Shared Flashcard Set

Details

Biochem test 1
all
174
Biochemistry
Undergraduate 3
10/20/2013

Additional Biochemistry Flashcards

 


 

Cards

Term
enolase and DNA polymerase are proteins that share which role in the body?
Definition
catalysis
Term
hemoglobin and lactose permease are proteins that share what duty in the body?
Definition
transport (hemoglobin transports blood; lactose permease carries lactose across the cell membrane)
Term
what are four main roles of proteins in biological systems? provide an example of each.
Definition
catalysis (DNA polymerase); transport (hemoglobin); structure (collagen); motion (myosin, actin)
Term
describe L-alanine and D-alanine
Definition
L-alanine has the NH3+ group on the LEFT (with an H on the right, and the CH3 R group on the bottom.)

D-alanine has the NH3+ amino group on the RIGHT.
Term
what is the difference between an L sugar and an R sugar?
Definition

L: the bottom -OH group is on the LEFT.

 

D: the bottom -OH group is on the RIGHT.

Term
what are the three aromatic amino acids? what test identifies them?
Definition

- phenylalanine

- tyrosine

- tryptophan

 

these guys are aromatic; aromatic amino acids absorb in the UV spectrum, not just the infrared spectrum like other amino acids. 

 

- they also display weak fluorescence

 

TRYPTOPHAN ONLY displays phosphorescence (which means it emits light for a long time.)

Term
hemoglobin is oligomeric and has two protomers. What does this mean?
Definition

oligomeric: it contains at least two polypeptide chains that are identical.

 

protomers: polypeptide chains which are identical.

Term
what is a conjugated protein?
Definition
a conjugated protein is a protein that contains permanantly associated chemical componenents in addition to amino acids. The non-amino acid part of a conjugated protein is called a PROSTHETIC GROUP. The prosthetic group can be a lipid (lipoprotein), a sugar (glycoprotein), or a metal (metalloprotein)
Term
what is dialysis?
Definition
seperating proteins from small solutes by allowing the small solutes to flow through a semipermeable membrane into a larger solution that draws them out
Term
how does ion-exchange chromotography work? what charge does a cation exchanger have? what about an anion exchanger?
Definition

resin beads with a certain charge stick to proteins with an opposite charge, keeping them from eluting as fast as those proteins with a similar charge.

a CATION exchanger attracts cations (is negatively charged)

 

an ANION exchanger attracts anions (is positively charged) 

Term
in size-exclusion chromotography, will larger or smaller proteins elute faster? why?
Definition
LARGER proteins will elute faster, because the smaller ones are trapped in the porous beads. the larger ones don't fit into the pores, so bypass the beads quickly.
Term
what is affinity chromotography?
Definition
you find the ligand that binds to your protein of interest and it becomes the stationary phase in your column. these are eluted last.
Term
two-dimensional electrophoresis
Definition
1. proteins are seperated based on isoelectric point (move to an area where the pH matches pI)

2. then those seperated proteins are bound to SDS and seperated by SIZE
Term

define: 

 

- activity

- specific activity

Definition

activity: the number of enzyme units in a solution

 

specific activity: the number of enzyme units/milligram of total protein

- specific activity is a measure of enzyme purity

Term
Sanger's N-terminus determination
Definition

1. react N-terminus with Sanger's Reagent

2. cleave all the bonds

3. check with amino group is bound to Sanger's Reagent

Term
Edman Degradation
Definition

amino acid reacted to PITC; cleaves N-terminus amino acids one by one

 

- becomes less accurate the bigger the protein is

- and you basically have to guess where the disulfide bonds are

Term
what are two methods of getting rid of disulfide bonds?
Definition

- reduction and oxidization

- reduction (turning into -SH) must be followed by carboxymethylaton to keep the -SH from reacting again into another disulfide bond

Term
define: protease
Definition
an enzyme that catalyzes the hydrolytic cleavage of peptide bonds
Term
Merrifeld peptide synthesis
Definition

1. protect the N-terminus of aa with Fmoc

2. bind C-terminus to reactive Cl-CH2-bead resin

3. protect N-terminus of a second aa and activate it's C-terminus with DCC

4. take of Fmoc from first aa

5. react N-terminus of first aa to activated c-terminus of second aa

6. remove Fmoc protective group from second aa

7. repeat

 

weaknesses: small differences in STEPWISE yield can strongly lower OVERALL yield.

