proteins and peptides

Question 1

What are the groups surrounding the central carbon on an amino acid? In what order are they arranged?

Answer 1

NH3, COO-, H, R groupCORN

Question 2

Name the non-polar, aliphatic amino acids.

Answer 2

Glycine, Alanine, Valine, Leucine, Methionine, Isoleucine

Question 3

Name the aromatic amino acids.

Answer 3

Tyrosine, Tryptophan, Phenylalanine

Question 4

Name the polar and uncharged amino acids.

Answer 4

Threonine, Serine, Cysteine, Proline, Asparagine, Glutamine

Question 5

Name the polar and positively charged amino acids.

Answer 5

Histidine, Lysine, Arginine

Question 6

Name the polar and negatively charged amino acids.

Answer 6

Aspartate, glutamate

Question 7

What is the role of disulfide bonds within proteins?

Answer 7

Stabilization and structure

Question 8

Post-translational modification: Why add a hydroxyl group to proline?What cofactor is needed?

Answer 8

Hydroxyproline is an important component of collagen.Vitamin C (don’t get scurvy!)

Question 9

Post-translational modification: Why add a carboxyl group to glutamate?What cofactor is needed?

Answer 9

Carboxyglutamate is a key component in blood clotting proteins.Vitamin K

Question 10

Post-translational modification: What three amino acids get glycosylated?What effects (2) does this have on the protein/cell?

Answer 10

Serine, Threonine, AsparagineProteins become more soluble, cells adhere to each other b/c of cell-cell glycoproteins.

Question 11

What happens when lysine and arginine get methylated or acetylated when part of a histone protein?

Answer 11

These positively charged proteins become neutralized, thus decreasing the histone-DNA attraction.

Question 12

What is a common post-translational modification found in signal transduction pathways?

Answer 12

Phosphorylation and dephosphorylation of serine, threonine, and tyrosine.

Question 13

What is ubiquitination?What does ubiquitination signal?

Answer 13

The addition of a 76 amino acid protein onto a lysine residue.It signals for the protein to be degraded by proteosomes.

Question 14

What are the three covalent bonds that make the backbone of a polypeptide chain?

Answer 14

Calpha-C, C-N, N-Calpha

Question 15

What determines the function of a protein?

Answer 15

Its amino acid sequence

Question 16

What do mutations in an amino acid sequence (peptide) cause?

Answer 16

genetic diseases

Question 17

What do proteases do?

Answer 17

Proteases hydrolyze peptide bonds at particular amino acid residues.They vary in specificity.

Question 18

What physiological functions depend on proteases?

Answer 18

Proteases activate digestive enzymes, insulin, complement enzymes, blood clotting enzymes, transcription factors, and enzymes involved in programmed cell death.

Question 19

How strong are hydrogen bonds?What are they often formed between?

Answer 19

1-7 kj/molMost often formed between N-H of backbone and O (C=O) of backbone.

Question 20

What role do hydrogen bonds play in secondary structure formation?

Answer 20

They help stabilize alpha helices and beta pleated sheets.

Question 21

What are the two major types of secondary protein structures?

Answer 21

Alpha helices, and beta pleated sheets.

Question 22

What does tertiary structure mean?Quaternary structure?

Answer 22

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).

Question 23

What role do loops play in protein structure and function?

Answer 23

Loops enable the peptide chain to form particular structures as opposed to staying extended. They also assist in interaction with other proteins (immunoglobulin).

Question 24

How does Kdrepresent the binding strength of proteins to molelcules?

Answer 24

Kd is the dissociation constant. A smaller Kd represents a higher binding affinity.

Question 25

How can binding specificity (ligand - protein) be achieved?

Answer 25

Through the lock and key complementary model” OR the “induced fit model”.”

Question 26

How does heme enable myoglobin to bind oxygen?

Answer 26

The heme has Fe2+at its center which has a high affinity for O2.

Question 27

Explain the molecular basis of CO poisoning.

Answer 27

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.

Question 28

Why is hemoglobin a good O2transporter?

Answer 28

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.

Question 29

What factors cause protein denaturation?

Answer 29

Heat + Chemicals.

Question 30

Ribonuclease Folding Experiment:What was the main conclusion?Who was the doc?

Answer 30

The primary sequence of a protein determines its structure.Dr. Chris Anfinson

Question 31

What are the two classes of protein chaperones and what are their functions?

Answer 31

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.

Question 32

Why is protein disulfide isomerase sometimes required for folding?

Answer 32

It catalyzes proper protein folding by breaking improper disulfide bonds and forming the correct bonds.

Question 33

Why is protein prolyl isomerase sometimes important for proper protein folding?

Answer 33

It helps catalyze the conversion between trans and cis proline which is often necessary for proper folding.

Question 34

What is the major cause of prion disease, alzheimer’s disease, parkinson’s disease, and amyloidosis?

Answer 34

Protein misfolding.

Question 35

What is the main secondary structure change in prion disease?What is the infectious agent?

Answer 35

Alpha helices to ß pleated sheetsMisfolded proteins

Question 36

What are the three major approaches for purifying proteins?

Answer 36

Gel filtration chromatographyIon exchange chromatographyGel electrophoresis

Question 37

How does gel filtration chromatography separate proteins?

Answer 37

Porous beads accept smaller proteins allowing bigger proteins to be eluted off the column.

Question 38

How does ion exchange chromatography work?

Answer 38

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.

Question 39

How does gel electrophoresis separate proteins

Answer 39

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.