1. Topics 3.2 and 3.3
Chromosomes and Meiosis (Core)

2. Prokaryotic DNA is comprised of one circular chromosome.
Prokaryotes and Eukaryotes have differences in their DNA.
Prokaryotic DNA is comprised of one circular chromosome.
Eukaryotic DNA is composed of linear DNA molecules, associated with histones. These are called chromosomes
Plasmids are also present in prokaryotic cells, which are strands of naked DNA scientists can use in genetic transfer.

3. Chromosome 1 – 3958 genes Chromosome 11 – 2364 genes
Different chromosomes within an organism contain different amounts of genes as well as genes for different traits
Chromosome 1 – 3958 genes
Chromosome 11 – 2364 genes
Notice the difference between these two human chromosomes.

4. Application: Comparison of the number of genes in humans with other species.
When looking at complexity, the number of genes an organism has does not necessarily correlate with the complexity of said organism.
Notice how the fruit fly and the chicken have very similar numbers of genes. This is an example of the breakdown of this trend.

5. Genome Length (millions of base pairs)
Application: Comparison of the genome size in T2 phage, E. coli, D. melanogaster, H. sapiens and P. japonica.
Name
Genome Length (millions of base pairs)
Number of Genes
T2 phage (Virus)
0.18
300
Escherichia coli (Bacteria) 5
4,377
Drosophila melanogaster (Fruit Fly)
140
17,000
Paris japonica (Plant)
150,000
Unknown
Homo sapiens (Human)
3,000
19-23,000
Notice – How does the trend of complexity vs. size of genome compare between species?

6. Skill: Use of a database to determine differences in the base sequence of a gene in two or more species.
One use of aligning base sequences is to determine the difference between species, which can show relationships in ancestry.
Your task is to analyze the differences in a gene sequence in three species, and to use the online Clustal tool to do so.
For each species, first you must gather the base sequence:
Go to the GenBank website
Next to the search bar, click and choose “Gene” from the dropdown menu.
Enter the name of one of the following genes:
AMY1A – Salivary Amylase
COX1 – Cytochrome oxidase
AND the binomial name for an organism (scientific names)
Click Search
Scroll down to ‘Genomic Regions, transcripts and products’ and click on FASTA
Save the sequence in a document. Repeat this process for two other species

7. Skill: Use of a database to determine differences in the base sequence of a gene in two or more species.
To align the sequences:
Go to Clustal Omega
In STEP 1 Select ‘DNA’ under ‘a set of’
Paste the chosen sequences into the box (TAKE CARE TO PUT EACH SEQUENCE ON A SEPARATE LINE)
Press Submit
Analysis:
Using ‘Alignments,’ you will be able to visually check your results
Under ‘Results Summary’ use the ‘Percent Identity Matrix’ to quantify the overall similarity (0-100)
Under ‘Phylogenetic Tree’ choose the ‘Real’ option for the Phylogram to get a visual of how similar the species are.
Have me come check when you are done!

8. Application: Comparison of the number of chromosomes between species.
Determine the number of chromosomes of the following species:
Species
Common Name
Number of Chromosomes
Homo sapiens
Humans
Pan troglodytes
Chimpanzee
Canis familiaris
Dog
Oryza sativa
Asian Rice
Parascaris equorum
Equine Roundworm

9. Species Common Name Number of Chromosomes
Ultimately, the number of chromosomes in the nuclei of the cells of an organism is what determines its characteristics.
Determine the number of chromosomes of the following species:
Species
Common Name
Number of Chromosomes
Homo sapiens
Humans 46
Pan troglodytes
Chimpanzee 48
Canis familiaris
Dog 78
Oryza sativa
Asian Rice 24
Parascaris equorum
Equine Roundworm 2
Notice – the trend of complexity does not hold here either!
Scientists are able to see the number of chromosomes present through a procedure known as Karyogramming, which generates an image like this:

10. The karyotype of this individual is 46, XY
Can you describe the difference between a karyotype and a karyogram?

11. Every somatic cell in your body is a diploid cell.
Ploidy is the term we use to refer to the number of copies of a genome that are present in the nucleus of a cell.
Every somatic cell in your body is a diploid cell.
Every gamete in your body is a haploid cell
Shown above are karyograms for a diploid and a haploid cell in humans. What is the difference?

