2. Components of Higher Eukaryotic Genomes Flashcards
What is the C-value paradox?
C-value paradox: organism’s genome size doesn’t predict its complexity
C-value: ‘constant’ value of haploid DNA content per nucleus
Does genome size predict gene number?
No, differences in genome size doesn’t predict differences in gene numbers
What are C0t renaturation curves?
C0t curves: kinetic curves representing DNA reassociation rate under specific conditions
-C0T value of DNA reassociation depends on DNA conc, temp., cation conc, viscosity
- C0t equation: C0t = C0 x t x buffer factor: C0 initial DNA conc (M), t renaturation rate (s), buffer accounts for cations
- Rate at which DNA reassociate is proportional to gene copy number present in genome -> more repeats - faster
Does a big part of human genome code for proteins?
No only 1.5% of genome codes for protein
What is the common structure of a gene?
- nc control sequences (promoters, enhancers, CpG islands in promoters)
- nc intervening sequences
- coding sequences
- 5’UTR, 3’ UTR
What are CpG islands?
CpG islands: DNA methylations regions in promoters - regulate gene expression through transcription silencing
Which nucleotides hold most genes?
GC: genes are more concentrated in GC rich areas
What is the fate of a duplicated gene copy?
If a gene is duplicated, the copy can:
- inactivated (pseudogenization)
- evolve into new function (neofunctionalization)
- take over some of the function from the original copy (subfunctionalization)
How can gene clusters produce variant proteins at different stages?
Regulate cluster expression - change protein variant expression:
ex fetal - adult hemoglobin
Fetal subunits are gamma - have higehr affinty for O2 - once born hemoglobin gene expression changes from gamma to beta
Are gene families found in the same locus?
Not necessarily - gene families (clusters) - can be spread across several discrete loci - in tandems repeats
What are the two types of repetitive genetic elements?
Repetitive genetic elements:
- interspersed repeats (SINEs and LINEs)
- tandem repeats
Explain interspersed repeats
Interspersed repeats:
- SINEs (short ex Alu): doesn’t encode reverese transcriptase
- LINEs (long ex L1): encodes reverse transcriptase
Long terminal repeats (LTRs): have/don’t have (??) how to classify
Spread by retrotransposition: sequence codes for reverse transcriptase (copy & paste)
Interspersed repeat retrotransposition can cause:
- insertional mutations
- genome rearrangements (intra-chromosomal recombination -> inversion)
Explain tandem repeats
Variable number tandem repeats (VNTRs):
- by length: micro- / mini- / satellite DNA
- arise from unequal crossing over / DNA replication slippage (forward or backward) / DNA repair
- VNTR repeat (microsatellite) number can determine disease
STR - short tandem repeat
How does unequal crossing over lead to variable VNTR repeats?
Unequal crossing over:
misalignment in meiosis -> unequal crossing over -> expansion of repeats
How does DNA replication slippage lead to variable VNTR repeats?
Backward: slippage on **5’->3’ **strand - additional repeat added of the slippage size
Forward: slippage on 3’->5’ strand
Give a specific example where microsatellite repeat number causes a phenotype
>40 CAG repeats in HTT gene -> higher risk for Huntington’s
What genentic elements are used for fingerprinting?
Minisatellite repeats (non-coding) highly variable - repeats can be inherited from parents
What techniques are used for DNA fingerprinting?
DNA extraction from blood -> restrcition enzymes -> PCR for minisatellite repeats -> electrophoresis -> transfer to membrane -> capillary electrophoresis/Southern blot with parent/crime scene DNA probes -> visualization
Lecture summary
Quiz 1
Quiz 2
Quiz 3
