Mol Bio Quiz 1

What is the structure of an amino acid?

H3N+CaHC(=O)O-

What amino acids have a negative charge?

Aspartic acid, glutamic acid

What amino acids have a positive charge?

Arginine, lysine, histidine

What amino acids are aromatic?

Tryptophan, phenylalanine, tyrosine

Why is the peptide bond stronger than other bonds in a protein?

The O=C-N has resonance giving it more strength than a single bond

What force holds alpha helices and beta sheets together?

Hydrogen bonds

What force mediates many protein-protein interactions?

Van der Waals

What does a ramachandran plot show?

The OBSERVED (phi, psi) dihedral angles of the residue

What amino acid has the most restrained ramachandran plot?

Proline

What amino acid covers the most of the ramachandran plot?

Glycine

In an alpha helix, where are the R groups pointed?

Out from the core helix

The lower the pKa…

The more acidic

Given the pKa of a molecule and the pH, what criteria is used to tell if the molecule will be protonated?

If the pH (inversely related to H+ concentration) is lower than the pKa (desire for molecule to loose its H), it will be protonated

What amino acid has a pKa close to biological conditions?

Histidine

What is a nucleophile?

An atom capable of sharing its electrons (typically electronegative)W

What is an electrophile?

An atom receiving the electrons from the nucleophile

What is the approximate wavelength of an X-ray?

1 angstrom

What is the theoretical limit of precision for X-ray crystallography?

About 1 angstrom

What is resolution?

The idea that two objects close to one another can be distinguished

On the collection film, what points represent the highest resolution?

The points on the outermost edge, these are atoms close to one another that have been scattered very far apart

Describe Anfinsen’s experiment

Ribonuclease is purified, then denatured and cystine bonds are broken. The protein is tested: when refolded and cysteine bonds are remade, or when cysteine bonds are remade and refolded, does the protein stil function?

What was the conclusion of Anfinsen’s experiment?

The instructions for protein folding are encoded in the amino acid sequence

What was Levinthal’s experiment?

If proteins sampled even just a small number of the possible conformations available to them, it would take many orders of magnitude too long to fild

What is the conclusion of Levinthal’s experiment?

Proteins do not sample all possible conformations while folding, but they fold along an ordered path

Is it true that a protein (artificially) split into two proteins could come together and reconstitute the same function?

Yes

What is special about alpha lytic protease?

Its amino acid sequence includes a folding enzyme to help the protein overcome an energy barrier in its own folding

What structure is an enzyme designed to bind?

The transition state in the reaction it is catalyzing

What do enzymes do, and how?

Lower the activation energy of a specific reaction by stabilizing the transition state via their shapes and charges

What is one strategy to inhibit an enzyme?

Mimicking the transition state of the reaction with a stable molecule

Enzymes catalyze the reaction, what might be some reasons it would favor one direction over another?

Product(s) may not bind as favorably

One or more products may be degraded as soon as they are produced

What enzyme catalyzes DNA growth?

DNA polymerase

How is the transition state stabilized in DNA polymerase?

5 oxygen atoms

What do the two magnesium atoms do?

One deprotonates the 3’ OH of the growing polynucleotide strand and stabilizes the phosphate O negative charge

The other stabilizes the other two phosphate groups making them a better leaving group

How are the magnesium atoms stabilized in DNA polymerase?

Two aspartic acids