Genome Structure and Function Flashcards
How are viruses genetically classified?
Based on their nucleic acid structure
What are the 4 genomic classifications of viruses?
- ssDNA
- dsDNA
- positive sense ssRNA
- negative sense ssRNA
- dsRNA
What does ss stand for?
Single stranded
What does ds stand for?
Double stranded
Can positive sense ssRNA be directly translated?
Yes
Can negative sense ssRNA be directly translated?
No
- it must be copied producing a positive sense complementary strand which can be translated
What is the most widely used method for sequencing genomes?
Whole genome sequencing (WGS)
What type of sequencing WGS?
Shotgun sequencing
How does WGS work?
- DNA cut into overlapping fragments by restriction enzymes, creating a series of contiguous fragments (‘contigs’)
- Overlapping sequenced fragments aligned using computer programming, assembling an entire chromosomes
What are the characteristics of prokaryotic genetic material?
- genes are tightly packed
- coding sequences on both strands
- coding sequences may overlap
- positive correlation between genome size and number of genes
- supercoiling leads to compaction of chromosomes
What is eukaryotic genetic material organised into?
- circular mitochondrial chromosomes
- linear nuclear chromosomes
What is a telomere?
The ends of each chromosome
Which arm is shorter, q or p?
p
Which arm is the top arm, p or q
p
Describe a metacentric chromosome
Both arms are equal in length
Describe a sub-metacentric chromosome
The p arm is slightly shorter than the q arm
Describe an acrocentric chromosome
The p arm is much shorter than the q arm
Describe a telocentric chromosome
There is no p arm just the q arm
What are the two types of chromosomes present in humans and some other eukaryotes?
- autosomes
- sex determining chromosomes
What is C value?
Amount of DNA in the haploid nuclear genome
What is satellite DNA?
Non-coding DNA present as multiple tandem repeats.
- the main component of centromeres and other heterochromatic regions
What is a tandem repeat?
A sequence of two or more DNA base pairs that is repeated that the repeats lie adjacent to each other on the chromosome
Name 4 repetitive elements of the genome
- multiple copy genes
- retrotransposons
- mini-satellites (VNTRs)
- micro-satellites (STRs)
What are the two types of retrotransposons?
- Short interspersed nuclear elements (SINES)
- Long interspersed nuclear elements (LINES)
Define autopolyploidy
Multiples of the same genome
Define allopoyploidy/amphidiploidy
Multiples of different genomes
How is sex determined in humans?
By the presence (male) or absence (female) of SRY
What are the two types of possible DNA damage?
- exogenous
- endogenous
What is exogenous DNA damage?
Damage from outside cell
What is endogenous DNA damage?
Damage from inside cell
Give 3 examples of exogenous DNA damage
- ionising radiation
- UV radiation
- chemicals in environment
Give 2 examples of endogenous DNA damage
- chemicals produced in the cell (e.g. oxygen free radicals)
- errors during DNA metabolism
Name the 5 types of oxidative DNA damage
- base modification
- depurination
- deamidation
- single strand break
- double strand break
Name the 4 types of DNA repair mechanisms
- direct reversal
- excision repair
- mismatch repair (MMR)
- double-strand break repair
What type of DNA repair mechanism is photoreactivation (PR)?
Direct reversal
What does PR do?
Repairs pyrimidine dimers
Name the 2 types of excision repair
- base excision repair (BER)
- nucleotide excision repair (NER)
What do mismatch repair, base excision repair, and nucleotide excision repair do?
Remove damaged nucleotides and replace them using the undamaged strand as a template
Name the 3 types of double-strand break repair
- homologous recombination (HR)
- non-homologous DNA end joint (NHEJ)
- microhomology-mediated end joining (MMEJ)
How does homologous repair work?
Repairs strand breaks using the homologous chromosome as a template