Term
what forces overcome the conformational entropy of an unfolded protein?
Definition
disulfide bonds and weak noncovalent interactions (hydrogen bonds)
Term
which are stronger, disulfide or weak noncovalent bonds? which predominate in strength in proteins, and why?
Definition
disulfide bonds are much stronger, but there are so many noncovalent bonds that they predominate in strength in proteins.
Term
what common rule of protein structure comes about because ordered water-protein interactions are unfavorable?
Definition
hydrophobic parts of the protein are shielded inside the protein. This minimizes the size of the solvation layer of water, minimizing it's ordered (and therefore entropically unfavorable) state.
Term
why do polar elements of proteins form H-bonds preferably with each other, and not with water?
Definition
because water H-bonds best with itself, it bonding with anything else, even a very polar protein, causes a net decrease in hydrogen bonding (causes an unfavorable decrease in overall water entropy). Therefore there is an entropic drive for water to bond with ITSELF and that leaves these polar groups free to bind with each other.
Term
what defines the "stability" of a protein?
Definition
stability = how well a protein is able to maintain its native conformation
Term
what are the most important weak interactions re: protein structure?
Definition
hydrophobic interactions (i.e. keeping the nonpolar molecules on the inside of the protein, away from water)
Term
what factor changes the strength of a salt bridge (covalent interaction within a protein)/ion pair?
Definition
the electrostatic environment - a polar environment makes the salt bridge have a smaller entropic advantage (less unfavorable to bind to water rather than each other), whereas a nonpolar environment makes it very entropically favorable to bind ion pairs to each other
Term
explain why polypeptide chains have a rigid structure.
Definition

the C-N bonds of a polypeptide chain have double bond character, making the =O (carbonyl oxygen) and the -H (hydrogen on the N) planar to each other, where they share electrons and therefore cannot rotate freely. Rotation is only possible between the Calpha and C=O carbons, and the N and C carbons.

 

this limits the number of conformations a polypeptide chain can have!

Term
how often does the regular structure of an alpha helix repeat? how many residues is this?
Definition

- 5.4 angstroms

 

- 3.6 residues

Term
which amino acid is most likely to form alpha-helical conformation?
Definition
alanine
Term
what is the charge relationship between amino acids 3 or 4 residues away from each other in alpha helixes? Why?
Definition
they are likely to be oppositely charged (form salt bridges); this is because when looking at the alpha-helix head on, these pairs interact with each other
Term
why would two aromatic amino acids be spaced 3 or 4 residues away from each other in an alpha helix?
Definition
because of the structure of the alpha helix, this would put them in close proximity to each other and facilitate hydrophobic interactions
Term
explain why proline is so unlikely to be in an alpha helix
Definition
its the only amino acid that has a "ring" R-group --> it's nitrogen has no hydrogen so it's unlikely to H-bond, decreasing the likelihood that it will show up in an alpha helix
Term
explain why glycine is unlikely to be in an alpha helix
Definition
with -H as its R group, it has a lot of conformational flexibility, so is unlikely to form a stable alpha helix
Term
which is more likely to be found at the amino terminus of an alpha helix, a positively or negatively charged amino acid? Why?
Definition
there is an overall dipole on the alpha helix, which results from the partial dipole on each carbonyl-nitrogen bond (one for every aa), and so increases with helix length. The charge rests on the terminal c-terminus (negative) and n-terminus (positive). Therefore positively charged aa are more likely to be found near the c-terminus end, and negatively charged aa are more likely to be found near the n-terminus end.
Term
what are the five things that determine how stable any given alpha helix structure is?
Definition

1. how likely each aa is to form an alpha helix

2. the interactions between the R-groups of aa making up the alpha helix, particularly those 3 or 4 residues apart

3. the bulkiness of adjacent R groups (if they are two big they push on each other and destabalize)

4. the more proline (ring that can't H-bond) and glycine (-H is -R so too flexible to reliably helix), the less likely to form an alpha helix

5. interactions between the aa at the ends of the chain and the overall dipole charges

Term
describe a beta turn
Definition

four amino acid residues

 

the carbonyl oxygen of the first forms a hydrogen bond with the nitrogen of the fourth

 

mostly happens with glycine (flexible) and proline (cis configuration is easy)

 

happen near the surface

Term
almost all peptide bonds are ________ configuration. However, with turns involving _______, which occur often in the ___________ structure, about 6% are ________.
Definition
almost all peptide bonds are TRANS configuration. However, with turns involving PROLINE, which occur often in the BETA TURN structure, about 6% are CIS.
Term
circular dichroism (CD)
Definition
a way to assess which common secondary structures are present in a protein. This measures the absorbtion spectrum for a protein; how the protein absorbs polarized light will change based on structure, so you can run your results against a beta-sheet and alpha-helix baseline.
Term
structure of alpha keratin
Definition

- made of two alpha helixes matched parallel (with n-terminus at the same end) and coiled together lefthandedly in a supracoil (quartenary structure)

 

-strength enhanced by covalent cross-linking: disulfide bonds

 

- forms hair, horn, etc.

Term
describe the structure of collagen
Definition

- made of three ALPHA CHAINS, which are NOT the same as alpha helixes. These guys have a lefthanded twist.

 

- they wrap around each other righthandedly.

