Lecture 12b Flashcards
What is the N-end of the protein?
This is the amino terminal end, also called the N-terminus end. This marks the beginning of the protein.
What is the N-end of the protein coded by?
This is coded by the codon on the most 5’ end of the mRNA.
What is the C-end of the protein?
This is the carboxyl terminal end. This marks the end of the protein.
What is the C-end of the protein coded by?
This is coded by the codon on the most 3’ end of the mRNA.
What is the R group of the polypeptide?
These are the structures that come off of the middle carbon on each amino acid. This is what differs between amino acids in the polypeptide chain.
How do we determine if an amino acid is hydrophobic?
Amino acids with non-polar and uncharged R groups are hydrophobic.
Where do we typically find hydrophobic amino acids relative to the folded protein?
Hydrophobic amino acids are often buried within the interior of a folded protein.
What are the two exceptions to hydrophobic/hydrophilic amino acids?
Tyrosine and Tryptophan
Why is Tyrosine an exception to hydrophobic/hydrophilic amino acids?
Tyrosine is a tweener amino acid that is right between hydrophobic and hydrophilic. However, we consider it to be slightly on the side of non-polar.
Why is Tryptophan an exception to hydrophobic/hydrophilic amino acids?
There is a nitrogen in Tryptophan that we would generally consider to be polar. However, there is a carbon ring surrounding the Nitrogen, which overwhelms it and makes the nitrogen hydrophobic.
How do we determine if an amino acid is hydrophilic?
Amino acids with polar or charged R groups are hydrophilic.
What are examples of polar or charged R groups?
The presence of an Oxygen or Nitrogen or both will make it polar. Additionally, charges in a molecule make it polar.
What are examples of non-polar or hydrophobic R groups?
C-H, C-S, and S-H bonds are nonpolar.
Where do we typically find hydrophilic amino acids relative to the folded protein?
These are more likely to be on the surface of the protein and in contact with the aqueous solution.
What is the primary structure of a protein?
A protein’s primary structure is its amino acid sequence.
Within the cell, how does the protein appear?
Within the cell, the protein is not found in a linear state. Rather, it will adapt a compact 3D structure that can begin folding during translation.
What dictates the progression from the primary to the 3D structure?
The amino acid sequence within the polypeptide decides how the protein will fold up.
What specifically in the amino acid sequence determines the 3D shape of the protein?
The R groups of the amino acids will determine how the protein folds up.
What is the secondary structure of proteins?
The primary structure of protein folds form regular, repeating shapes known as secondary structure.
What are the 2 most common secondary structures?
Alpha helices and beta sheets.
What are alpha helices?
A common secondary structure in which the proteins will assemble into a helix conformation. Hydrogen bonding will stabilize the formation.
What are beta sheets?
A common secondary structure in which the amino acid chain is stretched out. Hydrogen bonding will stabilize the formation and can occur regardless of direction.
What is the hydrogen bonding occurring between in alpha helices and beta sheets?
Hydrogen bonding will occur between the C=O and H-N.
Why is the hydrogen bonding beneficial in alpha helices and beta sheets?
The hydrogen bonding helps to stabilize the formation.
What is the tertiary structure of proteins?
The 3D shape of a single polypeptide structure.
What is the final conformation of proteins that are composed of a single polypeptide?
The tertiary structure of proteins.
