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Objectives:
Be familiar with the various subcellular compartments in eucaryotic cells.
Objectives:
Be familiar with the various subcellular compartments in eucaryotic cells.
Know types of proteins that would be found in the different subcellular
compartments.
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
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.
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.
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.
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.
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)
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-QWhat does this mean in the language of proteins?
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-QWhat does this mean in the language of proteins?
What would be the subcellular location of a protein with this
sequence of amino acids?
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-QWhat 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?
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-QWhat 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 ---> ---->
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.
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.
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.
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.
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.
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)
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)
Figure 7.16 Review: relationships among organelles of the endomembrane system
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.
Human diseases result from defects in integrin genes.
A defect in integrin beta3 causes prolonged bleeding, because
blood plateletes can’t 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
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.
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.
Other proteins are translated from their respective mRNA’s in the
cytosol and then delivered to different subcellular locations:
Mitochondria
Peroxisomes
Chloroplasts (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?
Mitochondria - e.g., Dehydrogenases
Peroxisomes - 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
Do all cells have all these different proteins and subcellular compartments?
Eucaryotes
Animals, flies, worms, yeast cells have these compartments and many
proteins that are homologous.
Do all cells have all these different proteins and subcellular compartments?
Eucaryotes
Animals, 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.
Do all cells have all these different proteins and subcellular compartments?
Eucaryotes
Animals, 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.
Do all cells have all these different proteins and subcellular compartments?
Eucaryotes
Animals, 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?
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?
Questions about the proteome:
What proteins are present?
Where are they?
When are they present - under what
conditions?
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
Animal cell - is a EUCARYOTE
Animal cell - is a EUCARYOTE - has a nucleus and other membrane
enclosed subcellular compartments, mitochondria, peroxisomes, etc.
Plant cell - is also a EUCARYOTE - has a nucleus, mitochondria,
peroxisomes, plus chloroplasts, central vacuole.
Vibrio
cholerae causes cholera
ATP drive motor protein complex
E. Coli - normal
inhabitant of
human gut
Bacterial cells - are PROCARYOTES
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.
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?
Organism
.
H. influenzae
(bacterium)
Genome size
(Megabases, 10^6)
1.8 Mb
Estimated number
of genes
1700
Type of
Organism
Procaryote,
no nucleus
.
Organism
.
Genome size
(Megabases, 10^6)
Estimated number
of genes
Type of
Organism
H. influenzae
(bacterium)
1.8 Mb
1700
Procaryote,
no nucleus
S. cerevisae
(Yeast)
12 Mb
6000
Eucaryote,
Unicellular
.
Organism
.
Genome size
(Megabases, 10^6)
Estimated number
of genes
Type of
Organism
.
H. influenzae
(bacterium)
1.8 Mb
1700
Procaryote,
no nucleus
S. cerevisae
(Yeast)
12 Mb
6000
Eucaryote,
Unicellular
C. elegans
(nematode worm)
97 Mb
19,000
Eucaryote,
Multicellular
Organism
.
Genome size
(Megabases, 10^6)
Estimated number
of genes
Type of
Organism
.
H. influenzae
(bacterium)
1.8 Mb
1700
Procaryote,
no nucleus
S. cerevisae
(Yeast)
12 Mb
6000
Eucaryote,
Unicellular
C. elegans
(nematode worm)
97 Mb
19,000
Eucaryote,
Multicellular
Arabidopsis
(plant)
100 Mb
25,000
Eucaryote
Multicellular
Organism
.
Genome size
(Megabases, 10^6)
Estimated number
of genes
Type of
Organism
.
H. influenzae
(bacterium)
1.8 Mb
1700
Procaryote,
no nucleus
S. cerevisae
(Yeast)
12 Mb
6000
Eucaryote,
Unicellular
C. elegans
(nematode worm)
97 Mb
19,000
Eucaryote,
Multicellular
Arabidopsis
(plant)
100 Mb
25,000
Eucaryote
Multicellular
Drosophila
(fruit fly)
180 Mb
13,000
Eucaryote
Multicellular
Organism
.
