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OSU / Microbiology / M 4000 / What is the complete set of genetic information?

What is the complete set of genetic information?

What is the complete set of genetic information?

Description

School: Ohio State University
Department: Microbiology
Course: Basic and Practical Microbiology
Professor: Tammy madhura pradhan
Term: Summer 2015
Tags: Microbiology, microbio, and Biology
Cost: 50
Name: Microbio 4000- Exam 2 Study Guide
Description: This study guide covers everything that was gone over in lecture on chapters 7, 8, 13, and 20; including all Top Hat questions.
Uploaded: 02/26/2018
62 Pages 66 Views 4 Unlocks
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Exam 2 Study Guide 


What is the complete set of genetic information?



Chapters 7, 8, 13, and 20 

Chapter 7: Bacterial Genetics 1

A. Genome

a. Complete set of genetic information

i. For cells, double stranded (dsDNA) is the genetic material

ii. Some viruses use single strands (ss) or RNA as their genome

iii. Functional unit of the genome is a Gene

b. Genomes In Bacteria: 

i. Chromosome + plasmids (if present) 

ii. Most are single, circular DNA molecules

c. Viruses have their own genomes

d. Gene expression = transcription and translation 

i. But does not always end in a protein Don't forget about the age old question of What is the function of chaperone proteins?

e. Humans have 1000x the amount of DNA as a bacterial cell


What enzyme synthesizes new dna?



i. We have a lot of DNA that isn’t used in expression (is not transcribed) B. Questions

a. DNA replication:

i. What enzyme synthesizes new DNA? When does this occur and what determines where replication of DNA will begin? 

1. DNA polymerase

2. Occurs before cell division

3. Origin of replication determines where this begins (Site where

DNA polymerase/other proteins bind and begin replication)

ii. DNA replication is semiconservative, bidirectional, and 

semi-discontinuous. What do each of these descriptions mean? We also discuss several other topics like What is the state of security?

1. Semiconservative = DNA has one original and one newly


What determines where replication of dna will begin?



synthesized strand

2. Bidirectional = 2 replication forks

3. Semi-discontinuous = leading strand is continuous, lagging

strand is discontinuous

b. Transcription:

i. What enzyme synthesizes RNA? When does this occur and what determines where transcription will begin and end? 

1. RNA polymerase

2. Promoter determines where it begins and terminators determine where it ends

ii. What roles do RNA transcripts have? 

1. Code for proteins, regulatory roles, transfer

c. Translation:

i. How is a molecule of mRNA (nucleic acid) “translated” into a peptide (protein) sequence of amino acids. What is needed to do this “decoding” ii. What is a codon and what is meant by “reading frame”? We also discuss several other topics like What is the known achievement of president andrew jackson?

C. DNA Replication

a. Occurs prior to cell division

b. Produces two copies of a DNA molecule

c. Each daughter cell receives one copy

d. In bacteria, replication is often slower than the generation time

e. Origin of Replication

i. Site in genomes where DNA polymerase and other replication proteins bind and begin replication

ii. Plasmids

f. DNA Polymerase:

i. Synthesize DNA 5’ 3’

ii. DNA template strand is needed

iii. Also used in DNA repair

g. Bidirectional

i. 2 replication forks; replicating 2 new strands at each

ii. Forks ultimately meet at terminating site and process complete (bacterial have circular genomes) We also discuss several other topics like What is the meaning of choosing my plate guidelines?

h. Semiconservative

i. DNA contains one original strand and one newly synthesized strand ii. Most important to us

i. Semi-Discontinuous

i. New DNA is synthesized only in the 5’ 3’ direction; But the rep. forks are bidirectional

ii. The leading strand is made continuously

1. fork and replication are moving in the same direction.

iii. The other lagging strand is synthesized discontinuously as short “Okazaki” fragments

1. fork and replication are moving in opposite directions If you want to learn more check out How do valence electrons affect atomic radius?

iv. Top strand = continuous, bottom strand = discontinuous, fragments D. Transcription

a. New RNA sequence is made Complementary and Antiparallel to the DNA template strand

i. Complementary = C to G, G to C, A to U, U to A

b. RNA transcript is the same sequence as the coding DNA strand (except U instead T)

c. RNA Polymerase:

i. Synthesize RNA 5’ 3’

ii. DNA template is needed

iii. Bind promoters (start)

iv. Stopped by terminators

v. RNAP

d. Promoter: signals start of transcription

i. upstream DNA sequence where RNA polymerase binds

ii. Promoter sequence orientation determines the direction of transcription and which DNA strand will be the template strand

iii. Different promoter sequences have different “strengths” or affinities for RNAP (affects how often transcription occurs)

e. Terminator: signals end of transcription If you want to learn more check out What is denoted when we say that the social security tax is regressive?

