Eukaryote Genome Organisation & Evolutionary genetics Flashcards
1
Q
Histone Proteins
A
- Small basic, positively charged amino acids (lysine & arginine) = ~ half all chromatin protein weight
- Histones bind & neutralize negatively charged DNA
- 5 types of histone: H1, H2A, H2B, H3, H4
o H2-4 = core histones – form nucleosome
o Linker histone (H1) joins histones to form the nucleosome - High level of sequence conservation of histones among diverse organisms.
2
Q
Non-Histone proteins
A
- Large variety (200-2,000,000) of non-histone proteins
- Therefore have large variety of functions:
o Scaffolding: backbone of chromosome (aid the compaction of chromosome)
o DNA replication: e.g. DNA polymerase
o Chromosome segregation: e.g. motor proteins of kinetochores
o Transcriptional regulation: transcription factors are largest group, regulate transcription during gene expression (5000 – 10 000 different transcription factors) - Occur in different amounts in different tissues
3
Q
Nucleosomes
A
- Fundamental unit of chromosome packaging
- Condensed DNA form chromatin fibres (string) with beads (nucleosomes)
- Have diameter of ±100 Â (Â = Angstrom = 10-10m); chromatin fibres have diameter of 20Â
- Each nucleosome = ~160bp of DNA wrapped twice around a core of 8 histones
- Nucleosome spacing is an important function and is inherited to daughter cells.
- Linker DNA links together nucleosomes & is about 40bp of DNA
- DNA sequence, spacing & structure affect genetic function
4
Q
Radial-loop Scaffolding Compaction
A
DNA compaction is sequential and progressive:
- First chromatin fibres (20Â) are wrapped around nucleosomes (100Â), which are supercoiled (300Â)
- Supercoiled chromatin undergoes compaction and forms loops held together by non-histone, scaffolding & non-scaffolding proteins.
- Chromatin loops form a rosette shape (daisy-like) held together by additional non-histone scaffold proteins
- Rosettes condense into compact bundles to rodlike chromosomes – this is 10 000 times more compact than naked DNA
5
Q
What is a Karyotype?
A
- Metaphase chromosomes stained with Giemsa have alternating bands of light and dark staining known as G banding
- Each band contains many DNA loops and ranges from 1 to 10 Mb in length
- Karyotype made from fully compacted metaphase chromosomes that have unique, reproducible banding patterns.
- Highly reproducible within a species & within an individual throughout its lifetime
6
Q
What are the uses of karyotypes?
A
- Locate genes on a chromosome
a. Chromosome divided into long and short arm joined by centromere - Reveals cause of genetic diseases
a. E.g. down syndrome (3 copies of Chr21) - Analyse chromosomal difference between species
7
Q
What are 3 specialised elements of Chromosomes?
A
- Origins of Replication
- Telomeres
- Centromeres
8
Q
Origins of replication
A
- Origins are accessible regions of DNA with NO nucleosomes -> relatively uncompacted
- Replication unit (replicon) – DNA running both ways from one origin to the endpoints. Replicons are AT rich
- Many origins of replication that are active at the same time (occurs at roughly 50 nucleotides/s)
- Replicons are scattered throughout the chromatin 30-300kb apart
9
Q
Telomeres
A
- Protective caps on the end of chromosomes
- Has protein enzyme telomerase – prevents shortening of telomeres
- Preserves the integrity of linear chromosomes & prevents fusion with other chromosomes
o Lagging strand RNA primer region must be removed leaving 2 uneven ends of a chromosome (called the DNA overhang)
o Chromosome would get shorter and shorter after each replication (by the length of a primer) - Consist of DNA + protein
- NO genes are present in telomeres
- Consist of TTAGGG repeated 250-1500 times; repeat number varies in cell types
10
Q
Centromeres
A
- Segregation of condensed chromosomes depends on centromeres
- Centromeres appear as constrictions on chromosomes and consist of:
o Blocks of repetitive, noncoding sequences called satellite DNA
o Satellite DNA consists of short sequences repeated many times - Can appear anywhere along the length of the chromosome, not just in the middle
- Centromeres have the following functions:
o Hold sister chromatids together
o Kinetochore – structure composed of DNA and protein that helps power chromosome movement
11
Q
What is a metacentric chromosome?
