformation

allows the protein to function

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3
Q

what is a native fold

what can be said about its energy

A

the properly folded, functional conformation of a protein

it has the lowest free energy

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4
Q

what does the native fold have and are examples of it

A

The native fold has a large number of favorable interactions within the protein for stability

example: ”burying” hydrophobic groups and maximizing H-bonding

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5
Q

how is protein conformation stabilized by

what do these combat

A

Disulfide bonds

Weak, non-covalent interactions

THESE COMBAT ENTROPY

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6
Q

what are the Favorable Interactions in Protein Folding used to Maintain a Native State (fold)?

A

hydrophobic effect

hydrogen bonds

van der waals interactions

electrostatic interactions

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7
Q

what does the Hydrophobic Effect do for the native fold

A

Release of water molecules from the structured solvation layer around the molecule as protein folds increases the net entropy

Correctly position hydrophobic side chains depending on the environment

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8
Q

what does hydrogen bonding do for the native fold

A

Interaction of N-H and C=O of the peptide bond leads to local regular structures such as α-helices and β-sheets

  • Side chain – side chain interactions. H-bonding between R-groups, H-bonding between backbone and R-groups.
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9
Q

what does van der waals do for the native fold

A

Weak attraction between all atoms contributes significantly to the stability in the interior of the protein

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10
Q

what do Electrostatic Interactions
dof ro native fold

A

Long-range strong interactions between permanently charged groups

Salt-bridges, especially buried in the hydrophobic environment strongly stabilize the protein

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11
Q

what does secondary structure start with

A

starts with primary structure

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12
Q

2 structures

describe the peptide bond

describe carbon-carbon bonds, what is another name for it

describe the carbon-nitrogen bond, what is another name for it

for psi/phi bonds, what can occur but what will be prevented

A

the peptide bond is rigid and planar, constraining the protein to certain, allowed conformations

Carbon-carbon (psi - Ψ) bonds can rotate

Carbon-nitrogen (peptide) bond (phi - Φ) cannot rotate

In theory, + / - 180° rotation for phi/psi bonds can occur,but…
- Steric Hinderance will prevent some angles from occurring…

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13
Q

what does steric hindrance effect and what is the result

A

steric hindrance can affect side chains and the backbone reduces possible rotations

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14
Q

what does a Ramachandran plot show

what does steric hindrance prevent

A

Shows common secondary structural elements and the acceptable range of rotation

Steric hindrance prevents all but a handful of secondarystructures

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15
Q

what is the structure of a peptide bond?

how many atoms does it have

A

is rigid and planar, constraining the protein to certain conformations

has 6 atoms

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16
Q

what do secondary structures consist of

A

alpha helix

beta-sheets

parallel beta sheets

antiparallel beta sheets

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17
Q

how is the helical backbone of an alpha helix held together?

what kind of direction is an alpha helix

what stabilizes the alpha helix

where are the side chains for the alpha helix

which residues align on top of each other

A

The helical backbone is held together by hydrogen bonds between the backbone amide of an “n” and carbonyl group of the “n + 4” amino acid

ann alpha helix is a right-handed helix

the hydrogen bond aligns roughly parallel with the helical axis and this stabilizes it

Side chains point out and are roughly perpendicular to the helical axis

residues 1 and 8 align on top of each other

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18
Q

describe the inner diameter of alpha helix, what can fit innside

describe the outer diameter of alpha helix, what can fit inside

what can amphipathic alpha helices form

what is the relatiionship between proline, glycines and alpha helices

does every polypeptide forrm a alpha helcies

what amino acids are strong helix formers

A

The inner diameter of the helix is about 4-5ÅToo small for anything to bind inside

The outer diameter of the helix (with side chains)is 10-12 Å. Fits into the major groove of dsDNA

Some amphipathic α-helices can form coiled-coildimers (stay tuned – keratin)

α-helices cannot be formed with Pro  kink(disrupts the helix). Gly is a helix breaker too.

Not all polypeptide sequences adopt α-helical structures

Small hydrophobic residues such as Ala and Leu are stronghelix formers.

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19
Q

what is the cause of the sheet-like zig zag structure of beta sheets

what holds together the sheet-like arrangement for beta sheet

where are the side chains in beta sheets

what amino acids are found in beta sheets

what amino acids are not found in beta sheets

A

The planarity of the peptide bond and tetrahedral geometry of the α-carbon create a pleated sheet-like structure (zigzag)

Sheet-like arrangement of the backbone is held together by hydrogen bonds between the backbone amides and carbonyl groups in different strands

Side chains protrude from the sheet alternating in up and down directions

Found in β-Sheets:
Large, aromatic (Y, F, W)
Branched (T, V, I)

NOT Found in β-Sheets:
G, P

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20
Q

in parallel beta sheet, where do the H-Bonds run and what does it result in

where can the individual strands be in the primary structure

A

In parallel β-sheets, the H-bonded strands run in the same direction,
Resulting in bent H-bonds (weaker)

Individual strands can be close, or distant, in the primary structure

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21
Q

in anti-parallel beta sheet, where do the H-Bonds run and what does it result in

where can the individual strands be in the primary structure

A

In antiparallel β-sheets, the H-bonded strands run in opposite directions, Resulting in linear H-bonds (stronger)

