Membranes - pas exams

Question 1

1. Which of the following features are characteristic for biomembranes? (4P)
   
   1. The average thickness varies from ~3.5 um
   2. Charged molecules can cross the membrane unhindered
   3. They can contain 25% of sterol lipids
   4. The have a hydrophilic and positively charged surface
   5. They are kept together by non-covalent interactions
   6. Water molecules can cross the membrane only via channels
   7. The can contain more than 70% proteins
   8. Triglycerols are one of the most common components of biomembranes

Answer 1

1. The average thickness varies from ~3.5 um - False
2. Charged molecules can cross the membrane unhindered - False
3. They can contain 25% of sterol lipids - True
4. The have a hydrophilic and positively charged surface - False
5. They are kept together by non-covalent interactions - True
6. Water molecules can cross the membrane only via channels - False
7. The can contain more than 70% proteins - True
8. Triglycerols are one of the most common components of biomembranes - False

Question 2

1. What is the difference between bilayer and non-bilayer lipids?
2. Why are there non-bilayer lipids in membranes?

Answer 2

1. What is the difference between bilayer and non-bilayer lipids?
   
   1. Bilayer lipids typically cylinder, non-bilayer typically cones
2. Why are there non-bilayer lipids in membranes?
   
   1. Non-bilayer lipids typically involved in adjustment of lipid bilayer, such as in hydrophobic mismatch, and membrane curvature.

Question 3

Which type of a) integral, b) anchored and c) peripheral membrane proteins exist? (6P)

Answer 3

1. Integral
   
   1. Alpha-helix
   2. Beta-barrel
2. Anchored
   
   1. GPI anchor
   2. Isoprenoid anchored
   3. Lipid anchored (e.g. palmitic)
3. Peripheral
   
   1. function as: cytoskeleton linkers, signal transducers, components of extracellular matrix (not 100% sure on this answer)

Question 4

1. Explain the term “hydrophobic mismatch and how it can be corrected in the context of a biomembrane? (3P)

Answer 4

1. If TM-region and lipid bilayer size do not match
2. Lipid bilayer can be adjusted to the protein size because lipid hydrocarbon chains are flexible and can be stretched squashed, or tilted
   
   1. Non-bilayer lipids are often involved in this adjustment
3. The protein can adjust to hydrophobic mismatch
   
   1. Changes in tilting angle of TM-helices can be employed to adjust proteins

Question 5

1. Explain in key words the functional mechanism of the Na+/K+ ATPase? (6P)

Answer 5

1. Is primary active antiporter
2. Description:
   
   1. Na+/K= ATPase is open to the inside and has high affinity for Na+
   2. One ATP transfers a phosphate group and induces conformational change
   3. The phosphorylated Na+/K+-ATPase is now open to the extracellular space and the 3Na+ are released there due to decreased affinity
   4. After binding of two K+, phosphate is cleaved off by a phosphate from Na+/K+ antiporter à Conformational change à release 2K+ in the cytosol à circle can start again
   5. Net 3Na+ out, 2K+ in, - potential
3. Process:
   
   1. Na+ binds
   2. Pump phosphorylates itself
   3. Phosphorylation triggers conformational change, Na+ ejected
   4. K+ binds
   5. Pump dephosphorylated
   6. Pump returns to original conformation, K+ ejected

Question 6

1. Identify the type of displayed lipid and label the marked structures (6P)

Answer 6

1. Phospholipid (or type of cetrimide) (from top to bottom): Hydrophilic part: (Head-group; Phosphate group); Hydrophobic part: (Glycerol; Fatty acid; fatty acid)
2. Glycosphingolipid (from top to bottom): Sugars; Sphingosine; Serine; Fatty acid; fatty acid
3. Sterol (cholesterol in this case) (from top to bottom): OH-/Hydroxy group; Isoprenoid

Question 7

1. You are asked to characterize a protein that was identified in the total membrane function of Arabidosis. Shortly describe 2 experimental set-ups to a) elucidate the precise subcellular localization and b) identify potential interaction partners. (6P)

