Genetics and Molecular Biology: DNA Structure, Replication, and Gene Regulation

Genome

The complete set of genetic material within a cell — all of the DNA that contains the information needed for the organism's structure, function, and reproduction.

Chromosomes

Large, organized DNA molecules containing most of the cell's genetic information.

Eukaryotes

Multiple, linear chromosomes located in the nucleus.

Prokaryotes

Single, circular chromosome found in the nucleoid region (cytoplasm).

Plasmids

Small, circular DNA molecules separate from the main chromosome. Found mainly in prokaryotes; carry nonessential genes such as antibiotic resistance or virulence factors.

Organelle DNA

In eukaryotes, mitochondria and chloroplasts have their own circular DNA, evidence of endosymbiosis.

Gene

A specific segment of DNA that contains the instructions (nucleotide sequence) to make a functional product — typically a protein or an RNA molecule.

Structural genes

Code for proteins that perform cellular functions (e.g., enzymes, structural components).

Regulatory genes

Control gene expression by coding for regulatory molecules like repressors or activators that turn genes on or off.

RNA genes

Code for functional RNA molecules (such as tRNA and rRNA) that are not translated into proteins but play roles in protein synthesis.

DNA Structure

DNA is a double-stranded molecule composed of nucleotides, each having a 5-carbon sugar (deoxyribose), a phosphate group, and a nitrogenous base.

Nucleotide

The basic building block of DNA, consisting of a 5-carbon sugar, a phosphate group, and a nitrogenous base.

Phosphodiester bonds

Links nucleotides together between the sugar of one nucleotide and the phosphate of the next, forming a sugar-phosphate backbone.

Hydrogen bonds

Hold the two strands of DNA together, with specific base pairing (A-T, G-C).

Double helix

The twisted structure of DNA formed by two complementary strands held together by hydrogen bonds.

Watson & Crick

Proposed the double helix model of DNA in 1953.

Franklin & Wilkins

Used X-ray diffraction to reveal the helical structure of DNA, providing key evidence for Watson and Crick's model.

Chargaff's rules

Discovered that the amount of adenine equals thymine and guanine equals cytosine, supporting base pairing.

DNA replication

The process by which a cell makes an exact copy of its DNA before cell division.

Semiconservative replication

Each new DNA molecule consists of one parental (old) strand and one newly synthesized strand.

Origin of replication (ori)

A specific DNA site where replication begins.

Helicase

Unwinds DNA ahead of the fork by breaking hydrogen bonds.

Single-stranded binding proteins (SSBPs)

Stabilize separated strands during DNA replication.

Primase

Synthesizes short RNA primers to provide a 3′-OH group for DNA polymerase to begin synthesis.

DNA Polymerase III

Continuously adds nucleotides to the new strand (5′→3′).

DNA Gyrase / Topoisomerase

Prevents overwinding ahead of replication fork.

Lagging Strand Synthesis Enzymes

Includes Primase, DNA Polymerase III, DNA Polymerase I, and DNA Ligase.

Primase (Lagging Strand)

Adds multiple RNA primers for each Okazaki fragment.

DNA Polymerase III (Lagging Strand)

Synthesizes DNA discontinuously between primers.

DNA Polymerase I

Removes RNA primers and replaces them with DNA.

DNA Ligase

Seals gaps between Okazaki fragments.

Leading Strand

Runs 3′→5′ (template), allowing continuous synthesis.

Lagging Strand

Runs 5′→3′ (template), requiring discontinuous synthesis in short segments (Okazaki fragments).

Transcription

The process by which information from DNA is copied into RNA.

RNA Polymerase

Binds to DNA and synthesizes an RNA strand complementary to the DNA template strand.

RNA Structure

Single-stranded molecule made of nucleotides with ribose sugar and bases A, U, C, G.

Gene Expression

The process of converting the genetic code to a protein through transcription and translation.

mRNA

Single-stranded copy of a gene; contains codons and carries genetic information from DNA to ribosomes for translation.

tRNA

Small (70-90 nucleotides), folded into a cloverleaf shape; brings the correct amino acid to the ribosome during protein synthesis.

rRNA

Longer, stable RNA that forms 60% of ribosome mass; ensures proper alignment of mRNA and tRNA during translation.

Transcription Direction

Transcription occurs in the 5′ → 3′ direction.

Template Strand

Only one strand of DNA is used as the template strand during transcription.

Coding Strand

The other strand of DNA that is identical to the mRNA sequence (except T → U).

Simultaneous Transcription and Translation

In prokaryotes, transcription and translation can occur simultaneously since there is no nucleus.

Promoter Region

RNA polymerase binds to this region upstream of the gene to initiate transcription.

Sigma Factor

Enables RNA polymerase to recognize and bind to the correct promoter.

RNA growth rate

RNA grows at about 40 nucleotides per second.

Uracil (U)

A nucleotide that replaces thymine as adenine's complement in RNA.

Rho-independent termination

A mechanism where RNA forms a hairpin loop that destabilizes the polymerase and stops transcription.

