(L9) Module 1 L9 - Molecules in biological environments

Question 1

What is pKa or pKb?

Answer 1

Shows how weak/strong concentration of an acid/base is.

Question 2

Do alcohols ionise?

Answer 2

alcohols do not ionise

Question 3

What’s hydrophobic? What’s hydrophilic? Meaning?

Answer 3

NP = hydrophobic, water hating
polar=hydrophilic, water loving

Question 4

What is a NP molecule?

Answer 4

One which doesn’t have any polar bonds or charged parts.

Question 5

Like dissolves like meaning

Answer 5

Like polarity will disolve like polarity. NP-NP P-P but not NP-P unless specific circumstances.

Question 6

What is hydration?

Answer 6

Polar nature of water enables electrostatic interaction with other charged molecules.

Question 7

Where is H bonding found?

Answer 7

1. solvation by water
2. within proteins
3. within DNA and RNA

Question 8

Requirements of H bonding:

Answer 8

1. H bond donor. 1st molecule has H attatch to F, O, N.
2. H bond acceptor. 2nd molecule has free lone pair of e’s to connect H bond to.

Question 9

What is ionisation status affected by:

Answer 9

1. pH status of the sorrounding aqueous environment
2. propensity of a functional group to ionise i.e the pKa

Question 10

What happens when weak base and conjugate base concentrations are the same?

Answer 10

pH=pKa

Question 11

What does it mean when pH = pKa

Answer 11

Half (50%) of the environment’s functional groups are ionised

Question 12

What does it mean if ph is less than 1 unit below pKa.
(>1 pH unit below pKa)

Answer 12

if (less than) >1 pH unit below pKa ~90% molecules pronated

Question 13

What does it mean if ph is less than 1 unit above pKa.
(>1 pH unit above pKa)

Answer 13

if (less than) >1 pH unit above pKa ~90% molecules depronated.

Question 14

A group is ____ when charged (+ve)

Answer 14

protonated

Question 15

A group is _____ when charged (-ve)

Answer 15

deprotonated

Question 16

What does ionise mean?

Answer 16

To remove electrons

Question 17

What’s approximate pKa of C. acid?

Answer 17

2-3, 2.5

Question 18

What’s approximate pKa of amino?

Answer 18

9-10. 9.5

Question 19

What is Kb or Ka?

Answer 19

Used to differentiate between strong/weak acid/base.
Acids dissociate MORE as Ka INCREASES.

Question 20

What happens when high Ka?

Answer 20

High Ka means acids dissociate more, meaning there’ll be a higher [H3O] concentration so higher pH.

Question 21

What is the buffer equation?

Answer 21

pH = pKa + log([A-] / [HA]) .. for a weak acid

Question 22

What is pH of a strong acid equation?

Answer 22

pH = -log[HA]

Question 23

pH +pOH?

Answer 23

14

Question 24

What is a peptide bond?

Answer 24

c. acid and amine

Question 25

What does creating a peptide bond do to atom

Answer 25

can't be acid/base means there's no pKa on the c.acid or amine side chain decides wether or not the particle is charged anymore.

Question 26

What does net charge of amino acid rely on?

Answer 26

1. The net charge of amino acid's rely on the ionisable side chain groups (R groups) 2. AND the N-, C- termini (at the end of the chain.)

Question 27

What's up with centre of proteins?

Answer 27

they get all weird and freaky. different pH's in centre of proteins

Question 28

How much of the body's processes happen in water?

Answer 28

98%

Question 29

Proper functionality of body requires side chains in certain charges. What controls this?

Answer 29

buffers - minimise variations of pH

Question 30

Why must proteins be positively charged?

Question 31

What's crucial for operation of some enzymes?

Answer 31

Ionisation state of amino acid side chains

Question 32

What is a catalytic triad?

Answer 32

3 amino acids side chains which work together to capitalise the reaction

Question 33

How does water attempt to hydraate NP molecules

Answer 33

Forms hydration shell around the molecule

Question 34

What do NP molecules do in water (aqueous solution/environment)

Answer 34

- NP molecules cluster together - NP regions hide from aqueous environment P parts are around outside NP parts are in centre as far from water as can be

Question 35

Phospholipid layout?

Answer 35

Polar head of phosphate group. NP tails.

Question 36

What is inside membrane for?

Answer 36

Storage of other hydrophobic molecules.

Question 37

What is cholesterol for?

Answer 37

Important part of membrane that assists in the structure and support of it.

Question 38

What is a transmembrane protein?

Answer 38

Has a hydrophobic internal trunk that sits within the cell membrane and a hydrophilic outsode branch which allows for the passage of particles. Hydrophilic particles line the insides.