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What is the structure of just the order of the amino acids in the protein?
Primary structure
What order of structure is the localized confirmation of the polypeptide backbone?
Secondary structure
What order of structure is the three dimensional structure of the entire polypeptide(backbone and sidechains)?
Tertiary structure
What order of structure is the spacial arrangement of polypeptide chains in a protein with multiple subunits?
Quaternary structure
What type of bonding is hydrogen bonding of electronegative atoms within the same molecule?
Intramolecular bonding
What type of bonding is hydrogen bonding between two different molecules?
Intermolecular bonding
What order of structure is a result of hydrogen bonding and is it inter or intra?
Secondary structure and intramolecular hydrogen bonding
What are the 2 most common patterns of folding?
alpha helix and beta sheet
What two functions can the amide functional group do leading to hydrogen bonding?
It can be both a hydrogen bond acceptor and a hydrogen bond donor
In the alpha helix, which way does the backbone twist?
In a right handed fashion
Where does the intramolecular hydrogen bond form in the secondary structure?
Between the NH and the C=O
How many residues down the alpha helix does the intramolecular hydrogen bond form?
4 residues down
Which amino acids prefer the alpha helix?
Ala, Glu, Leu, and Met
Which amino acid is a poor alph helix former?
Pro
Where is the only spot that proline can fit in the alpha helix well, and why is it not suited to fit in other spots in the alpha helix?
Only in the first spot, the side chain of proline causes steric hinderence in any other spot in the chain
What type of formation is from intramolecular bonds between neighboring strands?
Beta sheet
What two ways can the beta sheet be formed?
Parallel and antiparallel
What is the difference between parallel and antiparallel?
Parallel-Nterminal to Cterminal, Nterminal to Cterminal

Antiparallel-Nterminal to Cterminal, Cterminal to Nterminal
Which order of structure is usually a compact, globular shape?
Tertiary structure
What interactions form the tertiary structure?
Interactions with water and disulfide bridges alter the shape of the protein.
Which involves side chains, beta sheets or alpha helix?
Neither involve side chains
What type of bonds are involved in stabalizing the structure of the tertiary structure?
H-bonds, ionic bonds, hydophobic interactions, and disulfide bonds
What is the process called where the polypeptide chain aquires its correct 3-D shape to achieve its biologically active native state(folding state)
Protein folding
Do most polypeptide chains require assistance from enzymes and chaperones?
No, most of them form spontaniously
What is the major force favoring the native confirmation of the globular proteins?
Hydrophobic interactions
When a protein folds, 80% of the nonpolar sidechains are going to form on which side of the protein?(inside or outside)
They are folded into the protein, inside away from the solvent
What determines the chance that the side chain will be found in the core of the protein?
The hydrophobicity of the hydrophobic side chains
Hydrophobic interactions in the tertiary structures are reinforced by what 2 other forces?
Van Der Walls and aromatic stacking
Where are polar side chains found in tertiary structures?
Almost always located with a residue with the opposite charge, forming an ionic bond
What 4 things can easily cause a protein to go from the native (folding) state to the denatured (unfolded) state?
pH, temperature, pressure, and solvent medium changes
Is the energy change between the native and denatured state large or small?
Small
What are the two major contributors to the energy difference between the native and denatured states?
Entropy and Enthalpy
What is the term for the energy of the non-covalent interactions within the polypeptide chain?
Enthalpy
Are disulfide bonds covalent or non covalent?
Covalent
The non-covalent forces are stronger and more frequent in which state?
The native state(folded)
Which state has the larger energy contribution-Enthalpy?
Native state
What is the term for the measure of the disorder of a system?
Entropy
Which law of thermodynamics states that energy is required to create order?
2nd law of thermo
The _____ form of the protein has many confirmational states.
unfolded
The _______ form of the protein usually has one main confirmation
Native or folded
Increases in order cause a ________ in entropy
Decrease
A decrease in order of a solvent causes an increase in the _______ of the solvent
Entropy
Which state is thermodynamically unfavorable and causes folding of the protein?
Denatured(unfolded) state
Which state is thermodynamically favorable because there is an increse in entropy?
Native(folded) state
As the polypeptide goes through the mechanism of folding and associations into the native globular protein, there is also an increase in what?
Stability
____________ involved in all levels of the protein structure, local packing of the polypeptide chain, secondary elements, domains, and subunits.
Stabilization
Why does a protein sponsaniously fold?
In order to become thermodynamically favorable
__________ are macromolecules that catalyze all or most of the reactions in living cells
Proteins
_________ are workhorses that control virtuallty all of the cellular process
Proteins
Proteins also have an important role in what 2 things?
Drug transport and biologic activity of hormones
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