Individual strands can be close, or distant, in the primary structure

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22
Q

how are most proteins shaped

what is the reason for this shape

how many A.A residues are in turns or loops

what do the arrows in strands and sometimes in helices indicate

when do beta turns occur

how is the 180* turn accomplished

how are beta turns stabilized

what amino acid is found in beta turn type 1

what amino acid is found in beta turn type 2

A

Most proteins are globular in shape

the globular shape is due to of frequent turns or loops in the polypeptide chain that connects beta strands and alpha-helices

1/3 of AA residues are in turns or loops

Strands, and sometimes helices, will have arrows to indicate N- and C- termini of the 2° structural element

β turns occur frequently whenever strands in β sheets change direction (so whenever the beta sheets turn to change direction)

The 180° turn is accomplished over 4 amino acids

Turn stabilized by a H-bond

type 1: proline

type 2: glycine

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23
Q

what is the tertiary structure and what does it include

how is it stabilized

what interactions largely make it up

how else can it be stabilized

what Is also possible

what are two major of tertiary structure

A

Tertiary Structure – overall 3D arrangement of all atoms in a protein

Includes long-range contacts between AA’s in a single polypeptide chain

‘Stabilized by numerous weak interactions between amino acid side chains

Largely hydrophobic and polar interactions

Can be stabilized by disulfide bonds

Side chain with backbone interactions are also possible

Two Major Groups
- Fibrous (elongated; structural)
- Globular (enzymes, etc.)

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24
Q

what do tertiary structures often have and is it solute in water

what does it contain a high proportion of and what are examples of these

are the underlying structures complicated

what does it have a high proportion of

what does it have extensive of

what are examples of fibrous proteins

A

Often have structural rather than dynamic roles and are water insoluble

Typically contain high proportions of α-helices (keratin) or β-pleated sheets (fibroin)

High proportion of hydrophobic AAs–that is why it is water insoluble!!!!!!!!!

