Proteins Flashcards
Basic AA R groups
Can be protonated at physiological pH
Lysine, arginine, histidine
Spongiform Encephalopathy
Prp misfolds and caues other proteins to misfold
altered alpha helices to form beta sheets that cause them aggregate forms aggregates with amyloid plauques leading to neuronal loss and gliosis
What is the least hydrophobic of the non-polar AA?
Glycine
Cysteine
Cys C
Polar uncharged
what AA promote alpha helices?
hydrophobic Ala and Leu
Hsp70/Hsp40 in prokaryotes
prokaryoties are DnaK or DnaJ
bind to hydrophobic region to prevent aggregation
ATP hydrolysis
Sickle Cell Anemia
glutamine undergoes single amino acid change to make hemoglobin stickier and difficult to pass through capilary bed
what does alpha helices make
structural: keratin, myosin, fibrinogen
globlar: hemoglobin, myoglobin
Valine
Val V
Non polar aliphatic
How do aromatic groups absorb UV light?
at 280nm and its used to measure protein concentration. Absorbance is a function of concentration.
As concentration increases so does absorbance.
how does hemoglobin transport Co2?
CO2 is converted as Carbamate on amino terminal residues of hemoglobin
what AA promote Beta sheet formation
Trp, Ile, Val
DnaJ and DnaK
DnaJ binds to unfolded and facilitates DnaK binding.
DnaJ stimulates ATP hydrolysis by DnaK.
DnaK-ADP binds tightly to unfolded protein NT xchange factor stimulates release of ADP
ATP binds to DnaK to dissociate protein
What are the Aromatic AA?
hydrophobic as well as relatively non-polar
Phenylalanine, tyrosine, tryptophan
Isoleucine
Ile I
non-polar aliphatic
Beta turns
180 degree turn accomplished over 4 AA acids hydrogen bond between 1st A and 4th AA made
proline (2nd) or Glycine (3rd)
Relaxed Hemoglobin State
High affinity of O2 so when leaving the lungs it remains attached formation triggered by O2 binding.
Phenylalanine
Phe F
Aromatic R group
Hydrophobic least polar of the Aromatic group
Alpha helix
right hand screw
R groups pointing outward bond
between every 5 residues Carbonyl O and amine
Inner diameter is too small out
diameter fits in major groove of DNA
Aliphatic side chains - meaning
carbons in open chain conformation
Amyloidosis
generalized protein misfolded in rest of body leading to variety of disease (T2D to cardiac amyloidosis)
Lysine
Lys K Polar Basic (positively charged) pKa 10
L Isomer vs D isomer
L: with hydrogen backwards is CORN counterclockwise D: with hydrogen backwards is CORN clockwise All amino acids have L isomers
what is the signficance of 1 and 8 lining up in alpha helces
allows the formation of a leucine zipper
Serine
Ser S Polar, unchraged
Acetyl modificaiton
occurs on lysine, especially on histones
y-caroxyglutamate
A blood clotting prothrombin protein
Vitamin K added
carboxyl group
Warfarmin (Coudamin) prevents blood clotting
Tyrosine
Tyr T
Aromatic R Group hydrophobic and slightly polar (not really) can form H bonds
Triple Helix
rich in glycine and proline
rich in turns and loops, but proline are hydroxylated via vitamin C
allows massive H bonding E
very third residue is glycine in collagen
Chaperonin
a cap and 2 7 subunit rings in prok GroEL and GroES required for 10-15% coupled to ATP hydorlysis and conformational changes
Alanine
Ala A non-polar Aliphatic
Collagen
tensile strength, non-stretching tendons, cartilage, bones, cornea long
glycine and proline rich
Super helical triple helix higher tensile strength than steel wire.
Gel Filtration Chromatography
Purify proteins according to size Proteins run through filtration column large flow faster and small slower
what happens with pH>pKa
deprotonated base form denominates
What AA are non-polar, aliphatic
Glycine, alanine, valine, leucine, methionine, isoleucine
Why does Myoglobin use heme?
\generate free radicals
heme not generate free radicals!
myoglobin cant bind to O2 itself
Edman Degredation
label and remove N terminal AA one at a time and identify
Tense Hemoglobin site
Lower binding affinity so in high O2 region of lungs, O2 will bind very easily
Protein Prolyl Isomerase
Reforms proline from Trans to the cis
formation cis is important in Beta turns
Alpha Keratin
tough rigid, hard materials in nails and horns
cross linked alpha helices and S-S rich in hydrophobic residues form by alpha helices that coil together to form a coiled coil (left) to combine in a protofilmant and a protofibril and intermediate filament
Bortezomib
takes advantage of cancer cells always proliferating and proteasome is in high demand. acts on proteasome inhibitor and this has more pronounced effect on cancer cells. treats multiple myeloma
Methylation Modification
Occurs on lysine or arginine can have 1, 2, or 3 methyl groups methylation of histones
what aa do not promote beta sheet formation
Pro Gly
Polar R Group AA
Serine, Threonine, Cysteine, Asparagine, Glutamine
Disulfide Isomerase
correct disulfide bond formation between free cysteines especialy important when there are many free cysteines done on secreted of cell surface proteins
Leucine
Leu L non polar aliphatic
Tryptophan
Trp, W Aromatic R group Hydrophobic and slightly polar
Ion Exchange Chromatography
purify proteins according to charge run through cation exchange resin column with negatively charged beads. Positive charged particles stick and can be eluted with salt
Isoelectric Point
point at which the pH at which the protein carries equal number of + and - charge. pI is essentially pKa value pI > pH = positive charged (lysozyme) pI
Arginine
Arg, R Polar Basic (positively charged) pKa 12
Histidine
His, H Polar Basic (positively charged) pKa 6.5
Hydroxyproline
found in collagen and CT
Addition of OH group onto proline is responsible for strength
Facilitated by Vitamin C *Scurvy*
Slk Fibroin
soft, flexible fiber held together by Beta sheet and van der waals intercations
Immunoglobulin
one heavy chain composed of 4 beta sheets one ligh chain composed of 2 beta sheets dimers antigen binding domain
Asparagine
Asn N Polar, uncharged
Proline isomers
most peptide bonds are in trans conformation, but proline has 6% are in cis
Methionine
Met, M non-polar aliphatic
Histamine
formed from the removal of CO2 from histidine
Gleevec
tyrosine kinase inhibitor that treats chronic myelogenous leukemia binds to bcr-abl fused protein to inhibit the kinase
Asparate
Asp D Polar Negative (acid) pKa 4.4
Acidic AA R groups
Asparate and Glutamate Deprotonated at physiological pH
O linked vs N linked glycosylation
O: sugars added to Ser and Thr N linked: sugars added to Asp in sequnes XNX-S/T
Bohr effect
pH difference in lung vs tissue to increase O2 transfer
what AA do not promote alpha helices?
proline and glycine
how is hemoglobin influenced by pH
blood in lungs have higher pH than blood, O2 binds better PH in tissue is lower, thus O2 is released
Thryoid hormone
L-thyroxin is formed by modification of tyrosine
ALB protein
ALB is a kinase that normally phosphorylates and dephosphorylates as regulatory protein. When fused with BCR, it is always active and leads to continuous phosphorylation - thus leukemia.
what is scurvy caused by?
lack of vitamin C
Proline does not get hydroxylated so
4-hydroxyproline is not formed
Glutamine
Gln, Q polar, uncharged
Glutamate
Glu E Polar Negative (acid) pKa 4.4
Threonine
Thr, T polar uncharged
Kd
[p][L][pL] dissociation constant when Kd is higher, binding strength is low when Kd is low, binding strenth is high
