week 11 Flashcards by Queenie Mae

consists of 2.9 billion nucleotide base pairs of DNA organized into 23 chromosomes.

human genome

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humans inherit a haploid set of genes (23 chromosomes) from each parent, so humans have two copies of every
gene (except for some on the _ ).

diploid organisms
- X and Y chromosomes

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Each chromosome is a double helix of DNA, ranging from 246 million nucleotide base pairs in length in _ to 48
million nucleotide base pairs in _

chromosome 1 (the largest)
chromosome 21

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Genetic information is carried on the chromosomes in the
form of the order or sequence of nucleotides in the_

DNA helix

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is a trait or group of traits resulting from transcription and translation of these genes.

phenotype

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is the DNA nucleotide sequence responsible for
a phenotype. __ is performed to confirm or
predict this.

genotype
- Genotypic analysis

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mutations at the nucleotide-sequence level are detected using
_ or _ .

biochemical or molecular methods

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A transmissible (inheritable) change in the DNA sequence is a _ or _

mutation or polymorphism

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can affect a single nucleotide or millions of nucleotides, even whole chromosomes, and thus can be classified
into three categories:
1
2
3

DNA mutations
Gene
Chromosome
Genome mutations

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-affect single genes and are often, but not always, small changes in the DNA sequence.

Gene

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-affect the structures of entire chromosomes. These changes require movement
of large chromosomal regions (hundreds of thousands to millions of base pairs) either within the same chromosome or to another chromosome.

Chromosome

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-changes in the number of chromosomes.

Genome mutations

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*A cell or cell population with a normal complement of chromosomes is _.

euploid

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*Genome mutations result in cells that are _.

aneuploid

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is mostly observed as increased numbers of chromosomes because the loss of whole chromosomes is generally not compatible with survival.
> _ is an example of a disease resulting from it, where there are three copies, or trisomy, of chromosome 21.

Aneuploidy
- Down syndrome

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Detection of mutations in the laboratory ranges from
1
2

*Direct visualization of genome and chromosomal mutations under the microscope
*Molecular methods to detect single-base changes.

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Chromosome behavior is dependent on _ and _

chromosome structure
DNA sequence.

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_ will behave differently, depending on the
chromosomal location or the surrounding nucleotide sequence of the gene.

1 Genes with identical DNA sequences

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-a well-known phenomenon that a gene inserted or moved into a different
chromosomal location may be expressed (transcribed and translated) differently than it was in its original position.

Position effect

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DNA compaction into _ chromosomes.

metaphase

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_ forms the 10 11-nm chromatin strands found in
transcriptionally active 10-11 nm DNA.

Histone wrapped in DNA

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Further compaction results in the closed 30 nm fibers found in _

transcriptionally
silent DNA

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Before 1943, _ were thought to contain genetic information.
- Their function was later determined to be structural. It is now known that in addition to
their structural role, it control access to and expression of DNA.

histones

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Modification of histones, through__,__,__ or __
alters DNA access and plays a role in other cellular
functions, such as recombination, replication, and
gene expression

acetylation, methylation, phosphorylation, or ubiquitination,

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(state of compaction of the DNA double helix) affects gene activity.

Chromosome topology

Highly compacted DNA is less available for _

RNA transcription.

The more highly compacted state of DNA is _ or _ (in contrast to _ or _ ).

closed chromatin, or heterochromatin open chromatin, or euchromatin

*Members of a family of proteins, control chromosome condensation in eukaryotes and other aspects of chromosome behavior, including chromosome segregation in prokaryotes.

Smcproteins

Two of the SMC proteins, _ and _ *first isolated from frog eggs, are integral parts of the condens incomplex, a protein scaffold structure that can be isolated from both mitotic and interphase cells.

XCAP-C and XCAP-E

have been distinguished historically by their relative size and centromere placement.

