Biochem: Ch 8, 2, 3 Flashcards
fluid mosaic model
accounts for presence of lipids, proteins, and carbohydrates in a dynamic, semisolid plasma membrane that surrounds cells
carbohydrates in cell membrane
create glycoprotein coat
cell recognition
cell membrane dynamics
not static
- lipids move freely in membrane thru diffusion and can assemble into lipid rafts
- flippases maintain transport of lipids
- proteins and carbohydrates move within membrane but are relatively slowed by large size
lipid rafts
collections of similar lipids with or without associated proteins that serve as attachment points for other biomolecules
serve roles in signaling
flippases
specific membrane proteins that maintain the bidirectional transport of lipids between the layers of the phospholipid bilayer in cells
list the following membrane components in order from post plentiful to least: carbs, lipids, proteins, nucleic acids
lipids > proteins > carbs > nucleic acids
triacylglycerols/triglycerides
storage lipids involved in human metabolic processes
contain 3 fatty acid chains esterified to glycerol molecule
tryglycerides and free fatty acids in membrane
act as phospholipid precursors
found in low levels in membrane
unsaturated fatty acids
have one ore more double bonds
impart fluidity to membrane
saturated fatty acids
main components of animal fats
decrease overal membrane fluidity
unhealthy
glycerolphospholipids
replace one fatty acid with phosphate group, which is often linked to toehr hydrophilic groups
cholesterol in cell membrane
present in large amounts
cholesterol
contributes to membrane fluidity and stability
waxes in cell membrane
present in small amounts
most prevalent in plants
waxes
- extremely hydrophobic
- waterproofing and defense
- can provide stability and rigidity in nonpolar tail region of cell membrane
- composed of long chain fatty acid and long chain alcohol –> high melting point
proteins located within cell membrane act as
transporters, cell adhesion molecules, and enzymes
transmembrane proteins
pass completely through lipid bilayer
can have one or more hydrophobic domains
most likely to function as receptors or channels
embedded proteins
associated with only the interior or exterior surface of cell membrane
most likely part of catalytic complex or involved in cellular communication
membrane associated (peripheral) proteins
act as recognition molecules or enzymes
extracellular ligands
bind to membrane receptors, which function as channels or enzymes in second messenger pathways
gap junctions
aka connexons
- direct cell-cell communication
- allow for rapid exchange of ions and other small molecules between adjacent cells
- formed by alignment and interaction of pores composed of 6 molecules of connexin
tight junctions
- prevent paracellular transport
- prevent solutes from leaking into space between cells
- do not provide intercellular transport
- found in epithelial cells
desmosomes and hemidesmosomes
anchor layers of epithelial tissue together
phospholipids spontaneously assemble into
why?
micelles or liposomes
due to hydrophobic interactions
micelles
small monolayer vesciles
liposomes
bilayered vesicles
sphingolipids
contain hydrophilic region and two fatty acid derived hydrophobic tails
types of sphingolipids
ceramide, sphingomyelins, cerebrosides, gangliosides
desmosomes
bind adjacent cells by cnchoring to their cytoskeletons
hemidesmosomes
attach epithelial cells to underlying structures, esp basement membrane
three classes of membrane proteins
transmembrane proteins, embedded membrane proteins, membrane associated (peripheral) proteins
osmotic pressure
- pressure applied to pure solvent to prevent osmosis
- “sucking” pressure in which a solutions drawing water in, proportional to its conc
- used to express the conc of the solution
passive transport
does not require energy bc molecule is moving down conc gradient or from an area with higher conc to area w lower conc
types of passive transport
simple diffusion, osmosis, facilitated diffusion
simple diffusion
passive transport
small, nonpolar molecules passively move from area of high conc to area of low conc until equilibrium is achieved
does not require transporter
osmosis
passive transport
diffusion of water across selectively permeable membrane
facilitated diffusion
passive transport
uses transport proteins to move impermeable solutes across cell membrane
active tranport
requires energy in form of ATP or an existing favorable ion gradient
types of active transport
primary, secondary
types of secondary active transport
symport, antiport
pinocytosis
ingestion of liquid into the cell in vescles formed from the cell membrane
phagocytosis
ingestion of larger, solid molecules
passive vs active transport
temperature
passive transport - can inc in rate as temp inc
active transport - may or may not be affected - depends on enthalpy
hypotonic solution
conc of solutes inside cell is higher than surrounding soln
causes cell to swell as water rushes in –> lysis
hypertonic solution
soln that is more conc outside the cell than inside
