Intro Gen 5

What is chromatin?

A complex of DNA and protein in the nucleus

Describe the parts of chromatin:

1/3 DNA, 1/3 Histones (Proteins), 1/3 Nonhistone proteins, and RNA

What are the four histone proteins?

H1, H2, H3, and H4

What is a histone?

A small positively charged protein

Why is a histone positively charged? What does this allow it to do?

They have many positively charged amino acids on them; allows it to bind to negatively charged DNA

How do histone proteins help DNA?

They help compact DNA into chromatin (b/c DNA can’t fold up small enough on its own)

What does Histone H1 control?

The entry and exit of DNA

What do chemical modifications of H3 and H4 result in?

It affects overall gene expression

What are nonhistone proteins involved in?

Chromosome scaffold, replication, transcription, chromosome segregation, etc.

What are the 3 levels of chromosome compaction (in order)?

1. Nucleosome
2. Supercoiling
3. Radial-loop scaffold model

Describe the structure of the nucleosome (beads on a string):

DNA wraps twice around a core composed of histones (nucleosome core); Linker DNA connects one nucleosome to the next

When do nucleosomes form?

When DNA winds around histones

What is supercoiling?

A process of making a “spiral” of the beads on a string W

What is the radial-loop scaffold model?

Loops of DNA are formed by protein complexes called condensins

What is a condensing?

5 subunit complex that forms a ring around nucleosome-studded DNA where chromosome passes through the ring twice to form a loop

What stain is used during High Resolution G-Banding?

Metaphase chromosomes stand with Gisema (G-Stain)

What does each G-Band contain in H.R. G-Banding?

A large segment of DNA that contains many loops

What are the qualities of heterochromatin?

Highly condensed, transcriptionally inactive, and dark staining

What are the qualities of euchromatin?

Relaxed, usually transcriptionally active and light staining

What is Fluorescent in situ hybridization (FISH) used for?

Used to characterize genomes

What are the 4 steps of FISH?

1. Chromosomes spread on a glass slide and denatured to make them single stranded
2. DNA sequence is labeled with a fluorescent tag to make a probe
3. Probe hybridizes (anneals/binds to) chromosomes at complementary regions


1. Imaged by fluorescence microscopy

What does transcription require?

a change in chromosome structure and nucleosome position

How can promoters be exposed?

By removing or repositioning nucleosomes

Where are promoters of inactive genes hidden?

They are hidden in the nucleosome

What is one way a gene can be activated?

Some transcription factors can bind to enhancers and recruit chromatin remodeling proteins in order to activate a gene

What is epigenetics?

The study of changes in organisms caused by a modification in gene expression, rather than a change in the genetic code itself

What can epigenetics be caused by?

Chemical modifications of histone proteins

What happens when a methyl group is added to DNA?

It becomes a negative regulator of transcription

How does acetylation occur?

It occurs by histone acetyltransferases

What does acetylation do?

It prevents close packing of nucleosomes, **allowing for more transcription (euchromatin)**

How does methylation occur?

Occurs by histone methyltransferases

What is methylation associated with?

Reduction of transcription, but it can also have the opposite affect depending on the **amino acid that is being modified**

How can histone modifications be reversed?

They are reversed by histone deacetylases or demtheylases

What is the purpose of dosage compensation?

It occurs in mammals so that most X-Linked genes (in XX or XY individuals) are expressed **at the same leevel**

What is a Barr Body?

An inactive X chromosome

What is special about the descendants of someone who has an inactive Barr Body?

All the descendants will have the same inactive X (whether maternal or paternal)

Why are adult females considered mosaics?

Not all cells will have the same inactive X chromosome

What does the expression of the Xist gene lead to?

Heterochromatin formation

What does the random inactivation of all except one X chromosome in each result from?

Expression of the Xist gene on the inactive X

What is Xist RNA?

A large, non-coding, cis-acting regulatory type of RNA

What initiates histone modifications (methylation and deacetylation) that result in heterochromatin formation?

Xist RNA

What are the two main types of histone modification?

Methylation and Deacetylation

What are Yeast Artificial Chromosomes (YACs)?

Chromosomes that contain DNA elements that are required for **eukaryotic chromosome replication, segregation, and stability**

What is used for chromosome replication in eukaryotes?

The Ori/ARS: Origin of Replication

What is used for segregation in eukaryotes?

The centromere

What is used for stability in eukaryotes?

The telomere

What is an origin?

Accessible A-T rich regions of DNA that are devoid of nucleosomes

What is a centromere?

It holds sister chromatids together and is **needed** for chromosome segregation.

What is cohesion in mitosis?

A protein complex that holds sister chromatids along their length during metaphase; cleaved by separase during anaphase (to allow sisters to separate)

What is cohesion in meiosis?

