1. Microbial Genetics Genetics – the study of heredity
The science of genetics explores:
Transmission of biological traits from parent to offspring
Expression and variation of those traits
Structure and function of genetic material
How this material changes

2. Levels of Structure and Function of the Genome
Genome – sum total of genetic material of a cell (chromosomes + mitochondria/chloroplasts and/or plasmids)
Genome of cells – DNA
Genome of viruses – DNA or RNA

3. - DNA complexed with protein constitutes the genetic material as chromosomes
- Bacterial chromosomes are a single circular loop
- Eukaryotic chromosomes are multiple and linear

4. Chromosome is subdivided into genes, the fundamental unit of heredity
Segment of DNA that contains the necessary code to make a protein or RNA molecule
Three basic categories of genes:
Genes that code for proteins – structural genes
Genes that code for RNA
Genes that control gene expression – regulatory genes

5. Genotype - the genetic makeup of an organism
Phenotype - The expression of the genotype creates observable traits

6. Genomes Vary in Size Smallest virus – 4-5 genes
E. coli – single chromosome containing 4,288 genes; 1 mm; 1,000X longer than cell
Human cell – 46 chromosomes containing 31,000 genes; 6 feet; 180,000X longer than cell

7. DNA Two strands twisted into a double helix
Basic unit of DNA structure is a nucleotide
Each nucleotide consists of 3 parts:
A 5 carbon sugar – deoxyribose
A phosphate group
A nitrogenous base – adenine, guanine, thymine, cytosine
Nucleotides covalently bond to form a sugar-phosphate linkage – the backbone
Each sugar attaches to two phosphates –
5′ carbon and 3′ carbon

8. DNA
Nitrogenous bases covalently bond to the 1′ carbon of each sugar and span the center of the molecule to pair with an appropriate complementary base on the other strand
Adenine binds to Thymine with 2 hydrogen bonds
Guanine binds to Cytosine with 3 hydrogen bonds
Antiparallel strands 3′ to 5′ and 5′ to 3′
Order of bases constitutes the DNA code

10. Significance of DNA Structure
Maintenance of code during reproduction - Constancy of base pairing guarantees that the code will be retained
Providing variety - order of bases responsible for unique qualities of each organism

11. DNA Replication
Making an exact duplicate of the DNA involves 30 different enzymes
Begins at an origin of replication
Helicase unwinds and unzips the DNA double helix
An RNA primer is synthesized at the origin of replication
DNA polymerase III adds nucleotides in a 5′ to 3′ direction
Leading strand – synthesized continuously in 5′ to 3′ direction
Lagging strand – synthesized 5′ to 3′ in short segments; overall direction is 3′ to 5′

12. DNA polymerase I removes the RNA primers and replaces them with DNA
When replication forks meet, ligases link the DNA fragments along the lagging strand to complete the synthesis
Separation of the daughter molecules is complete

14. Completion of chromosome replication

15. DNA replication is semiconservative because each chromosome ends up with one new strand of DNA and one old strand.

16. Information stored on the DNA molecule is conveyed to RNA molecules through the process of transcription
The information contained in the RNA molecule is then used to produce proteins in the process of translation

18. Gene-Protein Connection
Each triplet of nucleotides on the RNA specifies a particular amino acid
A protein’s primary structure determines its shape and function
Proteins determine phenotype. Living things are what their proteins make them.
DNA is mainly a blueprint that tells the cell which kinds of proteins to make and how to make them

19. DNA-protein relationship

20. RNAs Single-stranded molecule made of nucleotides
5 carbon sugar is ribose (DNA has deoxyribose)
4 nitrogen bases – adenine, uracil, guanine, cytosine

21. RNA
3 types of RNA:
Messenger RNA (mRNA) – carries DNA message through complementary copy; message is in triplets called codons
Transfer RNA (tRNA) – made from DNA; secondary structure creates loops; bottom loop exposes a triplet of nucleotides called anticodon which designates specificity and complements mRNA; carries specific amino acids to ribosomes
Ribosomal RNA (rRNA) – component of ribosomes where protein synthesis occurs

23. Transcription: The First Stage of Gene Expression
RNA polymerase binds to promoter region upstream of the gene
RNA polymerase adds nucleotides complementary to the template strand of a segment of DNA in the 5′ to 3′ direction
Uracil is placed as adenine’s complement
At termination, RNA polymerase recognizes signals and releases the transcript
100-1,200 bases long

25. Translation: The Second Stage of Gene Expression
All the elements needed to synthesize protein are brought together on the ribosomes
The process occurs in five stages: initiation, elongation, termination, and protein folding and processing

27. The Genetic Code
Represented by the mRNA codons and the amino acids they specify
Code is universal
Code is redundant

30. Translation Ribosomes assemble on the 5′ end of an mRNA transcript
Ribosome scans the mRNA until it reaches the start codon, usually AUG
A tRNA molecule with the complementary anticodon and methionine amino acid enters the P site of the ribosome and binds to the mRNA

32. Translation
A second tRNA with the complementary anticodon fills the A site
A peptide bond is formed
The first tRNA is released and the ribosome slides down to the next codon
Another tRNA fills the A site and a peptide bond is formed
This process continues until a stop codon is encountered

34. Translation Termination
Termination codons – UAA, UAG, and UGA – are codons for which there is no corresponding tRNA
When this codon is reached, the ribosome falls off and the last tRNA is removed from the polypeptide

35. Prokaryotic transcription and translation Polyribosomal complex allows for the synthesis of many protein molecules simultaneously from the same mRNA molecule.

