BIOCH200 Lecture Notes - Lecture 7: Ammonia, Hydrogen Bond, Van Der Waals Force
5 May 2018
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What is pKa?
❏Index used to express strength of weak acid.
❏Smaller pKA the stronger the weak acid.
❏When [HA]=[A-] the pKa = pH (exactly half dissociated)
❏pH above pKa acid exists predominantly as A- (deprotonated form)
❏pH below pKA acid predominately as HA (protonated form)
❏The Stronger the acid the stronger the Ka and it can give up H+. A Weaker acid decreases Ka
and takes H+.
❏Therefore increase in Ka = decrease in pKa.
pH
❏Measures acidity of given solution by looking at the [H+]
pH and denaturation
❏Changing pH will cause a change in T(m) → affects protonation state of DNA and the ability to
H-bond.
❏pH > 10 → Some groups deprotonate because it is easier to give H+ up.
❏pH < 3 → some groups are protonated because easier to take H+
❏At pH below 3 the DNA may degrade.
pH and Salt concentrations
❏Affects T(m) → affects protonation state of DNA
❏Change in salt concentrations → Ions shield negative charges on the phosphate backbone
❏Mg 2+ and histones (positively charged proteins) help DNA come together (strands)
❏Low Salt → Decreases T(m) because it destabilizes the double helix → Easier to separate due to
repulsion of the negative charges of the backbone.
❏High Salt → Increases T(m) because it stabilizes the double helix → Neutralization of charge
therefore the strands come together.
Denaturation and Renaturation behaviour of nucleic acids enables Hybridization
❏Denature → occurs at high temperatures, pH above 10 and low salt concentrations.
❏Hybridization (strands come together) → occurs at high salt concentrations, low temperature and
pH of around 7.5.
RNA structure
❏A pairs with U, and is often single stranded, stabilized by hydrogen bonding and base stacking
interactions.
❏Intrastrand base pairing → pairs with bases within the strand.
❏DNA → interstrand base pairings → Pairs with other strands.
❏2’-OH makes RNA unstable due to increase of Hydrogen bonds → more susceptible to alkaline
hydrolysis.
RNA secondary structure
❏Stabilized by Hydrogen bonding base pairs (A/U. G/C and C/U which only occurs in the final 3-D
base pairing) and base stacking (helical right handed structure with hydrophobic/ van der waals
interactions).
❏RNA melting curve does not start at 0, it starts at 1 because it has single stranded regions prior to
“melting”
Introductory Biochemistry: Protein Structure and Function
Proteins have multiple tasks
1) Structure
2) Movement
3) Catalysis
Document Summary
Index used to express strength of weak acid. Smaller pka the stronger the weak acid. When [ha]=[a-] the pka = ph (exactly half dissociated) Ph above pka acid exists predominantly as a- (deprotonated form) Ph below pka acid predominately as ha (protonated form) The stronger the acid the stronger the ka and it can give up h+. A weaker acid decreases ka and takes h+. Therefore increase in ka = decrease in pka. Measures acidity of given solution by looking at the [h+] ph ph and denaturation. Changing ph will cause a change in t(m) affects protonation state of dna and the ability to. Ph > 10 some groups deprotonate because it is easier to give h+ up. Ph < 3 some groups are protonated because easier to take h+ At ph below 3 the dna may degrade. ph and salt concentrations. Affects t(m) affects protonation state of dna.