Mitotic chromosomes

the _ is the site of attachment of the chromosome to the spindle apparatus.

centromere

The connection is made between microtubules of the spindle and a protein complex, the _ , that assembles at the centromere sequences

kinetochore

The long arm of a chromosome

short arm is designated _.

chromosomes have a ratio of long arm length: short arm length from _

Acrocentric 3:1 to 10:1

Chromosomes _ _ _ _ are considered acrocentric, but may be classified as subtelocentric.

13 to 15, 21, and 22

The placement of the centromere divides the chromosome into _.

arms

Chromosomes are _,_ _ or _+ depending on the placement of the centromere

metacentric, submetacentric, acrocentric, or telocentric

centromere locates on the center both arms are equal length

metacentric

centromere locates near the center both arms are unequal

submetacentric

centromere locates near the end of chromosome

acrocentric (subtelocentric)

centromere locates at the end of chromosome

telocentric

GROUP A CHROMOSOMES

1,2 Large (metacentric) 3 Large submetacentric

GROUP B CHROMOSOMES

4,5 Large submetacentric

GROUP C CHROMOSOMES

6-12, X Medium size submetacentric

GROUP D CHROMOSOMES

13-15 Medium sized acrocentric w/ satellites

GROUP E CHROMOSOMES

16 Short metacentric 17, 18 short submetacentric

GROUP F CHROMOSOMES

19,20 Short metacentric

GROUP G CHROMOSOMES

21,22 Short acrocentric w/ satellites Y Short acrocentric

Conventional cytological stains, such as_, _ _ have been used to visualize chromosomes.

Feulgen, Wright, and hematoxylin

More Advanced in the recognition of individual chromosomes was the discovery that _ and _ can react with specific chromosome regions.

fluorescent stains and chemical dyes

When chromosomes are stained with the fluorescent dyes, _, _ and _ , the resulting fluorescence pattern visualized after staining is_ (This method was first demonstrated in 1970 by _, _ and _

quinacrine and quinacrine mustard - Q banding = Caspersson, Zech, and Johansson

*_ stains darkly by G or Q banding (left)

Heterochromatin

The chemical dye_ in patterns, or _- differs, depending on the treatment of the chromosomes before staining. Mild treatment (2 × standard saline citrate for 60 minutes at 60°C) yields the region-specific banding pattern comparable to that seen with fluorescent dyes.

Giemsa stains or G bands

can also be visualized after staining with acridine orange.

*R bands

Alkali treatment of chromosomes results in _, or _

centromere staining or C banding

The number of visualized bands can be increased from about 300 to 500 per chromosome by staining chromosomes before they reach maximal metaphase condensation. This is called __

high-resolution bandinG

- staining is another region-specific staining approach. Chromosomes treated with _ will stain specifically at the constricted regions, or stalks, on the acrocentric chromosomes.

Nucleolar organizing region (NOR) - silver nitrate

Staining of chromosomes with _ was first described in 1976 as a way to detect mycoplasmal contamination in cell cultures.

4 ′ ,6-diamidino-2-phenylindole (DAPI)

Genome mutations, or aneuploidy, can be detected by indirect methods, such as _ AND _

flow cytometre karyotyping.

A _ is the complete set of chromosomes in a cell.

karyotype

is the direct observation of metaphase chromosome structure by arranging metaphase chromosomes according to size. Done by the addition of a _, usually _.

Karyotyping - mitogen - phytohemagglutinin

can also be used to detect chromosomal mutations such as _, which are the exchange of genetic material between chromosomes.

Karyotyping - translocations

_ can be of several types. In _ , parts of two chromosomes exchange; that is, each chromosome breaks, and the broken chromosomes reassociate or recombine with one another

Translocations - reciprocal translocations

is a loss of chromosomal material. covering millions of base pairs can be detected using karyotyping; smaller microdeletions are not always easily seen using this technique.

deletion

An _ is a gain of chromosomal materials

insertion

result from excision, flipping, and reconnecting chromosomal material within the same chromosome.

inversions

include the centromere in the inverted region,

pericentric inversions

involve sequences within one arm of the chromosome.

paracentric inversions

An _ is a metacentric chromosome that results from transverse splitting of the centromere during cell division.

isochromosome

results from deletion of genetic regions from ends of the chromosome and a joining of the ends to form a ring.

ring chromosome

is an abnormal chromosome consisting of translocated or otherwise rearranged parts from two or more unidentified chromosomes joined to a normal chromosome.

derivative chromosome

A normal karyotype is _ in a female or _ in a male.

