7 Protein Structure

• 1. Alpha carbon (chiral except in glycine [R=H])
• 2. Hydrogen
• 3. R group (gives AA its properties)
• 4. Amine group (NH3+ at neutral pH)
• 5. Carboxylate acid group (COO- at neutral pH)

rich in hydrocarbons

hydrophobic interactions are on the INSIDE of a water-soluble protein

have oxygens, nitrogens & ESPECIALLY charged groups

linear chain formed by N & 2 C atoms



proteins adopt particular shapes to maximize favorable atomic interactions to make a shape with a function

the sum of weak, non-covalent (low energy) bonds [1-7 kcal/mol v. covalent forces: > 50 kcal/mol]

• some proteins don’t fold easily on their own & to do so require the assistance of chaperones

• destabilizing amino acid mutations disrupt fold(ing)

• unfolded proteins can aggregate & be improperly trafficked

by looking at its AA sequence & seeing if it’s homologous to other proteins’

the amount of activity per amount of purified protein

• insert a sample of protein in a spectrophotometer calibrated to detect absorbance of the sample at a wavelength of 280nm

• tryptophan & tyrosine absorb UV light at 280 nm

• amount of light produced ~ amount of protein?

secondary protein structure held together via hydrogen bonds that occur between the oxygen of a carbonyl group & the HN of an amino acid that is 4 residues down the polypeptide chain

• protein with charged residues (eg. Lys Lys) adjacent to each other in sequence can’t exist in a helix because the shape of it puts them too near each other

• CAN be AMPHIPATHIC (having both hydrophilic & phobic parts)

Proline: has a five-member ring & is referred to as the “helix breaker”

secondary protein structure held together via hydrogen bonds that occur between backbone atoms within stretches of amino acid residues

• at least 2 (usually more) extended polypeptide chains are involved

• prolines can exist in beta sheets

• adjacent R groups can be 180° apart so it’s a favorable conformation for AAs that have the same charge & exist next to each other in the peptide chain

transmembrane protein of the ATP Binding Cassette family with 5 domains

• activation allows passage of Cl^- ions through the PM via 2 methods (phosphorylation of the R domain & ATP binding + hydrolysis by NBD domains)

• • TM1, TM2: 2 transmembrane domains that are groups of 6 alpha helices that form a chloride channel
• - these helices are amphipathic: hydrophilic on the inside conducive to Cl- & hydrophobic on the outside conducive to placement in the PM

• • NBD1, NBD2: 2 cytoplasmic nucleotide binding domains that bind & hydrolyze ATP
• - a lot of mutations occur in the nucleotide binding domain

• R domain: a regulatory domain modified by phosphorylation

• R domain phosphorylation activates the channel

• ATP hydrolysis by NBD domains changes channel conformation & allows passage of Cl- ions through the PM

a treatment for CF patients with the G551D mutation

• fixes CFTR protein misfolding → allows it to fold properly

• only assists 4-5% of people with CF (75% have the deltaF508 mutation)

• has the smallest amino acid side chain (R = Hydrogen)

• allows for sharp bends in chains & for chains to come close to each other (eg. hairpin bend in p53 protein)

• can be hydrophilic or hydrophobic due to its minimal H side chain

• the CF G551 mutation is one that changes a Glycine to another AA → disrupting CFTR function

1. Elastin

2. Keratin

are relatively insoluble in water & are ELONGATED instead of being compact

• fibrous protein found in elastic tissue (eg. Lungs)
• the major kind of protein found in elastic tissue
• has no regular 2ndary structure
• is relatively water insoluble & elongated

a polypeptide connection involving four Lysines found only in elastin (springy connective tissue protein)

[connects spaghetti noodles that make up elastin]

• tough fibers rich in Cysteine
• contains tightly wound alpha-helices that are difficult to digested
• protein of hair, nails & skin

• disease in which there is increased acidity in the blood & other body tissue

• can result in growth defects, eg. bone formation issues, cognitive problems

• treatment is often ingesting bicarbonate

• causes problems in protein function because if protein isn’t at the right pH, it’s side chains will have wrong charge & may not function

• the negative log of the hydrogen ion concentration
• when [H⁺]=10^-7 M → pH = 7

the pH at which you have 50% of the conjugate acid & 50% of the conjugate base

• when the pH of a solution equals a molecule’s pKa, that solution can best absorb changes in pH (addition of other basic or acidic molecules)

• [pKa is when the concentration of the acid form of a molecule = the concentration of the base form of the same molecule]

when pH ~ pKa

• this is when the pH is most resistant to change upon addition of OH^- or H⁺

• relatively large additions in the amount of base (or acid) produce only small changes in pH → maximal buffering capacity

pH < pKa → acid form of the molecule predominates

pH > pKa → base predominates

[base is form of molecule with fewer hydrogens]

phosphate (pKa ~ 7)

H₂PO₄^- ↔ H⁺ + HPO₄^2-

Carbonic acid/Bicarbonate

H₂CO₃ ↔ H⁺ + HCO₃^-

• titratable groups on the amino acid side chains

• lots of amino groups & carboxyl groups (the AAs cyteine & histidine are especially good buffers)

• pKa of these groups differ depending on the side chain

• proteins have a considerable buffering capacity because the protein concentration in cells & plasma is quite high

• taking deep breaths → ↑ pH (CO₂ is released)

• pulmonary obstruction/holding one’s breath → ↓ pH (CO₂ builds up)

• • upon entering the stomach, Aspirin will be uncharged
• - stomach pH = 1.5
• - pKa of Aspirin = 3.5 [it’s a weak acid]
• - at a pH < pKa → Aspirin will exist in it’s acid form (more protons)
• - because of the acidic environment, Aspirin will be protonated (-COOH) & therefore uncharged

• as an uncharged molecule it can passively cross membranes

• when pH < pKa, molecule exists in its acidic form (RCOOH)

• when pH > pKa, molecule exists in its basic form (RCOO-)

• non-ionized molecules cross cell membranes passively whereas ionized molecules do not, more aspirin will be absorbed in the stomach than in the intestine

the pH at which a compound is electrically neutral, aka the net charge is zero

to find, average the 2 pKa's surrounding the isoelectric species

contains a ring that limits its flexibility & makes it incompatible with alpha helix formation (called the PRO helix breaker)

• both absorb UV light (280 nm) and makes protein detection easy

• tryptophan has a non-polar R group

• tyrosine has a polar R group

can form disulfide bonds between S's at the end of their R group

Cysteine: disulfide bonds are most often found in oxidizing environments such as outside of the cell

arginine, lysine, histidine

aspartate & glutamate (ate = negatively charged)

phenylalanine, tryptophan, and tyrosine (all have benzene rings)

Positively charged, because DNA carries a negative charge