causes water to move out of cell
isotonic solution
solutions inside and outside cell are equimolar
osmotic pressure eq
II = iMRT
II = osmotic pressure
i = vant hoff factor = number of particles obtained from the molecule when ins oln
T = temp
M = molarity
R = ideal gas constant
carriers
only open to one side of cell membrane at any given point
occluded state
carrrier is not open to either side of membrane
primary active transport
uses ATP or another energy molecule to directly power the transport of molecules across membrane
secondary active transport
uses energy to transport particles across membrane by harnessing energy released by one particle going down its gradient to drive a different particle up its gradent
antiport
when both particles in secondary active transport move in opposite directions
symport
when both particles in secondary active transport move in same direction
endocytosis
ell membrane invaginates and engulfs material to bring it into cell
exocytosis
secretory vesicles fuse with membrane, releasing material from inside cell to extracellular environment
simple diffusion ex molecules transported
small, nonpolar
(O2, CO2)
osmosis ex molecules transported
h2o
facilitated diffusion ex molecules transported
polar molecules (glucose)
ions (Na+, Cl-)
active transport ex molecules transported
polar molecules or ions (Na+, Cl-, K+)
as osmotic pressure increases, water will tend to flow…
into the compartment to decrease solute concentration
osmotic pressure
water moves toward
compartment with highest osmotic pressure
primary thermodynamic factor responsible for passive transport
entropy
membrane potential is maintained by
sodium potassium pump and leak channels
electric potential created by one ion can be calculated using
nernst eq
resting potential of membrane at physiological temp can be calculated useing
goldman hodgkin katz voltage eq
how does mitochondrial membrane differ from cell membrane
- outer mitochondrial membrane highly permeable to metabolic molecules and small proteins
- inner membrane
- citric acid cycle
- enzymes
- does not contain cholesterol
In the cell membrane, there are also the closely related Sphingolipids. Which of the following statements about Sphingolipids are true?
I. Sphingolipids lack Glycerol.
II. All Sphingolipids have a hydrophilic region and two fatty-acid like tails that form a hydrophobic region.
III. Some common Sphingolipids are Ceramide, Sphingomyelins, Gangliosides and Cerebrosides.
(A) II only
(B) I and II only
(C) I and III only
(D) I, II and III
(C) I and III only
Each of the following statements about Sphingolipids are true:
I. Sphingolipids lack Glycerol.
II. Sphingolipids have a hydrophilic region and can have either one or two fatty-acid like tails that form a hydrophobic region. Most have two, but not all do.
III. Some common Sphingolipids are Ceramide, Sphingomyelins, Gangliosides and Cerebrosides.
Describe whether or not each compound is able to pass through the Cell Membrane via Passive Diffusion:
(1) Gases
(2) Small, Polar Compounds
(3) Large, Non-polar Compounds
(4) Large, Polar Compounds
(5) Charged Compounds
(1) Gases - Yes, quickly.
(2) Small, Polar Compounds - Yes, slowly.
(3) Large, Non-polar Compounds - Yes, slowly.
(4) Large, Polar Compounds - No.
(5) Charged Compounds - No.
Which of the following are unable to pass through the Cell Membrane via Passive Diffusion?
I. Cholesterol
II. Na+
III. Glucose
(A) I Only
(B) I and II Only
(C) II and III Only
(D) I and III Only
(C) II and III Only
Cholesterol is a large, non-polar molecule, allowing it to pass through the Cell Membrane via Passive Diffusion at a slow rate.
Na+ is a charged compound, preventing it from utilizing Passive Diffusion.
Glucose is a large, polar compound, preventing it from utilizing Passive Diffusion.
Draw a Saturated Fatty Acid versus a Unsaturated Fatty Acid.
Compare Integral and Transmembrane Proteins.
Integral and Transmembrane proteins are the same exact thing! They both span the entire cell membrane from intracellular to extracellular.
Which of the following are roles that proteins play within a cell membrane?
I. Transport molecules
II. Transmit signals
III. Maintain the structural integrity of the cell membrane
(A) I Only
(B) II Only
(C) I and II Only
(D) I and III Only
(C) I and II Only
Proteins transport molecules across a cell membrane. They may also help transmit signals across a membrane.
CRB Define and draw a Glycoprotein.
Glycoprotiens are membrane-bound proteins that have an associated carbohydrate.
In this picture, the red is the membrane-bound protein.
Jack is studying a protein in his biochemistry class. He learns that this protein is located on the intracellular side of the cell membrane and converts one molecule into another molecule. This protein is known as a:
(A) lipidbound protein
(B) peripheral protein
(C) channel protein
(D) carrier protein
(B) peripheral protein
Peripheral proteins are on either the extracellular or intracellular side of the cell membrane but not both.
