5b

Question 1

what type of side chains are there

Answer 1

• nonpolar
• polar uncharged
• acidic (cooh)
• basic ( nh2)

Question 2

what are the side chain interactions responsible for

Answer 2

theyre responsible for the folding of polypeptides to give the complex’s 3d structure needed for their biological activity.

Question 3

name the 4 main different type of side r chain interactions we need to know

Answer 3

• ionic
• hydrogen bonds
• van der waals (dipoles + hydrophobic)
• disulfide bridges ( covalent )

Question 4

put these interactions in order of strength
- h bonding
- ionic
- dipole dipole
- london dispersion

Answer 4

• ionic
• hydrogen
• dipole dipole
• London dispersion

Question 5

interactions in a solvent medium involve what

Answer 5

they involve polarisation effects

Question 6

describe an ionic interaction

Answer 6

• its between two charged groups: cation and anion
• u draw the charge between the charges,, not the acc element
• ## strength depends on the distance between the ions and the medium theyre in

Question 7

whats the F and Ue in ionic interactions and what the equation and stuff in it

Answer 7

• F = force!!!
  Q1 Q2 / 4nEoEr r^2

where q is the charge of the ions,, n is pi, Eo is vaccum constant, Er is the solvents dielectric constant and r is the distance between them

• Ue = potential energy
  Q1Q2 / 4nEoEr r

Question 8

what does a negative potential energ ymean in terms of ions

Answer 8

it means there is attractive forces present!!!

if its negative that means they attract but when Ue is positive that means they repel !!!

if they repel the potential energy will be negative and that means that like charges are getting closer

Question 9

are ionic forces short o long ranger interactions

Answer 9

theyre short range interactions

Question 10

what are ionic forces strongly influenced by

Answer 10

theyre strongly influences by the solvent they are in and its dielectric constant (its relative permittivity) ,, Er.

aka how polar they are.

Question 11

will ionic interactions between the 2 same things be equal in all solvents

Answer 11

nope

their ionic interaction will differ majorly depending on what solvent theyre in!!!

Question 12

average ionic interaction strength

Answer 12

20 kjmol-1

Question 13

Er of the middle of a protein and Er of water

Answer 13

Er of the middle of a protein = 3-5

Er of water = 80

Question 14

briefly,, whats a salt bridge

Answer 14

• ionic interaction x hydrogen bonding interaction

Question 15

whats special about hydrogen bonding and therefore ionic interaction

Answer 15

• hydrogen bonds are directional meaning the atoms, the h and the h acceptor must be linear!!! aka in a straight line

Question 16

salt bridge interactions must be less that what distance apart

Answer 16

they need to be less that 4A apart!!

Question 17

are salt bridges stronger than just electrostatic interactions

Answer 17

yes bc salt bridges are the combo of an ionic interaction and hydrogen bonding

Question 18

name the 3 types of molecular dipole interactions

Answer 18

• permanent
• induced
• instantaneous

Question 19

describe and give an example of a permanent dipole

Answer 19

• when the e- in a bond are attracted to one of the atoms bc they have an electronegativity difference.
  HCl

Question 20

describe a induced dipole

Answer 20

• where a permanent dipole interacts with a polarisable molecule and induces a temporary dipole.

aka a molecule with an electronegativity difference affects a molecule that doesnt bc the e- move to align with the one with the permanent dipole.

Question 21

describe an instantaneous dipole

Answer 21

this is the dipole that occurs due to e- being mobile and moving.

their movement allows them to be more concentrated on one side of the molecule.

all based on chance an timing

Question 22

describe an ion permanent dipole interaction
- stronger /// weaker than ion ion interaction.

• strength of bond
• range interaction
• what is it responsible for

Answer 22

• its weaker than an ion ion interaction
• bond strength is around 15kjmol-1
• range ineteraction is lower than that of ion ion interaxctions. 1/r^2 meaning a small increase in distance causes the strngth of the bond to decrease by a lot.
• its responsible for solvation + dissolution of molecules. aka salt in water
  u have the Cl- anions surrounded by the H’s in water. and u have the Na+ cation surrounded by the O of the water.

ion being the Na and Cl and permanent dipole being the water bc O is more electronegative than H.

