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Intro Molecular Biology > Midterm 3 > Flashcards

Midterm 3 Flashcards

1
Q

What are membrane functions carried out by?

A

Membrane proteins

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2
Q

How much proteins make up animal membranes?

A

50% of the mass of most plasma membranes.

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3
Q

Glycolipids

A

Carbohydrates attached to lipids.

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4
Q

Glycoproteins

A

Proteins attached to lipids (short chains of sugars called oligosaccharides).

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5
Q

Why does the plasma membrane contain more lipid molecules?

A

Since they are much smaller, being over 50 more times prominent in the membrane.

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6
Q

Name a transporter protein and explain its function.

A

Na+ pump where it pumps Na+ out of the cell and K+ into.

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7
Q

Name an ion channel protein and explain its function.

A

K+ leak channel which allows K+ ions to leave the cell, having a great influence on cell excitability.

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8
Q

Name an anchor protein and explain its function.

A

Integrins which link intracellular actin filaments to extracellular matrix proteins.

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9
Q

Name a receptor protein and explain its function.

A

Platelet-derived growth factor (PDGF) receptor which binds extracellular PDGF, generating intracellular signals for the cell to grow and divide.

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10
Q

Name an enzyme protein and explain its function.

A

Adenylyl cyclase catalyzes the production of AMP in response to extracellular signals.

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11
Q

What are transmembrane proteins?

A

Proteins exist throughout the entire lipid bilayer, which part of their mass on each side (thus amphipathic).

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12
Q

How do the proteins on the cytosol side of the lipid bilayer associate with the membrane?

A

By an amphipathic alpha helix exposed on the surface of the protein.

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13
Q

How are the proteins that are entirely outside the bilayer, on either side, attached to the membrane?

A

Bound directly by one or more covalently attached lipid groups or indirectly through interactions with other membrane proteins.

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14
Q

How are integral membrane proteins removed from the bilayer?

A

By disrupting the bilayer with detergents.

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15
Q

How are peripheral membrane proteins removed from the membrane?

A

Gentle extraction procedures that interfere with protein-protein interactions but leave lipid bilayer intact.

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16
Q

How are the portions of a transmembrane protein connected?

A

By specialized membrane-spanning segments of the polypeptide chain.

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17
Q

What environment do these segments run through? What do they consist of?

A

Run through the hydrophobic environment of the interior of the lipid bilayer composed of amino acids of hydrophobic side chains (thus interact with the hydrophobic tails of the lipids).

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18
Q

What is the backbone of a polypeptide chain made of?

A

Protein amino acids, thus hydrophilic.

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19
Q

How do the atoms of the backbone interact with each other?

A

Can’t with interior of bilayer as no water, but hydrogen bond with one another.

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20
Q

How is hydrogen bonding maximized?

A

If the polypeptide chain forms a regular alpha helix.

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21
Q

How do the hydrophobic side chain and hydrophilic backbone exist in an alpha helix?

A

Hydrophobic side chain –> exposed on the outside of the helix to interact with hydrophobic lipid tails.
Hydrophilic backbone –> exist on the inside of the helix to form hydrogen bonds with one another.

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22
Q

What are single-pass transmembrane proteins? Give an example.

A

Its polypeptide chain only crosses the membrane once.
Ex. receptors for extracellular signals.

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23
Q

What are multipass transmembrane proteins? Give an example.

A

Those with series of alpha helices that cross the bilayer numerous times.
ex. channels

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24
Q

How are multipass transmembrane proteins arranged?

A

Amphipathic –> hydrophilic side chains fall one side of the helix and hydrophobic side chains on the others.

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25
Q

How is a transmembrane hydrophilic pore formed?

A

Multiple amphipathic alpha helices pack side by side to form a ring where the hydrophobic side chains are exposed to the lipids and the hydrophilic side chains form the lining of a hydrophilic pore.

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26
Q

How do transmembrane proteins cross the lipid bilayer as a beta sheet?

A

Amino acid side chains face the inside of the barrel to create a hydrophilic aqueous channel where the outside of the barrel is the hydrophobic core (interacts with the lipid bilayer).

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27
Q

What is a beta sheet?

