Genetics Exam 3 Lectures 21 and 22

Chromatin

Is a complex of DNA and protein found in eukaryotic cells. The primary function is to package long DNA molecules into more compact, denser structures

DNA+ Protein (histones)

Euchromatin

Lightly packed chromatin is rich in gene concentration and is most often under active transcription

Active? Have access to the DNA

Heterochromatin

Tightly packed chromatin consists mainly of genetically inactive sequences

Enzymes do not have access to the DNA

DNA is silenced in most cases because the DNA is so tightly packed we cannot get to it

Constitutive heterochromatin

Faculatative heterochromatin

VERY gene-poor; centromeres and telomeres: ALWAYS; All the time. Don’t want genes is something we can’t ever access

Gene silencing; Barr bodies - can go back and forth; go from tight to loose and back; silence particular genes (Barr body - is an inactivated X chromosome in a typical somatic cell of an individual with two X chromosomes). Its inactivation is an example of how chromatin packaging helps regulate gene expression)

Folded Fiber model (don’t really need to know)

Found few or no free fiber ends and concluded each chromatid must consist of a single fiber

Taking DNA and winding it up into the smallest thing you could make it

Nucleosome Model - Still used today

Most commonly accepted model for DNA packaging

Nucleosome

The simplest packaging structure of all eukaryotic chromatin localized areas of transcription; better fit for protein biosynthesis

Core Histones

H2A, H2B, H3, and H4 - Part of the core (2 of each in the core). Overall positive charge because the core is so basic

Consists of approximately 120 amino acids each in size

Highly conserved during evolution

In combination, form the core particle

VERY basic in charge (approx. 25% Lysine and Arginine)

Linker Histone

H1

Consists of approximately 200 amino acids

Tissue-specific expression and not highly conserved

Loosely associated with the core particle - Not considered part of the core! It is on the outside

Part of a nucleosome just not the core particle

Formation of the Nucleosome - 1st step of condensation

Core particles = 2 of each

DNA wraps around the core

10nm Fiber is another name for the nucleosome- primary packaging of the chromatin - beads on a string - G1 phase

Linker DNA - between the two nucleosomes - reduces length by 7 times

DNA is more of a negative charge, so it wrapping around the positive charge of the core allows it to stick to it and stay there

Formation of the Solenoid - 2nd Step

30nm Fiber - G2 phase

H1 Histone responsible for packaging - allows them to get tighter

Takes 6 nucleosomes and winds them together

Solenoid - helical coiling of 10nm fibers consisting of 6 nucleosomes

Another 7 times of condensation - but now that they are more closely wound together, it makes it harder to access the DNA

Can see right down the middle

How does Histone H1 work?

Binds two distinct regions of DNA

1) Linker DNA

2) Portion of the 146 bp core

Compaction 40x

- pinches the DNA strand together to make it occupy a smaller amount - we have to control how H1 tightly packs them together because we still need access to the DNA

“Alternate Model”

Formation of the Zig Zag Model

DNA backbone is not flexible enough to bend between nucleosomes

Straight linker DNA connects opposite nucleosomes

Has DNA in the middle, so you can not see through it - allows for more compaction than solenoid - so the argument is which one is true?

Experimental results show that both solenoid and zig-zag topologies may simultaneously be present in the chromatin fiber - depends on what the cell needs at a particular time

High-order chromatin - 3rd Step

300nm Fiber - G2 phase

“Chromatin loops” - rosettes - made up of the nucleosomes

Topoisomerase II - central core is made up of this

Compaction level of euchromatin

Last level of condensation where we can actually get access to the DNA →

Where we see most of the Euchromatin

Final Condensation

700nm Fiber - prophase, where we see true condensation occur

Spiral scaffold composed of Topoisomerase II and about 15 non-histone proteins are also a part of this

Compaction level of Heterochromatin

We can no longer access the DNA because it is wound up so tightly - proteins that need to interact with it can not

Can move facultatively from heterochromatin to euchromatin (from where you can’t access the DNA to where you can and back depending on what the cell needs at a specific time)

Metaphase chromosome

Is the most tightly wound - no access to it at all

How we enter the cell cycle

Goes from 700nm - up to around 1400nm

Cell Cycle

G1 = growth phase, getting ready for replication

S phase - where the DNA replicates

G2 = Growth phase, getting ready for cell division

Mitosis - Cell division

G1 - S- G2 = considered interphase - majority of the lifetime in the cell cycle - open and spread out, not fully condensed stay’s in the 300nm phase