Extensive supramolecular complexes

Fibrous Proteins: α-keratin, collagen, silk fibroin

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25
where can you find alpha keratin what is alpha keratin made of and what is ti strengthened by what is the fact from legally blonde how isa super tight coiled coil made how is permanent waving of hair done
Hair, nails, hooves, horns, outer skin made of Strong, RH α-helix; LH parallel super helix; strengthened by cross-links by covalent disulfide bonds – stabilizes! perm removes disulfide bonds Super-twisting helices, in a left-handed fashion, wrap around each other to make a very tight coiled-coil permanent waving of hair: reduce disulfide bonds, moist heat breaks H-bonds and causes uncoiling of alpha heckles, remove reducing again, add oxidizing agent, new SS bonds
26
what does collagen provide and how many different types are there where can collagen be found how does each protein fold what is the structure of collagen what amino acids are found in collagen which amino acid provides tensile strength for collagen how many variants are there in mammals
Provides tensile strength and structure (~30 types of collagen). can be found in Connective tissue (tendons, cartilage, organic matrix of bone, cornea) Each protein folds into a left-handed helix (α-chains; NOT α-helix) Coiled-coil of three separate α-chains supertwisted around each other in a right-handed manner to provide strength (like a rope). find Gly, Ala, Pro, HyLys and HyPro (essential! specific to collagen) Lys-HyLys (Hydroxylysine) form cross-links for added strength 30+ variants in mammals
27
in antiparallel beta sheets, where do H-bonds run does this make the H-Bonds linear or bent and does it make them stronger or weaker? what kind of amino acids is silk fibroin rich in what kind of structure is it mostly made of does it stretch what kind of interactions are within what kind of cross-links does it have, does it make it rigid or flexible
In antiparallel β-sheets, the H-bonded strands run in opposite directions Resulting in linear H-bonds (stronger) Individual strands can be close, or distant, in the primary structure Rich in Ala and Gly antiparallel β-sheets Fully extended: no stretching Extensive hydrogen bonding and van der Waals interactions between sheets, but no covalent cross-links for flexibility.
28
for silk fibroin what is it used for today? what are its characteristics? what structure is it made of what are its cross-links
used for silk soft and flexible filaments made of beta conformation no cross-links
29
for collagen of tendons, bone matrix how is it used today? what are its characteristics? what structure is it made of what are its cross links
tendons, connective tissues, organic bone matrix high tensile strength without stretch made of collagen triple helix – hydroxylysine (unique) cross-links  structure = function
30
for alpha keratin how is it used today? what are its characteristics? what structure is it made of
hair, feathers, and nails tough, insoluble protective structures of varying hardness and flexibility made of alpha helix, cross-linked by disulfide bonds
31
what are examples of globular proteins what structures can be found in them how are the different secondary structures arranged? what does the folding provide what is the general rule for globular proteins
examples: enzymes, transport proteins, molar proteins, regulatory proteins, immunoglobulins etc alpha helices, beta sheets, beta turns can all be found the different secondary structures are - compact conformation - folding provides structure diversity general rule: - bury nonpolar amino acid R-groups - distant segments may come together, but not the norm - optimize the number of weak interactions
32
what is an example of a globular protein? what does this protein bind and where is it found what is this protein related to but has a higher affinity for what what are the rules followed for this protein? what structures is this protein made of how many amino acids is it made of what kind of structure is it and what is at its center what is its prosthetic group? what is a prosthetic group? what amino acid is attached to what molecule in its center
myoglobin! binds iron and O2 and is found in muscles related to hemoglobin but has a higher affinity for O2 general rules: the hydrophobic R groups are buried made of alpha helices connected by loops made of 153 amino acids it is a porphyrin ring and has iron at its center heme is it a prosthetic group a prosthetic group is a nonprotein group forming part of or combined with a protein. a proximal histidine group is attached to the iron, a distal histidine group hovers near the opposite face
33
what are chymotrypsin ribonuclease carboxypeptidase cytochrome C lysosome myoglobin
they are secondary structures!
34
what are the steps taken for X-ray crystallography?
Purify the protein Crystallize the protein Collect diffraction data (light bending) Calculate electron density Fit residues into density
35
what are the pros and cons of X-Ray crystallography
Pros: - No size limits - High resolution - Well-established Cons: - Difficult for membrane proteins - The crystal form may not represent the protein in solution or in the cell - Not dynamic (cannot determine how the protein interacts with things)
36
what steps are taken for NMR
Steps Grow the protein with a NMR-active isotope (usually of Carbon-13) Purify the protein Collect NMR data Assign NMR signals Calculate the structure
37
what are the pros and cons of NMR
Pros: - No need to crystallize the protein - Dynamic studies possible - Interaction with ligands Cons: Difficult for insoluble proteins Works best with small proteins Nuclear Magnetic Resonance
38
what is a motif associated with what are motifs what are motifs composed of what are what a motif is composed of also considered motifs can be found as what what are proteins made of what are examples of secondary strcutures that can be found in motifs
Globular Proteins are associated with Motifs Motifs are stable arrangements of several secondary structure elements All alpha-helix All beta-sheet Combination These are sometimes considered supersecondary structures Motifs can be found as reoccurring structures in numerous proteins Motifs can be found as reoccurring structures in numerous proteins examples of secondary structures that can be found in motifs: twisted beta-sheet alpha alpha corner beta alpha beta loop beta barrel
39
what can you find in large motifs what are the two classes that a motif can be organized into
You can find small motifs as a part of large motifs People have determined the structure of so many proteins, so we must organize. Two classes of organization are shown here.
40
what are domains and where can they be found what can a domain have when do domains adopt the same folding pattern what can a single protein have
can be found in globular proteins Domains are relatively stable, independently folded regions within the tertiary structure of a globular protein Each domain may encompass one or more motifs and have the same combination of motifs (EF-hand) Domains having more than 30% of their amino acid sequence in common normally adopt the same folding pattern. A single protein can have several domains with each domain performing a different function (e.g., enzymatic, docking, regulatory, pore, membrane anchoring, etc)
