2.1.3 Nucleic acids

Question 1

Describe the structure of nucleotides generally

Answer 1

1. Nucleotides are composed of a pentose sugar
2. Carbon 1 is joined to a nitrogenous base by a glycosidic bond
3. Carbon 5 is joined to a phosphate group by an ester bond

Question 2

Discuss the nitrogenous bases in RNA and DNA

Answer 2

1. There are five nitrogenous bases, A, T (DNA), C, G and U (in RNA)
2. Adenine and guanine and purines, which means they have two rings in their structure
3. Thymine, cytosine and uracil are pyrimidines, which mean they have one ring in their structure
4. Base pairing occurs by complementary hydrogen bonding (between opposite partially charged groups)
5. Base pairing always occurs between a purine and a pyrimidine
6. A=T, C≡G, A=U

Question 3

Describe how polynucleotides can be formed from nucleotides

Answer 3

1. One nucleotide undergoes condensation reaction with another
2. (catalysed by DNA polymerase or RNA polymerase)
3. The 5’ phosphate group of the incoming nucleotide..
4. ..is joined to the 3’ hydroxyl group of the terminal nucleotide..
5. ..in the 5’ to 3’ direction
6. Connecting nucleotides with phosphodiester bonds

Question 4

Describe how polynucleotides can be broken down to nucleotides

Answer 4

1. Polynucleotides can be broken down to nucleotides with hydrolysis reactions
2. Involving the addition of water
3. Carried out be nuclease enzymes
4. exonucleases, which remove the terminal nucleotide
5. Or restriction endonucleases which cut polynucleotides in the ‘middle’

Question 5

Describe the structure of ADP and ATP

Answer 5

1. Modified adenine ribonucleotides
2. Adenine nitrogenous base, ribose pentose sugar, two (ADP) or three (ATP) phosphate groups

Question 6

Describe the structure of DNA

Answer 6

1. Deoxyribonucleotides are joined in condensation reactions by phosphodiester bonds
2. Forming polynucleotide DNA strands with ..
3. (pentose) sugar-phosphate backbones
4. And outwardly projecting nitrogenous bases
5. Two DNA strands with complementary sequence of bases will attract each other due to hydrogen bonding between complementary bases (A=T, C≡G)
6. The two strands are antiparallel (opposing 5’-3’ directions)
7. In an aqueous environment, the hydrophobic nitrogen bases and the hydrophilic sugar phosphate backbone result in the twisting of the two strands to form a helical structure, the alpha helix
8. DNA molecules are very long (and cannot leave the nucleus)

Question 7

Describe the structure of RNA

Answer 7

1. Composed of ribonucleotides joined in condensation reactions to form phosphodiester bonds
2. Forming a single stranded polynucleotide

Question 8

Compare the structure of DNA and RNA

Answer 8

1. They are both composed of nucleotides with a pentose sugar, nitrogenous base and phosphate group
2. The pentose sugar is DNA is deoxyribose (carbon 2 doesn’t have an -OH group), but the pentose sugar in RNA is ribose (carbon has an -OH group)
3. The nitrogenous bases in deoxyribonucleotide can be A, C, T and G, but in a ribonucleotide T is replaced with Uracil (U)
4. DNA and RNA nucleotides are joined by phosphodiester bonds
5. Both have sugar-phosphate backbones
6. DNA forms double-stranded molecules, RNA forms single-stranded molecules
7. DNA molecules are very long and RNA molecules are relatively shorter

Question 9

Describe how DNA can be purified by precipitation

Answer 9

1. Grinding biological material with a mortar and pestle, dissociates cells and breaks down cell wall if present
2. Detergent is added: this disrupts the phospholipid bilayer of cell membranes (such as cell surface membrane and nuclear envelope)
3. Add salt: this breaks the attractions between DNA and water
4. Add protease enzymes: this breaks down the histone proteins associated with DNA by hydrolysis
5. Add a layer of alcohol to the surface: DNA is insoluble in the alcohol, and so precipitates out, visible as a white solid

Question 10

Describe the process of semi-conservative DNA replication

Answer 10

1. DNA helicase causes the unwinding of the double-helix, and the separation of the two strands unzipping) by breaking the hydrogen bonds between the complementary nitrogenous bases
2. Free nucleotides in the nucleoplasm align to the newly exposed nitrogenous bases by complementary base pairing (A=T, C≡G)
3. DNA polymerase moves along the original strand catalysing condensation reactions between the newly aligned nucleotides and joining them with phosphodiester bonds
4. This occurs in the 3’ to 5’ direction continuously on one strand, and discontinuously on the other strand
5. When both original strands have a newly synthesised complementary strand, semi-consertive replication has occurred

Question 11

Describe the nature of the genetic code

Answer 11

1. The sequence of bases in DNA is what codes for the production of proteins with specific functions
2. Triplet code: it is sequences of three consecutive bases that code for specific amino acids. In the gene these three bases are referred to as triplets, while in the mRNA, they are called codons (anticodons in tRNA)
3. Universal code: the nature of the code is the same in all known living organisms
4. The code is degenerate: more than one triplet/codon can code for the same amino acid.
5. The code is specific: each triplet/codon cannot code for more than one amino acid
6. The code is non-overlapping: triplets/codons are read one after the other, and do not overlap

Question 12

Describe the process of transcription of a gene

Answer 12

1. DNA helicase unwinds and unzips a section of DNA corresponding to a gene
2. Free ribonucleotides align to the exposed bases on the template strand by complementary base pairing and hydrogen bonding
3. RNA polymerase moves along the template strand, catalysing condensation reactions to join the aligned ribonucleotides with phosphodiester bonds
4. At the end of the gene, RNA polymerase stops, detaches, the DNA rewinds, and mRNA separates, leaving via the nuclear pore

Question 13

Describe the process of translation of an mRNA

Answer 13

1. The mRNA binds to a ribosome
2. The ribosome reads the mRNA codon by codon
3. tRNA molecules (carrying specific amino acids) bind to their complementary codon on the mRNA via their anticodon
4. Thus, specific amino acids enter the Ribosome according to the sequence of codons on the mRNA
5. Two amino acids thus brought together are joined in the ribosome by peptide bonds (condensation reaction)
6. As the ribosome moves along the mRNA, amino acids are added according to the sequence of codons
7. This continues until the STOP codon is encountered, at which point the polypeptide separates from the ribosome

Question 14

State what a mutation is and how it can affect the function of a gene

Answer 14

1. Mutations are changes in the sequence of bases in a gene
2. These can occur during DNA replication (and made more likely by mutagens such as certain types of radiation and chemicals)
3. If mutations alter the triplets in the gene, the sequence of codons in the mRNA could be altered
4. If the sequence of codons in changed, the protein produced will have a different primary structure
5. The positions of amino acid side chains will be different, and the tertiary structure will be changed
6. If the tertiary structure is different, the function could be different (most likely, reduced)