Fates of Proteins in Cells
See also pages104-134 in
Goodman.
What does the genome do?
• “DNA serves as the blueprint for an organism”
• The protein-coding genes provide a parts list for
the organism
• Changes in the pattern of expression of genes
can create a substantially different organism
without major changes in the genes themselves
- so control of gene expression is very important.
Evolution of control genes is the most important
factor in species evolution.
Gene expression
• Differentiated cells express some definite
subset of their total protein-coding genome
– this determines the proteome of that cell:
the roster of protein types present in the
cell.
• What is gene ‘expression’?
• A gene is expressed if it is transcribed into
mRNA that results in the synthesis of the
corresponding protein.
One gene, one protein
• This statement was
once regarded as a
central dogma of
molecular biology
Central
dogma?
A relatively small number of genes can code for a
large number of proteins
• In the human genome, about 20-30
thousand genes code for more than 50
thousand proteins
Newly synthesized proteins are
addressed to particular parts of
the cell
Protein sorting- the first question is whether
the protein is to be secreted or not
Non-secreted proteins
• Step 1: rough ER or free ribosomes? Secreted
proteins have a signal sequence that causes the
ribosome to attach to the ER; proteins without
this sequence will remain in the cytoplasm
• Step 2 – proteins which have elements of their
sequences that direct them to specific organelles
or locations go to those locations – those without
such labels remain free as soluble cytoplasmic
proteins
Secreted Proteins
• proteins that are destined to be secreted
– Hormones
– Growth factors
– Extracellular matrix
– Extracellular enzymes
– Plasma proteins
In order for this to happen, secreted proteins
must enter the endoplasmic reticulum – a
membrane-bound box within a box inside the
cell.
Step 1 – translation starts
Step 2 – translation is halted shortly after a signal sequence is translated,
by binding of a signal recognition particle to the signal sequence
Step 3 – with the help of the signal recognition particle, the ribosome
associates with a translocon (channel in the ER membrane) and the signal
sequence is threaded through the translocon
Step 4 – once the leading end – the amino terminal end - of the protein is threaded
through the translocon, the signal sequence is clipped off by a specific peptidase
Step 5 – posttranslational modification of the growing protein may occur within the
ER – this typically occurs while the ER membrane is passing through the Golgi
apparatus- this protein is being glycosylated
Step 6 – when the ribosome reaches the end of the mRNA, the complete protein is
released into the ER lumen – It needs to undergo folding – usually with the help of a
chaperone protein that is not shown in this cartoon.
N-linked glycosylation
• When the nascent protein enters the ER
lumen, it gets glycosylated at sites called
sequons, determined by particular protein
sequence details. For example, an
asparagine (N) will be glycosylated, if it is
part of a sequon pattern -N-X-S- or -N-XT- where X is any amino acid, S is serine
and T is threonine, so long as X is not P
(proline).
Oligosaccharides are assembled on the
rough ER before being attached to protein
• Pro-oligosaccharides are assembled at the
cytoplasmic surface of the rough ER – during
this process they are anchored through
bisphospate to a membrane lipid called dolichol.
• The completed pro-oligosaccharide is then
translocated to the luminal side of the rough ER
• When a sequon passes through a translocon,
the oligosaccharide is attached to the
asparagine.
• The oligosaccharide may then be modified by
attachment of additional sugars or removal of
some of the original sugar structure.
N-glycosylation of a nascent
protein occurs when a
sequon of that protein enters
the ER. Oligosaccharides
that are waiting to be
attached to proteins are
attached to a membrane lipid
dolichol by bisphosphate
groups. The oligosaccharide
transferase moves the
oligosaccharide to the
asparagnine in the sequon.
Calnexin is a chaperone protein attached to the ER membrane at its blue end.
The protein’s arm embraces a newly-synthesized glycoprotein and causes it
to fold correctly.