41
what cause a Quarternary (4°) Structure how do the the polypeptide subunits associate into a larger functional cluster What drives Quarternary Association?
Results from the association of two or more polypeptide subunits into a larger functional cluster These polypeptide subunits associate into a larger functional cluster via side chain – side chain and side chain – polypeptide backbone interactions what drives quaternary association: Stability: reduction of surface to volume ratio Genetic economy and efficiency (using quarternary structure makes our genome more efficient) Bringing catalytic sites together Cooperativity (biological function may be regulated by complex interactions of multiple subunits)
42
what do Intrinsically Disordered Proteins or Protein Segments lack what can this type of protein remain as or what can it also do how many humans proteins fit this designation what amino acids form then and
Contain protein segments that lack a definable structure. Or, the entire protein The protein can remain in a primary structure indefinitely; or it may have a domain that can interact with other molecules, but the rest of the protein will remain disordered. Possibly 1/3 of all human proteins fit this designation.
43
what is Proteostasis how do proteins normally exiist what is involved in mainatining proteostasis
Proteostasis is Protein Stability;Proteostasis is the constant level of the active set of proteins in a cell. Proteins can exist in native conformation, or other conformations; flexibility is important Maintaining proteostasis is a complex process, involving: synthesis, folding, unfolding, degradation, modification, etc
44
most protein fucntion depends on what to be active what must a protein be what can the order of amino acids determine for a protein how can proteins denature
Most protein’s function depends on its 3D-structure. To be active a protein must be correctly folded (native conformation) The order of amino acids can help determine what this 3D conformation will be Loss of structural integrity and function/activity is called denaturation Proteins can be denatured by: 1. Strong acid or base 2. Organic solvents 3. Detergents 4. Reducing agents 5. Salt concentration 6. Heavy metal ions 7. Temperature 8. Mechanical stress
45
to what does a protein fold what determines the direction of a protein where can folding of 2ndary structure occur how do secondary structures interact when does protein synthesis being
Proteins fold to the lowest-energy (most stable) conformation in the microsecond to second-time scales. It is not a “search” The direction is biased towards thermodynamically and sterically possible conformations Nonpolar inside, polar outside! (we’ve gone over this Folding of secondary structures can occur at multiple sites at the same time. Then, secondary structures interact to find the lowest energy minima (conformation) Folding often begins before protein synthesis is complete!
46
what are chaperones what is Hso70 what are chaperonins What do Isomerases do?
another protein that promotes correct folding Hsp70 (Heat Shock Protein 70) family protects unfolded proteins from denaturation and aggregation Chaperonins promote correct folding Isomerases make sure we have the correct stereochemistry PDI – Protein disulfide isomerase PPI – Peptide prolyl cis-trans isomerase
47
what if protein is misfolded
normally misfolded proteins are fixed (rendked) or degraded defects n any of the ceeluar systems may affect the degree of protein misfolding
48
what is β-amyloid critical for and what shape must it be in what happens in alzheimers what does the misfolding promote what is lost due to misfolding then what happens to the brain
The native (correctly folded) β-amyloid is a soluble globular protein which is critical for neuronal growth, survival, and post-injury repair In Alzheimer’s disease, bet amyloid is clipped from the cell membrane, fragmented, and then, it misfolds This misfolding promotes aggregation Correctly folded helices are lost, and peptides form β strands, β helices, and β sheets  now insoluble These insoluble plaques collect around the neurons and disrupt their environment and connectivity
49
what is Parkinson’s Disease, Lewy-Body Dementia what is Huntington’s Disease
Parkinson’s Disease, Lewy-Body Dementia: misfolded α-synuclein forms aggregates  Lewy Bodies Huntington’s Disease: genetic mutation that increases CAG repeats (increases #of amino acids) causes misfolding and aggregation  neuronal death
50
what is a ligand? what is a binding site what is protein flexibility important for what else is important for binding what are the two parts that an enzyme comes into contact with what forces are responsible for binding and what does this allow for
a molecule that is reversiibily bound to a receptor specific location on protein protein flexibility is important for induced fit regulation is important for binding enzyme comes into contact with a substrate and catalytic (active) site binding is via noncovalent forces that dictate protein structure which allows for interactions to be transient
51
what can the high specificity of ligand binding be explained by what is Molecular complementarity due to what is the lock and key model are proteins rigid what is the induced fit model
High specificity can be explained by the complementary nature of the binding site and the ligand Molecular complementarity: size, shape, charge, hydrophobicity Lock and key model: proteins and ligands have a rigid interaction with each other Proteins are FLEXIBLE! Induced Fit Model: both the ligand and the protein can change conformations upon binding; makes binding site more complementary to the ligand
52
what is one example of Illustrating Protein Function that we are focusing on is O2 soluble what can transport O2 but what is the consequence of it because of the consequence, what do we need to do how do we sequester Fe what is a Heme a prosthetic group of what is a prosthetic group how does O2 bind what does O2 bind how manny sites does heme have and what binds those coordination sites
Illustrating Protein Function Through Oxygen Binding O2 is critically important (obvs), but poorly soluble Transition metals (esp. Fe) can transport O2 but can damage cells So there is a need to sequester Fe How? Heme! Heme is a prosthetic group – a porphyrin ring complex with an iron ion (Fe2+) Binds oxygen reversibly Oxygen binds via heme as amino acids cannot bind oxygen 6 coordination sites: 1-4 (nitrogen), 5 (amino acid), 6 (oxygen)
53
what is myoglobin (Mb) and what is it composed of with how many amino acids what is Mb mostly made of and what kind of regions does it have what is its job what does it contain what interacts with heme and O2 what does it sterically inhibit O2 from doing how is it folded and what is the result of this folding
