Unit 2: 3

Question 0

Define proteome

Answer 0

the contents of proteins within the cell at any given time

Question 1

What two factors determine protein functions?

Answer 1

1- polymer length
2- amino acid sequence
THese factors specify the unique three dimensional structure that dictates function

Question 2

Alzheimers Disease

Answer 2

Alzheimer’s disease is one of the most serious health threats to the aging population. Approx 10% of people develop AD by age 65. This figure doubles every decade thereafter until there is about a 50% likelihood of disease by age 85-90.

Question 3

What is Alzheimer’s disease characterized by and hot does it manifest in terms of pre- protein form?

Answer 3

AD is characterized by extensive deposits of misfolded proteins (amyloid fibers) in the brain. These fibers are associated with cell death and loss of brain function. The main component of these deposits is a 42 residue fragment from the Alzheimer precursor protein (APP). APP is normally cleaved to produce a 40-residue fragment. In AD the peptide is cleaved in the wrong place. THe extra two amino acids is enough to convert a normal soluble peptide to a toxic “sticky” peptide that build up in the brain. Although this may see like a subtle change even more minor changes lead to equally debilitating diseases.

Question 4

what causes cystic fibrousis?

Answer 4

A single amino acid deletion from the cystic fibrosis transmembrane conductance regulator protein - which is over 1400 amino acids long

Question 5

What are the only polymers that can spontaneously self-assemble?

Answer 5

PROTEINS

Question 6

What does a Ramachandran plot tell us?

Answer 6

tells you allowed and non-allowed phi and psi angle combinations.

• only a small fraction of phi and psi valued are allowed (dark grey in the plots) all structures must satisfy this plot. (backbone regions must lie in the grey regions)
• The limited amount of “space” allows only certain structures to form. Alpha helices and beta sheets, the two main secondary structural elements are found in these grey areas.
• The shapes of these plots arise simply from the way atoms are connected (bond lengths, angles and hard-sphere repulsion)
• Glycine has only a hydrogen for a side chain (very small). Therefore, it experiences fewer repulsion than other amino acids, as indicated by large grey areas on the right plot- regions of polypeptide chain containing Glycine will tend to be more flexible.

Question 7

Define and talk about pKa

Answer 7

pKa is the pH at which half of the ionizing groups are protonated and half are deprotonated

low pKa = binds H+ tightly
High pKa = binds H+ weakly

pH < pKa : lots of H+ in solution forces H+ onto ionizing groups
pH > pKa: low bulk H+ concentration draws off H+

Question 8

Defined dipole

Answer 8

a dipole is a molecule having partial positive and partial negative charges, without possessing a formal net charge