EXAM 3 Flashcards
1
Q
functions of membranes
A
boundaries of cell
allows import and export
retains metabolites and ions
senses external signals and transmits info into the cell
provides compartmentalization within eukaryotic cells
stores energy as a proton gradient
supports synthesis of ATP
2
Q
functions of membranes: import and export
A
selective import of nutrients and selective export of wastes and toxins
3
Q
functions of membranes: compartmentalization
A
separate energy-producing reactions from energy consuming ones
keeps proteolytic enzymes away from important cellular proteins
4
Q
membranes are composed of
A
variety of lipids and proteins
5
Q
some membrane lipids and proteins are
A
glycosylated
esp outer face of plasma membrane
6
Q
membrane bilayer
A
2 leaflets of lipid monolayers
7
Q
membrane bilayer is made up mostly of
A
glycerophospholipids (+sphingolipids and others)
8
Q
membrane bilayer spontaneously forms due to
A
hydrophobic effect
hydrophilic head groups interact w water
9
Q
glycerophospholipids
A
two fatty acids on C1 and C2 of glycerol
highly polar PO4 on C3 may be further esterified by an alcohol (head groups)
10
Q
sphingolipids
A
one fatty acid attached to sphingosine by amide linkage
head group may also be attached to sphingosine
11
Q
fluid mosaic model of membranes
A
singer and nicholson
lipids form a viscous, 2D solvent into which proteins are inserted and integrated
12
Q
two types of proteins in fluid mosaic model
A
integral and peripheral
13
Q
integral proteins
A
firmly associated with the membrane, often spanning the bilayer
14
Q
peripheral proteins
A
weakly associated to the surface of the bilayer via lipids or integral proteins and can be removed easily
15
Q
physical properties of membranes
A
dynamic and flexible
asymmetric
can undergo phase transitions
not permeable to larger polar solutes and ions
permeable to small polar solutes and nonpolar compounds
16
Q
composition of membranes: lipids
A
ratio of lipid to protein varies
type of phospholipid varies
abundance and type of sterols varries
17
Q
prokaryotes lack ______ in membranes
A
sterols
18
Q
cholesterol is found higher in ________ and absent in ______
A
higher in plasma membrane and absent in mitochondria
19
Q
asymmetry of membranes: lipids
A
outer and inner leaflets have different compositions
head groups on inner leaflet are smaller for smaller radius
20
Q
asymmetry of membranes: proteins
A
individual peripheral membrane proteins are only associated w one side of the membrane
integral proteins have different domains on different sides of the membrane
specific lipid anchors added to proteins target the protein to a specific leaflet
21
Q
asymmetry of membranes: carbs
A
only on outside of plasma cell membrane
22
Q
asymmetry of membranes: electric
A
inside is usually -50
23
Q
membrane phases
A
depending on their composition and the temperature, the lipid bilayer can be in the gel or fluid phase
gel
fluid
24
Q
gel phase
A
liquid ordered state
individual molecules do not move around
25
fluid phase
liquid disordered state
individual molecules can move around
26
membrane phases temperature
heating: gel to fluid
27
membrane under physiological conditions
membranes are more fluid like than gel like
28
adjusting membrane composition
fluidity is determined mainly by the fatty acid composition
29
shorter and more unsaturated fatty acids:
more fluid membranes
less interactions bc short
more kinks so less packing, lower Tm, more fluidity
30
high temperature membrane
more saturated fatty acids to maintain integrity
31
low temperature membrane
more unsaturated fatty acids to maintain fluidity
32
sterols in membranes
cholesterol: animals
phytosterols: plants
ergosterol: fungi
affect membrane rigidity and permeability
33
functions of proteins in membranes
receptors
enzymes
channels, gates, pumps
34
functions of proteins in membranes: receptors
detect signals from the outside
light (opsin)
hormones (insulin receptor)
NT (Ach receptor)
pheremones (taste and smell receptors)
35
functions of proteins in membranes: enzymes
lipid biosynthesis (acyltransferases)
ATP synthesis
36
functions of proteins in membranes: channels, gates, pumps
nutrients (maltoporin)
ions (K+ channel)
NT (SSRI)
37
peripheral membrane proteins
associate with the polar head groups on one side of membranes
loosely associated
noncovalent interactions with lipid head groups or aqueous domains of integral membrane proteins
can be removed by disrupting ionic/polar interactions either with high salt or change in pH
purified peripheral proteins are no longer associated with any lipids
38
integral membrane proteins
span the entire memrane or linked to membrane by lipid moiety
have asymmetry relative to the membrane; different segments in different compartments
tightly associated with the membrane
hydrophobic stretches in the protein interact with the hydrophobic regions of the membrane
removed by detergents that disrupt the membrane
purified integral membrane proteins still have phospholipids associated with them
39
lipid anchors
some membrane proteins are lipoproteins
contain a covalently linked lipid molecule
- long chain FA
- sterol
- isoprenoid
- glycosylated phosphotidylinositol (GPI)
lipid can become part of the membrane
protein is now anchored to the membrane
process is reversible if enzyme can cleave lipid moiety off the protein
allows targeting of proteins
40
types of integral membrane proteins: alpha helices
single transmembrane domain
many helices connected with loops
many domains not linked together