12. Two types of chromosomes in a cell:
How would this karyogram be different if the organism were different? Say drosophila melanogaster?
Autosomes (Outlined in Blue)
Sex Chromosomes (Outlined in Red)
Autosomes – determine characteristics that are common to both sexes
Sex Chromosomes – are the chromosomes that determine characteristics for the development of sexual characteristics (in addition to some other general genes)

13. The miracle of variation within a species
3.3 - Meiosis
The miracle of variation within a species

16. Check out this animation from Johnkyrk
Check out this animation from Johnkyrk.com, and see if you can identify what is happening in each of the steps of Meiosis

17. A homologous pair of chromosomes…

18. A homologous pair of chromosomes…
…replicates during S-phase of interphase…
DNA is replicated before meiosis so that all chromosomes consist of two sister chromatids.

19. A homologous pair of chromosomes…
…replicates during S-phase of interphase…
centromere
sister chromatids
…giving two pairs of sister chromatids,
each joined at the centromere.

20. The homologous pair associates during prophase I, through synapsis…

21. The homologous pair associates during prophase I, through synapsis…
…making a bivalent.

22. Crossing-over might take place between non-sister chromatids in prophase I…

23. Crossing-over might take place between non-sister chromatids in prophase I…
…leading to recombination of alleles.

24. In anaphase I, the homologous pair is separated but the sister chromatids remain attached.
This is the reduction division.

25. Meiosis Is a reduction division from
diploid somatic cells (2n) to produce
haploid gametes (n).
The reduction is in the chromosome number in each nucleus.
The halving of the chromosome number allows a sexual life cycle with fusion of gametes.

26. Interphase
In the S-phase of the interphase before meiosis begins, DNA replication takes place.
Chromosomes are replicated and these copies are attached to each other at the centromere.
The attached chromosome and its copy are known as sister chromatids.
Following S-phase, further growth and preparation take place for meiosis.

27. Prophase I
The homologous chromosomes associate with each other, to form bivalents.
The pairs of sister chromatids are joined by the centromere.
Non-sister chromatids are next to each other but not joined.
This bivalent is composed of:
One pair of homologous chromosomes
Which have replicated to form two pairs of sister chromatids.

28. Prophase I
The homologous chromosomes associate with each other, to form bivalents.
Crossing-over between non-sister chromatids can take place. This results in recombination of alleles and is a source of genetic variation in gametes.
The pairs of sister chromatids are joined by the centromere.
Non-sister chromatids are next to each other but not joined.
The homologous pair is separated in anaphase I. The joined sister chromatids are separated in anaphase II.
This bivalent is composed of:
One pair of homologous chromosomes
Which have replicated to form two pairs of sister chromatids.

29. Neighboring non-sister chromatids are cut at the same point.
Crossing-Over
Increases genetic variation through recombination of linked alleles.
Homologous chromosomes associate
Chiasmata Formation
Neighboring non-sister chromatids are cut at the same point.
DNA of the cut sections attach to the open end of the opposite non-sister chromatid.
Recombination
As a result, alleles are swapped between non-sister chromatids.

30. Prophase I The homologous chromosomes associate with each other.
Crossing-over between non-sister chromatids can take place. This results in recombination of alleles and is a source of genetic variation in gametes.
Crossing-over is more likely to occur between genes which are further apart. In this example, there will be more recombination between D and E than between C and D.
During prophase, the nuclear membrane also breaks down and the centrioles migrate to the poles of the cell.

31. Metaphase I The bivalents line up at the equator.
Random orientation occurs and is a significant source of genetic variation.
There are 2n possible orientations in metaphase I and II. That is 223 in humans – or 8,388,068 different combinations in gametes!

32. Anaphase I Spindle fibers contract.
Homologous pairs are separated and pulled to opposing poles.
This is the reduction division.
Non-disjunction here will affect the chromosome number of all four gametes.

36. Telophase I
New nuclei form and the cytoplasm begins to divide by cytokinesis.
The nuclei are no longer diploid.
They each contain one pair of sister chromatids for each of the species’ chromosomes.
If crossing-over and recombination has occurred then the sister chromatids will not be exact copies.

