Prokaryotic Genetics

 

 

 

GENETICS

l    The study of what genes are, how they carry information, how information is expressed, and how genes are replicated.

 

l    Genes

–    A segment of DNA that encodes a functional product, usually a protein.

 

l    Genome

–    All the genetic information in a cell

–    Genomics

l  Molecular study of genomes

 

Genome organized into chromosomes

▫          Chromosome: Structure containing DNA that physically carries hereditary information; the chromosomes contain the genes

 

 

l    Genotype

–    The genes of an organism

 

l    Phenotype

–    Expression of the genes

 

 

 

Flow of Genetic Information

 

 

 

DNA

l     Double helix associated with proteins

 

l     Polymers of nucleotides

–    Adenine, thymine, cytosine, and guanine

 

l     Deoxyribose-phosphate backbone

 

l     Strands are held together by hydrogen bonds between AT and CG.

 

l     Strands are antiparallel

 

l     Complimentary

–    Precise duplication

 

l     Diversity

–    Only 4 kinds of bases but each gene contains about 1000 of these bases

–    Arrangement of 41000 different ways

 

 

 

 

 

 

 

Bacterial DNA

l  Circular DNA

 

–  10% of volume

 

–  4 X 106 base pairs

 

–  1 mm long

 

 

 

 

DNA REPLICATION

l  One double stranded DNA from parent ΰ two double stranded daughter molecules

 

l  One strand acts as a template for another (complimentation)

 

l  Semiconservative replication

–  One old and one new

 

 

 

DNA REPLICATION

lDNA is copied by DNA polymerase

–    Additions to the 3’ end of DNA strand

l  In the 5’ΰ3’ direction

lSteps:

–    Parental unwinds

–    Replication fork

–    Leading strand

l  Synthesized continuously

–    Lagging strand

l  Synthesized discontinuously

l  Initiated by RNA primer

l  Okazaki fragments

–  DNA ligase

lBidirectional

lProofreading

 

 

 

 

DNA Replication

 

 

 

 

 

 

 

 

 

TRANSCRIPTION

l  DNA is transcribed to make RNA (mRNA, tRNA, and rRNA).

l  3 types of RNA: 

     ·  mRNA (messenger)ΰ carries info from DNA to ribosomes to make proteins

     ·  tRNA (transfer)ΰrecognizes specific RNA sequence and transports amino acids to appropriate regions during protein synthesis (translation)

     ·  rRNA (ribosomal)ΰforms the ribosomes which are the structures used to make the proteins

 

 

 

 

TRANSCRIPTION

l  Synthesis of a complementary strand of RNA from a DNA template

 

l   Nitrogenous base pairing

–   C-G, and T-A, but A-U

 

l   Transcription begins when RNA polymerase binds to the promoter sequence

 

l   Transcription proceeds in the 5’ to 3’ direction

 

l   Transcription stops when RNA polymerase moves along DNA until it reaches a terminator sequence.

 

 

 

 

TRANSCRIPTON

 

 

 

 

TRANSLATION

l    mRNA is translated in codons

 

l    Codons:  groups of 3 nucleotides

–    Each codon codes for one amino acid

–    64 possible codons and 20 amino acids

–    Degeneracy of the code ΰeach amino acid coded by more than one codon

▫          Sense codons ΰ code for amino acids

�   Translation of mRNA begins at the start codon: AUG

▫          Nonsense codons ΰ no amino acids coded (stop codons); translation ends

�   UAA, UAG, UGA are stop codons

 

l    Each tRNA carries the complementary anticodon

–    Anticodon pairs with codon and amino acid is transferred to match the codon

 

 

 

Translation

 

 

 

Translation (Initiation)

 

 

 

Translation (Elongation)

④Second tRNA with amino acid attaches at next codon (A site)

 

 

 

TRANSLATION (ELONGATION)

⑤Ribosome forms peptide bond between adjacent amino acids

 

 

 

 

TRANSLATION (ELONGATION)

⑥ tRNA at E site leaves while another tRNA attaches

 

 

 

 

TRANSCRIPTION (ELONGATION)

⑦Ribosome moves down mRNA

 

 

 

 

 

⑧A new peptide bond forms and next E site tRNA leaves, and ribosome moves again.

⑨Poly peptide formed

 

 

 

 

TRANSLATON (ELONGATION)

⑩Process continues until stop codon reached

 

 

 

Translation (Termination)

⑪Translation ends

⑫All tRNA leave, new protein leaves and ribosome subunits disassociate and leave.