Myoglobin is a compact globular protein composed of a single polypeptide chain (153 amino acids in length) Mainly α helices; there are 8. Also some intrinsically disordered regions (flexibility) Carries and stores oxygen (poorly soluble) for muscles Contains a heme prosthetic group Histidines interact with heme and O2 Sterically inhibits oxygen from binding perpendicularly to the heme plane (specific!) Shaped/folded to form a “cradle” that nestles the heme prosthetic group -----Protects iron from oxidation (free radicals  bad!)
54
in free heme, how does CO bind O2 compared to O2 In Mb, how does heme bind CO compared to O2 What does the protein structure act as what is the effect of histidine on ligands what does the histidine result in Why not evolve Mb to bind O2 more preferentially and tightly relative to CO?
In free heme, carbon monoxide (CO) binds 20,000x better than O2 In Mb, heme binds CO only 40X better than O2 The protein structure acts as a gate. The effect of histidine (His E7), forces ligands to bind at an angle. Significantly improves O2 vs CO binding
55
what does Keq equal what is the equation for the association constant and dissociation constant what does it mean that if the Kd is high using the Eqn what about if it is low using the Eqn what s Ks relationship to Ka
Keq = [products]/[reactants] Ka = [PL]/[P][L] Kd = [P][L]/[PL] high Kd means that there is more products which is [P] [L], so that means that the ligand would rather be dissociated from the receptor because t has a low affinity for for it low Kd means that there is more reactants which is [PL], so that means that the ligand would rather be associated from the receptor because t has a high affinity for for it use eqn of Kd to understand affinity!!!!!!!!!!! Kd = 1/Ka
56
what increases the amount of O2 bound to Mb what happens to the as the amount of O2 concentration increases sufficiently and what is the name for this what does fraction saturation equal and what is the symbol and eqn what determines that slope of the curve and what does it mean if it is very steep vs not as steep
the amount of O2 bound to Mb increases with O2 concentration as the [O2] increases sufficiently, the amount of binding reaches a maximum value and this is called saturation fraction saturation is the fraction (or half) of the protein that is bound to the ligand Y or theta = [PL]/[Ptotal] slope of the curve (how quickly we reach saturation) depends upon the affinity of the concentration steep slope = high affinity not so steep slope = low affinity
57
In a situation where P possesses one binding site for the ligand, what is the equation what does it mean when the concentration of protein bound to ligand [PL] equals the concentration of free protein [P] what does 50% saturation equal what can we say about Kd = [L]
Kd = [P][L]/[PL] originally Kd = [P]/[PL] ([L]) If the [PL] = [P] then [P]/[PL] = 1 and the concentration of free ligand [L] equals Kd Kd = 1 [L] For 50% saturation, Kd = L Kd = [L] at which half of the available ligand-binding sites are occupied, so when P binds half of the L
58
what does theta equal if [L] = 0 then theta equals if [L] >> Kd then theta equals f [L] << Kd then theta equal what happens to the curve if Kd gets smaller
theta is the fraction saturation which is [PL] = [Ptotal] which is occupied binding sites over the total protein eqn: theta = [L]/Kd + [L] if [L] = 0 then theta equals 0 if [L] >> Kd then theta equals 1 f [L] << Kd then theta equal 1/2 as the Kd gets smaller (binding is tigher) the binding curve is steepere
59
How do we know which of a series of candidate drugs is better than the others? How do we know what dosage to give someone? what is an agonist what is an antagonist
Agonist – a compound that causes a physiological response Antagonist – a compound that interferes with the physiological action of another compound
60
how is a gas concentration (hence ligand concentration) represented? How well does Mb bind to O2 according to the binding curve? looking into the binding curve, pO2 in the lungs is about 13 kPa, how well does O2 bind Mb accoridng to the curve looking into the binding curve, pO2 in the lungs is about 4 kPa, how well does O2 bind Mb according to the curve Is myoglobin a good transporter and deliverer of O2 in your body? Why? What does myoglobin do? is hemeglobin or Mb a better O2 transporter
as partial pressure so pO2 How well does myoglobin bind oxygen here?- very very well, indicated by the steep slope, so even a little bit of O2 is enough tot bind half of the ligands and then to saturate it to cause a plateau at 13 kPa, there is a plateau which means that there is saturation and almost all of the ligands are bound at 4 kPa, there is a forming plateau so there is almost saturation Mb is not a good transporter because it has a very very hgh affinity for O2 so it does not want to let it go Carries and stores oxygen (poorly soluble) for muscles Our body prefers to use hemoglobin rather than myoglobin as the oxygen carrier in the bloodstream. This is because hemoglobin not only binds oxygen weakly but more importantly binds oxygen cooperatively.
61
Myoglobin (Mb) and Hemoglobin (Hb) comparison Mb how many subunits what does it do for O2 how many heme groups Hb how many subunits what does it do for O2 how many heme groups
Myoglobin (Mb) 1 subunit O2 storage 1 heme group Hemoglobin (Hb) 4 subunits – 2α and 2β O2 transport 4 heme groups
62
T state of Hb what is called when is it more stable what affinity does it have O2 What is bound to it is it rigid and if so what makes it rigid what is a salt bridge and how are they broken
tense state more stable in absence of O2 Lower affinity for O2 tense state no O2 bound salt bridges makes it rigid salt bridges are ionic interactions between the R groups of the Hb Salt bridges are broken when the O2 binds to the heme groups, makes it more relaxed
63
R state of Hb what is called when is it more stable what affinity does it have O2 What is bound to it what interacts is it flexible and if so what makes it flexible what is a salt bridge and how are they broken
Relaxed state more stable in the presence of O2 higher affinity for O2 O2 bound Beta subunits interact salt bridges make it rigid Salt bridges are broken when the O2 binds to the heme groups, makes it more relaxed Relaxed state = fewer interactions, more flexible, higher affinity for O2
64
how many binding sites does Hb have for O2 What kind of protein iis Hb what does that mean what is cooperativity and what is it caused by what is + cooperativity what is - cooperativity
Recall that Hb has 4 O2 binding sites Hb is an allosteric protein: having more than one conformation; binding at one site affects the affinity of another site) This opens the door for something called cooperativity With the binding of each O2 molecule, (which changes the conformation of the binding subunity from T to R), the affinity of the whole protein for O2 increases. Positive Cooperativity: binding of a ligand increases the binding affinity of subsequent ligand Negative Cooperativity: binding of a ligand decrases the binding affinity of the subsequent ligand
65
what does the Hb curve look like when we add cooperativity? how does Hb bind O2 what does the curve look like for one binding site how many binding sites does Mb have for O2 and that explains what Mb can’t be cooperative. Why? what does a sigmoidal curve represent
