Course: PCB 3023, Cell Biology (University of Florida)
Difficulty: Intermediate Prerequisites: Basic chemistry (covalent bonds, hydrogen bonds, acids/bases). Familiarity with amino acids and protein structure helps for the histone material.
DNA is a double-stranded helix held together by complementary base pairing (A-T, G-C) along a sugar-phosphate backbone. The human genome is packaged into chromosomes by wrapping DNA around histone proteins to form nucleosomes, which then fold through several higher-order levels of compaction to produce the mitotic chromosomes visible during cell division. Understanding these structural layers, from the 2 nm helix up to the 1,400 nm mitotic chromosome, is the core of this chapter.
Sugar-phosphate backbone
The structural framework of each DNA strand, made of alternating deoxyribose sugars and phosphate groups linked by phosphodiester bonds. Think of it as the rails of a ladder; the bases are the rungs.
Complementary base pairing
The rule that adenine (A) always pairs with thymine (T) via two hydrogen bonds, and guanine (G) always pairs with cytosine (C) via three hydrogen bonds. In simple terms, if you know one strand's sequence, you can write the other.
Antiparallel strands
The two strands of the DNA double helix run in opposite directions: one 5' to 3', the other 3' to 5'. Think of it as two lanes of traffic running side by side in opposite directions.
Genome
The complete set of genetic information of an organism, encoded in its DNA. For humans, this refers to the DNA contained in a single haploid set of chromosomes (23 chromosomes, roughly 3.2 billion base pairs).
Chromatin
The complex of DNA and histone proteins that makes up chromosomes. In simple terms, chromatin is what chromosomes are made of. It exists in a more open form (euchromatin) during interphase and a highly condensed form during mitosis.
Nucleosome
The basic repeating unit of chromatin: about 200 bp of DNA wrapped around (and linking between) histone core particles. Think of it as a bead on a string, where the bead is the histone core and the string is the DNA.
Nucleosome core particle
An octamer of eight histone proteins (two each of H2A, H2B, H3, and H4) with 147 bp of DNA wrapped 1.7 times around it. The particle is roughly 11 nm in diameter.
Histones
Small, positively charged proteins rich in lysine and arginine that bind DNA and form the core of nucleosomes. Their positive charge attracts the negatively charged phosphate groups on DNA.
Histone modifications (covalent)
Chemical changes to histone tails (acetylation, methylation, phosphorylation) that alter chromatin structure and gene accessibility. Acetylation of lysine residues, for instance, loosens DNA-histone binding and opens chromatin for transcription or replication.
Nucleotide
The monomer (building block) of nucleic acids, consisting of a nitrogenous base, a five-carbon sugar, and one or more phosphate groups. DNA uses deoxyribonucleotides; RNA uses ribonucleotides. Eight distinct building blocks exist across DNA and RNA: dAMP, dGMP, dCMP, dTMP (DNA) and AMP, GMP, CMP, UMP (RNA).
The DNA double helix is composed of two polynucleotide strands wound around each other in a right-handed helix (B-form DNA under physiological conditions).
Each strand has a sugar-phosphate backbone on the outside and nitrogenous bases projecting inward.
Bases pair by hydrogen bonding: A pairs with T (2 H-bonds), G pairs with C (3 H-bonds).
The two strands are antiparallel: one runs 5' → 3', the other 3' → 5'.
Complementarity does not restrict the order of bases along one strand. Any sequence is possible on a single strand; the rule only dictates what the opposite strand must be.
The eight distinct building blocks of nucleic acids are:
DNA: dAMP, dGMP, dCMP, dTMP (deoxyribonucleotides)
RNA: AMP, GMP, CMP, UMP (ribonucleotides)
The difference: RNA uses ribose (with a 2'-OH) and uracil in place of thymine.
A genome is the complete set of genetic information in one haploid set of chromosomes.
The human genome comprises 23 distinct chromosomes (22 autosomes + 1 sex chromosome) and spans roughly 3.2 billion base pairs.
