Amino acids & Proteins part 2 Flashcards
Examples of post-translational modifications to amino acids?
Acetylation, Amidation, Phosphorylation, Hydroxylation, Methylation, Palmitoylation, Sulphation
Post translational modification that occurs at the N-terminus is
Acetylation
Post translational modification that happens to Ser, Tyr
Phosphorylation
Hydroxylation occurs at which amino acid
Pro
Methylation occurs at which amino acid(s)
Tyr, Lys
Palmitoylation occurs at which amino acid(s)
Ser, Thr
Are all amino acids except for glycine L or D?
All amino acids are L, except for glycine which is D
*all the amino acids have chiral carbons and exist as isomers…glycine is achiral b/c it has two Hydrogens attached to its central carbon
Thalidomide
An example of how the body recognizes different enantiomers; one has tetrogenic affects and one has the effect it was designed for
What does chirality describe?
The handedness of a molecule, the ability of a molecule to rotate the plane of polarized light either to the right, D, or to the left, L
Which form (d or l) of amino acids is incorporated into proteins in mammalian cells?
L-form
A chiral molecule and its mirror image molecule are called _______ or ______
Stereoisomers, or enantiomers
What is an enantiomer?
A non superimposable mirror image
What does it mean to be amphoteric?
The COOH and NH2 groups in amino acids are capable of ionizing. Since amino acids contain both a basic and an acidic group they are referred to as amphoteric
*The predominant form of the amino acid is dependent on the pH of the solution
At physiological pH (7.4) what is happening to the carboxyl group of an amino acid and the amino group?
The carboxyl group is unprotonated, and the amino group is protonated
Isoelectric point
The pH at which a molecule bears no net electric charge
Zwitterion
At physiological pH, the amino group is protonated (positive charge) while the carboxyl group is unprotonated (negative charge) therefore that amino acid can act as both an acid or a base, which is referred to as a zwitterion
Describe the titration of the non polar amino acid alanine with the use of a diagram
see notes
How do amino acids link together?
Amino acids can link together by a covalent bond between the alpha-carboxyl end of one amino acid and the alpha amino end of another
What type of reaction is the formation of a peptide bond?
A condensation reaction; water is lost
Who were the two individuals who analyzed the geometry and dimensions of peptide bonds in the crystal structures of molecules containing one or a few peptide bonds?
Linus pauling and robert corey
Pauling and corey rule #1
the peptidly C-N linkage and the four atoms to which the C and the N atoms are directly linked always form a planar structure as though the C-N linkages is a double bond
The C-N bond length of the peptide is 10% shorter than that found in usual C-N amine bonds as the peptide bond has some double bond character (40%) due to resonance which occurs with some amides
Pauling and Corey rule #2
the peptide carbonyl and the amino groups always form the maximum number of hydrogen bonds.
How to calculate the molecule weight of a peptide
Add the mass of the amino acids together then subtract the mass of a water molecule for each peptide bond formed
The torsion angles phi and psi are at which bond?
alpha C-N bond is phi
alpha C-C bond is psi
Primary structure
Linear sequence of amino acids that are joined together by peptide bonds.
Secondary structure
Refers to the amount of structural regularity or shape that the polypeptide chain adopts.
Two main types: alpha helix and beta pleated sheet
The alpha helix
The polypeptide folds by twisting into a right handed screw so that all the amino acids can form hydrogen bonds with each other. This high amount of hydrogen bonding stabilises the structure so that it forms a very strong rod-like structure.
What amino acid residue tends to destabilize the alpha-helix structure? Any others?
Pro
A sequence of Asp or Glu residues together can also destabilize the helix because they are highly negatively charged and thus repel each other; these repulsions are stronger than the H-bonding
How many residues are there per turn in an alpha helix?
3.6
What is the rise/residue in an alpha helix?
1.5 Å units
The beta sheet
More H-bonding is achieved by stretching out the polypeptide chain, and laying it side by side to form H-bonds between lengths of polypeptide chain. Thus providing both inter- and intra-H bonds.
The strands can run in opposite directions to give antiparallel beta-pleated sheet or they can run in same direction to give parallel beta-pleated sheets
Tertiary Structure
Concerns how the secondary structure units associate within a single polypeptide chain to give a 3D structure
Examples of tertiary structure
- disulfide bridges
- hydrogen bonding
- salt bridges
- hydrophobic interactions
Quaternary structure
How two or more polypeptide chains associate to form a native protein structure. Proteins with more than one polypeptide chain are said to be oligomeric
After folding into the quaternary structure what happens to the protein
The three dimensional, biologically active native conformation of the protein is maintained by hydrophobic interactions, electrostatic forces, Van der Waals forces, hydrogen bonding and if present covalent disulphide bonds, in addition to the peptide bonds between individual amino acids.
How many disulfide bonds are found in human insulin?
3
Name an example of a disease that is the result of a single amino acid change to a protein?
Sickle cell anemia
Globular proteins
Relatively spherical in shape: egg albumin, hemoglobin, myoglobin, insulin
Haemoglobin
Used to transport oxygen in the blood in red blood cells to tissue cells where it is used directly
-consists of 4 protein chains and 4 haem groups
Myoglobin
Present in skeletal muscles as an extra storage protein to enable muscle cells to have a readily available supply of oxygen
-consists of a single protein chain with 153 amino acids and one haem group that stores oxygen in the muscles
What metal ion is at the center of a haem group
Fe 2+
Which has a stronger affinity for oxygen: haemoglobin or myoglobin?
Myoglobin