Your bladder needs to contain water without it leaking out into the rest of your body’s tissues. The cells in your bladder most likely utilize which cell junction to allow for this ability?
(A) Synapse Junctions
(B) Gap Junctions
(C) Desmosomes
(D) Tight Junctions
(D) Tight Junctions
Tight Junctions are waterproof seals. They are common in areas that contain large amounts of water such as the bladder, intestines, and the Kidney.
Which of the following statements about Gap Junctions are true?
I. Gap Junctions can also be called Connexons.
II. The pores of Gap Junctions are formed by pores in interacting Connexin molecules.
III. Molecules that flow between cells at Gap Junctions are said to follow a Paracellular Route.
(A) II only
(B) I and II only
(C) I and III only
(D) I, II and III
(B) I and II only
The Paracellular route is related to Tight Junctions. Each of the following statements are true about Gap Junctions:
I. Gap Junctions can also be called Connexons.
II. The pores of Gap Junctions are formed by pores in interacting Connexin molecules.
Which are able to move faster in the Plasma Membrane, Lipid Rafts or Phospholipids, and why?
(A) Phospholipids, because they are diffusing from high concentration to low concentration.
(B) Lipid Rafts, because they are diffusing from high concentration to low concentration.
(C) Phospholipids, because they are smaller than Lipid Rafts.
(D) Lipid Rafts, because they are only on the surface of the Plasma Membrane, whereas Phospholipids have tails entering the middle of the membrane.
(C) Phospholipids, because they are smaller than Lipid Rafts.
enzymes
biological catalysts that are unchanged by the reactions they catalyze and are reusable
lower the activation energy necessary for biological reactions
specific for a particular reaction or class of reactions
oxidoreductases
enzymes that catalyze redox rxns that involve the transfer of electrons
transferases
enzymes that move a functional group from one molecule to another molecule
hydrolases
enzymes that catalyze cleavage with the addition of water
lyases
enzymes that catalyze cleavage without the addition of water and without the transfer of electrons
isomerases
enzymes that catalyze the interconversion of isomers, including both constitutional isomers and steroisomers
exergonic reactions
release energy
ΔG < 0
what do enzymes NOT alter?
thermodynamics: free energy or enthalpy
equilibrium constant
what do enzymes alter?
rate at which equilibrium is reached
kinetics
reductant
electron donor in reactions catalyzed by oxidoreductases
oxidant
electron acceptor in reactions catalyzed by oxidoreductases
enzymes with dehydrogenase or reductase in their names are usually
oxidoreductases
enzymes with oxidase in their names usually
have oxygen as the final electron acceptor
kinases
type of transferase
catalyze the transfer of phosphate group, generally from ATP, to another molecule
major enzyme classifications
LIL HOT
- Ligase
- Isomerase
- Lyase
- Hydrolase
- Oxidoreductase
- Transferase
synthase
catalyze the synthesis of two molecules into a single molecule
(type of lyase)
ligases
enzymes that catalyze addition or synthesis reations, generally between large similar molecules
often require ATP
endergonic reaction
requires energy
ΔG > 0
mechanisms of enzyme activity
stabilize transition state –> provide favorable microenvironment
bond with substrate molecules
active site
site of catlysis
lock and key theory
enzyme and substrate are exactly complementary
no alteration of tertiary or quaternary structure is necessary
induced fit model
enzyme and substrate undergo conformational changes to interact fully
cofactors
metal cations or inorganic molecules that activate enzymes
often ingested as dietary materials
coenzymes
small organic molecules that active enzymes
often vitamins or derivatives of vitamins such as NAD+, FAD, and coenzyme A
substrate
molecule upon which an enzyme acts
apoenzymes
enzymes without their cofactors
holoenzymes
enzymes containing their cofactors
prosthetic groups
tightly bound cofactors or coenzymes that are necessary for enzyme function
important coenzymes that must be replenished regularly and why
water soluble vitamins including B complex vitamins and ascorbic acid (vitamin C)
bc easily excreted
major classes of vitamins
fat and water soluble
enzymes experience ___ kinetics
saturation
saturation kinetics
as substrate conc inc, reaction rate inc until a max value is reached
cooperative enzymes display a sigmoidal curve on ___ plot because of
michaelis menton
the change in activity with substrate binding
vmax
enzyme is working at maximum velocity
only way to increase vmax
increasing enzyme conc
michaelis-menten plot of enzyme kinetics
michaelis menten rxn eq
ES complexes form at rate k1
ES dissociates at either rate k-1 or turn into E+P at rate kcat
[E] = enzyme
[S] = substrate
[P] = product
michaelis menten eq
Km
michaelis constant
- substrate conc at which half of the enzyme’s active sites are full
- can be a measure of the affinity of the enzyme for its substrate
- intrinsic property of ES system
- cannot be altered by changing conc
low Km