A typical human somatic cell (diploid) contains 46 chromosomes (two copies of each of the 23) and roughly 6.4 billion base pairs of DNA.
Human sperm and egg cells (haploid) contain 23 chromosomes.
Keep these numbers distinct: 23 chromosomes in the genome, 46 in a body cell, 23 in a gamete. The exam will test whether you can tell them apart.
Chromatin is the DNA-protein complex that constitutes chromosomes. DNA does not float free in the nucleus; it is packaged with proteins.
Nucleosome structure:
The nucleosome core particle contains an octamer of 8 histone proteins: two copies each of H2A, H2B, H3, and H4.
147 bp of DNA wraps 1.7 times around this octamer.
The core particle is approximately 11 nm in diameter.
A complete nucleosome includes the core particle plus linker DNA (total roughly 200 bp per nucleosome repeat).
Histone H1 (the linker histone) binds to the DNA entering and exiting the core particle, helping stabilise higher-order folding.
Why histones are positively charged:
Histones are rich in lysine and arginine (both positively charged amino acids).
This positive charge allows electrostatic attraction to the negatively charged phosphate groups in the DNA backbone, holding the DNA tightly on the histone surface.
Histone modifications (in vivo):
Covalent modifications to histone tails change how tightly DNA is packaged.
Acetylation (adding acetyl groups to lysine residues) neutralises the positive charge, weakening the histone-DNA interaction and opening the chromatin for transcription or replication.
Other modifications include methylation, phosphorylation, and ubiquitination. Each can signal for tighter or looser packaging depending on context.
Disassembling nucleosomes in vitro:
In the test tube, nucleosomes can be disrupted by increasing salt concentration (typically 2 M NaCl). The high ionic strength screens the electrostatic interactions between histones and DNA, causing the histones to release.
DNA must be compacted roughly 10,000-fold to fit inside the nucleus during mitosis.
Levels of compaction (from least to most condensed):
2 nm fibre: The naked DNA double helix itself.
11 nm fibre ("beads on a string"): DNA wrapped around nucleosome core particles, visible under the electron microscope after chromatin is spread at low ionic strength.
30 nm fibre: Nucleosomes fold into a more compact fibre, likely a solenoid or zigzag arrangement. Histone H1 and inter-nucleosome interactions stabilise this level. (The precise structure of the 30 nm fibre is still debated.)
Looped domains (300 nm): The 30 nm fibre forms loops anchored to a protein scaffold. Each loop contains roughly 50,000 to 100,000 bp.
700 nm condensed section: Further coiling of the looped domains.
1,400 nm mitotic chromosome: The final, most condensed state visible during metaphase. This is the classic X-shaped chromosome seen in textbook images.
The key idea: each level builds on the previous one, progressively shortening and thickening the chromosome.
Property | Value |
|---|---|
Width of the double helix | 2 nm |
Height of one complete turn | 3.4 nm |
Base pairs per turn | ~10 bp |
Distance between adjacent base pairs | 0.34 nm |
H-bonds in an A-T pair | 2 |
H-bonds in a G-C pair | 3 |
Helix sense | Right-handed (B-form) |
Nucleosome core particle diameter | ~11 nm |
DNA wrapped around core particle | 147 bp (1.7 turns) |
DNA per nucleosome repeat | ~200 bp |
Histone octamer composition | 2x each of H2A, H2B, H3, H4 |
Human haploid genome | ~3.2 billion bp, 23 chromosomes |
Human diploid cell | ~6.4 billion bp, 46 chromosomes |
"Complementarity restricts the sequence on one strand." It does not. Any order of bases is possible on a single strand. Complementarity only dictates what the other strand must be, given the first.
"The genome and the cell's total DNA are the same thing." The genome is the haploid set (23 chromosomes, ~3.2 Gbp). A diploid cell has two copies of the genome (46 chromosomes, ~6.4 Gbp). These are different numbers, and exams test exactly this distinction.
