Objectives:

1
Objectives Be familiar with the various
subcellular compartments in eucaryotic cells.
2
Objectives Be familiar with the various
subcellular compartments in eucaryotic
cells. Know types of proteins that would be
found in the different subcellular compartments.
3
Objectives Be familiar with the various
subcellular compartments in eucaryotic
cells. Know types of proteins that would be
found in the different subcellular
compartments. Use PubMed to find an article
about proteins present in bacteria
4
Objectives Be familiar with the various
subcellular compartments in eucaryotic
cells. Know types of proteins that would be
found in the different subcellular
compartments. Use PubMed to find an article
about proteins present in bacteria Recognize
amino acids by their single letter codes.
5
Objectives Be familiar with the various
subcellular compartments in eucaryotic
cells. Know types of proteins that would be
found in the different subcellular
compartments. Use PubMed to find an article
about proteins present in bacteria Recognize
amino acids by their single letter
codes. Identify positive, negative or
hydrophobic amino acid residues in a protein
sequence.
6
Objectives Be familiar with the various
subcellular compartments in eucaryotic
cells. Know types of proteins that would be
found in the different subcellular
compartments. Use PubMed to find an article
about proteins present in bacteria Recognize
amino acids by their single letter
codes. Identify positive, negative or
hydrophobic amino acid residues in a protein
sequence. Recognize patterns of amino acid
residues that serve as signals to target proteins
to subcellular locations.
7
Objectives Be familiar with the various
subcellular compartments in eucaryotic
cells. Know types of proteins that would be
found in the different subcellular
compartments. Use PubMed to find an article
about proteins present in bacteria Recognize
amino acids by their single letter
codes. Identify positive, negative or
hydrophobic amino acid residues in a protein
sequence. Recognize patterns of amino acid
residues that serve as signals to target proteins
to subcellular locations. Use amino acid
sequence information to identify a protein in the
NCBI data bases.
8
Objectives Be familiar with the various
subcellular compartments in eucaryotic
cells. Know types of proteins that would be
found in the different subcellular
compartments. Use PubMed to find an article
about proteins present in bacteria Recognize
amino acids by their single letter
codes. Identify positive, negative or
hydrophobic amino acid residues in a protein
sequence. Recognize patterns of amino acid
residues that serve as signals to target proteins
to subcellular locations. Use amino acid
sequence information to identify a protein in the
NCBI data bases. Use computational tools to
predict the subcellular location for a protein of
given sequence (homework)
9
M-M-S-F-V-S-L-L-L-V-G-I-L-F-W-A-T-E-A-E-Q-L-T-K-C
-E-V-F-Q- What does this mean in the language of
proteins?
10
M-M-S-F-V-S-L-L-L-V-G-I-L-F-W-A-T-E-A-E-Q-L-T-K-C
-E-V-F-Q- What does this mean in the language of
proteins? What would be the subcellular location
of a protein with this sequence of amino acids?
11
M-M-S-F-V-S-L-L-L-V-G-I-L-F-W-A-T-E-A-E-Q-L-T-K-C
-E-V-F-Q- What does this mean in the language of
proteins? What would be the subcellular location
of a protein with this sequence of amino
acids? How would such a protein be delivered to
its final location?
12
M-M-S-F-V-S-L-L-L-V-G-I-L-F-W-A-T-E-A-E-Q-L-T-K-C
-E-V-F-Q- What does this mean in the language of
proteins? What would be the subcellular location
of a protein with this sequence of amino
acids? How would such a protein be delivered to
its final location? First lets review the
possible locations in a cell ---gt ----gt
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Pathway to secretion of the protein to the
outside of the cell. For example, secretion of a
digestive enzyme such a lipase from a cell in the
pancreas. Transcription of the mRNA that codes
for the protein from DNA in the nucleus.
15
Pathway to secretion of the protein to the
outside of the cell. For example, secretion of a
digestive enzyme such a lipase from a cell in the
pancreas. Transcription of the mRNA that codes
for the protein from DNA in the nucleus.
Export of the mRNA from the nucleus through pores
in the nuclear envelope.
16
Pathway to secretion of the protein to the
outside of the cell. For example, secretion of a
digestive enzyme such a lipase from a cell in the
pancreas. Transcription of the mRNA that codes
for the protein from DNA in the nucleus.
Export of the mRNA from the nucleus through pores
in the nuclear envelope. Translation of the
mRNA on ribosomes on rough Endoplasmic Reticulum
(ER) to make the protein.
17
Pathway to secretion of the protein to the
outside of the cell. For example, secretion of a
digestive enzyme such a lipase from a cell in the
pancreas. Transcription of the mRNA that codes
for the protein from DNA in the nucleus.
Export of the mRNA from the nucleus through pores
in the nuclear envelope. Translation of the
mRNA on ribosomes on rough Endoplasmic Reticulum
(ER) to make the protein. The protein is
threaded into the lumen of the ER because of
signal sequence of amino acids (blue) near amino
terminus of the protein.
