S1) Introduction to DNA Flashcards
What is the role of nucleic acids?
Nucleic acids are required for the storage and expression of genetic information
Identify the two types of nucleic acid
- Deoxyribonucleic acid (DNA)
- Ribonucleic acid (RNA)
Describe the structure of DNA
- DNA is a polymer of deoxyribonucleoside monophosphates covalently linked by 3’→5’–phosphodiester bonds
- DNA exists as a double-stranded (ds) molecule, forming a double helix
Describe the bonds formed in the DNA molecule
Phosphodiester bonds join the 3’ end of one nucleotide to the 5’ end of an adjacent nucleotide through a phosphate group
Describe the polarity of the overall DNA chain
The resulting chain has polarity, with both a 5’-end (free phosphate) and a 3’-end (free hydroxyl) that are not attached to other nucleotides
How are bases in DNA written?
Bases are written in sequence from the 5’-end of the chain to the 3’-end
Compare and contrast the DNA found in eukaryotes with that found in prokaryotes
- Eukaryote: many chromosomes, linear molecule of dsDNA, bound to a complex of proteins to form chromatin
- Prokaryote: single circular and supercoiled chromosome, associated with non-histone proteins that condense the DNA to form a nucleoid
What are plasmids?
Plasmids are small, circular, extrachromosomal DNA molecules
What do plasmids do?
- Carry genes that convey antibiotic resistance to the host bacterium
- Facilitate the transfer of genetic information from one bacterium to another
Describe the structure of the double helix in the DNA molecule
- Two chains are coiled around an axis of symmetry in an anti-parallel manner
- The hydrophilic deoxyribose–phosphate backbone is on the outside and the hydrophobic bases are stacked inside
Describe base pairing in a DNA molecule
Bases of one strand are paired with the bases of the second strand:
- Adenine is always paired with a thymine (two H2 bonds)
- Cytosine is always paired with a guanine (three H2 bonds)
Explain how the separation of the DNA strands in a double helix might occur
- The two strands separate when hydrogen bonds between the paired bases are disrupted
- Disruption occurs if pH of the DNA solution is altered or if the solution is heated
What are telomeres?
Telomeres are complexes of noncoding DNA and proteins located at the ends of linear chromosomes
Describe the structure of telomeres
The single-stranded region folds back on itself, forming a loop structure that is stabilized by protein
What do telomeres do?
- Maintain the structural integrity of the chromosome, preventing attack by nucleases
- Allow repair systems to distinguish a true end from a break in dsDNA
Telomere shortening affects eukaryotic cells.
What is this phenomenon?
- After the removal of the RNA primer, there is no way to fill in the remaining gap with DNA
- Hence, in human somatic cells, telomeres shorten with each successive cell division until the cell becomes senescent
Identify the cells that are not affected by telomere shortening.
Explain why
The following cells contain telomerase, which maintains telomeric length:
- Germ cells
- Stem cells
- Cancer cells
What is telomerase and what does it do?
- Telomerase is a complex that contains a protein which acts as a reverse transcriptase using the RNA template to synthesize DNA in the usual 5’→3’ direction
- Telomerase then translocates to the newly synthesized end, and the process is repeated
What are reverse transcriptases?
Reverse transcriptases are RNA-directed DNA polymerases
Provide and example of a reverse transcriptase in human disease
Reverse transcriptases are involved in the replication of retroviruses e.g. HIV
Describe the inhibition of DNA synthesis by nucleoside analogs
- DNA chain growth can be blocked by the incorporation of nucleoside analogs that have been modified in the sugar portion of the nucleoside
- These compounds slow the division of rapidly growing cells and viruses e.g. araC (cancer) and AZT (HIV)
Describe 3 ways in which DNA damage can occur
- DNA synthesis errors
- Environmental insults alter/remove nucleotide bases
- Bases are also altered / lost spontaneously
Identify 2 agents which can damage DNA
- Chemicals e.g. nitrous acid changes bases
- -* Radiation e.g. UV light fuses pyramidines
What happens when damaged DNA is not repaired?
- A mutation is introduced that can result in any of a number of deleterious effects
- Effects include loss of control over the proliferation of the mutated cell, leading to cancer
Identify the three steps in DNA repair
- Recognition of the damage (lesion) on the DNA
- Removal or excision of the damage
- Replacement or filling the gap left by excision using the sister strand as a template for DNA synthesis and ligation
Describe methyl-directed mismatch repair
Mut proteins identify the mispaired nucleotide(s) and discriminate between the correct strand and the strand with the mismatch
Some bases experience alterations.
Describe the base alteration of cytosine
- Cytosine slowly undergoes deamination (the loss of its amino group) to form uracil
- Also occurs by action of deaminating or alkylating compounds
What can cause double-strand breaks in DNA?
- Natural errors in gene rearrangements
- High-energy radiation
- Oxidative free radicals
Explain the repair of double-strand breaks
Non-homologous end-joining repair brings together the ends of two DNA fragments by a group of proteins that effect their religation
What are the problems with non-homologous end pair joining?
- Some DNA is lost in the process and the mechanism is error prone and mutagenic
- Defects in this repair system are associated with a predisposition to cancer and immunodeficiency syndromes
