Genetics: DNA, Genome, Gene, Genotype, Phenotype

• Genetics studies inheritance and inherited traits.

DNA

• DNA is the polymer storing hereditary information
• RNA viruses are an exception to using DNA for storing hereditary information.

Genome

• Genome refers to all genetic information of a cell or virus.

Gene

• A gene is a "stretch" of DNA.
• Genes encode for a functional product like proteins or RNAs.

Genotype

• Genotype is the actual set of genes in an organism's genome.

Phenotype

• Phenotype refers to physical and functional features of a microbe
• Examples of microbes and their phenotypes include morphology or location of flagella.

Chromosome Structure

• Chromosomes contain DNA associated with proteins.
• Typical prokaryotic chromosomes feature a circular DNA molecule within the nucleoid.

Prokaryotic Cells

• Prokaryotic cells are haploid
• Prokaryotic cells typically have a single copy of the chromosome.

Plasmids

• Bacterial cells also carry plasmids, mobile genetic elements.

DNA Molecule

• DNA is a double-stranded molecule.
• Each strand is a polymer of nucleotides.

Nucleotides

• A nucleotide has a phosphate group, a sugar molecule, and a nitrogenous base.

Double Helix key components

• Sugar-phosphate backbones make up the double helix.

Nitrogenous Bases

• Nitrogenous bases are stacked within the helix
• The bases present are adenine (A), thymine (T), cytosine (C), and guanine (G).

Complementary Strands

• Complementary strands pair A with T and C with G

Antiparallel Strands

• Antiparallel strands run in opposite 5’ to 3’ direction.

DNA Replication

• A new DNA molecule contains one parental and one newly made (daughter) strand.

Template Strand

• Each strand of DNA functions as a template strand.

DNA Polymerase

• DNA polymerase relies on the template strand to synthesize a complementary, antiparallel "daughter" strand.

Bacterial Replication

• Replication initiates at a specific site: the origin of replication
• Termination occurs upon chromosome replication with two separated copies: the termination site

Helicase

• Helicase separates the two DNA strands
• Helicase then makes them available for synthesis.

DNA Gyrase or Topoisomerase

• DNA gyrase or topoisomerase alleviates supercoiling from unwinding.

Leading Strand Synthesis

• The leading strand is synthesized continuously as primase creates one RNA primer.
• Next, DNA polymerase III adds nucleotides in a 5’ to 3’ direction.

Lagging Strand Synthesis

• The lagging strand is made discontinuously by linking Okazaki fragments.

Fragments

• Each Okazaki fragment requires a primase-made RNA primer.
• Then, DNA polymerase III adds nucleotides in a 5’ to 3’ direction.

Removal

• Primers are removed.
• DNA polymerase I replaces removed primers with DNA.

Ligase

• Ligase seals the sugar-phosphate backbone, joining Okazaki fragments.

Genes

• Gene expression involves synthesizing a functional product.
• It's a segment of DNA the embodies a specific function.
• Genes often encode for proteins or RNAs like rRNA and tRNA.

Gene Expression two steps

• Transcription, which is the synthesis of mRNA from DNA.
• Synthesis of a protein (polypeptide) using the genetic information in mRNA is called translation.

Central Dogma

• Genetic information flows from DNA to mRNA and then proteins.

Bacterial Transcription

• The nucleotide sequence of a gene transcribes into mRNA via RNA polymerase.
• RNA polymerase makes RNA in a 5’ to 3’ direction.

Three key steps

• Transcription occurs in three segments
• The three stages are initiation, elongation, and termination.

Sigma factor

• The sigma factor is responsible for recognizing the promoter

Terminator

• The terminator signals the end of transcription.

Translation Defined

• The process of decoding genetic information in mRNA.

Translation Components

• Relies on mRNA, tRNAs, ribosomes, accessory proteins, GTP.

Nucleotide Sequence

• The nucleotide sequence of mRNA is translated into a sequence of amino acids.

Codons

• The nucleotide sequence is read in triplets called codons.
• Each codon carries the information for one amino acid.

Genetic Code

• Genetic information in mRNA is decoded

Start and Stop Codons

• There are 64 mRNA codons
• A start codon
• Three stop codons.

Codons and Amino Acids

• Multiple codons may code for a single amino acid.

Translation Begins

• Translation starts after the ribosome binding site on mRNA at the start codon.

Stop Codon

• Translation concludes by the stop codon.

tRNA

• tRNAs (transfer RNAs) carry amino acids to the ribosomes during translation.

Codon/Anticodon Recognition

• Codon/anticodon recognition enables addition of the correct amino acid.

mRNA

• mRNA carries the genetic information from DNA as a sequence of codons.

Ribosomes and Proteins

• Ribosomes construct proteins according to the mRNA's codon sequence.

Ribosomes and Covalent Bonds

• In translation, ribosomes link amino acids in translation using covalent, peptide bonds.

Translation: Start Codon

• Translation begins at the start codon: AUG.

Ribosomes Move

• Ribosomes move along the mRNA in a 5' to 3' direction, one codon per time.

