Proteins Flashcards
T or F: Proteins are branching (non-linear)
False: proteins are non-branching polymers (linear chain)
What does the aa sequence determine?
structure and .: function
What do proteins begin and end with?
Start with amino group, carboxylate group at the end
Name 3 ways of depicting chemical structure in proteins
- skeletal
- ball and stick
- space filling
What example protein is involved in cell signalling?
Insulin
What example proteins are involved in digestion? (2)
trypsin, amylase
What does HIV protease do?
- Breaks down proteins, effective in building up HIV virus
- HIV treated with protease inhibitor, blocks active site
What does insulin do (in terms of cell signalling)?
Binds to insulin receptors and signals cells to take up glucose
What does trypsin do?
Breaks down protein (protease) during digestion (in pancreas)
What does amylase do? Where is it found?
- Breaks down starch into sugars
- In saliva and pancreatic juices
What example proteins are involved in metabolism? (2)
Alcohol dehydrogenase
Hexokinase
What does Alcohol dehydrogenase do?
Helps metabolise ethanol (the alcohol you drink)
What is the role of a kinase?
adds phosphate
What example protein is involved in O2 transport?
hemoglobin
What example protein is involved in immune protection?
antibody
How does the SARS-CoV2 spike protein interact with our cells?
Binds to ACE2, unfolds a little and binds leaflet that sticks out
How can we block the interaction between the SARS-CoV2 spike protein and our cell? (2)
Need something that blocks interaction between leaflet and ACE2, or an antibody that inhibits the interaction
Which chiral form is generally chosen for by nature?
L form
What does the 2nd letter in a 3 digit mutation code (L#L) represent?
the new/mutated residue
Where are non-polar sidechains found within a folded protein? Why?
Proteins have to be soluble, so hydrophobic side chains tend to be buried within the protein
Which 2 aa are the odd ones out?
Glycine (G) and Proline (P)
Why is glycine special?
- R group is another H so not chiral
- No bulky R group, very flexible, used where a large side chain cannot be accommodated
Why is proline special?
- Technically an iminoacid
- Because side chain bonded back around to imine group = very stiff/rigid
Negatively charged (acidic) aa have what chemical feature?
2nd carboxylate group on side chain
How are negatively charged (acidic) aa found in solution?
as conj base
Positively charged (basic) aa tend to have what chemical feature?
Additional -NH2 group(s)
What is Phosphorylation? What is its biological function?
Phosphorylation: adding a phosphate group
· Used to control enzyme activity
· A chemical on/off switch
What is Hydroxylation? What is its biological function? What aa involved?
Hydroxylation: adding a hydroxyl group
· Needed to prevent connective tissue diseases, scurvy
· Often proline and lysine involved
What is Carboxylation? What is its biological function? What aa involved?
Carboxylation: adding a carboxyl group
· Needed for blood clotting
· Often glutamate involved
What is Glycosylation? What is its biological function? What aa involved?
Glycosylation: attaching elements of sugar molecule
· Asparagine, threonine often
· Glycosylated hemoglobin can be used to diagnose diabetes
How much double bond character does the peptide bond have? What property of a peptide bond does this lead to?
40% -> planar
What are the 3 characteristics of a peptide bond?
- PLANAR
- predominantly TRANS
- permanent DIPOLE
Why are aa in a protein referred to as residues?
b/c not complete/independent (don’t have the water part)
What makes up super secondary structure?
Elements of secondary structure (helices and strands) connected by turns or regions of less order structure called loops or coils
What are 4 common motifs of super secondary structure?
- helix-turn-helix
- B hairpin
- Greek key
- strand -helix-strand
What super 2ndary theme is found in Ca binding proteins? Where is the Ca atom held?
helix-turn-helix: EF hand arrangement where Ca atom held in turn, coordinated by C=O oxygens
Is the b hairpin parallel or anti-parallel?
anti-parallel (One strand up, one strand down)
how is a b-hairpin stabilised?
by H bonding across the strand
What is the greek key made up of?
4 antiparallel beta strands
In the strand, helix, strand, are the beta sheets parallel or antiparallel?
parallel, because of intervening helix
What is a protein domain?
- combination of super secondary elements
- independently folded regions which possess a specific function within the protein
- typically has a hydroPHOBIC core with hydroPHILIC parts on the surface near solvent.
Why do protein domains typically have a hydrophobic core?
for stability
T or F, small proteins contain as many protein domains as larger ones?
F - smaller proteins (<250bp) usually have 1 domain, larger proteins have multiple
What are the 3 families of proteins?
a domain family
a/B domain family
antiparallel B family
describe features of the alpha domain family
- mostly helical
- side chains of helices packed closely together
- hydrophobic core
describe the arrangement of helices in a 4 helix bindle
Cylinders have 20* tilt relative to binding protein so side chains pack better
the 3º structure of the globin fold fits within which family
alpha domain family
in the globin fold, packing occurs between non-adjacent helices. What does this mean?
- helices are not in order of when the chain comes out of the ribosome
- brings together elements widely separated in sequence
a/B family proteins are made up of…
a mix of a and B structures
antiparallel family proteins are made up of…
antiparallel b strands (no intervening helices)
What amino acids create protein turns?
proline and glycine
Describe the method of the Anfinsen Experiment.
- urea and alcohol used to open chain (break non covalent bonds)
- reacted -> didn’t react
- urea and alcohol removed, air oxidised
- protein refold and is functiona;
What does the Anfinsen Experiment show?
the instructions for protein folding is contained in the sequence
Outline the sequence of events for protein folding
- short 2º segments form
- subdomains form
- subdomains come together to make a partly folded domain - this is flexible and can be rearranged to minimize energy and maximize stability
- final domain emerges
What gives stability to a protein?
Non-covalent interactions, particularly the hydrophobic core
name and describe the 3 types of protein folding in regard to chaperones
- chaperone independent
- chaperone dependent - peptide has bits that tend to bond, chaperones keep this from happening
- chaperonin-dependent - need lots of help so go into special chamber with lid, needs ATP
What are prion diseases caused by?
PrP - a protein that changes shape (misfolded) then forms aggregates which cause brain damage
a -> B transformation
What are 3 examples of prion diseases?
Bovine spongiform encephalopathy (BSE)
Creutzfeldt-Jacob Disease (CJD)
Kuru