high affinity for substrate
(low [S] required for 50% enzyme saturation)
high Km
low affinity for the substrate
(high [S] required for 50% enzyme saturation)
when [S] < Km
changes in substrate conc will greatly affect reaction rate
when [S] > Km
reaction rate increases much more slowly as it approaches vmax
kcat
turnover number
measures number of substrate molecules “turned over” or converted to product per enzyme molecule per second
turnover number eq
vmax = [E]kcat
catalytic efficiency
= kcat/Km
high turnover results in
= large kcat
more efficient enzyme
low turnover results in
= small kcat
less efficient enzyme
lineweaver-burk plot
double reciprocal graph of Michaelis menten eq –> straight line
lineweaver-burk plot used to
calculate values of Km and vmax
determine type of inhibition that an enzyme is experiencing
lineweaver-burk plot
x intercept
-1/Km
lineweaver-burk plot
y intercept
1/vmax
subunits and enzymes exist in one of two states:
low affinity tense state (T)
high affinity relaxed state (R)
hill’s coefficient
quantifies cooperativity
indicates the nature of binding by the molecule
hill’s coefficient > 1
positively cooperative binding
hill’s coefficient < 1
negatively cooperative binding
hill’s coefficient = 1
no cooperative binding
positively cooperative binding
after one ligand is bound, the affinity of the enzyme for further ligands increases
negatively cooperative binding
after one ligand is bound, the affinity of the enzyme for further ligands decreases
effects of increasing [S] on enzyme kinetics
depends on how much substrate there is to begin with
- low [S]: inc in [S] -> inc in enzyme activty
- high [S]: inc in [S] -> no effect on activity bc vmax has already been attained
effects of increasing [E] on enzyme kinetics
increases vmax, regardless of starting conc of enzyme
as Km inc, enzyme’s affinity for its substrate ___
dec
effect on enzyme activity in vivo
temp and pH –> denaturing of enzyme and loss of activity due to loss of secondary, tertiary, or if present, quaternary structure
effect on enzyme activity in vitro
salinity can impact action of enzymes
ideal temp enzymes
37 deg C = 98 deg F = 310 K
ideal pH for most enzymes
7.4
feedback inhibition
aka negative feedback
regulatory mechanism whereby the catalytic activity of an enzyme is inhibited by the presence of high levels of a product later in the same pathway
reversible inhibition
ability to replace the inhibitor with a compound of greater affinity or to remove it using mild lab equipment
types of reversible inhibition
competitive, noncompetitive, mixed, uncompetitive
competitive inhibition
inhibitor is similar to substrate and binds at active site
how can competitive inhibition be overcome?
by adding more substrate
competitive inhibition
vmax and Km
vmax = unchanged
Km = increases –> [S] has to be higher to reach vmax in the presence of inhibitor
noncompetitive inhibition
inhibitor binds with equal affinity to the enzyme and the enzyme substrate complex
noncompetitive inhibition
vmax and Km
vmax = dec –> less enzyme available to react
Km = unchanged –> any copies of enzyme that are still active maintain same affinity
mixed inhibition
inhibitor binds with unequal affinity to enzyme and ES complex
mixed inhibition
vmax and Km
vmax = dec
Km = depends on if inhibitor has a higher affinity for E or ES complex
- if inhibitor preferentially binds to enzyme -> Km inc -> lowers the affinity
- if inhibitor preferentially binds to ES -> Km dec -> increases affinity
uncompetitive inhibition
inhibitor binds only with the ES complex and locks substrate into enzyme, preventing its release –> increases affinity between E and S
uncompetitive inhibition
vmax and Km
vmax = dec
Km = dec
feedforward regulation
enzymes regulated by intermediates that precede the enzyme in the pathway
irreversible inhibition
active site is made unavailable for prolonged period of time or enzyme is permanently altered
competitive inhibition
lineweaver burk plot
noncompetitive inhibition
lineweaver burk plot
uncompetitive inhibition
lineweaver burk plot
allosteric enzyme
alternate between active and inactive form
allosteric activator
binds to allosteric site and makes active site more available for binding to substrate
allosteric inhibitor
binds to allosteric site and makes active site less available for binding to substrate
enzymes can be covalently activated or deactivated by
phosphorylation or dephosphorylation
enzymes and glycosylation
covalent attachment of sugar moities
can tag an enzyme for transport within cell or can modify protein activity and selectivity
zymogens
precursors of active enzymes
why are some enzymes released as zymogens
it is critical that certain enzymes (like digestive enzymes of pancreas) remain inactive until arriving at their target site
structural proteins compose the
cytoskeleton, anchoring proteins, and much fo extracellular matrix
most common structural proteins
collagen, elastin, keratin, actin, tubulin
structural proteins
generally fibrous in nature
motor proteins
have one ore more heads capable of force generation through a conformational change
have catalytic activity, acting as ATPases to power movement
