Source: Lecture notes, textbook chapters on DNA structure
Tags: DNA structure, nucleotide, double helix, base pairing, antiparallel, Griffith, Hershey-Chase, Chargaff, Watson and Crick, BIO 311C
Difficulty: Intermediate | Prerequisites: Basic chemistry (chemical bonds, molecular structure), cell biology fundamentals (nucleus, proteins, enzymes)
This topic sits at the foundation of molecular biology. Before you can understand gene expression, protein synthesis, or genetic engineering, you need to know what DNA looks like, how it stores information, and why scientists concluded it was the hereditary molecule in the first place. The material here covers the physical structure of DNA (double helix, antiparallel strands, base pairing) and walks through the classic experiments that settled a decades-long debate over whether proteins or DNA carry genetic information. You should already be comfortable with basic organic chemistry (functional groups, hydrogen bonds) and the general layout of a eukaryotic cell.
DNA is a double-stranded helix made of nucleotides, held together by complementary base pairing (A with T, G with C) and running antiparallel. A series of landmark experiments, from Griffith's transformation work through Hershey-Chase's radioactive labelling, proved DNA (not protein) is the molecule that carries genetic information. Watson and Crick assembled these clues into the structural model we use today.
Chromatin
The loosely packed form of DNA in the nucleus, used as a template for RNA and DNA synthesis. Think of it as DNA in its "working" state, looking like tangled spaghetti inside the nucleus.
Chromosome
DNA condensed into a compact X-shaped structure for transmission from one cell to another during division. In simple terms, this is DNA packaged tightly for transport.
Nucleotide
The monomer (building block) of DNA, consisting of three parts: a phosphate group, a five-carbon sugar (deoxyribose), and a nitrogenous base. Think of it as one bead on a very long necklace.
Nitrogenous base
The variable part of a nucleotide that encodes genetic information. There are four types in DNA: adenine (A), thymine (T), guanine (G), and cytosine (C).
Purines
The larger, double-ringed nitrogenous bases: adenine (A) and guanine (G). In simple terms, the "big" bases.
Pyrimidines
The smaller, single-ringed nitrogenous bases: thymine (T) and cytosine (C). In simple terms, the "small" bases.
Complementary base pairing
The rule that A always pairs with T (two hydrogen bonds) and G always pairs with C (three hydrogen bonds). This is the mechanism that holds the two DNA strands together and makes replication possible.
Antiparallel
The orientation of the two DNA strands: one runs 5' to 3' while the other runs 3' to 5'. Think of it as two lanes of traffic going in opposite directions on the same road.
Double helix
The twisted-ladder shape of DNA, with the sugar-phosphate backbones as the rails and the base pairs as the rungs.
Transformation
A change in genotype and phenotype caused by the uptake of foreign DNA from the surrounding environment. First observed by Griffith when harmless bacteria picked up DNA from dead pathogenic bacteria and became pathogenic themselves.
Bacteriophage (phage)
A virus that infects bacteria, composed of protein and DNA. The T2 phage was central to the Hershey-Chase experiment. In simple terms, a bacterial parasite made of a protein shell around a DNA core.
Chargaff's rules
The observation that in any species, the amount of adenine equals the amount of thymine, and the amount of guanine equals the amount of cytosine (A = T, G = C). This only made sense once the double helix and base pairing were understood.
X-ray crystallography
A technique for determining molecular structure by firing X-rays at a crystallised sample and analysing the diffraction pattern. Rosalind Franklin's Photo 51, produced using this method, was crucial evidence for the double helix.
Semi-conservative replication
The model of DNA replication (confirmed by Meselson and Stahl) in which each new DNA molecule consists of one original (parental) strand and one newly synthesised strand. In simple terms, each daughter molecule keeps half of the original.
Chromatin: the loose, "spaghetti-like" form found in the nucleus during normal cell activity. This is the template form, used for synthesising RNA and copying DNA.
Chromosomes: the condensed, X-shaped form used when the cell is dividing and needs to move DNA from one cell to another.
Self-replication: DNA copies itself so genetic information passes to daughter cells.
Template for transcription: DNA serves as the blueprint from which RNA is made.
Both functions are possible because DNA nucleotides can base-pair with both ribose (RNA) and deoxyribose (DNA) nucleotides.
DNA is built from nucleotides, each containing three components: a phosphate group, a five-carbon deoxyribose sugar, and a nitrogenous base.
The sugar and phosphate groups alternate to form the sugar-phosphate backbone, the structural "rail" of the molecule.
Two strands are held together by hydrogen bonds between complementary nitrogenous bases (A–T and G–C). This is base pairing.
The two strands run antiparallel: one strand runs 5' to 3', the other runs 3' to 5'.
The 5' end has a free phosphate group.
The 3' end has a free hydroxyl (OH) group.