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Pathway to secretion of the protein to the
outside of the cell. For example, secretion of a
digestive enzyme such a lipase from a cell in the
pancreas. Transcription of the mRNA that codes
for the protein from DNA in the nucleus.
Export of the mRNA from the nucleus through pores
in the nuclear envelope. Translation of the
mRNA on ribosomes on rough Endoplasmic Reticulum
(ER) to make the protein. The protein is
threaded into the lumen of the ER because of
signal sequence of amino acids (blue) near amino
terminus of the protein. The protein is passed
on to the Golgi.
19
Pathway to secretion of the protein to the
outside of the cell. For example, secretion of a
digestive enzyme such a lipase from a cell in the
pancreas. Transcription of the mRNA that codes
for the protein from DNA in the nucleus.
Export of the mRNA from the nucleus through pores
in the nuclear envelope. Translation of the
mRNA on ribosomes on rough Endoplasmic Reticulum
(ER) to make the protein. The protein is
threaded into the lumen of the ER because of
signal sequence of amino acids (blue) near amino
terminus of the protein. The protein is passed
on to the Golgi. The protein is enclosed in a
membrane vesicle which leaves the Golgi and takes
it to the Plasma Membrane (PM)
20
Pathway to secretion of the protein to the
outside of the cell. For example, secretion of a
digestive enzyme such a lipase from a cell in the
pancreas. Transcription of the mRNA that codes
for the protein from DNA in the nucleus.
Export of the mRNA from the nucleus through pores
in the nuclear envelope. Translation of the
mRNA on ribosomes on rough Endoplasmic Reticulum
(ER) to make the protein. The protein is
threaded into the lumen of the ER because of
signal sequence of amino acids (blue) near amino
terminus of the protein. The protein is passed
on to the Golgi. The protein is enclosed in a
membrane vesicle which leaves the Golgi and takes
it to the Plasma Membrane (PM) The membrane of
the vesicle fuses with the PM releasing the
protein to the outside of the cell (eg., lipase
secreted from pancreatic cells)
21
Figure 7.16 Review relationships among
organelles of the endomembrane system 
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Proteins that follow this ER/Golgi pathway can
also go to - Plasma Membrane, eg.
Integrins Integrins are proteins that recognize
other cells, cause cells to stick together.
27
Human diseases result from defects in integrin
genes. A defect in integrin beta3 causes
prolonged bleeding, because blood plateletes
cant stick together. Glanzman's
Thrombasthenia. With defects in either alpha6
or beta4 integrin skin cells cannot stick
together well. Patients are born with blistering
epidermis and also have blisters within the mouth
and digestive tract...depending on the severity
of the disease. Some die within days and others
live. Junctional epidermolysis bullosa
28
Proteins that follow this ER/Golgi pathway can
also go to - Plasma Membrane, eg.
Integrins Integrins are proteins that recognize
other cells, cause cells to stick
together. Lysosomes, Hydrolases. Hydrolases
are digestive enzymes that use water to break
apart molecules such as proteins, DNA, lipids,
polysaccharides.
29
Proteins that follow this ER/Golgi pathway can
also go to - Plasma Membrane, eg.
Integrins Integrins are proteins that recognize
other cells, cause cells to stick
together. Lysosomes, Hydrolases. Hydrolases
are digestive enzymes that use water to break
apart molecules such as proteins, DNA, lipids,
polysaccharides. Defects in lysosomal genes
result in storage diseases If a hydrolase is
defective the molecules it digests accumulate in
lysosomes.
30
Other proteins are translated from their
respective mRNAs in the cytosol and then
delivered to different subcellular
locations Mitochondria Peroxisomes Chloroplast
s (in plant cells) - Nucleus Or some remain in
the cytosol - What types of proteins go to
these different locations and what information
directs them to those locations?
31
Mitochondria - e.g., Dehydrogenases Peroxisom
es - e.g., Oxidases Chloroplasts (in plant
cells) - proteins of photosynthesis Nucleus -
e.g., proteins that replicate DNA or regulate
genes Cytosol - e.g., enzymes that metabolize
glucose
32
Do all cells have all these different proteins
and subcellular compartments? Eucaryotes Animal
s, flies, worms, yeast cells have these
compartments and many proteins that are
homologous.
33
Do all cells have all these different proteins
and subcellular compartments? Eucaryotes Animal
s, flies, worms, yeast cells have these
compartments and many proteins that are
homologous. Plant cells have all the
compartments plus chloroplasts and a central
vacuole.
34
Do all cells have all these different proteins
and subcellular compartments? Eucaryotes Animal
s, flies, worms, yeast cells have these
compartments and many proteins that are
homologous. Plant cells have all the
compartments plus chloroplasts and a central
vacuole. Procaryotes Bacterial cells do not
have the compartments and have fewer genes, fewer
proteins.