37. Interphase
There is no Synthesis phase in Interphase II.

38. Prophase II
The nuclei break down.
No crossing-over occurs.

39. Metaphase II
Pairs of sister chromatids align at the equator. Spindle fibers form and attach at the centromeres.
Random orientation again contributes to variation in the gametes, though not to such an extent as in metaphase I.
This is because there is only a difference between chromatids where crossing-over has taken place.

40. Metaphase I vs II: Genetic Variation
Lots of variation in gametes produced
Random orientation of homologous pairs, which may have a great diversity in alleles present
Therefore many possible combinations of alleles could be pulled to each pole
Some variation in gametes produced
Random orientation of sister chromatids
Variation only in regions where crossing over has taken place in prophase I (recombination of alleles)

41. Anaphase II Spindle fibers contract and the centromeres are broken.
The pairs of sister chromatids are pulled to opposing poles.
Non-disjunction here will lead to two gametes containing the wrong chromosome number.

42. Telophase II New haploid nuclei are formed.
Cytokinesis begins, splitting the cells.
The end result of meiosis is four haploid gamete cells.
Fertilization of these haploid gametes will produce a diploid zygote.

46. Inquire and Share Activity
Your Task – To research one of the following methods of prenatal testing, and design a whiteboard to display important information about the procedure and the bioethics surrounding it.
Prenatal Testing Methods:
Nuchal Translucency Scan
Amniocentesis
Chorionic Villus Sampling
Maternal Blood Sampling
Maternal Serum Alpha-Fetoprotein
Whiteboard Components:
We will share and talk about
specific important parts of
each procedure.
Needed for IB
Procedure Name
Who gets it?
Availability
Cost vs
Effectiveness
Bioethics - Pros
Bioethics - Cons

55. Genetic Variation is almost infinite as a result of meiosis.
Crossing-over in prophase I
Leads to recombination of alleles on the chromosomes.
Random orientation in metaphase I
Huge number of maternal/paternal chromosome combinations possible in the final gametes. There are over 8million possible orientation in humans (223 orientations)
Random orientation in metaphase II
Further genetic variation arises where there are genetic differences between sister chromatids as a result of crossing-over in prophase I.

56. Genetic Variation is almost infinite as a result of meiosis.
Crossing-over in prophase I
Leads to recombination of alleles on the chromosomes.
Random orientation in metaphase I
Huge number of maternal/paternal chromosome combinations possible in the final gametes. There are over 8million possible orientation in humans (223 orientations)
Random orientation in metaphase II
Further genetic variation arises where there are genetic differences between sister chromatids as a result of crossing-over in prophase I.
Even more variation!
Random fertilization during sexual reproduction ensures even greater variation within the population.

57. Mendel’s Law of Independent Assortment
“The presence of an allele of one of the genes in a gamete has no influence over which allele of another gene is present.”
A and B are different genes on different chromosomes.
A is dominant over a.
B is dominant over b.
This only holds true for unlinked genes (genes on different chromosomes).

58. Random Orientation vs Independent Assortment
“The presence of an allele of one of the genes in a gamete has no influence over which allele of another gene is present.”
Random Orientation refers to the behavior of homologous pairs of chromosomes (metaphase I) or pairs of sister chromatids (metaphase II) in meiosis.
Independent assortment refers to the behavior of alleles of unlinked genes as a result of gamete production (meiosis).
Due to random orientation of the chromosomes in metaphase I, the alleles of these unlinked genes have become independently assorted into the gametes.
Animation from Sumanas:

59. Mendel and Meiosis
“The presence of an allele of one of the genes in a gamete has no influence over which allele of another gene is present.”
Mendel deduced that characteristics were determined by the interaction
between pairs of alleles long before the details of meiosis were known.
Where Mendel states that pairs of alleles of a gene separate independently during gamete production, we can now attribute this to random orientation of chromosomes during metaphase I.
Mendel made this deduction when working with pea plants. He investigated two separate traits (color and shape) and performed many test crosses, recording the ratios of phenotypes produced in subsequent generations.
It was rather fortunate that these two traits happened to be on separate chromosomes (unlinked genes)! Remember back then he did not know about the contents of the nucleus. Chromosomes and DNA were yet to be discovered.
We will use his work as an example of dihybrid crosses in the next section.
Animation from Sumanas: