Structure of DNA and DNA replication Flashcards
the natural form of DNA
dsDNA, double stranded DNA.
It is 2 polynucleotide strands wrapped around each other in a double helix
DNA name
Deoxyribonucleic acid. It is a nucleotide polymer
What is a nucleotide
A phosphate group PO4-
Pentose sugar
A nitrogenous base
The carbon atoms of the five-carbon deoxyribose are numbered 1ʹ, 2ʹ, 3ʹ, 4ʹ, and 5’
A nucleotide is simply a nucleoside with additional phosphate group or groups.
What is 5ʹ-3ʹ phosphodiester bonds
Links 2 nucleoside triphosphate together between the 3’ carbon and the 5’ carbon of the next nucleotide.
Phosphodiester bonding between nucleotides forms the sugar-phosphate backbone.
What is dNTP and describe the phosphate groups
Nucleoside triphosphate, a nucleotide which has a deoxyribose sugar, a nitrogenous base and 3 phosphate groups.
Phosphate groups are bound to the 5 prime carbon of the ribose sugar. The 5 prime carbon is the CH2, CH2 is bound to a oxygen of the PO4.
For each PO4, there is a negative charge and 1 oxygen is double bonded to phosphate. The final PO4 has -2 charge on both oxygen atoms with no double bonds.
The nitrogenous base is bound to the 1 prime carbon of the ribose sugar via a 1’ glycosidic bond.
Alpha, beta and gamma phosphate groups are the 1,2,3 phosphate groups respectively.
What are purines?
Purines are double ringed. They are adenine and guanine.
What are pyrimidines?
Pyrimidines are single ringed, They are uracil, cytosine and thymine. Uracil replaced thymine in RNA.
What is complimentary hydrogen bonding?
G and C bonds complimentarily via 3 hydrogen bonds.
A and T bond complimentarily via 2 hydrogen bonds.
What is a nucleoside
Pentose + nitrogenous base
What are the 4 key features of DNA
- Backbone of helix is composed of two chains with alternating sugar and phosphate units
- Bases in opposite strands hydrogen bonds according to ATGC rule
- 2 strands are antiparallel
- There are approximately 10 nucleotides in each strand per complete turn of the helix
- A complete turn is 3.4nm long
- Nitrogenous bases lie perpendicular to central axis, forming the “rungs” of the twisted ladder
- Alternating major and minor grooves
List the 2 types of nucleic acids
DNA
- Hereditary molecule (carries genetic material)
RNA
- Certain viruses (HIV, Coronavirus, Influence virus) use RNA as carrier of genetic information
List 6 difference of RNA from DNA
RNA contains ribose sugar whereas DNA contain deoxyribose sugar. Ribose has a OH on the 2’ carbon whereas deoxyribose has no OH on the 2’ carbon.
RNA uses uracil whereas DNA uses thymine.
RNA is commonly found in cytoplasm whereas DNA is commonly found in cell nuclei.
RNA is usually shorter than DNA
RNA is usually single stranded whereas DNA is usually double stranded.
RNA has 3 types, mRNA, tRNA and rRNA whereas DNA has 1 type.
List 4 function of DNA
- Storage of information Most cell contain a complete set of genetic information, only a part of this genetic information is expressed at any given point. - Expression of information - Replication - Variation by mutation
Describe the flow of genetic information
DNA -> Transcription -> mRNA + tRNA + rRNA (ribosomes) -> translation -> Protein
List the 2 types of cellular division
Mitosis - formation of diploid daughter cells, cellular replication
Meiosis - formation of gametes, cellular reproduction
Describe the steps in human DNA replication
Stage 1: Strand separation
DNA helicase breaks the hydrogen bonds between complimentary base pairs of the DNA. This creates a replication fork
1 of the strand is oriented in the 3’ to 5’ direction, towards the replication fork also known as leading strand. The other strand is oriented in the 5’ to 3’ direction, away from the replication fork also known as the lagging strand.
SSBP bind and stabilize the fork, prevent renaturation of DNA.
Gyrase relax the supercoiling and create nicks to allow coiling to occur.
Stage 2: Strand elongation
For the leading strand
A RNA primer, produced by primase comes along and bind to the leading strand. The primer acts as the starting point of DNA synthesis.
DNA polymerase 3 binds to the leading strand and goes along the leading strand to produce new complimentary molecules in the 5’ to 3’ direction.
This type of replication is continuous
For the lagging strand
Numerous RNA primers made by the primase binds at various points along the lagging strand.
Okazaki fragments are added to the lagging strand in the 5’ to 3’ direction.
This replication is discontinuous as the fragments have to be joined up later,
Stage 3: Termination
Once all bases are matched up, exonuclease removes the primers, DNA polymerase 1 fill the gap left by the primers with more complimentary molecules and proofread the new DNA to ensure there is no mistakes.
DNA ligase seals up the sequences of DNA into 2 continuous double strands.
The result is 2 DNA molecules consisting of 1 old and 1 new chains of nucleotides. Hence, DNA replication is semi-conservative as half of the new DNA template comes from the original DNA strand.
The DNA automatically rewinds into a double helix.
List the 5 types and general functions of the 5 E.coli DNA polymerases
1: Removes RNA primers and fills gap with
DNA (i.e. processing of Okazaki
fragments)
2: Participates in DNA repair
3: Replicates DNA and does
proof-reading
4 and 5: – Specialized DNA polymerases,
participates in DNA repair and replicating of damaged DNA
List the 3 raw materials for DNA synthesis
- > Free deoxyribonucleoside triphosphates (dNTPs)
- dATP, dTTP, dGTP, dCTP
-> Enzymes - e.g. DNA polymerase I and III, helicases,
ligase, gyrase
-> Template DNA - provides the base sequence that
specifies the complementary sequence of the new
DNA chain
Helicase
- Helicase unwind the DNA double helix at ori by breaking the hydrogen bonds and thus denatures the DNA, use ATP as energy source.
Topoisomerase
- Topoisomerase relax supercoiling of DNA in direction of replication fork, It also makes temporary single or double-stranded nicks in DNA backbone which allows uncoiling to occur, and subsequently repairs the nicks
Single stranded binding proteins
- Single stranded binding proteins bind to denatured single-stranded DNA to stabilize the open structure of replication fork and prevent strand renaturation
DNA polymerase 3
- > Requires a free 3’ OH end (i.e. from the short RNA primer synthesized by Primase)
- > Elongates the RNA primer by adding complementary bases in the 5’ to 3’ direction, using the parent DNA strand as a template
- > Proof-reading function i.e. a 3’ to 5’ exonuclease activity capable of detecting and excising mismatched bases on newly synthesized DNA strands
- > Fidelity of DNA replication - with only one error in every 100 million bases duplicated
DNA polymerase 1
- > Removes the RNA primer (5’ to 3’ exonuclease activity) and fills the gaps with complementary DNA
- > It is a template-dependent enzyme - it only adds nucleotides that correctly base pair with an existing DNA strand acting as a template
Ligase
- > Closes any nicks in the DNA backbone by catalyzing the formation of a phosphodiester bond between the adjacent 3’ OH and 5’ P groups
- > Joins Okazaki fragments together into a continuous strand of DNA