Complexity

Complicated, intricate

The state or quality of bring intricate or complicated

The state of having many parts and being difficult to understand or find an answer to

Biological Complexity

The result of the hierarchical organization of nested levels of cells, tissues and higher order part types interacting together

C value paradox

Excess DNA is present in the genome that does not seem to be essential for the development or evolutionary divergence of an organism

The C value paradox takes its name from our inability to account for the content of the genome in terms of known function

Genome size does not correlate with organismal complexity

G-value Paradox

The number of genes does not correlate with organismal complexity

Highly Repetitive DNA Sequence (HR)

Comprises about 10% of the human genome

Most is located in the heterochromatic regions around the centromere/telomere

“non-coding DNA regions”

Postulated functions include structural and organizational roles (centromeres and telomeres) to nothing more than junk

ex: Alpha satellite DNA - from 2 to more than 30 repeats of 171 bp tandem repeats

Moderately Repetitive DNA Sequence (MR)

Comprises about 30% of the human genome

Most is located in the euchromatin (facultative heterochromatin)

Average 300bp in size

Present at between 10-10^5 copies per genome

Function in length mutability, modulation of transcription factor binding, spacing between motor elements, cytosine methylation, alternative splicing, mRNA stability, transcription start and termination sites

Also includes ‘redundant’ genes for histones, and ribosomal RNA and proteins

Ex: microsatellite DNA (repeating sequences of 2-30 bp of DNA) interspersed with repetitive DNA (transposable elements)

Microsatellites

Variable-number tandem repeats typically occur in non-coding regions of the genome

di, tri, tetra

Used to identify different organisms

Useful genetic markers as they tend to be highly polymorphic

Used to sequence the human genome - markers for certain disease conditions - primary markers for DNA testing in forensic class

Occurs through a mutation process known as “slippage recognition” - DNA polymerase slips forward or backward

Single Copy DNA Sequence (unique)

Comprises about 1%-5%

Found throughout the euchromatin

“Coding DNA regions = GENES”

20,000 protein-coding genes

Present at single or low copy number per genome

Gene

Sequence of unique nucleotides (Genotype) that carry the genetic information which it to be expressed (phenotype)

“instruction manual for our bodies”

Every person. has two copies of each gene - one from mother, one from father

99.5% of the DNA, number of genes, types of genes, protein products, are the same in ALL people

<1% of the total number of genes contribute to each person’s unique physical features

Exon

Intron

- “coding sequences”

- “Intervening sequences” - areas of genes that generally don’t code for phenotype

5’ Untranslated Region

mRNA that is directly upstream from the initiation codon

• Differs in prokaryotes and Eukaryotes

• Mostly involved in regulation of Translation

• Recruitment of ribosomal subunits

3’ Untranslated Region

Section of messenger RNA (mRNA) that immediately follows the translation termination codon

Influences the localization, stability, export, and translation efficiency of an mrNA

Post-transcriptional influences on gene expression

Promotor

Promoter is a DNA sequence onto which the transcription machinery binds and initiates transcription

TATA Box

Highly conserved sequence in DNA serving as the binding site for transcription factors

Core DNA sequence

ON/OFF for transcription

“Basal level of transcription”

CAAT box

Consensus sequence that occurs upstream by 60-100 bases from the transcription site

Typically required for inducible genes to be produced in sufficient amounts

GC Bx

Region of DNA that can be bound with proteins (activators) to activate transcription of a gene or genes

RE1

Region of DNA that binds repressor proteins preventing neuronal genes from begin expressed in non-neural tissues

Termination

The end of the gene

Section of nucleic acid sequence that marks the end of a gene or operon in genomic DNA during transcription

Solitary Genes (unique)

A single copy of a gene (haploid situation); two copies in diploid

Comprises the bulk of euchromatin

Duplicated Genes

Process by which a portion of a chromosome is duplicated, resulting in an additional copy of a gene

Results in a copy of the original gene called a paralog gene

Either of the two genes may mutate and change the original function of the gene

Usually occurs due to an error during meiosis

Multigene Families

A set of several similar genes, formed by duplication of a single original gene and generally with similar biochemical functions

Most often located in similar regions of the chromosomes

Most often used or synthesized at different times

Pseudogenes

Dysfunctional relatives of genes that have lost their protein-coding ability

Often the result of multiple mutations within a gene