Exam 2 Study Guide - Nucleic Acids

Question 1

The structure of a nucleotide.

Answer 1

A nitrogenous base (pyrimidine or purine), a pentose sugar, and 1+ phosphates

Question 2

The difference between DNA and RNA: Structure

Answer 2

DNA (deoxyribonucleic acid)…2’ carbon in ribose sugar has only hydrogen atom, no oxygen “deoxy”; RNA (ribonucleic acid)

Question 3

The difference between DNA and RNA: Function

Answer 3

DNA provides storage of genetic material; RNA has many roles in protein synthesis, gene expression, catalytic properties, etc.

Question 4

Pyrimidines vs purines.

Answer 4

• Major pyrimidine bases: cytosine, thymine (only in DNA), uracil (only in RNA)
• Major purine bases: adenine and guanine

Question 5

Nucleic acids: Structure

Answer 5

Hydrophilic and negatively charged, double helix formation

Question 6

What does 5’ and 3’ mean?

Answer 6

Refers to the carbon atoms in a deoxyribose sugar that bind to the phosphate groups in DNA. DNA is always synthesized in the 5’ to 3’ direction and have antiparallel strands.

Question 7

Structure of the phosphodiester bond

Answer 7

Nucleotides join together by links of phosphodiester bonds (5’ carbon is linked to the phosphate; the phosphate is linked to the 3’ carbon on the next nucleotide)

Question 8

Base pairs: How are they connected

Answer 8

Hydrogen bonds between complementary strand of nucleic acids

Question 9

Which bases bind?

Answer 9

A bonds to T (or U in RNA); G bonds to C

Question 10

Base pairs: How many hydrogen bonds?

Answer 10

3 hydrogen bonds from between G and C; 2 hydrogen bonds form between A and T

Question 11

B-form DNA: Basic structure and where it is found

Answer 11

Watson-Crick structure; most stable for a random-sequence DNA molecule (normal DNA found in humans)

Question 12

A-form DNA: Basic structure and where it is found

Answer 12

Right-handed double helix with a wider helix (11 bp/turn), and a tilted plane; found in solutions devoid of water

Question 13

Z-form DNA: Basic structure and where it is found

Answer 13

Left-handed helix (12 bp/turn) and a backbone with a zig-zag appearance (slender and elongated); found in archaea, bacteria, some eukaryotes

Question 14

Palindromes

Answer 14

Region of DNA that is identical when read forward or backward (applied to region of DNA with inverted repeats)

Question 15

Hairpin and cruciform

Answer 15

Form from the self-complementarity within each strand

Question 16

Triplex DNAs

Answer 16

Form from Hoogsteen pairing (hydrogen bonding with a third DNA strand)

Question 17

Tetraplex DNAs

Answer 17

Occur when four DNA strands pairs (readily occurs with DNA sequences with a very high proportion of G residues)

Question 18

Messenger RNA

Answer 18

Portion of cellular RNA carrying the genetic information from DNA to the ribosome

Question 19

Transfer RNA

Answer 19

Carries and transfers an amino acid (anti-codon) to the polypeptide chain (required for protein translation)

Question 20

Ribosomal RNA

Answer 20

Ensures correct binding catalyzing the peptide bond (required for protein translation)

Question 21

Denaturation

Answer 21

Melting of the double helix (disrupts hydrogen bonds and base-stacking interactions); caused by pH or temperature extremes

Question 22

What is the Tm?

Answer 22

Temperature at which ½ of DNA is present as separated single strands

Question 23

What factors affect the Tm?

Answer 23

G-C content can increase the melting temperature…pair has three hydrogen bonds making them more difficult to melt

Question 24

Anneal

Answer 24

Process by which two strands spontaneously rewind when temperature or pH is returned to its normal range

Question 25

Mutation

Answer 25

Alterations in DNA structure that produce permanent changes in the genetic information encoded

Question 26

Deamination

Answer 26

Spontaneous loss of exocyclic amino groups (*deamination of cytosine to uracil*) uracil is recognized as foreign material and could be why DNA contains thymine instead

Question 27

What are the effects of UV light?

Answer 27

Mutations: Cyclobutene pyrimidine dimers and/or 6-4 photoproduct

Question 28

Ionizing radiation (X-rays and gamma rays)

Answer 28

Causes ring opening, base fragmentation, breaks in the covalent backbone of nucleic acids

Question 29

ROS

Answer 29

Reactive oxygen species can damage DNA…cells have antioxidants that defend and destroy ROS

Question 30

When DNA is run out on an agarose gel, the DNA moves toward the positive electrode. Explain why, include specifics about the structure of the molecule.

Answer 30

Nucleic acids are hydrophilic and negatively charged, due to its phosphate groups in the backbone. These phosphate groups have negatively charged oxygen atoms, giving DNA its negative charge. Therefore, when DNA is on an agarose gel, it will move toward the positive electrode, since it is the opposite charge (opposite charges attract each other).

Question 31

Which scientist demonstrated base-pair property?

Answer 31

Erwin Chargaff

Question 32

Provide 1 example of a nucleotide where the phosphate is not attached to the 5’ carbon.

Answer 32

One example is ribonucleoside (adenosine) 3’-monophosphates where the phosphate is attached to the 3’ carbon, hence its name. Ribonucleoside (adenosine) 3’-monophosphates is important because it’s the end product of RNA hydrolysis.

Question 33

Double stranded nucleic acids are antiparallel. Use what you know about the structure of DNA to explain what this means.

Answer 33

Nucleotide subunits are held together by phosphodiester bonds, linking the 5’ end of one sugar to the 3’ end of the next, hence the 3’ and 5’ orientation. The double stranded nucleic acids are antiparallel because the structure of DNA is oriented with opposite polarities. The antiparallel direction allows the strands to twist around one another to form the DNA double helix. Lastly, the polarity within the antiparallel strands give rise to the major and minor grooves in the DNA structure.

Question 34

What is a tautomer?

Answer 34

A tautomer is a structural isomer that can readily interconvert. Conversion occurs due to the relocation of a hydrogen atom within the compound. Examples are lactam, lactim, and double lactim.