35
Do all cells have all these different proteins
and subcellular compartments? Eucaryotes Animal
s, flies, worms, yeast cells have these
compartments and many proteins that are
homologous. Plant cells have all the
compartments plus chloroplasts and a central
vacuole. Procaryotes Bacterial cells do not
have the compartments and have fewer genes, fewer
proteins. Each cell of an organism has DNA that
encodes all the possible genes for that organism.
Are all the possible proteins present in every
cell of the organism?
36
Questions about the genome in an organism How
much DNA, how many nucleotides? How many genes
are there? What types of proteins appear to be
coded by these genes?
37
Questions about the proteome What proteins are
present? Where are they? When are they present
- under what conditions?
38
Questions about the proteome What proteins are
present? Where are they? When are they present
- under what conditions? What other proteins and
molecules does each protein interact with? It
depends on the type of cell, bacteria, yeast,
worm, fly, plant, human
39
Animal cell - is a EUCARYOTE
40
Animal cell - is a EUCARYOTE - has a nucleus and
other membrane enclosed subcellular compartments,
mitochondria, peroxisomes, etc.
41
Plant cell - is also a EUCARYOTE - has a nucleus,
mitochondria, peroxisomes, plus chloroplasts,
central vacuole.
42
Vibrio cholerae - causes cholera
ATP drive motor protein complex
E. Coli - normal inhabitant of human gut
Bacterial cells - are PROCARYOTES
43
Vibrio cholerae - causes cholera
ATP drive motor protein complex
E. Coli - normal inhabitant of human gut
Bacterial cells - are PROCARYOTES - NO nucleus,
NO membrane enclosed subcellular compartments, NO
mitochondria, NO peroxisomes, etc.
44
E. coli genome 4,639,221 nucleotide pairs
Protein-coding genes yellow or orange
bars genes coding only RNA green
arrows What are all the different types of RNAs?
45
Organism Genome size Estimated number Type
of . (Megabases, 106) of genes Organism
. H. influenzae 1.8 Mb 1700 Procaryote,
(bacterium) no nucleus
46
Organism Genome size Estimated number Type
of . (Megabases, 106) of genes Organism
. H. influenzae 1.8 Mb 1700 Procaryote,
(bacterium) no nucleus S. cerevisae 12
Mb 6000 Eucaryote, (Yeast) Unicellular

47
Organism Genome size Estimated number Type
of . (Megabases, 106) of genes Organism
. H. influenzae 1.8 Mb 1700 Procaryote,
(bacterium) no nucleus S. cerevisae 12
Mb 6000 Eucaryote, (Yeast) Unicellular C.
elegans 97 Mb 19,000 Eucaryote, (nematode
worm) Multicellular
48
Organism Genome size Estimated number Type
of . (Megabases, 106) of genes Organism
. H. influenzae 1.8 Mb 1700 Procaryote,
(bacterium) no nucleus S. cerevisae 12
Mb 6000 Eucaryote, (Yeast) Unicellular C.
elegans 97 Mb 19,000 Eucaryote, (nematode
worm) Multicellular Arabidopsis 100
Mb 25,000 Eucaryote (plant) Multicellular

49
Organism Genome size Estimated number Type
of . (Megabases, 106) of genes Organism
. H. influenzae 1.8 Mb 1700 Procaryote,
(bacterium) no nucleus S. cerevisae 12
Mb 6000 Eucaryote, (Yeast) Unicellular C.
elegans 97 Mb 19,000 Eucaryote, (nematode
worm) Multicellular Arabidopsis 100
Mb 25,000 Eucaryote (plant) Multicellular
Drosophila 180 Mb 13,000 Eucaryote (fruit
fly) Multicellular
50
Organism Genome size Estimated number Type
of . (Megabases, 106) of genes Organism
. H. influenzae 1.8 Mb 1700 Procaryote,
(bacterium) no nucleus S. cerevisae 12
Mb 6000 Eucaryote, (Yeast) Unicellular C.
elegans 97 Mb 19,000 Eucaryote, (nematode
worm) Multicellular Arabidopsis 100
Mb 25,000 Eucaryote (plant) Multicellular
Drosophila 180 Mb 13,000 Eucaryote (fruit
fly) Multicellular Homo sapiens 3200
Mb 40,000 Eucaryote (human) Multicellula
r
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Are all the genes in a cell producing proteins?
53
Egg cell genes determine nature of whole
multicellular organism.
Sea urchin egg gives rise to a sea urchin. (A,
B) Mouse egg gives rise to a mouse. (C,D) How
do sizes of egg cells compare to E.coli?
The different types of cells look like they would
have different proteins - hair, eyes, spines, etc.
54
Each cell contains a fixed set of DNA
moleculesits archive of genetic information.