lipid anchored
combo of anchor and helix
41
types of integral membrane proteins: beta sheets
barrels form with hydrogen bonds maximized by circle of beta strands
usually transporters
only found in bacteria, mitochondria, chloroplasts on the outer membrane
42
structure of integral membrane proteins: helices
proteins made of helices need helices of about 20 AA to cross the membrane
amino acids must be hydrophobic if interacting with the membrane; need to be hydrophilic if interacting with other helices or central to a pore
43
structure of integral membrane proteins: beta sheets
need 7-9 AA in a strand to cross the membrane
amino acids with R groups pointing towards membrane must be hydrophobic
AA with R groups into barrel must be hydrophilic
44
hydropathy index
```
positive = phobic
negative = philic
```
45
hydropathy plots
predicts helical transmembrane domains for most transmembrane proteins
hydropathy index vs amino acid
predictive plot
a way to look at known primary structure and try to determine if there are segments that form helices or cross the membrane
46
amino acids in membrane proteins cluster
transmembrane segments are predominantly hydrophobic
Tyr and Trp cluster at nonpolar/polar interface because hydrophaty indexes are around zero
—> associate with polar head groups of membranes at transition
charged AA found only in aqueous domains
47
membrane dynamics: lateral diffusion
individual lipids undergo fast lateral diffusion within the leaflet
48
membrane dynamics: transverse diffusion
spontaenous flips from one leaflet to another are rare; charged head group must transverse the hydrophobic tail region of the membrane
important for the composition of the membrane so we have to have a way for this to happen otherwise you don’t get the differential composition between the two leaflets
flippases
49
flippases
cause transverse movement of lipids
| some use energy of ATP to move lipids against the concentration gradient
50
floppases
moves phospholipids from cytosolic to outer leaflet
51
scramblase
moves lipids in either direction toward equilibrium, no ATP with gradient
52
flippase
PE and PS form outer to cytosolic leaflet
53
membrane fusion
membranes can fuse with each other without losing continuity
can be spontaneous or protein mediated
54
membrane fusions: proteins can
bend membranes to form a vesicle
bring a vesicle close enough to fuse with a membrane
55
examples of protein-mediated membrane fusion
entry of influenza virus into host cell
release of NTM at nerve synapses
56
cell membranes are permeable to
small nonpolar molecules that passively diffuse through the membrane
57
passive diffusion of polar molecules involves
desolvation and thus has a high activation energy barrier
58
transport across the membrane can be facilitated by proteins that provide an
alternative diffusion path (transporters)
59
passive transport must be energetically favorable
concentration dependence
electrochemical gradient
60
concentration dependence
solute moves towards equilibrium across the membrane high to low
61
electrochemical gradient
solute moves toward charge equilibrium across the membrane
62
active transport
solute moving isn’t energetically favorable to the system
63
polar solutes need alternative paths to cross cell membranes
protein helps with the desolvation process and keeps molecules from interacting with the hydrophobic core
lowers activation energy for transport, makes movement faster
64
C2
destination of molecule
65
C1
original location of molecule
66
dGt is negative if
C2 < C1
67
dPsi
charge on the membrane
68
dPsi is negative when
molecule is moving towards the negative side
69
dPsi is positive when
molecule is moving towards the positive side
70
integral membrane proteins: ion channels
passive transport
molecules move down their concentration gradient at rates close to diffisuion
generally don’t become saturated
71
integral membrane proteins: transporters
can be active or passive
move molecules slower than diffusion
can move molecules up their concentration gradient
can be saturated
72
cotransport
2 or more molecules
73
glucose transporter
12 transmembrane helices
amphipathic
hydrophilic core for glucose
74
glucose transporter model
2 conformations of glucose transporter
uniporter in either direction
passive transport
transport rarely stops because metabolism allows cell to keep glucose low inside or phosphorylates it so it cannot be bound by the transporters
we want [glucose] high = outside so it can enter the cell
75
glucose symporter
on apical surface
glucose and sodium secondary active
76
sodium potassium exchanger
prevents sodium buildup in the cell
77
glucose uniporter
basal surface
GLUT2
78
bicarbonate transporter
antiporter;
CO2 to lungs
antiport speeds up bicarbonate transport and maintains the electrochemical potential across the membrane
79
bicarbonate: in tissues
CO2 diffuses in and is converted to bicarbonate via carbonic anhydrase
bicarbonate transports out into the plasma via a Cl- bicarbonate exchanger
80
bicarbonate: in lungs
bicarbonates enters the blood cell via bicarbonate-Cl- exchanger
converted to CO2 via carbonic anhydrase and CO2 diffuses out into the lungs to be exhaled
81
ABC transporters
primary active
ATP Binding casette
uses ATP hydrolysis to drive transport of substrates
ATP hydrolysis occurs separately from the transporter and the hydrolysis changes the conformation of the protein and allows transport up a gradient
82
Proton transport