i. disrupts RNAP and transcription ends

ii. Often a sequence of RNA that forms a structure (hairpin)

f. Products of transcription = transcripts

i. Messenger RNA (mRNA) - codes for proteins

ii. Ribosomal RNA (rRNA)

1. Stable

iii. Transfer RNA (tRNA)

1. Stable

iv. Regulatory RNAs

E. Translation

a. Ribosome

i. Large complex of proteins and rRNA 

ii. Catalyzes peptide bond formation between amino acids

1. “Polypeptide”

2. That peptide folds into a protein

iii. RNA template is needed

iv. Ribosome maintains the correct Reading Frame and aligns tRNAs 1. So the proper amino acid is made

v. Finds Start codon (often AUG), moves along the mRNA template 5′ to 3′ 

b. Transfer RNAs (tRNAs)

i. deliver correct amino acids to the ribosome (tRNA sare recycled) c. The Genetic Code

i. 3 DNA bases = 1 Codon 

ii. Each codon codes for an amino acid (or a start or stop)

iii. 3 base code does not overlap in the message

1. (ATG CGT CAT TTA…)

iv. Degenerate- redundancy, or several codons code for the same amino acid

d. Open Reading Frame (ORF) - the region to be translated and is defined by sequences in the mRNA

i. Designated start and stop

e. Ribosome Binding Site (RBS)

i. Sequence in the mRNA that defines the correct start codon and sets the reading frame

f. Reading frame

i. 3 reading frames are possible on each strand of mRNA 

1. Top strand AND bottom strand can each give rise to 3 reading

frames (6 total)

ii. If the reading frame is incorrect, translation will yield a different, often nonfunctional, protein

F. Summary

a. Replication

i. Enzyme → DNA polymerase

ii. Template → DNA

iii. Recognition sequence → origin of replication

iv. Functional unit (what gets replicated) → genome

v. Product → DNA

b. Transcription and translation = gene and protein expression

c. Transcription

i. Enzyme → RNA polymerase

ii. Template → DNA

iii. Recognition sequence → promoter

iv. Functional unit (what gets transcribed) → gene

v. Product → RNA (mRNA, tRNA, rRNA, regulatory RNA)

d. Translation

i. Enzyme → ribosome

ii. Template → mRNA

iii. Recognition sequence → start codon and RBS (ribosome binding site) iv. Functional unit (what gets translated) → open reading frame

v. Product → peptide/protein

G. Top Hat

a. What would happen if the only promoter sequence of a gene was deleted? i. The encoded protein would not be produced

b. The template strand of a gene reads: 3’ ATGCGTAGGACTAAG 5’. What is the sequence of the RNA transcribed from this gene?

i. 5’ UACGCAUCCUGAUUC 3’

H. Gene Expression: Prokaryotic vs Eukaryotic

a. Location/timing:

i. In prokaryotes, transcription and translation are coupled

1. transcription/translation coupling- Translation begins before

transcription is complete

a. Important for gene regulation in prokaryotes

ii. In eukaryotes, they occur in separate locations in the cell

b. Genes per transcript:

i. In prokaryotes, genes are often arranged in operons and the mRNA is polycistronic

1. Operon- several genes transcribed together as a single RNA 

message

2. Polycistronic- multiple genes per mRNA

a. can encode more than one polypeptide separately within

the same RNA molecule

ii. In eukaryotes, mRNA is monocistronic

1. Monocistronic- one gene per mRNA

c. Processing:

i. In eukaryotes, pre-mRNA is processed through the addition of a 5’ cap and a 3’poly(A) tail

d. Introns and splicing:

i. Eukaryotic genes contain introns, which are removed from the RNA via splicing

1. Introns interrupt coding regions (exons)

ii. Prokaryotic mRNA does not get processed this way

1. Splicing does NOT occur in bacteria

I. Regulation of Bacterial Gene Expression

a. Microorganisms are constantly face changing environments

i. Nutrient availability, temperature, cell density, etc.

ii. Must be able to react quickly in order to survive

b. Sensing the environment (bacteria)

i. TWO-COMPONENT REGULATION

1. Bacteria cells are able to sense and respond to changes in their

environment 

2. Sensor protein

a. Detects changes in the environment

b. located in the membrane

3. Response regulator

a. Initiates changes in gene expression

4. Signal is relayed by the transfer of phosphate groups

5. Sometimes used to sense Quorum signals

ii. QUORUM SENSING:

