Biochem Exam 2

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204 Terms
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Ala, A, Non-polar
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Val, V, Non-polar
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Phe, F, Non-polar
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Trp, W, Non-polar
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Leu, L, Non-polar
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Ile, I, Non-polar
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Met, M, Non-polar
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Pro, P, Non-polar
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Ser, S, Polar
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Thr, T, Polar
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Tyr, Y, Polar
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Asn, N, Polar
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Gln, Q, Polar
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Cys, C, Polar (creates disulfide bonds with other cysteines
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His, H, Polar (can be charged)
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Lys, K, Basic (pos charge)
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Arg, R, Basic (pos charge)
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Aspartate (aspartic acid)
Asp, D, Acidic (neg charge)
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Glutamate (glutamic acid)
Glu, E, Acidic (neg charge)
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Gly, G, Not charged
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Rank the following according to their strength as acids--rank from strongest (1) to weakest (5).
A - 4 B - 3 C - 5 D - 2 E - 1
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Which of the following would NOT form a suitable buffer?
Hydrochloric acid/chloride
Under what conditions would a carboxyl group (COOH, pK 3.5) be mostly protonated?
pH < pK
Under what conditions would a carboxyl group (COOH, pK 3.5) be mostly deprotonated?
pH > pK
In aqueous solution, globules of up to several thousand amphiphilic molecules arranged with the hydrophilic groups on the surface and the hydrophobic groups buried in the center are called _____.
What term is used to describe the exclusion of nonpolar substances from an aqueous solution?
hydrophobic effect
Which of the following is an example of the hydrophobic effect?
all are examples of the hydrophobic effect
A molecule that has both a polar and nonpolar region is called _____________.
If the pK value for acetic acid (CH3COOH) is 4.76 at what pH would one observe equal amounts of CH3COO- and CH3COOH?
During metabolic acidosis, ______ ventilation excretes acid in the form of _____ .
increased; CO2
The LOWER the pK value of an acid the STRONGER the acid.
Which of the following bond forces are important in tertiary structure:
Hydrophobic effect Hydrogen bonds Disulfide bonds
Which of the following amino acid substitutions would be most likely to effect protein function?
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Select all the commonalities between alpha helices and b-pleated sheets. (i.e. select what is similar in both types of secondary structure)
prolines and glycines aren't suitable for the secondary structure hydrogen bonds between main chain CO and NH groups peptide bond is planar
The formation of a dipeptide from two amino acids involves A) side-chain complementarity. B) loss of water. C) oxidation of the alpha-carbon. D) reduction of the alpha-carbon. E) base catalysis.
The protein shown above is the human coronavirus protease. The structure contains 2 subunits, that have identical sequences. This protein can be classified as:
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At what pH would an amino acid bear both a COOH and an NH2 group?
All secondary structures in proteins involve helical forms.
Cys-Ala-Gly-Arg-Gln-Met In the above peptide, the amino-terminal amino acid is ____ and the carboxyl-terminal amino acid is ____
Cys; Met
For the amino acid structures shown above, the protonation state of structure A is shown at ______ pH, and the protonation state of structure B is shown at _______ pH.
low; high
Choose the amino acid that would be more likely to appear on the solvent-exposed (water facing) surface of a protein. Leu or Lys Ser or Ala Phe or Tyr Trp or Gln Asn or Ile
Lys Ser Tyr Gln Asn
The order in which the amino acids in a protein are linked by peptide bonds
The arrangement of the backbone atoms in a polypeptide chain
The arrangement of all the atoms in a protein (interactions between the R groups, hydrophobic ones inside of the protein)
the interaction of several polypeptide chains in a multisubunit protein
Examine the four amino acids given below: Indicate which of these amino acids are associated with the following properties:
branched aliphatic sidechain - C basic sidechain - D aromatic R group - B cyclic (nonaromatic) R group - A
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Which of the following amino acids carry a net positive charge at pH 7.0?
Arg, Lys
What is the net charge on the following peptide at pH 9.5? Lys-Ala-Glu-Gln-Cys-Ile
What is the net charge of the pentapeptide Ala-Cys-Ser-Glu-Asn at pH 7?
