52 notecards = 13 pages (4 cards per page)
What does NPH stand for?
Neutral Protein Hagadore
What's the basic structure of an amino acid?
1. Amino group (NH3+)
What catalyzes the dehydration synthesis that binds amino acids together?
Ribozymes (RNA enzymes)
Describe the formation of a peptide bond.
What is the implication of chiral amino acids.
All amino acids except Glyciene are chiral. They have D and L versions. All human proteins are L.
List the Aliphatic Amino Acids.
1. Glycine (Gly, G)
What are the properties of an Aliphatic Amino Acid?
Describe the structures of the Aliphatic Amino Acids.
1. Gly (H side chain)
List the aromatic amino acids
1. Phenylalanine (Phe, F)
What are the properties of the aromatic amino acids?
1. Absorbs UV light
List the polar amino acids.
1. Asparagine (Recognized for glycosylation) (Asn, N)
What are the properties of the polar amino acids?
List the sulfur-containing amino acids.
1. Methionine (Met, M)
What are the properties of the sulfur amino acids?
1. They can donate sulfur
List the Positive (Basic) Amino Acids.
1. Arginine (Arg, R)
What are the properties of the Basic Amino Acids?
1. Act as a base.
What are the properties of the Negative (Acidic) Amino Acids?
1. Aspartate (Asp, D)
What are the properties of the Acid Amino Acids?
1. Form salt bridges
What is pKa?
The point at which the number of protonated and unprotonated are equal.
What is PI?
-The point during a titration at which the solution becomes natural.
What are some the important amino acid interactions important for protein folding?
1. Hydrophobic interaction: Aromatics have the ability to stack
What can disrupt a salt bridge?
-Changes in pH
What is the primary structure of a protein?
The sequence/order of amino acids in a chain
What causes variation in primary structure?
1. Forward to backwards does not equal backwards to forwards
What are the two types of variations in protein primary structure?
1. Non critical: Sam Structure, Same Function
What should one consider when thinking about variation in primary structure of a protein?
-What group is being substituted for what?
What is a polymorphism?
Polymorphisms = sequence variations in an allele within a population
What is developmental variation?
-Certain variants of a protein family are differentially expressed based on the developmental stage of the organism.
Describe the developmental variations in hemoglobin.
Different forms of hemoglobin are associated with different affinities for O2. HbF has a higher affinity for O2 than HbA Thus, O2 can be exchanged at the placenta and then released in the embryonic tissues where the oxygen tension is very low. Subunit composition:
Describe Cell/Tissue Specific Variations in protein.
Different protein sequences are associated with slightly different functions and thus cell-type specific expression of particular isoforms are made.
Describe the application of variations to insulin.
-Bovine insulin differs from human insulin in simple amino acid substitutions.
How do we create injectable human insulin?
1. A residue that was once Pro-Lys was switched to Lys-Pro through genetic engineering.
Where are carbohydrates added on proteins?
O-glycosylation: OH of Ser, Thr, Tyr
Where are lipids added on proteins?
Palmitoylation: Internal SH of Cys
How are proteins modified for regulation?
Phosphorylation: OH of Ser, Thr, Tyr
How are proteins oxidized?
Occurs on the carbon of Pro, Lys
How are proteins carboxylyzed?
Occurs on the carbon of Glu
What are the levels of protein structure?
Primary: Amino Acid Sequence
Can peptide bonds spin?
No, peptide bonds are planar, and have restricted rotation.
Describe the location of R groups across a peptide backbone.
-R groups tend to alternate from side to side
What is the main stabilizing force of the alpha helix?
-There is a hydrogen bond between the NH group and the COO group of the peptide backbone. This causes the protein to twirl, and places the R groups on the outside.
What is the main stabilizing force of the Beta Pleated Sheet?
-Hydrogen bonds form between the peptide backbone of two proteins strands that run parallel. The R groups now alternate going "up" and "down" on the sheet.
What is a common structural motif in Beta Pleated Sheet?
What are the patterns of secondary structure that eventually lead to protein tertiary structure?
Give some examples of a tertiary structure.
Nucleotide Binding Fold
What is quaternary structure?
• Thespecificinteractionofdistinct polypeptide chain subunits.
What factors influence protein folding?
Where are hydrophobic residues on Globular, Fibrous, and Membrane proteins?
Globular: On the inside
What is a great example of a variety of protein folding?
What proteins assist the folding of other proteins in vivo?
￼Chaperones, Heat Shock Proteins, Isomerases
What are examples of protein folding diseases?
Prions (cause), ALS, Alzheimers
What leaks into the blood after muscular injury, or during a myocardial infarction?
•Myoglobin appears in the blood most rapidly, however, it is relatively nonspecific for cardiac injury.