1. Individual cells acting as a larger population to get something

done

2. How bacteria “sense” or “talk to” each other and detect Cell

Density (can be between friend or foe)

a. EX: Lots of signaling molecules = lots of bacterial cells

3. Different chemical signals are used

4. some bacteria use two-component regulation to detect the

quorum signal

5. some signals can cross the membrane

6. Examples of traits/behaviors that come of these gene expression changes:

a. Bioluminescence

b. Motility

c. Biofilm formation

d. Virulence

e. Horizontal gene transfer

i. Conjugation

ii. The regulatory genes get turned on by Quorum

sensing

7. Why is it beneficial for the cells to wait for a critical population density before turning on a gene?

a. Bacteria save their energy until there’s enough, so they

can ‘turn on’ all at once and pool their energy for a

greater effect

c. Regulon

i. Network of genes and operons controlled by a common regulatory mechanism

1. Can turn on a bunch of genes and pathways and inhibit others 2. Indicates which genes turn on/turn off with a specific signal ii. Ex: Two component regulation; response regulator affects several operons

iii. Remember: different from operon

1. Operon = several genes transcribed together as a single RNA message (polycistronic)

2. Regulon = many genes 

iv. Cells can be regulated at ALL points of gene expression

d. 2 Mechanisms that Control Transcription (readily reversible) i. Alternative Sigma Factors

1. Part of RNA polymerase 

a. Sigma factor is one of the subunits of RNA polymerase

2. Recognizes different promoters of specific networks of genes (regulons)

a. often global regulation

b. Different promoters are recognized by different sigma

factors

3. EX: Sporulation in Bacillus subtilis

a. Signal = starvation

b. Regulator = regulon

i. Cell starts to make a different sigma factor when it

realizes that it’s starving

ii. Different genes are now getting expressed, which

initiates sporulation

4. Very common in bacteria

ii. DNA-binding proteins

1. Block OR promote RNA polymerase-DNA binding 

2. Activator Protein - promotes 

a. Helps promote transcription (results in more transcription)

3. Repressor Protein- blocks 

a. Binds in front of RNA polymerase and blocks it

b. Prevents RNA polymerase from moving so transcription

cannot occur

c. EX: Corynebacterium diphtheriae - toxin expression

i. Host defense = limit Fe (starve the bacteria of

iron)

1. Repressor protein falls off

ii. Fe is present = transcription is prevented

1. Repressor protein turned on

4. EX: lactose utilization (genes that enable import and breakdown

of lactose)

a. Lac operon

5. Operons or genes can be:

a. Inducible

i. Usually OFF 

ii. Turns ON 

b. Repressible

i. Usually ON 

ii. Turns OFF 

c. Constitutive

i. Always ON 

e. Other factors affecting bacterial gene expression:

i. Factors that bind directly to RNA polymerase

ii. Structures on the mRNA

1. EX: block/occupy the ribosome binding site (RBS)

iii. Regulatory RNAs bind mRNA (effect can be positive or negative) iv. mRNA stability (how quickly the mRNA is degraded)

f. Regulation at the protein level:

i. Protein folding, processing, or stability

ii. Modification or regulation of proteins (activate/deactivate)

Chapter 8: Bacterial Genetics 2

Mutations and Horizontal Gene Transfer

A. Bacteria are faced with changing environments

a. Genes can be turned on and off in order for the cell to adjust to the conditions: i. Gene regulation (Ch. 7)

b. Genetic Changes can bring about new traits or functions enabling cells to adapt and survive (Ch. 8)

i. Change in genotype may bring on a new phenotype 

1. Genotype–DNA sequence

2. Phenotype– observable characteristic

B. Genetic Changes in Bacteria

a. Mutations –changes in the existing genome 

i. insertion/deletion

b. Horizontal gene transfer (HGT) – get new DNA 

i. DNA transferred between organisms

ii. Transferring DNA independently

c. Both Mutations and HGT events could be passed on to daughter cells i. Vertical gene transfer - DNA passed to progeny (cell division)

1. Can occur after a mutation or HGT

C. Mutations (Major Types)

a. Always occur in the DNA

b. A change in the DNA; can be neutral or bad

c. Two major types:

i. Base substitution mutations

ii. Addition/Deletion mutations

d. Base substitution mutations

i. Wrong nucleotide(s) used during DNA replication

1. Wrong base pair gets added

2. AAG-CGT → AGG-CGT

ii. Only some of the progeny gets the mutation because the mistake occurs during replication, which is semi-conservative

iii. What enzyme makes this mistake?

