BIOL413 Spring 2024 Homework 3 DUE 3/8 (but I suggest
doing before the exam)
1. Below are 3 -helical segments from 3 different proteins. Sketch and/or clearly describe how
each helix could individually interact with a lipid bilayer. If an -helix would not be able to
interact, simply state no interaction possible. Note: Each helix is 24-26 amino acids long, and
there is not a single amino acid that is "hiding" to invalidate your answer. The first two amino
acids of each are marked by an arrow to help orientate. B. Which of these might serve as signal
sequences and to what organelle might they target if in correct location in protein?
Helix B is primarily hydrophobic on the left side with the amino acids labeled in blue, and the
right side is mostly hydrophilic amino acids. This is an amphipathic helix, which is a signal for
the mitochondria. The membrane protein will have the hydrophobic half embedded in the
membrane.
Helix Z is entirely composed of hydrophobic amino acids. This protein is likely a
transmembrane protein. Proteins that have a sequence of hydrophobic amino acids at the N-
terminus are targeted to the ER.
Helix X will not interact with the lipid bilayer since it is mostly hydrophilic. It will not live in the
hydrophobic membrane.
1
, 2. For this question, do NOT spend too much time on scale. Use amino acid numbers to indicate
important positions. A. On the figure below, clearly indicate 2 regions that could have N-linked
glycosylation.
The nicotinic acetylcholine receptor is an ion channel in the plasma membrane of some neurons.
The hydropathy plot for the receptor is below. A. How many membrane-spanning α-helices do
you expect to exist? CIRCLE B. If the C-term is cytosolic when it is in the plasma membrane,
draw a model of this protein’s topology in the plasma membrane. Don’t forget to label the ends
of the protein (1st amino acid, last amino acid) and side of your membrane (cytosolic, extra
cellular).
+25
Hydropathy
index 0
–25
1 100 200 300 400
Residue number
The green circles indicate 4 expected membrane-spanning alpha helices.
Extracellular
Cytosolic
3. Which of the following proteins would you expect to have a signal sequence and which would
expect to lack one? BRIEFLY jusify.
a) histone2A – Should have a nuclear localization signal because it needs to interact with DNA.
b) cytochrome C (required for ATP synthesis in the mitochondria) – Should have a signal to
transport it from the cytosol to the mitochondria so it can participate in the ETC.
c) an actin binding protein – Actin is a molecule in the cytoplasm so this protein will have no
transport signal since the cytoplasm is the default location.
d) G protein coupled receptor – GCPR’s will be on the plasma membrane of the cell so different
extracellular conditions can cause a cascade of signaling events within the cell. For this to
occur the Transmembrane protein will first be co-translationally imported into the ER
2
doing before the exam)
1. Below are 3 -helical segments from 3 different proteins. Sketch and/or clearly describe how
each helix could individually interact with a lipid bilayer. If an -helix would not be able to
interact, simply state no interaction possible. Note: Each helix is 24-26 amino acids long, and
there is not a single amino acid that is "hiding" to invalidate your answer. The first two amino
acids of each are marked by an arrow to help orientate. B. Which of these might serve as signal
sequences and to what organelle might they target if in correct location in protein?
Helix B is primarily hydrophobic on the left side with the amino acids labeled in blue, and the
right side is mostly hydrophilic amino acids. This is an amphipathic helix, which is a signal for
the mitochondria. The membrane protein will have the hydrophobic half embedded in the
membrane.
Helix Z is entirely composed of hydrophobic amino acids. This protein is likely a
transmembrane protein. Proteins that have a sequence of hydrophobic amino acids at the N-
terminus are targeted to the ER.
Helix X will not interact with the lipid bilayer since it is mostly hydrophilic. It will not live in the
hydrophobic membrane.
1
, 2. For this question, do NOT spend too much time on scale. Use amino acid numbers to indicate
important positions. A. On the figure below, clearly indicate 2 regions that could have N-linked
glycosylation.
The nicotinic acetylcholine receptor is an ion channel in the plasma membrane of some neurons.
The hydropathy plot for the receptor is below. A. How many membrane-spanning α-helices do
you expect to exist? CIRCLE B. If the C-term is cytosolic when it is in the plasma membrane,
draw a model of this protein’s topology in the plasma membrane. Don’t forget to label the ends
of the protein (1st amino acid, last amino acid) and side of your membrane (cytosolic, extra
cellular).
+25
Hydropathy
index 0
–25
1 100 200 300 400
Residue number
The green circles indicate 4 expected membrane-spanning alpha helices.
Extracellular
Cytosolic
3. Which of the following proteins would you expect to have a signal sequence and which would
expect to lack one? BRIEFLY jusify.
a) histone2A – Should have a nuclear localization signal because it needs to interact with DNA.
b) cytochrome C (required for ATP synthesis in the mitochondria) – Should have a signal to
transport it from the cytosol to the mitochondria so it can participate in the ETC.
c) an actin binding protein – Actin is a molecule in the cytoplasm so this protein will have no
transport signal since the cytoplasm is the default location.
d) G protein coupled receptor – GCPR’s will be on the plasma membrane of the cell so different
extracellular conditions can cause a cascade of signaling events within the cell. For this to
occur the Transmembrane protein will first be co-translationally imported into the ER
2
