Biochemistry Chapter 2

In the structure of DNA, the bases in complementary strands interact through ___, while the bases within one strand interact through ___; lastly, phosphodiester groups interact with magnesium ions through ___

hydrogen bonds; pi-pi interactions; ionic interactions

What is the correct name of the structure?

• 2-deoxythymidine triphosphate

• phosphothymidylate

• 2-deoxythyminidine

• thymidylate triphosphate

2-deoxythymidine triphosphate

Which of the following statements about DNA and RNA is TRUE?

• DNA is synthesized in the 5’ to 3’ direction, whereas RNA is synthesized in the 3’ to 5’ direction

• DNA has a major groove whereas RNA has a minor groove

• The nitrogenous bases that are commonly found in both DNA and RNA are adenine, guanine, and cytosine

• DNA forms a double-stranded helical structure that contains base pairs whereas RNA is single stranded and does not form base pairs or adopt a double helical conformation

The nitrogenous bases that are commonly found in both DNA and RNA are adenine, guanine, and cytosine

Which of the following statements is TRUE regarding phosphodiester bonds that link adjacent nucleotides in both RNA and DNA?

• Phosphodiester bonds join the 3’ hydroxyl of one nucleotide to the 5’ hydroxyl of the next

• Phosphodiester bonds are uncharged at pH 7.0

• Phosphodiester bonds always link G with C and A with either T or U

• Phosphodiester bonds are positively charged

Phosphodiester bonds join the 3’ hydroxyl of one nucleotide to the 5’ hydroxyl of the next

Nucleotides play a central role in living organisms because ___

• they mediate transport of energy within the cell

• they are involved in oxidation-reduction reactions

• they are involved in intracellular signaling

• they function as building blocks for nucleic acids

• all of the above

all of the above

Which group is attached to the pyrimidine ring in thymine and is not present in uracil?

• ribose

• -CH₃

• -NH₂

• deoxyribose

• none of the above

-CH₃

Inside our cells, free nucleotides are almost always associated with ___

• cholesterol

• Mg²⁺ counterions

• proteins

• Cl^- counterions

• fatty acids

Mg2+ counterions

Nucleoside triphosphates carry energy in the form of ___

• amide linkages

• glycosidic bonds

• phosphoester bonds

• hydrogen bonds

• phosphoanhydride bonds

phosphoanhydride bonds

Knowledge about the tautomeric forms of the bases of nucleic acids is needed ___

• to understand H-bonding between the complementary bases

• to distinguish the 5’ end of a DNA strand from the 3’ end

• to understand how bases are linked to deoxyribose

• to understand how the bases are linked to ribose

• to understand the ability of nucleotides to act as energy carriers

to understand H-bonding between the complementary bases

Describe the structure of DNA molecule by listing the characteristics.

1) DNA forms a double ___

2) The two strands run ___

3) The sugar is ___

4) The sugar-phosphate groups ___

5) The location of the bases are ___

6) The bases are planar, and their plane is orientated ___ to the axis of the helix

7) There are ___ bases: ___, ___, ___, ___

8) The strand are held together by H-bonding between complementary bases: ___ to ____, and ___ to ___

9) The helix has a minor and a major ___ on its surface

1) helix

2) antiparallel

3) deoxyribose

4) are on the outside of the helix

5) are in the center of the helix

6) perpendicular

7) four; adenine, cytosine, guanine, thymine

8) A-T, G-C

9) groove

What type of bond is made between nucleoties?

• ester

• phosphoester

• phosphodiester

• glycosidic

• none of the above

phosphodiester

Which of the following correctly describes the B-DNA double helix?

• antiparallel strands

• right-handed helix

• base pairs are located in the center of the helix

• one helical rotation has a rise of 3.4 nm

• all of the above

all of the above

Phosphodiester bonds link DNA monomers to form a polymer by which mechanism?

• The OH group on the C-2 in the 2-deoxyribose monosaccharide forms a covalent bond to elongate the DNA polymer

• The OH group on C-2 in the ribose carbohydrate forms a covalent bond to elongate the DNA polymer

• The OH group on C-3 in the 2-deoxyribose carbohydrate forms a covalent bond to elongate the DNA chain

• The OH group on C-3 in the ribose carbohydrate forms a covalent bond to elongate the DNA chain

The OH group on C-3 in the 2-deoxyribose carbohydrate forms a covalent bond to elongate the DNA chain

What is the purpose of DNA polymerase?

• It facilitates annealing

• It is required for transcription in order to generate more DNA

• It adds the correct nitrogenous base to the template strand

• It is used to replicate DNA in the 5’ → 3’ direction

It is used to replicate DNA in the 5’ → 3’ direction

In most organisms, replication proceeds in a ___ manner from the ___

• bidirectional; replication origin

• bidirectional; theta site

• bidirectional; lagging strand

• unidirectional; chromosome ends

• none of the above

bidirectional; replication origin

Polypeptide synthesis proceeds from the ___ to the ___

• C-terminus; N-terminus

• peptidyl site; aminoacyl site

• N-terminus; C-terminus

• entrance site; exit site

• 50S subunit; 30S subunit

N-terminus; C-terminus

Dideoxy analogs are used in Sanger sequencing for what reason?

• they facilitate fluorescent DNA sequencing

• They facilitate polymerization of the DNA

• They facilitate elongation of the DNA fragments

• They block further elongation of the DNA

They block further elongation of the DNA

Which carbon(s) are deoxygenated for use with Sanger sequencing?

• 1

• 2

• 3

• 1 and 2

• 2 and 3

2 and 3

In Sanger dideoxy DNA sequencing, DNA polymerase 1 is used to add nucleotides to the ___ end of the growing polynucleotide chain

• 5’

• 3’

• dideoxy-nucleotide-containing

• sticky

• blunt

3’

DNA sequencing by the chain'-termination method uses DNA polymerase 1 to make a complementary copy of the target or template DNA molecule. A reaction with a 20 bp template and dideoxyadenosine nucleotides as terminators results in the production of a 5 bp fragment. Based on this result, we can conclude that the template contains ___

• a cytosine at position 5

• a thymine at position 5

• a thymine at position 16

• a uracil at position 5

• a cytosine at position 16

a thymine at position 16