session 4 - DNA

Describe how eukaryotic DNA is packaged in the cell:

DNA winds around histone proteins (H2A, H2B, H3, H4), the histone proteins are formed from positive charged amino acids, allowing the negative DNA to wind.

DNA-Histone complex forms chromatin, which is made from repeating units of nucleosome.

• Euchromatin = Less condensed, so more access to the proteins, so increased rate of transcription

• Heterochromatin = Highly condensed, so less access to the proteins, so decreased rate of transcription (darker colour of nucleus)

The chromatin then coils even more to form solenoid.

These solenoid condense even more to form the arms of the chromosomes.

DNA → Chromatin → Solenoid → Chromosome

Humans have 22 autosomal chromosomes and 2 sex chromosomes.

The structure of DNA

DNA structure:

• Deoxyribose sugar

• Nucleotide are the monomers:

  • Nucleosides: Sugar + nitrogenous base => Deoxyadenosine // Deoxyadenosine monophosphate

• Nitrogenous bases => joined by H-bonding (separated by heating)

  • Purines: Cyclical ring containing 9 atoms (Adenine and Guanine)

  • Pyrimidines: Single ring with 6 atoms (Thymine and Cytosine (Uracil, but found only in RNA))]

• Twists of DNA are uneven

  • Major: Allows for proteins to bind to DNA and start transcription

  • Minor: Exists because of the uneven base pairing

• Phosphodiester bonds: 5’ → sugar → Phosphate → Sugar → Phosphate → 3’

Describe and outline the primary, secondary, teritiary and quaternary structure of DNA

Primary: The sequence of nitrogenous bases

Secondary: Double helix formed by 2 identical copies of DNA bound via H-bonding

Tertiary: 3D geometrical structure of DNA

• A: Found in low humidity conditions, short and wider than B

• B: Found in high humidity conditions, longer and narrower than A

• Z: Not fully understood, but research says it plays role in disease (Alzhemier’s)

Quaternary: DNA associated with histone proteins, packaged into chromatin

Compare and contrast DNA and RNA

DNA:

• Deoxyribose sugar, where on the 2’C has H instead (more stable doesn’t have O so doesn’t undergo hydrolysis)

• DNA bases: A, T, C, G

RNA:

• Ribose sugar, where on the 2’C has OH instead of H (more likely to be hydrolysed, split)

• Contains: U, A, C, G

• Single stranded

Describe the general outline of the mechanism of DNA replication in prokaryotic and eukaryotes

Eukaryotes:

DNA unwinds at the point of origin, where there are many A and T (since only A=T 2 hydrogen bonds, easier to remove), Helicase separates them into a fork model.

Then Primase adds in an RNA primer, which allows DNA polymerase to bind, DNA polymerase catalyses DNA replication by adding nucleotides Triphosphates into the 3’ to 5’ end.

For the lagging strand, DNA ligase joins the short Okazaki fragments.

Checks are then made by replisome, which proof-reads the DNA replication, if there are mistakes then exonuclease removes it, leading the DNA polymerase to go back and add correct base pair.

DNA ligase is used to join together either side of replicated DNA.

Prokaryotes:

Similar overview:

Initiation → Elongation → Termination

Describe what is meant by semi-conservative replication

When DNA strand is separated, and each molecule is copied in parallel, forming two genetically identical DNA strands, each containing one newly synthesised and one old strand

Outline and explain the process occurring at a DNA replication fork

Once separation of strand occurs: Semi-discontinuous replication

• Leading strand: Copied as a single continuous piece of DNA, since copied in the 5’ to 3’ end

• Lagging strand: Copied in short sections called the Okazaki fragments, since lagging strand is reversely complementary starting at the 3’ end

Describe the main functions of the enzymes involved in the process of DNA replication

Helicase: Separates the 2 DNA strands from the origin

Primase: Synthesises RNA primer so that DNA polymerase can bind

DNA polymerase: Extends an existing molecule of DNA, with RNA molecule primer allows the DNA polymerase to work

DNA Ligase: Sticks together new pieces of DNA (joins the Okazaki fragments)

Topoisomerase: Changes the configuration (shape) of DNA by removing excess supercoiling

Replisome: Proof-reads the DNA strand

Exonuclease: Removes any incorrect nucleotide triphosphatase, where the DNA polymerase takes a step back and adds the correct base pair to continue the chain

What is the function of Telomeres?

• The RNA primer added by the primase, it cannot be replaced with DNA, by DNA polymerase, which will shorten the DNA overtime, leading to loss of DNA

• To overcome the issue, the ends of DNA contain repeat sequences called telomeres, recognised by telomerase.

  • Telomerase contains RNA and protein component

  • The telomerase binds to the overhaning strand of DNA and replaces it with RNA primer => the protein components replaces the RNA primer with a piece of DNA