Introduction to Bioinformatics ( Introduction to molecular biology )

Problem Set I

B2

Some antibiotics form rings that stack and create a pore through the membrane . Consider a cyclic

polypeptide antibiotic composed of the four amino acids : serine glycine , threonine , and alanine . If ?diameter ) to be 3 ?diameter (Show work

B10

Many proteins that form channels through membranes pass through the membrane multiple times

For example , rhodopsin , the light receptor protein in the rod cells of the retina , passes through the

membrane seven times as alpha-helical chains . Below is a cartoon showing the side view of part

of a

hypothetical channel-forming protein -- call it rhodopsin . The circles are amino acid residues , the ?-helices participate in the formation of a pore through the

membrane . The pore serves as the means by which protons can pass the membrane in response to

light

Congenital retinitis pigmentosa is a genetic disease leading to night-blindness . The disease exhibits a

variety of symptoms of different severities , which , in many cases , have been linked to specific

mutations in rhodopsin . For each given molecular outcome , choose one or more plausible amino acid

mutations that could account for it . In each case , explain , briefly , why your choice (s ) would lead to

the outcome

c . Overall structure of rhodopsin normal , but

channel does not conduct protons

C4

You isolate a new restriction enzyme EcoRX (an enzyme that cuts DNA at a specific position . You

find that the enzyme cuts the sequence ATGGTATACTGAACGAA once . Like many proteins that

recognize DNA , restriction enzymes generally recognize palindromic sequences

a . Presuming that...