Amino Acids, Peptides and Proteins-Napper Flashcards
Amino Acids
- small biomolecules that are the building blocks for proteins
- all have amino group, carboxyl group, alpha carbon and R group
- cannot be super imposed on themselves, therefore they are enantiomers
Gly, Ala, Pro, Val, Leu, Ile, Met
Nonpolar A.A., no potential for H bonding, found in the middle of peptide chains
F, Y, W
Aromatic A.A. have phenyl rings.
Ser, Thr, Cys, Asn, Gln
Polar AA, will H bond
S, T, Y
Serine, Threonine and Tyrosine all have OH(hydroxyl) groups which allow them to undergo post-translation modification through phosphorylation
Disulfide Bonds
-form through the oxidation of sulfhydryl groups of two cysteine AA, found in keratin
K, R, H
Positively charged AA, Histidine can be both charged and neutral at the bodys pH(about 90% uncharged)
D, E
Negatively charged AA, both have carboxyl COO- as part of side chain
Zwitterion
carrying both a + and - charge, all AA are zwitterions, because of COO- group and NH3+ group
Peptide Bonds
- formed between condensation reactions between carboxyl and amino groups
- rigid and planar with partial double bond characteristics
- almost always in trans configurations
- can accept and donate H bonds
- polar with permanent dipole moment
Amino Acid Chains
- numbered from NH3 end to COO- end
- different AA in chain called residues
How to approximate number of amino acids in a protein
-divide molecular weight by 110 to give approximate number of residues
Native Conformation
- the natural folding state of a protein at physiological conditions. Biological function depends on native conformation.
- native proteins are only marginally stable(stability is defined as their tendency to maintain a native conformation)
- the conformation with the lowest free energy (most stable) is usually the one with the maximum number of weak interactions
Weak interactions of a protein
- hydrogen bonds
- ionic interactions
- Van Der Waals forces
- hydrophobic interactions
Hydrogen Bonds
- 2.0-20.0 kJ/mol in strength
- 0.2 nm in length
- electrostatic interaction between two electronegative atoms
Ionic Interactions
- electrostatic interactions between charged particles(attraction or repulsion)
- strength of these interactions is greatly reduced by water
- important for molecular recognition and specificity of folding rather than stability
Salt Bridge
-ionic interaction between oppositely charged functional groups
Ion Pairs
-a salt bridge buried in hydrophobic interior of a protein. Stronger than surface salt bridge because not disrupted by water molecules.
Van Der Waals
- interactions between permanent and induced dipoles
- short range, low magnitude forces
Protein Denaturation
- the disruption of the native conformation of a protein, with loss of biological activity
- denaturing is cooperative(once some of it starts to go, the rest follows quickly and easily)
- some proteins can be renatured(refolded)
Primary Structure
- sequence of AA in a protein
- tells nothing of three dimensional characeristics
Secondary Structure
- formed mostly from hydrogen bonding
- major examples, alpha helix and beta sheet
- two key determinants 1) favoured conformation of peptide bond 2) optimization of hydrogen bonding potential
Phi Bond
- bond between alpha carbon and N
- on LEFT side of alpha carbon, has + or - 180 rotation
Psi Bond
- bond between alpha carbon and C
- on RIGHT side of alpha carbon, has + or - 180 rotation
Ramachadran Plot
-shows the allowable conformations of peptide chains, along with those actually found in nature
Alpha Helix
- right handed helix
- each carbonyl group hydrogen bonds with an amide group, carbonyl groups point towards the C-terminus
- 3.6 residues per turn, we use 4
- phi and psi bond angles are similar
- rarely see proline or glycine(helix breakers)
- helix has a net dipole, with N-terminus carrying partial positive and C-terminus a partial negative(body sometimes corrects for this, placing net negative AA at N-terminus and positives at C-terminus)
- hydrophobic side chains will bury themselves inside helix structure
Beta Strands
- polypeptide chains that are almost fully extended
- stabilized by hydrogen bonds between COO- and NH3 when paired with adjacent strands(in Beta sheet)
Beta Sheet
- made up of many beta strands
- side chains project above then below the plane, in an alternating fashion
- this could result in one side of beta sheet being hydrophobic, the other hydrophilic, (amphipathic beta sheet)
- can run in parallel or anti parallel with each other
- antiparallel Beta sheets are more stable because the hydrogen bonds are perpendicular to the side chains
Keratin
- principle component of hair, wool, horns, and nails
- primary structure, pseudo 7 repeat (a,b,c,d,e,f,g) where a and d are hydrophobic
- secondary structure, forms right handed helices (a and d hydrophobicity will give helix a hydrophobic streak)
- tertiary, nearly the full length of the protein is helical
- quaternary, two right handed helices of keratin will make a “coiled coil” in a LEFT handed fashion, effectively burying the hydrophobic regions together
- quaternary keratin then forms disulphide bonds, the amount of disulphide bonds decides how tough the keratin will be (horn has more disulphide bonds than hair)
Collagen
- major protein of vertebrates (25%of total protein) responsible for tendons and skin
- primary structure, multiple repeats of Gly-x-y where x is often proline and y is often hydroxyproline
- secondary structure, formation of left handed helices of THREE residues per turn(more like a zig zag look than helix to me)
- tertiary structure, same as keratin, nearly entire thing is helix
- quaternary structure, formation of “coiled coil” with three left handed helices coiling into a right handed helice
- structure of collagen is given when quaternary structures join together through covalent linkages, rather than disulphides, they occur from amino acid residues which undergo post translation modification (hydroxyproline and hydroxylysine)
- more of these cross linkages occur over time which makes connective tissue tougher
Hydroxy proline and lysine
- formed by enzyme hydroxylation reactions that require vitamin c
- needed to stabilize collagen
- no vitamin c leads to scurvy
Silk
- 200,000 psi strength
- primary structure, six residue repeat G,S,G,A,G,A
- fully extended polypeptide strength
- association of strands by hydrogen bonding(FLEXIBLE)
- association of sheets by Van Der Waals and hydrophobic interactions (flexible)
