Genomes, DNA Structure, Replication, and Protein Synthesis in Microbiology

Genotype, Phenotype, and Genome Organization

Genotype Determines Phenotype

The genotype refers to the genetic makeup of an organism, while the phenotype is the observable traits resulting from gene expression. Understanding the relationship between genotype and phenotype is fundamental in microbiology, as it explains how genetic information is translated into cellular functions and characteristics.

• Genetics: Study of genes, their function, and variation in genomes.

• Genome: The entire collection of genetic material in a cell or virus.

• Gregor Mendel: Pioneered genetics in the mid-1800s; traits are heritable and passed from generation to generation.

• Gene: Unit of genetic material that determines a particular trait.

• Genotype: The genetic makeup influencing physiological and physical traits.

• Phenotype: Observable characteristics determined by genotype.

• DNA and RNA: Cells have deoxyribonucleic acid (DNA) genomes; viruses may have DNA or ribonucleic acid (RNA) genomes.

Prokaryotic and Eukaryotic Genomes: Size and Organization

Genome Structure in Different Cell Types

Genome size and organization vary between prokaryotes and eukaryotes, affecting complexity and cellular processes.

• General Rule: More complex organisms have larger genomes.

• Prokaryotes: Example: Escherichia coli has about 4,600 genes; genome size ~4.7 million base pairs.

• Eukaryotes: Example: Human cells have about 20,000 genes; genome size ~3 billion base pairs.

• Chromosomes: Eukaryotes have multiple linear chromosomes; prokaryotes usually have a single circular chromosome.

• Histones: Eukaryotic DNA is organized with histone proteins; prokaryotes have histone-like proteins.

• Plasmids: Small, circular DNA molecules found in prokaryotes, often carrying genes for antibiotic resistance.

Factor	Prokaryotic Genomes	Eukaryotic Genomes
Complexity	Simple, more compact	Complex, less compact
Genome can include	Chromosomal DNA, plasmids	Chromosomal DNA, DNA in mitochondria/chloroplasts
Chromosomes	Single, circular	Multiple, linear
Location	Nucleoid region	Nucleus

Nucleic Acids: DNA and RNA Structure

DNA Structure and Function

DNA (deoxyribonucleic acid) is the hereditary material in most organisms. Its structure allows for the storage and transmission of genetic information.

• Nucleotide: Basic unit of DNA, consisting of a phosphate group, deoxyribose sugar, and nitrogen base.

• Nitrogen Bases: Adenine (A), Thymine (T), Guanine (G), Cytosine (C).

• Base Pairing: A pairs with T, G pairs with C.

• Double Helix: DNA is a double-stranded molecule with antiparallel strands (one runs 5' to 3', the other 3' to 5').

• Complementary: Each strand serves as a template for the other.

• Phosphodiester Bonds: Link nucleotides together, forming the backbone of DNA.

Nitrogen Base	DNA	RNA
Adenine (A)	Yes	Yes
Thymine (T)	Yes	No
Uracil (U)	No	Yes
Guanine (G)	Yes	Yes
Cytosine (C)	Yes	Yes

RNA (ribonucleic acid) differs from DNA by having ribose sugar and uracil (U) instead of thymine (T). RNA is usually single-stranded and can form complex secondary structures.

Central Dogma: Flow of Genetic Information

Genetic Information Typically Flows from DNA to RNA to Protein

The central dogma of molecular biology describes the flow of genetic information: DNA is transcribed into RNA, which is then translated into protein.

• Transcription: DNA is used as a template to synthesize RNA.

• Translation: RNA directs the synthesis of proteins.

• Types of RNA: Messenger RNA (mRNA), Transfer RNA (tRNA), Ribosomal RNA (rRNA).

DNA Replication

DNA Replication Allows Cells to Copy Their DNA

DNA replication is the process by which a cell duplicates its DNA before cell division. It is highly accurate, with proofreading mechanisms to minimize errors.

• Semiconservative Replication: Each new DNA molecule consists of one original (parental) strand and one newly synthesized strand.

• Enzymes Involved:

  • Helicase: Unwinds the DNA helix.

  • Primase: Synthesizes RNA primers.

  • DNA Polymerase III: Main enzyme that builds new DNA strands (5' to 3' direction).

  • DNA Polymerase I: Replaces RNA primers with DNA.

  • Ligase: Seals nicks in the DNA backbone.

  • Gyrase/Topoisomerase: Relieves tension ahead of the replication fork.

• Replication Fork: The area where DNA is actively being unwound and replicated.

• Leading Strand: Synthesized continuously toward the replication fork.

• Lagging Strand: Synthesized discontinuously away from the fork in short segments called Okazaki fragments.

Key Equations:

• Base pairing: $A = T$, $G = C$

• Antiparallel arrangement: 5' to 3' and 3' to 5'

Protein Synthesis: Transcription and Translation

Gene Expression and Protein Synthesis

Protein synthesis involves two main steps: transcription (DNA to RNA) and translation (RNA to protein). This process is essential for cell function and adaptation.

• Transcription: Occurs in the nucleus (eukaryotes) or cytoplasm (prokaryotes). RNA polymerase synthesizes RNA from DNA template.

• Translation: Ribosomes use mRNA to assemble proteins from amino acids.

• Three Main Types of RNA:

  • Messenger RNA (mRNA): Carries genetic code from DNA to ribosome.

  • Transfer RNA (tRNA): Brings amino acids to the ribosome, matching codons with anticodons.

  • Ribosomal RNA (rRNA): Forms the core of ribosome structure and catalyzes protein synthesis.

• Transcription Steps:

  1. Initiation: RNA polymerase binds to promoter region.

  2. Elongation: RNA strand is synthesized.

  3. Termination: RNA polymerase reaches terminator sequence and releases RNA.

• Translation Steps:

  1. Initiation: Ribosome assembles on mRNA.

  2. Elongation: tRNAs bring amino acids; peptide bonds form.

  3. Termination: Ribosome reaches stop codon; protein is released.

Reverse Transcription: Some viruses (e.g., retroviruses) can synthesize DNA from RNA using reverse transcriptase.

Additional info:

• Post-translational modifications can alter protein function after translation.

• Mutations and horizontal gene transfer contribute to genetic diversity in microbes.