 

- forms tendons, cartilage

Term
describe the side chains of myoglobin
Definition

hydrophobic side chains inside; hydrophilic side chains outside (and most are hydrated)

 

- the hydrophobic side chains are so closely packed that van-der-waals forces between them play a huge role in stabilizing the protein structure

Term
why is it important that the heme group in myoglobin is not exposed to solvent?
Definition
ferrous (Fe2+) bind oxygen; in oxygenated solvent, it's oxidized to ferric (Fe3+), which does NOT bind oxygen.
Term
what is a motif?
Definition
a part of a protein containing multiple elements of secondary structure (like betasheet-alphahelix-betasheet, or a beta barrel)
Term
what is a domain?
Definition
a part of a protein that is independently stable; if you cut it off from the rest of the protein, it would retain it's shape and function. These often have their own functions seperate from the other domains.
Term
NOESY
Definition
an NMR technique that measures distance-dependant coupling of nearby atoms
Term
TOCSY
Definition
an NMR technique that allows the measurement of distance-dependent coupling of atoms that are connected by COVALENT BONDS (like NOESY, but NOESY works on atoms that aren't connected covalently)
Term
when found together in a protein, alpha-helixes and beta-sheets are generally in different structural layers. Why?
Definition
because H-bonding between the two structures is difficult.
Term
connections between beta-sheets are generally ________ handed because of the _______ handed twist in beta strands.
Definition
connections between beta-sheets are generally RIGHT handed because of the RIGHT handed twist in beta strands.
Term
what do we learn from the fact that the denaturation/renaturation point of a given protein is very sudden?
Definition
it's a COOPERATIVE process - that is, destabilizing one part of the protein will destabilize the rest, and it will all suddenly come apart.
Term
Christian Anfinson and ribonuclease
Definition
experiment: denatured ribonuclease with urea and mercaptoethanol, causing denaturation. Later removed these, and it spontaneously refolded perfectly!
Term
Hsp70 and Hsp40 are molecular chaperones. What do they do?
Definition
they prevent inappropriate aggregation; they DON'T promote folding on their own.
Term
what does chaperonin do? How does that contrast with the other chaperone molecule (name it)?
Definition
chaperonins: actively fold the proteins. This is in contrast to Hsp 70 and Hsp 40, which PREVENT the protein from folding inappropriately
Term
PDI and PPI
Definition

these are two enzymes that catalyze protein folding.

 

PDI: messes with the sulfide bonds until the right ones are formed.

PPI: changes proline from cis to trans and back, speeding the unfolding process

Term
amyloid fiber formation
Definition

- protein with aromatic proteins making up a beta sheet

- these start to self associate

- then are joined by other proteins, lengthening the beta sheet/amyloid structure

Term
describe a heme group
Definition

present in heme proteins like myoglobin and hemoglobin. Is made of protoporphyrin IX, with a bound Fe2+ atom in the middle. It is bound between four N, which donate electrons to keep the Fe from oxidizing and not being able to bind oxygen anymore.

 

in addition, Fe has two available bonds not taken up by N. One of them is occupixed by a His residue, because two oxygens binding at once will also oxidize it.

Term

explain the location of the following protein based on the name:

 

His93

His F8

Definition

His93: the histidine residue 93 residues away from the amino terminus

 

His F8: the eighth his residue in the F alpha helix

Term
Ka (including units)
Definition

the association constant of a protein for a ligand. Ka = [PL]/[P][L]

Therefore the larger Ka is, the more the protein likes to stick to the ligand. 

 

units: M-1

 

Ka is also equal to ka/kd, which are the association/dissociation rate constants.

Term
What are the units of the rate constant of a first order reaction? Second order?
Definition

first order reaction (depends on concentration of one thing): s-1

 

second order reaction (depends on the concentration of two things): M-1s-1

Term
how do you find kd from ka?
Definition
kd = 1/ka and vice versa
Term
when concentration of free ligand [L] = kd, what is happening?
Definition
this is the point at which half of the available ligand is bound to protein
Term
if you say that P50 of oxygen is 0.26 kPa, what does that mean?
Definition
at a pressure of 0.26 kPa, 50% of oxygen present is bound to myoglobin. Since 0.26 is relatively low pressure, we can see that oxygen binds very happily to myoglobin.
Term
a lower kd represents a ___________ affinity of ligand to protein
Definition
a lower kd represents a HIGHER affinity of ligand to protein --> the lower kd, the more "sticky" the ligand/protein interaction (i.e. it dissociates less)
Term
why are you allowed to substitute [O2] for the partial pressure of O2 when finding the kd of oxygen?
Definition
because partial pressure is directly proportional to concentration of a gas
Term
if the partial pressure of oxygen in the blood is 13 kPa, and in the tissue is 4 kPa, and the kd of oxygen to myoglobin is 0.26, explain what would happen if we tried to use myoglobin as an oxygen carrier.
Definition
it would bind the oxygen really well in the blood; but it would hold on to it in the lungs! pOin the lungs is still much higher than kd, so way more than half of the oxygen would still be bound
Term
T state vs. R state of hemoglobin
Definition
T (tense) state does not bind oxygen as well as R (relaxed) state. Oxygen binding to T state causes transformation to R state.
Term
What stabilizes the T-state of hemoglobin where there is no oxygen bound? What happens when oxygen DOES bind?
Definition
T-state is stabilized by the presence of lots of ion pairs, mostly found in the alpha1/beta2 and alpha2/beta1 interfaces.