sigmoidal because Hb has a low affinity for O2 Hb binds O2 cooperatively One binding site  hyperbolic Mb has only 1 binding site for O2 and this has a hyperbolic curve Mb can’t be cooperative. Why? One binding site. Hb has a sigmoidal curve. Reflects a transition from low-affinity to high-affinity binding. This makes Hb highly sensitive to changes in [O2].
66
physiologcally, how must Hb bind O2 and where and what is the kPa physiologcally, where must Hb release O2and what is the kPa what does effective transport entail and there what must happen what is binding most sensitive to what regulates Hb what kind protein in Hb
Physiologically, Hb must bind O2 efficiently in the lungs (pO2 ~ 13.3 kPa) Hb must release O2 in tissues (pO2 ~ 4 kPa) Effective transport requires the ability to pick something up and drop if off. Therefore, affinities must change. Binding is much more sensitive to changes in oxygen concentration Other ligands bind Hb and change its oxygen-binding properties  Regulation! Hb is ALLOSTERIC!
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what does homotropic mean what does heterotropic mean what does Hb bind besides O2 Where does Hb bind O2 and CO2 what does binding CO2 or O2 result in what can high [CO2] result in due to what process What is the point of our circulation system
homotropic means the same ligands heterotropic means different ligands Hb binds CO2 Hb binds O2 & CO2 at different sites binding one reduces the affinity for the other high [CO2] raises the [H+] in circulation: - our RBCs have Hb and O2 from lungs - the O2 binds to Hb - Hb releases O2 to tissues
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besides CO2 & O2, what does Hb bind where is its binding site what does the [CO2] influence how is H+ formed what happens when Hb binds H+ What is the main buffer system in RBCs the affinity of Hb for O2 is what to the amount of what what are the consequences for this what s the name for it!
Hb binds H+ Binds at different binding site from O2 & CO2 The [CO2] influences the [H+]: H+ is formed when CO2 reacts with Hb or H2O CO2 + H2O <-> H2CO3 <-> H+ + HCO3 when Hb binds H+, its affinty for O2 decreases Hb is the main buffer system in RBCs the affinity of Hb for O2 is inversely proportional to amount of H+ & CO2 bound consequences are the Bohr effect - Peripheral tissues: high [CO2] and [H+]: low affinity - lungs: low [CO2] & [H+]: high O2 affinity
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what is BPG used for and does it stand for what is the [O2] at high altitudes where does BPG bind what does it stabilize what affinity does Hb have for O2 at T state
2,3-bisphosphoglycerate plays an important role in adaptation to high altitudes (low O2 partial pressure) BPG binds to Hb at a site far from the O2 binding site stabilizes the T state of Hb (low affinity for O2
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what happens to O2 at altitude what does BPG regulate does BPG share a binding ste what kind of modulator is BPG What does the stabilization of the T state mean for oxygen binding? what varies at sea level At altitude, since less oxygen is bound to Hb, that allows for BPG to do what
At altitude pO2 decreases BPG regulates the affinity of Hb for O2 It has its own binding site BPG is an allosteric modulator Stabilization of the T state decreases the affinity of Hb for O2. So Hb is Less willing to bind and less willing to *hold* onto O2 so oxygen gets dropped off The concentration of BPG varies in response to our altitude above sea level. At altitude, since less oxygen is bound to Hb, that allows for BPG to fit into its binding site
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Initially, at a lower pO2 (altitude), in the lungs, affinity of Hb for O2 is ______ what are the Kd values for when you are at lower altitude and what does this mean for the affinity compared to sea level Within hours of being at altitude, the concentration of BPG ______ from __ mM to __ mM what happened to the curve as BPG increased What does BPG do to the binding curve? Physiologically, what is happening?
Initially, at a lower pO2 (altitude), in the lungs, the affinity of Hb for O2 is reduced at altitude, there is a higher Kd so O2 has a low affinity for Hb (or vice versa) and does not bind very well, Kd is 8mM, maybe because there is less O2 at sea level the Kd is 5mM which is less than 5 and says that at sea level there is a higher affinity for Kd Within hours of being at altitude, the concentration of BPG increases from 5 mM to 8 mM the curve is looking more hyperbolic showing that there is an increased affinity for O2, BPG brings that back up to sea level – levels. What does BPG do to the binding curve?- Makes it more hyperbolic, BPG shifts the oxygen saturation curve to the right  Hb has less affinity for O2  allowing it to release oxygen to the tissues (more than it did before) Physiologically, what is happening? - Hb is gaining less affinity for O2 so it can drop it off at the tissues
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affinity in the lungs
Affinity for O2 in the lungs is reduced slightly, but in peripheral tissues more significantly; so, even though less is bound initially, more of it is released in the peripheral tissue; result: ~ 37% of bound O2 is delivered to peripheral tissue!
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a study of the binding of hormone Z by receptor protein 1022, yielded the following data. what is the Kd for the binding of Z to P-1022 0.5 x 10^-9 1.0 x 10^-9 4.0 x 10^-9 10 x 10^-9
if [Protein] = [protein + ligand] then you can say y50% of L its bound the answer is 4.0 x 10^-9 because. this is when the [protein] = [protein + ligand]
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catalysts
Catalysts: change rate of reaction without a net change of itself. So: they increase reaction rates without being used up; do not alter equilibrium (Keq)
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Enzyme Vast majority of biological catalysts are what how do globular proteins interact
a substance produced by a living organism that acts as a catalyst to bring about a specific biochemical reaction. Vast majority of biological catalysts are globular proteins globular protein interact via side-side chain interactions, h-bonding, ionic interactions and have subunits, domains and motifs
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Substrate Product Active Site:
Substrate: substance acted upon (specific!) Product: results Active Site: location in the enzyme where the reaction occurs
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what do enzymes do wihtout enzymes, biochemical rxns are fast or slow?
Enzymes Increase Reaction Rates by lowering the activation energy Without enzymes, biochemical reactions are slow. This is a good thing. Enzymes can increase reaction rates (depending on the reaction) up to 1017 X faster than the uncatalyzed reaction!
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what is the enzyme eqn what do enzymes not effect Interactions between enzyme and substrate at the active site occurs how what is the rate limting step
E+ S <-> ES <-> transition state <-> EP <-> E + P Many enzymes act in the forward and reverse reactions; helping the reaction reach equilibrium (but not affecting equilibrium, only rate) Interactions between enzyme and substrate at the active site  binding affinity