Answer 7

1. Subcellular localization methods
   
   1. Florescence label by tagging
      
      1. Add fluorescent label (e.g. GFP) to protein of interest to see its localization in the cell
   2. Immunogold labeling electron microscopy
      
      1. See the localization of your protein in electron microscopy after immune-gold labelling. Immunogold labelling occurs via antibodies
2. Interaction partner methods
   
   1. Ubiquitin-split-2-hybrid
      
      1. Protein of interest + potential interaction partner linked to Nub + Cub
      2. If the two proteins interact a transcription factor will be cleaved from the ubiquitin and trigger the transcription of a reporter gene
   2. Segregation of proteins by isoelectric point
      
      1. Protein complex should have
      2. Afterwards segregate complex via SDS-PAGE à identify components of complex

Question 8

1. Which of the following features are characteristic for biomembranes? (4P)
   
   1. Always bilayer in eukaryotes
   2. They have a hydrophilic core and a hydrophobic surface
   3. Their average thickness varies from ~3-5 um
   4. Charged molecules can cross the membrane unhindered
   5. They are comprised of lipids, proteins, sugars
   6. They from automatically under physiologically conditions
   7. Both monolayers always have the same composition
   8. They can contain 25% of sterol lipids

Answer 8

1. Always bilayer in eukaryotes - True
2. They have a hydrophilic core and a hydrophobic surface – false
   
   1. Have hydrophilic head group, and hydrophobic tails
3. Their average thickness varies from ~3-5 um – false
   
   1. Is 3-5 nm
4. Charged molecules can cross the membrane unhindered - false
5. They are comprised of lipids, proteins, sugars - true
6. They form automatically under physiologically conditions – True
7. Both monolayers always have the same composition - false
8. They can contain 25% of sterol lipids - true

Question 9

1. Label as detailed as possible (6P)

Answer 9

1. Phospholipid: Hydrophilic part: (Head-group; phosphor-group); Hydrophobic part: (Glycerol; fatty-acid; fatty-acid)
2. Glycolipid: Sugar; Sphingosine: (Serine + Fatty acid); Fatty acid
3. Sterol (Cholesterol): OH-/Hydroxy group; Isoprenoid

Question 10

1. Which type of amino acids are found preferentially where in a TM-α-helix and why? (4P)

Answer 10

1. Tryptophan and tyrosine: often within the aromatic belt
2. Lysine and arginine: snorkel just below the head region of the lipids
3. Phenylalanine, alanine, leucine, isoleucine and valine: predominantly located within the hydrophobic core region

Question 11

1. How do lipids move within Mono- and Bilayer and in-between membranes? (4P)

Answer 11

1. Within monolayer: Rotation, flexion, Lateral diffusion
2. Within bilayer: Transversal diffusion (flip-flop)
3. In-between membranes: Protein assisted movements, Vesicles

Question 12

What is the main phase transition temperature (Tm) and why is it important for membrane function? (3P)

Answer 12

1. The main phase transition temp (also known as the melting temp)
2. Temperature are which a phase transition occurs from normal liquid crystalline form to ordered crystalline/gel form
3. Will affect how lipids will behave in membranes:
   
   1. If temp is below Tm: Will be more solid (ordered crystalline structure)
   2. If temp is above Tm: Will be more fluid (liquid crstalline form)
4. Important for increasing or decreasing fluidity and flexibility of membranes as needed.