In the T-state, the molecule is bent; but when oxygen binds, it becomes planar. This forces the subunits to move slightly, breaking some of those ion pairs and forming new ones.
Term
why is hemoglobin a good transport protein for oxygen? talk about what a sigmoidal curve is.
Definition
hemoglobin has a sigmoidal binding curve, which means that in a low-oxygen environment it has low affinity and in a high-oxygen environment it has high affinity. This is possible because of cooperative binding; that is, it has various subunits and oxygen binding to one of them can alter the conformation of the rest, increasing the affinity for oxygen further. Therefore, when concentration of oxygen is high (in the blood) oxygen is bound; and when it's low (in the tissue), oxygen is released.
Term
how many oxygen molecules can bind to a single hemoglobin? which binds most easily?
Definition
four; the last one binds most easily (because oxygen bound means greater affinity for oxygen in hemoglobin - R state)
Term
what is an allosteric protein?
Definition
a protein in which binding of a ligand to one site affects the binding properties of another site at the same protein (like hemoglobin)
Term
what is the difference between a homotropic and heterotropic allosteric protein?
Definition

homotropic allosteric protein: the molecule that binds to the protein and changes its ligand affinity IS the ligand

 

heterotropic allosteric protein: the molecule that binds to the protein and changes its ligand affinity is a different molecule entirely than the ligand

Term
what does a sigmoidal binding curve indicate?
Definition
that the protein in question has cooperative binding (binding affects further  binding)
Term
what are the two requirements for a protein to be allosteric? (binding affinity changes)
Definition

- must have multiple binding sites

 

- must have subunits that are able to interact with each other (usually stable next to unstable segments)

Term
what is nH? What does it mean if it's 1? Greater than 1?
Definition
nis the Hill coefficient, a measure of cooperativity in a multi-binding-site protein. If it's 1, the sites don't cooperate or affect each other at all. The greater the number above 1, the more they cooperate and affect each other.
Term
what is the theoretical meaning of a protein with n= n?
Definition
that would mean that the level of cooperativity in the protein was equal to the number of binding sites; this would mean that you would never find a protein that was only partially ligand bound. This never actually happens.
Term
what does n< 1 signify?
Definition
that binding affinity is NEGATIVE; that is, binding of ligand to one subunit of the protein impedes further binding/lowers affinity
Term
in both it's low-affinity and high-affinity states, nof hemoglobin is...
Definition
n= 1
Term
MWC model
Definition
this is the all-or-nothing model of ligand cooperative binding. All binding sites always match in affinity --> if more successful binding happens, they all make the switch from low to high at once; but you'll never see a molecule with some low and some high affinity binding sites.
Term
sequential model of ligand binding
Definition
different subunits can have different conformations. Binding to one subunit increases the likelihood of binding to another subunit, and ALSO increases the likelihood of a positive affinity conformational change of the other subunits.
Term
carbonic anhydrase
Definition

hydrates carbon dioxide in the blood to bicarbonate (with H+ as a product). This is needed because carbon dioxide isn't very soluble in blood and otherwise would form bubbles. 

 

This causes the tissues to become more acidic.

Term
How and why do COand Hconcentration affect the binding of Oby hemoglobin? (BOHR EFFECT)
Definition

hemoglobin transports all three molecules. When there is a lot of carbon dioxide and hydrogen (low pH), they both bind to hemoglobin and lower the affinity for oxygen, causing oxygen to be deposited in the tissue.

 

In the lungs, however, carbon dioxide is breathed out of the body. This stops its conversion to bicarbonate and stops the production of H+, raising pH. Therefore oxygen is free to bind to hemoglobin - until it leaves the lungs, and carbon dioxide concentration increases again in the tissues/pH goes down, the oxygen is dropped off again in the tissues.

Term
what is the exact mechanism for the release of Owhen pH goes down?
Definition
when His146 is protonated, it forms a salt bridge with Asp94. This stabilizes the T state, RAISES the pKa, and promotes release of oxygen.
Term
carbamate
Definition
carbon dioxide that bonds covalently with the n-terminus of hemoglobin, stabilizing the T-state and causing dissociation of oxygen
Term
BPG
Definition

reduces affinity of hemoglobin for oxygen; BPG concentration changes based on altitude (when you go higher up, you have more of it, so more oxygen is released into your blood.)

