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M2M - Unit 1 > Peptides and Proteins > Flashcards

Flashcards in Peptides and Proteins Deck (39)
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1
Q

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

A

NH3, COO-, H, R groupCORN

2
Q

Name the non-polar, aliphatic amino acids.

A

Glycine, Alanine, Valine, Leucine, Methionine, Isoleucine

3
Q

Name the aromatic amino acids.

A

Tyrosine, Tryptophan, Phenylalanine

4
Q

Name the polar and uncharged amino acids.

A

Threonine, Serine, Cysteine, Proline, Asparagine, Glutamine

5
Q

Name the polar and positively charged amino acids.

A

Histidine, Lysine, Arginine

6
Q

Name the polar and negatively charged amino acids.

A

Aspartate, glutamate

7
Q

What is the role of disulfide bonds within proteins?

A

Stabilization and structure

8
Q

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

A

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

9
Q

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

A

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

10
Q

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

A

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

11
Q

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

A

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

12
Q

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

A

Phosphorylation and dephosphorylation of serine, threonine, and tyrosine.

13
Q

What is ubiquitination?What does ubiquitination signal?

A

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

14
Q

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

A

Calpha-C, C-N, N-Calpha

15
Q

What determines the function of a protein?

A

Its amino acid sequence

16
Q

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

A

genetic diseases

17
Q

What do proteases do?

A

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

18
Q

What physiological functions depend on proteases?

A

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

19
Q

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

A

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

20
Q

What role do hydrogen bonds play in secondary structure formation?

A

They help stabilize alpha helices and beta pleated sheets.

21
Q

What are the two major types of secondary protein structures?

A

Alpha helices, and beta pleated sheets.

22
Q

What does tertiary structure mean?Quaternary structure?

A

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).

23
Q

What role do loops play in protein structure and function?

A

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

24
Q

How does Kdrepresent the binding strength of proteins to molelcules?

A

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

25
Q

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

A

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

26
Q

How does heme enable myoglobin to bind oxygen?

A

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

27
Q

Explain the molecular basis of CO poisoning.

A

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.

28
Q

Why is hemoglobin a good O2transporter?

A

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.

29
Q

What factors cause protein denaturation?

A

Heat + Chemicals.

30
Q

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

A

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

31
Q

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

A

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.

32
Q

Why is protein disulfide isomerase sometimes required for folding?

A

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

33
Q

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

A

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

34
Q

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

A

Protein misfolding.

35
Q

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

A

Alpha helices to ß pleated sheetsMisfolded proteins

36
Q

What are the three major approaches for purifying proteins?

A

Gel filtration chromatographyIon exchange chromatographyGel electrophoresis

37
Q

How does gel filtration chromatography separate proteins?

A

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

38
Q

How does ion exchange chromatography work?

A

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.

39
Q

How does gel electrophoresis separate proteins

A

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.