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14 Mar 2019

For a DNA binding protein to recognize and bind a specific sequence of double stranded DNA, such as a regulatory element, where on the DNA double strand will it generally bind? The ribose sugars

The phosphates along the backbone

It will displace the phosphodiester bonds

To the nitrogenous bases via the major or minor groove

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Deanna HettingerLv2

16 Mar 2019

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The recognition of specific DNA sequences by proteins is thoughtto depend on two types of mechanisms: one that involves theformation of hydrogen bonds with specific bases, primarily in themajor groove, and one involving sequence-dependent deformations ofthe DNA helix. By comprehensively analyzing the three-dimensionalstructures of protein-DNA complexes, we show that the binding ofarginines to narrow minor grooves is a widely used mode forprotein-DNA recognition. This readout mechanism exploits thephenomenon that narrow minor grooves strongly enhance the negativeelectrostatic potential of the DNA. The nucleosome core particleoffers a striking example of this effect. Minor groove narrowing isoften associated with the presence of A-tracts, AT-rich sequencesthat exclude the flexible TpA step. These findings suggest that theability to detect local variations in DNA shape and electrostaticpotential is a general mechanism that enables proteins to useinformation in the minor groove, which otherwise offers fewopportunities for the formation of base-specific hydrogen bonds, toachieve DNA binding specificity

1. What three properties of the major groove are advantageous toalpha helix insertion?

2. Which nucleotides are prevalent in narrow minor grooves?

3. Which amino acid tends to bind to the minor groove and howare minor groove width and electrostatic potential correlated?

bronzegerbil134

1. Unlike DNA, RNA contains

deoxyribose

a double strand

phosphates

uracil

Nucleic acid structure

2. In transcription, uracil will bond with:

thymine

cytosine

adenine

guanine

Transcription

3. The first team of scientist to document the structure of DNA was:

Franklin and Wilkins

Watson and Crick

Pauling and Chargoff

None of the above

DNA structure

4. Organelles that synthesize protein are:

lysosomes

ribosomes

endoplasmic reticulum

golgi bodies

5. Most of the time in a cell's life, it's DNA is in the form of:

Chromatin

Chromatids

Replicated chromosomes

Spindle fibers

6. Uracil is a nitrogen base that pairs with adenine. Using this information, one could conclude that uracil is a:

Purine

Pyrimidine

Neither a purine or pyrimidine

Not enough information

7. a nucleotide does not consist of a:

polymerase

5-carbon sugar

phosphate group

nitrogen base

8. The genetic code in DNA of an individual depends on the sequence (order) of:

nucleotides

purines only

phosphates

sugars

9. Before a cell divides, it must duplicate its DNA in a process known as:

translation

transformation

transcription

replication

10. The basic unit (building block) of a protein is a (an):

carbohydrate

amino acid

lipid

hydrogen bond

11. Unlike DNA, RNA contains:

deoxyribose

a double strand

phosphates

uracil

12. The structure of DNA was first documented in:

1945

1953

1956

1962

13. In DNA replication, the new molecules produced are:

of unequal length

both assembled in the same direction

built with purines as the backbone

assembled in opposite directions

DNA replication

14. The "backbone" of DNA is composed of:

ribose and phosphates

deoxyribose and phosphates

ribose and uracil

deoxyribose and thymine

DNA structure

15. RNA differs from DNA in which of the following ways?

RNA is single-stranded

RNA contains ribose

RNA does not contain thymine

All of the above

DNA structure

16. Which of the following is NOT required for the transcription process itself?

RNA polymerase

DNA

uracil-containing nucleotides

ribosomes

skyhamster121

1) What is the difference between the leading strand and the lagging strand in DNA replication? Place the following steps of DNA replication in right chronological order.

1. Primase adds an ribonucleotide primer
2. Initiator proteins bind the origin of replication and helicase breaks hydrogen bonds between complementary bases of double stranded template DNA
3. DNA polymerase III extends by complementary base pairing deoxyribonucleotides to the template strands
4. Ligase phosphodiester bonds the nucleotides to connect okazaki fragments nad connect fragments at the origin and where the "crotches or forks" collide
5. DNA polymerase I removes RNA primer and replaces with Deoxyribonucleotides

2) Given the template DNA and primer sequences below, what bases will be added to the primer as DNA replication proceeds? (The bases should appear in the order that they will be added)

5'-GTCGTCTCCCTTTTTAAAAACCCCCCC-3'
5'-UUUUUAAAAAGGG-3'

3) Given the DNA sequence below, what could be a primer sequence used in its replication?
5'-CGTACGGCCCCAAAATTGCTACTCTGCTG-3'