common applications of motor proteins
muscle contraction, vesicle movement within cells, cell motility
most common motor proteins
myosin, kinesin, dynein
binding proteins
bind a specific substrate, either to sequester it in the body or hold its concentration at steady state
cell adhesion molecules (CAM)
allow cells to bind to other cells or surfaces
CAM examples
cadherins, integrins, selectins
cadherin
CAM
calcium dependent glycoproteins that hold similar cells together
integrins
CAM
permit cells to adhere to proteins in extracellular matrix
some also have signaling capabilities
selectins
CAM
allow cells to adhere to carbs on the surfaces of other cells
most commonly used in immune system
antibodies (Ig)
role + structure
used by immune system to target specific antigen
contain constant region and variable region
two identical heavy chains and tow identical light changes
held together by disulfide linkages and noncovalent interactions
motif
repetitive organization of secondary structural elements
collagen
makes up most of extracellular matrix of connective tissue
strength and flexibility
elastin
stretches and recoils, which restores original shape of tissue
keratins
intermediate filament proteins found in epithelial cells
found in hair and nails
actin
protein that makes up mcirofilaments and thin filaments in myofibrils
have a positive and negative side that allows motor proteins to travel along this filament
tubulin
makes up microtubules
negative and positive end
myosin
primary motor protein that interacts with actin
can be involved in cellular transport
kinesins and dyneins
motor proteins assoiated with microtubules
ungated channels
always open
voltage gated channels
open within a range of membrane potentials
ligand gated channels
open in presence of specific binding substance, usually hormone or neurotransmitter
enzyme linked receptors
participate in cell signaling thorugh extracellular ligand binding and imitation of second messenger cascades
g protein coupled receptors
have membrane bound protein associated with a trimeric G protein
initiate second messenger system
GPCR steps
- ligand binding engages G protein
- GDP replaced with GTP
- alpha subunit dissociates from beta and gamma subunits
- activated alpha subunit alters activity of adenylate cyclase or phospholipase C
- GTP is phosphorylated to GDP
- alpha subunit rebinds to beta and gamma subunits
membrane spanning domain
anchors receptor in cell membrane
ligand binding domain
stimulated by appropriate ligand and induces a conformational change that activates catalytic domain
classic example of second messenger cascade
receptor tyrosine kinases (RTKs) - phosphorylate other enzymes
electrophoresis
uses gel matrix to observe migration of proteins in response to electric field
subjects compounds to electric field, which moves them according to their net charge and size
native PAGE
gel electrophoresis
maintains protein’s shape, but results are difficult to compare because mass to charge ratio differs for each protein
SDS PAGE
gel electrophoresis
separates proteins on the basis of relative molecular mass alone
denatures the proteins and masks the active charge so that comparison of size is more accurate, but the functional protein cannot be recaptured from the gel
isoelectric focusing
gel electrophoresis
separates proteins by their isoelectric point
protein migrates toward an electrode until it reaches a region of the gel where pH = pI of the protein –> protein takes on neutral charge and will stop moving
chromatography
separates protein mixtures on bases of their affinity for a stationary or mobile phase
column chromatography
uses beads of polar compound with nonpolar solvent
ion exchange chromatography
uses charged column and variably saline eluent
size exclusion chromatography
relies on porous beads
larger molecules elute first
affinity chromatography
uses bound receptor or ligand and an eluent with free ligand or receptor for the protein of interest
homogenization
crushing, grinding, or blending the tissue of interest into evenly mixed solution
centrifugation
isolates proteins from much smaller molecules before other isolation techniques must be employed
electrophoresis
negatively charged compounds will migrate toward
positively charged anode
(A+ Anode has acidic gel and + charge)
electrophoresis
positively charged compounds will migrate toward
negatively charged cathode
polyacrylamide gel
standard medium for protein electrophroesis
allows smaller particles to pass through easily while retaining large particles
polyacrylamide gel
molecules will move faster if they are
small, highly charged, or placed in large electric field
polyacrylamide gel
molecules will move slower if they are
bigger, more convoluted, electrically neutral, or placed in small electric field
PAGE is most useful to
compare the molecular size or charge of proteins known to be similar in size from other analytic mehods
isoelectric point (pI)
pH at which the protein is electrically neutral
partioning
separation of components within stationary phase
what are two potential drawbacks of affinity chromatography?
