Week 6 & 7 Flashcards
Describe nucleotides and the parts (nitrogenous bases)
Nucleotides are the monomers of the polymer Nucleic Acids. It is the building blocks of DNA and RNA.
A nucleotide if formed by a phosphate group, a sugar group and a nitrogenous group.
The nitrogenous group has Pyrimidines (cytosine-C, thymine-T, Uracil-U => single stranded) & Purines (Adenine-A, Guanine-G => 2 rings). They are separated due to their structure.
The Phosphate group combines with the 5’ Carbon, while the Nitrogenous base combines with the 1’ Carbon. Nucleotides are added to 3’ Carbon.
How do nucleotides (monomer) polymerize(combines) into nucleic acids? (How nucleotides are combined to form DNA)
Via condensation reactions, therefore it will create a new bond called «phospodiester bond» (the bond between the nucleotides).
Compare DNA & RNA (components, structure and function)
DNA:
- Double stranded
- Nucleotide bases: A, C, T, G
- Sugar: Deoxyribose (it makes the backbones)
- Storage of genetic information
- Copied as cells divide
- Has the information to make proteins
RNA:
- Single stranded
- Nucleotide bases: A, C, G, U
- Sugar: Ribose
- mRNA, tRNA (trifles), rRNA (ribles)
- Involved in protein synthesis
Distinguish 5’ and 3’
Directional always written: 5’ -> 3’
Nucleotides are added to the 3’ end.
DNA is always read from 3’ to 5’.
DNA is always copied from 5’ to 3’.
Describe the helix structure of DNA (base pairing and hydrogen bonds)
The DNA is consisted of a double helix which is made of two strands; handrails and rungs. The center with bases is hydrophobic, it is why there is a twist.
‘’Handrails’’ are made of sugars and phosphates.
‘’Rungs’’ are made of nitrogenous bases.
Each strand is a chain of an antiparallel nucleotide.
The Helix: 1 turn = 10 bases = 3.4nm
The two strands are connected by hydrogen bonds between the nucleotides.
Base pairing: The number of purines in a DNA molecule is equal to the number of Pyrimidines.
What is the importance of antiparallel DNA strands?
It is important in DNA replication because it replicates the leading strand one way and the lagging strand the other way.
Describe the semi-conservative model of DNA replication
DNA opens each of the original strands to act as a template to make the opposite strand.
After replication, each new DNA helix contains 1 new and 1 original strand.
Relate DNA replication to cell division
In the Eukaryotes, while being in the Interphase phase for either mitosis or meiosis, DNA replication will occur.
In the Eukaryotes, the DNA replication will be located in the nucleus, while in the Prokaryotes, the reproduction will be in the cytoplasm.
Define origin of replication, replication fork & leading vs lagging strand
The origin of replication is a particular sequence in a genome at which replication is initiated.
Replication fork is the point at which the two strands of DNA are separated to allow replication of each strand.
The leading strand is the strand of nascent DNA which is synthesized in the same direction as the growing replication fork. The synthesis of leading strand is continuous. It is synthesized in the 5’ to 3’ direction. (Continuous)
The lagging strand is the strand of new DNA whose direction is opposite to the direction of the growing replication fork. It is synthesized in fragments called Okazaki fragments. It is synthesized in the 3’ to 5’ direction. (Discontinuous)
Identify enzymes used and their role (go practice identifying them on paper)
DNA Gyrase: It prevents the DNA of supercoiling
Helicase: It separates the DNA
Primase: It makes the primer (RNA) which synthesizes a short complementary RNA sequence
Polymerase III: It extends the chain
Polymerase I: It removes the primer
Ligase: It joins the fragments and then catalyzes the formation of the phosphodiester bond linkage that finally joins the two Okazaki fragments.
Explain all the steps of DNA replication
Step 1. DNA Helicase uncoils DNA helix and separates strands by breaking hydrogen bonds. At the same time, DNA gyrase will prevent the DNA of supercoiling the helix upstream of replication fork and Single-strand binding (SSB) proteins will prevent reannealing (binding) of two strands.
Step 2. Primase will synthesize a short complementary RNA sequence (RNA primer)
Step 3. DNA polymerase III will bind to RNA primer and will initiate DNA replication
Step 4. RNA primer will be replaced with DNA by DNA polymerase I
Step 5. DNA ligase will seal gaps in the leading and lagging strands
Discuss replication errors, DNA repair, mutations and consequences
DNA PROOFREADING
During DNA replication their could be an incorrect base that have been added to the growing chain. Therefore the DNA polymerase will immediately excise the incorrect base and replace it with the correct base before proceeding with replication.
MISMATCH REPAIR
During DNA replication there could be a base that has been mispaired and missed in proofreading. Therefore the mismatch repair proteins or enzymes will excise the mismatched base and some adjacent bases (they will remove a whole chunk). Then the DNA polymerase will add the correct bases and DNA ligase will repair the remaining nick.
The consequences if the DNA is not repaired is that it could cause cancer and diseases.