Question 13

1. How are sodium channels in the nerve axon regulated and which property is essential for the directed traveling of the signal? (3P)

Answer 13

1. Binding of neurotransmitter induces conformational change
2. Ion channel permeability changes, allowing flow of Na+
3. This changes the membrane potential, and it is depolarized
4. The membrane is eventually repolarized, causing sodium channels to close
5. Essential property: concentration gradient and membrane potential

Question 14

1. Explain (in keywords) the mechanism that guaranties the exclusive symport of one proton and one lactose molecule by LacY (6P)

Answer 14

1. Lactose permease is a secondary transporter
2. Is an example of coupled transport
3. A transported molecule (Lactose) is transported against the concentration gradient
4. This is done with the assistance of an ion (H+) that moves with the electrochemical gradient
5. Process:
   
   1. H+ binds from outside at Glu 269
   2. Protonated form binds lactose
   3. Conformational change happens
   4. Lactose is released
   5. H+ is released
   6. Conformational change reset

Question 15

1. Give an example for the direct involvement of a membrane lipid in signal transduction (2 P)

Answer 15

1. Phosphatidylinositol in membrane trafficking:
   
   1. Increases the affinity of membranes for peripheral membrane proteins
      
      1. Sorting protein cargo
      2. Docking and fusion of transport vesicles
      3. controls direction of membrane trafficking

Question 16

1. Label the numbered structures (5P)

Answer 16

1. 1 – Bi-molecular lipid layer
2. 2 – polar heads of lipid molecules
3. 3 – non-polar tails of phospholipid molecules
4. 4 – Carbohydrate of glycocalyx
5. 5 – Peripheral protein
6. 6 – glycoprotein
7. 7 – Integral protein
8. 8 – glycolipid
9. 9 – Cholesterol
10. 10 – Outward facing layer of phospholipids

Question 17

1. True/False statements about biomembranes:
   
   1. Bacteria have cholesterol
   2. They don’t have glycoproteins
   3. Thylakoids are rich in proteins
   4. Bacteria and archaea have terpenoids
   5. They only have unsaturated fatty acids
   6. Both monolayers always have the same composition

Answer 17

1. Bacteria have cholesterol – false (bacteria have Hoponoid sterols)
2. They don’t have glycoproteins – false (they do have them)
3. Thylakoids are rich in proteins – true (about 77% proteins)
4. Bacteria and archaea have terpenoids – true (archaea do not have sterols)
5. They only have unsaturated fatty acids - false
6. Both monolayers always have the same composition - false

Question 18

1. Draw a sketch of a glycerophospholipid, label its parts and mention an example

Answer 18

Question 19

1. Draw three sketches of examples of transmembrane proteins

Answer 19

1. Multi-pass transmembrane protein (polytopic) (example: rhodopsin)
2. Transmembrane β-barrel proteins (eg. Bacterial porins)
3. Oligomeric TM-helix protein (eg. Typical ion channels)
   
   1. Several subunits donate one or more TM helices that together form a multi-membrane-spanning holo protein

Question 20

How BAR domains stabilize membrane curvature?

Answer 20

1. Built from coiled coils
2. Dimerize into molecules with positively charged inner surface,
3. Allows them to preferentially interacts with lipid head groups to bend membranes.

Question 21

1. Three functions of protein glycosylation

Answer 21

1. Marks progression of protein folding in ER to golgi transport
2. Resistance to proteolytic cleavage
3. Protection against pathogens
4. Cell-cell recognition
5. signaling

Question 22

1. What happens with wrongly folded proteins in the ER?

Answer 22

1. Endoplasmic-reticulum-associated protein degradation (ERAD)
2. Misfolded proteins translocated out of ER via retro-translocation
3. Are degraded by the proteasome

Question 23

1. Explain fatty acid termination

Answer 23

1. A thioesterase (hydrolase) hydrolyzes acyl-ACP to a free fatty acid + ACP
2. Acyl-ACP + H2O –> fatty acid + ACP
3. Prevents continuation of fatty acid elongation/synthesis

Question 24

1. Explain the main steps of vesicle transport

Answer 24

1. Cargo loading
   
   1. Cargo binds to cargo receptor
   2. Adaptor proteins and coat proteins are summoned to begin vesicle formation
2. Budding
   
