lecture 3 - peptides Flashcards
what is a peptide
string of amino acids
condensation reactions
remove a water from 2 amino acids to form a peptide bond
hydrolysis reactions
add a water to 2 amino acids to break apart a peptide bond
where are N-term and C-term
N-term (amino) is on the left and C-term (carboxyl) is on the right
oligopeptide
several residues
polypeptide
many residues (~50-1000s)
proteins are the product of:
transcription and translation
define oligomer
protein with multiple subunits
homooligomer
have same polypeptides
heterooligomer
have different polypeptides
what non-amino acid components can proteins contain? (4)
- carbohydrates
- metal ions
- organic molecules
- lipids
3 rules for proteins
(1) no branching
(2) no restrictions on sequencing (any aa can follow another aa)
(3) no restrictions on composition ( some proteins are rich in a single aa where others are more uniform)
important properties for function and characterization (list both)
- hydrophobicity
- charge
hydrophobicity
-determined by?
- determined by aa composition
- especially by surface residues that will interact with other molecules (determines function)
charge
-determined by?
- determined by pH and pI
- pH = environment
- pI depends on aa composition
- net charge is important for interactions
why can histone bind dna?
- dna has neg phosphate backbone
- at neutral ph histone has pos charge
- because pI of histone > pH
pH > pK
positively charged
pH < pK
negatively charged
pH = pK
depends on if protein is neutral, negative or positively charged when protonated/deprotonated
charge for positive R groups when protonated/deprotonated
- protonated = positive
- deprotonated = neutral
charge for negative R groups when protonated/deprotonated
- protonated = neutral
- deprotonated = negative
how does environment affect pk values
can effect weak acid equilibrium
