chromosomes

I. The Chromosomal Basis of Genes and Heredity

• Genome organization

  • Nuclear DNA: linear chromosomes in nucleus, double-helix structure

  • Organelle DNA: circular chromosomes in mitochondria (and chloroplasts in plants/algae), typically lacking introns and with distinct replication processes

  • Nuclear envelope: key feature of eukaryotes, a double membrane that encloses the nucleus and controls molecular transport

II. The Eukaryotic Cell Division Cycle

1. Phases

• G1 (Gap 1): period of cell growth and normal metabolic roles, synthesizing proteins and organelles; prepares for DNA replication.

• S (Synthesis): DNA replication occurs, resulting in $2$ identical sister chromatids per chromosome.

• G2 (Gap 2): further growth, synthesis of proteins needed for mitosis; cell checks for DNA damage and completeness of replication.

• M (Mitosis + Cytokinesis): division of nucleus and cytoplasm

• Interphase = G1 + S + G2

• G0: quiescent, non-dividing state where cells exit the cell cycle and differentiate into specialized functions (e.g., neurons, muscle cells).

• Checkpoints: regulatory points (G1, G2, M) that monitor internal and external conditions, ensuring proper progression and preventing errors like incomplete replication or chromosome damage.

2. Chromosome/DNA content

• End of mitosis & G1/G0: 1 DNA molecule per chromosome

• After S-phase & G2: 2 DNA molecules (sister chromatids)

3. Key structures

• Telomeres: repetitive nucleotide sequences at the stable ends of linear chromosomes, protecting DNA from degradation and undesirable fusion.

• Centromere: constricted region joining sister chromatids, essential for proper chromosome segregation during cell division.

• Kinetochores: protein complexes assembled at centromeres, serving as attachment sites for spindle microtubules.

  

• Centrosome: microtubule-organizing center (pair of centrioles in animal cells); involved in forming the mitotic spindle(the pole).

III. DNA in the Eukaryotic Nucleus

Chromatin

• Decondensed DNA + histones (proteins that DNA wraps around to form nucleosomes)

• Condenses before cell division into visible chromosomes through further coiling and folding.

• Nucleosome = basic structural unit (DNA + histones)

Chromosomes

• Before replication: single DNA molecule

• After replication: two identical sister chromatids, joined at the centromere until anaphase.

• Classification by centromere location:

  • Metacentric (middle)

  • Submetacentric (near center)

  • Acrocentric (near end)

  • Telocentric (at end)

• Arms: p (short) and q (long)

IV. Genes, Loci, and Alleles

Gene

• Transmission genetics: unit of heredity that is passed from parent to offspring.

• Molecular genetics: region of DNA (or RNA) coding for a functional product (e.g., protein, tRNA, rRNA).

Locus

• Specific, fixed position or location on a chromosome where a particular gene is found.

Alleles

• Alternative forms of the same gene, residing at the same locus on homologous chromosomes.

Homologous chromosomes

• Pair of chromosomes (one from each parent) that are the same length, have the same centromere location, and carry genes for the same traits in the same loci order.

• May carry different alleles for those genes.

• Not sister chromatids (which are identical copies produced during replication).

V. Karyotypes and Ploidy

Karyotype

• Visual display of the complete set of chromosomes in a cell, arranged by size, centromere position, and banding patterns.

• Human: 22 pairs of autosomes + 1 pair of sex chromosomes (XX or XY); used to detect chromosomal abnormalities and determine sex.

Ploidy

• Diploid ($2n$): cells containing two sets of homologous chromosomes (e.g., somatic cells in humans, $2n=46$).

  

• Haploid ($n$): cells containing a single set of chromosomes (e.g., gametes like sperm and egg, $n=23$ in humans).

• Polyploid ($3n$, $4n$, etc.): cells or organisms containing more than two complete sets of chromosomes.

• Aneuploid: abnormal number of chromosomes that is not an exact multiple of the haploid set (e.g., monosomy (2n-1), trisomy (2n+1), such as not 46 in humans).

VI. Mitosis

any ploidy can undergo mitosis

1. Phases

• Prophase: chromatin condenses into visible chromosomes, mitotic spindle begins to form as centrosomes migrate to opposite poles.

• Prometaphase/Metaphase: nuclear envelope fragments; kinetochore microtubules attach to kinetochores on sister chromatids; non-kinetochore microtubules overlap; chromosomes align along the metaphase plate (equatorial plane).

• Four individual chromosomes go to the plate which is the main difference with mitosis and meiosis.

• Anaphase: sister chromatids separate and are pulled to opposite poles of the cell by the shortening of kinetochore microtubules. When separated they are now 8 chromosomes with one molecule of DNA each.

