BIOCHEMISTRY TUTORIAL

how does the hydrophobic effect influence the structures of large molecules

-nonpolar molecules are not easily solubilized in water and aggregate -polar groups are oriented on the surface, interacting with water

the equilibrium constant of ionization of H2O is

1.8 X 10 ^ -14 is KW but the K eq = 1.8 X 10 ^ -16 16!!!! MEMORIZE

each turn of an alpha helix contains ______________ amino acid residues

3.6

solution with an H+ concentration of 1.3 X 10 ^ -4. what is the concentration of OH-

7.7 X 10^-11

which one exhibits intermolecular hydrogen bonding

HF

human proteins contain

L-alpha- amino acids only

first step in 2D gel electrophoresis generates a series of protein bands by isoelectric focusing. In a second step a strip of this gel is turned 90 degrees placed on another gel containing SDS and electric current is again applied. In the second stage

Proteins with similar isoelectric points become further separated according to their molecular weights. isoelectric you will have a strip with pH it can go acidic to basic or vice versa. You put protein sample and will migrate when charge is placed until they reach pI. then separate by size to isolate proteins. An acidic protein has negative charge so it will migrated to the positive side. It will migrate towards the low pH where it is more positive.

which method would be used to check molecular weight of your purified protein with certainty

SDS PAGE, mass spectrometry and analytical SEC

a zwitterion is one which has in aqueous solution

a positive and negative charge

what is the starting point for selection of an IEX matrix for purification of a recombinant protein?

a) Prediction of isoelectric point (pI) from the amino acid sequence

the technique for specific purification of single proteins

affinity chromatography

which would be best to separate protein that binds strongly to a substrate

affinity chromotography -

in the alpha helix, the hydrogen bonds

are roughly parallel to the axis of the helix -hydrogen bonds occur mostly in the backbone but also in some R groups

which statement of acids and bases is true

at pH values above pka, more than 50% of a weak acid will be present in the dissociated state (conjugate base)

since pk values for aspartic acid are 2.0, 3.9, and 10.0, it follows that pI =

avg of 2.0 and 3,9

the term 'proteome" has been used to describe

basically all the proteins in an organisms. the complement of proteins encoded by an organisms DNA

at a pH below pI, an amino acid exists as a

cation

which is true when you have the addition of HCL to a soln with fluoride ions and hydrogen fluoride

concentration of fluoride ions will decrease and HF will increase

peptide bonds are formed by

dehydration

bonds formed between two cysteine residues are called

disulphide bonds

which mutant form of the protein is most likely closest to the normal form (due to conservative substitution) normal protein has glutamine at position 150. Each mutant has amino acid substituion at 150.

glutamine replaced by asparagine -glutamine polar uncharged

the only optically inactive amino acid is

glycine

the alpha helix is formed by the following bond

hydrogen bonds

which is not a form of chemical bonding

hydrogen bonds

which of the following occurs when proteins fold

in ribonucelase radioactivity allow to fold. They will always adopt lowest energy form. More ordered state requires more energy to hold that way. True -all of the above

which is not true about an alpha helix

involves multiple polypeptide chains TRUE -side chains extend radially outward -held together by H bonds

which of these chromatography types are suitable as a "capture" step in the purification of non tagged proteins

ion exchange chromatography

the double bond character of the peptide bond is important because it

limits free rotation about peptide bond. double bond character is stronger than single bond so it limits free rotation and it will not bend. peptide bond itself is super rigid.

a sulphur containing amino acid is

methionine

which mutant form is more likely to put amino acid 150 in the interior of the protein? normal protein has glutamine at position 150. Each mutant has amino acid substituion at 150.

nonpolar because it is in the inside. It has to be larger one because more HC chains means it is nonpolar. Aromatic hains (rings) are super nonpolar. glutamine has been replaced by phenylalanine

primary structure of a protein is formed by

peptide bonds

non-polar amino acids are often found in the trans- membrane domains of integral membrane proteins. name one reason you might find a polar amino acid within the same domain

polar amino acids form H bonds, and can stabilize trans-membrane domain structures.

amino acid that does not form an alpha helix

proline and glycine

the solubulity of most proteins is lowered at high salt concentrations. this process is called

salting out

in proteins, the alpha helix and beta pleated sheet are examples of

secondary structure

by adding SDS during the electrophoresis of proteins, it is possible to

separate proteins exclusively on the basis of molecular weight by giving it a negative charge so all of them are negatively charged SDS only separates by molecular weight

a hydroxyl group is present in the side chain of

serine

an amino acid having a hydrophilic side chain is -glycine -proline -methionine -serine

serine

the amino acid substitution that would most likely cause a change in tertiary structure of a protein is

tertiary- when polypeptide comes together to form subunit. has disulfide bridges and ionic peptide bond- covalent secondary- hydrogen bonds which amino acids can be charged side chains? 7 of them Lysine to Tyrosine because it is the only option that changes the charge. Tyrosine has a polar group but it is still classified as nonpolar aromatic.

in a solution when concentrations of a weak acid and its conjugate base are equal

the -log of H+ and ka are equal

in a mixture of the 5 proteins listed, which would elute second in size-exclusion (gel filtration)

the second largest (145,000)

which compounds would make best buffer at pH 8

tricine (pka = 8.15) because it is closer to the pH

which substances are present in a buffer

weak base or acid and its salt

is primary sequence in amino acids is enough to predict primary and secondary?

yes enough

at pI, an amino acid exists as a

zwitterion