Rho-dependent termination

A mechanism where a Rho protein binds the RNA and causes the release of RNA polymerase from the DNA template.

Promoter

A region upstream of a gene where RNA polymerase binds, containing -35 and -10 sequences.

Initiation site (+1)

The first nucleotide transcribed into RNA.

Upstream

DNA sequences before the initiation site, represented by negative numbers.

Downstream

DNA sequences after the initiation site, represented by positive numbers.

Terminator region

A sequence that signals RNA polymerase to stop transcription.

Gene regulation purpose

Cells conserve energy and resources by only expressing genes when their products (enzymes, proteins) are needed.

Constitutive genes

Genes that are always 'on', such as those for housekeeping proteins.

Enzyme production regulation

Enzymes are produced only when required; if a substrate or product is absent, enzymes for that pathway are turned off.

Homeostasis maintenance

The cell balances production and consumption of molecules.

Transcriptional regulation

Most bacterial regulation occurs at the transcriptional level, as it's more efficient to control mRNA synthesis than to destroy unneeded proteins later.

Gene regulation

The process of turning genes on or off depending on environmental conditions.

Enzyme Induction

The process where the presence of substrate (lactose) induces enzyme synthesis.

Lac Operon

Regulates production of enzymes that metabolize lactose in E. coli.

Regulator gene (lacI)

Codes for the repressor protein in the Lac Operon.

Operator (O)

The binding site for the repressor in the Lac Operon.

Structural genes (lacZ, lacY, lacA)

Encode enzymes to digest lactose (β-galactosidase, permease, transacetylase).

Enzyme Repression

The process where the presence of product (tryptophan) represses further synthesis.

Tryptophan Operon (trp operon)

Controls synthesis of tryptophan (an amino acid), normally on but turned off when tryptophan is abundant.

Regulator gene (trpR)

Codes for the inactive repressor protein in the Tryptophan Operon.

Structural genes (trpE, trpD, trpC, trpB, trpA)

Code for enzymes that synthesize tryptophan.

Regulator gene

Encodes the repressor protein (may be upstream).

Repressor protein

Binds to operator to inhibit transcription.

Inducer or Corepressor

Small molecules that activate or inactivate the repressor (e.g., allolactose = inducer; tryptophan = corepressor).

Trp operon

ON — enzymes produced to make tryptophan when end product (e.g., tryptophan) is low.

Attenuation

A fine-tuning mechanism of transcription control that depends on the rate of translation of a leader peptide.

Leader region of the trp operon (trpL)

Transcribed into a short mRNA that can form different hairpin loops (secondary structures).

Condition: Tryptophan scarce

Ribosome pauses at Trp codons → allows a 2-3 loop to form, transcription continues; full mRNA made → enzymes produced.

Condition: Tryptophan abundant

Ribosome does not pause → forms 3-4 loop (termination hairpin), transcription terminated early → no enzymes made.

Global regulation

The cell's ability to control multiple operons or pathways in response to overall environmental conditions (e.g., energy source availability).

Catabolite Repression

When multiple energy sources are available, E. coli prefers glucose, suppressing the expression of genes for using other sugars like lactose.

Mechanism of Catabolite Repression

When glucose is high, cAMP levels are low, preventing the formation of the CAP-cAMP complex.

cAMP (cyclic AMP)

Acts as a signal molecule inversely related to glucose levels. High when glucose is low.

CAP (Catabolite Activator Protein)

Binds with cAMP to form a complex that enhances RNA polymerase attachment to the promoter.

CAP-cAMP complex

Acts as a transcriptional activator for the lac operon and other sugar metabolism genes.

Mutation

A change in the nucleotide sequence of DNA that results in a change in the genotype, which may alter the phenotype (observable trait) of an organism.

Wild type (strain)

The natural, nonmutated form of an organism — the original reference sequence.

Mutant strain

Organism that carries a change (mutation) in its DNA; may differ in morphology, nutrient use, genetic regulation, or chemical resistance.

Spontaneous mutation

Random change in DNA due to replication errors or natural causes.

Induced mutation

Caused by exposure to mutagens (e.g., chemicals or radiation).

Mutagen

A physical or chemical agent that increases mutation rate.

Point mutation

Single base is added, deleted, or substituted. May change one amino acid.

Missense mutation

A different amino acid is coded for. Alters protein structure or function.

Nonsense mutation

Normal codon changed to a stop codon. Premature termination — truncated protein.

Silent mutation

Base change doesn't alter the amino acid. No effect on protein.

Frameshift mutation

Insertion or deletion changes reading frame. Alters every amino acid after the change.

Back-mutation

Mutated gene reverses to original sequence. Restores original function.

Impact of Mutations - Harmful

Most mutations cause nonfunctional or less efficient proteins → may be lethal.

Impact of Mutations - Neutral

Silent mutations have no effect on phenotype.

Impact of Mutations - Beneficial

Rare, but can confer advantages (e.g., antibiotic resistance, new metabolic abilities).

Evolutionary role of mutations

Source of genetic variation that drives natural selection and adaptation.