Genetics: DNA Structure and Nucleotides

Genetics

• Genetics refers to the scientific study of heredity.
• Molecular biology involves studying DNA and protein synthesis.
• The genome is the complete DNA content within a cell.
  • This includes chromosomes and plasmids.
• Genes reside on chromosomes.
  • Genes are DNA segments coding for functional products.
• DNA is a macromolecule composed of nucleotides.

Nucleotides

• Nucleotides consist of a nitrogenous base, deoxyribose sugar, and a phosphate group.
• DNA contains four nitrogenous bases.
  • Adenine (A)
  • Guanine (G)
  • Thymine (T)
  • Cytosine (C)

DNA Structure

• DNA has a double helix structure.
  • Two DNA strands are held together by hydrogen bonds between bases.
• Base pairing occurs between specific bases.
  • Adenine (A) pairs with Thymine (T) via two hydrogen bonds.
  • Guanine (G) pairs with Cytosine (C) via three hydrogen bonds.
  • G:::C and A::T represent these pairings.
• DNA strands are complementary.
  • The sequence of one strand determines the sequence of the other.
  • For example, 5'ACTGATT3' pairs with 3'TGACTAA5'.
• Adjacent nucleotides link via phosphodiester bonds.
• Carbon #5 of one nucleotide joins carbon #3 of the next.
  • These carbons are designated as 5' (5 prime) and 3' (3 prime).
• DNA directionality is from 5' to 3'.
  • DNA begins at the 5' end and finishes at the 3' end.

Genetic Flow

• DNA replicates before cell division, providing each offspring with a full genome copy.
• DNA is utilized within the cell to synthesize proteins.
• DNA can transfer between bacterial cells through recombination.

DNA Replication

• One double-stranded DNA creates two identical double-stranded DNA molecules.
• Since DNA strands are complementary, one strand acts as the template for the synthesis of the other.
  • A small segment of double-stranded DNA (dsDNA) unwinds, separating the strands to create a replication fork.
  • Each separated strand then serves as a template for synthesizing a complementary strand.
• The enzymes DNA gyrase and helicase unwind and separate DNA strands.
  • DNA gyrase is specific to bacteria, making it an antibiotic target.
• The enzyme primase synthesizes a short RNA primer.
  • The primer serves as an attachment point for adding new nucleotides to form a DNA strand.
• DNA polymerase synthesizes DNA.
  • Nucleotides are placed in the correct order based on the parent strand sequence.
  • DNA polymerase links nucleotides with phosphodiester bonds.
• Hydrogen bonds form between the new and parent strands.
• DNA polymerase adds nucleotides in the 5'-3' direction.
  • The template must be read in the 3'-5' direction.
  • The leading strand is synthesized continuously.
  • The lagging strand is synthesized discontinuously

Lagging Strand

• Lagging strand synthesis is slower than its leading counterpart
• DNA polymerase synthesizes the lagging strand in the 5' to 3' direction
  • The lagging strand requires the template to be read from 3' to 5'
  • Small DNA fragments, called Okazaki fragments, are created in the 5' to 3' direction.
  • The enzyme DNA ligase joins these small fragments together

RNA, Protein Synthesis

• RNA's nucleotide sugar is ribose, unlike DNA's deoxyribose.
• Uracil (U) replaces thymine (T) in RNA.
• The purpose of DNA is to direct protein synthesis.
• Genes, sections of DNA, contain instructions for a functional protein product.

Transcription

• Transcription refers to the synthesis of a complementary RNA strand from a DNA template.
• Three types of RNA exist.
  • Messenger RNA (mRNA) carries coded information for making specific proteins.
  • Ribosomal RNA (rRNA) is part of ribosomes, facilitating protein synthesis.
  • Transfer RNA (tRNA) carries specific amino acids to ribosomes to make proteins.
• mRNA is a short-term copy of a gene, directing protein synthesis.
• Both rRNA and tRNA facilitate protein synthesis.
• A strand of RNA is made from a particular gene.
• The mRNA produced is complementary to the gene.
• Uracil (U) replaces thymine (T) during synthesis.
• Transcription requires.
  • An RNA polymerase enzyme
  • A supply of RNA nucleotides
  • A DNA template
• Transcription steps.
  • RNA polymerase binds to DNA at a promoter site.
    • Only one DNA strand serves as a template.
    • Like DNA, RNA is made in a 5' to 3' direction.
  • Next, RNA polymerase assembles nucleotides into a new RNA chain using the DNA template.
  • Then RNA polymerase moves along the template as the new RNA chain grows.
  • RNA polymerase recognizes the gene terminator.
  • Lastly, RNA polymerase and the newly formed single-stranded RNA are released.