 

It binds to the T state and is NEGATIVELY charged, binding to the positively charged amino acids and stabilizing the T state. 

 

When oxygen binds, the cleft where BPG binds becomes smaller, expelling it, and raising oxygen affinity.

Term
sickle cell anemia
Definition

Glu-->Val mutation

 

Val, unlike Glu, has no negative charge.

 

- this creates a hydrophobic contact point on the outside surface

- and when hemoglobin is deoxygenated, these spots cause it to stick to other hemoglobins.

- this forms long, insoluble aggregates.

 

- these block capillaries

- and rupture easily, destroying a lot of the body's hemoglobin

Term
what is a globin?
Definition
an oxygen-binding protein
Term
why can't you bind oxygen with normal proteins? Why not with transition metals? why not pure heme groups? How DO you bind oxygen, if those two methods don't work?
Definition

normal protein side-chains: low affinity for oxygen

 

transition metals: generate free radicals in solution

 

heme group: would become oxidized to Fe3+ in solution, and stop binding oxygen

 

so you use a PROTEIN-BOUND HEME GROUP

Term
muscle contraction
Definition

myosin thick filament inside six actin thin filaments

 

myosin head: binds to actin.

 

atp binds to myosin --> myosin lets go of actin

 

 bound ATP hydrolized --> ADP + Phosphate still attached to myosin head

 

--> myosin changes conformation --> binds to actin filament further down the line --> phosphate is released

 

--> phosphate release causes myosin and actin to move relative to each other --> causes ADP to be released

 

--> now myosin head is holding tightly again

Term
tropomyosin and troponin
Definition
these are bound to actin when the muscle is relaxed, blocking myosin binding. When the muscle needs to contract, Ca2+ binds to troponin, causing a conformational change and moving them both out of the way so myosin can bind.
Term
what are the three things that an enzyme might need to work properly?
Definition

- cofactor (an inorganic metal ion)

 

- coenzyme (a complicated organic or organometallic molecule)

 

- prosthetic group - if either of these is covalently (or else very tightly) bound to the enzyme, either a cofactor or a coenzyme is called a prosthetic group

Term
holoenzyme vs. apoenzyme
Definition

holoenzyme: enzyme + cofactor/coenzyme/prosthetic group

 

apoenzyme: the enzyme without its cofactor/coenzyme/prosthetic group

Term

identify the functions of the following enzyme groups:

 

- oxidoreductases

 

- transferases

 

- hydrolases

 

- lyases

 

- isomerases

 

- ligases

Definition

oxidoreductases: transfer electrons (OH- or H+)

 

transferases: group transfer reactions

 

hydrolases: hydrolysis reactions 

 

lyases: cleavage resulting in elimination, or addition of groups to double bonds

 

isomerases: rearrangement of groups to yield isomeric forms

 

ligases: formation of organic bonds by condensation reactions - coupled to ATP or other cofactors

Term
what is the difference between ΔG° and ΔG'°?
Definition
ΔG° is the standard free energy change in a reaction; ΔG'° is the free energy change when that reaction is at biological pH, 7.0
Term
what is the difference between ΔG° and ΔG‡?
Definition

ΔG° is the change in free energy; i.e. the net energy difference between the substrate and the product of a reaction. 

 

ΔG‡ is the energy it takes to reach the TRANSITION STATE. This is what the reaction rate depends upon, NOT on ΔG°!

Term
What is affected about a reaction when an enzyme is present? What is NOT affected?
Definition

affected: the rate of reaction is much faster.

 

NOT affected: the reaction equilibrium remains the same.

Term
in a reaction with a rate constant k of 0.03-1s, how much substrate will be converted to product in 1s?
Definition
3%
Term
the relationship between the rate constant k of a reaction and ΔG‡ is __________ and _________
Definition

the relationship betwee rate constant k of a reaction and ΔG‡ is INVERSE and EXPONENTIAL.

 

This means that a higher activation energy means a slower reaction rate.

