Amino Acids/Proteins/Peptides Flashcards
Amino Acid Chemical Structure
The smallest protein constituents chemically composed of:
- Amino group (-NH2)
- Carboxylic group (-COOH)
- R group (determines property of amino acid)
- Alpha carbon
- **Note:
1. Amino & carboxylic groups do not have to branch from the same carbon
2. Not all amino acids are coded for by codons/not all of them are incorporated into proteins
3. Modification of some amino acids to others is possible
Proteinogenic Amino Acids
20 Alpha, chiral amino acids coded for by the human genome
***Glycine is the only achiral proteinogenic amino acid
Amino Acid Classes based on their Side Chain Property
- Nonpolar/Nonaromatic
- Polar
- Aromatic
- Negatively Charged
- Positively Charged
Nonpolar Amino Acids
- Glycine - [smallest amino acid -achiral with H R-group]
- Alanine- [CH3]
CH3
- Valine - [CH2-CH3]
CH3
- Leucine-[CH2-CH2-CH3]
CH3
- Isoleucine [CH2-CH2-CH3
- Proline - [Involves Amino group’s Nitrogen in a penta
cycline) - Methionine- [CH2-CH2-S-CH3]
Glaciers in Alaska victoriously Located Isolated Prowlers
Aromatic Amino Acids
- Phenylalanine [with a benzene group-is nonpolar]
- Tyrosine [Phenylalanine w -OH/relatively polar]
- Tryptophan [Double ring-contains N]
People still go to Alaska b/c of aroma of Pine, Timber & and other trees
Polar/NonAromatic Amino Acids
- Serine
- Threonine
* Both are highly polar due to their -OH group** - Asaparagine
- Glutamine
* Both have an amide group that does not become charged upon changes in pH*** - Cysteine
* Contains a thiol group (-SH) that is prone to oxidation****
Negatively Charged Amino Acids
at physiological pH of 7.4*
- Aspartic acid/Aspartate
- Glutamic acid/Glutamate
***These amino acids, unlike asparagine and glutamine that carry amide groups, carry carboxylic groups.
Aspartate and Glutamate are the deprotonated forms of these amino acids
Positively Charged Amino Acids
- Lysine [has primary amino group]
- Arginine [has positive charge delocalized over all 3 nitrogens in its side chain]
- Histadine [Has an aromatic ring with two nitrogen atoms]
Hydrophobic Vs. Hydrophilic Amino Acids
- Hydrophobic AA [Alanine, Valine, leucine, isoleucine, phenylalanine]
- Hydrophilic AA [(Negatively Charged: aspartate & glutamate) + (Positively Charged: lycine, arginine, histadine) + glutamine and aspargine]
The rest of the amino acids [ serine, threonine, cysteine, tyrosine, tryptophan, methionine, glycine & proline] lye somewhere in b/w with regards to their hydrophobic/philic nature
Amino Acid Acid/Base Behavior
Amino acids are amphoteric with 2 pkas for their 2 ionizable species (carboxylic acid & amino group)
-at ph
Buffer Solution
a solution in which the pH does not fluctuate much with acid or base titration
Pka1
Point at which only half of the carboxylic species of an amino acid are deprotonated
pI
Isoelectric point
Point at which all carboxylic species in an amino acid have been deprotonated and point at which amino acids exist as zwitterions or neutral species
- for acidic amino acids, pI can be obtained by averaging the pKa of carboxylic group and pKa of R-group
- for neutral amino acids, pI can be obtained by averaging pKa1 & pKa2
- for basic amino acids, pI can be obtained by averaging pka of amino group and that of the Rgroup.
pKa2
Point at which half of the amino groups of an amino acid are deprotonated
pH>pKa2
pH range in which all amino groups of an amino acid are deprotonated and the overall charge is positive
Titration Curve
Curve that shows the change in pH of a species with addition of base or acid
Elements of a titration curve consist of
pka1 —-nearly flat horizontal line b/c at pka1, [HA]=[A]; therefore solution serves as a buffer with little pH change
pI—–nearly vertical line b/c pH of neutral species is very sensitive to change w/ addition of acid/base.
pka2—-nearly flat horizontal line [see above]
Protonation/Deprotonation
pKa1= [deprotonated species of carboxylic acid]=[protonated species of carboxylic acid]
pI= [entirely deprotonated COOH]=[entirely protonated NH2]
pKa2= [deprotonated species of NH2]=[Protonated species of NH2]
Peptide Constituents/Types
Residues (amino acid subunits); dipeptides; tripeptides; oligopeptides; polypeptides
Peptide Bond
Aka Amide bond is formed through a condensation/dehydration rxn where the nucleophilic amino group of one amino acid attacks the electrophilic carbonyl carbon of another amino acid to connect the N of amino with with C of carbonyl while eliminating a water molecule.
***This reaction creates resonance structures where partial double bond character exists b/w Carbonyl C & O and between Carbonyl C and Amino N due to presence of delocalized electrons in the Carbonyl pi bond and on N as a lone pair.
The resonance Structure limits possibility of free rotation in peptide backbones, giving them very rigid structures.
Peptide bonds are read and drawn from N-Terminus (Free amino end) to (C-Terminus: free carbonyl end)
Peptide Breakdown Mechanism (Enzymes & Reactions)
Hydrolytic enzymes that break down Peptides in our bodies:
- Trypsin (starts cleavage at C-terminus of arginine & lysine)
- Chemotrypsin (starts cleavage at C-terminus of Phenylalanine, Tryptophan and Tyrosine)
Rxn:
- A hydrogen is added to the amino group and a hydroxide is added to the carbonyl group.
4 Levels of Protein Structure
- primary
- secondary
- tertiary
- quaternary
Primary Protein Structure
- Sequence of amino acids coded by DNA genes
- linearly linked with covalent, peptide bonds
- determined using SEQUENCING, a laboratory technique
Secondary Protein Structure
- hydrogen-bonded neighboring primary structures
2. 2 types: [Alpha helices & Beta-Pleated Sheets]
Alpha Helices
- Intramolecularly hydrogen bonded peptide chains that coil clockwise around a central axis
I: Side chains point away from the central axis
II: Hydrogen bonds exist b/w carbonyl oxygen of one
residue and amino hydrogen of another residue 4
residues down the chain - is a keratin component
Contains proline only at its begining due to its bulky structure
