Download Bio200 Au13 Lec19 10-29 Slides

Eukaryotic Gene Regulation: Data Set 4
Random Call for an
explanation of this…
Protein-coding mRNA
region for Gene Z
Amino-acid primary
Sequence for Gene Z
= Lysine
‘Life span’ of
the mutant
protein
(Life span of
non-mutant
protein Z)
Location of amino-acid-changing mutation
How to read this graph:
If you made a mutation in the 4th amino acid (blue), then the lifespan of the mutant protein would
be just a little bit shorter on average than the non-mutant protein Z.
Eukaryotic Gene Regulation:
Post-translational Ubiquitination
Eukaryotic Gene Regulation:
Other post-translational modifications
Ubiquitination by UbiE3s
Phosphates
Addition: kinase
Removal: phosphorylase
Acetylation
Cleavage by
proteases
Addition of
carbohydrates
Homework: Gene Regulation Chart
Type of regulation
Histone
acetylation
Enhancer site
Silencer-binding
protein
Splicing
Ubiquitin addition
to the product
5’ Cap and 3’
Poly-A tail
?
Found in
prokaryotes or
eukaryotes?
Mechanism?
Level
(dna, txn, tsl,
post-tsl?)
Increase or
decrease
expression?
Key Concepts
•  Eukaryotic gene regulation is typically more complex than regulation of
prokaryotes.
•  Eukaryotic DNA is packed onto histone proteins.
•  The looseness or tightness of this packing can effect expression.
•  DNA can be loosened by enzymatic addition of acetyl groups
•  Eukaryotic mRNA is heavily processed before being used
•  A 5’ protein cap and a 3’ poly-A tail are added to give stability
•  Non-coding introns are spliced out of the mRNA by the spliceosome
•  Eukaryotic genes can have promoter-influencing elements that are far
upstream or downstream of the protein-coding region.
•  These silencers and enhancers work through DNA binding proteins that
either help to recruit to repel RNA polymerase. DNA flexibility is essential.
•  Post-translational modifications can be used by the cell to regulate
enzyme activity
•  These can be additions, subtractions, or destructions of part or all of the
proteins.
•  These modifications are usually performed by other enzymes which may
have their own regulation schemes.
Oct 29th, 2013
Lecture 19 Outline Questions
Understanding Protein Trafficking and the Endomembrane System
•  What is the endomembrane system?
•  Why is the endomembrane system necessary?
–  How does the Rough ER help protein construction?
–  What is the common feature between the Rough ER and the Smooth ER?
–  Why does Golgi vesicle movement result in sorting of proteins?
•  How are proteins directed to particular regions of the cell?
–  Where is the trafficking information stored?
–  What molecular factors assist in protein transport and direction?
Translation into the Rough ER: Signal Sequence
Cytosol
Ribosome
SRP
RNA
Signal sequence
Emerging Protein
Lumen of
rough ER
SRP receptor
Protein
EMS Organelles: The Rough ER
A Protein Synthesis and Processing Complex
• 
• 
• 
• 
The rough ER is contiguous
with the nuclear membrane
New proteins are directly
inserted into the ER
Microenvironment: noncytoplasmic molecular
conditions for protein folding
Lumen of
After processing, proteins are
transported to other destinations rough ER
by controlled vesicle budding
Ribosomes
on outside
Free ribosomes
in cytoplasm
EMS Organelles: Smooth ER
A Lipid-Handling Center and Storage Site
•  The smooth ER is the major
processing zone for lipids
•  Smooth ER lacks ribosomes,
naturally
•  ER hosts non-cytoplasmic
molecular conditions and
specialized enzymes
•  After processing, lipids are
transported to other
destinations by controlled
vesicle budding
Smooth endoplasmic reticulum
Lumen of
smooth ER
Golgi apparatus: The cellular “post office”
11
EMS Organelles: The Golgi Apparatus
A Site of Protein Processing
The cis face is oriented
towards the rough ER
• 
• 
• 
• 
A site for carbohydrate
modification of proteins
Packaging and transport to
cellular locations with
vesicles
Formed by a series of
stacked flat membranous
sacs called cisternae.
Receives products from
the rough ER and sends
finished products to the
cell surface in vesicles.
The trans face is oriented
away from the rough ER Golgi apparatus
cis face
Vesicle
Lumen
Cisternae
Vesicles
trans face
How do proteins get where they need to go in the cell?
Different protein ZIP codes …..
different destinations
13
Key Concepts
•  Protein trafficking is the process of:
–  translating,
–  folding, and
–  transporting proteins
•  Proteins that are sent through the endomembrane
system are eventually active in:
–  organelles,
–  the plasma membrane, or
–  outside of the cell.
•  Trafficking signals are embedded information in the
structure of the molecules.
–  In proteins, this is often in the form of small trafficking ‘tags’ that are
short stretches of amino-acids.
–  These tags are recognized by mediating molecules.
•  The endoplasmic reticulums process molecules for use in
non-cytoplasmic environments.
–  The Rough ER processes proteins.
–  The Smooth ER processes lipids.
–  Molecules are sent by vesicle through the Golgi apparatus for
movement to different parts of the cell.