Flashcards in Biochemistry Deck (556)
What is pK(a)?
The pH at which 50% of the HA (acid) has ionised
What is the Henderson-Hasselbalch equation?
pH = pK + log[A-]/[HA]
What is the relationship between pH, pKa and ionisation?
If the pKa is higher than pH, acid is less likely to be ionised
What is critical pH?
pH at which tooth becomes unsaturated with respect to Ca and PO43- allowing hydroxyapatite in enamel to dissolve
Region of pH 5.2-5.5
How does saliva protect teeth from decay?
Produces many buffers (principally bicarbonate) which prevent resting pH falling much lower than pH 6.3
What are the main buffers in saliva and how effective are they?
Proteins - not effective as nearly all charged groups from peptide bonds
Phosphate - good but not in high enough conc. to be effective
Bicarbonate - good
What is the role of bicarbonate in plaque?
Acts to neutralise acid rather than buffer acid
Produces H+ pushing reaction to right producing CO2 and H2O - CO2 released as mouth open system
What conc. does carbonic acid stay at in the mouth and what changes?
pH and [HCO3-] change, bicarbonate varies with flow rate
What must all AAs have?
Amino (NH2), carboxyl (COOH), H and R group
a-carbon is C atom amino and carboxyl groups are attached
What is the role of side chains?
Are the functional groups
Determine structure, function and charge of AAs
Charged, polar or hydrophilic R groups exposed on surface
Non-polar, hydrophobic R groups buried in interior
What confers an AAs' optical activity?
An asymmetric C atom - C attached to 4 different groups
All AAs except GLYCINE (R group = H) are asymmetric
What does being asymmetric mean?
Means compound has spatially distinct but chemically identical isomers that are mirror images of each other (enamtiomers)
Both are optically active (rotate plane polarised light) to right (Dextro) or to left (Levo - majority of AAs)
What is a zwitterion?
A molecule that bears groups of opposite polarity
As amino and carboxylic acid groups readily ionise AAs are dipolar/zwitterions
How does the charge of AAs change with increasing pH?
Low pH - amino protonated, carboxyl normal
pH 7 - amino protonated, carboxyl ionised
High pH - amino normal, carboxyl ionised
Molecules that have both acidic and basic groups
AAs are amphoteric
A negative ions from gain of e-
+ve charged molecule
Name the aliphatic AAs? (Hydrophobic/non-polar)
V - valine
I - isoleucine
G - glycine
A - alanine
L - leucine
Name the aromatic AAs
Phenylalanine (phenol - aromatic)
Tryptophan (Y + T = aromatic)
Tyrosine (Y + T)
Name the sulphur containing AAs
M - methionine
C - cysteine (can from S-S, stabilise proteins)
Name the neutral polar AAs
Amide derivates of Acids
What is the ImIno acid?
Proline - causes bends in polypeptides
Name acidic AAs
COOH R group - ionised at pH 7
Name the basic AAs
Larry is basic
L - lysine
Ar - arginine
His - histidine
LArHis - extra +ve charge
What formula is used to calculate the isoelectric point? How is this calculated for amino acids with 2 carboxyl/amino groups?
pI = (pKa + pKb)/2
a (acidic) = COOH b (basic) = NH2
For 2 carboxyl groups the (pKa1 + pKa2)/2 is used
What is a dalton?
Da is a unit of molecular weight equivalent to 1 H atom
Compares how heavy something is to H
Describe the primary structure of a protein
Unique sequence of AAs held by peptide bonds
Compare structure to find common sequences suggesting members of a multigene family
Describe the secondary structure of proteins
H bonding determines secondary structure either a-helix or B-pleated sheet
Describe boding in and structure of an a-helix
N atom in peptide bond shares H atom with CO group 4 residues upstream
Polypeptide twists around in a spiral, each turn takes 3.6 AAs residues