55
Each cell contains a fixed set of DNA
moleculesits archive of genetic information.
A given segment of this DNA serves to guide the
synthesis of many identical RNA transcripts,
which serve as working copies of the information
stored in the archive.
56
Each cell contains a fixed set of DNA
moleculesits archive of genetic information.
A given segment of this DNA serves to guide the
synthesis of many identical RNA transcripts,
which serve as working copies of the information
stored in the archive. Many different sets of
RNA molecules can be made by transcribing
selected parts of a long DNA sequence, allowing
each cell to use its information store
differently.
57
Kirkpatrick C, Maurer LM, Oyelakin NE, Yoncheva
YN, Maurer R, Slonczewski JL. Acetate and
formate stress opposite responses in the
proteome of Escherichia coli.J Bacteriol. 2001
Nov183(21)6466-77.
Do cells produce proteins from all their genes?
What technique can be used to find out?
Open Netscape or Explorer. Go to PubMed at
http//www.ncbi.nih.gov/entrez/query.fcgi Search
PubMed for Slonczewski JL
Pairs of students work together What type of
cell are they working on? What question are they
trying to answer? What techinques are they
using? Open one of the figures. Tell everyone
how to find that figure. Explain what is seen
in that figure. How were the proteins
identified? What were the conclusions?
Blankenhorn D, Phillips J, Slonczewski JL.
Acid- and base-induced proteins during aerobic
and anaerobic growth of Escherichia coli revealed
by two-dimensional gel electrophoresis. J
Bacteriol. 1999 Apr181(7)2209-16.
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E. coli (bacteria) Saccharomyces
(Yeast) Procaryote Eucaryote, single
cells No nucleus or Nucleus,
Mitochondria, organelles ER, Golgi,
peroxisomes Genome 4,640,000 12,050,000
nucleotides Proteins for Metabolism,
energy 890 820
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E. coli (bacteria) Saccharomyces
(Yeast) Procaryote Eucaryote, single
cells No nucleus or Nucleus,
Mitochondria, organelles ER, Golgi,
peroxisomes Genome 4,640,000 12,050,000
nucleotides Proteins for Metabolism,
energy 890 820 DNA replication,
repair 120 175 Transcription of
RNA 230 400
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E. coli (bacteria) Saccharomyces
(Yeast) Procaryote Eucaryote, single
cells No nucleus or Nucleus,
Mitochondria, organelles ER, Golgi,
peroxisomes Genome 4,640,000 12,050,000
nucleotides Proteins for Metabolism,
energy 890 820 DNA replication,
repair 120 175 Transcription of
RNA 230 400 Translation 180 350 Cell
Structure 180 250 Protein targeting,
secretion 35 430
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E. coli (bacteria) Saccharomyces
(Yeast) Procaryote Eucaryote, single
cells No nucleus or Nucleus,
Mitochondria, organelles ER, Golgi,
peroxisomes Genome 4,640,000 12,050,000
nucleotides Proteins for Metabolism,
energy 890 820 DNA replication,
repair 120 175 Transcription of
RNA 230 400 Translation 180 350 Cell
Structure 180 250 Protein targeting,
secretion 35 430 Does E.coli produce all
proteins constantly, or selected ones? Where are
the proteins located in the yeast cell?
62
This is the sequence of amino acids at the end of
a protein that is targeted to a certain
subcellular compartment. M-M-S-F-V-S-L-L-L-V-G-I-
L-F-W-A-T-E-A-E-Q-L-T-K-C-E-V-F-Q- What does
this mean in the language of proteins?
63
This is the sequence of amino acids at the end of
a protein that is targeted to a certain
subcellular compartment. M-M-S-F-V-S-L-L-L-V-G-I-
L-F-W-A-T-E-A-E-Q-L-T-K-C-E-V-F-Q- What does
this mean in the language of proteins? What
would be the subcellular location of a protein
with this sequence of amino acids?
64
This is the sequence of amino acids at the end of
a protein that is targeted to a certain
subcellular compartment. M-M-S-F-V-S-L-L-L-V-G-I-
L-F-W-A-T-E-A-E-Q-L-T-K-C-E-V-F-Q- What does
this mean in the language of proteins? What
would be the subcellular location of a protein
with this sequence of amino acids? How would
such a protein be delivered to its final
location? What are the functions of protein in
this subcellular location?
65
To understand the information in proteins that
targets them to the respective subcellular
compartments you need to be able read amino acid
sequences. Also, amino acid sequences can
indicate the function of the protein.
66
You need to recognize the amino acids by their
single letter abbreviations. Recognize those
that are non-polar, hydrophobic. Recognize the
polar, hydrophyllic ones. Recognize the
charged ones, positive or negative.
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You need to recognize the amino acids by their
single letter abbreviations. Recognize those
that are non-polar, hydrophobic. Recognize the
polar, hydrophyllic ones. Recognize the
charged ones, positive or negative. Glycine is
the simplest amino acid.
