Amino Acids Flashcards
Glycine (G, gly)
Nonpolar
properties: achiral, good if you need a small side chain tends to destabilize proteins, flexible.
Alanine (A, ala)
Nonpolar
properties: tetris AA (packs nicely in interior of proteins)
Leucine (L, leu)
Nonpolar
properties: tetris AA (packs nicely in interior of proteins)
Isoleucine (I, ile)
Nonpolar
properties: tetris AA (packs nicely in interior of proteins)
Methionine (M, met)
Nonpolar
properties: tetris AA (packs nicely in interior of proteins), S is inert
Tryptophan (W, trp)
Nonpolar
Phenylalanine (F, phe)
Nonpolar
Proline (P, pro)
Nonpolar
properties: imino acid, 15% in cis, stabilizing effect on protein
Serine (S, ser)
Uncharged polar
properties: Hydrogen binding, can be phosphorylated, O-linked glycosylation
Threonine (T, thr)
Uncharged polar
properties: can be phosphorylated, H bonding, )-linked glycosylation
Tyrosine (Y, tyr)
Uncharged polar
properties: H bonding, phosphorylation
Asparagine (N, asn)
Uncharged polar
properties: amide, good for H bonding, N-linking glycosylation
*(think N for everything!)*
Glutamine (Q, gln)
Uncharged polar
properties: good N donor, high concentraion in cells for N donating
*too long for other properties*
Cysteine (Y, cys)
Uncharged polar
properties: sulfhydryl, able to form cross-links via disulfide bonds
disulfide bonds- only occurs in oxidizing environments (typically outside cells) or lysosomes, stabilize the structure, requires specific orientations and distances, can be intrachain or interchain
Glutamic acid (E, glu)
Acidic
pKa: 4
properties: N donor
Aspartic Acid (D, asp)
Acidic
pKa: 4
properties: H bonds, catalyzes reactions, nucleophile
Histidine (H, his)
Basic
pKa: 6
properties: imidazole
Lysine (K, lys)
Basic
pKa: 10
properties: guanidinium, planar, good H bonding
Properties of Amino Acids
Free AA exists in this form
stereochem: L-Configuration in proteins (“CORN” looking from H down to C)
pKa amino group: 9
pKa carboxyl group: 2
Properties of the Peptide Bond
N terminus –> C terminus
2 amino acids comes together, lose a water, and form a C-N bond
The two alpha carbons form a planar backbone
peptide bond is polar (neutralize polarity via H bonds on the insideof proteins)
sp2 hybrid orbitals (π bond)
Configurations of Peptide Bonds
mostly in trans (except for 15% prolines in cis)
backbone in a plane with C alphas in the corners
angles to allow planes to rotate relative to eachother:
- Φ: C alpha (@ point in both planes) to N
- Ψ C alpha (@ point in both planes) to C’
Primary Structure
amino acid sequence, defined by covalent bonds including disulfide bridges (between cysteine)
Secondary Structure
Local arrangements of the peptide backbone, often defined by H-bonds
if repeated phi psi angles:
Alpha helix & beta sheet
if non repeating phi psi angles:
loops & turns
Tertiary Structure
Arrangement of secondary structure elements into compact domain…i.e. a globular unit
Quaternary Structure
arrangement of multiple polypeptide chains in a multisubunit protein (oligomers like hemoglobin)
Alpha Helix
H bonding, polarity, and dimensions
right handed
C=O points to C terminus (dipole)
residues separated by 3 positions for H bonds between backbone atoms
* (bonds are formed bw C=O of residue I to H of residue i+4)
dimensions: 3.6 residues/turn, 5.4 A/turn, 1.5 A rise/ residue
Classification of Helices
can be hyrophobic (buried) or polar (exposed) but most are amphipathic…meaning half polar half hydrophobic
when this protein packs, the nonpolar residues will be buried on the inside and the polar residues will be exposed on the surface of the protein
Beta Sheets
directions and dimensions
come together via H bonding in parallel or antiparallel strands to form sheets
directions:
strands in one plane with side chains above and below the sheet
dimensions: 3.5 A / residue
Beta sheets
characteristics of parallel sheets
hydrophobic residues above and below plane.. so typically buried
wrapping with amphipathic helices from the N terminus to the C terminus called “Beta bends”
Beta sheets
characteristics of anti-parallel sheets
amphipathic (hydrophobic residues above, hydrophilic residues below), so exposed ons urface of proteins
easy to connect N with C (sm amino acid chane, dont have to cross over the plain like in parallel sheets)
Turns and Loops
characteristics
non-repetitive secondary structure
make up 50% of proteins
FUNCTIONAL residues:
occur on surfaces of proteins (exposed to solvents/binding sites)
Motifs
(supersecondary structures)
A: helix-loop-helix
B: B-hairpin
C: Greek Key
D: B-a-B
Average molecular weight of an amino acid residue
110 Da
Fibrous proteins
structural proteins
elongated and LARGE in mass
ex) used in tissue formation (collagen, elastin)
Globular proteins
dynamin functions
spherical
examples) used in transport, immune system, metabolism, catalysis (enzymes), gene expression, muscle contraction
Forces that stabilize proteins
Hyrdrophobic: side chains pack to form core
Van der Waals: weak but numerous
Hydrogen bonds: stabilize and neutralize backbone
Ionic interactions: charged residues (amino + carbox)
Disulfide bridges: cysteine covalently binds two chains together
primarily alpha proteins
can be parallel or perpendicular
primarily B proteins
form a barrel to bury hyrdophobic residues
top: anti-parallel and contiguous
bottom: anti-parallel and two greek keys that join at a face
alpha/beta proteins (most common for proteins)
top: alpha helix are all parallel, beta sheets forming a barrel
bottom: domain 2