In anaphase I, if it is along chromosome arms it is enzymatically cleaved; however if cohesion is at the centromere it is not cleaved because of protection by **Shugoshin** (homologs separate, but not sisters); Shugoshin is removed and centromeric cohesion is separated to allow sis

How long are satellite DNAs? Where are they found?

They are repetitive noncoding sequences that are 5-300bp long; found in centromeres

What is a telomere?

Highly repeated sequences of DNA that cap the ends of linear DNA

What lengthens DNA?

Telomerase

What happens to chromosomes with age? Telomerase?

They shorten with age; Telomerase activity also decreases with age

Why do telomeres shorten with age? How do they counteract this?

DNAP cannot copy the 5’ end of linear DNA molecules (it needs the 3’ OH); They counteract this by having repeated sequences that can be extended by telomerase

How long are telomeres?

250-1000 repeats

How does DNA copying work in eukaryotes? Is there one origin at a time or multiple?

DNA copying initiates simultaneously at thousands of origins of replication

Where are there high levels of telomerase?

Germ, skin, and tumor cells

What is telomerase RNA?

RNA that is complementary to telomere repeat sequences

What is the level of expression of telomerase in somatic ells?

Low; telomeres shorten at each cell division

What can chromosomal rearrangements be caused by?

DNA breakage or illegitimate crossing over

What is a deletion?

Information is lost via **the removal of base pairs**

What is a duplication?

Sequences are duplicated via the addition of base pairs

What is an inversion?

180° flip of DNA

What is translocation?

Two non-homologous chromosomes swap parts; a piece of one chromosome is attached to a different one

What problems can rearranged chromosomes cause?

When in heterozygosity, there can be problems in **gametogenesis** when homologs pair and recombine

What “malfunctions” can cause all four types of chromosomal rearrangement?

DNA breakage and Aberrant crossing over

What is DNA breakage?

Double strand breaks followed by non homologous end joining (can be caused by things such as X-Rays

What is aberrant crossing over?

Crossing over between repeated sequences on homologous or non homologous chromosomes

What can deletions be caused by?

1. Double-stranded breaks in DNA
2. Intrachromosomal recombinations between direct repeats
3. Unequal crossing over

How can novel (new) phenotypes occur from deletions?

1. Fewer gene copies (altered gene dosage; haploinsufficiency)
2. Existing recessive mutant allele on “non-deletion” homolog
3. New chromosomal context (altered gene expression)

What is new chromosomal context (altered gene expression) referring to?

The level of chromosome compaction

Altered gene dosage is also known as ____?

Fewer gene copies

New chromosomal context is also referred to as ______?

Altered gene expression

What is haploinsufficiency?

Only half of the normal gene dosage is present, and it’s not enough to produce protein products for a normal phenotype

What happens if a deletion appears in homozygosity?

It’s lethal or harmful

What can cause deletions?

Double stranded breaks in DNA and unequal crossing over

How can novel phenotypes arise for duplications?

More gene copies and new chromosomal context

What can inversions be caused by?

Double stranded breaks in DNA; a rotation of chromosome segments; intrachromosomal recombination between inverted repeat sequences

How can novel phenotypes arise with inversions?

New chromosomal context (altered gene expression) and disruption of a gene by an inversion breakpoint

Does gene dosage change in inversions? Why or why not?

There is no change in gene dosage (# of gene copies) b/c nothing is getting added or deleted. Things are simply moving around.

Pericentric

Inversions that include the centromere

Paracentric

Inversions that exclude the centromere

What are translocations caused by?

double stranded breaks in DNA

What is a reciprocal translocation?

Non-homologs swap parts

What is robertsonian translocation?

Chromosomal breaks that occur at/near the centromere of two afrocentric chromosomes; this results in one large metacentric chromosome and a small chromosome that is lost

How can novel phenotypes arise from translocations?

New chromosomal context (altered gene expression) and disruption/alteration of a gene by a translocation breakpoint

What is chromosome segregation like in the **translocation homozygote?**

Homologs separate normally during Meiosis I

What is chromosome segregation like in the **translocation heterozygote?**

Abnormal pairing of homologs in prophase I leads to unbalanced gametes

What is a transposable element (jumping genes)?

Any segment of DNA that evolves the ability to move from one place to another in the genome (ex: transposon, retroposon)

How much of the genome is made up of transposable elements?

44%

What is aneuploidy?

The loss or gan of one or more chromosomes

What are aneuploids?

Individuals whose chromosome number is not an exact multiple of the diploid (2n) # for that species?

What is euploidy?

Normal diploid state where there are 2 copies of each chromosome present (2n)

Nullisomy

(2n-2); 2 sets of chromosomes are missing

Monosomy

(2n-1); 1 chromosome is missing from a set

What is the only viable monosomy in humans?

Turner Syndrome (female with only 1 X chromosome)

Trisomy

(2n+1); Chromosome is added

What are the 3 viable trisomies?

Trisomy 21, 13, and 18

Trisomy 21

Down syndrome