Genome size
(Megabases, 10^6)
Estimated number
of genes
Type of
Organism
.
H. influenzae
(bacterium)
1.8 Mb
1700
Procaryote,
no nucleus
S. cerevisae
(Yeast)
12 Mb
6000
Eucaryote,
Unicellular
C. elegans
(nematode worm)
97 Mb
19,000
Eucaryote,
Multicellular
Arabidopsis
(plant)
100 Mb
25,000
Eucaryote
Multicellular
Drosophila
(fruit fly)
180 Mb
13,000
Eucaryote
Multicellular
Homo sapiens
(human)
3200 Mb
40,000
Eucaryote
Multicellular
Are all the genes in a cell producing proteins?
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)
The different types of cells look like they would
have different proteins - hair, eyes, spines, etc.
How do sizes of
egg cells
compare to
E.coli?
Each cell contains a fixed set of DNA molecules—its archive of
genetic information.
Each cell contains a fixed set of DNA molecules—its 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.
Each cell contains a fixed set of DNA molecules—its 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.
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?
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 Nov;183(21):6466-77.
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 Apr;181(7):2209-16.
Genome
Proteins for:
Metabolism, energy
E. coli (bacteria)
Procaryote
No nucleus or
organelles
Saccharomyces (Yeast)
Eucaryote, single cells
Nucleus, Mitochondria,
ER, Golgi, peroxisomes
4,640,000
12,050,000 nucleotides
890
820
Genome
E. coli (bacteria)
Procaryote
No nucleus or
organelles
Saccharomyces (Yeast)
Eucaryote, single cells
Nucleus, Mitochondria,
ER, Golgi, peroxisomes
4,640,000
12,050,000 nucleotides
Proteins for:
Metabolism, energy
DNA replication, repair
Transcription of RNA
890
120
230
820
175
400
Genome
E. coli (bacteria)
Procaryote
No nucleus or
organelles
Saccharomyces (Yeast)
Eucaryote, single cells
Nucleus, Mitochondria,
ER, Golgi, peroxisomes
4,640,000
12,050,000 nucleotides
Proteins for:
Metabolism, energy
DNA replication, repair
Transcription of RNA
Translation
Cell Structure
Protein targeting, secretion
890
120
230
180
180
35
820
175
400
350
250
430
Genome
E. coli (bacteria)
Procaryote
No nucleus or
organelles
Saccharomyces (Yeast)
Eucaryote, single cells
Nucleus, Mitochondria,
ER, Golgi, peroxisomes
4,640,000
12,050,000 nucleotides
Proteins for:
Metabolism, energy
DNA replication, repair
Transcription of RNA
Translation
Cell Structure
Protein targeting, secretion
890
120
230
180
180
35
820
175
400
350
250
430
Does E.coli produce all proteins constantly, or selected ones?
Where are the proteins located in the yeast cell?
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-QWhat does this mean in the language of proteins?
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-QWhat does this mean in the language of proteins?
What would be the subcellular location of a protein with this
sequence of amino acids?
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-QWhat 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?
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.
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.
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.
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.
Its single letter abbreviation is
G
G
G
A
G
A
V
Hydrophobic
L
I
G
A
V
Hydrophobic
M
L
I
G
A
V
L
I
Hydrophobic
M
F
W
P
S
T
Hydrophyllic
S
T
C
Hydrophyllic
Y
N
Q
S
T
C
Hydrophyllic
D
E
Y
N
Q
S
T
C
Y
N
Q
R
H
Hydrophyllic
D
E
K
Figure 5.16 Making a polypeptide chain
Figure 5.16 Making a polypeptide chain
amino
end
carboxyl
end
Figure 5.16 Making a polypeptide chain
Figure 5.16 Making a polypeptide chain
What are the names
of these amino acid
residues?