36. Eukaryotic Transcription and Translation
Do not occur simultaneously – transcription occurs in the nucleus and translation occurs in the cytoplasm
Eukaryotic start codon is AUG, but it does not use formyl-methionine
Eukaryotic mRNA encodes a single protein, unlike bacterial mRNA which encodes many
Eukaryotic DNA contains introns – intervening sequences of noncoding DNA – which have to be spliced out of the final mRNA transcript

38. Regulation of Protein Synthesis and Metabolism
Genes are regulated to be active only when their products are required
In prokaryotes this regulation is coordinated by operons, a set of genes, all of which are regulated as a single unit

39. Operons 2 types of operons:
Inducible – operon is turned ON by substrate: catabolic operons - enzymes needed to metabolize a nutrient are produced when needed
Repressible – genes in a series are turned OFF by the product synthesized; anabolic operon –enzymes used to synthesize an amino acid stop being produced when they are not needed

40. Lactose Operon: Inducible Operon
Made of 3 segments:
Regulator – gene that codes for repressor
Control locus – composed of promoter and operator
Structural locus – made of 3 genes each coding for an enzyme needed to catabolize lactose –
b-galactosidase – hydrolyzes lactose
permease – brings lactose across cell membrane
b-galactosidase transacetylase – uncertain function

41. Lac Operon Normally off Lactose turns the operon on
In the absence of lactose, the repressor binds with the operator locus and blocks transcription of downstream structural genes
Lactose turns the operon on
Binding of lactose to the repressor protein changes its shape and causes it to fall off the operator. RNA polymerase can bind to the promoter. Structural genes are transcribed.

43. Arginine Operon: Repressible
Normally on and will be turned off when the product of the pathway is no longer required
When excess arginine is present, it binds to the repressor and changes it. Then the repressor binds to the operator and blocks arginine synthesis.

45. Mutations: Changes in the Genetic Code
A change in phenotype due to a change in genotype (nitrogen base sequence of DNA) is called a mutation
A natural, nonmutated characteristic is known as a wild type (wild strain)
An organism that has a mutation is a mutant strain, showing variance in morphology, nutritional characteristics, genetic control mechanisms, resistance to chemicals, etc.

46. Causes of Mutations
Spontaneous mutations – random change in the DNA due to errors in replication that occur without known cause
Induced mutations – result from exposure to known mutagens, physical (primarily radiation) or chemical agents that interact with DNA in a disruptive manner

47. Categories of Mutations
Point mutation – addition, deletion, or substitution of a few bases
Missense mutation – causes change in a single amino acid
Nonsense mutation – changes a normal codon into a stop codon
Silent mutation – alters a base but does not change the amino acid

48. Categories of Mutations
Back-mutation – when a mutated gene reverses to its original base composition
Frameshift mutation – when the reading frame of the mRNA is altered

50. Repair of Mutations
Since mutations can be potentially fatal, the cell has several enzymatic repair mechanisms in place to find and repair damaged DNA
DNA polymerase – proofreads nucleotides during DNA replication
Mismatch repair – locates and repairs mismatched nitrogen bases that were not repaired by DNA polymerase
Light repair – for UV light damage
Excision repair – locates and repairs incorrect sequence by removing a segment of the DNA and then adding the correct nucleotides

52. Positive and Negative Effects of Mutations
Mutations leading to nonfunctional proteins are harmful, possibly fatal
Organisms with mutations that are beneficial in their environment can readily adapt, survive, and reproduce – these mutations are the basis of change in populations
Any change that confers an advantage during selection pressure will be retained by the population

53. DNA Recombination Events (Horizontal gene transfer – HGT)
Genetic recombination – occurs when an organism acquires and expresses genes that originated in another organism
3 means for genetic recombination in bacteria:
Conjugation
Transformation
Transduction

54. Conjugation
Conjugation – transfer of a plasmid or chromosomal fragment from a donor cell to a recipient cell via a direct connection
Gram-negative cell donor has a fertility plasmid (F plasmid, F′ factor) that allows the synthesis of a conjugative pilus
Recipient cell is a related species or genus without a fertility plasmid
Donor transfers fertility plasmid to recipient through pilus

57. Conjugation
High-frequency recombination – donor’s fertility plasmid has been integrated into the bacterial chromosome
When conjugation occurs, a portion of the chromosome and a portion of the fertility plasmid are transferred to the recipient

59. Transformation
Transformation – chromosome fragments from a lysed cell are accepted by a recipient cell; the genetic code of the DNA fragment is acquired by the recipient
Donor and recipient cells can be unrelated
Useful tool in recombinant DNA technology

60. Insert figure 9.23
transformation

61. Transduction
Transduction – bacteriophage serves as a carrier of DNA from a donor cell to a recipient cell
Two types:
Generalized transduction – random fragments of disintegrating host DNA are picked up by the phage during assembly; any gene can be transmitted this way
Specialized transduction – a highly specific part of the host genome is regularly incorporated into the virus

62. Generalized
transduction

63. Specialized
transduction