   1. In case of clathrin coated vesicles, clathrin triskelion is bound to adaptor protein, forming a clathrin coated vesicle
   2. Membrane-bending and fission proteins bend inner membrane, and sever vesicle from mebrane (involves dynamin and other cytosolic factors)
   3. Clathrin and adaptor proteins come off (uncoating) once vesicle is formed (naked transport vesicle)
3. Movement
   
   1. Vesicles transported along cytoskeleton
   2. Motor protein, receptor and energy
   3. Transport along actin filaments is assisted by myosin
   4. Transport along microtubules is mediated by kinesin-Dynein
   5. Transport is regulated spatially, temporally and directionally
4. Tethering/docking
   
   1. Protein complexes ensure than proteins are fusing with the correct acceptor membrane
   2. Rab tethering
      
      1. Rab proteins: monomeric GTPases
      2. Rab effectors (binds to Rab on both membranes)
   3. SNARE mediated vesicle fusion
      
      1. Vesicle has v-SNARE, target membrane has t-SNARE together forming a trans-SNARE complex
5. Fusion and cargo release
   
   1. Two lipid bilayers have to fuse
   2. Membrane contact, fusion of bi-layer, pore opening
   3. Stalk formation à hemifusion stalk à hemifusion diaphragm à fusion pore
   4. Theory 1: automatic fusion (lipid lined pore), Theory 2: SNAREs facilitate pore formation (protein-lined pore)

Question 25

1. Characteristics of unsaturated fatty acids

Answer 25

1. Contain one or more C-C double bonds
2. Liquid at room temp or lower depending on saturation
3. Lipids with unsaturated fatty acids are less tightly packed and have higher potential for movement in a membrane

Question 26

1. In which compartments lipid synthesis takes place in animals and plants? Mention which specific step happens in each cell compartment

Answer 26

1. Animals:
   
   1. Mitochondria: synthesis of cardiolipin
   2. Cytosol: Fatty acid biosynthesis (eukaryotes)
   3. ER: Fatty acid elongation and lipid synthesis
2. Plants:
   
   1. Mitochondria: Synthesis of cardiolipin
   2. Plastid: Malonyl-CoA synthesis and fatty acid synthesis (prokaryotes)
   3. Cytosol: Malonyl-CoA synthesis for fatty acid elongation (eukaryotes)
   4. ER: Fatty acid elongation and lipid synthesis

Question 27

1. Which compartments are related to vesicle transport?

Answer 27

1. ER
2. Golgi
3. Lysosome
4. Vacuole
5. Cell surface/plasma membrane

Question 28

1. How does depolarization occur in the neuron cell?

Answer 28

1. Resting state: all gated Na+ and K+ channels closed (-60 mV) (uneven distribution of Na+ and K+ in this state)
2. Threshold potential: Ion fluxes from synapses changes membrane potential to about 20 mV (the threshold potential) – leads to opening of voltage gates sodium channels
3. Depolarization: opening of Na+ channels results in a reversal of membrane potential to around +40 mV
4. Repolarization: opening of voltage gated potassium channels and closing of sodium channels à reversal of membrane potential to below -60 mV
   
   1. Sodium channels are inactivated, which limits repetitive firing rate of neuron. This is essential for directional signal transduction

Question 29

1. Differences between a F-Type and V-type ATPase and mention an example

Answer 29

1. V-type ATPase:
   
   1. Found in vacuoles of eukarytes and in bacteria
   2. Proton pumps: 2-3 H+/ATP, leads to acidification of vacuole
   3. Uses energy from ATP hydrolysis to produce a proton gradient
   4. Example: proton gradient across yeast vacuolar membrane generated by V-ATPases drives calcium uptake into vacuole through H+/Ca2+ antiporter system
2. F-type ATPases
   
   1. In mitochondria, chloroplasts and bacteria
   2. Function as ATP synthases
   3. Use proton motive force to produce ATP
   4. Example: ATP-synthase in inner mitochondrial membrane uses proton motive force to produce ATP, with F1 part projecting into mitochondrial matrix