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You need to recognize the amino acids by their
single letter abbreviations. Recognize those
that are non-polar, hydrophobic. Recognize the
polar, hydrophyllic ones. Recognize the
charged ones, positive or negative. Glycine is
the simplest amino acid.
G
Its single letter abbreviation is
69
G
70
G
A
71
G
A
V
L
I
Hydrophobic
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G
A
V
L
I
Hydrophobic
M
73
G
A
V
L
I
Hydrophobic
M
F
W
P
74
S
T
Hydrophyllic
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S
T
C
Y
N
Q
Hydrophyllic
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S
T
C
Y
N
Q
Hydrophyllic
E
D
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S
T
C
Y
N
Q
Hydrophyllic
E
D
K
R
H
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Figure 5.16 Making a polypeptide chain
79
Figure 5.16 Making a polypeptide chain
carboxyl end
amino end
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Figure 5.16 Making a polypeptide chain
81
Figure 5.16 Making a polypeptide chain
What are the names of these amino acid residues?
82
Figure 5.18 The primary structure of a protein
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Figure 5.20 The secondary structure of a protein
84
Figure 5.17 Conformation of a protein, the
enzyme Lysozyme
85
Figure 5.19 A single amino acid substitution in
a protein causes sickle-cell disease
A change in one amino acid can change the
structure and function of a protein
What chemical difference between Glu and Val?
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Figure 5.19 A single amino acid substitution in
a protein causes sickle-cell disease
A change in one amino acid can change the
structure and function of a protein
What chemical difference between Glu and Val?
87
Some Typical Signal Sequences that direct
proteins to different subcellular
compartments Import into ER M-M-S-F-V-S-L-L-L-V-G
-I-L-F-W-A-T-E-A-E-Q-L-T-K-C-E-V-F-Q- Retention
in lumen of ER -K-D-E-L
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Some Typical Signal Sequences that direct
proteins to different subcellular
compartments Import into ER M-M-S-F-V-S-L-L-L-V-G
-I-L-F-W-A-T-E-A-E-Q-L-T-K-C-E-V-F-Q- Retention
in lumen of ER -K-D-E-L Import into
mitochondria M-L-S-L-R-Q-S-I-R-F-F-K-P-A-T-R-T-L
-C-S-S-R-Y-L-L-
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Some Typical Signal Sequences that direct
proteins to different subcellular
compartments Import into ER M-M-S-F-V-S-L-L-L-V-G
-I-L-F-W-A-T-E-A-E-Q-L-T-K-C-E-V-F-Q- Retention
in lumen of ER -K-D-E-L Import into
mitochondria M-L-S-L-R-Q-S-I-R-F-F-K-P-A-T-R-T-L
-C-S-S-R-Y-L-L- Import into nucleus
-P-P-K-K-K-R-K-V- Import into peroxisomes
-S-K-L
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Some Typical Signal Sequences Import into
ER M-M-S-F-V-S-L-L-L-V-G-I-L-F-W-A-T-E-A-E-Q-L-T-K
-C-E-V-F-Q- Retention in lumen of ER
-K-D-E-L Import into mitochondria
M-L-S-L-R-Q-S-I-R-F-F-K-P-A-T-R-T-L-C-S-S-R-Y-L-
L- Import into nucleus -P-P-K-K-K-R-K-V- Impor
t into peroxisomes -S-K-L An extended block of
hydrophobic amino acids is shown in blue. The
amino terminus of a protein is toward the left
the carboxyl terminus to the right. Which ones
are positively or negatively charged??
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Import into ER M-M-S-F-V-S-L-L-L-V-G-I-L-F-W-A-T-E
-A-E-Q-L-T-K-C-E-V-F-Q- A hydrophobic series
near the amino terminus Retention in lumen of ER
-K-D-E-L At the carboxyl terminus Import into
mitochondria M-L-S-L-R-Q-S-I-R-F-F-K-P-A-T-R-T-L
-C-S-S-R-Y-L-L- Regularly spaced positive
residues near amino terminus Import into nucleus
-P-P-K-K-K-R-K-V- A patch of positive
residues in the middle Import into peroxisomes
-S-K-L A small residue, positive residue,
hydrophobic at carboxyl Positively charged amino
acids are shown in green, and negatively charged
amino acids in red. An extended block of
hydrophobic amino acids is shown in blue. The
amino terminus of a protein is toward the left
the carboxyl terminus to the right.
