1. Chromosomes
Subtopic 3.2

2. 3.2.1 Bacterial Chromosomes (prokaryotes)
Most only have 1 chromosome.
Which means, it only contains a single copy of each gene (except during cell division when chromosomes are replicated).
Has circular DNA that contains all genes needed for basic life processes of the cell.
DNA is “naked” – not associated with proteins.

3. Plasmids Small extra DNA molecules.
Common in prokaryotes, very unusual in eukaryotes.
Plasmids have small, circular and naked DNA, and contains few genes.
Genes on plasmids are useful to the cell, but are non-essential for life processes.
Ex: Antibiotic resistance genes are usually located in plasmids. Such gene is only useful when antibiotic is present.
Plasmids are not always replicated at the same time as chromosomes or at the same rate.
Plasmids can be transferred from one cell to another.
They can even cross the species barrier, when a dead prokaryotic cell gets absorbed by a cell of a different species.
Plasmids can also be used to artificially transfer genes between species.

4. Plasmids cont.
Diagram of a plasmid that carries two genes, making the bacterial cell resistant against ampicillin and tetracycline - two commonly used antibiotics.
Plasmids can be easily exchanged between bacteria, providing a mechanism by which antibiotic resistance spreads. Antibiotic resistant bacteria are a major problem in hospitals.

5. Autoradiography
This technique was used in the 1940’s to discover where specific substances were located in cells or tissues.
In the 1960’s John Cairns used the technique a different way to obtain images of whole DNA molecules from E. Coli bacteria, as well as measuring the length of DNA molecules.
The significance of his images:
Showed that bacterial chromosome was a single DNA molecule
Showed replication forks in DNA
Technique became used by other scientists.

6. Autoradiography – Cairns’ technique
Produced images of DNA molecules from Escherichia coli (E.coli).
E.coli was cultured in a medium containing labelled ribonucleotide thymidine (an important component in DNA comprising of deoxyribose sugar linked to the base thymine). This later was labelled with the heavy isotope of hydrogen, 3H, so that the newly replicated molecule synthesized by incorporating thymidine could be visualized through autoradiography.
He then lysed the E. Coli cells to release the cell content including the intact bacterial DNA on slides.
Next, he covered the slides with photographic emulsion and stored them in the dark for two months.
During that period the particles emitted by thymidine (incorporated in the DNA) caused the appearance of dark areas on the photographic emulsion.
The pattern of dark spots indicated the presence of labelled DNA (as shown in Figure 1).
The length of the DNA could then be measured and was worked out to about 1mm.

7. Pattern of dark spots indicating the presence of labeled DNA.
The autoradiographs developed by Cairns also showed that E. Coli contains a single circular DNA and demonstrated that replication occurs in a semi-conservative way.
DNA replication starts at the origin of replication and proceeds in both directions to give rise to two replication forks.
Showing an autoradiograph obtained by Cairns' (A) and its interpretation in terms of DNA (B) - the DNA is undergoing its second replication cycle in this case and appears as a θ (theta) shaped figure.

8. Improvements in technology and equipment allow development in scientific research.
Molecules are difficult to observe by direct observation even with the most powerful electron microscopes in use today. John Cairns overcame this difficulty by developing auto radiography in  
If a molecule has radioactive atoms or molecules incorporated into its structure, it will leave a trace on a photographic plate which can allow it to be identified or measured. Because of the large variety of biological molecules, the radioactive molecules have to be chosen so that they are only incorporated into the target molecule, Cairns used radioactive thymidine.  
John Cairns applied autoradiography to bacterial DNA molecules. He used radioactive thymidine as a nutrient which was incorporated into bacterial DNA on replication. The bacterial cell walls were damaged and the DNA leaked out of the cell. The bacteria were placed in a gel on a photographic plate. The radioactive DNA left a photographic trace which could be measured giving tangible evidence of the length of the DNA molecule in the bacteria.

9. Eukaryote Chromosomes
Chromosomes in eukaryotes are composed of DNA and protein.
DNA is a single very long linear DNA molecule.
DNA is associated with histone proteins.
Adjacent histones in the chromosome are separated by short stretches of DNA molecules not in contact with histones, giving it an appearance of a string of beads during interphase.
Chromosomes are not visible with a light microscope during interphase.
During cell division (mitosis and meiosis), chromosomes condense (become shorter and fatter) by supercoiling.

10. Eukaryotic chromosomes during interphase
Only visible during interphase
Referred to as chromatin

11. Eukaryotic chromosomes during cell division
- In the first stage of mitosis (and meiosis), the chromosomes appear as duplicated structures because they have been replicated, and they become more condensed; a process called supercoiling. Each chromosome consists of two chromatids.

12. Differences between chromosomes
Length
Position of the centromere
Humans have 23 different types of chromosomes.
Every eukaryote has at least 2 different kinds.

13. Locus The location of a specific gene on a chromosome.
Each chromosome type carries a specific sequence of genes arranged along a linear DNA molecule.

14. Homologous chromosomes
Carry the same sequence of genes, but not necessarily the same alleles.
Remember alleles are different versions of the same gene.

15. Interbreeding
Interbreeding happens among organisms of the same species.
This is possible because each chromosome in of the organism is homologous with at least one chromosome in the other.

