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Questions and Answers
What is the purpose of telomeres in chromosomes?
What occurs when telomeres get too short?
What is a characteristic of cancer cells?
What is the primary function of transposons?
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What is a characteristic of retrotransposons?
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What percentage of the human genome is composed of mobile genetic elements and remnants?
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What is the purpose of using ddNTPs in the Sanger chain termination method?
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What is the main advantage of Next Generation Sequencing over traditional Sanger sequencing?
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What is the primary factor determining the melting temperature of DNA?
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What is the term for the phenomenon where the size of an organism's genome does not correlate with its complexity?
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What is the approximate percentage of non-coding DNA in the human genome?
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What is the term for the short, repetitive sequences found at telomeres and centromeres?
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What is the enzyme responsible for adding telomere repeats to the ends of chromosomes?
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What is the primary function of centromeres in chromosomes?
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What is the majority of the non-coding DNA in the human genome composed of?
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What is the main characteristic of segmental duplications in the human genome?
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What is the function of centromeres in determining the structure of chromosomes?
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What type of DNA is found in large tandem arrays at centromeres?
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What is the location of tandem repeats in the human genome?
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What is the repetitive sequence found in human telomeres?
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What type of DNA structure forms at the end of chromosomes?
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What is the point at which telomeres get too short and cells stop dividing?
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What is unique about the telomerase enzyme?
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What is a characteristic of cancer cells?
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Study Notes
Chain Termination Method
- Devised by Sanger, uses ddNTPs and dNTPs
- ddNTPs cannot be added onto as no OH group on 3’ carbon
- Replication randomly terminated at different points in four tubes with different ddNTPs
- Resolve by electrophoresis and label DNA fragments, determine sequence
Next Generation Sequencing
- Relies on massively parallel sequencing – sequence short reads (25-30bp)
- Reads are assembled into chromosomes/genomes by computers
- Rate of annealing gives information on complexity, composition, and size of genome
DNA Hybridisation
- DNA separation by raising temperature above melting temperature
- Depends on DNA length and ionic composition of solvent
- G:C rich higher melting point than AT rich
- De-natured strands can reanneal when fall below melting temperature
C-Value Paradox
- Lack of correlation between genome size and organism complexity
- Complex organisms tend to have larger genomes
- Lack of correlation between genome size and number of genes
Human Genome
- 98.5% of human genome = non-coding
- 25% = footprint of gene, 75% no known function
- Non-coding DNA contains sequence repeats – tandem repeats and interspersed repeats
- Interspersed repeats include mobile genetic elements like transposons and Alu repeats
Segmental Duplications
- 1-400kb, have high sequence identity, 5% of genome
- Include low-copy repeats
Telomeres and Centromeres
- Major regions of heterochromatin
- Centromere position determines length of arms of chromosomes
- Telomere DNA sequence = TTAGGG in humans, repeated about 1000 times
- Telomere added by telomerase = self-templating reverse transcriptase
Telomere Function
- T-LOOP closes off end of chromosomes
- QUADRUPLEX DNA = four GGG triplets forming stacked planar G quartets held by HOOGSTEEN HYDROGEN BONDS
- Stops chromosomes being damaged by cell
- HALYFLICK LIMIT = point where telomeres get too short, and cells stop dividing
- Introduction of telomerase allows continuation of division
- Cancers have elevated telomerase
Mobile Genetic Elements
- Many repetitive sequences derived from mobile genetic elements
- Cause mutations where they insert
- TRANSPOSONS are DNA that move around genome by TRANSPOSASE
- RETROTRANSPOSONS – DNA transcribed to RNA; RNA reverse transcribed to DNA which is inserted into a different part of the genome
- 45% of human genome = mobile genetic elements/remnants, most have lost mobility
- Transposons can cause muscular dystrophy and haemophilia but can be useful for evolution and immune system diversity
- RECOMBINASES that mediate antibody diversity generation are related to transposon-coded enzymes
Human Genome Composition
- The majority of the human genome, approximately 98.5%, is non-coding.
Function and Characteristics of Non-Coding DNA
- Only 25% of non-coding DNA has a known function, such as coding for lncRNA (long non-coding RNA) and miRNA, leaving 75% with unknown function.
- Non-coding DNA contains sequence repeats, including:
- Tandem repeats: short nucleotide stretches in a head-to-tail arrangement, primarily found at telomeres and centromeres.
- Interspersed repeats: mobile genetic elements that can move around the genome, including transposons and Alu repeats.
Segmental Duplications
- Segmental duplications, also known as low-copy repeats, are 1-400kb in length and have high sequence identity, covering approximately 5% of the genome.
Telomeres and Centromeres
- Telomeres and centromeres are major regions of heterochromatin.
- The position of the centromere determines the length of the arms of chromosomes.
- Centromeres contain large tandem arrays called satellite DNA, which is 171bp long.
Telomere Structure and Function
- Telomere DNA sequence in humans is TTAGGG, repeated approximately 1000 times.
- Telomeres protect chromosomes from damage by capping the ends, allowing for proper cell division.
Telomere Maintenance
- Telomeres are added by telomerase, a self-templating reverse transcriptase that uses RNA as a template for DNA synthesis.
- Telomeraseallows for the extension of telomeres, which would otherwise shorten with each cell division.
Telomere Protection Mechanism
- The T-LOOP structure at the end of chromosomes is formed, which prevents chromosomes from being damaged by the cell.
- Quadruplex DNA, consisting of four GGG triplets, forms stacked planar G quartets held together by Hoogsteen hydrogen bonds, ensuring chromosome stability.
Telomere Limitations
- The Hayflick limit is the point at which telomeres become too short, and cells stop dividing.
- Introduction of telomerase can overcome the Hayflick limit, allowing cells to continue dividing.
Telomerase and Cancer
- Cancers are characterized by elevated levels of telomerase, enabling unlimited cell division and contributing to tumor growth.
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Description
This quiz covers the Sanger's chain termination method, a DNA sequencing technique that uses ddNTPs and dNTPs to terminate replication at different points, followed by electrophoresis and labeling to determine the sequence. It also touches on next-generation sequencing methods.
