BCEM 3201 - Foundations

Nonpolar R groups increase in hydrophobicity with..?

increasing number of carbon atoms

pH < pKa

protonated

pH > pKa

deprotonated

At a neutral pH, amino acids exist as..?

zwitterions

zwitterion

can act as acid (proton donor) or base (proton acceptor) with net zero charge

Ampholytes

substances with dual acid-base nature

Protonic equillibria

Titration curve example

worst pH regions for buffering power

endpoints and equivalence points

Isoelectric point (pI)

pH where molecule had zero net charge

pI = (pKa1+pKa2)/2 (except for basic AAs)

pI in acidic AAs

average of pKa1 and pKaR

pI in basic AAs

pKaR and pKa2

Peptide bonds are formed through which reaction?

Condesation reaction (removal of water)

Breaking of peptide bonds is called…?

Hydrolysis

What are the 4 levels of protein structure?

Primary, secondary, tertiary and quarternary

Primary structure

linear amino acid sequence from N to C termini, dictates structure and function of proteins

Secondary structure

Repetitive conformation along short sections of polypeptide

Formed by H-bonding between carbonyl group of one peptide bond and amino group of another

In secondary structure, the irregular arrangement of the polypeptide chain is called a..?

random coil

α-Helix

Stabilized by H-bonding, side chain groups point outwards from helix

Right-handed helix with 3.6 residues (5.4 Å) per turn

Which residues are strong helix formers?

Small hydrophobic residues

Helix breakers

Proline (rotation around N-C bond is impossible, no amino-H for H-bonding)

Glycine (tiny R group supports other conformations)

alpha helix models

β-Sheets

sheet like arrangement of backbone, side chains protrude from sheet alternating in up/down direction

Held together by H-bonding of amide and carbonyl group of peptide bond from opposite strands

β-Sheet orientations

Antiparallel and Parallel

Antiparellel B-sheets are ____ than parallel

stronger, due to possessing linear H-bonds rather than bent

B-Turns

Connecting elements allow polypeptide chain to reverse direction

Stabilized by H-bond from carbonyl oxygen to amide hydrogen three residues down sequence

Which residues are often found in turns?

Proline and Glycine

psi (Ψ) angle around alpha carbon

carbonyl carbon bond (C-Ca)

phi (Φ) angle around alpha carbon

amide nitrogen bond (N-Ca)

Rotation around the pepide bond (C-N) is..?

not permitted, due to resonance structure

Though peptide bonds cannot rotate, they can..?

flip between cis and trans (trans is more stable)

In a fully extended polypeptide, bot phi and psi are…?

180°

Ramachandran plot

Each amino acid has a phi and psi angle, and each secondary structure has its own preferred phi and psi angle

Circular dichroism (CD) spectroscopy

measures secondary structure;

measures difference in absorption between left and right-handed polarized light

Tertiary structure

overall 3D structure of polypeptide chain

interacting AA’s not next to eachother in primary sequence

Tertiary structure determined by..?

Hydrophobic interactions

disulfide bridges

hydrogen bonds

ionic/electrostatic interactions

Structural motifs

specific arrangement of 2 or more secondary structure

Domain

combination of different motifs

Independent folding units in a tertiary structure of a protein

Classes of proteins in tertiary structure

Globular and fibrous proteins

globular proteins

polypeptide chain coiled into compact
spherical shape

soluble in water

mobile within cells

Fibrous proteins

polypeptide chains arranged side by side in long filaments

mechanically strong, water insoluble

Structural and protective Functions

a-Keratin

key structural material of hair

moist heat stretches hair from a-helix to B-sheet

Quarternary structure

organization of subunits in protein with multiple subunits

Subunits held together by non-covalent interactions

protein folding

Driven by need to “bury” hydrophobic AA’s from aqueous environment

Can be spontaneous or occur with help of molecular chaperones

Protein denaturation

destruction of protein conformation (loss of function), disruption of forces that stabilize 2o, 3o and 4o structures

Denaturing agents

acids/bases

metal cations

salts

organic solvents

high temperatures

Tm (melting temperature)

midpoint of temperature range where denaturation occurs

Chaotropic agents

denaturing agent, breaks H-bonds

Protein renaturation