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What is this protein? Where is it
located? http//www.ncbi.nlm.nih.gov/blast/ use
the Standard Protein-Protein Blast Enter the
amino acid sequence and submit it to the Blast
search gtP11310 MAAGFGRCCRVLRSISRFHWRSQHTKANRQREPG
LGFSFEFTEQQKEFQATARKFAREEIIPVAAEYDKTGEYPVPLIRRAWEL
GLMNTHIPENCGGLGLGTFDACLISEELAYGCTGVQTAIEGNSLGQMPII
IAGNDQQKKKYLGRMTEEPLMCAYCVTEPGAGSDVAGIKTKAEKKGDEYI
INGQKMWITNGGKANWYFLLARSDPDPKAPANKAFTGFIVEADTPGIQIG
RKELNMGQRCSDTRGIVFEDVKVPKENVLIGDGAGFKVAMGAFDKTRPVV
AAGAVGLAQRALDEATKYALERKTFGKLLVEHQAISFMLAEMAMKVELAR
MSYQRAAWEVDSGRRNTYYASIAKAFAGDIANQLATDAVQILGGNGFNTE
YPVEKLMRDAKIYQIYEGTSQIQRLIVAREHIDKYKN
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gtP11310 is ACYL-COA DEHYDROGENASE, MEDIUM-CHAIN
SPECIFIC PRECURSOR It is delivered to the
Mitochondria
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What is this protein? http//www.ncbi.nlm.nih.gov/
blast/ use the Standard Protein-Protein
Blast Enter the amino acid sequence and submit it
to the Blast search gtgi17560134refNP_508036.1
MNRYICEGDNPDITEERKKASFNVDKLTEYYYGGEKRLKARREVEKCVED
HKELQDLKPTPFMSRDELIDNSVRKLAGMAKNYKMIDLTNIEKTTYFLQL
VHVRDSMAFSLHYLMFLPVLQSQASPEQLAEWMPRALSGTIIGTYAQTEM
GHGTNLSKLETTATYGQKTSEFVLHTPTISGAKWWPGSLGKFCNFAIIVA
NLWTNGVCVGPHPFLVQIRDLKTHKTLPNIKLGDIGPKLGSNGSDNGYLV
FTNYRISRGNMLMRHSKVHPDGTYQKPPHSKLAYGGMVFVRSMMVRDIAN
YLANAVTIATRYSTVRRQGEPLPGAGEVKILDYQTQQYRILPYIAKTIAF
RMAGEELQQAFLNISKDLRQGNASLLPDLHSLSSGLKAVVTFEVQQGIEQ
CRLACGGHGYSHASGIPELSAFSCGSCTYEGDNIVLLLQVANECELYPEH
EAWNRCSIELCKAARWHVRLYIVRNFLQKVCTAPKDLQPVLRALSNLYIF
DLQVSNKGHFMENGYMTSQQIDQLKMGINESLSTIRPDAVSIVDGFAIHE
FELKSVLGRRDGNVYPGLFEWTKHSQLNNKEVHPAFDKYLTPIMDKIRAK
M
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gi17560134refNP_508036.1 is Acyl-Coenzyme A
oxidase peroxisomal like family member from the
nematode worm Caenorhabditis elegans. It is
targeted to Peroxisomes by the three amino acids
at its carboxyl terminus
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The typical Signal Sequences that direct proteins
to different subcellular compartments Import
into ER M-M-S-F-V-S-L-L-L-V-G-I-L-F-W-A-T-E-A-E-Q-
L-T-K-C-E-V-F-Q- A hydrophobic series near the
amino terminus Retention in lumen of ER
-K-D-E-L At the carboxyl terminus Import into
mitochondria M-L-S-L-R-Q-S-I-R-F-F-K-P-A-T-R-T-L
-C-S-S-R-Y-L-L- Regularly spaced positive
residues near amino terminus Import into nucleus
-P-P-K-K-K-R-K-V- A patch of positive
residues in the middle Import into peroxisomes
-S-K-L or A-K-M or similar, A small residue,
positive residue, hydrophobic at carboxyl
97
What are the functions of the proteins that are
targeted to the different subcellular
locations? ER/Golgi pathway Secreted proteins -
e.g., pancreatic digestive enzymes, proteases
such as trypsin Lysosomal enzymes - e.g., acid
hydrolases such as acid proteases, lipases,
DNAases, etc. Plasma Membrane proteins - e.g.,
Integrins.
98
What are the functions of the proteins that are
targeted to the different subcellular
locations? ER/Golgi pathway Secreted proteins -
e.g., pancreatic digestive enzymes, proteases
such as trypsin Lysosomal enzymes - e.g., acid
hydrolases such as acid proteases, lipases,
DNAases, etc. Plasma Membrane proteins - e.g.,
Integrins. Chloroplasts (in plant cells)?
