Biochem Lecture 2 Flashcards
(32 cards)
What are the two chemical groups common to all amino acids?
Carboxyl group (COO-) Amino group (NH3+)
What is a peptide?
Amino acids bonded together through a peptide bond.
What is a residue?
When an amino acid is part of a peptide or protein, it is called a residue.
Is a peptide bond charged or polar?
It is an uncharged polar bond. The O has a partial neg charge and the N has a partial pos.
How do residues participate in hydrogen bonding?
The partial charges on the O and N molecules of the amino and carboxyl groups now bonded together make them able to undergo hydrogen bonding. The O is attracted to the H on the N.
In which direction are polypeptides read?
By convention, they are read from Amino terminus to carboxy terminus.
What is the primary structure of proteins?
It is the linear sequence of amino acids which is determined by the genetic code.
What are the secondary structures of proteins?
alpha helices, beta pleated sheets,
loops
What stabilizes the secondary structures of proteins?
Hydrogen bonding between the C=O and the N-H. Allows all amino acid sequences to form these secondary structures.
Where are the R-groups in an alpha helix?
There is no room inside the helix, so the R-groups are directed towards the outside.
What is a coiled coil?
Two alpha helices combine and wrap around each other. This can be because of polar and nonpolar residues grouping.
What is an alpha chain?
Three polypeptide chains coil together in a spiraled triple helix.
How are beta sheets stabilized?
Hydrogen bonding between the C=O and the N-H across strands in the sheet.
Where are the R-groups in a pleated sheet?
They are above and below the plain.
What is a loop, and what can it do?
Part of the sequence not part of a regular folding. Serves as a connecting region.
How are loops stabilized?
Loops can be different shapes and sizes for any given protein, but they are not random and are stabilized by covalent and non-covalent interactions.
What are short loops called that have five or less residues?
Turns.
What are supersecondary structures?
AKA Motifs. These are patterns in secondary structures such as orientation of strands in beta sheets and interaction between alpha helices and sheets. Examples are greek key, beta meander, and beta barrel.
What makes tertiary protein structures?
Folding and packing together of secondary structures.
What is the hydrophobic effect?
Proteins in solution generally fold so that their hydrophobic residues are inside and their polar, hydrophilic residues are outside. This is one of the major driving force in the folding of proteins.
What interactions stabilize tertiary structures?
Disulfide bridges,
hydrophobic interactions,
hydrogen bonds,
ionic bonds
What are the two global classifications of tertiary structure?
Globular: spherical
Fibrous: rod-like
What is a domain?
Stable structural elements within a protein that have individual functions. A separate structural and functional entity.
What is the difference between identical sequences and conserved sequences?
In the primary structure of two proteins, identical residues are exactly the same and conserved have several residues interchanged with ones having the same chemical properties.