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Enzyme activity is regulated by: how many enzymes require metal ions Holoenzyme Coenzymes Enzymes can be regulated
regulated by: pH Temperature [enzyme] [substrate] [cofactors/coenzymes] (stay tuned) 1/3 of all known enzymes require metal ions (metalloenzymes) Holoenzyme: apoenzyme (inactive) + cofactor/coenzyme/metal ion (prosthetic group) Coenzymes are often vitamins and essential to our diet. Enzymes can be regulated: enzymes can be activated (phosphorylated) or inactivated (de-)
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activation energy (Ea) what is the free energy of activation ∆G‡ what does Ea equal in a graph what does the rate of rxn relate to A higher ∆G‡ corresponds to a fast or slow rxn what is ∆G and is it changed by enzyme
the minimum amount of energy that colliding molecules have in order for a chemical rxn to take place In biochemistry, activation energy is this is free energy of activation ∆G‡ on a graph, Ea is the difference between energy levels of the ground state and the transition state (typically higher energy than both ground states) The rate of a reaction relates to activation energy. A higher ∆G‡ corresponds to a slower reaction. ∆G is the energy difference between the substrate and product! NOT CHANGED BY ENZYME
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enzymes increase rxn rates by shifting equilibrium to the substrates shifting equilibrium to the products decreasing ∆G‡ increasing ∆G‡ decreasing ∆G‡ increasing ∆G‡
decreasing ∆G‡
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what is not changed by an enzyme what instead is changed by the enzyme how are rxn rates set what is the rate-limiting step what does a catalyst do what is ∆G‡ chemically
∆G (substrate and product) is not changed by an enzyme The free energy difference between the substrate and the transition state ∆G‡ is changed by an enzyme Reaction rates are set by the activation energy. The activation energy “hill”, therefore, is the rate-limiting step! A catalyst reduces the activation energy of a reaction! ∆G‡ is the amount of energy needed to convert 1 mol of the substrate from the ground state to the transition state
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the binding site of an enzyme is most complementary to the substrate transition state product equilibrium
transition state
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The more molecules reaching the transition state means what what does the enzyme bind the best and what kind of interactions are there
The more molecules reaching the transition state means the more likely product forms, meaning the faster the reaction rate to reach equilibrium. Enzymes bind the transition state BEST (more weak interactions). Induced fit and molecular complementarity
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enzyme-substrate complex what is the enzyme-substrate complex mediated by what does induced fit lead to and what does it increase Enzymes act as catalysts because of their ability to:
Enzyme-catalyzed reactions begin with the substrate entering the active site to form the enzyme-substrate complex This is mediated by shape and weak, noncovalent interactions Induced fit leads to both enzyme and substrate shape changes. This increases noncovalent interactions (desolvation - strip away H2O - Entropy?) Enzymes act as catalysts because of their ability to: 1. Bring substrate(s) and active sites together: proximity effect 2. Hold substrate(s) at the exact distance and exact orientation necessary for the reaction: orientation effect 3. Provide acidic, basic, or other types of groups required for catalysis: catalytic effect 4. Lower the energy barrier by inducing strain in bonds in the substrate molecule: energy effect
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How Enzymes Work: Catalytic Effect Mechanisms on their substrates General acid-base catalysis Covalent catalysis Metal ion catalyst
General acid-base catalysis: proton donation/removal by an acid/base lowers free energy of the transition state Covalent catalysis: acceleration through transient formation of an enzyme-substrate bond Metal ion catalysis: metal ions In reality, many enzymes use a combination of these strategies participate in the reaction mechanism
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Acid catalysis Base catalysis Amino Acids:
Acid catalysis: proton transfer from an acid lowers the free energy of the reaction’s transition state Base catalysis: proton removal by a base lowers the free energy of the reaction’s transition state Amino Acids: Glu, Asp, Lys, Arg, Cys, His, Ser, Tyr
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metal ion + acid-base
Metal ions bound to the enzyme Metal ions: help orient the substrate for the reaction Stabilize negative charges Mediate oxidation-reduction reactions
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If we understand how enzymes catalyze reactions what can we do Key Factors Affecting Rate: Usually [E] << [S]. Under these conditions…
If we understand how enzymes catalyze reactions, we can determine how to inhibit or stimulate them. Key Factors Affecting Rate: concentrations of enzyme ([E]) and substrate(s) ([S]) The maximum achievable reaction rate is proportional to the concentration of the limiting reactant [E].
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Michaelis and Menten developed a series of mathematical relationships to explain the behavior of many nonallosteric enzymes. what does nonallosteric mean The initial reaction velocity (V0) is The maximum velocity, (Vmax) is where this process looks a lot like
nonallosteric means only 1 binding site The initial reaction velocity (V0) is the rate at which substrate is consumed or product (molarity/time) is formed at the START of the reaction The maximum velocity, (Vmax) is where the rate plateaus looks like Kd Note: Vmax is not an inherent property of an enzyme. It depends on reaction conditions  [E] At low [S], V0 increases with an increase in [S]. At higher [S], V0 increases by smaller and smaller amounts in response to increased [S]. The rate never exceeds a maximum rate, Vmax
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What is Km Small Km indicates High Km indicates Km is the
Km is a constant; it is intrinsic to the particular enzyme-substrate pair. For a given enzyme, each substrate has its own Km Small Km indicates tight binding (curve shifted to the left) High Km indicates weak binding (curve shifted to the right) Km is the [S] at which half of the enzyme molecules have their active sites occupied with S and are generating ES. Km is the [S] at which V0 = ½ Vmax
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what do enzymes do what does it do to the: transition state activation energy rate constant (k) delta G
promote the formation of a transition state lower the activation energy increase the magnitude of the rate constant for both the forward and reverse reactions, as the enzyme catalyzes both reactions. cannot change the delta G (which is also equilibrium)
