Nucleic Acids and Chromosome Structure (Chapters 1–6) 9/4/25 genetics
Nucleotide components and naming (DNA vs RNA)
Nucleotide components: each nucleotide consists of three parts:
a five-carbon sugar (ribose in RNA; deoxyribose in DNA),
a nitrogenous base (DNA uses A, G, C, T; RNA uses A, G, C, and U instead of T),
a phosphate group.
In the diagrams discussed, the nucleotide is shown as the complete unit (base + sugar + phosphate), not just the base.
Common naming convention for DNA nucleotides (examples):
dAMP, dGMP, dTMP, dCMP (deoxyribonucleotide monophosphates)
These are often abbreviated as dA, dG, dT, dC when needed; the “d” denotes deoxyribose.
When discussing chain building, note that the 5′ carbon of the sugar is the attachment site for the base and the phosphate group of the nucleotide, and the 3′ carbon is involved in linking to the next nucleotide.
Important distinction emphasized: the five-prime end and the three-prime end define the directionality of a strand (5′ → 3′). The nitrogenous base attaches at the 1′ carbon of the sugar; the phosphate group links the 5′ end of one nucleotide to the 3′ end of the preceding nucleotide in the chain (phosphodiester linkage).
Directionality and linking rule discussed: the phosphate group attached to the 5′ carbon of a nucleotide’s sugar connects to the phosphate group of the next nucleotide, forming the backbone. The 3′ carbon of the sugar in the first nucleotide forms the linkage to the phosphate of the next nucleotide. (Note: actual biochemical processes are described as phosphodiester bonds formed between the 3′-OH of one sugar and the 5′-phosphate of the next; the transcript presents a schematic view emphasizing ends and linkage direction.)
Two key consequences of this structure:
The strand has a defined 5′ end and 3′ end.
The nitrogenous bases are attached to the sugar and project toward the interior of the molecule along the backbone.
Base composition and pairing (DNA)
Nitrogenous bases in DNA: A, T, G, C. In RNA, T is replaced by U (uracil).
Base-pairing rule for double-stranded DNA:
Adenine pairs with thymine via two hydrogen bonds: \text{A} \leftrightarrow \text{T} with 2 hydrogen bonds.
Guanine pairs with cytosine via three hydrogen bonds: \text{G} \leftrightarrow \text{C} with 3 hydrogen bonds.
Observed base composition patterns (historical measurements) indicate that in double-stranded DNA, the percent of A equals the percent of T, and the percent of G equals the percent of C (A ≈ T and G ≈ C) due to complementarity.
Example reasoning (SNP/sequence variation context): If a DNA strand contains 15% adenine (A), then:
T must also be 15% (A = T).
Combined A+T = 30%; the remaining bases (G and C) sum to 70%, so G = C = 35% each.
This explains why A% ≈ T% and G% ≈ C% in double-stranded DNA.
In single-stranded contexts, these pairing rules do not apply across strands, so base percentages need not match in the same way.
Structural overview of nucleic acids (historical context)
Rosalind Franklin’s X-ray diffraction work enabled measurements of distances between components in DNA and the overall width of the molecule, informing the three-dimensional model.
Key measurements from diffraction studies:
The width of the DNA molecule is approximately 2\ \text{nm}.
The distance between base pairs along the helix and various spacings helped infer the helical structure.
Watson and Crick integrated Franklin’s data with other evidence to propose the double helix model.
The double-helix arrangement features two antiparallel strands with a sugar-phosphate backbone on the outside and paired bases on the inside, stabilized by hydrogen bonds.
Conceptual constraint from base shapes:
Pyrimidines (single-ring bases: C, T/U) pair with purines (two-ring bases: A, G) to yield the characteristic 2 nm width of DNA; pairing pyrimidine-pyrimidine would be too narrow and purine-purine would be too wide (Goldilocks principle).
The double helix supports the observed base-pairing proportions (A≈T; G≈C).
Antiparallel geometry and the backbone
The two DNA strands run in opposite directions (antiparallel): one strand is 5′→3′ in one direction, the other is 5′→3′ in the opposite direction.
Backbone arrangement:
The sugar-phosphate backbones are on the outside of the helix.
Nitrogenous bases are inside, paired across the two strands.