Question 23

what is a dipole dipole interaction

Answer 23

an interaction between molecules that both have dipoles

Question 24

what i the strength of a dipole dipole interaction similar to

Answer 24

its similar to hydrogen bonding strength : 4-12 kjmol-1

Question 25

dipole dipole interactions are anisotropic,, what does that mean

Answer 25

it means the interction depends on the orientation of the molecule

Question 26

what are the 3 types of dipole dipole interaction

Answer 26

permanent permanent permanent induced induced induced

Question 27

describe permanent permanent dipole interactions and what things they can occur between

Answer 27

- an interaction between molecules who both have a dipole - u can see it between two carbonyls: the o from one and the c of another. when theyre in the head tail orientation - they must be less than 5A apart in a medium of Er 4 ( aka in a protein)

Question 28

describe the perm perm dipole ditance thing

Answer 28

its 1/r^3 meaning a tiny increase in dif=stance significantly reduces the strength of the bond

Question 29

whats the dipole moment of a carbonyl in debye units

Answer 29

its around 1.3 debye units

Question 30

what do hydrogen bonds form between

Answer 30

- N O F H - electronegative elements - H donor = what provides the H bond with the H - H acceptor = what has the electronegative atom

Question 31

hydrogen bonds contain what type pf character

Answer 31

they contain a bit of covalent character the bond isnt as polarised as an ionic bond.

Question 32

whats special about the h bonds

Answer 32

everythign needs to be linearrrrrrrr aka i na straight line

Question 33

diff WDW interactions

Answer 33

- dipole dipole - dipole and induced dipole - instantaneous

Question 34

describe an induced dipole

Answer 34

- e- wizz around and cause polarisation - these can change the e- density in other compounds as the e- will align to form attractive interactions ( aka complementary dipoles)

Question 35

are induced dipoles strong or weak

Answer 35

theyre weak bc they depend on the random movement of e-!! theyr eimportant tho bc theyres normally loads of them so their strength increases

Question 36

induced dipoles // vdw interactions are seen where

Answer 36

in hydrocarbon chains theyre maxamised when theyre closer together

Question 37

as induced dipoles are seen in hydrocarbon chainsa dn theyre stronger when theyre closer together,, will a branched or linear hydrocarbon be srtronger

Answer 37

the linear oneeee!! bc its more compact and therefore has a larger boiling point than the branched one. the longer the chain,, the larger the boiling point.

Question 38

where are VDW interactions seen

Answer 38

theyre seen in hydrocarbon // hydrophobic side R chains

Question 39

whats the hydrophobic effect

Answer 39

when the entropy of water is maximised when VDW interactions occur between side chains between different amino acids. bc normally there would be an organised shell of water around the amino acids,, forming hydrogen bonds with other water molecules around it,, but when the amin oacids form the VDW intercation and get closer they push the water molecules in that area apart, freeing them and increasing the entropy of the water.

Question 40

what part of the protein is hydrophobic and hydrophilic

Answer 40

the inside of a proetin is hydrophobic,,, Er = 3ish its surface is hydrophilic tho!!

Question 41

what largely determines the 3d shape of a protein

Answer 41

the vdw and hydrophobic interactions largely determine he 3d structure of proteins

Question 42

whats a disulphide bridge

Answer 42

a covalent interaction between 2 sulphides u have 2 thiols and they undergo oxidation to form a disulphide bond + 2H+ and 2e-. the amin oacids are covalently koined and so theyre super strong and have a BDE of 250kjmol-1 this is still 40% weaker than CC or CH bonds tho

Question 43

covalent bonds:

Answer 43

disulphide

Question 44

H bonds

Answer 44

H shared between electronegative atoms

Question 45

electrostatic forces

Answer 45

attraction between opposite charges

Question 46

VDW

Answer 46

fluctuation in e- clouds around molecules,, oppositely polarised neighbouring atoms

Question 47

hydrophobic forces

Answer 47

hydrophobic groupsninteract with eachother to exclude water moelcules.