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what terms are important for enzymatic reactions
[S] Vo Vmax Km
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what is Km how does Km relate to Vmax what is the Michaelis-Menten Equation what does the graph look like
The substrate concentration at which half of the enzyme active sites are bound by substrate! Km is the [S] that generates a rate of 1/2 Vmax Vo = (Vmax)([S])/(Km + [S]) graph looks like a hyperbola
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do we. always want some reactions to keep going? so what do we do what can you do if you know a lot about the strcuture of an enzyme how do many drugs work
Sometimes we want reactions to stop, so we inhibit enzymes Alternatively, if you know a lot about the enzyme’s structure, one can rationally design an inhibitor to fit the active site (target-based design). Many drugs, and toxic agents, act by inhibiting enzymes!
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what are inhibitors what do irreversible inhibitors do to an enzyme what can one inhibitory molecule do what are 2 examples of this
Irreversible Inhibitors (inactivators) Usually cause stable, covalent alterations in the enzyme. One inhibitory molecule can permanently shut off one enzyme molecule. Often powerful toxins, but also drugs. Example: organophosphorous compounds (sarin, insecticides malathion and parathion) bind to and inhibit acetylcholinesterase Example: aspirin binds to and inhibits cyclooxygenase (COX) Example: penicillin binds to and inhibits transpeptidase which makes bacterial cell walls
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how do reversible inhibitors bind an enzyme? how are they related to substrates? they are used as drugs to do what what are the 2 categories
Bind to, and dissociate from the enzyme (binding is easily reversed) Interact with the enzyme through noncovalent association/dissociation reactions They are often structural analogs of substrates (fit and inhibit) or products (feedback) They are often used as drugs to slow down an enzyme The fall into two major categories - Competitive - Not Competitive Uncompetitive Mixed
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Reversible Enzyme Inhibition: what can it bind to what do they resemble what do they do for the active site? does it affect the catalysis for substrate to products, what does that mean for Vmax how does increasing the [S] affect the type of inhibition, what does that mean for the Km
what kind of inhibitions is this can bind - the free enzyme and prevent binding of the substrate (Competitive) - The enzyme-substrate complex and prevent the SP reaction Competitive Inhibitors - Resemble the normal substrate molecule - Compete for admission into the active site Inhibitor does not affect catalysis of SP, Vmax is unchanged! Increasing the [S] favors the likelihood of S binding to the enzyme instead of the inhibitor, I. Km shifts to the right on the graph and thus has a lower affinity
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is competitive inhibition permanent what is dihydrofolate what is methotrexate
not permanent Dihydrofolate is a substrate used for nucleotide synthesis Cancer cells manufacture significant amounts of nucleotides necessary for rapid cell division Methotrexate (inhibitor) is used for the treatment of some cancers (high doses) and for the treatment of various immunologic diseases such as rheumatoid arthritis
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The Kinetics of Competitive Inhibition what does increasing inhibition do to Km even if we increase the inhibitor, does the Vmax change or stay the same what is the inhibitor competing for what happens if the [S] is really high summary for competitive inhibtion
moves km to the right and lowers the affinity Vmax stays the same Compare the top blue curve (no inhibitor) with the other lines (increased [inhibitor]) Remember Km? Vmax? Note: the presence of the inhibitor lowers and shifts the curve; affecting Km All curves will eventually reach the same plateau, and therefore the same Vmax I is competing with S for the active site of E. If [S] is really high, it will “win” the competition for the active site The Km has moved to the right in the presence of I, but Vmax is unchanged.
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what does the lineweaver-Burk plot show what is it the inverse of and what can it show us
Lineweaver-Burk (double-reciprocal) plots can be used to distinguish types of inhibition Using the reciprocal of the Michaelis-Menten the equation allows a more simplistic way to compare different types of inhibition and easily extract kinetic values.
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Competitive Inhibition what does the y-intercept equal and does it change what is the slope and does it change what is the x-intercept and does it change
Competitive Inhibition: Increases Km; Vmax the same Competitive Inhibition: Increases Km; Vmax the same Pay attention to the slope… (Km/Vmax) The y-intercept (1/Vmax) is always the same The slope (Km/Vmax) increases with the inhibitor The x-intercept (-1/Km) shifts to the right to show an increased Km in the presence of an inhibitor.
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Reversible Enzyme Inhibition: Uncompetitive what can reversible inhibitors bind what does it bind to how is its binding site created how can inhibition be overcome
Reversible Inhibitors can bind to: The free enzyme and prevents binding of the substrate (Competitive) The enzyme-substrate complex and prevent the SP reaction (Uncompetitive) Uncompetitive Inhibitors - Binds only to the enzyme-substrate [ES] complex The binding site for the inhibitor isn’t created until the enzyme binds the substrate Inhibition cannot be overcome by the addition of more substrate
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The Kinetics of Uncompetitive Inhibition what does it bind are any products formed? do Km and Vmax increase, decrease or remain the same what does it decrease
Compare the top blue curve (no inhibitor) with the other lines (increased [inhibitor]) In uncompetitive inhibition, the inhibitor binds only to the ES complex. This E-S-I complex does not go to form any product. Remember Vmax? With a decreased Vmax, by definition, the Km must also decrease by the same amount as Vmax Uncompetitive inhibition decreases Vmax and Km (though can be hard to see).
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L/B Plots of Uncompetitive Inhibition are Km and Vmax decreased, increased or remain the same does the slope remain the same why or why not does 1/Vmax (which is what) increase, decrease or remain the same does the -1/Km shift right or left and what does that mean on the plot, how are the lines in reference to each other
Uncompetitive Inhibition: Decreases Km and Vmax Pay attention to the slope… (Km/Vmax) The slope remains unchanged because Km and Vmax are reduced by equal amounts The y-intercept (1/Vmax) decreases The x-intercept (-1/Km) shifts to the left to show an decreased Km in the presence of inhibitor. parallel lines!
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in enzymology what is the rate-limiting step
transition state