BJU Bio 409 (Genetics): Unit 2 Test - Ch. 8, 11, and 20

metacentric

Type of chromosome where the centromere is located approximately in the middle, so the chromosome has two arms of equal length

submetacentric

Type of chromosome where the centromere is displaced toward one end, creating a long arm and a short arm (on human chromosomes, the short arm is designated by the letter p and the long arm by the letter q)

arocentric

type of chromosome where the centromere is near one end, producing a long arm and a knob, or satellite, at the other end.

telocentric

type of chromosome where the centromere is at or very near the end of the chromosome

karyotype

the complete set of chromosomes possessed by an organism

G bands = A-T rich regions

What are the different bands that appear with Giemsa staining? And what regions do these bands represent

Q bands = A-T rich regions (bright) and C-G rich regions (dull)

What are the different bands that appear with Quinacrine mustard + UV light? And what regions do these bands represent?

R bands = C-G rich regions

What are the different bands that appear with hot phosphate buffer + Giemsa dye? What regions do these bands represent?

C bands = centromeric heterochromatin

What are the different bands that appear with denaturing chromosomes and then applying Giemsa staining? What regions do these bands represent?

telomeres

The stable ends of chromosomes

Centromere

a constricted region of the chromosome where the kinetochores form and the spindle microtubules attach.

In the following order:

• Chromosome #

• Arm (p or q)

• region #

• band #

.

• sub-band #

Example: 7q31.2

How is the location of the gene in a chromosome communicated?

Chromosome mutations

Difference from WT in structure or number of one or more chromosomes

structural variants

Type of mutation where there is a change in structure of single chromosomes

Chromosome rearrangements (duplication)

Type of mutation included in structural variants where there is a change from WT in structure of one or more chromosomes

2n = 6

copy number variation

Type of mutation included in structural variants where there is a difference between individuals in the number of copies of a >1000-bp sequence

aneuploidy (trisomy)

Type of mutation that has a change from WT in the number of individual chromosomes

2n + 1 = 7

Polyploidy

Type of mutation where there is an increase from WT chromosomes in the number of sets of chromosomes

3n = 9

Species usually have a characteristic chromosome number because chromosome number is inherited during reproduction, and changes in chromosome number can interfere with successful reproduction.

• Chromosomes must pair correctly during meiosis

• Chromosome-number changes can disrupt gene dosage

• Natural selection tends to preserve chromosome arrangements that reproduce successfully

Why do species usually have a characteristic number of chromosomes? Why don't we see many species where chromosome number varies within the species, with some individuals, say, having 2n = 20 and others having 2n = 24?

duplication

Mutation where a segment of the chromosome is duplicated

deletion

mutation where a segment of the chromosome is deleted

inversion

mutation where a segment of the chromosome is turned 180 degrees

translocation

mutation where a segment of a chromosome moves from one chromosome to a nonhomologous chromosome or to another place on the same chromosome

• Pericentric inversion extends across the centromere and involves both parts of the chromosome (p and q)

• Paracentric inversion occurs entirely within one chromosome arm
  
  

Difference between pericentric and paracentric inversion?

Aneuploidy = an abnormal number of individual chromosomes. An organism gains or loses one or more chromosomes rather than a complete set.

Ex: 2n ± #

Polyploidy = having more than two complete sets of chromosomes. Instead of gaining or losing individual chromosomes, an organism gains entire chromosome sets.

Difference between aneuploidy and polypoidy?

If the twins separate from the same early embryo, but the chromosome error occurs in a cell lineage that contributes to only one twin, one twin can develop with trisomy 21 (47 chromosomes) while the other has the normal number (46 chromosomes).

A recent study examined a pair of monozygotic (identical) twins in which one of the twins had trisomy 21 and the other had two normal copies of chromosome 21. Explain how two identical twins could differ in their number of chromosomes

How it works:

• XIST produces an RNA molecule that coats an X chromosome and triggers its inactivation.

• Researchers can introduce or activate XIST on the extra copy of chromosome 21.

• The XIST RNA may then silence much of the extra chromosome’s gene expression, potentially making the cells function more like cells with the normal two copies of chromosome 21.

Challenges for using this approach in patients:

1. Delivering the gene: Researchers would need to deliver and activate XIST in enough of the patient's cells, potentially across many tissues and organs.

2. Silencing the correct chromosome: XIST would need to target the extra chromosome 21 without silencing the two normal copies.

3. Incomplete silencing: Not every gene on chromosome 21 may be fully inactivated, so some effects of trisomy 21 could remain.

4. Timing of treatment: Some developmental differences begin before birth. Silencing the extra chromosome later in life may not reverse changes that have already occurred.

5. Safety: Researchers would need to ensure that introducing XIST does not unintentionally alter gene expression elsewhere or cause harmful effects.

Geneticist have been exploring ways to suppress the expression of the extra chromosome 21 in individuals with Down syndrome in hopes of preventing the medical problems and intellectual disability of individuals with trisomy 21. One approach involves modifying a gene that is already present in human cells and using it to suppress the expression of the extra copy of chromosome 21. What approach, do you think, are they taking, and what may be some of the challenges for using it in patients?

