1. Fates of Proteins in Cells See also pages104-134 in Goodman.

2. 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.

3. 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.

4. One gene, one protein This statement was once regarded as a central dogma of molecular biology Central dog ma?

5. 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

6. Newly synthesized proteins are addressed to particular parts of the cell

7. Protein sorting- the first question is whether the protein is to be secreted or not

8. 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

9. 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.

10. 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

11. 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.

12. 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-X- T- where X is any amino acid, S is serine and T is threonine, so long as X is not P (proline).

13. 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.

14. 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.

15. 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.