BIOL 4093 : Study Guide Questions Answered For All 4 Tests
Study questions for Exam #1
1. Define the major non-covalent interactions in biological systems.
• Electrostatic Interactions
o Typically 1-2 kcal/mol
o Coulomb’s Law- E=kq1q2/ (er^2)
o q1, q2 : charges on 2 atoms; r : distance between 2 atoms(m) ; k: Coulomb’s law
constant (Nm^2/C^2); e : dielectric constant (1 Coulomb= 6.242e18 electrons).
o Dielectric constant varies based on medium (i.e. vacuum, air, glass, rubber,
wood, water, etc)
• Hydrogen bonds
o Typically 1-5 kcal/mol
o N, F, O
o Strong hydrogen bonds are arranged in a straight line
• Van der Waals Interactions
o Typically .5-1 kcal/mol
o Dipole-dipole forces
• Hydrophobic Interactions
o Water tends to squeeze hydrophobic molecules together (oil in water)
o They contribute to stabilization of structures of biological molecules
2. Structure, one-letter and three-letter symbols of 20 amino acid residues in proteins. What are the
essential amino acids, aromatic amino acids, basic amino acids, and acidic amino acids?
See flashcards for structures.
• Aliphatic amino acids: 9
• Basic amino acids: 3
• Acidic amino acids: 2
• Acidic amino acids neutralized with carboxaminde group: 2
• Aromatic amino acids: 3
• Structurally unusual amino acid: 1
• Amino acids contain sulfur atom: 2
3. The peptide bond and its arrangement of atoms within bond. Be able to recognize peptide bonds in
polypeptides. What are the ф and ψ angles in polypeptide?
• ф (Phi) is the angle of rotation about the bond between the N and the a-carbon.
• ψ (Psi) is the angle of rotation about the bond between the a-carbon and the carbon of the
C=O group.
• Peptide bond is essentially planar and has double bond characteristics
o Single bond (C-N)= 1.49A, Double Bond (C=N)= 1.27A. Peptide bond is 1.32 A.
4. Four levels of protein structure. Know the dimensions of alpha-helix and beta sheet and able to draw
the alpha-helix wheel. Recognize the anti-parallel and parallel beta sheet in the protein structure.
• Primary structure
o The specific amino acids found in a protein
o Size of protein can be determined-mean molecular weight of AA residues is
about 110 gram/mol
o Primary sequence determines the structure and function of the protein
• Secondary structure
o Alpha Helices
▪ Each amino acide turns about 100 degrees i.e. about 3.6 residues per
turn.
▪ Diameter of helix is about 12 A
▪ Each AA advances about 1.5 A along helical axis.
▪ Right handed helix is more common than left handed helix.
o Beta-sheets
▪ Distance between adjacent AA is about 3.5 A
▪ Beta sheets can be together through H-bonds
▪ Anti-parallel- opposite direction of AA
▪ Parallel- same direction of AA
▪ Mixed beta sheet- both parallel and anti-parallel.
o Turns and Loops
▪ Often on the surface of proteins
▪ Important for protein-protein interaction, catalytic and other functions
• Tertiary structure
o How alpha helixes, beta sheets and turns and loops work together
o Overall structure of polypeptide chain
• Quaternary structure
o Spatial arrangement of subunits and the nature of their interactions
o Homo-, hetero-
o Dimer, trimer, tetramer, etc…
5. Understand the Herdeson-Hasselbach Equation and related calculations for the protonated and de-
protonated forms of amino acids. Calculate the net charge of a given protein at specific pH.
• Henderson-Hasselbach equation= pH=pKa +log{[A-]/[HA]}
• pH = pK1 + log{([Z]+[D])/[H]}
• pH = pK2 + log{[D]/([H]+[Z])}
• H=protonated form; Z=Dipolar form; D=Deprotonated form.
• To find charge of a protein
o pH = pKa + log {[A]/HA+]}
o multiply the charge(z) by number of residues(n) to obtain a total charge
o see homework problem
6. The major strategies for purifying protein. How would you use the anionic and cationic exchange and
gel filtration columns to purify proteins? What is the principle for the protein purification in each case?
• Based on protein solubility
o Change the net charge of proteins
▪ Least soluble at pI (isoelectric point)
▪ pI- a pH point at which the net charge of a protein is zero
o Ionic precipitation
o Organic solvents (ethanol) precipitation
o Nonionic polymers (polyethylene glycol (PEG)) precipitation
o Temperature precipitation
o Use of Ammonium Sulfate to “salt out” specific proteins
• Based on protein charge
o Positive charged AA residues= Arginine, lysine, histidine
o Negatively charged AA residues= Aspartic acid, Glutamatic acid
o Anion Exchange- matrix is positively charged: load, wash and elute out
negatively charged proteins
▪ Popular positively charged matrix options: DEAE-Cellulose
(diethylaminoethyl cellulose) and Mono Q (quaternary ammonium)
o Cation exchange- matrix is negatively charged: load, wash and elute out
positively charged proteins
▪ Popular negatively charged matrix options: Carboxymethyl-cellulose,
phosphor-cellulose, and MonoS(sulfonate)
• Based on protein polarity
Document Summary
Be able to recognize peptide bonds in polypeptides. C=o group: peptide bond is essentially planar and has double bond characteristics, single bond (c-n)= 1. 49a, double bond (c=n)= 1. 27a. Peptide bond is 1. 32 a: four levels of protein structure. Know the dimensions of alpha-helix and beta sheet and able to draw the alpha-helix wheel. Important for protein-protein interaction, catalytic and other functions. Tertiary structure: how alpha helixes, beta sheets and turns and loops work together, overall structure of polypeptide chain. Quaternary structure: spatial arrangement of subunits and the nature of their interactions, homo-, hetero, dimer, trimer, tetramer, etc , understand the herdeson-hasselbach equation and related calculations for the protonated and de- protonated forms of amino acids. Large molecules are left in dialysis bag: gel filtration (size exclusion) column. Chapter 8: six major types of enzymes, oxidoreductases, oxidation-reduction, example lactate dehydrogenase, pyruvate + nadh + h+ Lactate + nad: transferases, group transfer, example- protein kinase, protein-oh + atp.
