Studied by 78 peopleTags & Description
What are the positively charged Amino Acids?
His (H) Lys (K) Arg (R)
What are the negatively charged Amino Acids?
Asp (D) Glu (E)
The amino acid sequence that makes up the protein
Primary Protein Structure
Local areas of repeating main chain structure
Secondary Protein Structure
A spatial arrangement of the secondary structural elements in one polypeptide chain
Tertiary Protein Structure
The spatial arrangement of multiple polypeptide chains to form multisubunit complexes
Quaternary Protein Structure
-3.6 AA per turn
Helix rises 5.4 A every turn -i-th AA forms H-bonds with i+3-th or i+4-th AA
Alpha helix
Which way do the side chains radiate on a alpha helix?
They radiate away
How is the alpha helix stabilized?
The hydrogen bonds between AA
What are the partial oxygen levels for the following
Lungs
Resting Tissue
Exercising Tissue
100 mmHg
40 mmHg
20 mmHg
-The whole thing consists of 2 strands -Has parallel and antiparallel orientations
Beta Sheets
How are neighboring side chains positioned on a Beta sheet?
They are positioned on opposite faces of the sheet
How are Beta sheets stabalized?
Main chain hydrogen bonds between adjacent Beta strands
3 AA every turn
helix rises 6 A
3*10 helix
approximately 1/3 of the residues are prolines
forms a left-handed helix
not stabilized by hydrogen
Polypeptide II helix
What is the phi range for Beta strands?
-150 to -100
What is the phi range for alpha helices?
-70 to -60
What is the phi range for 3*10 helices?
-70 to -60
What is the phi range for Polypeptide II helices?
-80 to -60
What is the psi range for Beta strands?
120 to 160
What is the psi range for alpha helices?
-50 to -40
What is the psi range for 3*10 helices?
-30 to -10
What is the psi range for Polypeptide II helices?
130 to 160
Contain polypeptide chains organized approximately parallel along a single axis
Fibrous proteins
-Made of large sheets -Mechanically strong -Insoluble -Important for structural roles in nature
Fibrous proteins
What order structure is a Fibrous protein?
Secondary
Name the types of Fibrous proteins?
-Collagen -alpha keratin -silk fibroin
-Have diverse structures with varying amounts of helix, sheet, and loop regions -Often contain two or more distinct domains of the compact folded structure
Globular proteins
What order structure is a globular protein?
Tertiary
How many AA are in a domain?
about 200 will fold independently
How is a globular proteins characterized?
By the context of helix and sheet secondary structures as well as defined turns that link the secondary structures
True or False: A globular protein can not contain a mixture of helix and sheet secondary structures?
False
Region that can not be categorized as helix, sheet, or turn
random coil
-Have a nonpolar (hydrophobic) interior -Beta sheets are usually twisted or wrapped into barrel structures -The polypeptide chain can turn corners
Globular proteins
What chemical reduces denatures tertiary and quaternary structures?
Urea/BME
How does a tertiary protein reform after being denatured and reduced?
Remove Urea
Oxidize
What happens if a denatured tertiary/quaternary protein is oxidized before Urea is removed?
Proteins with randomly formed disulfide bonds are created
What is important to remember about enthalpy? (Delta H)
It does not change, but molecules always occupy all the space
What is important to remember about entropy? (Delta S)
Systems of molecules have a tendency to become less ordered
What is important to remember about Gibbs Free energy? (Delta G)
The portion of total energy change that is available to do useful work at constant temperature and pressure
How is the enthalpy of protein thermodynamically favored?
-charge-charge interactions -intermolecular hydrogen bonds -van der Waals interactions
True or False: Folded protein is entropically favored by the solvent
True
As the hydrophobic side chains cluster in the interior, they release ordered solvent molecules from clathrate structures
Hydrophobic effect
What would happen if a disulfide bond was removed from a Bovine trypsin inhibitor?
The melting temperature would decrease, and the structure would be less stable
What protein corrects the formation of non-native disulfide bonds?
disulfide isomerase
Protein complexes that facilitate protein folding
Chaperonins
How do chaperonins work?
An unfolded protein with a hydrophobic face enters the GroEL ring which has a hydrophobic interior at this stage.