A
Centromere is in the middle
12
Q
What is an Acrocentric chromosome?
A
Chromosome in non-symmetrical.
13
Q
Heterochromatin
A
- Darkly stained regions of chromosome and highly compacted (even during interphase) (i.e. not actively transcribe during non-division phases)
- Common at the centromere
- Constitutive heterochromatin: condensed most of time in all cells (e.g. Y chromosome)
- Facultative heterochromatin: condensed in only some cells & relaxed in other cells (e.g. position effect variegation, X chromosome)
- Can silence gene expression
o If an inversion happens that brings genes close to heterochromatin, the compaction of the heterochromatin will block the unwinding of the euchromatin section
14
Q
BARR bodies
A
o One of the X chromosomes appears as a darkly stained heterochromatin mass in interphase cells; example of facultative heterochromatin
o One of the 2 X chromosomes is randomly inactivated -> BARR body
o Example of dosage compensation, if more than 1 X chromosome, all other copies of X are inactivated
15
Q
Chromosomal deletions
A
- Removal of a segment of DNA
- Phenotypic consequences of deletions:
o Deletion homozygotes: normally lethal
o Deletion heterozygotes: often detrimental due to decreased ‘dose’ of gene - Humans cant survive deletion heterozygotes when >3% of genome is deleted
16
Q
Chromosomal Duplications
A
- Add copies of a chromosomal region to genome
- Arise from chromosomal breakage & faulty repair, unequal cross over or errors in DNA duplication
- Most duplications have no obvious phenotype and only often seen by molecular analysis
- Duplication loop forms (in Prophase I) to maximise the parings of homologous chromosomes in heterozygotes prior to meiosis. (i.e. duplications need to be looped out)
- Effect on phenotype:
o May produce novel phenotypes
o More gene copies: 1 copy retains original function and other copy can gain new function
o Duplicated genes can be placed in a new environment – alters their expression
o Humans duplication heterozygotes can cope with no more than 5% of haploid genome or its lethal.
17
Q
Chromosomal Inversions
A
- Reorganise the DNA sequence of a chromosome
- Produced by a 180 deg rotation of chromosomal regions after a double-stranded break
- Can also result from rare crossovers between related DNA sequences in opposite orientation.
- Can affect phenotype if it disrupts a gene (the break is in the middle of the gene so half of it gets flipped away)
- PROBLEM: inversion heterozygotes reduce the number of recombinant progeny because gametes are unbalanced
o Loop is formed in order to maximise best possible alignment of homologous chromosomes prior to meiosis
o If cross-over occurs in this loop then 50% of gametes produced from heterozygote inversion will be unbalanced which means they will not have normal haploid genome content.
o Zygotes produced form unbalanced gametes do not normally survive.
18
Q
What is a paracentric Inversion?
A
Doesn’t include the centromere.
- A cross-over in the inversion loop of a paracentric inversion forms an acentric chromosome (no centromere) which is lost in meiosis and a dicentric chromosome (2 centromeres) which breaks resulting in deletion fragments.
Therefore only the 2 chromatids that don’t take part in crossing over result in viable gametes
19
Q
What Is a pericentric inversion?
A
Includes the centromere
20
Q
Types of chromosomal translocations
A
- Non-reciprocal translocation: part of 1 chromosome breaks off and is joined to a non-homologous chromosome
- Reciprocal translocation: 2 non-homologous chromosomes swap genetic material
- Reciprocal translocation can be balanced (no genetic material is lost) or unbalanced
- Translocation heterozygotes (often show no phenotype) are semi-sterile because only 50% of gametes are viable (have complete complement of genetic material)
21
Q
Reciprocal Translocations
A
- Quadrivalent: 4 chromosome structure formed during reciprocal translocation
o 2 of these chromosomes pass into gametes - Can promote myelogenous leukaemia (uncontrolled cell division of white blood cells in bone marrow)
o Reciprocal translocation between chromosome 9 & 22 - Unbalanced reciprocal translocation:
o Leads to loss of genetic material
22
Q
What are Robertsonian Translocations?