Question 30

1. Explain how a secondary active transporter works

Answer 30

1. Symport:
   
   1. Electrochemical potential gradient of substrate goes against concentration gradient
   2. Moves in same direction as ion
   3. Example: Lactose permease in E. coli
      
      1. H+ follows its concentration gradient, binds to transporter from outside
      2. Protonated form binds lactose
      3. A conformational change of transporter occurs
      4. Lactose is released inside, against lactose concentration gradient
      5. H+ is released with its concentration gradient
      6. Conformational change and transporter is reset
2. Antiport:
   
   1. Electrochemical potential gradient of substrate goes against concentration gradient
   2. Moves in opposite direction as ion

Question 31

1. Difference between a non-bilayer and bilayer lipids. Mention and example of each.

Answer 31

1. Non-bilayer lipids:
   
   1. Typically cones
   2. Found in membranes (e.g. required for membrane curvature)
   3. Example: Phosphatidylethanolamine (PE)
      
      1. Dominates in bacteria
      2. 45% of lipid content in brain and nerves
      3. Modulates membrane curvature
2. Bilayer lipids:
   
   1. Typically cylinders
   2. Example: phosphatidylserine (PS)
      
      1. Enriched in brain and retina
      2. Low in mitochondrial inner membranes
      3. Serves as signal for apoptosis

Question 32

1. How a protein is co-translationally transported from the ribosomes into the ER?

Answer 32

1. Ribosome starts translating protein
2. Signal sequence is recognized by Signal recognition particle (SRP)
3. SRP binds signal sequence, halts translation. GDP phosphorylated to GTP
4. SRP guides ribosome to ER and binds SRP receptor
5. GTP hydrolysis leads to transfer of ribosome to transfer away of SRP and SRP receptor and opening of translocon
6. SRP dissociation allows translation to continue through translocon into ER lumen

Question 33

1. What is snorkeling?

Answer 33

1. Can be done by positively charged amino acids with long hydrophobic chains (such as lysine and arginine)
2. Hydrophobic chain is in the bilayer, polar head on the surface
3. Transmembrane domains often flanked by these snorkels
4. Lysine and arginine snorkel just below the head region of lipids

Question 34

Which is the restrictive step in fatty acid synthesis and mention the enzyme.

Answer 34

1. Rate limiting step is formation of malonyl-CoA
2. Carboxyltransferase subunit of ACCase (Acetyl-CoA carboxylase) is enzyme

Question 35

1. Which are the ABC transporter domains and explain its function

Answer 35

1. Binding protein
   
   1. Substrate binding
   2. In periplasmic space in Gram-negative bacteria
2. 2 Transmembrane domains
   
   1. Within membrane
   2. α-helical, pore forming
   3. without ATP, without substrate, changes between open and closed states
   4. Conformational change upon binding substrate.
3. 2 ATP binding domains
   
   1. On cytoplasm side of membrane
   2. Name: ATP-binding-cassette transporter
   3. Upon substrate binding, ATP affinity increases,
   4. 1 ATP binds to each domain, changing conformation, and ABC domains interact
   5. Energy consumption (converts ATP to ADP + Pi)
   6. ATP hydrolysis resets transporter to initial state

Question 36

1. True/false statements about membranes (10 in total)
   
   1. Can contain more than 70% protein
   2. Have a hydrophilic surface
   3. β-barrel proteins are always membrane proteins
   4. lipids are stabilized by covalent interactions
   5. membranes contain only saturated fatty acids

Answer 36

1. Can contain more than 70% protein - true
2. Have a hydrophilic surface - true
3. β-barrel proteins are always membrane proteins - false
4. lipids are stabilized by covalent interactions - false
5. membranes contain only saturated fatty acids - false

Question 37

1. Draw a glycerophospholipid, name all the structures and give an example of such a lipid.

Answer 37

Question 38

Name domains/co-factor of ACCase and reaction catalyzed by this

Answer 38

1. Co-factor: Biotin carboxyl carrier protein
2. Biotin carboxylase
3. Carboxyltransferase
4. First step: transfer of CO2 to biotin carboxyl carrier protein catalyzed by biotin carboxylase
5. 2^nd step: transfer of carboxyl group to acetyl-CoA to form malonyl CoA, catalyzed by carboxyltransferase
6. ATP is not needed to change acetyl-CoA to malonyl CoA, but it is needed to replace the COO- on biotin with the CO2 group

Question 39

Cardiolipin: where in the cell is synthesized and what is special about it?

