TBBOL- Week 4

What are nucleotides?

The building blocks for nucleic acid polymers.

What does DNA stand for?

Deoxyribonucleic acid.

What does RNA stand for?

Ribonucleic acid.

What is formed between nucleotides during a condensation reaction?

Phosphodiester linkages.

What is complementary base pairing?

Purines pair with pyrimidines by hydrogen bonds.

What is the chemical structure of RNA?

Single stranded with unique secondary structures through base pairing.

What is the chemical structure of DNA?

Double strand with anti-parallel strands and a double helix.

In what two ways does DNA transmit information?

Replication and transcription.

During the European Renaissance, how did most people believe forms of life arose?

Spontaneous generation.

Who disproved spontaneous generation in 1668?

Francesco Redi.

What are the two theories on the origin of life?

Small molecules of life came from space and chemical evolution on primitive Earth.

What happened when Miller opened the tubes of ammonia, hydrogen cyanide and water?

They contained amino acids and nucleotide bases.

What may have been responsible for some of the small organic molecules?

Volcanoes.

What may have been responsible for the synthesis of polymers?

Hot pools at ocean edges and hydrothermal vents.

What does the ‘RNA world'' hypothesis consist of?

RNA both stored genetic information and catalysed chemical reactions in primitive cells.

What are some examples of RNA carrying genetic information?

mRNA and the fact that some virus genomes are composed solely of RNA.

What do many RNA structures also contain?

Conserved motifs.

What is a ribozyme?

RNA with catalytic activity.

What are some of the biochemical reactions that can be catalysed by ribozymes?

RNA/DNA cleavage, RNA ligation and RNA splicing.

What is one of the key chemical reactions RNA can catalyse?

Template-dependant RNA synthesis.

In the prebiotic world, what can be generated?

Nucleotides and random RNA sequences to some extent.

Where would have early cells had their hereditary information stored?

DNA.

What enzyme is used to convert ribose into deoxyribose?

Ribonucleotide reductase.

Why is RNA unstable under alkaline conditions?

The 2’-OH group.

Why is RNA more susceptible to degradation?

RNA is less hydrophobic.

In what process are DNA sequences copied into RNA?

Transcription.

In what process do RNAs code for a sequence of amino acids in a polypeptide?

Translation.

What is the name of sequences of DNA that encode specific proteins?

Genes.

What enzymes catalyses the synthesis of DNA from RNA in retroviruses?

Reverse transcriptase.

What was used to show that DNA was in the correct place in cells?

Staining.

What could be genetically transformed by dead material from one strain to another strain?

One living strain of bacteria.

What was used to determine whether DNA or protein is the genetic material of cells?

Bacteriophage T2 virus.

What is used to demonstrate transfection?

A genetic marker.

What does each nucleotide consist of?

Deoxyribose, a phosphate group and a nitrogen containing base.

What occurs in DNA because of the arrangement of bases?

A major and a minor groove.

What is the major and minor groove of DNA dependant on?

How far away the sugar phosphate backbone is from each other.

Is replication conservative, semiconservative or dispersive?

Semiconservative.

What does DNA replication start with?

A large protein complex called the pre-replication complex.

Where does the pre-replication complex bind to?

The origin of replication.

In what direction is a new strand formed in?

5’ —> 3’ direction.

How many replication forks are there in DNA replication?

Two.

How does DNA proceed in bacteria?

Bidirectionally from a single origin on its circular genome.

How does DNA proceed in eukaryotes?

Multiple replication forks that move away from each other.

What binds to the template strand during DNA replication?

DNA polymerase.

How is DNA polymerase shaped?

Like an open right hand, the palm brings the active site and the substrates into contact. The “fingers recognise the nucleotide bases.

What does DNA polymerase require?

A primer.

What is a primer?

A short starter strand- usually RNA.

What synthesises a primer?

A primase.

What opens the double stranded DNA to expose template strands for DNA polymerase?

DNA helicase.

How does the leading strand synthesise DNA?

Continuously.

What is the name of the fragments formed by the lagging strand?

Okazaki fragments.

How does the lagging strand synthesise DNA?

Discontinuously.

What is primase’s role in the lagging strand?

It lays down RNA primers to provide a 3’ end.

What recognises any mismatches if DNA polymerase III incorporates the wrong nucleotide?

3’ —> 5’ exonuclease.

What joins the Okazaki fragments together?

DNA ligase.

In the lagging strand, what hydrolyses the primer and replaces it with DNA?

DNA polymerase I

What happens during mismatch replication?

The mismatch repair proteins excise the mismatched nucleotide and some adjacent nucleotides and DNA polymerase I adds the correct nucleotides.

What happens during excision repair?

The excision repair proteins excise the damaged nucleotide and some adjacent nucleotides. DNA polymerase I adds the correct nucleotides.