Any peptide which contains 2 sulfur-containing amino acids can form an internal disulfide bond.
The interactions that stabilize multisubunit complexes are different than those that stabilize tertiary structure.
Myoglobin is _____; hemoglobin is _____.
monomeric; tetrameric
The individual hemoglobin subunits and myoglobin share similar primary structure but have rather different secondary structure.
Which of the following fibers is correctly paired with the protein that forms the fiber?
extracellular support fibers: collagen microtubules: tubulin microfilaments: actin intermediate filaments: keratin (all are true)
Which amino acid is critical for crosslinking of keratin fibers?
Cys (disulfide bonds)
The idea that binding of one molecule of oxygen to hemoglobin enhances further binding of oxygen to hemoglobin is called _____.
What is the most prevalent secondary structure observed in the proteins of intermediate filaments?
alpha helices
Which of the following statements about actin are true?
Monomeric G-actin polymerizes to form F-actin. Actin filaments are polar (the ends can be distinguished).
Several oxygen dissociation curves are shown in the figure below. Assuming that curve 3 corresponds to isolated hemoglobin placed in a solution containing physiologic concentrations of CO2 and BPG at a pH of 7.0, indicate which of the curves reflects the following changes in conditions:
Increased BPG concentration 4 Increased pH 2 Dissociation of hemoglobin into subunits. 1
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Match the feature of hemoglobin with the proper structural level.
Amino acid sequence in each of the alpha and beta polypeptide chains. Primary Structure 8 alpha helices in each of the subunits. Secondary Structure Spatial relationship between every atom in the individual subunits. Tertiary Structure Spatial relationship between the four polypeptide chains. Quaternary Structure
The presence of 2,3-BPG causes hemoglobin's affinity for oxygen to______.
Which amino acid is involved in heme coordination in both hemoglobin and myoglobin and is highly conserved?
Calculate the fractional saturation for myoglobin when pO2 is a. 20 torr and b. 80 torr. Assume K=2.8.
a. 0.88 b. 0.97
Both myoglobin and hemoglobin exhibit cooperative binding to oxygen.
Conservative amino acid mutations (i.e. Val to Leu) are likely to affect stability or function of a protein.
Which of the following fatty acids have the lowest melting point?
Linoleate (18:2)
Which of the following types of lipids can be found in cell membranes?
glycerophospholipids cholesterol cerebrosides gangliosides
Select the statements the describe fatty acids:
can either be saturated or unsaturated. mostly found with an even number of carbons
In what way(s) do sphingolipids differ from glycerophospholipids?
Sphingolipids are not built on a glycerol backbone. Sphingolipids contain an acyl group attached via an amide bond on the serine potion of the sphingosine.
Show which are characteristics of peripheral membrane proteins and which are characteristics of integral membrane proteins.
peripheral bind to the surface of membranes integral have transmembrane domains
Which of the following is most likely to be an unnatural fatty acid?
17:3△t9,12,15 (uneven number of carbons)
Sphingosine is not a component of:
Select the fatty acid in each pair that has the higher melting temperature.
16:1c9 or 16:2c9,12 - 16:1c9 18:0 or 18:1c9 - 18:0 18:0 or 20:0 - 20:0
Membranes are generally symmetrical, i.e., the outer face is composed of the same number and types of phospholipids as the inner face.
Phospholipids can freely diffuse from the interior leaflet of the plasma membrane to the exterior leaflet without the assistance of enzymes.
Triglycerides are fat storage molecules not typically found in membranes.
Match the description given with the correct lipid. (Answers may be used more than once)
Primary storage form of lipids. Triacylglycerols. Provides stability in the plasma membrane. Cholesterol Isoprene derivative Cholesterol Commonly found in nervous tissue Sphingomyelin Sphingosine backbone with several carbohydrates attached Ganglioside Glycerol backbone with two fatty acyl groups Glycerophospholipid
A membrane's fluidity is largely determined by the percentage of _____________.
unsaturated fats
The concentration of Ca2+ in the endoplasmic reticulum (outside) is 1 mM, and the concentration of Ca2+ in the cytosol (inside) is 0.1 μM. Calculate ΔG at 37°C when the membrane potential is −50 mV (cytosol negative)
Which of the following is/are true regarding the glucose transporter?
it transports glucose down it's concentration gradient binding of glucose causes a conformational change so that the transporter is never open on both sides of the membrane
Match the transporter (A- blue, B- green, C- light purple) with it's description.