Answer 39

1. Mostly found in inner mitochondrial membrane of animals and plants – constitutes 20% of total lipid content (also in thylakoids of plants)
2. Is based on 2 diacyglycerols (DAGs)
3. Also found in cell membrane of most bacteria; archaea contain analog of cardiolipin.
4. Only eukaryotic lipid synthesized in mitochondria (supports endosymbiosis theory)
5. Essential component of several complexes of the respiratory chain
6. Additional roles in apoptosis

Question 40

1. SERCA: which type of pump? Describe the mechanism of a muscle cell.

Answer 40

1. Calcium ATPase-type P-ATPase
2. Is in the sarcoplasmic reticulum within myocytes
3. Transfers Ca2+ from cytosol of cell to lumen of ER at expense of ATP hydrolysis during muscle relaxation

Question 41

1. Main difference between transporter and channels in membranes.

Answer 41

1. Transporters: can go against electrochemical gradient
   
   1. Can be active or passive
   2. Requires conformational change to transport
   3. Binding pocket interaction with ligand determines selectivity
2. Channels: always with the electrochemical gradient
   
   1. Regulated by opening and closing
   2. Selectivity of the channel is based on the size and the charge

Question 42

Name two amino acids located in the aromatic belt and why they fit in there ideally.

Answer 42

1. Tryptophan and tyrosine
2. Ring system is perfect for positioning in the polar-apolar interphase of the membrane surface.
3. Not phenylalanine because it is hydrophobic

Question 43

1. At which steps of vesicle transport are GTPases involved?

Answer 43

1. Vesicle scission:
   
   1. GTP-dependent dimerization of G-domains of dynamin, GTP hydrolysis and resulting membrane constriction
2. Vesicle tethering:
   
   1. Rab proteins are monomeric GTPases

Question 44

How can proteins be associated with a membrane?

Answer 44

1. Integral:
   
   1. Directly embedded in bilayer
   2. Alpha helical and beta barrel
2. Non-integral
   
   1. Hydrophobic membrane anchor (lipid chain or oligosaccharide glycolipid (GPI) linker)
   2. Interaction with an integral membrane protein

Question 45

Differences between bacterial and archaea membrane

Answer 45

1. Bacteria:
   
   1. Principally bilayer structure
   2. Ester-linkage of fatty acids with glycerol
2. Archaea:
   
   1. have monolayer in addition to bilayer
   2. Ether-linkage of isoprenoids with glycerol = more stable

Question 46

Name two features of typical transmembrane helices.

Answer 46

1. Exposed R-residues on helix surface are non-polar
2. Don’t contain proline
3. 3.6 residues per turn
4. Right handed
5. Usually spans whole membranes (~15-20 AAs)
6. Alanine, leucine, isoleucine, valine common in bilayer because are hydrophobic non-polar
7. Can be angled in membrane up to 40°

Question 47

Name 3 physical properties of lipids and by which structure they are defined

Answer 47

1. Length – determined by acyl chain
2. Width – determined by saturation of acyl chain
3. Charge – determined only by head group

Question 48

1. What mechanism is responsible selectivity of aquaporin channel and what prevents proton hopping?

Answer 48

1. Narrow pore size to prevent ion diffusion
2. Two Asn residues interact with the oxygen atom of the central H2O molecule
   
   1. This prevents proton hopping because them interacting with central oxygen prevents protons from transferring to the central oxygen
3. Bipolarity (pore on outside is hydrophobic)

