A1.2 Nucleic Acids

How is DNA evidence of common ancestry

DNA is universal to all living organisms

What are the components of a nucleotide

Phosphate group

Five-carbon monosaccharide (pentose sugar)

nitrogenous base

How are nucleotides bonded together and why

3’ carbon is covalently bonded to phosphate group of next nucleotide (phosphodiester bond).

sugar phosphate bonding makes a continous chain of covalently bonded atoms in each strand of DNA or RNA nucleotides

This bond is a result of condensation reactions.

Covalent bonds are relatively strong and thus a nucleic acid polymer made of nucleotides is quite stable.

What are the nitrogenous bases in DNA and the number of H bonds formed

Adenine - Thymine (2 hydrogen bonds)

Cytosine - Guanine (3 hydrogen bonds)

What are the nitrogenous bases in RNA and the number of H bonds formed

Adenine - Uracil (2 bonds)

Cytosine - Guanine (3 bonds)

Which nucleotides are purines

Adenine and guanine

Which nucleotides are pyrimidines

Thymine/Uracil and cytosine

Draw the nucleotide bases

Are DNA and RNA nucleotides identical

No. Nucleotides in RNA contain ribose, nucleotides in DNA contain deoxyribose.

Uracil only occurs in RNA

Thymine only occurs in DNA

How many different nucleotides are there in total

8

4 DNA, 4 RNA

Draw a RNA nucleotide

Students should be able to draw and recognize diagrams of the structure of single nucleotides and RNA polymers.

Draw DNA as a double helix

In diagrams of DNA structure, students should draw the two strands antiparallel, but are not required to draw the helical shape.

Students should show adenine (A) paired with thymine (T), and guanine (G) paired with cytosine (C).

Students are not required to memorize the relative lengths of the purine and pyrimidine bases, or the numbers of hydrogen bonds.

Marking Rubric

• sugar, phosphate and base linked correctly to form at least one nucleotide

  • ignore labelling of the subunits of the nucleotide. Carbon atoms in deoxyribose do not have to be numbered but the phosphate should be linked to C5 and the base to C1. Shapes other than circles and rectangles could be used for the phosphate and base.

• deoxyribose, phosphate and named base labelled at least once

• adenine paired with thymine and cytosine paired with guanine

  • Full names of all four bases are required, but not relative sizes of the purine and pyrimidine bases.

• two antiparallel chains of nucleotides linked by hydrogen bonds with all sugar-phosphate bonds in correct position

  • a bond should connect the C3 of deoxyribose on one nucleotide to the phosphate on the adjacent nucleotide. Two nucleotides in each strand is sufficient.

  • this picture uses solid lines to draw hydrogen bonds. Try NOT to do that, use dotted lines instead.

Difference in structure, location, and length of DNA and RNA

DNA	RNA
Double stranded	Single stranded
Consists of two polynucleotide strands of complementary base pairs in the form of a double helix	Consists of single strands in three functional forms - mRNA, tRNA, rRNA
Deoxyribose as sugar	Ribose as sugar
Thymine instead of uracil	Uracil instead of thymine
Occurs in the nucleus	Occurs in the nucleus and cytoplasm, particularly in ribosomes
Very long strands, usually several million nucleotides	Relatively short strands, 100-several thousand nucleotides

Common Mistake

Must be careful when explaining the difference in location of DNA and RNA

RNA can occur in the nucleus (its synthesised there), but most of the time it will be found in the cytoplasm with the ribosomes -> it is false that RNA only appear in the cytoplasm

Why is DNA called antiparallel

Because the two strands are upside down in comparison to each other, but parallel, they are said to be antiparallel to each other.

Examples of nucleic acids

DNA

messenger RNA

transfer RNA

ribosomal RNA

Adenosine Triphosphate

Importance of complementary base pairing

• Complementary base pairing is important for DNA replication.

  • based on hydrogen bonding, where adenine and thymine only form H bonds with each other, and likewise for cytosine and guanine

• During DNA replication, both sides of the original DNA are used as a template.

  • After DNA has been unzipped (opened up into two single strands), the free-floating individual nucleotides in solution will begin pairing with the unmatched nucleotides.

  • An exact copy of the original molecule can be made.

Diversity of possible DNA sequences

Explain that diversity by any length of DNA molecule and any base sequence is possible. (using P&C)

Emphasize the enormous capacity of DNA for storing data with great economy.

Start codon

TAC (DNA)

AUG (mRNA)

Stop codons

ATT, ATC, ACT (DNA)

UAA, UAG, UGA (mRNA)

Importance of directionality

• When RNA or DNA is formed, one nucleotide at a time is added to the molecule.

  • The nucleotide is not added at a random spot: it is added as the next nucleotide in a growing chain.

• As all nucleotides have a phosphate group, pentose sugar and nitrogenous base, you can trace this formation by looking for the first nucleotide in the sequence.

  • That first nucleotide will always be the 5' end of the strand.

  • This is important when a new nucleic acid strand is formed.

• When DNA replicates, the two strands separate from each other in a particular area, and each separated strand acts as a template for a new strand to be formed.

  • A new strand will always begin with the 5'-end nucleotide first.

  • Similarly, transcription synthesises the 5’ end of RNA first

  • Translation starts from the 5’ end of the RNA

How does purine to pyrimidine bonding contribute to the stability of the DNA helix

• Pyrimidines are smaller as they contain a single-ring structure, whereas purines are larger as they contain a double-ring structure.

• When bonding the two strands of DNA together to make the double helix, a purine is always bonded to a pyrimidine.

• Adenine-thymine (A-T) and cytosine-guanine (C-G) pairs have equal length, so the DNA helix has the same three-dimensional structure regardless of the base sequence

What is the structure of a nucleosome

A DNA molecule wrapped around a core of eight histone proteins (an octamer) held together by an additional histone protein attached to linker DNA.

*linker DNA is the DNA that extends from one nucleosome to the next is called linker DNA.

What is the function of nucleosomes

• Nucleosomes help to supercoil chromosomes.

• Its function is to regulate gene expression - DNA bound to histones cannot be transcribed

Do prokaryotes have nucleosomes

No

What is the hershey-chase experiment and its conclusions.

Radioisotopes of phosphorous (phosphorous 32) and sulfur (sulfur 35) were used.

Bacteriophages were grown in separate solutions of these radioisotopes.

The phosphorous was detected in the DNA of the virus.

The sulfur was detected in the protein outer coat of the virus, as DNA does not contain sulfur. Two of the 20 amino acids contain sulfur.

The e coli infected with the phosphorous 32 bacteriophage had radioactivity, which indicated DNA.

The e coli infected with sulfur 35 had no radioactivity.

This led to the conclusion that DNA, not protein, is the genetic material.

Identify the curves from the hershey-chase experiment

This is a possible MCQ question where they ask you to identify the curves. Take not that there will not be a 100% or 0% result, but there will be a noticeable difference between the sulfur and phosphorus curves.

What is Chargaff’s rule

DNA contains the same number of adenine as thymine nucleotides, as well as the same number of guanine and cytosine nucleotides.

What is chargaff’s experiment and its results

From the results for the DNA Chargaff extracted from the thymus gland of a calf, there is almost the same ratio of adenine to thymine, and also the same ratio of guanine to cytosine.

This showed that the tetranucleotide theory is false.

The tetranucleotide theory, if correct, would have resulted in the proportion of all of the nitrogenous bases being equal, in other words, the same quantities of A, T, C and G.

The data did not show equal proportions of all four bases, and thus the tetranucleotide idea was falsified.