Chapter 5: Genes and genomes Flashcards
What is the genetic material of all organisms?
Deoxyribosenucleic acid / DNA
Define Gene
A heritible unit of DNA that encodes a product - either a protein or a functional RNA
What is a genome?
The entire genetic material of an organism
What are the key features of DNA that make it suitable to be heritable instructions?
- It has a stable structure
- Is able to accurately replicate (complementary base pairing and able to separate strands)
- Contains the information is a suitable form
Describe the structure of DNA
2 nucleic acid polymers, formed of nucleotides, wrapped around eachother in a right handed double helix, anti-parallel to eachother.
Each strand has a sugar-phosphate backbone (deoxyribose sugar and a phosphate group), and are connected through hydrogen bonds between each nucleotides nitrogenous base - either Adenine, Guanine, Thymine or Adenine.
What are the complementary base pairing rules in DNA?
Adenine (A) — Thymine (T)
Guanine (G) — Cytosine (C)
How many hydrogen bonds form between each complementary base pair found in DNA?
A - T: 2 hydrogen bonds
G - C: 3 hydrogen bonds
Thymine, Cytosine and Uracil are what type of bases?
Pyrimidines
Guanine and Adenine are what type of bases?
Purines
What is the structure of a purine?
A 6 membered nitrogen-containing ring fused to a 5 membered nitrogen-containing ring
What is the structure of a pyrimidine?
A six-membered nitrogen-containing ring
What is the name of the two strands of DNA in regards to DNA replication? What are the newly made strands called?
Template strand and Lagging strand (DNA)
Complementary strand (newly synthesized)
What is the function of helicase in DNA replication?
To separate the two DNA strands
What is the function of DNA polymerase in DNA replication?
To synthesise the next strand by catalysing polymerisation of nucleotides
What must be formed before DNA replication can take place?
Pre-replication complex
What is the approximate rate of error in DNA replication in humans?
1 in every million base pairs copied
Does DNA have an overall positive, negative, or neutral charge?
negative due to negative oxygen molecules on the attached phosphate group
What are the two types of grooves of DNA and what is their importance?
Major and minor grooves
- Allow access to the DNA for recognition and binding proteins
Draw a deoxyribose nucleotide!
Idk look it up :)
What type of bonding occurs between nucloetides and which areas bond?
- Covalent
- Between the sugar of one and the phosphate of the other
On which carbon of deoxyribose nucleotide is the phosphate group found?
5’
On which carbon of deoxyribose nucleotide is the -OH group found?
3’
What type of bonds form between the nitrogenous bases of DNA?
Hydrogen bonds
Which direction is DNA synthesised?
5’ –> 3’
The origin or replication contains high amounts of what type of base pairing? Why is this?
A-T pairings
Adenine and Thymine have 2 hydrogen bonds compared to the 3 between Guanine and Cytosine meaning the bonds will require less energy overall to separate the DNA strands.
What is the replication complex?
A protein complex containing a number of molecules and enzymes required for DNA replication. It binds to the origin of replication?
Where does the replication complex bind during DNA replication?
The origin of replication
What are replication forks?
The areas formed at either end of the replication bubble.
What is the function of helicase?
The separation of base bairs between the two DNA strands
Which direction does helicase travel down the DNA?
Bidirectionally
What is the function of single-stranded DNA binding proteins?
- Prevent base pairs from reannealing
- Protect DNA strands from nucleases that would break down the nucleic acid polymers.
What is formed when the two strands of DNA at the origin or replication are separated?
The replication bubble
What is the risk of supercoils forming?
Would eventually cause the prevention of strand separation and therefore prevent DNA replication.
What is the type of stress contained within a supercoil?
Torsional stress
What enzyme prevents supercoils that could prevent DNA replication?
DNA Topoisomerase
How does DNA Topoisomerase reduce the torsional stress of supercoils within DNA?
DNA Topoisomerase makes cuts in the sugar-phosphate backbone of a DNA-strand allowing the supercoils to unwind and therefore reduces the torsional stress. It then reseals the cuts.