DNA synthesis can only proceed in the 5' to 3' direction. This constraint is the reason the lagging strand must be synthesised in fragments.
The overall shape is a double helix, a twisted ladder.
The sequence of bases along a DNA or mRNA polymer is unique for each gene.
For any molecule to serve as genetic material, it must satisfy four requirements:
Sufficient variability to encode complex information (DNA's four bases in varying sequences provide this).
Ability to replicate, to make copies of itself.
Accessibility, so the stored information can be read and expressed (gene expression).
Imperfect copying, because occasional errors (mutations) produce the variation that drives evolution and gives rise to different phenotypes and genotypes.
Early scientists assumed proteins were the genetic material because proteins have 20 different amino acids (giving enormous structural variety) and were already known to control cell reactions. DNA, by contrast, has only four nucleotides, appears uniform and "stringy" under the microscope, and stays in the nucleus. It took several clever experiments to prove DNA was the carrier of hereditary information.
Worked with two strains of Streptococcus pneumoniae: S (smooth, pathogenic) and R (rough, harmless).
Four conditions tested:
Living S cells injected into mouse: mouse dies.
Living R cells injected into mouse: mouse lives.
Heat-killed S cells injected into mouse: mouse lives.
Heat-killed S cells mixed with living R cells injected into mouse: mouse dies, and living S cells are found in the dead mouse.
Conclusion: something from the dead S cells "transformed" the living R cells, making them pathogenic. Griffith called this transformation.
Transformation is now defined as a change in genotype and phenotype due to the uptake and incorporation of foreign DNA.
The transformation was heritable: descendants of the transformed R cells remained pathogenic.
Built on Griffith's work to determine which molecule carried the transforming ability.
Steps:
Removed lipids and carbohydrates from heat-killed S cells, leaving proteins, RNA, and DNA.
Treated separate samples with enzymes that destroyed either proteins, RNA, or DNA.
Added each treated sample to living R cells and checked for transformation.
Result: transformation occurred when proteins were destroyed and when RNA was destroyed, but did not occur when DNA was destroyed.
Conclusion: DNA is the transforming agent.
Used T2 bacteriophage (a virus made of protein and DNA) that infects E. coli.
Designed two parallel experiments to determine whether DNA or protein enters the host cell during infection.
Experiment 1, testing protein:
Phage protein coats labelled with radioactive sulfur (³⁵S), because sulfur is found in protein but not in DNA.
Phages infect bacteria, then phage coats are separated by centrifugation.
Radioactivity found in the supernatant (outside the cells), not in the bacterial pellet.
Conclusion: protein does not enter the cell, so protein is not the genetic material.
Experiment 2, testing DNA:
Phage DNA labelled with radioactive phosphorus (³²P), because phosphorus is found in DNA but not in protein.
Phages infect bacteria, then separated by centrifugation.
Radioactivity found in the pellet (inside the cells).
Conclusion: DNA enters the cell and is the genetic material.
Why not use nitrogen as the label? Both DNA and proteins contain nitrogen, so radioactive nitrogen would not distinguish between the two.
Erwin Chargaff analysed the base composition of DNA from multiple species.
Found that base composition varies between species, making DNA a more credible candidate for genetic material (it has the variability needed to encode different organisms).
The rules:
The percentage of A always equals the percentage of T.
The percentage of G always equals the percentage of C.
Stated differently: purines (A + G) = pyrimidines (T + C).
These ratios were not fully explained until Watson and Crick proposed complementary base pairing in the double helix.
Rosalind Franklin used X-ray crystallography to study DNA's molecular structure.
Produced Photo 51, a diffraction image that strongly suggested DNA is a helix.
The image revealed the width of the helix and the regular spacing of the bases.
Used Franklin's Photo 51, Chargaff's base-ratio data, and existing chemical knowledge to build their model.
Key insights:
DNA is composed of two strands wound into a double helix.
Complementary base pairing (A–T, G–C) explains Chargaff's rules and gives DNA a uniform diameter (one purine paired with one pyrimidine at each rung).
The two strands fit best in an antiparallel arrangement.
After completing the model, it became clear that DNA could carry vast amounts of hereditary information through the sequence of bases.
Watson and Crick's structure also suggested a mechanism for replication: because the strands are complementary, each can serve as a template for building a new partner strand.
Before this experiment, three models of replication were debated: conservative, semi-conservative, and dispersive.
Meselson and Stahl's results supported the semi-conservative model, in which each daughter DNA molecule contains one parental strand and one newly synthesised strand.
This experiment is worth reviewing from your textbook and BioNinja notes for full procedural detail.
Students often think Griffith's experiment proved DNA is the genetic material. It did not. Griffith showed that transformation occurs but never identified which molecule was responsible. It took Avery, McCarty, and MacLeod to pinpoint DNA.
