biochem ch1 amino acids Flashcards
What are the different groups in an amino?
The amine group, the carboxy group, the hydrogen, and the variable side chain
On a fisher projection how can you know if an amino acid is an L or D amino acid
In a fisher projection, the amino group will be on the left side in an amino acid L for left
What form of amino acids are found in the body L or D
L amino acids
what direction are the vertical and horizontal bonds in a Fischer projection facing
The vertical bonds are facing away into the paper or the screen
The horizontal bonds are coming toward you
What are enantiomers
Molecules that are mirror images of each other that are non-superimposable
How are peptide bonds formed?
Nucleophilic edition elimination reactions between the Amine group of one amino acid and the carboxy group of another amino acid
What are the two types of hydrolysis which can break down peptide bonds?
Strong acid hydrolysis breaks down peptides with the use of a strong acid and heat to breakdown peptide bonds non-specifically
Proteolysis is the use of an enzyme called protease to breakdown peptide bonds specifically
what is special about the amino acid histidine
It has a pKa of around 6.5 which is close to physiological pH of 7.4 which allows it to stabilize and destabilize substrates at active sites of proteins.
when pH>pKa of an amino acid what be said about the aa
the aa will be in it’s deprotonated form.
when pH<pKa of an amino acid what be said about the aa
the aa will be in it’s protonated form.
What is special about the amino acids, proline and glycine
Proline’s R group wraps around itself and connect to the Amine group
Glycine’s R group is an H
These amino acids are both special because they can cause kinks in the alpha helix secondary structure of proteins. They are known as alpha helix breakers.
What is special about the amino acid cysteine?
It’s our group contains a thiol or an SH which can form bridges with other cysteines.
In reducing environments like the intracellular space, they do not form a bridge in
oxidizing environments like the extracellular space They do form a bridge.
What is the isoelectric point?
It is the pH of an amino acid when the amino acid is neutral and has zero charge
What is a zwitterion?
It is when a molecule has a positive and negative charge present at the same time
Describe the primary structure of an amino acid chain
It is the basic linear sequence of amino acids in a polypeptide chain held together by peptide bonds
Describe the secondary structure of proteins
It is the folding of linear primary structure, polypeptide chains into structures which include alpha helices, and beta sheets
What is a solvation shell, and how does it relate to protein?
Otherwise, known as the hydration shell in Aqua environments, it is the layer of water or solution directly outside of a protein that helps to stabilize it
When the solvation shell is water, the electronegative oxygen of the water interacts with the positive polar amino acids further stabilizing it
what are four ways that denaturation can occur
By increasing the temperature
By changing the pH
By adding chemical denaturants
By adding enzymes