A - Symporter B - Uniporter C - Antiporter
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Indicate whether the following compounds are likely to cross a membrane by simple diffusion or facilitated diffusion transport:
aspartic acid facilitated carbon dioxide simple glucose facilitated
Which of the following will cause the opening or closing of a gated ion channel?
voltage change
What substance will be transported through an aquaporin?
In the sodium-potassium pump:
sodium is transported out of the cell and potassium into the cell, both against concentration gradients
Active transport is uniquely characterized by:
the tight coupling of an input of energy, with the species going from a lesser concentration to a greater concentration.
Facilitated (Mediated) diffusion across a biological membrane:
is driven by a difference in solute concentration.
Energy requiring transport mechanisms include
Active transport
Inside a nerve cell at rest, [Na +] is ____ and [K+] _____ relative to the concentrations seen outside the cell.
low, high
The Hydrophobic Effect
The exclusion of nonpolar substances from an aqueous solution
experience both hydrophilic interactions and the hydrophobic effect. most lipids are amphiphilic.
the pH scale
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The ionization of water can be described by a dissociation constant, K:
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substance that can donate a proton
a substance that can accept a proton
pK helps to
determine the strength of an acid (lower pK = stronger acid, higher pK = weaker acid)
Henderson-Hasselbalch Equation
*pK is the specific pH where there are equal concentrations of base and acid *log > 1 --> always positive, pH rises *log < 1 --> always negative, pH lowers
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pH < pK
everything will be protonated
*weak acid/conj base system* aids in resisting changes in the pH of a system
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Amino Acids (L and D groups)
L --> amino group to the left of the alpha carbon D --> amino group to the right of the alpha carbon L is the most common in nature
Amino acids are linked via a
condensation reaction
Amino acid residues
only the residual atoms remain.
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enzymes that act from the end of the chain
enzymes that act from the middle of the chain
several amino acids linked together (8-20 usually)
many amino acids together (20+)
Directionality of a protein
N-terminus to the C-terminus (N-terminus = the amino group, C-terminus = COOH)
The two types of secondary structures
- alpha helices (helix) - beta pleated sheets
The α helix
- Hydrogen bonds along the helical axis stabilize this structure - Right-handed (R groups face out) - HB only form between neighboring or very close carbons
Hydrogen Bonding β Sheets
- Parallel --> all amino groups run on the same end - Antiparallel --> amino groups run in opposite direction
Tertiary structures are heavily influenced by ...
the hydrophobic effect ... the interactions between R groups and whether they are polar or nonpolar plays an important part. nonpolar R groups will be folded inside of the protein and the polar R groups will face outward. (also impacted by HB, electrostatic, and Van Der Waals)
The only covalent bonds found in tertiary structures are ...
disulfide bonds formed between two cysteines.
Why do globular proteins have a hydrophobic core and hydrophilic surface?
because of the hydrophobic effect and its influence on the tertiary structure
Advantages of quaternary structures
Large proteins can be constructed incrementally Allows for some proteins to be assembled outside the cell Minimized impact of errors in transcription and translation Affords an opportunity for subunits to influence and regulate each other (cooperative behavior)
Nomenclature for quaternary structures
Monomer (no quaternary structure) Dimer Trimer Tetramer Pentamer Hexamer Homodimer - same subunits Heterodimer - different subunits
Fates of misfolded protein
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the main way of isolating proteins - separating proteins based on a specific characteristic - Size Exclusion Chromatography - Ion Exchange Chromatography - Affinity Chromatography - High Performance Liquid Chromatography (HPLC)
a method in which charged molecules move through a gel-like matrix under the influence of an electric field
Mass Spectroscopy
a method for analyzing protein structure by measuring the size of peptide fragments.
when pI = pH
there is a 0 net charge
the pI is ...
