(L9) Module 1 L9 - Molecules in biological environments Flashcards
What is pKa or pKb?
Shows how weak/strong concentration of an acid/base is.
Do alcohols ionise?
alcohols do not ionise
What’s hydrophobic? What’s hydrophilic? Meaning?
NP = hydrophobic, water hating
polar=hydrophilic, water loving
What is a NP molecule?
One which doesn’t have any polar bonds or charged parts.
Like dissolves like meaning
Like polarity will disolve like polarity. NP-NP P-P but not NP-P unless specific circumstances.
What is hydration?
Polar nature of water enables electrostatic interaction with other charged molecules.
Where is H bonding found?
- solvation by water
- within proteins
- within DNA and RNA
Requirements of H bonding:
- H bond donor. 1st molecule has H attatch to F, O, N.
- H bond acceptor. 2nd molecule has free lone pair of e’s to connect H bond to.
What is ionisation status affected by:
- pH status of the sorrounding aqueous environment
- propensity of a functional group to ionise i.e the pKa
What happens when weak base and conjugate base concentrations are the same?
pH=pKa
What does it mean when pH = pKa
Half (50%) of the environment’s functional groups are ionised
What does it mean if ph is less than 1 unit below pKa.
(>1 pH unit below pKa)
if (less than) >1 pH unit below pKa ~90% molecules pronated
What does it mean if ph is less than 1 unit above pKa.
(>1 pH unit above pKa)
if (less than) >1 pH unit above pKa ~90% molecules depronated.
A group is ____ when charged (+ve)
protonated
A group is _____ when charged (-ve)
deprotonated
What does ionise mean?
To remove electrons
What’s approximate pKa of C. acid?
2-3, 2.5
What’s approximate pKa of amino?
9-10. 9.5
What is Kb or Ka?
Used to differentiate between strong/weak acid/base.
Acids dissociate MORE as Ka INCREASES.
What happens when high Ka?
High Ka means acids dissociate more, meaning there’ll be a higher [H3O] concentration so higher pH.
What is the buffer equation?
pH = pKa + log([A-] / [HA]) .. for a weak acid
What is pH of a strong acid equation?
pH = -log[HA]
pH +pOH?
14
What is a peptide bond?
c. acid and amine
What does creating a peptide bond do to atom
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.
What does net charge of amino acid rely on?
- The net charge of amino acid’s rely on the ionisable side chain groups (R groups)
- AND the N-, C- termini (at the end of the chain.)
What’s up with centre of proteins?
they get all weird and freaky. different pH’s in centre of proteins
How much of the body’s processes happen in water?
98%
Proper functionality of body requires side chains in certain charges. What controls this?
buffers - minimise variations of pH
Why must proteins be positively charged?
What’s crucial for operation of some enzymes?
Ionisation state of amino acid side chains
What is a catalytic triad?
3 amino acids side chains which work together to capitalise the reaction
How does water attempt to hydraate NP molecules
Forms hydration shell around the molecule
What do NP molecules do in water (aqueous solution/environment)
- 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
Phospholipid layout?
Polar head of phosphate group.
NP tails.
What is inside membrane for?
Storage of other hydrophobic molecules.
What is cholesterol for?
Important part of membrane that assists in the structure and support of it.
What is a transmembrane protein?
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.