Question 49

1. A) Which overall shape have so-called non-bilayer lipids?
2. B) in which two ways can this shape be achieved?
3. C) why are non-bilayer lipids present in biomembranes? (3P)

Answer 49

1. A) Which overall shape have so-called non-bilayer lipids?
   
   1. Cone shape
2. B) in which two ways can this shape be achieved?
   
   1. Determined by head group and hydrophobic part
   2. Thermodynamically favorable structure is formed according to equation P=V/A*L
      
      1. If P < 1/3 it is cone shaped
3. C) why are non-bilayer lipids present in biomembranes? (3P)
   
   1. Curvature of membrane
   2. Can form aggregates like micelles and liposomes

Question 50

Which distinctive structural features can be found in membrane lipids from Archaea? (3P)

Answer 50

1. No sterols
2. Isoprenoids linked to glycerol through an ether link
3. Monolayer in addition to bilayer

Question 51

1. Which of the following features are characteristic for biomembranes? (6P)
   
   1. They have a hydrophilic core and a hydrophobic surface
   2. Their average thickness varies from ~3-5 um
   3. Charged molecules can cross the membrane unhindered
   4. They are composed of lipids, proteins, and sugars
   5. They form automatically under physiological conditions
   6. Both monolayers always have the same lipid composition
   7. They can contain 25% of sterol lipids
   8. They have a hydrophilic and positively charged surface
   9. They are kept together by non-covalent interactions
   10. Water molecules can cross the membrane unhindered
   11. Triglycerols are one of the most common components of biomembranes

Answer 51

1. Which of the following features are characteristic for biomembranes? (6P)
   
   1. They have a hydrophilic core and a hydrophobic surface – false (it’s the opposite)
   2. Their average thickness varies from ~3-5 um – false (its ~3.5 nm)
   3. Charged molecules can cross the membrane unhindered - false
   4. They are composed of lipids, proteins, and sugars - true
   5. They form automatically under physiological conditions - true
   6. Both monolayers always have the same lipid composition - false
   7. They can contain 25% of sterol lipids - true
   8. They have a hydrophilic and positively charged surface – false (surface is hydrophilic, but is not necessarily positively charged)
   9. They are kept together by non-covalent interactions - true
   10. Water molecules can cross the membrane unhindered – true? (seems to be able to based on slide 366, but slowly maybe)
   11. Triglycerols are one of the most common components of biomembranes - false

Question 52

Why can the amino acids R and K snorkel by neither D, E, nor N, Q? (4P

Answer 52

1. R (arginine), K (lysine)
   
   1. Long enough hydrophobic chains to allow snorkeling
2. N (asparagine), Q (glutamine)
   
   1. Too short
3. D (aspartate), E (Glutamate)
   
   1. Because too short and negative R-group

Question 53

1. A) How many amino acids per turn are found in the most common TM-Helices?
2. B) Which other two variants can be found in nature?
3. C) what are the physical consequences, when the number of amino acids per turn changes? (4P)
4. D) How does T_m change when saturases change the fatty acids of the lipids from a desaturated to a saturated form? (2P)

Answer 53

1. A) How many amino acids per turn are found in the most common TM-Helices?
   
   1. 3.6
2. B) Which other two variants can be found in nature?
   
   1. 3 residues per turn (3₁₀ helix)
   2. 4.1 (π helix)
3. C) what are the physical consequences, when the number of amino acids per turn changes? (4P)
   
   1. Width changes
      
      1. (with π helix, will create a bulge)
      2. With 3 residues its narrower
4. D) How does T_m change when saturases change the fatty acids of the lipids from a desaturated to a saturated form? (2P)
   
   1. Will increase the Tm because can pack more tightly in saturated form
      
      1. Due to lack of kinks from double bonds

Question 54

1. Explain in 10 (only have 8 actually) keywords/short statements the principle steps from the reception of a photon in the disc region of a rod cell to the transmission of the signal to the interneuron at the synaptic region. (10 P)