What does Primase synthesise?
RNA primer
What is the function of RNA primer?
Faciliates the synthesis of DNA by RNA polymerase by providing an 3’ -OH group to begin synthesis from.
In which direction does Primase synthesise RNA primer?
5’ - 3’
Which specific DNA polymerase is involved in DNA replication
DNA Polymerase type III
Which direction does DNA polymerase read and synthesise?
Reads 3’ - 5’
Synthesises 5’ - 3’
What is the function of ligase in DNA replication?
Covalently bonds the DNA fragments/Ozaki fragments together
What are Ozaki fragments?
Short sections of the lagging strands newly replicated complementary strand.
‘DNA,RNA,DNA,RNA,DNA,RNA…’
What does pattern represent?
The lagging strands newly replicated complementary strands, showing the RNA primers and Ozaki fragments.
In DNA replication what is each strand of the parent DNA called?
3’ - 5’ is the leading strand
5’ - 3’ is the lagging strand
In what type of cells would replication bubbles eventually meet?
Prokaryotic
What can the polymerase chain reaction (PCR) be used for?
- DNA sequencing
- Gene cloning
What are the advantages of PCR?
- specific targeting of sequences
- Exponential inrease of yield
Describe the process of the polymerase chain reaction
- Denaturation | DNA is separated into two single strands
- Primer annealing | Oligonucleotide primers bind to their complementary sequences on the DNA strands
- Elongation | DNA polymerase initiates synthesis at primer, synthesises new DNA strands
What biomolecules are required to carry out the polymerase chain reaction?
- Double stranded template DNA
- DNA polymerase
- The four dNTPS (dATP, dGTP, dTTP, and dCTP)
- Two oligonucleotides (short single strands of DNA ~20 nucleotides long) that act as primers
What are the three steps of DNA replication?
- Initiation
- Elongation
- Termination
From what organism is DNA polymerase often extracted to use in PCR?
Thermus Aquaticus (Bacterium adapted to high temperatures)
What is mismatch repair (MMR)?
The repair system of DNA that can recognise and change incorrectly incorporated nucleotides in newly synthesises strands.
What carries out mismatch repair?
Mismatch repair enzymes
How do mismatch repair enzymes recognise the newly synthesises strand in some bacteria?
By its lack of methylation
Describe the process of mismatch repair?
- Complex of MMR enzymes cut new strand near distortion
- Unwinds short section
- Exonuclease degrades section of new strand starting at the cut, including the mismatch
- DNA polymerase synthesises new DNA in 5’ - 3’ direction using other strand as template
- DNA ligase joins newly synthesised section to rest of DNA
Done :)
What can the characteristic ‘molecular lesions’ of DNA be caused by? Give 2.
- Electromagnetic radiation | xyrays, gamma rays, UV light
- Toxic chemicals | Cigarette smoke, by-products of normal biochemical processes like reactive oxygen species.
What is deamination?
The removal of an amine group e.g., the deamination of cytosine to uracil
What is base excision repair (BER)?
Cellular mechanism of repair that removes a single damaged base from DNA and corrects it.
What kind of site would it be if a single base (not the sugar-phosphate backbone) was removed from a DNA strand?
Abasic site
Describe the process of Base excision repair (BER).
- ‘base name’ DNA glycosylase breaks bond between base and deoxyribose and removes damages base
- Sugar-phosphate unti is removed
- DNA polymerase adds new nucleotide
- DNA ligase seals single gap
Which bases can be affected by deamination?
Cytosine
Guanine
Adenine
What is depurination?
The complete loss of a guanine or adenine base leaving an abasic site.
Name two types of DNA damage that can be repaired by Base Excision Repair (BER)?
Deamination
Depurination
Name the three types of UV given out by the sun. Which is the most damaging to DNA?
UV-A, UV-B, and UV-C
UV-B is the most damaging to DNA
What can UV-B cause the formation of in DNA?
Pyrimidine dimers | Adjacent thymine or cytosine undergoing photochemical reactions leading to the covalent bonding of the bases, creating a kink in the DNA