What are the groups surrounding the central carbon on an amino acid? In what order are they arranged?
NH3, COO-, H, R groupCORN
Name the non-polar, aliphatic amino acids.
Glycine, Alanine, Valine, Leucine, Methionine, Isoleucine
Name the aromatic amino acids.
Tyrosine, Tryptophan, Phenylalanine
Name the polar and uncharged amino acids.
Threonine, Serine, Cysteine, Proline, Asparagine, Glutamine
Name the polar and positively charged amino acids.
Histidine, Lysine, Arginine
Name the polar and negatively charged amino acids.
What is the role of disulfide bonds within proteins?
Stabilization and structure
Post-translational modification: Why add a hydroxyl group to proline?What cofactor is needed?
Hydroxyproline is an important component of collagen.Vitamin C (don’t get scurvy!)
Post-translational modification: Why add a carboxyl group to glutamate?What cofactor is needed?
Carboxyglutamate is a key component in blood clotting proteins.Vitamin K
Post-translational modification: What three amino acids get glycosylated?What effects (2) does this have on the protein/cell?
Serine, Threonine, AsparagineProteins become more soluble, cells adhere to each other b/c of cell-cell glycoproteins.
What happens when lysine and arginine get methylated or acetylated when part of a histone protein?
These positively charged proteins become neutralized, thus decreasing the histone-DNA attraction.
What is a common post-translational modification found in signal transduction pathways?
Phosphorylation and dephosphorylation of serine, threonine, and tyrosine.
What is ubiquitination?What does ubiquitination signal?
The addition of a 76 amino acid protein onto a lysine residue.It signals for the protein to be degraded by proteosomes.
What are the three covalent bonds that make the backbone of a polypeptide chain?
Calpha-C, C-N, N-Calpha
What determines the function of a protein?
Its amino acid sequence
What do mutations in an amino acid sequence (peptide) cause?
What do proteases do?
Proteases hydrolyze peptide bonds at particular amino acid residues.They vary in specificity.
What physiological functions depend on proteases?
Proteases activate digestive enzymes, insulin, complement enzymes, blood clotting enzymes, transcription factors, and enzymes involved in programmed cell death.
How strong are hydrogen bonds?What are they often formed between?
1-7 kj/molMost often formed between N-H of backbone and O (C=O) of backbone.
What role do hydrogen bonds play in secondary structure formation?
They help stabilize alpha helices and beta pleated sheets.
What are the two major types of secondary protein structures?
Alpha helices, and beta pleated sheets.
What does tertiary structure mean?Quaternary structure?
The spatial arrangement of a polypeptide chain usually grouped into fibrous or globular structures.The name given to a protein with multiple polypeptides (i.e. hemoglobin).
What role do loops play in protein structure and function?
Loops enable the peptide chain to form particular structures as opposed to staying extended. They also assist in interaction with other proteins (immunoglobulin).
How does Kdrepresent the binding strength of proteins to molelcules?
Kd is the dissociation constant. A smaller Kd represents a higher binding affinity.
How can binding specificity (ligand - protein) be achieved?
Through the lock and key complementary model” OR the “induced fit model”.”
How does heme enable myoglobin to bind oxygen?
The heme has Fe2+at its center which has a high affinity for O2.
Explain the molecular basis of CO poisoning.
CO binds heme much tighter than O2. Thus, CO ends up binding to all hemoglobin proteins - which prevents oxygen from binding and traveling to distal tissues.
Why is hemoglobin a good O2transporter?
Hemoglobin has four binding sites. It also has a tensed and relaxed state which enables it to respond to changes in the partial pressure of O2.
What factors cause protein denaturation?
Heat + Chemicals.
Ribonuclease Folding Experiment:What was the main conclusion?Who was the doc?
The primary sequence of a protein determines its structure.Dr. Chris Anfinson
What are the two classes of protein chaperones and what are their functions?
Hsp70: induced by heat, binds to hydrophobic areas to prevent aggregation - giving protein a chance to fold.GroEL: Acts the same way but not heat induced. Much more generic.
Why is protein disulfide isomerase sometimes required for folding?
It catalyzes proper protein folding by breaking improper disulfide bonds and forming the correct bonds.
Why is protein prolyl isomerase sometimes important for proper protein folding?
It helps catalyze the conversion between trans and cis proline which is often necessary for proper folding.
What is the major cause of prion disease, alzheimer’s disease, parkinson’s disease, and amyloidosis?
What is the main secondary structure change in prion disease?What is the infectious agent?
Alpha helices to ß pleated sheetsMisfolded proteins
What are the three major approaches for purifying proteins?
Gel filtration chromatographyIon exchange chromatographyGel electrophoresis
How does gel filtration chromatography separate proteins?
Porous beads accept smaller proteins allowing bigger proteins to be eluted off the column.
How does ion exchange chromatography work?
Proteins are sent through a charged column of beads. Positive proteins stick to negatively charged beads allowing negatively charged proteins to flow through. And vice versa.
How does gel electrophoresis separate proteins
Proteins are coated with charge (using a detergent such as SDS) and run through a polyacrylamide gel using an electric field. Small proteins make it further, big lag behind.