- protein of interest may not elute from column bc its affinity is too high
- may be permanently bound to free receptor in eluent
x ray crystallography
determines protein structure after protein is isolated
measures electron density on high res scale
edman degradation
sequential degradation for amino acid sequencing
uses cleavage to sequence proteins
how are activity levels for enzymatic samples determined?
following the process of a known reaction, often accompanied by a color change
protein conc can be determined
colorimetrically, either by UV spectroscopy or through color change reaction
assays that test for protein
BCA assay, Lowry reagent assay, Bradford protein assay
bradford protein assay
uses color change from brown-green to blue
most common assay
protein structure can be determined through
X-ray crystallography and NMR spectroscopry
CRB Compare Enzymes and Catalysts.
Catalysts are any material that are not used up in a reaction, but can speed up the process of a reaction.
Enzymes are Biological Catalysts made of proteins. Also note that there are Ribozymes (RNA that can have catalytic functions similar to protein enzymes).
Describe the relationship between antibodies and antigens
Antigens are the ligands of antibodies. If an antigen is not recognized as belonging to the host, the antibody can recognize and flag this protein for elimination or degradation.
Which motor protein(s) is/are specifically responsible for intracellular transport?
I. Myosin
II. Kinesin
III. Dynein
(A) I Only
(B) III Only
(C) I and II Only
(D) II and III Only
(D) II and III Only
Kinesin and dynein are motor proteins that are responsible for intracellular transport.
At which point of a reaction do the enzyme and substrate bind at their maximum strength?
(A) Just before the Transition State
(B) During the Transition State
(C) Just after the Transition State
(D) At the end of a reaction
(B) During the Transition State
The enzyme is most tightly bound to its substrate during the transition state (induced fit stage).
What occurs at the active sites vs. allosteric sites of an enzyme?
The active site is where the reaction takes place, while the allosteric site is where regulation takes place.
Describe the mechanism of action for a ligase enzyme.
Ligase enzymes catalyze reactions between molecule A and molecule B to form a complex molecule AB.
Describe the mechanism of action for an oxidoreductase enzyme? Oxidase enzyme? Reductase enzyme?
Oxidoreductase enzymes can catalyze both oxidation and reduction reactions.
Oxidase enzymes catalyze reactions that take electrons away from a molecule.
Reductase enzymes catalyze reactions that give electrons to a molecule.
Fill in the blanks: In an Oxidoreductase enzyme’s reactions, the electron donor is called the _____________, and the electron acceptor is called the ____________. This is more closely related to the ____________ definition of Acids and Bases.
(A) Reductant, Oxidant, Bronsted-Lowry
(B) Reductant, Oxidant, Lewis
(C) Oxidant, Reductant, Bronsted-Lowry
(D) Oxidant, Reductant, Lewis
(B) Reductant, Oxidant, Lewis
In an Oxidoreductase enzyme’s reactions, the electron donor is called the Reductant, and the electron acceptor is called the Oxidant. This is more closely related to the Lewis definition of Acids and Bases.
During DNA replication, two strands of DNA are joined together. What kind of enzyme would be involved in this reaction?
(A) Hydrolase
(B) Ligase
(C) Lyase
(D) Transferase
(B) Ligase
A ligase enzyme (DNA ligase) is involved in DNA replication because two separate DNA strands (molecules) are being joined to form a single strand.
CRB Compare Lyases and Ligases.
Both Lyases and Ligases can catalyze synthesis reactions without Oxidation-Reduction occurring.
Lyases can also catalyze the splitting of these bonds without water or Oxidation-Reduction occurring, and typically work with small molecules. This 2nd reaction is what lyases are typically known for.
Ligases typically work with larger molecules and require ATP.
What is the difference between vitamins and minerals?
Vitamins are carbon-based (organic) co-enzymes, whereas minerals are inorganic or metallic co-factors. Minerals may also help structurally, such as calcium, which is an important component of bone and teeth.
How can we increase the rate of a reaction assuming the rate constant (k) is constant?
