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84 Cards in this Set
- Front
- Back
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What is a Shine Dalgarno Sequence? |
Prokaryotic mRNA A ribosomal binding site located on the mRNA upstream from the AUG start codon |
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Why is the Shine Dalgarno sequence so important in prokaryotic mRNA? |
Prokaryotic mRNA is polycistronic so there needs to be a ay to find the start codon for each polypeptide |
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What is the difference between the scanning mechanism in Eukaryotes vs the Shine Dalgarno sequence in prokaryotes? |
Eukaryotic mRNA is monocistronic so there is no need for a Shine Dalgarno sequence Instead ribosomes move towards the 3' end searching for a translation start site The first AUG encountered is the start site. |
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What does UTR stand for? |
Untranslated Region |
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What is post-translational modification? |
Side chains of specific amino acids can be modified = post translational modification |
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What enzyme adds the poly A tail to a pre mRNA strand? |
Poly A polymerase |
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When does post-translational modification occur? |
Occurs while the proteins are still attached to the ribosome (cotranslational) or after synthesis is complete (post translational) |
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Why is post-translational modification so important? |
Essential for regulating protein function |
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What are the 4 main reasons proteins are modified? |
1) Regulation of activity - on or off & different function 2) Protein-protein interaction - modification site may be binding surface 3) Subcellular localization - targeting signal & membrane anchor 4) Aging - Identify for degradation |
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Name 4 forms of post-translational modification |
Glycosylation Hydroxylation Phosphorylation Methylation |
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How is proteolytic cleavage a post-translational modification? |
Hydrolysis of specific peptide bonds by proteases can lead to protein alteration (uses water and no ATP) |
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What are 2 functional examples of proteolytic cleavage? |
Conversion of inactive precursor to it's active form 1) Insulin 2) Zymogens |
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How is insulin activated through proteolytic cleavage? |
1) Preproinsulin - removal of N terminal peptide 2) Proinsulin - Removal of C chain 3) Insulin |
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How is Trypsin activated through proteolytic cleavage? |
Trypsinogen > trypsin |
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Pepsinogen becomes what and where through proteolytic cleavage? |
Pepsin In stomach |
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Chymotrypsinogen becomes what and where through proteolytic cleavage? |
Chymotrypsin In Pancreas |
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What is glycosylation? |
Addition of CHO to a protein i.e. glycoproteins and proteoglycans |
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What is the function of glycosylation? |
Stabilize proteins against proteolysis Adds to 3D conformation Modulation of immune response |
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Where are glycoproteins and proteoglycans found? |
Collagen, ABO blood group, MHC proteins, transferring, blood clotting factors |
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Where in the cell does glycosylation occur? |
Occurs in ER Or golgi |
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What proteins are mostly formed in ER? |
Glycoproteins |
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What sugars are typically added during glycosylation? |
Glucose, mannose, N-acetylglucosamine |
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Name the 2 types of glycosylation |
1) N- linked - attachment of CHO to N of ASN 2) O- linked - attachment of CHO to O of SER or THR |
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How does glycosylation modulate the immune response? |
1) Selectins weakly bind to oligosaccharides 2) Concentrates lymphocytes in lymphoid organs 3) Attracts WBC's and platelets to sites of inflammation |
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Describe the 2 steps of glycosylation in the ER |
1. Oligosaccharide is assembled and attached to dolichol phosphate (lipid molecule in ER membrane) 2) Oligosaccharide is then transferred to an ASN residue of a protein by glycosyl transferase |
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What amino acids are hydroxylated in proteins? |
Proline and Lysine |
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Where is hydroxyproline found? |
Present in collagen and elastin |
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Where is hydroxylysine found? |
Present in collagen only |
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What structure requires hydroxylation? |
Connective Tissue proteins |
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Where does hydroxylation occur? |
In the lumen of the ER |
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What enzyme is used to hydroxylate pro and lys? |
Oxygenases |
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What cofactors and coenzymes are required for hydroxylation? |
Oxygen Ferrous And Vitamin C |
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What does vitamin C do to iron? |
Reduces Fe3+ to Fe2+ |
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What is the most common form of PTM? |
Phosphorylation - in 30% of eukaryote proteins |
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What are major regulation pathways affected by phosphorylation? |
1) Metabolic 2) Signal transduction 3) Protein- Protein interaction |
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What is the function of a protein kinase? and give some specific examples |
Phosphorylate
Ser/Thr kinases : Acceptor is OH Tyr Kinases : Acceptor is OH |
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What is the function of protein phosphatase? |
Dephosphorylation |
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What is the major function of lipophilic modification? |
Improves membrane binding capacity or certain protein-protein interactions |
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What are some types of lipophilic modifications? |
Acylation Prenylation (isoprenoids) N-Myristoylation (C14:0 fatty acid) |
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What proteins are typically affected by lipophilic modification? |
Signal transduction proteins |
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How is Ras anchored to the membrane? |
By a farnesyl group |
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What amino acids are typically methylated and what enzyme carries out this reaction? |
Methyltransferase Aspartate, His, Lys, Arginine |
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What is an example of methylation of histidine? |
Methylation of histidine in histones (H3 and H4) can increase or decrease gene transcription |
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What proteins only have disulphide bonds? |
Only in secreted proteins NOT in cytoplasmic proteins This is because disulphide bonds are broken apart in reducing environments and the cytoplasm has a high concentration of glutathione to act as a reducing agent |
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Where are the disulphide bonds formed in secreted proteins? |
