Chapter 8: Microbial Genetics and Genetic Engineering

genetics

• the study of inheritance (heredity) of living things; it is wide-ranging and explores:

  • The transmission of biological traits from parent to offspring

  • How those traits are expressed in an organism

  • The structure and function of the genetic material

  • How this material changes

genome

the sum total of genetic material of an organism

chromosomes

most genomes exist as these

plasmids

some genomes may be these

DNA

cell genomes are these

DNA or RNA

virus genomes are these

chromosome

a distinct cellular structure composed of a neatly packaged DNA molecule

eukaryotic chromosomes 

• DNA wound around histone proteins

• Located in the nucleus

• Diploid (in pairs) or haploid (single)

• Linear and double-stranded

bacterial chromosomes

• DNA condensed into a packet by histone-like proteins

• One, two, or sometimes several chromosomes

• DNA is circular and double-stranded

genes

provide information for certain cell functions; encode for protein and RNA molecules

structural genes that code for proteins, genes that code for RNA machinery, regulatory genes that control for gene expression

What are the three categories of genes?

genotype

the sum of all gene types; an organism’s distinctive genetic makeup

phenotype

the expression of the genotype creates traits (structures or functions)

nucleotide

• basic unit of DNA structure

  • Phosphate, deoxyribose, and nitrogenous base

covalently

Nucleotides ___________ bond to each other creating a sugar-phosphate backbone

5’, 3’

Sugars attach in a repetitive pattern to two phosphates; One of the bonds is to the number ___ carbon on deoxyribose, and other to ____ carbon

adenine and guanine

What are the purine bases?

thymine and cytosine

What are the pyrimidine bases?

hydrogen

Bases interact using these bonds; they are weak, making it easy for them to be easily unzipped and gain access to the information encoded in the bases

antiparallel arrangement

• one strand runs in opposite direction of other

• One side runs 5′ to 3′, the other side runs 3′ to 5′

• Important factor in DNA synthesis and protein production

DNA replication

• Enzymes separate existing DNA strands and copy them to create two daughter molecules

• Daughter molecules are identical to parent in composition

• Process is semiconservative

  • Each daughter molecule has one new strand and one parent strand

transcription

production of RNA from a DNA template

translation

transcribed RNA used to produce protein

some viruses can convert RNA to RNA or RNA to DNA

What are the exceptions to transcription and translation?

initiation, elongation, and termination

What are the steps in transcription?

initiation

phase of transcription when the DNA is unwinded and the first RNA chain is synthesized

elongation

phase of transcription when the RNA polymerase lengthens an RNA strand by adding complementary nucleotides, producing the full RNA transcript

termination

phase of transcription where RNA polymerase stops synthesizing an RNA molecule, releasing it along with the enzyme from the DNA template

RNA

• Single-stranded, helical molecule

• Can form secondary and tertiary structures

• Makes specialized forms (tRNA and rRNA)

• Contains uracil (U) instead of thymine

  • A pairs with U;  G pairs with C

• Contains ribose rather than deoxyribose

translational RNAs

ribosomal RNA, transfer RNA, messenger RNA; function in protein production

Regulatory RNAs

•micro RNA, anti-sense RNA, riboswitches, small interfering RNA, primer RNA, ribozymes; function in regulating protein production

ribosomes

align mRNA with tRNA during translation

70S

size of ribosomes in bacteria, mitochondria, and chloroplasts

80S

eukaryotic ribosomes size

small subunit

this binds mRNA

large subunit

this supplies enzymes for making peptide bonds

codon

• groups of 3 nucleotides

• Determine which amino acid is added to growing peptide chain

redundancy

• Same amino acid represented by several codons

• If mistakes occur (in replication or transcription) the correct amino acid may still be inserted

