Amino Acids And Proteins Flashcards
What are the strongest bonds?
Covalent bonds
E.g. Peptide bonds, disulfide bonds
What are covalent bonds?
When two atoms share electrons
What are ionic bonds?
Interactions of ions with one a full positive and the other a full negative
E.g. Salt
What is a hydrogen bond?
A dipole-dipole interaction between a partially positive hydrogen atom and partially negative oxygen (FONS and H)
What are van dear walks interactions?
Dipole dipole interactions
These are the weakest electrostatic bonds
What are hydrophobes?
Nonpolar, hydrophobic molecules
E.g. The inside of the plasma membrane
Why do hydrophobes tend to cluster together?
Nonpolar molecules tend to break the hydrogen bonds of water increasing enthalpy. To counteract this they cluster together in order to achieve to lowest possible enthalpy.
Enthalphy = energy state
What do the core of proteins usually contain? (Usually globular proteins)
They have a hydrophobic center
What is the hydropathy index?
Measure of hydrophobicity of amino acids
What is a glycophorin?
An erythrocyte membrane spanning protein
-used as an example for hydropathy plots
What are the four components of an amino acid?
Amino acid
Carbonyl group
Side chain (-R group)
Hydrogen
-all bound to central carbon
What determines the chemical properties of the protein? E.g. Whether is is nonpolar, charged, polar uncharged
The R group
What are the abbreviations for Alanine, Arginine, Asparagine, Aspartic acid?
Ala, A
Arg, R
Asn, N
Asp, D
What are the abbreviations for Cysteine, glutamine, glutamic acid, glycine?
Cys, C
Gln, Q
Glu, E
Gly, G
What are the abbreviations for Histidine, Isoleuine, leucine, lysine?
His, H
Ile, I
Leu, L
Lys, K
What are the abbreviations for Methionine, phenylalanine, proline and serine?
Met, M
Phe, F
Pro, P
Ser, S
What are the abbreviations of Threonine, Tryptophan, Tyrosine, Valine?
Thr, T
Trp, W
Tyr, Y
Val, V
Which are the essential amino acids?
Phe, Val, Trp
Thr, Ile, Met,
His, Arg, Leu, Lys
“PVT TIM HALL”
Which are the branched chain amino acids?
Leucine, isoleucine and valine
“LIV”
Which amino acids are aliphtic (non-aromatic)?
Pro Ala Val Ile Leu "My friend PAVIL is not charismatic (aromatic)"
Which amino acids are only mildly hydrophobic?
Gly
Ala
Pro
“The reason why there’s a GAP inside proteins”
What is special about glycine?
Only mildly hydrophobic but confers flexility in proteins
What is different about Cys?
It has a polar side chain -SH but acts more hydrophobic than glycine or alanine
It is considered a hydrophobic amino acid
Which amino acids are aromatic?
Tyrosine
-hydrophobic
Tryptophan
Phenylalanine
-Phen/Phan indicate an aromatic
How can proteins be differentiated from nucleic acids using UV light?
Proteins absorbs at 280 nm
Nucleic acids absorb at 260
List the order of absorbance for the aromatic compounds.
Most Trp, Tyr, Phe least
Which amino acids are un charge at physiological pH?
Cysteine Asparagine Threonine Serine Glutamine
“My CATS a G”
Which amino acids are basic ?
Lysine
Arginine
Histidine
Which amino acids are negatively charged? (These are acidic)
Aspartate
Glutamate
What are the kinds of secondary protein structures?
Alpha helix
Pleated sheet
Beta turn
What kind of reactions forms a peptide bond?
Condensation (dehydration)
What is a peptide bond?
A covalent, amide bond between the alpha-carbonyl group of one amino acid and the alpha-amino group of another
(“NCC-NCC-NCC” each NCC is an amino acid)
What are the characteristics of a pepdtide bone?
Rigid (no rotation)
Planar. (Flat)
Has dipole (slightly positive on one side and slightly negative on the other side)
What part of the peptide bond holds a dipole?
Carbonyl oxygen holds a negative dipole
Amide nitrogen holds a positive dipole
What is a primary structure of a protein?
The linear sequence of amino acids in the polypeptide chain
In which order is a protein written in?
From the N-terminus to the C-terminus
“NCC-NCC-NCC”
What is a secondary structure?
Where regions of amino acids fol into a limited number of distinct structures
What kind of bonds form secondary structures?
Hydrogen bonds between carbonyl and amide groups in the peptide bond
-the R groups are usually not involved
What is an alpha helix?
A rigid, right handed helix forming a rod-like structure. (3.6 amino acids per turn)
What forms an alpha helix?
H bonding between peptide bonds (4 residues apart)
Which amino acid destabilizes alpha helixes?
Proline because it is bulky and has a charged R group
What amino acid is to involved in alpha helixes because it allows too much flexibility?
Glycine
What is a beta sheet?
When 2 or more peptide chains are arranged parallel or anti parallel to each other
Form a “pleated sheet”
What forms a beta sheet?
Hydrogen bonds between adjacent peptide chain