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MCB2020F > Eukaryote Genome Organisation & Evolutionary genetics > Flashcards

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.
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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
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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
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4
Q

Radial-loop Scaffolding Compaction

A

DNA compaction is sequential and progressive:

  1. First chromatin fibres (20Â) are wrapped around nucleosomes (100Â), which are supercoiled (300Â)
  2. Supercoiled chromatin undergoes compaction and forms loops held together by non-histone, scaffolding & non-scaffolding proteins.
  3. Chromatin loops form a rosette shape (daisy-like) held together by additional non-histone scaffold proteins
  4. Rosettes condense into compact bundles to rodlike chromosomes – this is 10 000 times more compact than naked DNA
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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
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6
Q

What are the uses of karyotypes?

A
  1. Locate genes on a chromosome
    a. Chromosome divided into long and short arm joined by centromere
  2. Reveals cause of genetic diseases
    a. E.g. down syndrome (3 copies of Chr21)
  3. Analyse chromosomal difference between species
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7
Q

What are 3 specialised elements of Chromosomes?

A
  1. Origins of Replication
  2. Telomeres
  3. Centromeres
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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
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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
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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
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11
Q

What is a metacentric chromosome?

A

Centromere is in the middle

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12
Q

What is an Acrocentric chromosome?

A

Chromosome in non-symmetrical.

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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
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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

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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
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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.
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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.
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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

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19
Q

What Is a pericentric inversion?

A

Includes the centromere

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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)
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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
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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
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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
  1. 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
  1. Both chloroplasts and mitochondria have their own circular supercoiled DNA like bacteria
  2. mtDNA & cpDNA are NOT organised into nucleosomes by histones (similar to bacteria)
  3. Mitochondrial genomes use N-formylmethionine and tRNAfmet in translation (like bacteria)
  4. Inhibitors of bacterial translation also inhibit mitochondrial translation, but not eukaryotic cytoplasmic protein synthesis
  5. Chloroplasts & mitochondria genomes are organised with functionally related proteins close together & often expressed as single unit (like operons)
  6. Ribosome particles have subunits the same size as prokaryotes
  7. 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
  1. The population has an infinite number of individuals
  2. Individuals mate at random
  3. No new mutations appear
  4. No migration into or out of the population
  5. 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

MCB2020F (6 decks)

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