A

A formation of a polypeptide chain that is rolled into a cylinder, forming a keg-like structure called a beta barrel.

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28
Q

What is an example of a beta barrel?

A

Porin proteins

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29
Q

What are porin proteins?

A

Form large, water-filled pores in mitochondrial and bacterial outer membranes.

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30
Q

What is the purpose of a porin protein?

A

Allow the passage of small nutrients, metabolites, and inorganic ions across the outer membranes.

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31
Q

What is the first step of separating membrane proteins?

A

Solubilizing the membrane with agents that destroy the lipid bilayer by disrupting hydrophobic associations.

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32
Q

What is the most widely used disruptive agent?

A

Detergents

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33
Q

How do detergents differ from membrane phospholipids?

A

Only a single hydrophobic tail.

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34
Q

What does the single hydrophobic tail of detergents allow?

A

One tail shapes it like a cone where they aggregate into small clusters in water forming micelles (spherical).

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35
Q

How do detergents disrupt the membrane?

A

The hydrophobic ends interact with hydrophobic regions of transmembrane proteins and tails of phospholipids, disrupting the lipid bilayer and separating the proteins from most of the phospholipids.

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36
Q

How does the detergent solubilize the membrane?

A

The hydrophilic ends interact, bringing the membrane proteins into solution as protein-detergent complexes that can be separated from one another.

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37
Q

How to determine a protein’s 3D structure?

A

X-ray crystallography

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38
Q

Why are membrane proteins harder to crystallize?

A

Purified in detergent micelles that are often heterogenous in size.

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39
Q

What is bacteriorhodopsin?

A

A small protein of 250 amino acids that are found in larger amounts of the plasma membrane of the Halobacterium halobium.

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40
Q

What does bacteriorhodopsin act as? Function?

A

A membrane transport protein (pump protein) that pumps H+ out of the cell.

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41
Q

How does bacteriorhodopsin gets its energy to pump H+ out of the cell?

A

Sunlight

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42
Q

What is the purpose of retinal in bacteriorhodopsin?

A

A light-absorbing non protein that gives the protein and bacteria a deep purple colour.

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43
Q

How is retinal attached to bacteriorhodopsin?

A

The hydrophobic molecule is covalently attached to one of bacteriorhodopsin’s seven transmembrane alpha helices.

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44
Q

What happens when retinal absorbs a photon of light?

A

It changes shape, causing the protein embedded in the lipid bilayer to undergo a series of small conformational changes.

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45
Q

What do the structural changes of bacteriorhodopsin result in?

A

The transfer of one H+ from the retinal to the outside of the bacterium.

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46
Q

How does the protein return to its original conformation (in terms of retinal)?

A

Retinal is regenerated by taking up a H+ from the cytosol, returning the protein to its original shape.

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47
Q

What is a pump protein?

A

A class of transmembrane proteins that actively move small organic molecules and inorganic ions into and out of cells.

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48
Q

How does bacteriorhodopsin create a concentration gradient?

A

When in the presence of sunlight, thousands of them pump H+ out of the cell generating a concentration gradient of H+ across the plasma membrane.

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49
Q

How are cell membranes strengthened and supported?

A

By a framework of proteins, attached to the membrane via transmembrane proteins.

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50
Q

What are plant’s plasma membrane encased by?

A

A cell wall

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51
Q

Explain the composition of a cell wall.

A

A meshwork of proteins, sugars, and other macromolecules.

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52
Q

What is the plasma membrane of an animal cell stabilized by?

A

Cell cortex.

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53
Q

What is the cell cortex made of?

A

A meshwork of fibrous proteins.

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54
Q

Where is the cell cortex attached?

A

On the underside of the plasma membrane (inside the cell).

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55
Q

What is the shape of red blood cells?

A

Biconcave shape

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56
Q

What is the main component of the cell cortex in red blood cells?

A

Dimeric protein spectrin

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57
Q

What is the structure of dimeric protein spectrin?

A

A long, flexible rod about 100nm in length.

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58
Q

How is the spectrin meshwork attached to the membrane?

A

Through intracellular attachment proteins the link it to specific transmembrane proteins.

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59
Q

What are the structures of anemic blood?

A

Red cells are spherical and fragile.

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60
Q

What are the main components of the cortex in animal cells?

A

Actin and motor protein myosin.

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61
Q

What is the purpose of the cortex?

A

Red blood cells need it to provide mechanical strength; need it to allow them to selectively take up materials from their environment; and cells use it to restrain the diffusion of proteins within the plasma membrane.

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62
Q

How was the lateral diffusion of proteins within the lipid bilayer shown?

A

Fusing a mouse cell with a human cell to form double-sized hybrid cell and then monitoring the distribution of certain mouse and human plasma membranes:
- confined to own halves of the newly formed cell
- time passes, and the two sets of proteins become evenly mixed over the entire cell surface

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63
Q

Membrane domains

A

Functionally specialized regions by confining particular proteins to localized areas within the bilayer membrane.

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64
Q

What can the plasma membrane tether itself to on the outside of the cell?

A

Membrane proteins attach to extracellular matrix or on an adjacent cell.

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65
Q

Can membrane domains interact?

A

Yes and no, as the cell can create barriers that restrict particular membrane components to one membrane domain.

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66
Q

Where must proteins that are involved in the uptake of nutrients from the gut located?

A

Apical surface (surface that faces the gut contents).

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67
Q

Where must proteins involved in the export of solutes out of epithelial cells into tissue and bloodstream located?

A

Basal and lateral surfaces.

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68
Q

What is the purpose of a tight junction?

A

Creates a seal between adjacent plasma membranes from specialized junction proteins forming a belt, thus not allowing membrane proteins to diffuse past it.

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69
Q

Proteoglycans

A

Membrane protein that contain one or more long polysaccharide chains.

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70
Q

Where are the carbohydrates attached to glycoproteins and glycolipids located? What do they form?

A

Located on the outside of the plasma membrane forming a sugar coating called glycocalyx.

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71
Q

What is the purpose of the glycocalyx?

A

Protect the cell surface from mechanical damage.

72
Q

How does the glycocalyx layer become slimy?

A

When oligosaccharides and polysaccharides absorb water.

73
Q

What is the purpose of the glycocalyx’s slimy surface?

A

Helps motile cells squeeze through narrow spaces and prevent blood cells from sticking to one another or to the walls of blood vessels.

74
Q

What do cell surface carbohydrates help in?

A

Protect, lubricate, cell-cell recoginition, and adhesion.

75
Q

What is the purpose of lectins?

A

Proteins that are specialized to bind to particular oligosaccharide side chains.

76
Q

How are the oligosaccharide side chains joined together?

A

Sugars are joined together in many different arrangements by covalent linkages forming branched structures.

77
Q

How does the carbohydrate layer on the surface of cells help with cell-cell recognition?

A

Very distinctive and recognized by other cell types that interact with it.

78
Q

Give two examples of cell-cell recognition with the surface carbohydrate later.

A
  1. Recognition of an egg by a sperm due to specific oligosaccharides
  2. Carbohydrate surface in white blood cells - neutrophils - is recognized by lectin on cells lining the blood vessels at the site of infection; neutrophils then bind to blood vessel wall and migrate to infected tissue to destroy invading bacteria.
79
Q

Explain synthetic lipid bilayer studies of membrane proteins.

A
  1. Membrane protein isolated
  2. Protein of interest is purified and reformed in artificial phospholipid vesicles (addition and removal of detergent to make happen)
  3. Lipids allow the purified protein to maintain its proper structure and function
80
Q

What do transporters pass through the membrane?

A

Shift small organic molecules or inorganic ions.

81
Q

How do transporters allow molecules to pass the membrane?

A

By changing shapes.

82
Q

What do channels form?

A

Tiny, hydrophilic pores across the membrane.

83
Q

Ion channels

A

Those that allow the passage of inorganic ions.

84
Q

What happens when ions cross the membrane?

A

Create a powerful electric force or voltage due to ions being electrically charged.

85
Q

Simple diffusion

A

Molecules moving from high to low concentrations without the assistance of transporters.

86
Q

Facilitated diffusion

A

Molecules moving from high to low concentrations with the assistance of specialized membrane transport proteins.

87
Q

Why can’t hydrophilic, polar molecules simply cross lipid bilayers?

A

Simple diffusion occurs too slow, thus they need the aid of membrane transport proteins.

88
Q

What molecules diffuse rapidly across the membrane?

A

The smaller the molecule and more hydrophobic, nonpolar, it is.

89
Q

What molecules diffuse rapidly across cells through simple diffusion?

A

Small nonpolar molecules like carbon dioxide and molecular oxygen.

90
Q

What is the purpose of O2 and CO2 in cells?

A

Cell respiration processes.

91
Q

How do uncharged polar molecules cross the membrane? What kinds?

A

Diffuse readily across the bilayer if they are small enough (simple diffusion) like ethanol and water. Larger uncharged polar molecules like glucose cross hardly at all.

92
Q

How do charged molecules cross the membrane? Why?

A

Inorganic ions can’t enter the bilayer due to their charges and strong electrical attraction to water.

93
Q

What inorganic ions are crucial for a cell?

A

Na+, K+, Ca2+, Cl-, and H+.

94
Q

What do the movement of inorganic ions allow for a cell?

A

Production of ATP and communication between cells, specifically nerve ones.

95
Q

What ion exists the most inside the cell?

A

K+

96
Q

What ion exists the most outside the cell?

A

Na+

97
Q

How does a cell avoid being torn apart by electrical forces?

A

The quantity of positive charges inside the cell must be balanced by an almost exactly equal quantity of negative charge; this goes for the fluid surrounding the cell.

98
Q

What is the high concentration of Na+ outside the cell balanced by?

A

Cl-

99
Q

What is the high concentration of K+ inside the cell balanced by?

A

Negatively charged organic and inorganic ions, like nucleic acids, proteins, and many cell metabolites.

100
Q

Membrane potential

A

Electrical imbalances that generate a voltage difference across the membrane.

101
Q

Rest membarne potential

A

When the excahnge of anion and cations across the mebrane are balanced, but not zero.

102
Q

What is the resting membrane potential in animal cells?

A

Between -20 and -200 mV

103
Q

Why is the resting membrane potential negatve?

A

Because the interior of the cell is more negatively charged than the exterior.

104
Q

What does the membrane potential allow for the cells?

A

The power to transport of certain metabolites and provides those excitable cells to communicate with their neighbours.

105
Q

What principles do channels transport solutes on?

A

Size and electric charge.

106
Q

What happens when the channel is open?

A

Ano ion or molecule that is small enough and carries the appropriate charge can pass through.

107
Q

What principles do transporters transport solutes on?

A

Great specificity

108
Q

How does a transporter transport a solute?

A

Transfers only those molecules or ions that fit into specific binding sites on the protein.

109
Q

What is the opening and closing of channels controlled by?

A

An external stimulus or conditions within the cell.

110
Q

Passive transport

A

When molecules spontaneously move down high to low concentrations without using energy by the transport protein.

111
Q

Why doesn’t passive transport use energy?

A

More solute will move in than out until the two concentrations equalize.

112
Q

What membrane proteins use passive transport?

A

All channels and some transporters.

113
Q

Active transport

A

When solutes move against the concentration gradient using the input of energy from ATP hydrolysis, a transmembrane ion gradient, or sunlight.

114
Q

What membrane proteins use active transport?

A

Special types of transporters called pumps.

115
Q

What is the direction of passive transport determined by for an uncharged molecule?

A

Its concentration gradient.

116
Q

What does the membrane potential act on?

A

Exerts a force on any molecule that carries an electric charge.

117
Q

What does the membrane potential pull in and out of the cell?

A

The membrane potential pulls positive charges into the cell (due to the negative potential in the cytosol) and drives negative ones out.

118
Q

Electrochemical graident

A

A net driving forces that drives a charged solute across a cell membrane.

119
Q

What are the two forces of the electrochemical gradient?

A

One is the concentration gradient and the other is a membrane potential.

120
Q

What does the electrochemical gradient determine?

A

The direction that each solute will flow across the membrane by passive transport.

121
Q

What happens when the voltage and concentration gradients work in the same direction?

A

It creates a very steep and powerful electrochemical gradient.

122
Q

What ion has a strong electrochemical gradient? What does this do?

A

Na+ which tend to enter the cells if given the opportunity.

123
Q

What happens if the voltage and concentration gradients work in the opposite directions?

A

A small electrochemical gradient.

124
Q

What ions has a small electrochemical gradient? What does this do?

A

K+ where there is little net movement of K+ across the membrane even when K+ channels are open.

125
Q

How much does water make up of a cell?

A

Generally about 70% by weight.

126
Q

Aquaporins

A

Specialized channel proteins that allow the flow of water molecules.

127
Q

Osmolarity

A

The total concentration of solute particles inside the cell.

128
Q

What way does water flow normally in cells?

A

Down its concentration gradient from high water concentrations to low ones also known as osmosis.

129
Q

Why does water normally flow into cells?

A

Because the total concentration of solute particles, charged molecules and ions, sindie the cell exceed the solute concentration outside the cell.

130
Q

How do animal cells withstand cell swelling?

A

Cells have a gel-like cytoplasm that resist osmotic swelling.

131
Q

How do protozoans resists osmotic swelling?

A

Use contractile vacuoles that periodically discharge their contents to the exterior.

132
Q

How do plant cells resist osmotic swelling?

A

Tough cell walls

133
Q

What is the purpose of turgor pressure?

A

Keep cell walls tense, so that stems of plants are rigid and its leaves are extended. If no turgor pressure, the plants wilt.

134
Q

What transporters do plasma membranes contain?

A

Those that import nutrients like sugars and amino acids.

135
Q

What transporters do lysosomal membranes contains?

A

H+ transporter that import H+ to acidify the interior and others that move digestion products out.

136
Q

Explain the conformations of the glucose transporter.

A

One exposes the binding sites for glucose to the exterior of the cell and the other conformation exposes the sites to the cell interior.

137
Q

What component of an electrochemical gradient determines the direction of the glucose transporter?

A

The concentration gradient of glucose.

138
Q

How does the electrical component of the electrochemical gradient of glucose exist? Why?

A

It’s zero since glucose is uncharged.

139
Q

What happens when glucose levels are high oustide of cells? Explain in terms of glucose transporter.

A

The sugar binds to the transporter’s binding sites and the protein than switches conformations, carrying the bound sugar unward to release into the cytosol.

140
Q

What happens when glucose levels are low in the blood? Explain in terms of a glucose transporter.

A

Glucagon that is broken down inside liver cells binds to the internally displaying binding sites on the transporter, and the protein switches conformation in the opposite direction where glucose is released into the blood.

141
Q

What are the three pumps for active transport?

A
  1. ATP-driven pumps: hydrolyze ATP to drive uphill transport
  2. Coupled pumps that link the uphill transport of one solute to the downhill transport of another
  3. Light-driven pumps: energy from the sun to drive uphill transport
142
Q

How is Na+ transport linked to others?

A

The Na+ pumps Na+ out of the cell against its electrochemical gradient, thus it can flow back into the cell via its electrochemical gradient where the influx of incoming Na+ provide energy for the active transport of other substances into the cell AGAINST their electrochemical gradients.

143
Q

What would happen to the Na+ couple pumps if the Na+ pump stopped?

A

They would stop since the the Na+ gradient doesn’t run or provide energy.

144
Q

What organism do Na+ pumps exist most in?

A

Plasma membranes of animal cells.

145
Q

What is bacteria’s version of Na+ pumps? Explain.

A

ATP-driven H+ pumps where in pumping H+ out of the cell, it creates an electrochemical gradient of H+ across the plasma membrane that is used for other solute transport.

146
Q

How much ATP does the Na+ pump use?

A

30% or more of total ATP consumption.

147
Q

How do conformation changes occur in Na+/K+ pump?

A

The energy from ATP hydrolysis and the phosphate group removed attaches to the pump.

148
Q

What does ouabain do for the Na+/K+ pump?

A

Inhibits the pump by preventing the binding of extracellular K+.

149
Q

What allows the Na+/K+ pump to avoid using useless ATP hydrolysis?

A

The tight coupling between steps ensures that it only operates when the appropriate ions are present.

150
Q

How many Na+ are transported out of the cell during one cycle out the Na+/K+ pump? K+?

A

Na+ = 3 out
K+ = 2 in

151
Q

How does the Na+/K+ pump ensure that Na+ in the cytosol is way lower in the cell and K+ is way higher (10-30 times)?

A

Expels the Na+ that constantly enters the cell through other transporters and ion channels in the plasma membrane.

152
Q

Why does Na+ want to go back into the cell?

A

Due to the large electrochemical gradient crated from the steep concentration gradient of Na+ across the membrane acting with its membrane potential.

153
Q

What happens to the other pumps when the ouabain stop the Na+ pump?

A

The stored energy of the high concentration of Na+ outside the cell drives other pumps that drive na+ into the cell for a couple of minutes.

154
Q

How are Ca2+ concentrations?

A

Low concentration in the cytosol and large concentration in the extracellular fluid.

155
Q

What does an influx of Ca2+ into the cytosol via channels cause?

A

Intracellular signal to trigger cell processes like muscle contraction and nerve cell communication.

156
Q

Where do ATP driven Ca2+ pumps exist?

A

In the plasma membrane and the endoplasmic reticulum membrane.

157
Q

Why do eukaryotic cells want a low concentration of free Ca2+ in their cytosol?

A

The lower the free Ca2+ in the cytosol, the more sensitive the cell is to an increase in it, thus triggering faster and stronger signals.

158
Q

What is the main difference between Ca2+ and Na+ pumps?

A

Ca2+ pumps return to their original conformation without a requirement for binding and transporting a second ion.

159
Q

How many Ca2+ ions are driven out of the cytosol?

A

2

160
Q

What shows that Na+ and Ca2+ have common evolutionary origin?

A

Have similar amino acid sequences and structures.

161
Q

How do coupled pumps work?

A

They couple the movement of one (in)organic ion to the movement of another.

162
Q

Symport

A

The pump move both solutes in the same direction across the membrane.

163
Q

Antiport

A

Moves the solutes in opposite directions.

164
Q

Uniport

A

Not a coupled transporter since it move only one type of solute.

165
Q

Explain symports in epithelial cells that line the gut.

A

A glucose-Na+ symport:
- Electrochemical gradient for Na+ is steep, so Na+ moves into the cell down its gradient, pulling glucose into the cell with it (even though the concentration of glucose is higher in the cell).

166
Q

Cooperative binding

A

The binding of one enhances the binding of the other, where both must be present to occur.

167
Q

Where does the glucose-Na+ symport exist? Why?

A

In the apical domain of the plasma membrane which faces the gut lumen to create a high glucose concentration in the cytosol, so that glucose can be pumped into the blood.

168
Q

Where do the glucose uniports exist? Why?

A

In the basal and lateral domains of the plasma membranes so that glucose can move down its concentration gradient for use by other tissues.

169
Q

How are the two glucose transporters separated?

A

A diffusion barrier formed by a tight junction around the apex of the cell.

170
Q

Explain the Na+-H+ antiport.

A

Uses the downhill influx of Na+ into the cell to pump H+ out of the cell.

171
Q

Why are Na+-H+ antiports used?

A

To control the pH in the cytosol of animal cells by preventing the cell interior from becoming too acidic.

172
Q

What do plant cells and bacteria rely on for their electrochemical gradient?

A

Those created by H+ pumps that pump H+ out of the cell, thus H+ symports to transport sugars into cells.

173
Q

What are the H+ pumps in photosynthetic bacteria?

A

Bacteriorhodopsin that uses the activity of light driven H+ pumps to create the gradient.

174
Q

Are some H+ pumps similar to Na+ ones?

A

Yes, in the sense that they create the gradient using the energy of ATP hydrolysis.

175
Q

What is the purpose of ATP H+ pumps in intracellular organelles like lysosomes and central vacuoles?

A

Transport H+ out of the actively transport H+ out of the cytosol into the organelle keeping the pH of the cytosol neutral and the pH of the interior of the organelle acidic.

Intro Molecular Biology (5 decks)

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