could you explain to me in detail how to work out these problem! thanks Shown below is the structure of Drug 1, that binds to the E. coli ribosome. Indicate whether each circled regioncould possibly form ionic bonds, hydrogen bonds, or hydrophobic interactions with another molecule by filling outthe table below. Fill in the table with "yes" if that type of bond is possible, "no" if it is not.a)Part(0)(11)(iii)(iv)Could this part formionic bondsH₂Asn 231 )Ribosome from:E. coliSpeciesSpeciesLys 101HNA representation of the drug bound to the E. coli ribosome is shown below. Three amino acids of the ribosomethat are important for binding are shown. If this drug can bind to different bacterial ribosomes, it may be useful asan antibiotic. The ability of this drug to bind to the ribosomes of two different species is examined. The drug bindsto the ribosome of species 1, but does not bind to the ribosome of species 2.H(CH, (in))RibosomeHN101LysGluArgCould this part formhydrogen bondsCH, (m)231AsnSerGluCHCH (iv)CH₂Amino acid found atCH₂H312CH (iv)CH₂LeuVallleCH,b) The table shows the differences between the ribosomes. Given this information, complete the table indicatingwhich would be from species 1 (drug binds) and which would be from species 2 (drug does not bind).Could this part be involved in ahydrophobic interactionLeu 312For your information:Amino acidlleValAsnGluLysSerLeuArgSide chainCHCH₂CH₂CH₂CHCH₂CH₂CH,CONH,CH₂CH₂COO™(CH,),NH,+CH₂OHCH₂CHCH₂CH₂(CH2)NHC(NH2)*c) What specific amino acid or amino acids prevents the ribosome from species 2 from binding Drug 1?d) In terms of the specific non-covalent interactions, explain why the ribosome from species 2 will NOT bind Drug1, but the ribosomes from E. coli and species 1 will. This is the structure of an antibodyantigen-binding siteH₂NH₂NHOOClight chainS-Sheavy chain.hingeregionsHOOCCOOHCOOHantigen-binding siteNH₂light chainheavy chainNH₂Total MW=150,0004 polypeptides:• 2 Light Chains, MW = 25,000 daltons(each)• 2 Heavy Chains, MW = 50,000daltons (each)The 4 polypeptides are held togetherby disulfide bondsQuestions:1. Draw a picture of the lane of an SDS-PAGE gel if you ran a sample of the antibodyprotein after treating with DTT. Include mw standards of 150 kd, 100 kd, 50 kd, and25 kd.2. Draw a picture of the lane of an SDS-PAGE gel if you ran a sample of the antibodyprotein after treating without DTT. Include mw standards of 150 kd, 100 kd, 50 kd,and 25 kd.

Answered: Shown below is the structure of Drug 1,…

Biochemistry

9th Edition

ISBN:9781319114671

Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Publisher:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Chapter1: Biochemistry: An Evolving Science

Section: Chapter Questions

Problem 1P

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Related questions

Question

could you explain to me in detail how to work out these problem! thanks

Shown below is the structure of Drug 1, that binds to the E. coli ribosome. Indicate whether each circled region
could possibly form ionic bonds, hydrogen bonds, or hydrophobic interactions with another molecule by filling out
the table below. Fill in the table with "yes" if that type of bond is possible, "no" if it is not.
a)
Part
(0)
(11)
(iii)
(iv)
Could this part form
ionic bonds
H₂
Asn 231 )
Ribosome from:
E. coli
Species
Species
Lys 101
HN
A representation of the drug bound to the E. coli ribosome is shown below. Three amino acids of the ribosome
that are important for binding are shown. If this drug can bind to different bacterial ribosomes, it may be useful as
an antibiotic. The ability of this drug to bind to the ribosomes of two different species is examined. The drug binds
to the ribosome of species 1, but does not bind to the ribosome of species 2.
H
(CH, (in))
Ribosome
HN
101
Lys
Glu
Arg
Could this part form
hydrogen bonds
CH, (m)
231
Asn
Ser
Glu
CH
CH (iv)
CH₂
Amino acid found at
CH₂
H
312
CH (iv)
CH₂
Leu
Val
lle
CH,
b) The table shows the differences between the ribosomes. Given this information, complete the table indicating
which would be from species 1 (drug binds) and which would be from species 2 (drug does not bind).
Could this part be involved in a
hydrophobic interaction
Leu 312
For your information:
Amino acid
lle
Val
Asn
Glu
Lys
Ser
Leu
Arg
Side chain
CHCH₂CH₂CH₂
CHCH₂CH₂
CH,CONH,
CH₂CH₂COO™
(CH,),NH,+
CH₂OH
CH₂CHCH₂CH₂
(CH2)NHC(NH2)*
c) What specific amino acid or amino acids prevents the ribosome from species 2 from binding Drug 1?
d) In terms of the specific non-covalent interactions, explain why the ribosome from species 2 will NOT bind Drug
1, but the ribosomes from E. coli and species 1 will.

This is the structure of an antibody
antigen-
binding site
H₂N
H₂N
HOOC
light chain
S-S
heavy chain.
hinge
regions
HOOC
COOH
COOH
antigen-
binding site
NH₂
light chain
heavy chain
NH₂
Total MW=150,000
4 polypeptides:
• 2 Light Chains, MW = 25,000 daltons
(each)
• 2 Heavy Chains, MW = 50,000
daltons (each)
The 4 polypeptides are held together
by disulfide bonds
Questions:
1. Draw a picture of the lane of an SDS-PAGE gel if you ran a sample of the antibody
protein after treating with DTT. Include mw standards of 150 kd, 100 kd, 50 kd, and
25 kd.
2. Draw a picture of the lane of an SDS-PAGE gel if you ran a sample of the antibody
protein after treating without DTT. Include mw standards of 150 kd, 100 kd, 50 kd,
and 25 kd.

Expert Solution

Step 1

Since, you have asked multiple questions from multiple concepts, we have answered all 4 subparts of first question. Kindly post the other questions separately to get it answered. Thanks.

Amino acids can interact with drugs in several ways. Some of the most common types of interactions include:

Hydrogen bonding: This type of interaction occurs when the positively charged hydrogen atoms on an amino acid bond with the negatively charged atoms of a drug molecule.
Ion pairing: This interaction occurs when the positively charged amino acid residues form an ionic bond with the negatively charged drug molecules.
Hydrophobic interaction: This interaction occurs between hydrophobic amino acid residues and hydrophobic regions of drug molecules, which can cause the drug to become trapped within the protein structure.
Van der Waals interaction: This interaction occurs between the nonpolar regions of amino acids and drugs and is driven by the attraction between the temporary dipoles in the molecule.
Covalent bonding: This interaction occurs when a covalent bond is formed between the drug molecule and the amino acid residue, typically through a reaction between the drug molecule's electrophilic center and the nucleophilic center of the amino acid residue.