energy of ATP hydrolysis can be used to pump protons across the membrane against a gradient (Ftype ATPase)
pH control
energy of proton gradient can be used to synthesize ATP
ATP synthase in chloroplast and mitochondrial membranes
83
ion channels
passive transport
potassium enters cavity of channel, hydrated by water molecules
helix in transporters have diples; negative dipole helps binding of the K+ ion
K+ interacts with the carbonyl oxygens on amino acids in the binding site
binding slots desolvate K+ ions with oxygens on carbonyls
K+ fits into alternating slots
84
hydrolysis of ATP is favorable under standard conditions
charge separation in products makes the reaction favorable
products are better solvated
products are stabilized with resonance, making the reaction more favorable
85
the actual free energy change of a process
depends on the standard free energy (-30.5 for ATP hydrolysis)
actual concentrations of reactants and products
86
the free-energy change is more favorable if
the ratio of reactant concentration to product concentration exceeds that at standard concentration
[ATP] is kept high in cells
if [ATP] levels get low, fewer molecules and less energy to drive reactions
87
dG for ATP hydrolysis in erythrocytes
-52kJ/mol
88
many phosphorylated compounds have a large dG’* for hydrolysis
electrostatic repulsion with the reactant is relieved
the products are stabilized with resonance or more favorable solvation
product undergoes tautomerization
89
phosphates can be transfered from
compounds with more negative dG to those with less negative dG
90
NTP reactions: activation of a reaction
1. Pi or PPi or NMP (AMP) is bound to substrate or enzyme
| 2. phosphate containing moiety is displaced
91
energy quantities
phosphoenolpyruvate
1,3-bisphosphoglycerate
phosphocreatine
ATP
glucose-6P
glycerol-6P
92
in some instances ATP or GTP are hydrolyzed directly
provides energy for movement
| ribosome movement on mRNA
93
phosphorylation of proteins can change conformation
to cause activity
Na+K+ATPase transports ions using cycling of phosphorylation
94
2ADP —> ATP + AMP
when ATP is low
| can run in reverse when ATP is high
95
thioesters
sulfer atom replaces oxygen
hydrolysis generates a carboxyllic acid
product is resonance stabilized
dG’* is negative
96
most common types of redox reactions in biological systems
transfer of single electrons with or without simultaneous transfer of protons
transfer of a hydride ion
transfer of electrons to molecular oxygen
incorporation of one or both oxygen atoms from O2 into a substrate
97
most common types of redox reactions in biological systems: transfer of single electrons
with or without simultaneous transfer of protons
enzymes require cofactors
occur predominantly in mitochondria as part of the electron transport chain and in chloroplasts or cyanobacteria in photosynthesis
98
enzymes involved in transfering of single electrons: cofactors
hemes (change in oxidation state of iron between Fe2+ and Fe3+)
iron-sulfur proteins
copper ions (Cu+/Cu2+)
flavin nucleotides (FMN or FAD)
99
most common types of redox reactions in biological systems: transfer of a hydride ion
one proton plus 2 electrons
NAD+/NADH and NADP+/NADPH are usually involved
catalyzed by dehydrogenases or reductases
100
most common types of redox reactions in biological systems: transfer of electrons to molecular oxygens
reduced to water or H2O2 in this process
catalyzed by oxidases
101
most common types of redox reactions in biological systems: incorporation of one or both oxygen atoms from O2 into a substrate
catalyzed by oxygenases
102
reduced organic compounds
serve as fuels from which electrons can be stripped off during oxidation
103
oxidation reduction reactions
many biochemical oxidation-reduction reactions involve transfer of 2 electrons
in order to keep the charges in balance, proton transfer often accompanies electron transfer
in many dehydrogenases, the reaction proceeds by a stepwise transfer of proton and hydride
104
measuring the standard reduction potential of a redox pair
measures electron movement
test cell with equal lactate and pyruvate conjugate redox pair
at standard hydrogen electrode: water half reaction takes place
if the electron affinity of the oxidized form of the conjugate redox pair is higher than the electron affinity of H3O+, the standard reduction potential is positive; if not, it is negative
* *electrons go to test cell —> higher reduction potential
* * electrons go to reference cell —> lower reduction potential
105
reduction potential (E)
affinity for electrons; interest of molecule to take electrons and be reduced
electrons transfered from molecules with lower E to higher E
pH of 7 and 1M concentrations assumed
106
NAD+ and NADP+
common redox cofactors
coenzymes (can dissociate from enzyme after the reaction and react elsewhere to return to original redox state)
hydride from an alcohol is transferred to NAD+ giving NADH
107
NADPH
usually used to reduce other molecules
108
NAD+
breakdown of molecules
109
NADP+
synthesis
110
tossman fold
proteins have specific domains for NAD(H) or NADP(H) binding
111
flavin cofactors
allow single and double electron transfers
organic cofactor used in oxidative phosphorylation and photosynthesis as an electron carrier in electron transport
prosthetic groups (tightly bound to enzymes)
FAD or FMN can accept one electron and one hydrogen at a time to make FADH2 or FMNH2
can also pass or accept 2 electrons and 2 hydrogens (usually intermediary between NAD+/NADH and metal ions)
112
FMN or fAD
depends on the enzyme