The difference is that the X chromosome can largely compensate for having an extra copy through X-inactivation, whereas chromosomes 4 and 5 do not have a similar chromosome-wide inactivation mechanism.

The human X chromosome is about the same size as human chromosomes 4 and 5. Trisomy of the X chromosome occurs about once in every 1,000 human female births, and yet trisomy 4 and trisomy 5 are almost never seen among living humans. Why do these differences in the frequency of trisomic individuals occur, in spite of similar chromosome size?

euchromatin is loosely packed and generally accessible for gene expression

heterochromatin is tightly packed and generally less accessible for gene expression.

Difference between heterochromatin and euchromatin

• DNA-only transposons

  • Short inverted repeats at each end; require transposase for movement; move as DNA, either by cut-and-paste or replicative pathways

• Retroviral-like retrotransposons

  • Directly repeated long terminal repeats (LTRs) at each end; require reverse transcriptase and integrase for movement; moves via an RNA intermediate produced by a promoter in the LTR

• Nonretroviral retrotransposons

  • Poly A at 3’ end of RNA transcript; 5’ end is often truncated; require reverse transcriptase and endonuclease; moves via an RNA intermediate that is often produced from a neighboring promoter

What are the three major classes of transposable elements?

structural genomics

Branch of genomics that studies the organization and sequence of information contained within genomes

comparative genomcis

branch of genomics that studies similarities and differences in gene content, function, and organization among genomes of different organisms

functional genomics

branch of genomics that studies the functions of the genetic information contained within genomes.

structural genomics

The ultimate goal of ______________ is to determine the ordered nucleotide sequences of entire genomes of organisms, providing the sequence information that is used to answer other questions.

Using recombination frequencies determined by testcrosses

how are genetic maps constructed?

The physical distance map shows the actual location of the genes. It has greater resolution and accuracy.

Genetic maps are created from recombination frequency data and has limited accuracy

What is the difference between a physical distance map and a genetic map?

Map-based

1. Generate overlapping BAC “Clones” with unique “markers.” Each resulting “contig” represents a large chunk of a chromosome

2. Generate BAC “subclones” with smaller inserts

3. Sequence each subclone

4. “stitch” together overlapping subclone sequences

What was the public strategy for the human genome project?

Whole-Genome shotgun sequencing (faster, cheaper, but not perfect)

1. The chromosomes are identical for most of the DNA sequences

2. Variation in a single base constitutes each SNP

3. Each haplotype is made up of a particular set of alleles at each SNP

What was the private strategy for the human genome project?

• Homology searches

• Protein domains

• Transcriptomics (i.e., Microarrays / RNA sequencing)

• Visualize gene expression patterns

• Genome-wide mutagenesis

What are the different genomic approaches to determine gene function?

• Homologs = related through common ancestry

  • Genes or proteins that descended from a common ancestral gene. The umbrella term that includes both orthologs and paralogs.

• Orthologs = genes separated in speciation

  • Homologous genes in different species that descended from the same ancestral gene when a species split into two species. They occur in different species, but their common ancestor existed before the species diverged. They often retain similar functions, although not guaranteed.

• Paralogs = genes separated by gene duplication

  • Homologous genes that originated when an ancestral gene was duplicated.

Difference between homologs, paralogs, and orthologs in homology searches?

1. A microarray consists of DNA probes fixed to a solid support, such as a nylon membrane or glass slide.

2. Each spot consists of a different DNA probe

3. Cancer and noncancer cells removed from 78 women with breast cancer.

4. Messenger RNA from the cells is converted into cDNA and labeled with red (cancer cells) or green (noncancer cells) fluorescent nucleotides

5. The cDNAs are mixed and hybridized to DNA probes on a chip

6. The chip is scanned spot by spot. Yellow fluorescence (red + green) indicates equal expression of the gene in both types of cells; red indicates more expression in cancer cells; and green indicates more expression in noncancer cells.

Results

• Each spot represents the expression of one gene in one patient’s tumor compared with the expression of that gene in her noncancer cells.

• Tumors above the solid yellow line came primarily from patients who remained cancer free for at least 5 years.

• Tumors below the solid yellow line came primarily from patients in whom the cancer spread within 5 years of diagnosis

Know the process/how to read microarrays

1. Total cellular RNA is isolated from cells

2. The RNA of interest (e.g. mRNA) is isolated.

3. The enzyme reverse transcriptase is used to make complimentary DNA (cDNA) from mRNA

4. The cDNA is broken into overlapping fragments

5. Adapters with sequences for amplification and sequencing are added to the ends of the fragments

6. The fragments are amplified with PCR and sequenced using next generation sequencing.

7. The sequence reads are assembled into RNA transcripts

Know the process of RNA sequencing

1. Male zebrafish are treated with EMS to produce mutations in their sperm and are then crossed with wild-type females

2. progeny fish are screened for mutant phenotypes. Recessive mutations (m²) will not be expressed in the F1 phenotype.

3. Variant fish may posses a dominant mutation (M^1).

4. Progeny fish with normal phenotypes are mated with wild-type fish and backcrossed to reveal recessive mutations

5. Some fish homozygous for recessive mutations are produced

The mutagenesis screen produces fish with a mutation affecting the trait. These fish are further analyzed to identify the mutation.

Know the process of genome-wide mutagenesis