DNA

Question 1

What is DNA?

Answer 1

DNA is a nucleic acid

Question 2

What is DNA made up of?

Answer 2

DNA is made up of two anti parallel polynucleotide chains which are formed in a 5’ to 3’ direction (both strands are formed and run in the 5’ to 3’ direction)

Question 3

What is each DNA polynucleotide made up of?

Answer 3

Each polynucleotide chain is made up of many nucleotides

Question 4

What are nucleotides made up of?

Answer 4

Each nucleotide consists of a 5 carbon sugar (pentose sugar) (deoxyribose), a nitrogen containing base and a phosphate group. The phosphate group and the nitrogen containing base are attached to the pentose sugar. Nitrogen containing base is attached to the 1’ carbon by a glycosidic bond and the phosphate group is attached to the 5’ carbon by a phosphodiester bond

Question 5

What are the 4 different nucleotides found in DNA and how are they different?

Answer 5

• There are 4 different nucleotides found in DNA, differing only in the nitrogenous base. - Adenine, Thymine, Guanine and Cytosine. - - The order and combination of these bases signal different protein molecules to come and unwind the DNA in a temporal and spacial way.
• Adenine and Guanine are purines and have long bases (2 benzene rings)
• Thymine and Cytosine are pyrimidines and have short bases (1 benzene ring)
• All 4 bases take up similar space inside the nucleus

Question 6

What is a nucleotide made up of?

Answer 6

Nucleotide = pentose sugar + phosphate group + nitrogenous base

Question 7

What is a nucleoside made up of?

Answer 7

Nucleoside = pentose sugar + nitrogenous base

Question 8

Why is the DNA helix important?

Answer 8

It forms major and minor grooves which are essential for the enzymes used replication and transcription because enzymes can identify these regions allowing for uncoiling so other protein factors can enter

Question 9

How can the knowledge that DNA is written 5’ to 3’ be useful?

Answer 9

DNA is not static, so identification of the 5’ end of the 3’ end is useful

Question 10

How does a phosphodieser bond form between two nucleotides?

Answer 10

3’,5’ Phosphodiester bond forms between the phosphate group on the 5’ carbon and the hydroxyl group on the 3’ carbon in a condensation reaction (expulsion of water)

Question 11

How do the bases pair?

Answer 11

• Adenine and Thymine pair by 2 hydrogen bonds

- Cytosine and Guanine pair by 3 hydrogen bonds

Question 12

What must occur during DNA replication?

Answer 12

Both daughter cells must receive a complete set of genes so the DNA molecules (chromosomes) must replicate accurately before division

Question 13

When does DNA replication occur?

Answer 13

DNA replicates at set points during the cell cycle

Question 14

In which cells does DNA rep produce completely identical cells?

Answer 14

Specialised, terminally differentiated cells

Question 15

What do differences in DNA rep cause

Answer 15

• Differentiation
• Mutations which may or may not be advantageous or which have no effect on expression (no change to phenotype) depends on location and type of mutation

Question 16

Why is DNA rep semi conservative?

Answer 16

One strand of DNA is used as a template to make the new daughter strand

Question 17

How does replication occur in prokaryotes?

Answer 17

• All DNA is contained on one circular chromosome
• Single chromosome replicates to produce 2 identical chromosomes (except in mutation)
• Two chromosomes move to opposite sides of the cell and the cell divides into 2 identical daughter cells in the process of partitioning
• Only 1 origin of replication

Question 18

How does DNA rep occur in eukaryotes?

Answer 18

• Many chromosomes that need replicating and they are replicated at the same time
• DNA replicates during S phase of the cell cycle
• Transcription cannot occur at the same time as replication
• Transcription (gene expression) occurs during the gap phases (G1 and G2 and sometimes S depending on when replication is occurring)
• A highly expressed gene will be replicated early on in S phase so it is ready as soon as the cell has completed division
• Less used genes will be replicated late
• Nuclear division (mitosis) occurs during mitosis
• Cytokinesis occurs at the end of mitosis

Question 19

In what order are enzymes/proteins active during DNA rep?

Answer 19

• Helicase
• Single stranded binding proteins
• Primase
• DNA polymerase
• Exonuclease
• Ligase
• Gyrase
• Telomerase

Question 20

What is the role of helicase in DNA rep?

Answer 20

INITIATION Helicase unwinds double helical DNA (forming the replication fork)

Question 21

What is the role of the single stranded binding proteins in DNA rep?

Answer 21

INITIATION Single-strand binding proteins bind to and stabilise the single strand to keep the DNA unwound (attraction between the bases would cause the double helix to reform)

Question 22

What is the role of primase in DNA rep?

Answer 22

INITIATION Primase adds ribonucleoside triphosates which synthesise an RNA primer (presence of uracil allows us to locate the RNA primer). Primase binds at the initiation point on the 3’-5’ parent chain to synthesise the RNA primer in the 5’ to 3’ direction

Question 23

What is the role of DNA polymerase in DNA rep?

Answer 23

ELONGATION DNA Polymerase locates the RNA primer and attaches itself to it (must have the primer and the template strand, adds 1000 bases per second, proceeds in a 5’ to 3’ direction, uses and adds all 4 DNA nucleotides (deoxyribonucleotides) and has proof reading ability (lays down a set number of deoxyribonucleotides then backtracks to check they are correct on the new daughter strand))

Question 24

What is the role of exonuclease in DNA rep?

Answer 24

Exonuclease removes any excess nucleotides (works 5’ to 3’ and 3’ to 5’) from the ends of the DNA strands and removes the RNA primer by identifying the ribose

Question 25

What is the role of ligase in DNA rep?

Answer 25

Ligase joins the ends of single DNA strands by forming new phosphodiester bonds in condensation reactions

Question 26

What is the role of gyrase in DNA rep?

Answer 26

• Gyrase (topoisomerase) ensures the DNA double helix is not twisted (major and minor groves will not form)

Question 27

What is the role of telomerase in DNA rep?

Answer 27

• Telomerase uses a short RNA template to add short DNA repeats (Telomere) to the short ends of linear chromosomes when the last primer is removed using RNA template to protect the DNA
• Every time DNA repeats the telomere formed gets shorter therefore as you get older your genome is more venerable therefore more likely to get age related diseases

Question 28

Why is a leading and lagging strand formed?

Answer 28

• Both strands are replicated at the same time
• Leading strand is formed continuously from the template strand
• Lagging strand is formed in Okazaki fragments (joined by ligase) (5’ to 3’) because primer can only be added once helicase has unwound the DNA double helix due to the rotation of the DNA strands

Question 29

How do the origins of replication differ in pro and eukaryotes?

Answer 29

• In prokaryotes there is only one origin of replication
• In eukaryotes there are multiple origins of replication in each chromosome
• Replication of whole mammalian genome takes approx 8 hours
• Checkpoints give DNA polymerase opportunities to go back and check the replicated strand for mutations
• Replication can happen at multiple points along the genome (speeds up replication)