Chromatin structure

Chromosome

Structure in which genetics material is carried

DNA compaction

DNA is crammed into a compact enviroment

Viral Chromosomes

-Single double stranded DNA or RNA

-Circular or linear molecules 

-DNA has few or no proteins

Bacteral Chromosomes

-Circular, double stranded DNA

-Not that many proteins

-readily replicated and transcribed

Bacterial chromosomes compacted into

A nucleoid

A Nucleoide  

-found inside bacterial chromosome

-not surrounded by a membrane

-center of the cell

Binding proteins:

HU 

H-NS

HU

wraps and bends DNA

H-NS (Histone-like Nucleoid Structuring Protein)

Compact DNA and regulate gene expressions

Regulate gene expressions

controlling how much, when, and where a gene is turned on or off

Coils

Way DNA twists and loops to become more compact

Mitochondria and Chloroplasts:

-Have their own DNA

-Comes from the mothers egg cell

-Eggs cytoplasm contains these organelles 

Mitochondria and Chloroplasts are similar to

Viral and Bacterial DNA

How are Mitochondria and Chloroplasts are similar to Viral and Bacterial DNA ?

-Circular

-few proteins attached

-only 1 piece

-smaller than DNA in nucleous

Mitochondria and Chloroplasts have what independent cells need:

-Own DNA
-Own ribosomes

-own cell membrane

-own cytoplasm

Endosymbiosis

Believed organelles came from free living bacteria that got inside bigger cells

Endosymbiosis steps:

Primitive eukaryotic cell, swalled small bacterium

instead of digesting it—> formed partnership 

(save place to live, new abilities)

Chromatin

Complex of DNA, RNA, proteins inside cell nucleus 

-uncompacted DNA used throughout cell cycle 

Chromatides 

(mitotic chromosomes).

-Highly compacted “X” shaped in mitosis 

During interphase, chromatin is dispersed

Throughout the nucleus 

Chromatin is made up of

nucleosomes

Nucleosomes

basic unit of DNA packaging in eukaryotic cells

-DNA wrapped around histones

Histones

postive charged proteins

bind to the negatively charged DNA.

Histones are

Most abudent protein

5 main histones:

-H1

-H2A

-H2B

-H3

-H4

What helps help histones bind tightly to DNA?

Lysine and Arginine

(small, positively charged amino acids)

Nucleosome core particle contains a

histone octamer

Histone octamer

-core structure made of 8 histone proteins.

-It forms the central part of a nucleosome, which DNA wraps around

Histone octamer has two copies of:

-H2A, H2B, H3, and H4

-with 147 base pairs of DNA wrapped around it.

Linker DNA

Stretch of DNA

Connects nucleosome 

Histone H1

Binds to Linker DNA

packs nucleosomes close 

1st level of Nucleosome packing:

-formation of nucleosome

-DNA wraps around histone Octamer 

-11 Mn wide 

DNA wrapped around histones to form nucleosomes (~11 nm fiber).

2nd level of packing

-Further coil to a thicker fiber: 30nm

-This fiber is called “Solenoid”

-Histone H1 helps compact pack nucleosomes tighter

(most common form of chromatin during interphase (when the cell is not dividing)

(nucleosomes coil into a 30-nm fiber (solenoid) with the help of histone H1)

Further packing:

Looped Domains

-The 30-nm fiber forms large loops attached to a protein scaffold inside the nucleus

Coiled Chromatin Fibers

• These looped domains can coil even more tightly, creating a thicker fiber.

Chromatids

• When the cell enters mitosis, chromatin fibers fold and coil extensively to form the chromatids of the visible mitotic chromosomes

Chromatin fibers

DNA-protein complexes at various levels of folding, from nucleosomes to tightly coiled fibers, that organize and compact DNA inside cells. (11 and 30mn)

Chromatin Remodeling

Chromatin structure changes

allows DNA-binding proteins access to DNA

Chromatin Remodeling is essential for:

-DNA replication

-Gene expression

DNA replication

Copying DNA before cell divison

Gene expression

Turning Genes on and off

Chemical modification of histones

Adding or removing of

-Acetyl group

-methyl group

-Phosphate group 

Acetyl group

-Adds Negative charge

-loosens DNA—> turns genes on

Methyl group

-No charge change

Can turn genes on and off

Phosphorylation (Phosphate group)

- Adds Negative charge

-Can signal DNA damage, or affect gene expression and cell division

Histone tails

loose, flexible ends of histone proteins that stick out from the nucleosome and can be chemically modified to help control how tightly DNA is packed and how genes are turned on or off.

Histone acetylation is often linked

gene activation (turning on)

Euchromatin

-less condensed (loosely packed)

-Active and transcribed (used to make RNA and proteins)

-30-nm fiber

Heterochromatin

-tightly packed part of chromosome

-nactive (not being used)

-loop domains that are compacted even more than euchromatin

Repetitive DNA

-sections of DNA that repeat many times in a row or throughout the genome

-60% of our DNA

Why is repetitive DNA important?

• vary a lot between different people.

• Because of this variation, these repetitive regions are used for DNA fingerprinting

Highly Repetitive Satellite DNA

short sequences repeated many times in a row

Highly Repetitive Satellite DNA Location:

Centromeres

telomeres

other heterochromatin regions

Minisatellites (Variable Number Tandem Repeats - VNTRs)

-15-100 base pairs

-used in DNA fingerprinting 

Microsatellites: short tandem repeats (STRs)

-Very short repeats like 2 to 5 base pairs (di-, tri-, tetra-, penta-nucleotide repeats).

Multiple Copy Genes

-genes are duplicated many times in a row.

-Tandem

-common for ribosomal RNA genes.

Interspersed transposon elements:

-SINES

-LINES

SINES

Small sequences about 200–300 base pairs long

-1/3 of human genome

-inactive

LINES

Much longer, about 6,000 base pairs long

-1/3 of human genome 

-inactive

Protein-Coding Genes

-small part of the genome—about 2–10%

-

Single-Copy Noncoding Regions

only one copy, not repeated

Gene regulatory sequences

Control when and where genes are turned on or off (like promoters and enhancers).

Promoters

tells us where to begin copying DNA to RNA

Enhancers

make gene expressions stronger

Pseudogenes

Broken or “dead” copies of genes with mutations, usually not made into RNA or protein.

Noncoding RNA genes

Make RNA molecules that don’t code for proteins but have important functions, such as:

• rRNAs (ribosomal RNA)

• tRNAs (transfer RNA)

• microRNAs and long noncoding RNAs (regulate gene expression and other processess