bis 102

midterm 2

Structes

Primary structure

see if angiogenin destroys RNase (meaning there is enzyme activity)

in the x-ray, some x rays get deflected at different angles (dark sopts are where it is hit) comes up with 3d structure were all atoms are

helps determine second and tertiary struct

sequence a protein

stategy 1. generate small fragments

2. look for overlapping sequeces

Tools that Sanger had

trypsin down K and down R

chumotryspin aromatic a.a down

Sanger N-terminal chemistry

DNP is yellow

we need the yellow guy and run through stnadards to find who he is

thin layer crmo togrsahy

arrow is polar solvent (polyamide plate)

plate si never homegenoues

nonpolar for the secon picture

Overlapping sequences

trypsin cuts right hand side

Secondary structure
reverse turn

one h bond holds reversre turn

many times its a proline not 2 though

cant have big guys or repusion

no di sulifde bonds

α-helix

most are right handded because most are made o l amino acids

rgroups on the outside are pointing down

residue 1h bond with residue 4

(-60,-50

# of h bonds=n-4 (n=residues)

avg length 10 aa residues

What causes an α-helix to form?

-glycine too flexible

roline wrong geo no h on N

-/- +/+ repulsion

W-W F-F steric hinderance

seerine mpefer h bond with h20

α-helix

dots are h bonds, in gray is the planes that are formed by the atoms), r groips are yellow

β-pleated sheea

serveral hydrogen bonds (how many depends on length) weaker if they are not in striaght line, both diagrams can make different mixture toghter

a helix stand by itslrf byt b can have family vin diseal

Ramachandran plot

organe is anti b pleated beta sheet

Myoglobin

this protien is sittign in muscles cells

etc is where o becomes water

mb has a tricky taks: how do yuo carry )2 without becoming oxdized

Mb 17000MW

the functional protein has heme ← protroporphin IX +Fe2+

apoprotein with out function

heme

letters are ring systems, iron i bound to N from cov. bonds, 5 covanletn bonds 4 ring and 1 from behind , amino acid is histdine base form

90-degree heme

all bottom arrows are illed

Side view of heme in Hb subunit (α or β

~13+/- on left (salt bridges)

Where are all of these salt bridges?

5 salt brdiges in the central cavity of the molecule at the end of the channel

Other salt bridges of deoxy Hb

CO2

bottom forms new+/ -

-0 to Nh is carbamate

carbmate+ H

binding co2 is alllosteric not binfin whereo2 binds but inderctly affect O2

Wherre do protones binds

where is ther net bindin of H+ at these sites

1 dramtic changes in pka oxy Hb →← deoxy HB

2. more H+ in tissues

Ph= pka +log b/a

7.6=6.2 +log b/a

hence no salt bridge

1. virtually no + charge on H

2. r is too far away coulomb’s Law

for tissue 7.2=7.7+logb/a

a=1/1.316=76%

What environmental factors affect a pKa

2 which xharge is thermo favored

what will lead to the lower energy

3. up to accpmlish thiw

2. which charge is thermo favored

3. pka down to accomplisjed

Cl-

pka up

dr ani

urea know struct, it forms h bonds

top 1% activity 1/105

→ trace amounts mercapteothanol 10gr 4C

bottom 95% actvitvit

red dots are urea, at time zeor no urea so net flow is out

con.1. all info is in the 1

2. 3 is the ost thermo stbale

3. disuslfide bonds prodive strngth but weak bonds are more important

in viv they are syntg as inactive precursors

proinsulin (took pic)

What if all of the RNase A was not completely denatured?

amino acids→synthesice RNase A

Kinetics of protein folding

How then does protein folding occur?

How then does protein folding occur?

no one path to fnial 3 struct

right is order collpased

Several diseases are associated with improper protein folding:

1. protein disulfuide isomerase

   catalyzes disulfide reaction in the ER

2. proline race mase

trans 1000 cis 1

trans 4 csi 1

← proloene racemarse

3. chaperionins proten complexes that allo phobi interactions a second chance

inerior holds 90000mw

red is incorreclty folded

interior loines with bydrophobic residues

bottom atp hydrolysis

lid off then gren ort

protien does not fild faster

What if a protein cannot be repaired?

ubiquitin proteasome