Hydrogen bonding holds the base pairs together: A–T has 2 hydrogen bonds; G–C has 3 hydrogen bonds.
Consequence for strand transitions: the 5′ end and 3′ end are oriented in opposite directions on the two strands.
Nucleotide connectivity and structure visuals
In a linear view of a portion of a strand, you can identify:
The phosphate group attached to the 5′ carbon of the sugar at the 5′ end.
The next nucleotide linked via the phosphodiester bond to the 3′ carbon of the current sugar.
In the middle of a strand, each interior nucleotide bears two phosphates (one connecting to the preceding 3′ end and one to the following 5′ end) in terms of phosphate groups across the polymer chain.
Summary of ends:
5′ end: phosphate group attached to the 5′ carbon of the terminal sugar.
3′ end: free 3′ hydroxyl of the terminal sugar (or its equivalent in a given barcode context).
Structural properties and historical context of DNA (summary)
DNA is a double-stranded molecule with two antiparallel strands.
It has a sugar-phosphate backbone with bases pairing in the interior via hydrogen bonds.
The basic width and base-pairing rules reflect the need for stable, uniform geometry across sequences.
The content of A, T, G, C varies across organisms but obeys the A=T and G=C rules in double-stranded DNA.
Four key structural levels of DNA and RNA
Primary structure: the nucleotide sequence (the order of A, T, C, G).
Secondary structure: the actual double-helix arrangement in DNA (or a single-stranded secondary structure in RNA that folds back on itself).
Tertiary structure: higher-order organization within a cell, including packaging into chromatin in eukaryotes.
In double-stranded DNA, the canonical secondary structure is the B-form double helix (right-handed, typically ~10 base pairs per turn).
In RNA, and sometimes under certain conditions, alternative conformations can occur (A-form, Z-form in DNA under specific conditions).
Primary structure variations and types
Sequence variation among species can be visualized by aligning sequences to highlight differences.
Types of variation include:
SNPs (single nucleotide polymorphisms): a single nucleotide differs at a position (e.g., G vs T).
Indels: insertions or deletions of one or more nucleotides relative to another sequence.
Sequence variation can influence secondary structure and function.
Secondary structure varieties
For double-stranded DNA, the classic form is B-DNA (right-handed, ~10 bp/turn).
A-DNA form (also right-handed) is broader and occurs under certain conditions (e.g., dehydrated samples, RNA-DNA hybrids).
Z-DNA form is left-handed and has ~12 bp/turn; tends to be GC-rich regions or transiently during transcription.
Single-stranded nucleic acids can form intramolecular base pairing, yielding structures such as:
Hairpins (stem-loop) with a stem of paired bases and a loop of unpaired bases.
Bulges (unpaired bases that create a bulge in the pairing region).
Pseudoknots (complex multifold structures formed by base-pairing interactions that cross within the same strand).
Palindromic motifs can promote self-pairing in single-stranded nucleic acids.
Tertiary structure and chromatin organization (eukaryotes)
In eukaryotes, DNA is packaged into chromatin, which organizes into higher-order structures.
Core concept: DNA wraps around histone proteins to form nucleosomes, which resemble "beads on a string".
Nucleosome structure:
Core histones: H2A, H2B, H3, and H4 form the octamer around which DNA is wrapped.
H1 histone acts as a linker/clamp to secure DNA on the core particle.
The DNA wraps around the histone core ~1.65 turns per nucleosome, forming the basic repeating unit of chromatin.
Electrostatic interactions: histones are positively charged, DNA is negatively charged, which promotes tight association.
Beads-on-a-string organization can be further condensed into higher-order chromatin structures and ultimately into condensed chromosomes during mitosis.
Post-translational histone modifications regulate chromatin state:
Acetylation of histones generally promotes a more open (decondensed) chromatin state and active transcription.
Deacetylation promotes condensation and transcriptional repression.
Euchromatin vs. heterochromatin:
Euchromatin: less condensed, gene-rich regions that are transcriptionally active; more accessible to transcription machinery; during interphase, typically decondensed.
Heterochromatin: highly condensed regions, often gene-poor; transcriptionally less active; often remains condensed through the cell cycle; enriched near centromeres and telomeres.
Visual representations include nucleus images and karyotypes showing dark (heterochromatin) vs light (euchromatin) bands; euchromatin tends to be lighter in staining, heterochromatin darker.