"Histones are negatively charged because they bind DNA." The opposite: histones are positively charged (rich in lysine and arginine), which is precisely why they attract the negatively charged DNA backbone.
"Acetylation tightens chromatin." Acetylation loosens chromatin by neutralising the positive charges on histone tails. This is one of the most commonly reversed facts on exams.
⚠️ Know the vital statistics table cold: width (2 nm), turn height (3.4 nm), bp per turn (~10), distance between bp (0.34 nm), H-bonds per pair (2 for A-T, 3 for G-C).
⚠️ Be precise about chromosome numbers: 23 in the genome (haploid set), 46 in a somatic cell (diploid), 23 in a gamete. The review sheet flags that each of these questions has a different answer.
⚠️ Know the nucleosome core particle composition by heart: 8 histones (2x H2A, H2B, H3, H4), 147 bp of DNA, 11 nm diameter.
⚠️ Understand the distinction between in vivo histone modification (acetylation, methylation, phosphorylation) and in vitro nucleosome disassembly (high salt concentration). This is a common exam comparison.
⚠️ Be able to list the levels of DNA compaction in order from 2 nm to 1,400 nm, naming each structure.
True or False: The two strands of DNA run in the same direction (both 5' to 3').
Fill in the blank: An A-T base pair is held together by ___ hydrogen bonds, while a G-C pair has ___.
True or False: The human genome contains 46 chromosomes.
Fill in the blank: The nucleosome core particle contains ___ histone proteins and ___ bp of DNA.
True or False: Acetylation of histone tails makes chromatin more condensed.
Answers: 1. False (antiparallel). 2. Two; three. 3. False (23 in the genome; 46 in a diploid cell). 4. Eight (the octamer); 147 bp. 5. False (acetylation loosens chromatin).
Q: Describe the sugar-phosphate backbone and explain what holds the two strands of the double helix together.
A: Each strand is built from deoxyribose sugars linked by phosphodiester bonds to phosphate groups, forming the backbone. The two strands are held together by hydrogen bonds between complementary bases (A-T and G-C) projecting inward from each backbone.
Q: Does complementary base pairing restrict the sequence of bases along one strand of DNA?
A: No. Any sequence of bases is possible on a single strand. Complementarity only determines the sequence of the opposite strand.
Q: How many chromosomes are in (a) the human genome, (b) a typical human somatic cell, and (c) a human gamete?
A: (a) 23 chromosomes (the haploid set). (b) 46 chromosomes (diploid). (c) 23 chromosomes (haploid).
Q: Name the eight histone proteins in a nucleosome core particle and state how much DNA wraps around it.
A: Two copies each of H2A, H2B, H3, and H4 (eight total). 147 base pairs of DNA wrap 1.7 times around the octamer.
Q: Why are histones positively charged, and how does acetylation affect their interaction with DNA?
A: Histones are rich in lysine and arginine, both positively charged amino acids, allowing electrostatic binding to the negatively charged DNA backbone. Acetylation neutralises these positive charges, weakening the interaction and opening the chromatin.
Q: How are nucleosomes disassembled in vitro?
A: By raising the salt concentration (e.g. 2 M NaCl), which screens the electrostatic interactions between the positively charged histones and the negatively charged DNA, releasing the histones.
Q: List the levels of DNA compaction from the double helix to the mitotic chromosome.
A: 2 nm (bare double helix) → 11 nm (beads on a string/nucleosome fibre) → 30 nm (chromatin fibre) → 300 nm (looped domains) → 700 nm (condensed section) → 1,400 nm (mitotic chromosome).
This material connects directly to Chapter 6 (DNA Replication and Repair), because the replication machinery must navigate chromatin structure. Nucleosomes must be disassembled ahead of the replication fork and reassembled behind it.
Histone modifications also tie into gene regulation (typically covered later in the course). Acetylation and methylation patterns determine which genes are accessible for transcription, linking chromosome structure to gene expression.
The concept of antiparallel strands is essential for understanding why leading and lagging strand synthesis differ during replication (Chapter 6).
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