2.1.3 Nucleotides and Nucleic Acids

What is a nucleotide?

monomer of nucleic acid

What do nucleotides consist of?

A phosphate group, a pentose sugar and a nitrogenous base

What type of bond connects the phosphate group to the pentose sugar in a nucleotide?

Phosphodiester bond

What type of bond connects the pentose sugar to the nitrogenous base?

Glycosidic bond

What are the components of a DNA nucleotide?

A deoxyribose sugar with a hydrogen on the 2' position, a phosphate group, and one of 4 nitrogenous bases (including thymine)

What are the components of a RNA nucleotide?

A ribose sugar with a hydroxyl on the 2' position, a phosphate group, and one of 4 nitrogenous bases (including uracil)

Why is it important that DNA is a stable molecule?

So that the integrity of the code within the base sequences is protected

How is the bonding between A-T and C-G different?

AT only has two hydrogen bonds whereas CG has three, so CG is a stronger base pair

What is a polynucleotide?

long chain of nucleotides

How are polynucleotides broken down?

Phosphodiester bonds are broken by hydrolysis reactions, releasing the individual nucleotides

How are polynucleotides synthesised?

Condensation reactions between the phosphate group of one nucleotide and the pentose sugar of another join them together with a phosphodiester bond and release a molecule of water.

What are the two different categories of bases?

Purines and pyrimidines

What bases are purines?

Adenine and Guanine

What bases are pyrimidines?

Thymine, cytosine and uracil (RNA)

What is the structure of purines?

A double ring with one six carbon and one 5 carbon ring

What is the structure of pyrimidines?

A single six sided ring structure

How many strands are there in DNA?

2

How many strands are there in RNA?

1

What does a molecule of ADP consist of?

A pentose sugar (ribose), adenine and 2 phosphate groups

What does a molecule of ATP consist of?

A pentose sugar (ribose), adenine and 3 phosphate groups

How does ATP release energy?

Energy is released when a phosphate group is removed to create ADP

What is Chargaff's rule?

A=T and G=C ie the percentage of adenine is equal to the percentage of thymine etc

What does DNA stand for?

deoxyribonucleic acid

How is DNA structured?

2 antiparallel polynucleotide strands made up of deoxyribose sugars and phosphate groups bonded together to form the backbone. The nitrogenous base of each nucleotide is inside the molecule and hydrogen bonds between the nitrogenous bases hold the molecule together. The DNA molecule is then twisted to form its double helix shape.

What name is given the the pairings between bases?

Complementary base pairing

Describe 3 ways DNA is suited to its function

Strong sugar-phosphate backbone prevents chain from breaking and the code being disrupted, coiled structure allows a large amount of information to be fit in the nucleus, and weak hydrogen bonds allows DNA to be separated in transcription

What is dispersive replication?

Parental DNA broken down and nucleotides replicated ie new and old parts of DNA are scattered randomly throughout the molecule

What is conservative replication?

DNA remains intact and new daughter DNA made from scratch

What is the name given to DNA's style of replication?

Semi-conservative

What is semi-conservative replication?

DNA splits and each strand acts as a template for replication. This means the new molecule will have one strand from the old DNA and one strand from the new DNA

How do you purify DNA (outline)?

Through a precipitation reaction. Break the cells and disrupt the nuclear membrane to release the DNA, use enzymes to denature and remove the proteins (histones) associated with DNA, then finally precipitate the DNA

Explain how you would perform a DNA purification experiment

Break up the solute and then add to some detergent to break down the nuclear membranes. Place into a water bath for 10 mins then cool in an ice bath to stop the DNA itself from breaking down. Add protease enzyme to denature the histones and finally add ice cold ethanol.

Describe DNA replication

1. The DNA unwinds 2. The two strands unzip due to the hydrogen bonds being broken; this is catalysed by helicase 3. A primer marks the starting point for the construction of the new strand 4. DNA polymerase binds to the primer and starts adding free nucleotides in the 5' to 3' direction 5. The lagging strand is made in small chunks 6. All the primers are removed by exonuclease 7. Ligase seals the fragments

What are Okazaki fragments?

Relatively short fragment of DNA synthesized on the lagging strand during DNA replication.

Why can the lagging strand not be made continuously?

DNA polymerase only works in the 5' to 3' direction so it has to add to the lagging strand in small chunks

How is the energy provided for the phosphodiester bonds during replication?

Hydrolysis of the extra phosphate group on the activated nucleotides supplies the energy to form bonds between the sugar on one nucleotide and the phosphate group on another

What does helicase do during replication?

Breaks the hydrogen bonds and allows the helix to unzip

What does DNA polymerase do?

Joins individual nucleotides to make complementary strands during replication

What does DNA ligase do?

joins Okazaki fragments together

What is a mutation?

change in DNA sequence

How do mutations occur?

Can occur spontaneously when DNA polymerase makes a mistake, but the rate of mutation is affected by external factors

Give 3 examples of external factors that could affect mutations

UV radiation, free radicals produced during metabolism or mutagenic agents

What are the 3 types of mutations?

substitution, insertion, deletion

What is a substitution mutation?

Replacement of a single nucleotide by another nucleotide e.g ATCGA becomes ATCGG

What is an insertion mutation?

Where a nucleotide base is added as an extra e.g ATCGA becomes ATCGAA

What is a deletion mutation?

Where a nucleotide base is deleted e.g ATCGA becomes ATCG

Why might mutations not have any effects?

The code is degenerate so substitution changes may have no effect, or the mutation occurs in an intron

Why can DNA be described as degenerate?

For the majority of the amino acids, there is more than one base triplet

Give 3 words that describe the nature of the genetic code?

Universal, degenerate and non-overlapping

Why can DNA be described as non-overlapping?

It is read starting from a fixed point

What is a gene?

segment of DNA that codes for a protein

Why can DNA be described as a triplet?

3 bases code for one amino acid in a protein so you have more than enough amino acids coded for

Give 3 ways RNA is different from DNA

The sugar molecule in RNA is ribose, it has Uracil instead of Thymine and it has a single-stranded chain

What is transcription (not detailed summary)

Production of mRNA using DNA as a template

How does transcription work?

Helicase unwinds and unzips a gene, causing the hydrogen bonds between nucleotide bases to break. Free RNA nucleotides pair to the exposed bases on the template strand, and RNA polymerase forms sugar-phosphate bonds between them. The mRNA strand then detaches from the template DNA, and the two DNA strands join back up. The mRNA strand is then modified and moves out of a nuclear pore

How is the mRNA strand modified?

Introns are removed by enzymes, leaving only the exons

How does translation work?

In the cytoplasm a ribosome attaches to the start codon on the mRNA. tRNA molecules bind with their specific amino acid and bring them to the mRNA molecule. The anticodon on the tRNA bonds with the codon on the mRNA. Two tRNA molecules do this at any one time, and so bring their amino acids next to each other. A peptide bond is formed between the amino acids and this process continues until a stop codon is reached. The amino acid chain then forms the final polypeptide

Where are tRNA molecules made?

nucleolus

What is a codon?

a three-nucleotide sequence that codes for an amino acid

What is an anticodon?

An anticodon is the three unpaired bases on a tRNA that is complementary to one mRNA.

What is the role of tRNA in translation?

Carry amino acid to the ribosome, anticodon then binds to the codon, tRNA molecules hold amino acids in place whilst peptide bond is formed, then they detach and are reused

What is the sense strand?

coding strand ie the strand that the mRNA is identical to

What does rRNA do?

forms ribosomes