Answer 54

1. One rhodopsin molecule absorbs one photon
2. 500 G-protein (transducin) molecules are activated
3. 500 cyclic GMP phosphodiesterase molecules are activated
4. 10⁵ cyclic GMP molecules are hydrolyzed
5. 250 cation channels close
6. 10⁶ – 10⁷ Na+ ions per second are prevented from entered the cell for a period of ~1 second
7. Membrane potential is altered by 1 mV
8. Signal relayed to brain

Question 55

Which distinctive structural feature has cardiolipin? (2P

Answer 55

1. Is based on 2 diacyglycerols (DAGs)

Question 56

1. Which of the following characteristics for biomembranes? (4P)
   
   1. Their average thickness varies from ~3-5 nm
   2. Charged molecules can cross the membrane unhindered
   3. They have to contain sterol lipids
   4. The surface is formed by an aromatic layer
   5. They are stabilized by covalent bonds between fatty acids
   6. Water molecules can cross the membrane only via channels
   7. They can contain more than 70% proteins
   8. Diaglycerides are the most common components of biomembranes

Answer 56

1. Which of the following characteristics for biomembranes? (4P)
   
   1. Their average thickness varies from ~3-5 nm - true
   2. Charged molecules can cross the membrane unhindered - false
   3. They have to contain sterol lipids – false
   4. The surface is formed by an aromatic layer – false
   5. They are stabilized by covalent bonds between fatty acids - false
   6. Water molecules can cross the membrane only via channels - false
   7. They can contain more than 70% proteins - true
   8. Diaglycerides are the most common components of biomembranes - true

Question 57

1. A) which process is described by the term “transversial diffusion”?
2. B) why is it often so slow?
3. C) How is this process sped-up in nature? (3P)

Answer 57

1. A) which process is described by the term “transversial diffusion”?
   
   1. Movement within the bilayer, is the “flip-flop”
2. B) why is it often so slow?
   
   1. Because the head groups are polar
3. C) How is this process sped-up in nature? (3P)
   
   1. Via enzymes: flippases and flopases

Question 58

1. A) How many AAs/turn are found in the most common type of TM-helix?
2. B) Which other two variants can be found in nature and how many AAs/turn do they have?
3. C) How many turns has an average TM helix consequently within the membrane? (5P)

Answer 58

1. A) How many AAs/turn are found in the most common type of TM-helix?
   
   1. 3.6 per turn
2. B) Which other two variants can be found in nature and how many AAs/turn do they have?
   
   1. 3 (3₁₀)
   2. 4.1 (π helix)
3. C) How many turns has an average TM helix consequently within the membrane? (5P)
   
   1. 15-20 residues per helix
   2. Usual is 3.6 per turn
   3. Do the math (20/~4 = ~5 ish)

Question 59

1. A) how can organisms change the main phase transition temperature (T_m) of their membranes?
2. B) why is that necessary? (4P)

Answer 59

1. A) how can organisms change the main phase transition temperature (T_m) of their membranes?
   
   1. By changing saturation and lipid composition
2. B) why is that necessary? (4P)
   
   1. Because fluidity is required for:
      
      1. Membrane protein function
      2. Permeability
      3. Temperature adaptation

Question 60

1. Why is the opening of sodium channels in the nerve axon voltage-gated?
2. B) which other property of these channels is essential for the directed traveling of the signal? (3 P)

Answer 60

1. Why is the opening of sodium channels in the nerve axon voltage-gated?
   
   1. Open upon reaching threshold potential (+20 mV) due to action potential changes in response to some stimulus
2. B) which other property of these channels is essential for the directed traveling of the signal? (3 P)
   
   1. Sodium channels are inactivated, which limits repetitive firing rate of neuron. This is essential for directional signal transduction.

Question 61

Which function has the NA+/K+ ATPase in the transmission of signals along the axon of neurons? (1P)

Answer 61

1. RE-establishes the resting membrane potential by pumping against electrochemical gradient by using ATP
2. Pumping Na+ out and pumping K+ in