Protein Structure 2 Flashcards
What determines the charge on the protein?
The pH and the number and type of each amino acid residues with ionisable sidechains
What is the pH inside lysosomes and why?
pH is 4.5/5
to activate the enzymes
Van der Waal interactions
What range is its effect?
Is it weak or strong?
How is it broken?
Very short range effect
Weak electrostatic forces
Broken by heat and denaturing agents
What energy is the best for protein folding?
Lowest energy minimum
What are protein domains?
Areas of protein that fold independently
these often perform a specific function
Is amorphous aggregation is non specific ?
It is non specific
Why is Amyloid proteins cause illness?
They can form multiple disordered proteins spontaneously
What 5 things can disrupt protein structure
Ionic Strength pH heat ( 20-40C) denaturing agent UV / oxidative / radiation damage
Can proteins be modified after they are made?
yes
Interactions can be what?
Interactions can be transient or stable
Name an example of how a protein can be modified
Can have prosthetic groups
proteins compete for binding sites
What percentage of proteins have a form that differs from their genetic sequence?
44%
What is a proteoform?
proteoform is used to denote all the molecular forms in which the protein product of a single gene can be found
When do reactions of sidechains that drive the addition of chemical groups?
It occurs post translation
Name 7 modifications that can occur to a protein
Phosphates Lipids Acetylation Methylation Proteins Glycans/carbs Proteolytic maturation
Which three amino acids commonly phosphate
S T Y
What is phosphorylation important in?
Important in downstream cellular signal
What enzyme phosphorylates?
Kinase
What enzyme dephosphorylates?
Phoslase
Describe glycosylation
Addition of complex carbohydrate groups
N-linked to Asn or O-linked to Ser/ Thr
What is palmitoylation?
Long lipid groups help anchor proteins in membrane
Modification on cysteine, glycine, lysine
Which amino acids side chain can be used to make isopeptide bonds?
The lysine side chain can be used to make isopeptide bonds with the carboxyl
terminus of ubiquitin
What are Zymogens?
Precursors of enzymes that are activated in a proteolytic cascade after release as granules into the duodenum
Name 3 examples of groups that can be conjugated that are non protein
Heam
Lipid
Mental ion
Nucleic Acid
What is the meaning of homomeric and hetromeric?
Homomeric= all the same units Heteromeric= differing units
What do oligomeric interactions of the proteins require?
What are these driven by?
Complementary interfaces , often dormains or motifs
Driven by hydrophobic packing or electrostatic/ polar interactions
Interactions between protein can be
t_____ or s_____
Transient or Stable
What is PKR?
PKR= kinase that is activated when double stranded RNA is present in the cell
What is often a sign of a viral infection in the cell?
Double stranded RNA
How does PKR help stop a viral infection
Double stranded RNA binds to the PKR which causes a conformational change and dimerisation so the kinase becomes activated
Activated PKR then phosphylates the substrate and switches off general translation hence inhibits the viruses replication
Which protein acts in blood to decrease the circulation of elastase?
Alpha-1-antirypsin