Figure 5.18 The primary structure of a protein
Figure 5.20 The secondary structure of a protein
Figure 5.17 Conformation of a protein, the enzyme Lysozyme
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?
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?
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
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-
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
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-QRetention 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-LImport into nucleus
-P-P-K-K-K-R-K-V-
Import 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??
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-QA hydrophobic series near the amino terminus
Retention in lumen of ER
At the carboxyl terminus
-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-LRegularly spaced positive residues near amino terminus
Import into nucleus
-P-P-K-K-K-R-K-VA 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.
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
>P11310
MAAGFGRCCRVLRSISRFHWRSQHTKANRQREPGLGFSFEFTEQQKEFQATARKF
AREEIIPVAAEYDKTGEYPVPLIRRAWELGLMNTHIPENCGGLGLGTFDACLISEE
LAYGCTGVQTAIEGNSLGQMPIIIAGNDQQKKKYLGRMTEEPLMCAYCVTEPGA
GSDVAGIKTKAEKKGDEYIINGQKMWITNGGKANWYFLLARSDPDPKAPANKA
FTGFIVEADTPGIQIGRKELNMGQRCSDTRGIVFEDVKVPKENVLIGDGAGFKVA
MGAFDKTRPVVAAGAVGLAQRALDEATKYALERKTFGKLLVEHQAISFMLAEM
AMKVELARMSYQRAAWEVDSGRRNTYYASIAKAFAGDIANQLATDAVQILGGN
GFNTEYPVEKLMRDAKIYQIYEGTSQIQRLIVAREHIDKYKN
>P11310 is
ACYL-COA DEHYDROGENASE, MEDIUM-CHAIN SPECIFIC
PRECURSOR
It is delivered to the Mitochondria
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
>gi|17560134|ref|NP_508036.1
MNRYICEGDNPDITEERKKASFNVDKLTEYYYGGEKRLKARREVEKCVEDHKELQD
LKPTPFMSRDELIDNSVRKLAGMAKNYKMIDLTNIEKTTYFLQLVHVRDSMAFSLHY
LMFLPVLQSQASPEQLAEWMPRALSGTIIGTYAQTEMGHGTNLSKLETTATYGQKTS
EFVLHTPTISGAKWWPGSLGKFCNFAIIVANLWTNGVCVGPHPFLVQIRDLKTHKTLP
NIKLGDIGPKLGSNGSDNGYLVFTNYRISRGNMLMRHSKVHPDGTYQKPPHSKLAYG
GMVFVRSMMVRDIANYLANAVTIATRYSTVRRQGEPLPGAGEVKILDYQTQQYRILP
YIAKTIAFRMAGEELQQAFLNISKDLRQGNASLLPDLHSLSSGLKAVVTFEVQQGIEQ
CRLACGGHGYSHASGIPELSAFSCGSCTYEGDNIVLLLQVANECELYPEHEAWNRCSI
ELCKAARWHVRLYIVRNFLQKVCTAPKDLQPVLRALSNLYIFDLQVSNKGHFMENG
YMTSQQIDQLKMGINESLSTIRPDAVSIVDGFAIHEFELKSVLGRRDGNVYPGLFEWT
KHSQLNNKEVHPAFDKYLTPIMDKIRAKM
gi|17560134|ref|NP_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
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-QA hydrophobic series near the amino terminus
Retention in lumen of ER
At the carboxyl terminus
-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-LRegularly spaced positive residues near amino terminus
Import into nucleus
-P-P-K-K-K-R-K-VA 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
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.
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)?
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
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 ? ?
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
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
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
Figure 7.9 The nucleus and its envelope
Figure 7.x1 Nuclei and F-actin in BPAEC cells
Figure 7.17 The mitochondrion, site of cellular respiration
Figure 7.19 Peroxisomes
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
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
(2H’s) from the fatty acid.
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
(2H’s) from the fatty acid.
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
(2H’s) from the fatty acid.