They are formed spontaneously as the polypeptide emerges into the lumen of the RER ER is a more oxidizing environment |
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What is disulphide exchange? |
Disulphide bonds migrate from one position to another until the most stable structure is achieved |
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What are the two types of ribosomes? |
1) Free in cytosol 2) Bound to the ER > RER |
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Where are transmembrane and secretory proteins made? |
Ribosomes bound to the ER |
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Where does peptide growth begin? |
The N Terminus |
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Where do N-linked and O-linked oligosaccharides undergo further modification? |
Golgi |
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Define Cotranslational transfer |
Translocation of a polypeptide during ongoing protein synthesis |
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What are Signal recognition particle? (SRPs) |
Protein-RNA complexes Recognize and target proteins to the ER |
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What is the signal hypothesis? |
Explains the translocation of polypeptides across the RER |
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What is a translocon |
Transmembrane protein that mediates translocation of polypeptide across the membrane |
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Describe the process of cotranlsational transfer across the RER |
1) SRP binds to ER signal sequence (pauses translation) 2) SRP binds to SRP receptor 3) Translation restarts and growing polypeptide inserts into the membrane 4) SRP is released and polypeptide translocates through the translocon |
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Is energy required for cotranslational transfer? If so, where does it attach? |
GTP hydrolysis provides the energy to push the protein across the RER Both SRP And SRP receptor bind GTP |
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What is a signal sequence? |
1) Short regions of proteins that act as targeting signals to direct the protein to a specific sub cellular localization 2) Help insert the polypeptide into appropriate membrane |
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What is the charge of a signal sequence? |
Consists of a positively charged region followed by a central hydrophobic region |
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Where are signal sequences typically found on the polypeptide and how many residues long? |
NH2 terminus (13-35 residues) |
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What happens when the signal sequence protrudes beyond the ribosome? |
It binds to a signal recognition particle (SRP) |
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What is the function of signal peptidase? |
Cleaves off the signal sequence releasing the mature protein into the ER lumen |
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How are integral membrane proteins contained in the ER membrane? |
They contain a "stop transfer" sequence within the polypeptide that leads to the release of the protein into the ER Membrane |
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How does RNA editing occur? |
1) Nucleotide insertion 2) Nucleotide deletion 3) Nucleotide modification |
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What is the most common form of RNA editing in mammals? |
Formation of inosine through adenosine deamination |
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Give two examples of RNA substitution editing |
1) Adenosine deaminase ( Adenosine to inosine) 2) Cytidine deaminase (Cytidine to uridine) |
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What happens to APOB gene in the intestines? How is it catalyzed? |
RNA editing Modification of C (glutamine) to U (stop codon) in codon 2153 The modification is catalyzed by cytidine deaminase Translation of the mRNA stops early forming apolipoprotein B-48 which aids in the absorption of dietary lipids in the intestine |
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What happens to APOB gene in the liver? |
No RNA editing Function of the polypeptide is to transport cholesterol in the blood |
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What happens to APOB in the intestine? |
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What is the purpose of introns? |
1) Introns permit Alternative splicing = multiple proteins from 1 gene 2) Introns may also facilitate the evolution of new genes via 'exon shuffling' |
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Give an example of polyadenylation modification |
The switch between membrane-bound and secreted immunoglobulins is regulated by RNA cleavage depending on the polyadenylation sites |
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How does a poly A tail lead to a membrane bound immunoglobulin? |
Has a poly-A tail at the membrane coding sequence which leads to cleavage of the secretion coding sequence which leads to a membrane- bound immunoglobulin |
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How does no poly A tail lead to a secreted immunoglobulin |
Has a poly A tail that attaches to the secretion coding sequence after the cleavage of the membrane coding sequence and leads to a soluble C-terminus = secreted immunoglobulins
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What does Nuclear Export of RNA require? |
1) Nuclear Export signals 2) Cap binding and other proteins |
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Where does the nuclear cap-binding complex (CBC) attach? |
5' cap and this end leads the way through he nuclear pore complex (NPC) |
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How is rate of degradation controlled in mRNA? |
palindromes or hairpin loops - prevent degradation by nucleases
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What is the translation rate of mRNA dependant on? |
Rate of synthesis and rate of degradation |
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What contributes to mRNA stability? |
1) Reversible adenylation/deadenylation at the 3' end of the mRNA 2) Poly A binding proteins |
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How is translation controlled negatively? |
The binding of repressor proteins at the 5' ends of the mRNA - blocks the binding and scanning of ribosomes |
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What is ferritin? |
Cytosolic iron-binding protein expressed when iron is abundant in the cell - STORAGE
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What is transferrin? |
plasma membrane receptor important for import of iron into the cytosol |
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How is iron regulated? |
Ferritin and transferrin are coordinately regulated in opposite directions When repressor proteins binds to 5' end of ferritin mRNA translation is blocked (made when not bound) When repressor protein is bound to the 3' end transferrin receptor is made (not made when not bound) |
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What is initiation factor phosphorylation? |
Phosphorylation of proteins such as elFs that aid in translation and can affect the translation of specific mRNAs |
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Initiation Factor phosphorylation can help cells alter protein synthesis in response to these two changing environments.... |
1) Nutrient Availability - low nutrient levels down regulates translation 2) Growth factor signals - Stimulation of cll division upregulates translation |
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Describe the process of elF2 phosphorylation and how this controls translation. |
elF2 is inactive when phosphorylated i.e if you don't have enough amino acids you don't want to initiate translation because you will make inadequate proteins |