the average of the pK values of all ionizable groups in a molecule
When calculating pI
1. order pK values 2. determine charge (is it protonated/deprotonated at that pH) 3. use those charges to determine what pH will get a net charge of 0 pI=(pK+pK)/2
Mass spec reveals ...
the amino acid/primary structure
NMR is good for ...
looking at small proteins
When identifying the amino acids on our exam ...
it will spell out a word
For amino acids with no other ionizable groups (other than the amino group and the COOH)
the pI will be equal to 6.75
- globular structure - monomer (no quaternary structure) (1 alpha subunit or 1 beta subunit) - 8 alpha helices - contains a heme group which binds to the oxygen
Heme is a ____ group
prosthetic (covalently bonded organic molecule)
Structure of heme
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Iron is coordinated by 6 different atoms
- 4 nitrogens - a histidine residue - and oxygen that bids to the top
K of Myoglobin
K=2.8 torr for human myoglobin (K values will be given on exam)
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Fractional Saturation (Y)
the proportion of myoglobin molecules that have bound O2
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Mb and Hb are similar in their ____ and ____ structures
secondary, tertiary
- tetramer - 2 alpha subunits, 2 beta subunits - binds 4 O2 molecules
Mb and Hb are only ~___% identical in primary sequence
Mb & Hb primary structures
- Invariant --> cannot change, must be the same in both - Conservative --> can change but must have similar properties (if nonpolar, the new one also needs to be nonpolar) - Variable --> can and will change, doesn't matter how different they may be
Hb _____ O2 in high concentrations
Hemoglobin structure changes when oxygen is bound to it
When binding occurs, it causes a shift so that the next heme group is open and receptive for binding until the fourth (last) oxygen binds to the molecule.
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Bohr effect
In high pHs & areas of higher O2 concentration, the hemoglobin is more prone to being in the relaxed (oxy) state where it takes up oxygen (ie the lungs). In areas of low O2 concentration and low pH, the hemoglobin shifts to the tense (deoxy) state where it releases the oxygen it's carrying (ie tissues).
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BPG binds only to the ___ conformation of Hb
tense (deoxy)
Myoglobin is ____ likely to give up its oxygen than hemoglobin
Three types of cytoskeletal filaments
- Actin filaments - Intermediate filaments - Microtubules
Actin is the ...
ATP binding protein
Actin has a globular subunit that
acts in a double chain to create a microfilament.
- filamentous - long strings of multiple g-actins together - positive end --> quicker addition of the monomers - negative end --> slow addition of monomers
Dimers (tubulin)
composed of both alpha and beta tubulin dimers contain the GTP binding sites
- hollow fibers built from tubulin fibers - usually contain 13 protofilaments
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- intermediate filament - 2 alpha helices twist together: coiled-coil - left-handed twist - link together through covalent disulfide bonds
- intermediate fiber - has hydroxyproline in it - triple helix (3 twisted together is a mature collagen fiber)
Fatty acids
- long-chain hydrocarbons - the even-numbered C16 and C18 species are most common in plants and animals - can be saturated with hydrogens ** saturated will not have a double bond - can be unsaturated or polyunsaturated ** unsaturated contains one or more double bonds ** double bonds are usually in the cis position
Delta and Omega Naming Systems
Delta: - start from the COOH carbon - Number of Carbons:Number of Double Bonds(superscript(Delta)Carbons where double bond starts) Omega: - Start from the Me carbon - Number of Carbons:Number of Double Bonds(omega)-Carbon where first double bond is seen
Only storage lipid we spoke about
- the ester bond linking each acyl group is the result of a condensation reaction - 3 fatty acids linked to a glycerol backbone
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2 fatty acids linked to a glycerol, with a phosphate group attached to the glycerol. (glycero --> from the glycerol, phospho --> phosphate group). has many different phosphate groups that it could be.
cleave glycerophospholipids at specific sites
Sphignolipids: glycolipid
- some have CHOs as a head group ** cerebroside --> monosaccharide ** ganglioside --> polysaccharides/disaccharides (gang of sugars)
has a phosphocholine or phophoethanolamine head group
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derived from palmitate and serine
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Lipids that are isoprene derivatives
- cholesterol - fat soluble vitamins (A,D,E,K) are as well
- RING STRUCTURE - amphiphilic isoprenoid - Important in membranes and steroids
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A lipid bilayer
Forms spontaneously due to the hydrophobic effect - made up of: glycerophospholipids, sphingolipids, cholesterol, and proteins
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The double bonds in a lipid ...
