2nd law of thermodynamics - ANSWER -nature tends to become more
distorted
-entropy does not decrease in a closed system (entropy will stay the same or
increase)
What is the relationship between delta G and K (equilibrium constant)? -
ANSWER As K increases, delta decreases.
Relationship between K and Q? - ANSWER Q < K --> Reactions proceed
forwards
Q = K --> equilibrium
Q > K --> Reactions proceed backwards
Other amino acids - ANSWER -4-hydroxyproline: found in collagen
-ornithine and citrulline are metabolism intermediates
Adding positive charges to the amino acid solution will... - ANSWER lower
the pKa because the amino acid will be more likely to give a proton
Adding negative charges to the amino acid solution will... - ANSWER raise
the pKa because the amino acid will be more likely to keep its proton to avoid
resulting in negative-negative interactions
Amino acids are counted from... - ANSWER the N-terminal end to the C-
terminal end
Structure of peptide bond - ANSWER -planar
-normally trans
Rotation of bonds - ANSWER -C-N bond cannot rotate
-alpha-C's can rotate about their bonds
, Proline unique conformation - ANSWER All amino acids are in the trans form
except proline, which may have some in the cis form due to the steric
hindrances caused by the ring
Disulfide bonds intracellularly and extracellularly - ANSWER -Disulfide
bonds don't typically exist intracellularly
-Exist outside the cell to maintain protein structure in the harsh external
environment to maintain protein structure
-Extracellular environment is oxidizing, resulting in disulfide bonds
Alpha helix structure - ANSWER -backbone atoms follow helical pathway
-held together by hydrogen bonds between every fourth carbon (i+3)
Beta sheet structure - ANSWER -formed using carbon backbone
-can be parallel or anti-parallel
Difference between alpha helix and beta sheet - ANSWER -alpha helix is
formed from a single chain of amino acids
-beta sheet is formed from several short contiguous amino acid chains placed
side by side
Anti-parallel vs. parallel beta sheet - ANSWER Must have longer loops for
parallel structure than anti-parallel structure
Ramachandran plot - ANSWER -only some of the phi, psi angle combinations
occur (cluster in certain regions)
-sterics explain why only certain combinations occur (side chains may run into
each other in certain phi, psi angle combinations)
Motif - ANSWER some kind of reoccurring structure that combines certain
secondary structural sections
Surface vs. ribbon structure - ANSWER -surface: shows all components of the
protein (surface shapes)
-ribbon: shows mostly the backbone of the protein
3 types of tertiary protein structure - ANSWER 1. all alpha helix
2. mixed alpha helix/beta sheet
distorted
-entropy does not decrease in a closed system (entropy will stay the same or
increase)
What is the relationship between delta G and K (equilibrium constant)? -
ANSWER As K increases, delta decreases.
Relationship between K and Q? - ANSWER Q < K --> Reactions proceed
forwards
Q = K --> equilibrium
Q > K --> Reactions proceed backwards
Other amino acids - ANSWER -4-hydroxyproline: found in collagen
-ornithine and citrulline are metabolism intermediates
Adding positive charges to the amino acid solution will... - ANSWER lower
the pKa because the amino acid will be more likely to give a proton
Adding negative charges to the amino acid solution will... - ANSWER raise
the pKa because the amino acid will be more likely to keep its proton to avoid
resulting in negative-negative interactions
Amino acids are counted from... - ANSWER the N-terminal end to the C-
terminal end
Structure of peptide bond - ANSWER -planar
-normally trans
Rotation of bonds - ANSWER -C-N bond cannot rotate
-alpha-C's can rotate about their bonds
, Proline unique conformation - ANSWER All amino acids are in the trans form
except proline, which may have some in the cis form due to the steric
hindrances caused by the ring
Disulfide bonds intracellularly and extracellularly - ANSWER -Disulfide
bonds don't typically exist intracellularly
-Exist outside the cell to maintain protein structure in the harsh external
environment to maintain protein structure
-Extracellular environment is oxidizing, resulting in disulfide bonds
Alpha helix structure - ANSWER -backbone atoms follow helical pathway
-held together by hydrogen bonds between every fourth carbon (i+3)
Beta sheet structure - ANSWER -formed using carbon backbone
-can be parallel or anti-parallel
Difference between alpha helix and beta sheet - ANSWER -alpha helix is
formed from a single chain of amino acids
-beta sheet is formed from several short contiguous amino acid chains placed
side by side
Anti-parallel vs. parallel beta sheet - ANSWER Must have longer loops for
parallel structure than anti-parallel structure
Ramachandran plot - ANSWER -only some of the phi, psi angle combinations
occur (cluster in certain regions)
-sterics explain why only certain combinations occur (side chains may run into
each other in certain phi, psi angle combinations)
Motif - ANSWER some kind of reoccurring structure that combines certain
secondary structural sections
Surface vs. ribbon structure - ANSWER -surface: shows all components of the
protein (surface shapes)
-ribbon: shows mostly the backbone of the protein
3 types of tertiary protein structure - ANSWER 1. all alpha helix
2. mixed alpha helix/beta sheet
