What is a peptide bond
Covalent linkages between the carboxyl group of one amino acid and amino group from another amino acid
Peptide bonds form by condensation reactions involving the generation of what?
A water molecule
Within the main chain of a polypeptide the linkage is a repeating bond. What is it?
NCCNCC
Rotation around the C-N bond is restricted due to? As a result of the partial double bond, the six atoms of the peptide group are?
-Its partial double bond characteristic
-Rigid and planar
The partial double bond of the peptide structure creates
cis-trans isomers
What are the four levels of protein structure?
Primary structure
Secondary structure
Tertiary structure
Quarternary structure
What is the structure description of each level of protein structure?
Primary: Linear sequence of amino acids not in 3D space
Secondary: Localized folding within the peptide chain
Tertiary: The final folding pattern of a single polypeptide
Quarternary: Folding pattern when multiple polypeptides are involved
What groups in the Amino acids are the start terminus and the end terminus?
Primary structure is presented from the N amino terminus to the C carboxyl terminus
What group must start the polypeptide chain
N (amino group)
Viable forms of secondary protein structures must
1.Optimize the hydrogen bonding potential of main chain carbonyl and amide groups.
2.Represent a favoured conformation of the polypeptide chain.
Each peptide bond has both hydrogen bond donor and acceptor groups. TRUE OR FALSE?
True
What are the alpha helix properties
Right handed helix with 3.6 residues/turn
What amino acids are less likely to be bonded inside of an alpha helix?
Proline and Valine
What residue are you most likely to find at the N and C terminal cap of an alpha helix
N terminal: ASP or GLU
C terminal: LYS, ASN, HIS
What causes an amphipathic helix to have both polar and non-polar faces?
The positioning of hydrophobic and hydrophilic residues within the primary structure generates an amphipathic helix with polar and non-polar faces.
In parallel b sheets, which direction do the strands run?
Same direction
In anti-parallel b sheets, which direction do the strands run?
Opposite directions
What causes a beta sheet to be amphipathic (have both polar and non-polar sides)?
Alternating polar and non-polar residues within the primary structure of a beta sheet result in an amphipathic beta sheet.
What determines the stability of a protein?
The stability of a protein reflects the difference in the free energies of the folded and unfolded states.
What is denaturation?
The disruption of native conformation with loss of biological activity
Protein folding and denaturation is a cooperative process, what does this mean?
It means that once folding (or unfolding) begins, it rapidly spreads through the entire protein—interactions between parts of the molecule make the process all-or-none rather than gradual.
protein folding is…
-Rapid
-Cooperative
-Reversible
Biological advantages of quarternary structures
-May help stabilize subunits and prolong life of protein.
-Unique active sites produced at the interfaces between subunits.
-Help facilitate unique and dynamic combinations of structure/function through physiological changes in tertiary and
quaternary structure (Hemoglobin) .
-Conservation of functional subunits more efficient than selection for new protein with ideal function.
Biological roles of protein (general)
-Enzymes
-Storage and transport
-Physical cell support and shape
-Mechanical movement
-Decoding cell information
-Hormones and/or hormone receptors
-Many other specialized functions
