mod. 4: genome I DNA structure and chromosomes

what is non-coding DNA?

regulatory structural repetitive DNA

what is the structure of DNA?

double helix, complementary, enables replikcation

what are the bonds holding together nucleotides?

phosphodiester bonds, polar

what is base pairing bonded by?

H-bonds`

what is translation?

DNA→mRNA

what is transcription?

mRNA→proteins

what is chromatin?

DNA and histone proteins

what are nucleosomes?

DNA wrapped around histones

what is euchromatin?

loosley packed active genes

what is heterochromatin?

tightly packed inactive regions

what are chromosomes?

highly organized compacted DNA

what is the packing ratio?

10,000:1 packing ratio

what are the levels of DNA packing?

double helix→nucleosome→ chromatin fiber→ looped domains→ condensed chromosomes

what is chromatin?

DNA+ histones + non histone proteins

what does chromatin do?

enables DNA compaction and gene regulation~roughly 1/3 its length of naked DNA when packaged

what is a nucleosome?

DNA+ histones “beads on a string”

has core particle- octamer (8 histones)

linker DNA-connects through nucleotide pairs

Histone Hl-linker histone binds outside to stabilize highr order structure.

what is the structure of a histone composed of?

3 alpha helicies that mediate histone-histone interactions.

and a histone tail at the N-terminus that are key regulatory sites.( this is the site of modification bc its more accesible here)

what are some properties of histones

• rich in arginine and lysine that binds charged DNA

• highly conserved across species

• interactions are reversible allowing chromatin remodeling

• **histone-DNA interactions depend on charge; neutralization loosens DNA

what is a chromatin fiber?

long super coiled looped of DNA scaffolding proteins.

contains cohesion rings- that maintain loop structure, hold DNA strands together during mitosis

what are SMC ring complexes?

structural maintainence of chromosomes form ring complexes around DNA.

they use ATP hydrolysis to open and close the ring.

DNA loops grow as SMC’s pull DNA through the ring( like a molecular motor)

what controls the chromatin loop?

clamp proteins- stop loop growth at specific DNA sequences. loop sizes determines which genes share the same regulatory environment.

1. cohesion binds DNA and forces small loop

2. ATP hydrolysis enlarges loop.

how does packing for mitosis occur?

cells open or compact chromatin using ATP dependent remodeling complexes and histone modifying enzymes.

euchromatin; access for transcription, replication, repair

heterochromatin; condensed, transcriptionally silent; can spread or be inherited through cell divisions.

** chromatin structure is dynamic and regulated gene accessibility.

what are the types and subtypes of chromatin?

euchromatin: loosely packed

heterochromatin: tightly packed

• constitutive heterochromatin: always condensed silent DNA, highly repeated sequences, few genes

• facultative heterochromatin: inactivated during certain portions of organisms life or in all cells types→ gene silencing (X chromosome, barr body)((calico cats))

what is the histone code hypothesis?

activity of chromatin region depends on degree of chemical modification of histone tails

they can serve as docking sites to recruit non-histone proteins 

they can alter the way histones of neighboring nucleosomes interact ( more effects of wider regions)

what does the N termini site modify for amino acids?

proteins may bind selectively to modifiy H3 or H4 residues

interphase chromatin fibers in distinct territories have different locations related to levels of chromosome activity.