16. Comparing the chromosomes of mice and humans.
Numbers and colors are used to indicate sections of mouse chromosomes that are homologous to sections of human chromosomes.
the majority of human chromosome 1 is composed of (i.e. is syntenic to) mouse chromosome 4, 3 and 1.

17. Genome size Organism Genome Size (mbp) Description T2 Phage 0.18
Virus that attacks E. coli
Escherichia coli 5
Gut bacterium
Drosophila melanogaster
140
Fruit fly
Homo sapiens
3,000
Humans
Paris japonica
150,000
Woodland plant
Genome size depends of eukaryotes depends on the size and number of chromosomes.
Genome size is correlated with the complexity of the organism, but it is not directionally proportional.
This is because the proportion of the DNA that acts as functional genes is very variable and also the amount of gene duplication varies.

18. Haploid nuclei
Haploid nuclei have one chromosome of each chromosome type.
Haploid cells in humans have 23 chromosomes.
Gametes = sex cells
Humans:
egg and sperm
23 chromosomes
Mosses are unusual because their cells are haploid.

19. Diploid nuclei
Diploid nuclei have pairs of homologous chromosomes found in its species.
Two chromosomes of each type.
Somatic cells = body cells.
Humans: 23 pairs, two copies of each gene, one maternal copy and one paternal copy of each gene.
Genetic advantage:
the effects of harmful recessive mutations can be avoided if a dominant allele is present.
Organisms are often more vigorous if they have two different alleles of genes, instead of just one.

20. Chromosome numbers
Chromosome number is a characteristic feature of members of a species.
Organisms with different number of chromosomes are unlikely to be able to interbreed.
The number of chromosomes can change during the evolution of a species.
Decrease if chromosomes fuse, or increase if chromosomes split. It may even double.
Such events are rare, and chromosome numbers tend to remain unchanged over millions of years of evolution.

21. Differences in chromosome number.
Table 1. Diploid chromosome number of some species.
Organism
Diploid chromosome number
Myrmecia pilosula (jack jumper ant) 4
Aedes aegypti (mosquito) 6
Caenorhabditis elegans (round worm) 12
Sarcophilus harrisii (tasmanian devil) 14
Phascolarctos cinereus (koala) 16
Cannabis sativa (hemp) 20
Ailuropoda melanoleuca (giant panda) 42
Homo sapiens (humans) 46
Homo neanderthalensis (neanderthals)
46 (most likely estimate)
Agrodiaetus shahrami (a type of butterfly)
268
Ophioglossum reticulatum (adder's tongue; a fern)
1,260 (Largest known chromosome number)
Pan troglodytes (chimpanzee) 48
Canis familiaris (domestic dog) 78
Oryza sativa (rice plant) 24
Parascaris equorum (equine roundworm)
You should be able to compare the diploid chromosome numbers of Homo sapiens, Pan troglodytes, Canis familiaris, Oryza sativa, Parascaris equorum.

22. Sex determination Sex is determined by the sex chromosomes.
Autosomes are chromosomes that do not determine the gender of the organism, but instead they control the inheritance of all traits except the sex-linked ones, which are under the control of sex chromosomes.
There are two kinds of sex chromosomes:
X – relatively large, and centromere near the middle.
Contain genes essential in both genders. That’s why all humans have at least 1 X.
Y – much smaller, and centromere near the end.
Contains a small number of genes.
A small part of the Y chromosome has the same genes as the X, but the rest of the genes on the Y chromosome is not needed for female development.

23. Autosomal chromosomes & Sex chromosomes

24. Male development 1 X chromosome and 1 Y chromosome (XY).
Determined by the gene SRY (sex-determining region Y) or TDF (testis-determining factor).
Gene responsible for initiating the development of male features.
Testes and testosterone.

25. Female development Two X chromosomes (XX)
Females do not have a Y chromosome, and therefore do not have the TDF gene.
Genes such as Wnt-4 and DAX-1 (anti-testis gene) necessary for initiation of female pathway ovary development.
Develops ovaries and female sex hormones.
In female mammals one X chromosome in every cell is inactivated.
Females can only pass on X chromosomes to their offspring.

26. Karyograms
Shows chromosomes of an organism in homologous pairs of decreasing length.

27. Karyogram

28. Mistakes in meiosis
During meiosis, when the gametes are formed, ova or sperm cells can sometimes contain an extra copy of a chromosome.
Trisomy - Zygotes formed from a gamete with an extra chromosome, give rise to individuals with three copies of one particular chromosome.
Ex:  trisomy 21, where there are three copies of chromosome 21 present - giving rise to Down syndrome. This syndrome causes hearing loss, heart and vision problems, as well as mental and growth retardation. There is no cure for this syndrome.

29. 3.2.5 Using Databases
Know how to navigate the OMIM database!!!

30. International mindedness - International cooperation to sequence the rice genome
In 1997 at a conference in Singapore, scientists agreed to cooperate on the sequencing of one variety of rice and, importantly, to immediately release their data to all members of the group.  
The complete genome is approximately 420 million base pairs. Each group sequenced part of the genome and the initial project was rapidly concluded in 2002 due to the cooperative nature of the effort. Further research then began on sequencing all of the many cultivars of rice grown throughout the world to compare their genomes with the aim of developing varieties with higher productivity and greater resistance to pests.