8- bio targets I

Question 1

what are proteins?

Answer 1

Linear chain of amino acids, connected by Amide bonds (peptide) and very strong linkage, but can be taken apart

Question 2

what are nucleic acids?

Answer 2

Linear chain of nucleotides and connected by Phosphate esters

Question 3

what are polysaccharides?

Answer 3

linear chains of sugars, some are branched. connected by acetals

Question 4

what are lipids?

Answer 4

linear chains of acetate or propionate

Question 5

what do the four modular bio molecules have in common?

Answer 5

they’re all linear

Question 6

what molecule is usually modified in the lipids?

Answer 6

oxygen, the underlying units are usually hidden, you need to do fundamental research to determine if it is an acetate or propionate

Question 7

how many enzyme systems are needed for each biomolecule type and function?

Answer 7

1, as proteins are made by ribosomes and they are also disassembled by proteasome.

Question 8

what do you do once you are done with the molecule, and how is this possible?

Answer 8

you can easily disassemble the complex structures and regenerate parts or re-use, as they are complex structures made using simple molecule components

Question 9

how do drugs produce effects?

Answer 9

by binding to biomolecules, they need a physical interaction

Question 10

what is the most common target, and the less common target?

Answer 10

proteins, and nucleic acid

Question 11

what determines the binding of the 3D shapes of the biomolecules?

Answer 11

the shape and pattern of electron density determines the binding, as there are some parts that are more negative and positive. this is made up of non covalent interactions

Question 12

why do some drugs react chemically with biological molecules?

Answer 12

covalent bonds, not every drug reacts this way (some advantages and big disadvantages)

Question 13

what do amino acids share? and what do they not share?

Answer 13

backbone and stereochemistry, but they differ from sidechain (R) as the chemical properties of the side chains vary

Question 14

what kind of configuration do amino acids have? and where?

Answer 14

S, where the amine and side chain meet

Question 15

explain the characteristics of the non polar side chains, alkyl? list five of them

Answer 15

interact with van der waals. alanine, valine, leucine, isoleucine, methionine. miss meth is very nonpolar because of the sulfur

Question 16

explain the characteristics of the non polar side chains, aromatic? list three of them

Answer 16

tyrosine and tryptophan have possibility to do polar interactions but are typically weak, phenylalanine is third molecule

Question 17

explain the characteristics of the acidic side chains?

Answer 17

aspartic acid and glutamic acid. there’s a nomenclature problem because when they’re in protonated form, the functional groups are acidic- when at pH 7.4, for proteins, the side chains tend to be deprotonated and negatively charged (act as bases)

Question 18

explain the characteristics of the basic side chains? list (3)

Answer 18

the nomenclature issue, at pH 7.4 it becomes positively charged and acts as an acid. lysine arginine, histidine

Question 19

explain the characteristics of the polar side chains? list (5)

Answer 19

they have ability to participate in H bonding, have strong dipole bonding. aspagine, glutamine, serine, cysteine, threonine

Question 20

explain the specialness of glycine and proline

Answer 20

because of the side chain and connectivity, allow protein to adopt special conformations

Question 21

what are proteins and peptides and their relation?

Answer 21

they are long peptides folded into a particular shape- peptides are the series of amino acids connected to each other

Question 22

what is the leaving group in a living system usually?

Answer 22

the tRNA

Question 23

what is the structure of an amine group with another acid?

Answer 23

react the leaving group with an amine from another acid → left with amide bond in between the two structures

Question 24

what happens during the nucleophilic substitution of carboxylates?

Answer 24

Nu donates electrons to the carbonyl carbon of the amino acid
pi bond breaks, going up to the O (O-)
kick off leaving group by reforming pi bond

Question 25

what happens during base catalysis of amide bond formation?

Answer 25

• base catalysis: amino group donates its electrons of the carbonyl carbon which causes the double bond to break → forms the intermediate
• the base removes the proton from the hydrogen because that is the easiest bond to break → forms second intermediate
• the X group leaves, oxygen reforms double bond

Question 26

what happens during acid catalysis of amide bond formation?

Answer 26

• same sequence but reversed protonation step
• base donates a proton
• nucleophile donates a pair of electrons to the carbonyl carbon, breaking the pi bond
• then the base comes backs and steals the proton, donating the electron to the nitrogen (making it a neutral intermediate)
• the X group then leaves, allowing the oxygen to donate its pair of electrons to reform the double bond
• final step is the base comes back to steal a proton making the oxygen neutral charged