VL 17 (George Soultoukis)

Question 1

Important key terms

Answer 1

Viral genome:
the entire genetic sequence of a virus

Nucleoid:
the condensed genetic material of a prokaryote (vs. nucleolus in eukaryotes, or nucleotides, a monomer unit)

Heterochromatin and euchromatin:
two states of inactive and active chromatin

Histone octamer:
a protein complex comprising nucleosomes

Nucleosome and nucleosome arrays:
the subunits that make up condensed chromatin

DNA supercoiling:
topoisomeric modulation of DNA double helices

Open vs. Closed DNA regions: accessible vs. non-accessible DNA regions

Telomere:
chromosomal caps and lost with cellular senescence

Question 2

Viral genomes

Answer 2

Viruses:
infectious, self-replicating molecular engines

• Evolved from bacteria or plasmids (bacteria/archaea, “cellular origin hypothesis”) vs. “virus first hypothesis”
  –> paleovirology
• Viral genomes can be made of DNA or RNA, and code the basic machinery for viral particle reproduction i.e. of replicating all components of a viable virus
• DNA density (compaction): prokaryotic cell (x1) < eukaryotic cell (x10) < virus capsule (x50)
• Viruses have an outer shell, a viral protein coat known as capsid, which surrounds the self-replicating nuclei acid molecule

Viroids: plant pathogens without a protein coat

Question 3

Explain DNA supercoiling

Answer 3

• A relaxed B-DNA contains 10.5 bp / twist around the helical axis
• Introducing additional twists imposes a strain:
  –> a single „O“ DNA molecule will turn into an „8“
• For each new twist, a new coil („writhe“) will be produced.
• Underwound coiled DNA is negatively twisted, and represents the state of most DNA helices in most species

Topoisomerases can sense supercoiling tension, and either dissipate it (release) or increase it

Question 4

Eukaryotic cell nucleus

Answer 4

• Cell nucleus contains all DNA apart from organellar DNA
• Lipid bilayer known as nuclear envelope encases all nuclear DNA and related proteins (TFs, histones, …)
• Nuclear membrane is embedded with signalling proteins, transport/carrier proteins, and other protein complexes that coordinate nuclear processes such as transcription, mitosis, and others.
• Nuclear pore complexes (NPCs) transport:
  –> RNA
  –> Ribosomal proteins
  –> Lipids and carbohydrates
  –> Signaling molecules

Question 5

Chromosomes

Answer 5

• Each chromosome contains a single double-stranded DNA molecule tightly compacted around proteins
• The entire complex fibrous-like structure of DNA and proteins forms chromatin
• Chromatin condenses during cell division (mitosis, prophase), and can be seen as chromosomes (metaphase)
• Present in most cells, with some exceptions (e.g. erythrocytes)
• Highly variable numbers of chromosomes between species a result of evolution and speciation

Question 6

Chromosomal segregation during mitosis/meiosis can alter cell division during evolution

Answer 6

• The two species co-existed for tens of thousands of year, and exchanged genes, until „real WWI“ ~30,000 ago (Watson 2003)
• Neanderthals were physically stronger with thicker bones and muscle mass, more tools and earlier, and are thought to be the first species that buried their dead and were creative (wall paintings and other representational art)
• Mutation in genes Casc5, Spag5, and Kif18a in occurred in Homo sapiens, compared to Homo neanderthalensis, affecting the human kinetochore function during stem cell division in neurons, potentially affecting brain development and brain size changes between the two species (Svante Pääbo et al. 2022)

Question 7

Chromatin structure

Answer 7

• Heterochromatin (transcriptionally silent DNA) and euchromatin (transcriptionally active DNA)
• Heterochromatin can be facultative (inactivated X, reverses to euchromatin state) or constructive (centromeres and telomeres)

Question 7

Explain Histones and nucleosomes

Answer 7

• The nucleosome is the subunit of all chromatin
• A single nucleosome consists of about 160 bp of DNA sequence wrapped around a core of histone proteins
• Nucleosome arrays across DNA domains and regions are arragned as „beads on a string“
  –> Arrays are folded to form chromatin fibers
• Chromatin fibers are compacted and condensed to form a chromosome
• A nucleosome consists of a segment of DNA wound around eight histone proteins (octamer)
• The histone octamer consist of two copies each of the histone proteins H2A, H2B, H3, and H4
• Each human cell contains around 30 million nucleosomes, each carrying its own epigenetic signature
• Nucleosome positions in the genome are not random, and determine accessibility of DNA to regulatory proteins
• A polynucleosome is a chain of mononucleosomes linked by DNA and histone proteins

Question 8

Open vs- closed DNA regions

Answer 8

Question 9

What are chromosomal telomeres and what do they have to do with aging?

Answer 9

• Telomeres seal and protect the end of chromosomes from degradation
• They therefore prevent unwanted DNA annealing („sticking“) of chromosomal ends with other chromosomes.
• Consists of long series of short tandem repeat sequences, in mammals and plants: Cn(A/T)m where n>1 and m≤4
• Telomeres are added by telomerase, but telomerase is not active in somatic cells (only in gametes & cancer cells)

Aging
* Telomeres are lost in each cell division, so in each mitosis the telomeres shorten slightly

• Somatic cell division can only occur a certain amount of times under normal physiological conditions, before cell division stops
• Leonard Hayflick determines this to be somewhere between 40-60 times (1961)
• Once telomeres reach a critical length, cell division will cease, which was referred to as cellular senescence
• The ageing of cell populations is positively correlated with the physical ageing of an organism
• The Hayflick limit correlates with the length of the telomeric region at the end of chromosomes
• During DNA replication of a chromosome, small segments of terminal DNA are not copied and are lost
• Cell lines are immortalised cells with high telomerase activity

Question 10

What is X Chromosomae inactivation

Answer 10

• To avoid gene expression misregulation, one of the two X chromosomes in females is inactivated (randomly or skewed between parental chromosomes)
• This results in a haploid chromosome pair 23
• One of the two inherited chromosomes becomes densely supercoiled with multiple superloops of chromatin, and forms a compact structure that is referred to as a Barr body
• Anchoring the superloops is a DNA satellite sequence called DXZ4 (macrosatellite)
• Loss or hypermutation of DXZ4 causes the superloops to unravel, which can lead to chromosomal activation

Question 11

What is homologous recombination?

Answer 11