I. Increase Substrate Concentration
II. Increase Enzyme Concentration
III. Increase Mixed Inhibitor Concentration
(A) I Only
(B) I and II Only
(C) II and III Only
(D) I, II, and III
(B) I and II Only
We can increase the rate of reaction by increasing the substrate or enzyme concentration.
Adding any type of inhibitor will not increase the rate of a reaction.
What is the steady-state assumption when talking about enzyme kinetics?
(A) [ES] is constant
(B) [S] is constant
(C) [P] is constant
(D) [I] is constant
(A) [ES] is constant
The steady state assumption means that the concentration of the enzyme-substrate complex (ES) is constant, which means that the formation of ES is equal to the dissociation of ES.
The catalytic efficiency for a certain reaction increases. What happens to the reaction rate?
(A) It would increase
(B) It would remain the same
(C) It would decrease
(D) It would stop
(A) It would increase
Catalytic efficiency is basically an enzyme’s ability to catalyze reactions. If it increases so too will the rate of the reaction.
What is the equation for the enzyme turnover number (Kcat)?
Kcat = Vmax/ [E]T
Vmax is the maximum velocity of the enzyme
[E]T is the concentration of the enzyme.
unit: 1/sec
What does the enzyme turnover number (Kcat) really mean?
The enzyme turnover number (Kcat) basically tells us how many substrates a single enzyme can turn into product in one second at its maximum speed.
Draw a Lineweaver-Burke plot. What is the equation for the x- and y- intercept? What about the slope?
Which type of inhibitor will decrease Vmax but does not apparently alter the value of Km?
(A) Competitive
(B) Uncompetitive
(C) Noncompetitive
(D) Mixed
(C) Noncompetitive
A noncompetitive Inhibitor will decrease Vmax and not alter the value Km.
A noncompetitive inhibitor decreases Vmax because it binds to enzyme and the enzyme-substrate complex, thus creating less available enzymes to react.
The inhibitor binds ES, shifting the reaction (E + S –> ES) to the right. The inhibitor also binds to E, shifting the reaction to the left. Furthermore, the inhibitor binds to ES and E with the same affinity; this means these shifts cancel each other out, resulting in no change to affinity (Km).
What type of inhibitor does not change the apparent Km value?
(A) Competitive
(B) Uncompetitive
(C) Noncompetitive
(D) Mixed
(C) Noncompetitive
A noncompetitive inhibitor does not change the apparent Km value because the inhibitor binds equally well to the enzyme and enzyme-substrate complex.
What type of inhibitor does not change the Vmax value?
(A) Competitive
(B) Uncompetitive
(C) Noncompetitive
(D) Mixed
(A) Competitive
Competitive inhibitor does not change the Vmax value because if enough substrates are added, it will outcompete the inhibitor and be able to run the reaction at maximum velocity.
On a Michaelis-Menten plot please draw what the curves would look like for enzymes with non-cooperative binding, positive-cooperative binding, and negative-cooperative binding.
An enzyme with non-cooperative binding will have a hyperbolic shaped curve.
An enzyme with positive-cooperative binding will have a sigmoidal “S” shaped curve.
An enzyme with negative-cooperative binding will have an altered hyperbolic shape with a steeper initial curve than non-cooperative binding.
Draw the percent saturation curves of Hemoglobin and Myoglobin. How do they differ?
Hemoglobin has a sigmoidal “S” shaped curve because it exhibits positive-cooperative binding. Myoglobin has a hyperbolic curve since it exhibits non-cooperative binding.
CRB Compare how drastically increasing and decreasing pH can differently cause Denaturation.
Increasing pH will cause deprotonation of key residues in the active site and affect hydrogen bonding of the secondary structure. Decreasing pH could protonate key residues in the active site, also affecting the hydrogen bonding of the secondary structure, and could also protonate the Cystines, breaking all disulfide bonds.
How could dramatically increasing the Salinity of an solution with enzymes denature the enzyme?
(A) It could disrupt the Primary Structure by breaking only covalent bonds.
(B) It could disrupt Secondary Structure by disrupting only Hydrogen Bonds.
(C) It could disrupt Tertiary and Quaternary Structure by disrupting only Ionic Bonds.
(D) It could disrupt Secondary, Tertiary and Quaternary Structure by disrupting both Hydrogen and Ionic Bonds.
(D) Increased Salinity could disrupt Secondary, Tertiary and Quaternary Structure by disrupting both Hydrogen and Ionic Bonds.
Compare the two types of enzyme regulators – allosteric activators vs. inhibitors. How does each affect Km and Vmax?
Allosteric activators increase enzyme activity. They increase Vmax and decrease Km.
