What is the entity used to make DNA using a DNA template called?
What is the entity used to make RNA using a DNA template called?
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:
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?
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?
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?
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
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?
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?
What are the two forces that destabalize the DNA double helix?
2.) Negative charges on phosphate in backbone
How does heat cause denaturation of DNA?
Thermal energy increases the mobility of molecules, tending to unwind the 2 DNA strands
How do negative charges on the phosphate in the DNA backbone cause DNA denaturation?
The repulsive forces on the negatively charged phosphates on the DNA backbone tend to push the two DNA strands apart
What is hyperchromicity?
The increase in absorbance of a material, such as when double stranded DNA denatures to single stranded DNA.
What is Residual hyperchromicity?
The further increase in absorbance that occurs when single stranded DNA is broken up into nucleotides.
What is meant by "relative absorbance"?
Ratios that apply to any DNA concentration
Why is the Tm of GC-rich DNA higher than the Tm of AT-rich DNA?
Stacking interactions involving G and C are greater than those involving A and T
How does salt stabilize the double helix?
The cations (+ charges) sheild the repulsive forces of the negatively charged phosphates (forces that tend to destabilize the helix)
What are two factors that affect the Tm of DNA?
1.) The amount of GC content
2.) The monovalent cation concentration
What are 2 ways to lower stringency?
Raising salt concentration and Decreasing temperature
What does "Tm" stand for?
Thermal denaturation midpoint - It is the point at which the DNA is half double-stranded and half single-stranded
also referred to as melting temperature
How do you determine the handedness of DNA?
What causes torsional stress?
Overwinding or Underwinding in the primary coil
What can relieve torsional stress due to overwinding?
Formation of supercoils in the opposite handedness of the primary coiling
What can relieve torsional stress due to underwinding?
Formation of supercoils of the same handedness of the primary coiling
What drives supercoiling?
Torsional Stress in the primary coil
What are Topological Isomers (or Topoisomers)?
DNA molecules of identical sequence but different linking numbers
What is a Linking Number?
The total number of times that 2 DNA strands cross over eachother in space
What is the "Twist"?
A property of the primary helix -- the number of times one srand crosses over the other in the primary helix
What is the "Writhe"?
A number that represents the twisting of the axis of the double helix about itself in space (i.e. Supercoiling)
What is the "Ideal Linking Number"?
1.) Lowest Energetic State
3.) No Writhe
4.) Twist = 10 bp/turn
When does Negative Torsional Stress occur?
When the linking number is lower than the ideal linking number
What is a special sequence requirement in order for cruciforms to be formed?
What is a special sequence requirement for the formation of Z-DNA?
Alternation of purines and pyrimadines
What are four ways of attaining optimal twist in torsionally stressed molecules?
4.) Some bp completely unwound
What is the role of Type II Topoisomerases?
They make transient cuts in both strands of DNA and change linking numbers in increments of 2
Can: Introduce negative supercoils (ATP required)
Can: Relax positive or negative supercoils (no ATP required)
What is the role of Type I Topoisomerases?
They make transient cuts in one strand of DNA and change linking numbers in increments of 1
can: relax positive or negative supercoils (no ATP required)
How does Type II Isomerase "resolve" a positive supercoil?
By converting it to a negative supercoil and reducing the linking number by 2
What is a Toroidal Supercoil?
A supercoil that occurs when DNA coils around another object but there is no apparent crossing of the DNA axis over itself as in normal supercoiling.
Left-handed toroidal supercoils are actually right-handed regular supercoils
What are the signs for Twist and Writhe in accordance to Right-handed and Left-handed DNA?
If a torsionally constrained B-form DNA molecule (without supercoils, cruciforms, unpaired regions or Z-DNA) is found to have a right-handed twist of 8 bp per turn, would the molecule be underwound, overwound or relaxed?
As RNA polymerase transcribes DNA, what happens to the DNA ahead of the polymerase and the DNA behind the polymerase?
The DNA ahead of the polymerase becomes overwound and the DNA behind the polymerase becomes underwound
How can E. coli Gyrase (Topoisomerase II) introduce supercoils in relaxed DNA?
By untwisting the two DNA strands using the energy of ATP
What is the difference between Southern Blots, Northern Blots, and Western Blots?
1.) In Southern Blots, the molecule blotted is DNA
2.) In Northern Blots, the molecule blotted is RNA
3.) In Western Blots, proteins are blotted
Which amino acids are most likely to be found in alpha-helices?
Glutamate, Alanine, and Leucine
Which 2 amino acids are least likely to be found in alpha-helices?
Proline and Glycine
What are the three types of domains in transcription factors?
1.) Dimerization Domains (protein-protein interactions)
2.) DNA-binding Domains (protein-DNA interactions)
3.) Activation Domains (protein-protein interactions)
How does GAL4 activate transcription?
By binding to UAS (upstream activating sites) in enhancers
What does it mean when hybrids have "mismatches"?
"Mismatch" means that there are places where sequences are not perfectly complementary between two hybrids
Explain what "hybridiziation with heterologous DNA" means
The process in which DNA-DNA hybrids are made when a strand of DNA from one source hybridizes with a DNA strand from another source
What happens when you lower the temperature in a hybridization reaction?
It makes the hybrids more stable, therefore more forgiving of mismatches
For what situation would it be necessary to use high stringency conditions?
If you want to isolate a specific gene within a gene family
What 3 factors does light absorbance depend on?
1.) The wavelength of light
2.) The characteristics of the absorbing molecules
3.) The concentration of the absorbing molecules