Students confuse purines and pyrimidines. Remember: purines (A, G) are the big double-ringed bases; pyrimidines (T, C) are the smaller single-ringed ones. A common mnemonic: "CUT the PYrimidines" (C, U, T).
Students assume Hershey and Chase used nitrogen to label DNA. They used phosphorus (³²P), because nitrogen is present in both DNA and protein and would not distinguish between them.
Students sometimes think antiparallel means the strands run in the same direction. Antiparallel means the opposite: one strand runs 5' to 3' while the other runs 3' to 5'.
⚠️ Know the order and logic of the landmark experiments: Griffith → Avery/McCarty/MacLeod → Hershey-Chase. Each builds on the previous one. Be able to explain what each experiment showed and, just as importantly, what it did not show.
⚠️ Be able to explain why sulfur and phosphorus were chosen as labels in the Hershey-Chase experiment, and why nitrogen would not work.
⚠️ Chargaff's rules (A = T, G = C) are frequently tested. Know the rules themselves and understand that they are a consequence of complementary base pairing.
⚠️ Understand what "antiparallel" means and why it matters for replication (it forces the lagging strand to be made in fragments).
⚠️ Be ready to distinguish the three proposed models of replication (conservative, semi-conservative, dispersive) and know that Meselson-Stahl confirmed the semi-conservative model.
True or false: Griffith's experiment identified DNA as the transforming agent. (False. Griffith showed transformation occurred but did not identify the molecule. Avery, McCarty, and MacLeod did that.)
Fill in the blank: In Chargaff's rules, the amount of adenine equals the amount of ______, and guanine equals ______. (thymine; cytosine)
True or false: In the Hershey-Chase experiment, radioactive phosphorus was found in the supernatant after centrifugation. (False. Radioactive phosphorus was found in the pellet, inside the bacterial cells, confirming DNA enters the cell.)
Fill in the blank: The two strands of DNA run in opposite directions, a property called ______. (antiparallel)
True or false: DNA synthesis proceeds in the 3' to 5' direction. (False. DNA synthesis proceeds in the 5' to 3' direction.)
Q: In the Hershey-Chase experiment, why was sulfur used to label protein coats and phosphorus to label DNA?
A: Sulfur is present in certain amino acids (methionine, cysteine) but absent from DNA. Phosphorus is present in the sugar-phosphate backbone of DNA but absent from proteins. This allowed the researchers to track each molecule independently.
Q: If Griffith had used purified DNA from heat-killed S cells instead of whole heat-killed S cells, would the R cells still have been transformed?
A: Yes. The transforming agent is DNA, so purified DNA from S cells would still transform R cells (this is essentially what Avery, McCarty, and MacLeod demonstrated).
Q: A sample of DNA is found to contain 30% adenine. What are the percentages of thymine, guanine, and cytosine?
A: By Chargaff's rules, thymine = 30% (since A = T). That accounts for 60%, leaving 40% split equally between guanine and cytosine: 20% each.
Q: Why does the structure of DNA run antiparallel, and what consequence does this have for replication?
A: The antiparallel orientation is a consequence of how the sugar-phosphate backbone is assembled. Because DNA polymerase can only add nucleotides to the 3' end (synthesising 5' to 3'), only one strand (the leading strand) can be synthesised continuously toward the replication fork. The other strand (the lagging strand) must be synthesised in short fragments (Okazaki fragments) in the direction away from the fork.
Q: What was the significance of Rosalind Franklin's Photo 51?
A: Photo 51, an X-ray diffraction image of DNA, provided critical evidence that DNA has a helical structure. It also revealed the width of the helix and the spacing of the bases, which Watson and Crick used to build their double helix model.
This material connects directly to DNA replication (covered in the companion study notes), because the double helix structure and base pairing rules determine how replication works at the molecular level. It also underpins transcription and translation: the sequence of bases in DNA is transcribed into mRNA, which is then translated into protein. Understanding mutations (introduced here as "imperfect copying") connects to evolution, natural selection, and genetic variation, topics you will revisit later in the course.
DNA structure, double helix, nucleotide, nitrogenous base, base pairing, complementary base pairing, antiparallel, 5' to 3' direction, sugar-phosphate backbone, deoxyribose, phosphodiester bond, chromatin, chromosome, purine, pyrimidine, adenine, thymine, guanine, cytosine, Griffith experiment, transformation, Avery McCarty MacLeod, Hershey-Chase experiment, bacteriophage, T2 phage, radioactive labelling, sulfur-35, phosphorus-32, Chargaff's rules, base composition, X-ray crystallography, Photo 51, Rosalind Franklin, Watson and Crick, double helix model, semi-conservative replication, Meselson and Stahl, hereditary molecule, genetic material, BIO 311C, intro biology, University of Texas