Understanding Chromosomes

Definition of a Chromosome

• German biologist Walter Flemming discovered chromosomes during cell division in the 1880s.
• During cell division, nuclear material assembles into visible, thread-like structures.
• These structures, which stain deeply with basic dyes, received the name chromosomes.
• Chromosome translates to "colored bodies," referring to their affinity for stains.
• Chromosomes are defined as a highly organized arrangement of DNA and proteins.
• Chromosomes contain numerous genes, hereditary units, regulatory elements, and nucleotide sequences.
• DNA-bound proteins within chromosomes package DNA and control its functions
• Chromosomes vary in number and structure across different organisms.
• The number of chromosomes is a characteristic feature of each species.
• Benden and Bovery reported in 1887 that the number of chromosomes is constant in each species.
• Sutton and Boveri suggested in 1902 that chromosomes are the messengers of heredity

Chromosome Composition and Structure

• Chromosomes consist of tightly coiled DNA around basic histone proteins.
• Histone proteins facilitate the tight packing of DNA.
• DNA exists as chromatin during interphase, and it is not tightly coiled into chromosomes.
• Chemically, chromosomes contain proteins mainly composed of protamines, histones, and smaller amounts of acidic proteins and nucleic acids.
• Nucleic acids are deoxyribose nucleic acids (DNA), and genes are segments of DNA.
• Eukaryotic DNA undergoes condensation to fit within the nucleus.
• The degree of DNA condensation is expressed as a packing ratio.
• Packing ratio is the length of DNA divided by the length into which it is packaged into chromatin along with proteins.

Morphology

• Chromosome size is normally measured at mitotic metaphase.
• Chromosomes range from 0.25μm in fungi and birds to 30 μm in some plants like Trillium.
• Most mitotic chromosomes range from 3μm in Drosophila to 5μm in humans, and 8-12μm in maize.
• Monocots contain larger chromosomes than dicots.
• Organisms with fewer chromosomes tend to have larger chromosomes.
• Chromosome shape changes from phase to phase during cell growth and division.
• Chromosomes appear as thin, coiled, elastic, contractile, thread-like stainable structures called chromatin threads during interphase.
• In metaphase and anaphase, chromosomes become thick and filamentous.
• Each chromosome contains a clear zone known as the centromere or kinetochore along its length.
• The centromere divides the chromosome into two parts, each called a chromosome arm.
• The centromere's position varies, giving chromosomes different shapes and the shape is the name to describe them:
• Telocentric: Centromere is located at the proximal end of the chromosome.
• Acrocentric: Centromere positioned at one end, resulting in one very short arm and one long arm.
• Submetacentric: J or L-shaped chromosome with the centromere near the center.
• Metacentric: V-shaped with the centromere located at the center.

Structure of Chromosome

• A chromosome at mitotic metaphase includes two symmetrical structures, called chromatids.
• Each chromatid consists of a single DNA molecule.
• Chromatids are attached to each other by the centromere, separating at the beginning of anaphase.
• Chromomeres are bead-like accumulations of chromatin material.
• Chromomeres sometimes become visible along interphase chromosomes.
• A chromomere bearing chromatin looks like a necklace with several beads on a string.
• Chromomeres are regions of tightly folded DNA, and they become prominent in polytene chromosomes.
• The centromere in a chromosome has specific DNA sequences with special proteins that form a disc-shaped structure, called the kinetochore.
• Under an electron microscope, the kinetochore displays as a plate or cup-like disc with a diameter of 0.20-0.25 nm.
• The kinetochore is located upon the primary constriction, or centromere.
• Most organisms' chromosomes contain only one centromere and are known as monocentric chromosomes.
• Centromeres are condensed regions within the chromosome, that ensure correct segregation of the replicated chromosome during mitosis and meiosis.
• When chromosomes are stained, a dark-stained region, namely the centromere, is typically visible.
• The kinetochore is the location where spindle fibers attach and it consists of DNA and protein.
• The DNA sequence inside these regions is CEN DNA
• CEN DNA can be moved from one chromosome to another and continue to allow segregation.
• CEN DNA is about 120 base pairs long and contains sub-domains: CDE-I, CDE-II and CDE-III.
• Mutations in the CDE-I and CDE-II sub-domains do not affect segregation.
• But a point mutation in the CDE-III sub-domain eliminates the centromere's ability to function during chromosome segregation.