A
- Most common type of unbalanced reciprocal translocation
- Occurs between 2 acrocentric chromosomes
- Generates large metacentric and small chromosome which is often lost
- If between 14-21 leads to Down Syndrome
23
Q
What is aneuploidy?
A
Change in chromosome number
24
Q
3 types of anueploidy
A
- Monosomy (2n-1)
- Trisomy (2n+1)
- Tetrasomy (2n + 2)
- Because of dosage compensation humans can tolerate aneuploidy of sex chromosomes if its on the X chromosome
25
Q
What is euploidy?
A
The complete set of chromosomes in a cell
26
Q
What is polyploidy?
A
More than the normal diploid number of chromosome SETS
- Triploidy (3n)
- Tetraploidy (4n)
27
Q
How does aneuploidy form?
A
As a result of nondisjunction in meiosis
28
Q
what is nondisjunction?
A
Failure of chromatids to separate during mitotic anaphase
29
Q
Mitochondrial DNA General information
A
- mtDNA is found in matrix of mitochondria (between 2 membranes) in nucleoids
- Nucleoids = condensed DNA-containing structures
- 4-5 mtDNA mols/nucleoid; 10-30 nucleoids/mitochondria; ±40 mitochondria/cell
- Different cells/tissues have different numbers of mtDNA mols
- Size and gene content of mtDNA can vary from organism to organism
- Mitochondria can fuse/divide and generally first doubles in size, then divide into half in each cell generation
- Replication of mitochondria is random and not limited to the S-phase of the cell cycle.
- To have a fully functional organelle:
o Mitochondrial and chloroplast genomes must have co-op between organelle genomes and nuclear genomes - ANIMAL mtDNA does not use universal genetic code (but plant does)
30
Q
Structure of animal mtDNA
A
- Genome is circular & supercoiled
- Genome size is ±17kbp
- 37 genes and NO introns
- 100-1000’s of copies in cell
- D-loop (control loop) doesn’t code for anything, its where synthesis begins
31
Q
Yeast mtDNA genome features
A
- 4x longer than human/animal mtDNA
- Long intergenic sequences separate genes (makes up about ½ of yeast mtDNA genome)
- Introns from about 25% of yeast genome
32
Q
Plant mtDNA genome
A
- Large mtDNA genome
- More genes than animals or fungi
o 12 e- transport genes
o 16 ribosomal protein genes
o 20 genes of unknown function
33
Q
mtDNA Genetic Diseases
A
- Mitochondria are maternally inherited in higher animals because the egg is the major source of cytoplasm to the zygote
- Therefore:
Child will inherit mothers phenotype - Some mtDNA mutations result in disease which decreases ATP-generating capacity of the mitochondria:
o Affect function of muscle and nerve cells
o Could lead to blindness, deafness and stroke - mtDNA diseases are lethal, or can be variable in their severity
o because tissues can have different proportions of normal vs abnormal mtDNA
34
Q
What is MERRF?
A
- Myoclonic epilepsy & ragged red fibre disease
- It is caused by mutation in tRNA-Lys which affect the synthesis of all proteins coded in mitochondria
o MERRF is lethal if there are no normal mitochondria
35
Q
What is heteroplasmy?
A
When there are 2 types of mtDNA present in the same cell
36
Q
What is homoplasmy?
A
When there is 1 type of mtDNA present in the same cell
37
Q
What affects the range of severity of mtDNA genetic disease phenotypes?
A
- Ratio of disease:normal mtDNA in the same cell
2. Which cell type has highest proportion of mutated mtDNA
38
Q
Mitochondrial inheritance in identical twins
A
- Mitochondrial genomes are NOT the same in twins although the nuclear genomes are identical
- For e.g. the symptoms of neurodegenerative diseases or other mutations may manifest in one twin, but not the other twin
- Different mitochondrial genomes in twins because the mother is heteroplasmic mother and probability of disease phenotype in each twin depends:
o How the mutant mtDNA is partitions after fertilization
o Which tissue receives the mutation during development
39
Q
Mechanisms of uniparental inheritance
A
- Differences in gamete size
- Degradation of organelles in male gametes of some organisms
o Here the zygote destroys paternal organelle after fertilization - Paternal organelles are excluded from some organisms
40
Q
What is the endosymbiont theory?