Peptide Bond Synthesis

• Peptide bonds are the result of a catalysis that joins together amino acids.

Translation Termination

• Translation stops when the ribosome reaches the stop codon on mRNA.

Ribosome Assembly

• The ribosome assembles at the ribosome binding site of mRNA.

Translation Steps

• Translation occurs in three main stages
• The segments are initiation, elongation, and termination.

Binding: For each AA

• For the binding of each amino acid, Codon/anticodon must bind in the A Site

Peptide Bond Formation

• A peptide bond needs to be formed by a ribozyme

Ribosome Movement

• The ribosome moves from one codon to the 3’ end of mRNA

Elongation

• Translation continues until reaching a stop codon.

Enzyme Release

• Enzymes promote free the polypeptide via breaking covalent bonds.
• Breaking the polypeptide joins the tRNA in the P site.

Ribosome Dissasembly

• The ribosome falls off and disassembles.

Prokaryotes and Gene Expression

• Transcription and translation occur simultaneously in prokaryotes.

Overview of Gene Transfer in Prokaryotes

• Mutations are stable changes in the nucleotide sequence of DNA.
• Mutations prompt changes in proteins and their functions.

Mutations key result

• Spontaneous mutations result from errors during DNA replication or repair.
• Induced mutations are caused by mutagens.
• Mutagens include chemicals or physical agents like UV radiation.

Point mutations affects

• Affect only a few nucleotide pairs in DNA.

Base Substitutions

• Silent mutation: no change in amino acid sequence
• Missense mutation: slightly different amino acid sequence
• Nonsense mutation: polypeptide synthesis ceases.

Mutagens and Nucleotide Mutations

• Nucleotide sequence changes are due to chemical and physical agents called mutagens.

Types of Mutagens

• Chemicals and radiation are key mutagens.

Mutations by Base Analogs

• Base analogs lead to base substitutions.

Example Mutation

• A TA base pair will be replaced by CG

Consequences

• Ultraviolet radiation affects thymine dimers.
• UV leads to Covalent bonds between adjacent thymines .
• Double helixes cannot form, resulting in distortion.

Damage stalling

• Replication and transcription stall at the distortion site.

Survival

• Cells must repair damaged DNA.

DNA Repair Mechanisms

• Damages to DNA, if not repaired, lead to cell death or cancer.
• Mutations are rare as changes in DNA are generally fixed

Spontaneous Repair and Effects and the Mechanisms Behind Them

• Wrong nucleotide incorporated during DNA replication
• Use proofreading by DNA polymerase, and this causes potential mutations to be eliminated
• Mismatch Repair
  • The repair mechanisms is binding a protein the the mismatched site and cutting the strand, leading to eliminated potential mutations
• Oxidized Guanine in DNA
• Using action of glycosylase, using glycosylases to remove oxidized Guanine leads to eliminated potential mutations

Mutagen Induced repair and effects and the mechanisms behind them

• Wrong nucleotide incorporated during DNA replication
• Proofreading and mismatch repair is used which causes elimination of potential mutation
• Use UV light to cause thymine dimer formation
• Photoreactivation is what breaks the covalent bonds and restores the original DNA molecule
• UV light being used to cause Excision repair
• Removing them using strands containing thymine and letting polymearse synthesize
• UV light being uses to trigger SOS repair
• The result of this repair is that the cell survives but produces numerous mutations

Photoreactivation

• Light repair involves photolyase a light activated enzyme.

Nucleotide excision repair

• A type of single strand repair which is a type if direct repair

Horizontal Gene Transfer

• Processes that enable bacteria to exchange or transfer genetic information.

Transformation

• Naked DNA uptake from the surrounding environment.

Recombination

• Uptake becomes part of the cell's DNA

Recipient Cells and competence

• Cells that must be able to take up large molecules.

Avery, MacLeod, and McCarty

• In 1944, they determined the transforming agent was DNA.

Bacteriophages

• The transferor of transfer is done by viruses

Donor Host

• DNA transfers from the donor host cell to a recipient cell by a phage particle

Transferred DNA

• The transferred DNA can be integrated into the chromosome
• The host cell is now leading to recombination

Generalized Transduction

• Any segment of a donor host cell chromosome transfers to a recipient host, acting as a transducing particle

Bacterial Plasmids

• F plasmid Conjugation relies of a conjugation pilus or sex pilus

F+ cell

• The donor cell, has the plasmid

F- Cell

• The receiver cell, has no plasmid

Plasmid

• Plasmids can remain in the cell's, or incorporate the chromosome

Antibiotic Resistance

• R (resistance plasmids)
• Code for antibiotic resistance.

Genetic elements

• Mobile genetic elements known as transposons

Chromosomes

• DNA segments move location within a chromosome.

Plasmids

• Move from chromosomes to plasmids

Spread Of Resistance

• Patients infected with S. aureus, they may be susceptible to Vancomycin

Strain Of E faecalis

• Contains the vancomycin resistance

Transfer Of S Aureus

• E. faecalis transfers the transposon by conjugation

Vancomycin

• S Aureus then becomes resistant