ATP and the GroES cap bind and the unfolded protein begins to fold as the interior is hydrophilic at this stage.
3)ADP and the GroES cap cleave from the GroEL ring and the folded protein is repelled out.
Infectious agents that cause disease by inducing amyloid formation on contact
Prions
Shows repeating patterns of side chain polarity every 3-4 residues
Amphiphilic alpha helix
Shows repeating patterns of side chain polarity every other residue
Amphiphilic beta strand
Interactions among identical asymmetric protein subunits
homotypic
Interactions among different asymmetric protein subunits
heterotypic
One axis of symmetry
C*2 (two fold)
One threefold axis
C*3
Three twofold axes
D*2
One fourfold axes and two twofold axes
D*4
What is important about helical symmetry?
They are capable of indefinite growth in length
What type of quaternary symmetry does a Beta Sandwich have?
C*2
What wavelength does protein absorb?
280
What wavelength does DNA absorb?
260
What does SDS-PAGE measure?
How long the peptides are
What is the importance of the DTT and BME reducing agents in SDS-PAGE?
They dissolve disulfide bonds
Where will the shortest and longest polypeptide chains appear on a SDS-PAGE test?
The shortest is furthest (lower kDa) and the longest is closest (higher kDa)
How do cross-linked networks form and how do they interact?
The binding of two epitopes on antigens by each antibody forms cross-linked networks. They precipitate as an aggregate
Where do effector cells come from?
B-lyphocytes proliferates
-Secrete a soluble form of the antibody -Circulate in the bloodstream -Plasma -Adaptive Immune system
Effector Cells
How are memory cells different than effector cells?
-Membrane bound antibodies -Larger response to secondary exposure
Where does enzymatic cleavage happen?
the hinge region
What are the fragments that result from the enzymatic cleavage of IgG?
2 F(ab) fragments 1 F(c) fragment
-has 1 antigen binding site -has a variation and constant region
F(ab) fragment
What stabilizes the constant region of IgG?
Carbohydrate (CHO)
composed of two antiparallel Beta sheets stacked face to face
IgG
-hypervariable -located at the ends of the antibody variable regions
Complementary-determining regions (CDR loops)
How are antibody-antigen interactions mediated?
shape and charge complementarity
Identifying a known protein structure
Western Blotting
Detection of a specific DNA sequence in DNA samples
Southern blotting
Detection of a specific RNA sequence in RNA sample
Northern Blotting
a monomeric heme protein that binds and releases O2 in tissues
Myoglobin
a tetrameric heme protein that transports O2 from lungs/gills to peripheral tissues and returns CO2 to lungs/gills for exhalation
Hemoglobin
How is hemoglobin transported?
red blood cells
What is the heme made of?
Fe2+ and protoporphyrin IX
Mb and Hb with no heme
apoprotein
Mb and Hb with heme
holoprotein
What occupies the sixth coordinating position of Fe2+?
The proximal His (H) of the globin protein
What stabilizes the O2 binding to Fe2+?
The distal His (H) of the globin using hydrogen bonding
partial pressure of Oxygen
Po2
the fraction of sites occupied
Yo2
a constant that reflects the binding affinity of myoglobin to oxygen
P50
True or False: A higher P50 means a higher oxygen affinity
False
What is the ideal behavior for something to deliver oxygen?
nearly 100% capacity at lungs and 60% capacity at the capillaries
Binding event on one site of a protein or protein complex affects the binding event in a distal and distinct site
Allosteric effect
n>1
A larger n means a more "S" shaped curve
Binding O2 at one subunit changes conformation at that subunit facilitating transition at adjacent subunits in the same molecule
KNF model
The more you bind, the stronger the binding affinity
KNF model
O2 binding perturbs the T state to R state equilibrium toward the R state, and O2 release favors the T state
MWC model
What orientation change occurs when hemoglobin goes from T to R state?
One alpha-beta dimer rotates 15 degrees with respect to the second dimer
more salt bridges/H-bonds are present between alpha-beta and beta-beta interfaces
T state
-All noncovalent interactions are broken -Unfavorable enthalpy loss is compensated by favorable O2-heme binding interactions
R state
What bonds stabilize R state Hb?
Fe-O2 bond
True or False: T state is thermodynamically favored without ligand over R-state
True
Note
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