99
What are the functions of the proteins that are
targeted to the different subcellular
locations? ER/Golgi pathway Secreted proteins -
e.g., pancreatic digestive enzymes, proteases
such as trypsin Lysosomal enzymes - e.g., acid
hydrolases such as acid proteases, lipases,
DNAases, etc. Plasma Membrane proteins - e.g.,
Integrins. Chloroplasts (in plant cells) -
proteins of photosynthesis
100
What are the functions of the proteins that are
targeted to the different subcellular
locations? ER/Golgi pathway Secreted proteins -
e.g., pancreatic digestive enzymes, proteases
such as trypsin Lysosomal enzymes - e.g., acid
hydrolases such as acid proteases, lipases,
DNAases, etc. Plasma Membrane proteins - e.g.,
Integrins. Chloroplasts (in plant cells) -
proteins of photosynthesis Nucleus ? ?
101
What are the functions of the proteins that are
targeted to the different subcellular
locations? ER/Golgi pathway Secreted proteins -
e.g., pancreatic digestive enzymes, proteases
such as trypsin Lysosomal enzymes - e.g., acid
hydrolases such as acid proteases, lipases,
DNAases, etc. Plasma Membrane proteins - e.g.,
Integrins. Chloroplasts (in plant cells) -
proteins of photosynthesis Nucleus - e.g.,
proteins that replicate DNA or regulate genes,
transcription factors
102
What are the functions of the proteins that are
targeted to the different subcellular
locations? ER/Golgi pathway Secreted proteins -
e.g., pancreatic digestive enzymes, proteases
such as trypsin Lysosomal enzymes - e.g., acid
hydrolases such as acid proteases, lipases,
DNAases, etc. Plasma Membrane proteins - e.g.,
Integrins. Chloroplasts (in plant cells) -
proteins of photosynthesis Nucleus - e.g.,
proteins that replicate DNA or regulate genes,
transcription factors Cytosol - e.g., enzymes
that metabolize glucose Mitochondria - e.g.,
Dehydrogenases, metabolism to obtain energy
103
What are the functions of the proteins that are
targeted to the different subcellular
locations? ER/Golgi pathway Secreted proteins -
e.g., pancreatic digestive enzymes, proteases
such as trypsin Lysosomal enzymes - e.g., acid
hydrolases such as acid proteases, lipases,
DNAases, etc. Plasma Membrane proteins - e.g.,
Integrins. Chloroplasts (in plant cells) -
proteins of photosynthesis Nucleus - e.g.,
proteins that replicate DNA or regulate genes,
transcription factors Cytosol - e.g., enzymes
that metabolize glucose Mitochondria - e.g.,
Dehydrogenases, metabolism to obtain
energy Peroxisomes - e.g., Oxidases, metabolism
when energy is not needed
104
Figure 7.9 The nucleus and its envelope 
105
Figure 7.x1 Nuclei and F-actin in BPAEC cells
106
Figure 7.17 The mitochondrion, site of cellular
respiration
107
Figure 7.19 Peroxisomes
108
A comparison of a mitochondrial dehydrogenase to
a peroxisomal oxidase, both of which metabolize
fat.
H H H H H H H H H-C-C-C-C-C-C-C-C-COOH H H H
H H H H H
A Fatty acid, which can be oxidized in
mitochondria or peroxisomes
109
Dehydrogenase
H H H H H H H H H-C-C-C-C-C-C-C-C-COOH H H H
H H H H H
In mitochondria a Dehydrogenase takes two
Hydrogens (2Hs) from the fatty acid.
110
Dehydrogenase
H H H H H H H H H-C-C-C-C-C-C-C-C-COOH H H H
H H H H H
In mitochondria a Dehydrogenase takes two
Hydrogens (2Hs) from the fatty acid.
111
Dehydrogenase
H H H H H H H H H-C-C-C-C-C-C-C-C-COOH H H H
H H H H H
In mitochondria a Dehydrogenase takes two
Hydrogens (2Hs) from the fatty acid.
112
Dehydrogenase
2Hs
H H H H H H H H-C-C-C-C-CC-C-C-COOH H H H
H H H H
In mitochondria a Dehydrogenase takes two
Hydrogens (2Hs) from the fatty acid. Creates a
double bond.
113
Dehydrogenase
2Hs
H H H H H H H H-C-C-C-C-CC-C-C-COOH H H H
H H H H
In mitochondria a Dehydrogenase takes two
Hydrogens (2Hs) from the fatty acid. Creates a
double bond.
114
Dehydrogenase
2Hs
H H H H H H H H-C-C-C-C-CC-C-C-COOH H H H
H H H H
In mitochondria a Dehydrogenase takes two
Hydrogens (2Hs) from the fatty acid. Creates a
double bond.
115
Dehydrogenase
2Hs
NAD
H H H H H H H H-C-C-C-C-CC-C-C-COOH H H H
H H H H
The mitochondrial Dehydrogenase transfers the two
Hydrogens (2Hs) to NAD. Creates a double bond.
116
Dehydrogenase
2Hs
NAD
H H H H H H H H-C-C-C-C-CC-C-C-COOH H H H
H H H H
The mitochondrial Dehydrogenase transfers the two
Hydrogens (2Hs) to NAD. Creates a double bond.