Term
what are the two interactions between enzyme and substrate that lower the activation energy of the reaction?
Definition

- covalent

 

- noncovalent (this produces BINDING ENERGY)

Term
ΔGB
Definition
BINDING ENERGY --> the energy that is released from the weak interactions of the enzyme-substrate complex formation. This is a MAJOR source of free energy used by enzymes to lower the activation energies of reactions.
Term
the enzyme is complementary to the ________ of the substrate
Definition
the enzyme is complementary to the TRANSITION STATE of the substrate
Term
how do enzymes result in entropy reduction?
Definition
they hold the substrate in a way that it's physically easier (lower energy) to react. For example, it can make a second-order reaction react as if it were a first-order reaction by holding the two molecules together.
Term
desolvation
Definition
a way that enzymes reduce the transition state energy and increase the rate. The new weak interactions formed in the ES complex replace the hydrogen bonds between the water and the substrate that would otherwise impede the reaction.
Term
why are acid-base catalysts necesary in enzymatic reactions?
Definition
in an enzyme, the substrate is shielded from water in the enzyme active site. In a normal reaction, water can donate or accept electrons and stabilize the transition state of a reaction before it breaks down to reactants again. When water can't reach the molecule to stabilize it, certain amino acids have to act as the acid-base stabilizers.
Term
what is specific acid-base catalysis? General acid-base catalysis?
Definition

specific: when water is the electron donor and acceptor that stabilizes the reaction

 

general: when an enzyme does it

Term
what are two possible ways that metal ion catalysis works?
Definition

1. the metal ions that are bound to the enzyme can interact with the substrate and orient the substrate for reaction, or stabilize charged transition sites. 

 

2. metals can become oxidized or reduced to mediate oxydization/reduction reactions.

Term
how does the large size of enzymes aid its function?
Definition
it has a lot of available interactions that can donate energy to offset the activation energy
Term
what is the steady-state assumption in Michaelis-Menton kinetics?
Definition
that when saturated with [S], ES levels are constant
Term
what did Michaelis-Menton assume was the rate limiting step in an enzymatic reaction?
Definition
the breakdown of the ES complex to E + P
Term
what is the practical definition of Km?
Definition
Km is equal to the substrate concentration [S] where reaction rate is half of maximum.
Term
what is kcat?
Definition

1. the rate constant of the rate-limiting step in an enzyme-catalyzed reaction

 

2. the TURNOVER NUMBER - kcat is the number of substrate molecules converted to product in a given unit of time on a SINGLE enzyme molecule, when enzyme is saturated with substrate.

 

the unit is s-1

Term
what is the specificity constant?
Definition

kcat/km : turnover rate (how many molecules of substrate are turned to product for one enzyme unit in one time unit at enzyme saturation) over michaelis-menton constant ([S] when v = 1/2 vmax.

 

between 10and 10is the ideal value for specificity constant; the nearer it is to this value (which is a maximum value), the more efficient catalysis is of an enzyme.

Term
what are three common mechanisms for enzyme-catalyzed bisustrate treactions?
Definition

1. enzyme binds S1 and then S2 (must be in this order) and then releases them in a specific order

 

2. enzyme binds S1 and S2 in no specific order, and then releases them in no specific order

 

3. enzyme binds S1, then releases it, in the process having its conformation changed. This enables it to pick up and release S2, changing its conformation back to its original state.

Term
what do intersecting lines in a steady-state analysis of bisubstrate reactions indicate about the mechanism? What about nonintersecting lines?
Definition

intersecting lines: it's ordered or non-ordered, but it involves a ternery complex (both substrates bound to the enzyme at once.)

 

nonintersecting lines: ping-pong mechanism - there's no ternery complex; first one S binds, changes the conformation, is released, second S binds, returns conformation to normal upon release

Term
what are the two types of enzyme inhibitions?
Definition
reversible and irreversible
Term
describe the three types of reversible inhibition, their equilibrium constants, and where they bind
Definition

1. competitive inhibition; KI (the smaller this is, the better the inhibitor is at sticking); binds to E (in the active zone)

 

2. noncompetitive inhibition; K'I (the smaller this is, the better the inhibitor is at stickin); binds to ES complex, NOT just the enzyme!

 

3. mixed inhibition; this does NOT bind at the active site, but can bind either to the enzyme or the ES complex.

Term
what is α regarding enzyme inhibitors?
Definition
the factor by which km appears to increase when there's an inhibitor present (i.e. it takes more [S] to overpower the I, but if you don't know the I is there, km just looks bigger than it actually is.)
Term
what are two things that a noncompetitive inhibitor changes about the reaction kinetics?
Definition

- appears to raise Km

 

- lowers Vmax

Term
what is an irreversible inhibitor?
Definition
an inhibitor that either binds covalently to the enzyme or destroys it.
Term
why do enzymes function optimally at specific pH ranges?
Definition
pH change can deactivate the proper charge needed on the amino acids in the active sites; and on the charges on the protein ionized side chains, both of which have weak interaction roles that can be disrupted if their charges are messed with.
Term
protease
Definition
an enzyme that catalyzes the hydrolytic cleavage of peptide bonds
Term
bovine pancreatic chymotrypsin
Definition

- is a protease (catalyses hydrolytic cleavage of peptide bonds)

 

- cuts after aromatic amino acids (Trp, Phe, Tyr)

 

- has a two-step mechanism:

1. peptide bond cleaved --> enzyme bound by ester linkage to the carbonyl carbon (fast)

