2.1.3 NULEOTIDES AND NUCLEIC ACIDS

What is the structure of a nucleotide

It has pentose sugar with 5 carbon atoms, a nitrogenous base and a phosphate group.

What is the difference between DNA nucleotide and RNA nucleotide?

DNA nucleotide has a deoxyribose sugar while RNA nucleotide has a ribose sugar. DNA nucleotide has the base thymine while RNA nucleotide replaces thymine with uracil. DNA nucleotide has two polynucleotide strands in a double helix while RNA consists of one polynucleotide strand. DNA nucleotide is found in chromosomes in the nucleus. RNA nucleotide is found in the cytoplasm. DNA is an extremely long molecule. RNA is a relatively short molecule.

What is the difference between purine and pyrimidines

Purine has 2 hydrogen bonds and 2 carbon-nitrogen rings joined together so it is a base larger than pyrimidines. Pyrimidines have 3 hydrogen bonds and one carbon-nitrogen ring so therefore smaller than a purine base. 

Which bases are purines

Adenine, guanine

Which bases are pyrimidines

Thymine, cytosine

Explain the synthesis of polynucleotides with the formation of phosphodiester bonds

Polynucleotides are formed by condensation reactions between nucleotides. The phosphate group of one nucleotide joins to the hydroxyl group on the 3′ carbon of the sugar on another nucleotide, forming a phosphodiester bond and releasing a molecule of water. This produces the sugar–phosphate backbone of the polynucleotide chain.

Explain the breakdown of polynucleotides by the breakage of phosphodiester bonds

During hydrolysis, water is used to break the phosphodiester bonds, leading to the breakdown of polynucleotides.

How can you form polynucleotides

By joining nucleotides

How many hydrogen bonds does guanine and cytosine form

3 hydrogen bonds

How many hydrogen bonds does adenine and thymine form

2 hydrogen bonds

Explain the steps of semi-conservative DNA replication

1) The enzyme DNA helicase attaches to the DNA molecule and causes the hydrogen bonds between the two polynucleotide DNA strands and the complementary bases to break. 2) This causes the two polynucleotide strands to separate from eachother and so the double helix structure unzips forming two single strands. 3) The free nucleotides (floating in the nucleus) line up and pair up with the complementary exposed unpaired bases. 4) The free nucleotides are held in place by the hydrogen bonds between the complementary bases 5) DNA polymerase moves down the molecule and catalyses the formation of phosphodiester bonds between these new nucleotides and join the nucleotides of the new strand together. This is an example of a condensation reaction. 6) The result is two double strands of DNA : each new helix is made from one “original” strand and one “new” strand.

When DNA polymerase does its role, there are two types of strands. What is the strand that is unzipped from the 3’ end.

What is the strand unzipped from the 5’ end?

The other strand is unzipped from the 5’ end so DNA polymerase has to wait until a section of the strand has unzipped and then work back along the strand. This results in DNA being produced in sections of copied DNA, the Okazaki fragments which are created on the strand called the lagging strand and is said to undergo discontinuous replication. 

Why is it important that DNA is copied continuously?

In order to conserve the genetic information with accuracy and to minimise the occurence of random, spontaneous mutations. 

What is the nature of the genetic code?

• The genetic code is near universal because in almost all living organism the same triplet DNA bases code for the same amino acid

• The genetic code is described as degenerate, because for all amino acids there is more than one base triplet. This may reduce the effect of point mutations as a change in one base of the triplet could produce another base triplet that still codes for the same amino acid

• The genetic code is non-overlapping and is read started from a fixed point in groups of three bases. If a base is added or deleted, then it cases a frame shift, as each base triplet after than, and hence every amino acid coded for is changed. 

Describe how a polynucleotide is formed from its monomers

(more than two) nucleotides joined by phosphodiester bonds in a condensation reaction

Explain the stages of transcription.

Occurs in the nucleus. 1) Starts when RNA polymerase which has helicase activity attaches to the DNA double helix at the beginning of a gene 2) The hydrogen bonds between the two DNA strands and complementary bases break seperating the strands and the DNA molecule uncoils. 3) One of the strands is then used as a template to make an mRNA molecule by RNA polymerase. The DNA template is called the anti-sense strand. 4) The RNA polymerase lines up the free floating RNA nucleotides with complementary exposed bases on the template strand. Base T is replaced with U. 5) RNA polymerase catalyses the formation of phosphodiester bonds joining adjacent RNA nucleotides together. 6) The hydrogen bonds between the uncoiled strands of DNA re-form once the RNA polymerase has passed by and the strands coil back into a double helix. 7) When the RNA polymerase reaches a “stop codon” the chain is terminated and mRNA then moves out of the nucleus through a nuclear pore and attaches to a ribosome in the cytoplasm to start translation.

What are the events that occur when mRNA is made during transcription

 The enzyme RNA polymerase attaches to one strand of the DNA. The DNA molecule opens up in the region of a gene. The RNA polymerase runs along the strand. Free RNA nucleotides are paired up opposite the DNA template using complementary base pairing.

Explain the stages of translation

Occurs at the ribosomes in the cytoplasm. Amino acids join together to form a polypeptide chain. 1) mRNA attaches to a ribosome and tRNA collects amino acids from the cytoplasm and carries them to the ribosome. 2) tRNA molecules attach to the ribosome, and their anticodons pair up with the appropriate codons on the mRNA. 

What is tRNA

tRNA is a single stranded molecule with a binding site at one end thus it can only carry one type of amino acid, and a triplet of bases at the other