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What is the entity used to make DNA using a DNA template called?

DNA polymerase


What is the entity used to make RNA using a DNA template called?

RNA polymerase


What is the entity responsible for covalently linking amino acids to make proteins called?



If the R group of an amino acid is a hydrocarbon, what will the amino acid will be classified as?



Name the three neutral amino acids with R groups that contain hydroxyls (OH)

Serine, Threonine, Tyrosine


If Cysteine is involved in cross-linking in proteins, what would happen to the sulfhydryl groups?

They would be oxidized


When a peptide bond is formed, what is formed as a by-product?



The enzyme that is used in the laboratory to make cDNA by copying RNA is called:

Reverse Transcriptase


If you wanted to follow the incorporation of radioactive phosphate (32P) from a nucleotide into a nucleic acid, at which position would you want to have the labeled phosphate on the free nucleotides?

5' alpha


If you wanted to follow the incorporation of radioactive phosphate (32P) from ATP into glucose to make glucose phosphate, at which position would you want to have the labeled phosphate on the ATP?

5' gamma


Why are zinc fingers important in cellular regulation?

Because they are a structural motif in many DNA-binding proteins


Which type of interaction is likely to be the most important determinant of equilibrium constant in the interaction of two biological macromolecules?

Hydrophobic Interactions


According to the Law of Mass Action, what happens if the concentration of molecules increases?

The ratio of combined to uncombined entities increases


What are hydropathy plots used to predict?

They are used to predict the tertiary structure of proteins and to identfy functional homologs.

Bars above 0 are interior regions of the protein

Bars below 0 are exterior regions of the protein


Which domain of a transcription factor interacts with an enhancer?

DNA binding domain


What is the role of restriction enzymes?

To cut DNA at specific bp sequence


How does the lexA/GAL4 domain swap protein activate transcription?

By binding to the lexA operator in enhancers


What are the four major secondary structures?

1.) alpha helix

2.) beta-sheet

3.) beta-turn

4.) random coil


Which type of bonds are used to stablilize beta-sheets?

Hydrogen bonds between C=O and NH


Which amino acid is least likely to be found in alpha-helices?

Proline -- it cannot form hydrogen bonds due to ring structure


What are the Chou-Fasman Rules used for?

Predicting (not determining) secondary structure in proteins


What is a reason why you might expect a hydrophobic portion of a protein to be on the outside of a protein rather than the inside?

1.) If a portion of the protein is involved in an interaction with another macromolecule through hydrophobic interactions (i.e. Quaternary structure -- protein-protein interactions)

2.) If a protein spans a membrane


What is Homology Modeling?

Constructing a model of a protein based on its known amino acid sequence and known 3D sequence of a related protein with similar function


What are the 4 major types of weak chemical interactions?

1.) Van Der Waals forces (1 kcal/mole)

2.) Hydrogen bonds (1-7 kcal/mole)

3.) Ionic bonds (5-10 kcal/mole)

4.) Hydrophobic interactions (20-25 kcal/mole)


What types of weak chemical interactions are responsible for Recognition and Specificity?

Van Der Waals, Hydrogen bonds, and Ionic bonds


What type of weak chemical interaction is the driving force, or the most important consideration in the overall strength of interaction between 2 macromolecules?

Hydrophobic Interaction


What are 4 structural features of DNA?

1.) Plectonemic or Plexonemic

2.) Anti-parallel Arrangement

3.) Hydrogen Bonding

4.) Base Stacking


Why is G/C rich DNA more stable than A/T rich DNA?

1.) Hydrophobic stacking interactions

2.) There are 3 H-bonds between G/C pairs and only 2 H-bonds between A/T pairs


Which form of DNA is the most common?

B-form DNA


What are the two forces that destabalize the DNA double helix?

1.) Heat

2.) Negative charges on phosphate in backbone