Lecture 2: Nucleic Acids

What are the three chemical components of a nucleotide?

1. A nitrogenous base (Adenine, Guanine, Cytosine, and Thymine/Uracil)

2. A 5-carbon pentose sugar (deoxyribose or ribose)

3. At least one phosphate group

What is the structural difference between a nucleoside and a nucleotide?

• Nucleoside: Nitrogenous base + 5-carbon sugar.

• Nucleotide: Nitrogenous base + 5-carbon sugar + phosphate group(s) (i.e., a nucleoside with a phosphate).

How do purines and pyrimidines differ chemically and which bases belong to each group?

• Purines: Double-ring structure (6-membered ring fused to a 5-membered ring) → Adenine (A) and Guanine (G).

• Pyrimidines: Single 6-membered ring → Cytosine (C), Thymine (T) (DNA), and Uracil (U) (RNA).

What is the exact chemical difference between the sugar in DNA (deoxyribose) and RNA (ribose)?

• Ribose (RNA): Has a hydroxyl group (−OH) attached to the 2′ carbon.

• Deoxyribose (DNA): Lacks an oxygen at the 2′ carbon (has a hydrogen atom, −H, instead of −OH)

What is the structural/chemical difference between Thymine and Uracil?

Thymine has a methyl group (−CH3​) at the C5 position of the pyrimidine ring, whereas Uracil has a hydrogen (−H) at that position.

What is the cellular location and typical strandedness of DNA vs. RNA?

• DNA: Typically double-stranded; located in the nucleus, mitochondria, and chloroplasts in eukaryotes, and in the nucleoid in prokaryotes.

• RNA: Typically single-stranded (with secondary structure); found in the nucleus and cytoplasm in eukaryotes.

Why are polynucleotide chains directional, and how is that direction defined chemically?

• Directionality is defined from 5′ to 3′.

• The linkage occurs via a phosphodiester bond connecting the phosphate on the 5′ carbon of one sugar to the hydroxyl group on the 3′ carbon of the adjacent sugar.

What holds the two strands of a double-stranded DNA molecule together, and what is meant by "reverse complement" (antiparallel)?

• Strands are held together by hydrogen bonds between complementary nitrogenous base pairs (A–T and G–C).

• Antiparallel/Reverse complement: The two paired strands run in opposite chemical directions (one runs 5′→3′, the complementary strand runs 3′→5′).

How many hydrogen bonds form between Adenine–Thymine vs. Cytosine–Guanine pairs?

• A=T: 2 hydrogen bonds.

• G≡C: 3 hydrogen bonds.

Why must a purine pair with a pyrimidine in the double helix (rather than purine-purine or pyrimidine-pyrimidine)?

• Purine + Purine: Too wide (>2.0 nm).

• Pyrimidine + Pyrimidine: Too narrow (<2.0 nm).

• Purine + Pyrimidine: Generates the exact, uniform 2.0 nm diameter observed in X-ray diffraction data.

What structural dimensions of the DNA double helix were revealed by Rosalind Franklin’s X-ray diffraction data?

• Helix diameter: Constant at 2.0 nm.

• Pitch (1 complete turn): 3.4 nm (≈10.5 bp/turn).

• Base stacking distance: 0.34 nm between adjacent nitrogenous base pairs.

• Phosphates: Positioned on the outside of the helix.

What determines whether DNA adopts a right-handed helix (A-form / B-form) vs. a left-handed helix (Z-form)?

The hydration state and the specific nucleotide sequence of the nucleic acid determine the helical form and twist direction.

What is the linear length of human DNA in a single cell compared to the size of the nucleus?

• Linear DNA length: 3 billion bases×0.34 nm/base≈1×109 nm=1 meter.

• Nuclear diameter: 5–10 μm (1 μm=1×10−6 m).

How does the cell fit 1 meter of DNA inside a 5–10 μm nucleus?

DNA associates with proteins to form chromatin particles, which condense to form chromosomes, compacting the linear dsDNA molecule over 100,000-fold.

What percentage of the human genome codes for proteins, and how many chromosomes exist in human somatic vs. sex cells?

• Protein-coding portion: Only about 2% of the human genome.

• Somatic cells: 46 chromosomes (22 pairs of autosomes + 2 sex chromosomes).

• Sex cells (gametes): 23 chromosomes.

Describe Griffith’s Transformation Experiment (1928): design, findings, and conclusion.

• Design: Injected mice with virulent encapsulated strain (died), nonvirulent nonencapsulated strain (lived), heat-killed virulent (lived), and a mixture of heat-killed virulent + live nonvirulent (died).

• Finding: Live virulent bacteria were recovered from the dead mice given the mixture.

• Conclusion: A "transforming principle" from dead virulent cells permanently altered the genotype and phenotype of nonpathogenic bugs.

Describe Avery, MacLeod, and McCarty’s Experiment (1944)

• Method: Fractionated heat-killed virulent bacteria into purified macromolecules (DNA, RNA, proteins) and tested each for the ability to transform nonvirulent bacteria.

• Result: Only DNA was able to transform bacteria, demonstrating DNA is the transforming substance.

Describe the Hershey-Chase Bacteriophage Experiment (1952): isotopes used and conclusion

• Isotopes: 35S (labels sulfur in viral proteins) and 32P (labels phosphorus in viral DNA).

• Method: Infected bacteria with labeled phage, agitated in a blender to detach capsids, and centrifuged.

• Result: 32P entered the bacterial pellet and was passed to progeny phages; 35S remained in the supernatant.

• Conclusion: DNA, not protein, is the genetic material injected by viruses to direct replication.

What is Chargaff’s Rule

Chargaff's Rule states that in any given DNA molecule, the amount of adenine (A) is equal to thymine (T), and the amount of cytosine (C) is equal to guanine (G). This reflects the base pairing rules in the DNA structure.

What is the Central Dogma of molecular biology, and what enzymes catalyze each step?

The Central Dogma of molecular biology describes the flow of genetic information from DNA to RNA to protein. The key enzymes involved are DNA polymerase for DNA replication, RNA polymerase for transcription, and ribosomes for translation.

What are two notable exceptions to the classic flow of genetic information in the Central Dogma?

• Reverse Transcription: RNA is reverse transcribed into DNA via Reverse Transcriptase (e.g., retroviruses).

• Functional non-coding RNAs: Some RNA molecules do not code for proteins but act directly as functional molecules (e.g., rRNA in ribosomes, tRNAs).

Distinguish between Genotype and Phenotype.

Genotype refers to the genetic makeup of an organism, including all alleles inherited from parents, while phenotype is the observable physical or biochemical characteristics resulting from the genotype and environmental influences.

What are the three phenotypic consequences of base sequence changes (mutations), and how do mutations affect inheritance?

1. Damaging: Produces a defective protein or alters phenotype negatively.

2. Neutral: Does not alter the phenotype of the cell.

3. Productive: Yields a more viable or better protein product (basis of evolution).

• Inheritance: Mutations in somatic cells pass to daughter cells during mitosis; only mutations in germ/sex cells transmit to individual offspring (meiosis).

What is the famous quote from Watson and Crick's 1953 paper regarding DNA structure and replication?

• "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material."

• Because each strand is the reverse complement of the other, each original strand serves as a template during replication.