Amino acids, peptides, and proteins Flashcards
Atom naming of amino acids
Organic nomencalture: start from one end
Biochemical designation: start from alpha-carbon and go down to R-group
Basics about alpha-amino acids
Most alpha-amino acids are chiral
The alpha-carbon always has 4 substituents - tetrahedral
All (except proline) have an acidic carboxyl group, a basic amino group, and an alpha-hydrogen connected to the alpha-carbon
Each has a unique 4th substituent R group
In glycine, the R group is a hydrogen
Five basic groups of amino acids
Nonpolar, aliphatic
Aromatic
Polar, uncharged
Positively charged
Negatively charged
Nonpolar, aliphatic R groups
What primary characteristic?
Which amino acids beloing to this group?
Side chains are hydrophobic
- Glycine
- Alanine
- Proline
- Valine
- Leucine
- Isoleucine
- Methionine
Aromatic R groups
What primary characteristic?
Which amino acids beloing to this group?
Side chains absorb UV light at 270-280nm
- Phenylalanine
- Tyrosine
- Tryptophan
Polar, uncharged R groups
What primary characteristic?
Which amino acids beloing to this group?
Side chains can form hydrogen bonds - Cysteine can form disulfide bonds
- Serine
- Threonine
- Cysteine
- Asparagine
- Glutamine
Positively charged (basic) R groups
What primary characteristic?
Which amino acids beloing to this group?
Most hydrophilic (along with negative), positive charge at pH 7.0
- Lysine
- Arginine
- Histidine
Negatively charged (acidic) R groups
What primary characteristic?
Which amino acids beloing to this group?
Most hydrophilic (along with positively charged), negative charge at pH 7.0
- Aspartate
- Glutamate
What happens when amino acids are ionized:
At acidic pH?
At neutral pH?
At alkaline pH?
Acidic - Carboxyl group is protonated, amino acid in the cationic form
Neutral - Carboxyl group is deprotonoated, amino group is protonated, net charge is zero –> known as Zwitterions
Alkaline pH - Amino group is neutral -NH2, and the amino acid is in the anionic form
What is a Zwitterion?
An ion with a net charge of zero, occurring at neutral pH, when the carboxyl group is deprotonated and the amino group is protonated
What is the isoelectric point?
The point at which the amino acid carries a net charge of zero
For amino acids without ionizable side chains, pI = pK1 + pK2 / 2
Amino acids with uncharged side chains have 2 pK values, acting as a buffer in 2 different regimes
What are peptides and how are they formed? (Basic)
They are small condensation products of amino acids, small compared to proteins (<10 kDa)
Name all amino acids (and their 3 and 1 letter abbreviations)
Nonpolar aliphatic
- Glycine - Gly - G
- Alanine - Ala - A
- Proline - Pro - P
- Valine - Val - V
- Leucine - Leu - L
- Isoleucine - Ile - I
- Methionine - Met - M
Aromatic
- Phenylalanine - Phe - F
- Tyrosine - Tyr - Y
- Tryptophan - Trp - W
Polar, uncharged
- Serine - Ser - S
- Threonine - Thr - T
- Cysteine - Cys - C
- Asparagine - Asn - N
- Glutamine - Gln - Q
Positively charged
- Lysine - Lys - K
- Histidine - His - H
- Arginine - Arg - R
Negatively charged
- Aspartate - Asp - D
- Glutamate - Glu - E
Functions of peptides
Hormones and pheromones
- Insulin
- Oxytocin
- Sex-peptides
Neuropeptides
- Substance P (pain mediator)
Antibiotics
- Polymyxin B
- Bacitracin
Protection, e.g. toxins
- Amanitin
- Conotoxin
- Chlorotoxin
Protein functions
Cofactors (functional non-amino acid component, metal ions or organic molecules)
Coenzymes (organic cofactors, NAD+)
Prosthetic groups (covalently attached cofactors, heme in myoglobin)
Other modifications
