Topic 8- Genome & Chromatin Structure

What is supercoiling?

• + supercoiling?

• - supercoiling?

Twisting of DNA (compacts DNA, Affects gene expression)

• + → more rotations, less bp/ rotation (tighter)

• - → less rotations more bp/ rotation (looser)

What is different between Eukaryotic and Bacterial DNA

Bacterial DNA is not assocciated with histones

Bacteria DNA is segmented into twisted loops

Topoisomerase I?

Topoisomerase II?

Both function to relieve supercoiling tension

I) cuts1 strand of the duplex, relieving tension, no ATP

II) cuts 2 strands, uses ATP, can untangle intertwined DNA (for pulling out specific sequences)

What is chromatin?

• Heterochromatin?

• Euchromatin?

DNA associated with protein (1/3 DNA, 2/3 protein)

Heterochromatin:

• densely packed

• Transcriptionally silent

• Often repetitive

• @ telomeres and centromeres

(% varies among cells, increases as cells become more differentiated)

Euchromatin:

• Loosely packed

• Transcriptionally active

• Genes expressed

When is heterochromatin replicated?

@ the end of S-phase.

(because it needs to unfold 1st)

What is a nucleosome?

What is a histone?

• 8 histone proteins wrapped by DNA 1.65x

• + charged proteins, DNA wraps around them

- H1, H2, H3, H4 (2 of each)

What are Polytene Chromosomes

Found in Drosophila salivary glands.

They form when DNA replicates repeatedly, cell doesnt divide

Result:

• Giant chromosomes

• Visible banding pattern

• “Puffs” = regions actively being transcribe

What is the role of Histone 1

It clamps the DNA on the nucleosome.

What is the ENCODE project?

Large research project to identify all functional elements in the human genome

INCLUDING:

• Regulatory regions

• Noncoding functional DNA

Pseudogenes

Nonfunctional copies of DNA (dont produce functional protein)

Not expressed, rotting away

How do unique, moderately and highly repetitive DNA differ?

Unique DNA

• Single-copy sequences

• Most protein-coding genes

Moderately repetitive

• Present dozens–thousands of times

• rRNA genes, transposons

Highly repetitive

• Short sequences repeated millions of times

• Often structural (centromeres, telomeres)

What are Satellites

what are they, what do they do, where are they found?

Highly repetitive segments of DNA

found at centromeres

structural role

What are microsatellites?

• AKA Short Tandem Repeats

• 1–8 base pair repeats (ex: CACACACA)

• No known function

• Highly variable between individuals

• Used in DNA fingerprinting (counts # repeats)

How is DNA fingerprinting conducted?

Process:

1. Extract DNA

2. PCR amplify repeat regions

3. Separate by size

4. Compare patterns

What is a Telomere?

• what happens when they wear down?

• what kind of cell has the longest telomere

Caps on DNA to prevent loss of genes (at the end of a chromosome.)

• non-coding

• shorter withe each division

when the wear down the cell becomes SCENESCENT

sperm and egg have LONGEST telomeres

What is a Centromere?

• Region where spindle fibers attach, ensures proper chromosome segregation

• LARGE array of repetitive DNA

• The sequence is unimportant, but SHAPE = CRUCIAL, very conserved

What is Alu DNA

10% of genome

Cancerous DNA, working against organism

we are also 17% viral DNA

What is a NOR

What is CODUS

Combined DNA Index System (CODIS)

forensic DNA database operated by the FBI

stores DNA profiles based on STRs

Genetically, CODIS works because:

CODIS uses allele length variation at 13/20 core STR loci to uniquely identify individuals.

What is the C-value paradox

There is a high correlation between Prokaryote genome size and organism size,

BUT

the same is NOT true for Eukaryotes.

What is the C-value

haploid amount of DNA

differs by organism

What type of organism would have a higher amount of G & C than A & T

high temperature organism

prevents against melting and denaturation

What are Transcription Factories

in oil bubbles keeps condensin loops

DNA is moved and brought to RNA polymerase

(all DNA required for s specific job)

Transcription factories are nuclear clusters of RNA polymerase and transcription machinery where multiple genes are transcribed simultaneously as DNA loops into these active transcription hubs.

What is Condensin

Condensin is a protein complex that organizes and FOLDS chromosomes during mitosis and meiosis.

• positive supercoils and

• stabilizes loops

• ensures accurate chromosome segregation.

Why are phosphorylation and dephosphorylation important for chromosome condensation?

1. Phosphorylation = “Turn On”

   • Adds a phosphate group to proteins (like condensin or histones).

   • Causes chromosomes to condense during mitosis.

2. Dephosphorylation = “Turn Off”

   • Removes the phosphate group.

   • Causes chromosomes to relax after mitosis, so the cell can read genes again.

Why it matters:

• Makes sure chromosomes condense only during cell division.

• Prevents mistakes in gene expression or chromosome separation.

What is a Retrovirus

A virus that has RNA as its genetic material

Uses reverse transcriptase RNA → DNA

• Integrates its DNA into the host’s genome.

• Hijacks the host cell’s machinery to make more viruses.

• lots of MUTATIONS

Ex: HIV

What is an ERV

Endogenous Retrovirus

• Entered germline cells → passed to offspring (permanently integrated into host genome)

• Needs host to live, ensures survival

• Mostly silent

Ex: HERV-W

What is HERV-W

An ERV that produces protein that fuses cells together:

THIN PLACENTA

• Fuses cells to form syncytiotrophoblast

• Shows how humans co-opted a viral gene for essential reproduction.

What are Microevolutionary changes

Small-scale changes in allele frequencies within a population over a short time (years to centuries).

ex- Antibiotic resistance in bacteria, peppered moth color change

Macroevolution

large-scale evolutionary changes over long periods (thousands to millions of years) that can create new species or higher taxa.

changes to gene regulation

ex- divergence of Darwin’s finches.

What are DNA transposons (Class II)

“cut-and-paste” transposable elements

Insertion sequences

• Carries only the genetic information needed for

transposition

Composite transposons

• Flanked by two copies of an insertion sequence that

may itself transpose

What is a flanking direct repeat

A short identical DNA sequence found on both sides of a transposon after it inserts into the genome.

• Created when transposase makes staggered cuts in the target DNA.

• DNA polymerase fills the gaps, duplicating the target sequence.

• The duplicated sequences appear on both sides of the transposon

What is Transposase?

Cleaves the ends of the transposon, freeing it from its initial location.

Cleaves target sites where the element is to be inserted.

What are Inverted repeats?

Inverted repeats are short DNA sequences at the ends of a transposon that are reverse complements of each other.

Key points:

• Part of the transposon itself

• Located at both ends of the element

• Recognized by the enzyme transposase

• Help the transposon be excised and inserted into a new location

Reverse Transcriptase

• Enzyme used by retrotransposons

• Converts RNA → DNA

• Allows the element to copy itself and insert a new copy

What are LINES

Retrotransposons

copy & paste

use reverse transcriptase

RNA → DNA

What are LINEs (Long Interspersed Nuclear Elements)?

JUNK GENES

retrovirus genomes, repeated ~140,000 times; comprise 20.7% of human

genome-the commonest is LINE-1 (14.6%) which is the only one still active

What are SINES

Notochord?

Short Interspersed Nuclear Elements

short non-autonomous retrotransposons

• cannot move on their own

• rely on LINE reverse transcriptase to copy and insert into new genomic locations.

Alu SINE insertions near the notochord gene, which caused alternative splicing.

This altered gene expression and likely contributed to tail loss in apes and humans during evolution.

What are Composite Transposons