Allosteric inhibitors decrease enzyme activity. They decrease Vmax and increase Km.
A single reaction in a pathway would be a great control point for regulation if it has a very:
(A) positive ΔG.
(B) negative ΔG.
(C) positive ΔS.
(D) negative ΔS.
(B) negative ΔG.
A reaction with a negative ΔG would be a great “committing” step for a pathway because that reaction is unlikely to be reversed. That reaction’s products would then be committed to moving forward in the pathway. Phosphofructokinase’s reaction has a very negative ΔG; thus, it is a great control point for glycolysis.
Match each of the following types of Gel Electrophoresis with their descriptions.
I. Polyacrylamide Gel.
II. Native PAGE
III. SDS-PAGE
(A) Can only give mass-to-charge ratios, so could have decreased separation of proteins with different masses or charges. This does NOT denature the protein.
(B) The typical medium used for protein electrophoresis.
(C) Uses a Detergent to break all noncovalent interactions, including affecting the charges of proteins. They are only separated based on size.
Note that PAGE stands for Polyacrylamide Gel Electrophoresis
I. Polyacrylamide Gel - (B) The typical medium used for protein electrophoresis.
II. Native PAGE - (A) Can only give mass-to-charge ratios, so could have decreased separation of proteins with different masses or charges. This does NOT denature the protein.
III. SDS-PAGE - (C) Uses a Detergent to break all noncovalent interactions, including affecting the charges of proteins. They are only separated based on size.
Which of the following descriptions of Isoelectric Focusing are true?
I. The gel that the samples are separated in has a pH gradient, ranging from acidic to basic.
II. The protein will settle at the pH where the protein’s R-groups are fully deprotonated.
III. As proteins move towards the Cathode, the pH increases.
(A) I only
(B) I and III only
(C) II and III only
(D) I, II and III
(B) I and III only
Each of the following statements are true about Isoelectric Focusing:
I. The gel that the samples are separated in has a pH gradient, ranging from acidic to basic.
II. The protein will settle at the pH equal to the protein’s pI.
III. As proteins move towards the Cathode, the pH increases.
CRB True or false? In isoelectric focusing, the proteins are loaded near the Anode, where there is a low pH and the proteins will be protonated and positively charged.
True. In isoelectric focusing, the proteins are loaded near the Anode, where there is a low pH and the proteins will be protonated and positively charged.
Which of the following are examples of Membrane Receptors?
I. Ligand-gated Ion Channels
II. G-protein Coupled Receptors
III. Enzyme Linked Receptors
(A) I and II Only
(B) II and III Only
(C) I and III Only
(D) I, II, and III
(D) I, II, and III
The following are examples of Membrane Receptors:
I. Ligand-gated Ion Channels
II. G-protein Coupled Receptors
III. Enzyme Linked Receptors
The GPCR mechanism is extremely important to know. Please draw out this mechanism, including the α, β, and γ subunits of the G Protein.
Epinephrine is a classic example of a molecule that binds to a GPCR. In this case, the activated α-subunit binds to Adenylate Cyclase. What does Adenylate Cyclase then do?
Adenylate Cyclase converts ATP into cAMP (Cyclic AMP), which will then activate and alter other proteins within the cell, ultimately resulting in increased heart rate, dilated blood vessels, glycogenolysis, etc.
Receptor Tyrosine Kinases (RTKs) are classic examples of Enzyme linked receptors. After a ligand binds to the Ligand Binding Domain, what cascade of events occurs in order to activate intracellular proteins?
Upon activation, neighboring RTKs will move close together and form cross-linked dimers. Next the Tyrosine amino acids in the Enzymatic Domain will phosphorylate each other. Now, these Phosphorylated Tyrosine amino acids can bind to intracellular proteins and activate them.
CRB Recall the equation for Gibbs Free Energy. What must be increasing to make Passive Transport have a negative ΔG?
It is illogical to think that this Passive Transport will significantly increase temperature, so this Passive Transport must increase Entropy.
CRB What is the significance of the Van’t Hoff Factor in that Osmotic Pressure equation?
The Van’t Hoff Factor is the number of particles that are in solution for each molecule of the substance that dissolved. This is how you account for the number of molecules in solution being different when ionic solutions dissolve into multiple particles!
CRB Mitochondria also have two membranes. Compare the permeabilities of each membrane.
The Outer Mitochondrial membrane has many large pores, allowing ions and small proteins to move freely, including electron carriers.
The Inner Mitochondrial Membrane is much less permeable, requiring the integral proteins that are part of the Electron Transport Chain and ATP Synthase for the passage of ions to occur.