Translation

• Translation involves decoding mRNA to synthesize proteins.
• The information is in the form of a group of 3 nucleotides (codons).
  • For example, AUG, GGC, or AAA.
• Each codon containing 3 nucleotides signals for a specific amino acid.
• The specific mRNA codon sequence dictates the sequence of amino acids in the protein.
  • This sequence defines the genetic code.
• UAG, UAA, and UGA codons are stop or nonsense codons, signaling the end of translation.
• Translation Steps include.
  • The mRNA attaches to the ribosome.
  • tRNA carrying an amino acid enters the ribosome and binds to mRNA.
  • The next tRNA with an amino acid enters the ribosome to bind.
  • Two amino acids join via a peptide bond.
  • The ribosome moves along the mRNA in a 5' to 3' direction, repeating the addition of amino acids.
  • The process continues in a 5' to 3' direction until a stop codon is reached and translation ends.
  • With the process completed, the mRNA and newly-formed protein are released.

Mutation

• Mutations are changes to the nucleotide sequence of DNA.
  • They can cause changes in the protein encoded by a gene.
• There are different types of mutation.
  • Point mutations (substitution) involve replacing a single by another nucleotide.
    • DNA replication may result in a substituted base pair.
    • Incorrect transcription/translation can produce an incorrect amino acid - a missense mutation.
  • However, it can also result in in the same amino acid with redundant genetic code.
    • Stop codons can be introduced prematurely.
      • This leads to shorter (truncated) proteins.
• Frameshift mutations involve the addition (insertion) or removal (deletion) of a nucleotide.
  • The mRNA reading frame is changed.
  • The protein sequence is changed downstream from the mutation.

Occurrence of mutations

• Mutations can occur in different ways
  • Spontaneous mutations can occur due to occasional mistakes in DNA replication in the absence of mutagens
  • Other mutations can be caused by UV light, radiation and certain chemicals
• Regardless of the origins, mutations can cause different outcomes.
  • Incomplete, non-functional, truncated proteins
  • Proteins with altered sequence and function
  • Functional proteins with no effect on the protein

Plasmids

• Plasmids are self-replicating, double-stranded DNA molecules.
• Plasmids contain non-essential genes, such as those for penicillin resistance.
• F Plasmids
  • F-factor, fertility plasmid
  • Carry genes to make F pili
  • Involved in bacterial mating (conjugation)
  • Allow the transfer of genetic material in between bacteria
• R Plasmids
  • Resistance factors
  • Carry genes for antibiotic resistance
  • Example: enzymes that degrade antibiotics
• Vir Plasmids
  • Virulence factors
  • Carry genes for toxin production

Genetic Transfer

• Genetic material moves between bacterial cells in several ways.
• Horizontal Gene Transfer
  • DNA moves to other bacterial cells instead of progeny.
  • Transformation involves naked DNA uptake by a bacterial cell.
  • This DNA can originate from dead cells or be released as plasmids.
  • As recombination, these DNA pieces integrate to the chromosome.
• Conjugation requires bacterial mating between a donor (F+) and recipient (F-).
  • F+ contains F pili
  • The F pilus facilitates F+ to F- cell attachment.
  • An F plasmid copy moves through a hollow tube to the F- cell.
  • The F- recipient then becomes F+.
• Transduction
  • Small DNA fragments move between bacteria by a virus.
  • Bacteriophages are viruses infecting bacteria.
  • The phage connects to and injects its DNA to the bacterial cell wall.
  • The phage DNA is replicated inside the bacterial cell.
  • The phage DNA promotes protein synthesis for new phages.
  • The new phages assemble and accidentally package bacterial DNA into the phage protein coat.
  • The accident phage then infects another bacterial cell.
    • The bacterial DNA is injected into the next cell.
  • The bacterial DNA can incorporate into the bacterial chromosome.