Study Guide for Midterm 1

Study Guide for Midterm 1 / BIBC 100 / Structural Biochemistry / Key

1. Create a sequence of peptides containing 10 amino acids. Chose any of the 20 amino acid types in any combination. You can choose an amino acid type more than once. Make the peptides

- hydrophobicexample VAFLIMLAAF

- hydrophilicuse S TC N Q Y

- positively chargeduse K R

- negatively chargeuse D E

- neutral (one with a glutamic acid, and one with no charged residues). Use single letter codes/three letter codes (you should make 6 peptides).

2. What molecular properties determine the solubility of polar molecules in water? dipole moments, charges What is the importance of electrostatic interaction in protein secondary structures? hydrogen bonds restrict torsion angel rotation Which type of interaction is mostly involved in the presence of chemical groups containing oxygen, nitrogen, but not carbon atoms? hydrogen bonds Which amino acid residues should you avoid when designing a water soluble peptide? Hydrophobic amino acidsHow many amino acids do you need in a peptide to span a distance of 30 Angstroms in alpha helical conformation? 20 amino acids form 30A alpha helix

3. Transfer RNA contains a high amount of unusual bases. During the synthesis of a tRNA molecule, however, only ATP, GTP, UTP and CTP are used, and are enzymatically modified after transcription. Imagine a cell that is defective in an enzyme that methylates guanine bases in tRNA's. What would the effect be on tRNA-mRNA interaction? phenylalanyl-tRNA has a methylated G at the first anticodon position allowing for a wobble (loose) interaction with the third codon base on the mRNA

4. What stabilizes the supramolecular structure of a phospholipid membrane? Define the interior of the membrane with the dielectric property of the system. What does 'amphipathic' mean, and how does this property relate to the stability of membranes? Could you imagine amphipathic peptides behaving like phospholipids in aqueous solution? hydrophobic effect, dielectric constant 2 in membrane, amphipathic molecules contain both polar and non-polar parts, phospholipids are amphipathic, peptides do not form membranes (bilayers), but need phospholipids to become part of membranes

5. Explain in your words the melting temperature of DNA? Would you expect a melting temperature behavior of tRNA? What makes the base pairing of nucleotides in DNA precise? How does the base pair stacking contribute to the stability of hydrogen bonds in AT and GC pairs? tRNA also shows melting temperatures, hydrogen bonds restrict conformational space

6. Why do proteins in a protein crystal need to be ordered? Why not in protein solutions for NMR analysis? X-ray diffraction occurs at electrons that are at the same lattice within the crystal structure and are getting amplified (disordered crystals do not contain regular patterns because the electron distribution is not regular), NMR measures chemical shift from nearby nuclei (absolute orientation not important)

7. Define the chemical bonds between units in the three major biochemical macromolecules: proteins, nucleic acids, polysaccharides. Write down the generic reaction equation for each type (substrate Û product) and name enzymes involved in the catalysis for both the forth and back reactions. peptide bonds, phosphodiester bonds, glycosidic bonds etc.

8. Draw the water structure around a:

a)Na⁺ ion

b)oil droplet

What major difference in solute-solvent interaction would explain your solutions to problems a and b respectively? hydration shell of ions: water dipole interact with charge/electric field of ion, water molecules do not H-bond with each other; structured water layer of oil drop: water can interact only through low energy Van der Waals binding with solute

9. Cellulose Fibers are composed of many polysaccharide strands of several thousand glucose molecules. Monomeric glucose is water soluble, whereas cellulose is not. Why?all hydrogen bonds are formed within cellulose fiber, glucose solubilised by hydrogen bonds with water molecules

10. Chargaff's rule says that the G+C content of DNA differs from organism to organism. You have extracted the DNA from two bacterial strains ('F' and 'H') which you found in a soil sample from Cuyuamaca State Park. A denaturation experiment shows that strain 'F' has a higher G+C content than strain 'H'. Draw the melting curves for both DNA's on a single figure and indicate them with 'F' and 'H'. If the melting temperature(Tm) of strain 'H' is 76 degrees Celsius, what could you say about the corresponding Tm of strain 'F'? Tm of strain F DNA is higher than 76 deg Celsius

11. Using the single letter code, design a 15 amino acid peptide for each of the following properties(write the sequence only). You can choose only among the following 10 amino acids types(more than once, of course):

Ala, Val, Phe, Ser, Thr, Met, Glu, Asn, Lys, Pro

(a) Sequence of a peptide that shows a bend in the alpha-helix use P

(b) Sequence of a peptide which contains a sulfur group use M

(use A, V, F, M, P)

12. You study the helical structure of a short piece of double stranded nucleic acid, diluted in water buffered and pH 7.4, with sequence:

5' A G G T C T A A C T 3'

3' T C C A G A T T G A 5'

Give the name of the helix type, the number of base pairs per turn, and the length of the particular piece of nucleic acid in Angstroms. B-DNA, 10 bp, 34 Angstrom

13. You are designing a short protein and have two peptides as intermediates.

(read the sequences left to right)

peptide I:M S K F S C I R Epeptide II:M F S T W C D

(a) Identify the non-polar residues in both peptides (circle in above sequences) and give the net charge at physiological pH. (M,F,C,I,W)+1, 0

(b) Which peptide can span a phospholipid membrane(25 Angstroms) in alpha helical form:nonebeta strand form: I

(c) Give all possible overall sequences of the products of covalently linking the two peptides together(minimum of three)

M S K F S C I R E M F S T W C D

M F S T W C D M S K F S C I R E

in addition disulfide bonds