Prokaryotic vs. eukaryotic chromosome organization
Prokaryotes (bacteria): circular genomes packaged through supercoiling (positive or negative) to compact DNA; topoisomerases introduce or relieve supercoils by breaking and resealing DNA strands.
Positive supercoiling increases compaction but can impede transcription; negative supercoiling often correlates with active transcription.
Eukaryotes: linear chromosomes packaged into chromatin; DNA is wrapped around histones to form nucleosomes; organized into higher-order structures and condensed into mitotic chromosomes during cell division.
Centromeres, telomeres, and satellite DNA
Telomeres:
Ends of linear chromosomes; composed of short tandem repeats (STRs) that are repeated hundreds of times (telomeric repeats).
Telomeres protect chromosome ends from being recognized as DNA breaks and help with replication of chromosome ends.
Shelterin complex helps protect telomeres; specialized structures such as T-loops and V-loops help cap the ends and prevent unwanted repair.
Telomeres generally exhibit a repetitive DNA signature and are often packaged into heterochromatin to protect genomic integrity.
Centromeres:
The constricted region of a chromosome; important for proper chromosome segregation during mitosis/meiosis.
Surrounding the centromere is satellite DNA (SAT DNA): short repetitive sequences repeated many times.
SAT DNA is typically associated with heterochromatin and contributes to the dense packaging required at centromeres.
Visual and functional implications:
Karyotypes show dark bands (heterochromatin, SAT-rich regions) and light bands (euchromatin); this staining pattern corresponds to DNA packing density and gene content.
SAT DNA near centromeres contributes to the dense heterochromatic state at these regions.
An illustrative note from imaging examples: SAT DNA labeled with fluorescent probes highlights centromere locations; telomeres often appear less pink due to lower SAT DNA content.
Chromatin organization and dynamics in the cell cycle
Nucleosome: a fundamental repeating unit of chromatin; DNA wraps around a histone core; histone H1 clamps the DNA to the core.
Beads-on-a-string model: a linear array of nucleosomes connected by linker DNA; can be further condensed to higher-order chromatin structures.
Condensation processes:
Histone acetylation opens up chromatin (euchromatin state) and promotes transcription.
Deacetylation or other repressive marks lead to condensed chromatin (heterochromatin).
During interphase, chromatin is generally less condensed to permit transcription; during mitosis, chromatin condenses into tightly packed mitotic chromosomes.
Quick practice prompt (from the session)
Given a single-stranded DNA sequence that forms a hairpin structure of 5 bases, propose three possible nucleotide sequences for the remaining portion that would allow a 5-base-pair hairpin to form.
Remember to consider palindromic complementarity and feasible base-pairing in the stem region of a hairpin.
Summary of key numerical facts (quick reference)
DNA width: 2\ \text{nm}
B-form DNA: approximately 10\ \text{bp per turn} (right-handed).
A-form DNA: right-handed, more base pairs per turn and wider than B-form (context-dependent).
Z-form DNA: left-handed, approximately 12\ \text{bp per turn} (GC-rich regions or transcriptionally active zones).
Hydrogen bonding in base pairs:
AT pairs: 2 hydrogen bonds.
GC pairs: 3 hydrogen bonds.
Major and minor grooves arise from the helical geometry and base-pairing patterns; these grooves influence protein-DNA interactions.
General qualitative relationships:
GC-rich sequences tend to have higher melting temperatures due to more hydrogen bonds per pair.
GC content influences stability and denaturation behavior of DNA.
Connections to broader biology and real-world relevance
The antiparallel double-helix structure explains how genetic information is stored, replicated, and transcribed with high fidelity.
Base-pairing rules enforce complementarity, enabling precise DNA replication and repair mechanisms.
Chromatin packaging regulates gene accessibility; alterations in histone modification patterns can influence gene expression and cell fate.
Structural variations (SNPs, indels) can have functional consequences, affecting protein coding, regulatory elements, or RNA structure.
Telomeres and centromeres serve essential roles in genome stability and cell division; defects in these regions can lead to genomic instability and disease.
Prokaryotic genome organization illustrates how cells compact DNA efficiently without a nucleus, while eukaryotes use chromatin-based regulation to manage gene expression across large genomes.