 

 

 

 

 

Prokaryote vs Eukaryote – Fig 8.12

l    In prokaryotes, transcription and translation occurs in cytoplasm

–    Translation may begin before the transcription of a particular mRNA is complete

 

l    Prokaryotes and eukaryotes have different ribosomes

 

l    Eukaryotes:

o    Transcription in nucleus

o    RNA is processed before translation

o   Exons (expressed DNA)

o   Introns (intervening DNA)

o   Introns are removed from RNA transcript and exons are joined by ribozymes before translation which occurs at the ER in cytoplasm

 

RNA processing in Eukaryotes

 

 

 

 

REGULATION – Fig 8.13

l   Constitutive versus regulated

 

l   Repression (transcriptional level regulation)

•    Over abundance of a metabolic product

•    Repressors block RNA polymerase from initiating transcription of the enzyme that creates the metabolic product.

 

l   Induction (transcriptional level regulation)

•    When there is a need for a certain metabolic product

•    Inducers induce transcription of the inducible enzyme that creates that product.

 

 

 

Operon Model

l  Operon

–  Promoter

–  Operator

–  Structural gene

 

 

 

Mutations – Fig 8.17a,b

l   Change in genetic material

l   Mutations may be neutral, beneficial, or harmful.

l   Often silent (Degeneracy of the code)

l   Types of Mutation

–   Base substitution (point mutation)

l  Change in one base

l  Three types:

–   Missense = changes the codon and codes for different amino acid
–   Nonsense= changes the codon and codes for a stop codon
–   Silent= changes the codon, but codes for same amino acid

–   Frameshift mutation

l  Insertion or deletion of a few nucleotides causing a shift

l  Often involves a long stretch of altered amino acids leaving a non functional protein

 

 

 

 

Example of Point Mutations

 

 

 

Example of Frameshift Mutations

 

 

 

Types of Mutagens

l    Mutagens

–    Agents that causes mutations.

–    Spontaneous mutations

l  Occur in the absence of a mutagen

 

l    Chemical

–    Nucleoside analogs

l  AZT to treat HIV

 

l    Radiation

–    Ionizing radiation (X rays and gamma rays)

l  Causes the formation of ions that can react with nucleotides and the deoxyribose-phosphate backbone

–    Nonionizing radiation (UV light)

l  Causes thymine dimers, which leads to problems with replication and transcription

 

 

 

Repair Mechanism

l  Nucleotide excision

–  Repairs mutations

 

 

 

Gene Transfer

l    Vertical gene transfer

–    Occurs during reproduction between generations of cells

–    Genes from parent to offspring

–    Passage of entire chromosome in this event

–    Replication must occur first then binary fission

–    All organisms

 

l    Horizontal Gene transfer

–    The transfer of genes between cells of the same generation

–    Genes to others in same generation (sister to sister cell)

–    Only SOME DNA is transferred; never a whole chromosome and not always an entire gene

–    Prokaryotes only

–    Mechanisms:  conjugation, transformation, and transduction

 

 

 

RECOMBINATION        

l   What happens to the DNA after it is transferred?

l   Is it expressed?

l   It is only expressed if it meets one of the following criteria:

–   It is in plasmid form (i.e.  The method of transfer was conjugation)

–   It recombines with the recipient’s chromosome through a process called RECOMBINATION

 

 

 

Recombination

l    Exchange of genes between two DNA molecules

 

l    Occurs naturally within a genome

 

l    Occurs with DNA transferred by conjugation, transformation, and transduction

 

l    Crossing over occurs when two chromosomes break and rejoin

 

 

 

Transferring DNA

l  Donor DNA is transferred to recipient cell in 3 possible ways

 

–  Transformation:  donor DNA is free in the environment

–  Transduction:  donor DNA transfer is mediated by a virus

–  Conjugation:  donor DNA is transferred by cell to cell contact

 

 

 

 

TRANSFORMATION

 

l   Recipient takes up donor DNA through cell membrane

l   DNA must recombine to notice possible change in genotype.

–   Recombination necessary for expression

Conjugation

l   Transfer of the F plasmid (from F+ to F- cell)

l   Sex pilus forms

l   Replication and transfer of F plasmid by rolling circle replication

 

 

 

TRANSDUCTION

l    Phage injects DNA into host

 

l    Chromosomal DNA of host is chopped up

 

l    Meanwhile, Phage forces host to make phage DNA and phage proteins

 

l    Phage protein coat (capsid) surround pieces of DNA to make new phage offspring and offspring are released from host (burst).

 

l    Normal offspring phage are released and infect new hosts