Involvement of CDE-III

• Must be actively involved in the binding of the spindle fibers to the centromere.
• The protein component of the kinetochore is now under characterization.
• A complex of three proteins called Cbf-III binds to normal CDE-III regions.
• Cbf-III cannot bind to a CDE-III region with a point mutation that prevents mitotic segregation.
• Mutants of the genes encoding the Cbf-III proteins eliminate the ability for chromosomes to segregate during mitosis.
• Further analyses of the DNA and protein components of the centromere are required to fully understand how chromosome segregation works.
• Some species feature diffused centromeres.
• Microtubules attach along the length of the chromosomes: holocentric chromosomes.
• Chromosomes of Ascaris megalocephala: examples of diffused centromeric chromosomes.

Telomeres

• Telomeres are "caps" at the end of the chromosome that consist of repetitive DNA sequences.
• Prevents fusions of chromosomes with each other
• Stabilizes chromosome structure
• Certain bacteria have telomeres in their linear genetic material, and they can be either a hairpin telomere or an invertron telomere.
• Hairpin Telomere: bend around from the end of one DNA strand to the end of the complimentary strand.
• Invertron Telomere: allow an overlap between the ends of the complimentary DNA strands.

Telomere Replication

• An important step in DNA replication.
• The primary difficulty with telomeres is the replication of the lagging strand.
• DNA synthesis requires a RNA template (that provides the free 3'-OH group) to prime DNA replication.
• This template is eventually degraded.
• A single-stranded region is left at the end of the chromosome.
• This region is susceptible to enzymes that degrade single-stranded DNA.
• This reduces the length of the chromosome after each division called, the end replication problem.
• Telomerase enzymes ensure the lagging strands ends are replicated correctly.
• Telomerase contains an RNA primer that is complementary to the end of the G-rich strand.
• The G-rich strand extends past the C-rich strand.
• The telomerase RNA binds to the protruding end of the G-rich strand and acts as a template for adding nucleotides onto the 3' terminus of the strand.
• A segment of DNA is synthesized,
• The telomerase RNA slides to the new end of the strand being elongated.
• Serves as the template for the incorporation of additional nucleotides.
• The gap in the complementary strand is filled by the replication enzymes polymerase α-primase.
• Telomerase activity is retained in germ cells and zygotes, while somatic cells do not show such activities after a few cell division cycles.
• Telomeres shrink, which causes chromosome shortening.
• This causes the cell to stop growing and dividing.
• Werner’s syndrome is an inherited disease causes aging much more rapidly caused by abnormal telomere maintenance.
• Besides the primary constrictions or centromeres, chromosomes also posses secondary constriction at any point, in a constant position and extent.
• These constrictions determine particular chromosomes.
• Chromosomes also contain nucleolar organizers.
• Secondary constrictions contain genes coding for 5.8S, 18S and 28S ribosomal RNA.
• Induce the formation of nucleoli.
• Sometimes chromosomes bear round, elongated, or knob-like appendages called satellites.
• The satellite is connected to the rest of the chromosomes by a thin chromatin filament.
• Each chromosome has a p and q arm known as the p and q arm
• p (petit) = the short arm
• q = the long arm
• Some chromosomes (13, 14, and 15) have small p arms.
• The q arm is placed at the bottom, and the p on the top when a karyotype is made.
• Arms are separated by a region known as the centromere, a pinched area of the chromosome.
• Eukaryotic chromosomes are composed of chromatin fiber in eukaryotes.
• Chromatin fiber: nucleosomes or histone octamers: a DNA strand attached to and wrapped around it.
• Chromatin fibers are packaged by proteins into a condensed structure named chromatin
• Chromatin carries the bulk of DNA and a small amount inherited maternally, can be found in the mitochondria.
• Chromatin is present in most cells other than red blood cells.
• Chromatin allows large DNA molecules fit into the cell nucleus.
• The DNA Molecules either Duplicated or Unduplicated.
• Unduplicated chromosomes consist of single double helixes
• Duplicated chromosomes have two identical copies (called chromatids or sister chromatids) joined by a centromere.
• Each chromosome has a constriction point: the centromere
• The centromere divides the chromosome into two sections known as arms:
• short arm = “p arm” and a long arm = “q arm.”
• The centromere's place gives the chromosome its shape.