Dehydrogenase
H H 2H’s
H H
H H H
H-C-C-C-C-C=C-C-C-COOH
H H H H H
H H
In mitochondria a Dehydrogenase takes two Hydrogens
(2H’s) from the fatty acid.
Creates a double bond.
Dehydrogenase
2H’s
H H H H
H H H
H-C-C-C-C-C=C-C-C-COOH
H H H H H
H H
In mitochondria a Dehydrogenase takes two Hydrogens
(2H’s) from the fatty acid.
Creates a double bond.
Dehydrogenase
2H’s
H H H H
H H H
H-C-C-C-C-C=C-C-C-COOH
H H H H H
H H
In mitochondria a Dehydrogenase takes two Hydrogens
(2H’s) from the fatty acid.
Creates a double bond.
Dehydrogenase
2H’s
NAD
H H H H
H H H
H-C-C-C-C-C=C-C-C-COOH
H H H H H
H H
The mitochondrial Dehydrogenase transfers the two Hydrogens
(2H’s) to NAD.
Creates a double bond.
Dehydrogenase
2H’s NAD
H H H H
H H H
H-C-C-C-C-C=C-C-C-COOH
H H H H H
H H
The mitochondrial Dehydrogenase transfers the two Hydrogens
(2H’s) to NAD.
Creates a double bond.
Dehydrogenase
NADH2
H H H H
H H H
H-C-C-C-C-C=C-C-C-COOH
H H H H H
H H
The mitochondrial Dehydrogenase transfers the two Hydrogens
(2H’s) to NAD.
Creates a double bond.
Dehydrogenase
NADH2
H H H H
H H H
H-C-C-C-C-C=C-C-C-COOH
H H H H H
H H
The mitochondrial Dehydrogenase transfers the two Hydrogens
(2H’s) to NAD.
Dehydrogenase
NADH2
H H H H
H H H
H-C-C-C-C-C=C-C-C-COOH
H H H H H
H H
The mitochondrial Dehydrogenase transfers the two Hydrogens
(2H’s) to NAD.
Dehydrogenase
NADH2
H H H H
H H H
H-C-C-C-C-C=C-C-C-COOH
H H H H H
H H
The mitochondrial Dehydrogenase transfers the two Hydrogens
(2H’s) to NAD.
Dehydrogenase
NADH2
H H H H
H H H
H-C-C-C-C-C=C-C-C-COOH
H H H H H
H H
ATP
The Hydrogens are delivered to the inner membrane to make ATP
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
(2H’s) from a fatty acid.
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
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
Oxidase
H H 2H’s
H H
H H H
H-C-C-C-C-C=C-C-C-COOH
H H H H H
H H
Oxidase
2H’s
H H H H
H H H
H-C-C-C-C-C=C-C-C-COOH
H H H H H
H H
Oxidase
2H’s
H H H H
H H H
H-C-C-C-C-C=C-C-C-COOH
H H H H H
H H
Oxidase
2H’s
O2
H H H H
H H H
H-C-C-C-C-C=C-C-C-COOH
H H H H H
H H
Oxidase
2H’s
O2
H H H H
H H H
H-C-C-C-C-C=C-C-C-COOH
H H H H H
H H
Oxidase
H2 O2
H H H H
H H H
H-C-C-C-C-C=C-C-C-COOH
H H H H H
H H
Oxidase
H2 O2
H H H H
H H H
H-C-C-C-C-C=C-C-C-COOH
H H H H H
H H
The Peroxisomal Oxidase transfers the two Hydrogens
(2H’s) to Oxygen to make Hydrogen Peroxide (H2O2).
Oxidase
H2 O2
H H H H
H H H
H-C-C-C-C-C=C-C-C-COOH
H H H H H
H H
The Peroxisomal Oxidase transfers the two Hydrogens
(2H’s) to Oxygen to make Hydrogen Peroxide (H2O2)
No ATP is made in Peroxisomes
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.
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 (Lorenzo’s Oil).
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 (Lorenzo’s 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.
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.