MCB Unit 1

Hydrophobic interaction is not considered as a type of electrostatic interaction why?

there are no ions involved and it is the molecules releasing water out which takes little to no energy h-bong, ionic interaction and vanderwaals interaction are all weak non-polar bonds

What drives the folding of proteins and the assembly of membranes?

the hydrophobic effect drives the folding of proteins and assembly of membranes

Why is it important to finely control pH in living systems as well as in biochemical experiments? How may changing pH impact DNA and protein? Why does raising pH disrupt double helical structure of DNA? How does altering pH impact the net charge of a protein?

1. Changes in pH in cells or body fluids can have profound clinical significance and if untreated can be fatal

2. Changing pH may impact DNA and protein bc for DNA it can disrupt the double helix bc i leads to deprotonation of guanine losing a crucial hydrogen bond donor. Changing pH may impact proteins bc it alters their surface charge which can impact their functions.

What are the 3 major buffering systems for biological pH control? What is carbonic anhydrase considered an important enzyme in pH control? How does elimination or retention of CO2 affect pH in our body?

1. the three major buffering systems for biological pH control is the carbonic-acid bicarbonate buffer system, dihydrogen phosphate-hydrogen phosphate system, and proteins

2. Carbonic anhydrase is considered an important enzyme in pH control bc the pH of blood is primarily regulated by this enzyme

3. elimination or retention of CO2 affects the pH in our body. Retention of CO2 shifts the equilibrium from CO2 to H2CO3 to H+ which prevents the loss of H+ from the blood leading to a restoration of blood pH back to normal.

what is the one exception to L-amino acids having s-configuration

Cysteine

Why is it possible to use spectrophotometer to estimate the concentration of proteins in a solution? Would this method work for proteins without Trp and Tyr?

1. bc of the aromatic side chains

2. yes bc other methods can be used to estimate protein concentration

The side chains of proline and glycine are classified as non-polar, but why are they often found on the surface of a globular protein?

the are found on the turn region of a protein, turns are always on the surface of a protein.

what are the essential amino acids

essential amino acids are amino acids that are found in diet

histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine

what are the non essential aminio acids

amino acids that must be made and are able to be synthesized

arginine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, tyrosine

what are the corresponding keto acids to ala, asp, and glu

pyruvate, oxaloacetate, and a-ketoglutate

what is the function of the shikimate pathway?

the function of the shikimate pathway is to syntehsize aromatic amino acids in plants and bacteria

what is post-translational modification? what residues are likely to be phosphorylated into eukaryotes?

post translational modicication→ after incorporated into the proteins the side chains of certain aminio acids can be further chemically modified.

In Eukaryotes it is hydroxyproline, collagen, phosphoresce, and glycosylation

what are the amino acids with ionizable side chains?

aspartate, glutamate, histidine, lysine, arginine, tyrosine, lysine

how does pH affect the ionic state of amino acids?

-at physiological pH amino acids are zwitterions

-at very acidic pH amino acids are cations

-at very basic pH amino acids are anions

what are the characteristic of peptide bond: planar and partial double bond feature

1. shorter bond length

2. no free rotation

3. six atoms on a plane

   planar : peptide bond resonates between single bond and double bond