• 64 triplet codes, but only 20 amino acids

control mechanisms

• ensure genes are active only when required

  • Enzymes only produced when needed

bacteria, archaea, and eukaryotes

use regulatory RNAs (micro RNAs, antisense RNAs, etc.) to control protein production

operons

groups of genes regulated as a single unit; only in bacteria and archaea

inducible operons

• turned on by enzyme substrate

• Often catabolic enzymes (needed when substrate is present)

repressible operons

• turned off by enzyme product

• Often anabolic enzymes (stopped when enough product is made)

phase variation

• bacteria turn on/off genes that lead to obvious phenotypic changes

• Mediated by regulatory proteins

• Usually applied to traits affecting surface of bacterial cell

produce an attachment fimbriae

What is the phase variation of Neisseria gonorrhoeae?

produce a capsule

What is the phase variation of Streptococcus pneumoniae?

bacteria

have no exact equivalent to sexual reproduction

recombination

• One bacterium donates DNA to another

• Results in new strain different from DNA donor and recipient

• Plasmids are adept at interchanging genes

• Provides genes for antimicrobial resistance, new metabolic capabilities, increased virulence, and adaptation to the environment

recombinant 

an organism containing genes originating from another organism

vertical gene transfer

• flow of genetic information from one generation to the next

  • Occurs during replication

horizontal gene transfer

transfer of genes between cells of the same generation; new genes did not come from parent organisms

plasmids

• Small, circular pieces of DNA

• Contain their own origin of replication

• Replicate independently

• Not necessary for survival

• Can carry useful traits

chromosomal fragments

Must integrate into the bacterial chromosome in order to be replicated

conjugation

genetic material transferred from one bacterium to another through direct contact

gram negative conjugation

• genetic material transferred by pilus

  • Fertility (F factor) creates pilus

gram positive conjugation

genetic material passes from one cell to another through openings in cell envelope

resistance (R) plasmids

• Commonly shared by conjugation

• Can transfer genes for:

  • Resistance to multiple antibiotics

  • Resistance to heavy metals

  • Virulence factors such as toxins, enzymes, and adhesion molecules

transformation

• Uptake of small DNA fragments from environment (from lysed cells)

  • Aided by DNA-binding proteins on cell wall

  • Competent cells can accept genetic material

• Requires no special appendages; donor and recipient cells do not have to be in direct contact

• Useful for recombinant DNA technology

transduction

DNA transfer from donor cell to recipient by a bacteriophage

generalized transduction

Random fragments of disintegrating host DNA are taken up by the bacteriophage

specialized transduction

• specific part of host genome transferred by a lysogenic phage

  • Prophage DNA separates from bacterial chromosome, carrying a small segment of host genes with it

  • In lytic cycle, viral and host genes are incorporated into virions and carried to another bacterial cell

transposons

• Pieces of DNA capable of shifting from one part of genome to another

• Can move from a chromosome to a plasmid, or vice versa; or from one cell to another

• Involved in:

  • Trait changes (colony morphology, pigmentation, etc.)

  • Transfer of drug resistance (in bacteria)

direct

Is conjugation direct or indirect contact?

indirect

Is transformation direct or indirect contact?

indirect

Is transduction direct or indirect contact?

conjugation

Name the mode of horizontal gene transfer:

Factors involved: donor cell with pilus, fertility plasmid in donor, both donor and recipient alive, and bridge forms between cells to transfer DNA

transformation

Name the mode of horizontal gene transfer:

Factors involved: free donor DNA (fragment); live, competent recipient cell

transduction

Name the mode of horizontal gene transfer:
Factors involved: donor is lysed in bacterial cell, defective bacteriophage is carrier of donor DNA, live recipient cell of same species as donor

drug resistance, resistance to metals, toxin production, enzymes, and adherence molecules

What are the genes commonly transferred in nature via conjugation?

polysaccharide capsule

What are the genes commonly transferred in nature via transformation?

toxins, enzymes for sugar fermentation, and drug resistance

What are the genes commonly transferred in nature via transduction?