Chromosomes in Prokaryotes vs. Eukaryotes

• Prokaryotic Chromosome: Absent of typical chromosome formation, only a single chromosome, Comparatively shorter, Has C ovalently closed circular DNA and codes for few proteins. Is free in the cell center, and can touch the cytoplasm. Sometimes has mesosomes, and DNA is not in histone proteins. Nucleosomes aren't formed, only has one for of replication, negative charge reversed by Mg ions and centromeres doesn't form.
• Eukaryotic Chromosomes: Has genetic material and multiple chromosomes, has linear DNA with 2 ends and has many different proteins. Has enclosed cells and aren't in contact with cytoplasm, cannot produce plasmic membrane, the DNA in histone proteins and nucleosmes are produced. Also has many replications, produces lots of histone proteins and forms centromeres

Chromatin Composition

• Chemical composition: DNA, RNA and protein. Proteins are further divided into histones and non-histones.
• DNA is the most important chemical component, playing a central role in controlling heredity. It's measured in picograms.
• Besides chromosome number, the amount of DNA in a haploid cell also defines an organism's genome.

Histones

• Histones: arginine and lysine. At physiological pH, they are cationic and interact with anionic nucleic acids.
• Form a highly condensed structure. There are five types of histones: H1, H2A, H2B, H3, and H4.
• Are conserved during evolution among eukaryotes.
• H1 is the least conserved and loosely bound with DNA and is absent in Sacharomyces cerevisiae.
• Non-histones include are involved in a range of activities, including DNA replication and gene expression. Highly diverse
• Roger Kornberg described the basic structural unit of chromatin as the nucleosome in 1974.
• Histones are positive charged proteins that wrap up DNA.
• DNA--Histone complex formed by eight histone molecules.
• 2x H3--H4
• 2x H2A--H2B and are and are kept together by H1 histone
• Each nucleosomes have two turns of DNA
• The length of DNA per nucleosome varies from 154-‐260bp.

Chromatin

• Euchromatin: Lightly-stained regions; contains single-copy, genetically-active DNA. Chromatin condensation varies, and is essential to regulating gene expression. Chromatin are decondensed, known as euchromatin.
• Heterochromatin: Coined by Heil based on cytological observations in nucleosomal arrays. Accounts for 10% of the chromatin which are in high density. Two Types of Heterochromatin: constitutive and facultative heterochromatin. The regions where the cells are at all points, these areas contain repetitive DNA. Constitutive heterochromatin is located by mammals' telomeres arm.

Effects of Genes

• Constitutive heterochromatin possesses has lead to transcriptional inactivation of nearby genes and inhibits recombination.
• This phenomenon is “position effect”.
• Facultative heterochromatin is chromatin that is inactivated during certain phases of an organism's life.

Chromosome Function

• Chromosomes are self-duplicating: DNA strands unwind, and each template DNA forms its complementary strand in double-helix form.
• Aided expression: expression of characteristics in cell.
• Conversion from the old to the new molecules duplicate chromosome.A definite protein is accumulated to produce the definite character.