Introduction to the structure of DNA part 1

Question 1

Explain how DNA is packaged in the cell.

Answer 1

DNA is assembled into nucleosomes (DNA wrapped around a histone core).
These form chromatin - repeating nucleosome subunits.
The chromatin can be twisted around each other to form a solenoid with diameter of about 30nm.

Question 2

What is the role of helicase?

Answer 2

Untwists the DNA strands in both directions from the origin of replication.

Question 3

What is the role of primase?

Answer 3

Makes RNA primer to allow DNA polymerase to bind.

Question 4

What is the role of DNA polymerase?

Answer 4

Copies the DNA in a 3’ to 5’ direction. Polymerase cannot initiate transcription, it can only extend an existing molecule.

Question 5

What is the role of DNA ligase?

Answer 5

Sticks together pieces of DNA.

Question 6

What is the role of topoisomerase?

Answer 6

Changes the configuration of DNA, removing excess supercoiling.

Question 7

What is the role of exonuclease?

Answer 7

Removes nucleotides from the end of a DNA molecule.

Question 8

What is the difference between heterochromatin and euchromatin?

Answer 8

Both contain DNA.
Heterochromatin: More heavily condensed (darker). Solenoid 30nm fibre. Genes not expressed.
Euchromatin: Less condensed (lighter). Beads on a string. Genes expressed.

Chromosomes shuttle between the two forms (takes hours).

Question 9

What is the histone core?

Answer 9

Positively charged histone proteins that DNA (-ve) is wrapped around. This is called chromatin.

A nucleosome is DNA wrapped around a histone core. Nucleosomes coil around each other to save space, this makes a solonoid structure which forms loops on the chromosome arms.

Histone is an octamer made of 8 subunits.

Question 10

During which phase of the cell cycle is DNA replicated?

Answer 10

The S (synthase) phase.

Question 11

How is DNA replicated?

Answer 11

1. DNA strand is unwound by helicase.
2. each half is copied in parallel. This is called semi-conservative replication - each DNA molecule contains 1 strand of the parental DNA.
3. DNA growth is directional from 5’ to 3’ and 2 identical copies (leading and lagging strands) are produced.

DNA replication is catalysed by polymerase. It links the 3’C of an existing nucleotide to the 5’C of the new nucleotide.

Question 12

Describe the overall DNA replication in eukaryotes.

Answer 12

Initiation: Starts copying 3’ end, so new DNA is synthesised in this direction. This end is called the 5’ end in the new strand.

Elongation: A second DNA polymerase binds to the 3’ end of the lagging strand. Leading strand is copied as one continuous piece of DNA, lagging strand is copied in Okazaki fragments.

Question 13

What are Okazaki fragmants?

Answer 13

Short fragments which the lagging strand is copied in a series of.

This is semi-discontinuous replication.
DNA ligase binds these together.

Question 14

How is the newly-synthesised DNA proof-read?

Answer 14

The replisome proof-reads it and the enzyme exonuclease removes an incorrect nucleotide. DNA polymerase then adds the correct base pair.

Question 15

What’s the difference between DNA and RNA?

Answer 15

DNA:
- Stores genetic info.
- Can replicate itself without mistake.
- Double helix.

RNA:
- Carried genetic material in viruses and bacteria.
- Comes in different forms in eukaryotes - mRNA, rRNA, tRNA, microRNA, picoRNA.
- Single and double stranded forms.

Question 16

What is the structure of DNA?

Answer 16

A double-stranded helix with a right-hand turn.
Outside of rope ladder made from sugar phosphate backbone. Internal steps made from nitrogenous bases that carry genetic info.

Question 17

What are the functions of the major and minor groove in DNA?
And how are they formed?

Answer 17

Major groove permits proteins to bind the DNA molecule and control its transcription.

Uneven pairing between bases in the centre of the molecule mean the coils are not equally spaced.

Question 18

What is the name of the bond that links monomer units together that make up the DNA backbone?

Answer 18

Phosphodiester bonds.
Strong covalent bond, giving rigidity to the molecule.

The 5’ C of the first nucleotide is linked to the 3’ C of the next nucleotide.

Question 19

What’s the difference between a nucleoside and a nucleotide?

Answer 19

Nucleoside = nitrogenous base bonded to a pentose sugar.

Nucleotide = phosphate group added to a nucleoside.

Question 20

What is the difference between DNA and RNA structure?

Answer 20

DNA has an H at the second C whereas, RNA has an OH there.

The OH is more likely to be hydrolysed, meaning RNA molecules are more likely to be degraded than DNA.

Question 21

What are the two types of nitrogenous bases and name them?

Answer 21

Purines: Cyclical ring containing 9 C atoms.
ADENINE
GUANINE

Pyramidines: Cyclical ring containing 6 C atoms.
THYMINE (dna) or URACIL (rna)
CYTOSINE

Longer molecule has shorter name.

Question 22

What is the name of a nucleoside with adenine and what would the nucleotide be called?

Answer 22

Deoxyadenosine.

Deoxyadenosine monophosphate.

Question 23

What other forces occur in DNA?

Answer 23

Hydrogen bonding: join the bases that form the centre of the DNA. Separated by heating DNA.

Van der Waals: further stabilise double helix.

Question 24

Is the G and C or T and A bond stronger?

Answer 24

G and C as it binds with 3 H bonds whereas. T and A only have 2.

Question 25

How is the coding sequence to make a protein transcribed?

Answer 25

mRNA exits nucleus via a pore and is translated into a protein by ribosomes on the RER.

The sequences that make up the genes contain introns and exons.
Exons contain coding sequence that is translated to make a protein. Introns contain regulatory elements. Introns are removed by splicing before translation.

Question 26

Why is splicing important?

Answer 26

To remove the introns. It prevents different versions of the genes (splice variants) from arising.

Question 27

What is a genome?

Answer 27

The organism in which the entirety of the DNA sequence is contained.

It is contained on chromosomes.

Question 28

How many chromosomes do humans have?

Answer 28

The genome contains 24 chromosomes - 22 autososomes (non-sex) and 2 sex chromosomes.

Humans are diploid, so each ell contains two copies of the genome. 46 chromosomes - 44 autosomes and still 2 sex chromosomes.

Question 29

How are different cell types in the body given rise to?

Answer 29

Each cell contains a copy of every gene, but only some of them are activated in each cell.

Question 30

What is semidiscontinuous replication?

Answer 30

The process of copying the lagging strand.

Question 31

What are telomeres?

Answer 31

The final RNA primer cannot be replaced with DNA by the polymerase enzyme. This would result in a bit of DNA getting chopped off each time it was copied.

To solve this, the end of each chromosome contains repeat sequences called telomeres which are recognised by the telomerase enzyme. This replaces the RNA primer with a piece of DNA.

Question 32

What is a centromere?

Answer 32

Joins 2 identical DNA molecules.

Question 33

What are isoenzymes?

Answer 33

A group of enzymes which catalyse the same reaction, but have different enzyme forms and catalytic efficiencies.

Question 34

What’s a zymogen?

Answer 34

A protein that displays no catalytic activity, but is transformed within an organism into an enzyme, especially one which catalyses a reaction involving the breakdown of proteins.

Question 35

How does covalent modification regulate enzyme activity?

Answer 35

A functional group is transferred from a molecule onto the enzyme or protein which activates or deactivates the enzyme (turns it on or off).