DNA Structure & Chromatin

50 vocabulary flashcards covering DNA structure and chromatin based on the provided lecture notes. Each flashcard presents a term and its definition.

DNA stability compared to RNA

DNA lacks a 2′ OH group, reducing susceptibility to hydrolysis.

Cytosine deamination product

Uracil.

Reason DNA uses thymine instead of uracil

To distinguish uracil from deaminated cytosine.

Hydrogen bonds between A–T

2 hydrogen bonds.

Hydrogen bonds between G–C

3 hydrogen bonds.

Bond holding sugar-phosphate backbone together

Phosphodiester bonds.

Bonds holding complementary base pairs together

Hydrogen bonds.

Additional force stabilizing DNA

Base stacking (hydrophobic interactions between aromatic bases).

DNA denaturation process

The two strands separate as hydrogen bonds break.

DNA renaturation

Annealing (reformation of double helix).

Melting temperature (Tm) dependence

G–C content (higher GC = higher Tm).

Most common DNA form under physiological conditions

B-form DNA.

A-form DNA characteristics

Right-handed, shorter/wider, found in dehydrated samples or DNA–RNA hybrids.

Z-form DNA characteristics

Left-handed and occurs with alternating G–C sequences.

DNA groove for sequence-specific protein binding

Major groove.

Groove/backbone interaction used by DNA polymerases

Minor groove and backbone.

Topoisomerase I function

Introduces or removes supercoils by cutting one strand.

Topoisomerase II function

Cuts both strands to resolve concatenated DNA.

Proteins packaging eukaryotic DNA into nucleosomes

Histones.

Four core histones in the nucleosome

H2A, H2B, H3, H4 (two of each).

Linker histone

H1.

Base pairs wrapping around a nucleosome

~147 bp (~1.7 turns).

Reason histones are highly basic

They contain many lysines and arginines, which are positively charged.

Significance of histone positive charge

It interacts with negatively charged DNA backbone.

Histone tail modification

Yes, by methylation, acetylation, phosphorylation, etc.

Effect of histone modifications

Regulate DNA compaction and accessibility.

Effect of acetylation of histone tails

Reduced compaction → more transcriptionally active.

Cell cycle phase with most DNA compaction

Metaphase of mitosis.

Euchromatin

Less condensed, transcriptionally active chromatin.

Heterochromatin

More condensed, transcriptionally inactive chromatin.

Nature of nucleosome structures

No, they are dynamic and can slide or be removed.

Nucleosome remodeling complexes function

Shift or reposition nucleosomes on DNA.

Histone modifying enzymes function

Add or remove covalent modifications from histone tails.

Consequence of DNA wrapping around nucleosomes for protein access

It can block access to major/minor grooves facing inward.

Enzyme used experimentally to cut linker DNA

MNase (micrococcal nuclease).

DNA fragment size from MNase digestion

~160 bp fragments (nucleosome + linker).

MNase-seq application

Mapping nucleosome positions genome-wide.

Reason MNase cannot cut wrapped DNA

Because the DNA is tightly bound to histones and inaccessible.

Model organism for studying histone variants

Yeast (has conserved histones).

Method to test histone variant association with specific genes

MNase digestion followed by sequencing.

H2A.Z

A histone variant often enriched at promoters, regulating accessibility.

γH2AX

A histone variant associated with DNA damage sites.

H3.3

A histone variant enriched in regions of active transcription (less compact).

Reason histones do not need strict sequence specificity to bind DNA

Binding is mostly electrostatic with the phosphate backbone.

Primary interaction site for proteins with DNA bases

Major groove.

Reason inward-facing grooves in nucleosomes might be inaccessible

They are blocked by histone surface contacts.

Supercoiling

Over- or under-winding of the DNA helix.

Consequence of unresolved supercoiling

Replication and transcription are hindered.

Power source for nucleosome remodeling complexes

ATP-dependent dsDNA translocases.

Reason for dynamic DNA compaction

To balance genome protection with accessibility for replication, repair, and transcription.