A
- Mitochondria & chloroplasts originated > 1bya as free living cells
- Ancient archaea cells engulfed bacteria and established symbiotic relationship (formed mitochondria)
- Endosymbiont then engulfed cyanobacteria and formed chloroplast
41
Q
Evidence for endosymbiont theory
A
- Both chloroplasts and mitochondria have their own circular supercoiled DNA like bacteria
- mtDNA & cpDNA are NOT organised into nucleosomes by histones (similar to bacteria)
- Mitochondrial genomes use N-formylmethionine and tRNAfmet in translation (like bacteria)
- Inhibitors of bacterial translation also inhibit mitochondrial translation, but not eukaryotic cytoplasmic protein synthesis
- Chloroplasts & mitochondria genomes are organised with functionally related proteins close together & often expressed as single unit (like operons)
- Ribosome particles have subunits the same size as prokaryotes
- Sequences of chloroplast ribosomes similar to cyanobacteria & even E. coli
42
Q
mtDNA/cpDNA rate of mutation
A
- Animal mtDNA has mutation rate 10x higher than nuclear DNA
o Reflects more errors in replication
o Reason is less efficient repair mechanisms & high levels of reactive oxygen species due to oxidative phosphorylation
o Means they have fewer tRNA than required to make all amino acids - cpDNA has mutation rate faster than nuclear DNA
43
Q
Multi-Regional hypothesis
A
- Theory for origin of humans
- H. erectus migrated out of Africa 1-2MYA
- H. erectus gives rise to archaic humans in different regions
o i.e., homo sapiens evolved 4 times independently of each other in 4 different regions - These regions (subspecies) maintain some gene flow and eventually give rise to modern humans in multiple locations
44
Q
Out of Africa hypothesis
A
- H. erectus migrated out of Africa 1-2 MYA
- H. erectus gives rise to archaic humans in different regions BUT goes extinct except in Africa
- H. sapiens evolved in Africa ± 100 000 years ago
- H. sapiens subsequently spread to other regions and displaces other hominid species
45
Q
Results of Cann, Stoneking & Wilson mtDNA studies
A
- Common ancestor to modern humans = 200 000 – 290 000 years ago
- Oldest individuals are African individuals. Oldest Africans have a high sequence divergence – evidence of recent evolution of modern humans and out of Africa hypothesis
- Non-Africans have multiple origins in one branch only (the more recent branch)
- Greatest variation exists in African lineage = found in many places on tree
- Earliest branch only contains Africans; therefore an ‘African Genesis’ is implied (mitochondrial Eve)
46
Q
What is a Population?
A
Group of interbreeding individuals of the same species that inhabit the same space at the same time and exchange genes
47
Q
What is a Gene pool?
A
Sum total of alleles carried by all members of a population
48
Q
What is Microevolution?
A
Changes in allele frequency within a population
49
Q
What is Phenotype frequency?
A
Proportion of individuals in a population that have a particular phenotype
50
Q
What is Genotype frequency?
A
Proportion of individuals in a population that carry a particular genotype
51
Q
What can cause changes to the gene pool?
A
- Mutation
- Immigration of new individuals into or out of the population
- Selection
52
Q
Hardy-Weinberg Law Assumptions
A
- The population has an infinite number of individuals
- Individuals mate at random
- No new mutations appear
- No migration into or out of the population
- Genotypes have no effect on ability to survive and transmit alleles to the next generation
53
Q
What are Founder Effects?
A
Occur when a few individuals separate from a larger population and establish a new population
Results in reducing allele frequencies
54
Q
What is Population bottlenecks?
A
A large proportion of individuals die
Survivors are equivalent to a founder population and will have a different allele frequency to the original population
55
Q
What is natural selection?
A
The process that progressively decreases/eliminates genotypes with a lower fitness in a population
56
Q
Random Genetic Drift
A
- Major cause of genetic variation among populations especially small populations
- Occurs because populations are NOT infinitely large
- Only a few gametes participate in fertilisation & contribute to zygotes in the next generation
o i.e. alleles are lost because not all the individuals participated in fertilisation