- kink the acyl change - account for the fluidity/fluid nature of some lipids - make it less efficient for packing together
The lipid membrane is ...
made up of both saturated and unsaturated fatty acids to help keep it fluid but not too fluid
Melting points of saturated vs unsaturated fats
Saturated fats with more carbons have the highest melting points. Saturated fats in general will have higher MPs. Unsaturated fats with one double bond will be higher than ones with more DBs, but still lower than saturated fats. Aka ... more carbons and no double bonds = high melting points, more double bonds = lower melting points.
Diffusion in membranes
Lateral --> favored Transverse --> not favored (the center of the membrane is hydrophobic, takes more energy to do this)
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Protein associations with a membrane
- Integral membrane proteins - Peripheral membrane proteins - Lipid linked membrane proteins
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Membrane proteins can span the bilayer
A membrane-spanning 𝛼 helix - Part of the protein bacteriorhodopsin - One can identify a transmembrane helix by its sequence (rich in highly hydrophobic amino acids) Beta Barrel - fully hydrogen-bonded where they span the width of the bilayer. hydrophobic side chains (green) on the barrel exterior face the bilayer core. aromatic residues (gold) are located mostly near the lipid head groups.
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The fluid mosaic model
proteins can move laterally across a membrane but not transversely
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switches to the inside side of a membrane or to the outside side of a membrane
flips to the inside
flips to the outside
Gibbs free energy, G
A measure of the free energy of a system based on H and S Units = J • mol
ΔG = Gibbs free energy change ΔH = Enthalpy change ΔS = Entropy change
When ΔG <0
the reaction is spontaneous or exergonic. (generates energy)
When ΔG >0
the reaction is nonspontaneous or endergonic (requires energy)
Free Energy Changes in Coupled Chemical Reactions
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The voltage across a membrane caused by
ion transport is the membrane potential **equation and other constants will be given on exam**
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The equation reduces to the following when: monovalent ion (Z=1) at 20℃
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An Action Potential
1. Depolarization --> membrane shifts from -70mV to +50mV --> caused by Na+ channels opening causing Na+ to enter the axon 2. Repolarization --> K+ channels open, K+ moves out of the cell
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Propagation of a Nerve Impulse
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Due to the hydrophobicity of the lipid bilayer, small ions like K+ are unable to leave the cell by simple diffusion.
True: charged ions are impermeable to the membrane
What is responsible for the extremely rapid propagation of axon potential?
Axons are insulated with a myelin sheath which prevents ion movement except at the nodes between myelinated segments.
Which of the following does occur when neurons are stimulated?
Neighboring Na+ channels open in response to the change in membrane potential, resulting in a wave of depolarization. Depolarization stimulates the opening of voltage-gated K+ channels, resulting in repolarization. Recovery involves the movement of Na+ out of the cell and K+ into the cell.
- always open - trimers - pores - high to low concentration - OmpF --> connects
Structure of the K+ Channel from S. lividans
4 subunits, alpha helices
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K+ Channels ...
selectively filter
Operation of the Voltage-Gated K+ Channel
- open or close in response to the concentration gradient (or otherwise called the voltage differences across the membrane) - still a passive transport
Structure of an Aquaporin Subunit
- full aquaporin (not pictured) is made up of four subunits (single subunit pictured)
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Operation of the Red Blood Cell Glucose Transporter
1. Glucose binds to a site on the transporter that faces the cell exterior 2. Glucose binding triggers a conformational change that exposes the glucose-binding site to the cell interior. 3. Glucose dissociates from the transporter. 4. The transporter reverts to its original conformation.
Types of Membrane Transport Systems
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A pore that simultaneously transports two different molecules in different directions is called a(n)
A pore that simultaneously transports two different molecules in the same direction is called a(n)