46,XX 46,XY

A karyotype showing __denotes a deletion in the long arm q of chromosome 7 at region 1, band 3.

46,XX,del(7)(q13)

A karyotype showing _ denotes a translocation t between the short arms p of chromosomes 5 and 17 and region 1, band 3, subband3, and region 1, band 3, respectively.

46,XY,t(5;17)(p13.3;p13)

A karyotype showing _ is the karyotype of a female with Down syndrome resulting from an extra chromosome 21.

47,XX + 21

is caused by an extra X chromosome in males, for example, 47,XXY.

Klinefelter syndrome

is a method widely used to detect protein and RNA as well as DNA structures in place in the cell, or in situ.

Fluorescence in situ hybridization (FISH)

offers a more rapid assay with higher resolution and flexibility than karyotyping.

FISH

targets specific sequences of chromosomes with fluorescent probes. *Probes are designed to hybridize to critical areas that are amplified, deleted, translocated, or otherwise rearranged in disease states

FISH

* In contrast to karyotyping, it does not require culturing of cells. Because growing cells in culture is not required.

Interphase FISH

are used commonly to study prenatal samples, tumors, and hematological malignancies, not all of which are conveniently brought into metaphase in culture.

Interphase FISH methods

, the bound probe is visualized under a fluorescent microscope as a point of fluorescent light in the nucleus of the cell.

interphase FISH

The sensitivity of interphase FISH analysis for the detection of translocations is increased through the use of _ or _ *These probes are mixtures of two single probes, each labeled with a different fluorescent dye. *They are designed to bind to regions spanning the breakpoint of translocations.-

dual-color probes, or dual-fusion probes.

analysis has been enhanced by the development of fluorescent probes that bind to metaphase chromosomal regions or to whole chromosomes.

Metaphase FISH

allows analysis of small regions not visible by regular chromosome banding.

metaphase FISH

Probes that cover the entire chromosome, or whole chromosome paints, are valuable for detecting these small or complex rearrangements (__ can distinguish all 23 chromosomes by chromosome-specific colors).

Metaphase FISH spectral karyotyping

This type of analysis can detect abnormalities that affect multiple chromosomes, as is sometimes found in cancer cells or immortalized cell lines

Metaphase FISH

is the analysis of repeated sequences by assessing the relative intensity of probe signals. * Microscopic images are digitized on a charge-coupled device (CCD). * The signals are then measured by imaging software, quantifying FISH signals from each digital image. * The relative intensity is compared between signals. * The __ has been applied to studies on telomere length.

Quantitative FISH - telomere Q-FISH technique

* Intrachromosomal amplifications or deletions can be detected by it * In this method, DNA from test and reference samples is labeled and used as a probe on a normal metaphase chromosome spread

COMPARATIVE GENOME HYBRIDIZATION (CGH) 37

its capability to identify the location of deletions or amplifications throughout the genome

COMPARATIVE GENOME HYBRIDIZATION (CGH) 37

, the test DNA is isolated and labeled along with a reference DNA.

CGH

Two colorimetrically distinct cyanine dyes, commonly_ and _ , are used as fluorescent labels for the test and reference DNA.

Cy3 and Cy5

, which fluoresces at a wavelength of 550 nm, is often represented as “green,”

Cy3

, which fluoresces in the far-red region of the spectrum (650 to 667 nm), is represented as “red.”

Cy5

* Derivatives of these dyes, such as _which fluoresces in the red-orange region.

Cy3.5,

A DNA sequence change that is present in a relatively small proportion of a population is a _

mutation

A variant that is present in at least 1% to 2% of a population is considered a _.

polymorphism