2. this linkage is hydrolized and the enzyme is regenerated (slow)

Term
how was the release of p-nitrophenol used to prove the acyl-enzyme intermediate of chymotrypsin?
Definition
at first, lots of p-nitrophenol is released (almost stoichiometric with the amount of chymotrypsin.) This reflects the fast acyl-formation step. Then, this release rate slows down, because the cleavage and regen step is slower.
Term
a molecule with n chiral centers has how many enantiomers?
Definition
2n
Term
what would be the name of the 5-carbon ketose corresponding to the 5-carbon aldose D-ribose?
Definition
D-ribulose
Term
what is an epimer?
Definition
two sugars that differ only in the configuration around ONE chiral center is called an epimer
Term
what is the name of the molecule you get when you react an aldose sugar with an alcohol? A ketose sugar?
Definition

aldose sugar: ACETAL

 

ketose sugar: KETAL

Term
what is mutarotation?
Definition
interconversion between alpha and beta configuration of cyclic sugar forms (rotation around the anomeric carbon)
Term
what are the five-membered sugar rings called? the six-membered ones?
Definition
five-membered: furanose

six membered: pyranose (MUCH more stable)
Term
what is an aldonic acid?
Definition

what you get when you oxidize the aldehyde carbon of a sugar HO-C=O

          |

Term
what is a reducing sugar?
Definition
a sugar whose carbon can be oxidized - ALDOSES, not ketoses (with some exceptions where it can be first turned into an aldose.)
Term
what is the reducing end of a polysaccharide?
Definition
the one sugar on the polypeptide chain that doesn't have its anomeric carbon bound in a glycocidic linkage, and can therefore become linear, and can therefore be oxidized to aldonic acid
Term
what are the two categories of polysaccharides describing the structure?
Definition

homopolysaccharides/heteropolysaccharides (contains one repeated monomer or different kinds)

 

branched/unbranched

Term
glycoseaminoglycans
Definition

molecules made up of alternating:

 

- uronic acids

- amino sugar residues (N-acetylglucoseamine or N-acetylgalactoseamine)

 

they are VERY negatively charged and hang out in the extracellular matrix. To keep the negative charges (uronic acids and esterified sulfide groups) away from each other, it winds into a helix with these charges on opposite sides.

Term
starch, glycogen, and cellulose
Definition

starch: stores energy in plants. It's a homopolysaccharide for glucose. Amylose is linear, amylopectin is branched.

 

glycogen: energy storage in aminals. Homopolysaccharide for animals. branched.

 

cellulose: structural support in plants. Homopolysaccharide for glucose. Branched.

Term
what is the unit that comprises both glycogen and starch?
Definition
D-glucose with (α1-->4) linkages
Term
what is the repeating unit of both chitin and cellulose?
Definition
D-glucose in (β1-->4) linkages
Term
proteoglycan
Definition
a glycosaminoglycan (uronic acid-amino sugar) bound covalently to a membrane protein (or secreted protein). Then the charged glycosaminoglycan chain can interact with extracellular goings-on.
Term
glycoproteins
Definition

one or more oligosaccharides bound covelently to a protein. Found on outer face of plasma membrane, in ECM, and in the blood; also sometimes inside the cell on the organelles. 

 

- form highly specific recognition sites for binding by lectins

Term
how are proteoglycans linked? (how is the glucosaminoglycan linked to the protein?)
Definition
by a tetrasaccharide linker connected to a SERINE residue in the protein.
Term
what is an NS domain?
Definition
a very sulfonated (highly negatively charged) domain of a proteoglycan
Term
what are four types of protein interactions with the NS domains of a proteoglycan?
Definition

1. conformational activation --> binding to the NS domain changes the conformation of protein, allowing it to accept a factor

 

2. enhanced protein-protein interaction --> binding of each protein to NS holds them in a way that makes it easier to bind to each other

 

3. coreceptor for extracellular ligands --> NS binds both a cofactor and its ligand, bringing them together

 

4. cell surface localization/concentration --> NS ionically attracts positively charged molecules and holds them in a certain place they need to be

Term
describe the two kinds of oligosaccharide-protein bonds in glycoproteins
Definition

1. O-linked

 

the carbohydrate is attached by its anomeric carbon to the -OH of a SER or THR

 

2. N-linked

 

the carbohydrate is attached by its anomeric carbon to the AMIDE NITROGEN of ASN

Term
categorize the following: heparan sulfate, chondroitin sulfate, dermatan sulfate, keratan sulfate
Definition
glucosaminoglycans - uronicacid-aminosugar with sulfonated side chains
Term
what are the two ways a glycosaminoglycan can be attached to the outside of a plasma membrane to form a proteoglycan?
Definition

1. covalently attached lipid

 

2. transmembrane protein

Term
viruses, bacterium, cell-cell interactions through [se]lectins, and receptors within the cell all interact with _____________, which are _______________ attached to the plasma membrane.
Definition
viruses, bacterium, cell-cell signalling interactions through [se]lectins, and receptors within the cell all interact with OLIGOSACCHARIDES, which are componants of glycolipids or glycoproteins associated with the membrane surface.
Term
what does the introduction of unsaturated fatty acids do to the packing of other fatty acids?
Definition
makes it less stable - the bend caused by the double bond in the hydrocarbon tail disrupts neat packing.
Term
in biological fatty acids, the configuration of double bonds is almost always _______
Definition
cis
Term
a fatty acid that is a solid at room temperature is likely to be ____________
Definition
UNSATURATED - it packs better and is more stable.
Term
why is it more efficient to store energy as fats?
Definition

triacylglycerols (fats) have more reduced double bonds than carbohydrates, so when you oxidize them you get lots more energy than glycogen breakdown. 

 

Also! 

 

they are hydrophobic, so you don't carry the extra water weight when storing them as you do with glucose.

 

 

Term

[image]

 

is an example of what kind of membrane lipid?

Definition
glycerophospholipid
Term

[image]

 

what kind of membrane lipid is this?

Definition
it's a glycerophospholipid - and an ether lipid (see the ether bond on top, instead of an ester bond?)
Term
describe the structure of a sphingolipid
Definition

- sphingosine backbone

 

- C2 has a long chain fatty acid with an AMIDE linkage

 

- C3 has either a phospholipid or a sugar attached

Term

[image]

 

what kind of membrane lipid is this?

Definition
sphingolipid
Term
what is the difference between gangliosides and cerebrosides?
Definition
both are kinds of sphingolipids. A ganglioside has a complex sugar as its polar head group; a cerebroside has a single sugar.
Term
are you more likely to find cholesterol in the plasma membrane, or mitochondrial membrane?
Definition
plasma membrane
Term
what holds integral membrane proteins in against the nonpolar lipid molecules of the phospholipid bilayer?
Definition
nonpolar interactions between the nonpolar side chains and the lipid chains
Term
phosphotidylserine (PS) moving to the outer leaflet of a membrane bilayer is a signal for what to happen?
Definition
either platelet activation, or apoptosis
Term
how would one remove an integral membrane protein?
Definition
it's stuck fast by hydrophobic interactions into the lipid bilayer, so you could take it out with a detergent  that interfered with the hydrophobic interactions.
Term
how are peripheral membrane proteins bound to the bilayer?
Definition
by electrostatic or hydrogen bonding to the hydrophilic domains of membrane proteins, or with the head groups of membrane lipids.
Term
what is an amphitropic protein?
Definition
a protein that is found both in the cytosol AND associated with membranes. Sometimes these are associated with the membrane through noncovalent interactions with a membrane protein or lipid. Sometimes, they are bound covalently to a membrane lipid. Generally speaking, their association with the membrane is REGULATED
Term
GPI linkages
Definition
glycosilated PI linked proteins. These are found only on the outer membrane.
Term
what makes a membrane stucturally and functionally asymmetric?
Definition
the proteins and lipids that make it up are inserted with "sidedness"
Term
what effect does the presence of sterols have on the fluidity of the plasma membrane?
Definition
sterols force the acyl chains into extended confirmation because they are rigid. This promotes the liquid-ordered phase (reducing fluidity in the bilayer)
Term
FRAP
Definition
fluorescence recovery after photobleaching - way to prove that LATERAL phospholipid diffusion throughout the membrane happens very fast.
Term
which two molecules associate to form microdomain "rafts"? Why these two, as opposed to _______?
Definition
sphingolipids and cholesterol associate because the long unsaturated acyl chains of sphingolipids mesh better with the rigid structure of cholesterol. Glycerophospholipids have shorter, unsaturated chains that don't bind as well.
Term
primary active transport vs. secondary active transport
Definition

primary active transport: transfer of something against its electronic or concentration gradient is coupled directly to an energy-generating reaction

 

secondary active transport: when endergonic "uphill" transport of one thing is coupled to exergonic "downhill" transport of another, that was originally pumped "uphill" by primary active transport.

Term
A high dielectric constant does what to the attractive forces between oppositely charged ions in a salt crystal?
Definition
DECREASES the attraction (as in water, which has a very high dielectric constant)
Term
describe the hydrophobic effect
Definition
i.e. hydrophobic interactions - in minimizing the ordered contact of water with a molecule, the nonpolar regions of that moleclue aggragate tightly together.
Term
why do acid-base reactions in aqueous solution move so incredibly fast?
Definition

PROTON HOPPING

 

protons being transferred between water molecules in a chain causes a NET movement of a proton (or OH-) over a long distance very quickly.

Term
what is osmotic pressure?
Definition
the pressure needed to resist water movement
Supporting users have an ad free experience!