Molecular biology and Biochemistry: SEMESTER 1

Which is more reactive, DNA or RNA?

RNA

Which is more stable, RNA or DNA?

DNA

Why does DNA not have uracil?

Cytosine spontaneously delaminates to uracil but DNA removes uracil.

State some features of the double helix DNA strands

Run anti parallel, have major and minor grooves, is a right handed helix, bases stack offset

Why do the DNA bases stack offsets slightly?

To reduce repulsion

Why is RNA less stable than DNA?

RNA is an internal nucleophile, so has internal displacement reactions that allows RNA to change shape

Why can RNA not have thymine?

Thymine is methylated uracil, RNA cannot methylate, therefore thymine cannot be produced.

How many hydrogen bonds do AT base pairings have?

2

How many hydrogen bonds do GC base pairings have?

3 hydrogen bonds

What bond forms between a sugar and a base?

Glysocidic

What bond forms between a sugar and a phosphate?

Phosphodiester

Which 2 bases are purines?

Adenine and guanine

Which 2 bases are pyrimidines?

Cytosine and thymine

What is the difference between a major and minor grooves?

Major is more easily accessed for DNA replication by DNA binding proteins

State the process of DNA replication

1. DNA primate produces a short RNA primer that provides the 3’ OH group

2. DNA polymerase III extends the primer

3. DNA polymerase I removes the primer and replaces it with DNA nucleotides

4. DNA ligase joins all of the nicks together

State the function of single stranded DNA proteins

Prevents annealing as it stops hydrogen bonds from forming between the two single strands

State the function of DNA helicase

Breaks the hydrogen bonds between the double strand

State the function of topoisomerase

Relieves tension in the helix as it unwinds, runs slightly before DNA helicase.

Which direction does DNA replication move in? (Which end to which end)

5’ to 3’

Which end is at the replication fork for the lagging strand?

5’

Which end is at the replication fork for the leading strand?

3’

What is made on the lagging strand as DNA replication goes on?

Okazaki fragments

What is the function of the sliding clamp in DNA replication?

Prevents a frame shift

What is the feature of DNA polymerase III aids in DNA replication?

Proof reads DNA and can pause replication if a mutation takes place

State the process of transcription?

1. RNA polymerase binds to the promoter region of the template strand

2. RNA polymerase transcribes RNA nucleotides to make a transcript

3. RNA polymerase reaches the termination region and ends transcription

4. RNA transcript exits the nucleus via the exit channel

What is a transcription factor?

An activator that encourages RNA polymerase action

What does a repressor do?

Blocks the promoter region

What feature of promoters is the same for everyone and why?

They are very AT rich as it allows the opening of the double helix to be greater due to less hydrogen bonds

What is the strand called where the RNA is transcribed?

Template strand

What is the code called that isn’t used in transcription?

The coding strand

What is a promoter region?

A specific sequence where RNA polymerase can bind

Which direction does transcription move? (which end to which end)

5’ to 3’

What modifications can be made to eukaryotic DNA in transcription?

• 5’ end can be modified by adding a base early on in transcription (5’ cap)

• 3’ end can be modified (polyA tail)

What are the advantages of the polyA tail?

• help RNA exit the nucleus

• Adds stability

What is meant by alternative splicing

Exons can be joined at different combinations

State the initiation step in eukaryotic mRNA for translation

Begins at the 5’ cap, small subunit binds to tRNAi-meth and scans until a start codon is reached.

State the initiation step for prokaryotic mRNA in translation

Ribosomal RNA pairs the sequence in the mRNA until a start codon is found

State the process of translocation

1. tRNA scans until it reaches a start codon

2. tRNAi-meth binds at the P site, the A site accepts a new tRNA molecule

3. The new tRNA aligns so that codon anticodon pairing takes place

4. A peptide bond forms between the two amino acids as the covalent bond between the tRNA molecule and the amino acid at the p site is hydrolysed

5. The uncharged tRNA molecule unbinds from the P site and exits via the E site

6. The tRNA at the a site shifts 3 bases to the P site, a new tRNA binds to the A site. The polypeptide chain gets longer again and the process repeats until a stop codon is reached

7. At the stop codon, release factors stimulate the hydrolysis of the bond between the tRNA and polypeptide. The subunits dissociate.

What is the code of the start codon?

AUG

How is mRNA described?

• unambiguous

• Degenerate

• Informative

Define unambiguous in relation to mRNA

A triplet will always code for the same amino acid

Define degenerate in relation to mRNA

Amino acids can be coded for by multiple different triplet codes

Define informative in relation to mRNA

Every codon codes for an amino acid

What is an open frame and what type of mRNA is it seen in?

An open stretch of mRNA that is coded for during transcription, prokaryotic mRNA

What are operon and what type of mRNA are they seen in?

Genes required in the same pathway that can be transcribed into a single mRNA, prokaryotic mRNA

What is the difference between prokaryotic and eukaryotic ribosomes?

Size. Prokaryotic - 70s eukaryotic - 80s

What type bond forms in aminoacyl-tRNA?

Covalent bonding

Name the enzyme that synthesises the joining of an amino acid and a tRNA molecule

Aminoacyl-tRNA synthase

Where is an amino acid added to a tRNA molecule?

At the 3’ end of the tRNA molecule

How can the tRNA be describes when it forms aminoacyl-tRNA?

Charged

Name the 3 sites in ribosomes

A site, P site and E site

What subunit of a ribosome does mRNA run through during translation?

The small subunit

What subunit of a ribosome does the polypeptide chain form in during translation?

The large subunit

What carbon is the hydroxyl group found on in DNA?

3

What carbon is the phosphate found on in DNA?

5

Why do DNA binding proteins prefer to bind to the major groove of DNA rather than the minor groove?

• more chemical differences between base pairs in the major groove

• helps DNA binding proteins distinguish between the sequences

• Allows sequence-specific binding

What effect does a higher percentage of GC base pairs have when trying to split the double helix of DNA?

• GC base pairs have 3 hydrogen bonds between them

• Greater energy needed to overcome more hydrogen bonds to separate the strands

What effect does a higher concentration of NaCl solution have when trying to split the double helix of DNA?

• higher concentration = more Na+ ions in solution

• Sugar phosphate backbone is negatively charged so Na+ ions neutralise the repulsion between two strands

• Therefore more concentrated NaCl, more energy needed to separate the strands

Which strand are Okazaki fragments seen on?

Lagging strand

What is a missense mutation?

A mutation that results in an amino acid change but does not change the reading frame of the protein

What is a silent mutation?

A mutation that does not result in a change in amino acid

What is a frame shift mutation?

A mutation involving insertion or deletion of bases that is not a multiple of three, shifting the reading frame in all codons following the site of the mutation.

What is a nonsense mutation?

A mutation that changes a codon specifying an amino acid into a stop/termination codon.