• Telophase: DNA decondenses, chromosomes arrive at poles, and nuclear envelopes reform around the two sets of chromosomes; mitotic spindle disassembles.

• Cytokinesis: cytoplasm divides; in animal cells, a cleavage furrow forms; in plant cells, a cell plate forms to create new cell walls.

• Outcome: 2 diploid ($2n$) daughter cells, genetically identical to the parent cell; crucial for growth, repair, and asexual reproduction.

VII. Meiosis

germ cells and has to be able to form pairs Diploid only or an even multiple of the haploid number

Overview

• Specialized division $\to$ gametes (animals) /spores (plants); (in sexually reproducing organisms).

• Involves two successive divisions (Meiosis I and Meiosis II) leading to $4$ haploid cells.

• Outcome: 4 haploid ($1n$) cells, genetically unique due to crossing over and independent assortment; crucial for sexual reproduction and genetic diversity.

  

Meiosis I (Reductional division)

• Homologous chromosomes pair $\to$ tetrads (bivalents).

  

• Synaptonemal complex: protein structure mediates stable pairing of homologous chromosomes (synapsis) and assists in crossing over. The cell makes enzymes which means it wants this to happen.

  

• Prophase I substages:

  1. Leptotene – DNA begins condensing, chromosomes become visible as long, thin threads.

  2. Zygotene – homologs pair (synapsis) side by side, forming tetrads/bivalents; synaptonemal complex forms.

  3. Pachytene – crossing over occurs between non-sister chromatids, exchanging genetic material; this is often the longest substage.

  4. Diplotene – homologous chromosomes start to separate but remain joined at chiasmata (sites where crossing over previously occurred).

  5. Diakinesis – final condensation of chromosomes; nuclear envelope fragments; spindle fibers begin to form.

     

• Anaphase I: homologous chromosomes segregate and move to opposite poles; sister chromatids remain attached.

• Homologous pairs of chromosomes line up along the metaphase plate is the main difference with mitosis and meiosis.

  

• Outcome: 2 haploid ($1n$) daughter cells (not identical) but each chromosome still consists of two sister chromatids.

Meiosis II (Equational division)

• Sister chromatids disjoin; very similar to mitosis but occurs in haploid cells.

• Outcome: 4 haploid gametes (or spores in plants/fungi), each with a single set of unduplicated chromosomes.

Comparisons

• Mitosis: occurs in somatic cells for growth, repair, and asexual reproduction; no homolog pairing or crossing over; results in 2 genetically identical diploid cells.

• Meiosis: occurs in germ line cells for sexual reproduction; involves homolog pairing, crossing over, and two divisions; results in 4 genetically unique haploid gametes.

VIII. Gametogenesis

• Spermatogenesis: process in males leading to sperm formation; involves equal cytokinesis $\to$ 4 functional sperm cells from one primary spermatocyte.

• Oogenesis: process in females leading to egg formation; involves unequal cytokinesis $\to$ 1 large functional egg (ovum) + 2 or 3 small polar bodies (which degenerate) from one primary oocyte.

• Fertilization: fusion of male and female gametes (sperm and egg) restores the diploid state, forming a zygote.

IX. Yeast Life Cycle (Saccharomyces cerevisiae)

• Exists as diploid ($2n$) or haploid ($n$) cells.

• Both can divide mitotically to produce more cells of their respective ploidy.

• Haploids of opposite mating type (a and $\alpha$) can fuse ($\to$ diploid zygote), which then grows mitotically.

• Diploid cells under environmental stress (e.g., nutrient depletion) can undergo meiosis $\to$ 4 haploid spores inside an ascus (a sac).

X. Meiotic Failures

• Refer to situations where chromosome numbers are not even multiples of the haploid number, often leading to sterility.

• Triploids ($3n$): organisms with three sets of chromosomes; typically sterile because homologous chromosomes cannot properly pair and segregate during meiosis, leading to unbalanced gametes.

• Examples:

  • Seedless watermelon: often produced by crossing a tetraploid ($4n$) parent with a diploid ($2n$) parent, resulting in a triploid ($3n$) hybrid that cannot produce viable seeds due to meiotic irregularity.

  • Mules: sterile hybrids resulting from a cross between a horse and a donkey, which have different chromosome numbers, leading to unpaired chromosomes in meiosis.

XI. Nondisjunction

• Failure of homologous chromosomes (in Anaphase I of meiosis) or sister chromatids (in Anaphase II of meiosis or Anaphase of mitosis) to separate properly.

• Consequences: leads to aneuploidies (abnormal chromosome numbers in gametes or somatic cells).

  • Trisomy: presence of an extra copy of a chromosome ($2n+1$).

  • Monosomy: absence of one copy of a chromosome ($2n-1$).