117
Dehydrogenase
NADH2
H H H H H H H H-C-C-C-C-CC-C-C-COOH H H H
H H H H
The mitochondrial Dehydrogenase transfers the two
Hydrogens (2Hs) to NAD. Creates a double bond.
118
Dehydrogenase
NADH2
H H H H H H H H-C-C-C-C-CC-C-C-COOH H H H
H H H H
The mitochondrial Dehydrogenase transfers the two
Hydrogens (2Hs) to NAD.
119
Dehydrogenase
NADH2
H H H H H H H H-C-C-C-C-CC-C-C-COOH H H H
H H H H
The mitochondrial Dehydrogenase transfers the two
Hydrogens (2Hs) to NAD.
120
Dehydrogenase
NADH2
H H H H H H H H-C-C-C-C-CC-C-C-COOH H H H
H H H H
The mitochondrial Dehydrogenase transfers the two
Hydrogens (2Hs) to NAD.
121
Dehydrogenase
NADH2
H H H H H H H H-C-C-C-C-CC-C-C-COOH H H H
H H H H
ATP
The Hydrogens are delivered to the inner membrane
to make ATP
122
Oxidase
H H H H H H H H H-C-C-C-C-C-C-C-C-COOH H H H
H H H H H
In Peroxisomes an Oxidase takes two
Hydrogens (2Hs) from a fatty acid.
123
Oxidase
H H H H H H H H H-C-C-C-C-C-C-C-C-COOH H H H
H H H H H
124
Oxidase
H H H H H H H H H-C-C-C-C-C-C-C-C-COOH H H H
H H H H H
125
Oxidase
2Hs
H H H H H H H H-C-C-C-C-CC-C-C-COOH H H H
H H H H
126
Oxidase
2Hs
H H H H H H H H-C-C-C-C-CC-C-C-COOH H H H
H H H H
127
Oxidase
2Hs
H H H H H H H H-C-C-C-C-CC-C-C-COOH H H H
H H H H
128
Oxidase
2Hs
O2
H H H H H H H H-C-C-C-C-CC-C-C-COOH H H H
H H H H
129
Oxidase
2Hs
O2
H H H H H H H H-C-C-C-C-CC-C-C-COOH H H H
H H H H
130
Oxidase
H2O2
H H H H H H H H-C-C-C-C-CC-C-C-COOH H H H
H H H H
131
Oxidase
H2O2
H H H H H H H H-C-C-C-C-CC-C-C-COOH H H H
H H H H
The Peroxisomal Oxidase transfers the two
Hydrogens (2Hs) to Oxygen to make Hydrogen
Peroxide (H2O2).
132
Oxidase
H2O2
H H H H H H H H-C-C-C-C-CC-C-C-COOH H H H
H H H H
The Peroxisomal Oxidase transfers the two
Hydrogens (2Hs) to Oxygen to make Hydrogen
Peroxide (H2O2) No ATP is made in Peroxisomes
133
What happens if there is a genetic defect in a
peroxisomal protein? If one of the nucleotides
is changed in the gene, in the DNA, then an amino
acid may be changed and the resulting protein may
no longer function.
134
What happens if there is a genetic defect in a
peroxisomal protein? If one of the nucleotides
is changed in the gene, in the DNA, then an amino
acid may be changed and the resulting protein may
no longer function. If the protein is a fatty
acid oxidase, then unmetabolized fatty acid will
accumulate, damage nervous system, and result in
mental degeneration after several years of life -
Adrenoleukodystrophy (Lorenzos Oil).
135
What happens if there is a genetic defect in a
peroxisomal protein? If one of the nucleotides
is changed in the gene, in the DNA, then an amino
acid may be changed and the resulting protein may
no longer function. If the protein is a fatty
acid oxidase, then unmetabolized fatty acid will
accumulate, damage nervous system, and result in
mental degeneration after several years of life -
Adrenoleukodystrophy (Lorenzos Oil). If the
protein is the receptor that recognizes the
Signal Sequence (-SKL) then most proteins will
not be imported into peroxisomes. Infant does
not survive - Zellwegers Syndrome.
136
(No Transcript)
137
Each protein contains much information, to be
recognized by other proteins, to recognize the
molecules it acts on. The specific functions of
a cell depend on groups of proteins interacting
with each other and with other molecules, DNA,
small molecules. To understand these complex
interactions computational tools can be employed
to predict the functions of individual proteins
and groups of proteins. The Howard Hughes
Medical Institute (HHMI) is supporting the GWU
program to involve undergraduate students in
research that involves computational approaches
to biological problems. New insights on
biological functions and disease will come from
researchers and doctors who know biology and
computational tools. The HHMI program has funds
to support summer undergraduate research
internships, new computer science courses for
biologists, new courses where biology and
computer science students will work together to
investigate biological problems.