1. DNA polymerase

iv. Point Mutation- A single base change

v. Wild type – typical phenotype of strains isolated in nature

vi. 3 potential outcomes:

1. Silent mutation - Codes for the same amino acid 

a. Even though the mutation occurred, you still get the

correct amino acid

2. Missense mutation - Codes for a different amino acid 

3. Nonsense mutation - Codes for a STOP codon 

a. Get a premature STOP in transcription

b. Get a truncated protein

e. Addition/Deletion Mutations

i. Frameshift Mutation - An addition or deletion can shift the reading frame 

1. The encoded peptide sequence is different

ii. Knockout Mutation (or null) - Gene product is inactivated

1. Missense and Nonsense mutations from base substitution can

be knockout mutations

2. Product of the gene is no longer functional 

3. Is not a type of mutation, but the result of a mutation that leads to a nonfunctional gene

f. Reversion - a shift back to the wild type sequence or phenotype i. Could be a different base pair sequence from the wild type, but codes for the SAME amino acid

ii. Could be the same base pair sequence

D. Transposons (Large Addition Mutations)

a. Piece of DNA moves from one place in the genome to another, random location → “jumping genes” 

b. Cannot replicate independently

c. Encode transposase that helps move the DNA to a new location i. “cut and paste” 

d. Often will inactivate gene into which it inserts → “knockout” 

e. Some move by “copy paste” → replicative transposon

f. Insertion Sequence - Just transposase gene and repeats

i. Only the transposon gets transferred

g. Composite transposon - Mobile element contains additional genes i. Something else that has nothing to do with the transposon also gets transferred

ii. ex. antibiotic resistance or toxins

h. Transposons can be passed on DNA during HGT

i. EX: plasmids

E. Spontaneous Mutations

a. Referring to HOW the mutation came about

b. Mutations that occur during normal cell processes

c. Random and infrequent, but at characteristic rates (Mutation Rates) i. The probability of/how often mutations are occurring

d. Cells in a population (e.g. colony) are not identical

i. allows for diversity and adaptation to environment

e. Wrong Nucleotide Paired during replication

i. Mistake by DNA polymerase 

ii. Sometimes can be corrected by DNA polymerase Proofreading activity 1. Double checking the correct nucleotide was being inserted

f. Reactive Oxygen Species (ROS)

i. damage DNA, making mispairing by DNA polymerase more likely ii. Base substitutions are more common in aerobic environments

g. Mutation Rate: probability of a mutation with each cell division

i. Typically between 1 in 10–4 and 1 in 10–12 for a given gene

h. Vertical transfer - Spontaneous mutations (if not repaired) are passed to daughter cells

i. A second mutation could change the sequence back to the original sequence - reversion

i. Mutations are not permanent 

j. Beneficial or Not?

i. Depends… the environment provides Selective Pressure and the cells that are “fit” are able to survive and reproduce

ii. If the mutation does not provide a benefit to the organism, it will be selected out of the population and will not remain in the genepool

iii. Natural selection 

F. Induced Mutations

a. Referring to HOW the mutation came about

b. When an outside agent (mutagen) damages or changes DNA, increasing the mutation rate

c. Chemical mutagens:

i. Can modify DNA OR resemble DNA bases, often results in base pairing mistakes

1. EX: alkylating agents modify DNA by adding an alkyl group and

changing which base pair gets added

2. EX: base analogs resemble DNA bases and increase likelihood

of base mispairing

a. Used as substrates for DNA replication

b. Less specific with what it pairs with – mispairings occur

during the next round of replication

ii. Intercalating Agents - modify the DNA by inserting and distorting it 1. frameshifting often results

d. Radiation as a Mutagen:

i. Ultraviolet (UV)

1. Induces thymine dimer formation- distorts DNA, mutations during replication result

ii. X rays

1. Breaks in DNA backbone; can also alter bases 

G. Top Hat

a. In order to test if a chemical is a mutagen, you need to measure: i. Its affect on mutation rate

b. Aside from sequencing, a simple way to determine if a mutation (change in genotype) has occurred is to:

i. Observe a change in a correlated phenotype

c. Match the genotype with the phenotype. Note: Glucose-salts agar LACKS amino acids such as histidine

i. Knockout mutation in a histidine biosynthesis gene

1. His- (auxotroph) CANNOT grow on glucose-salts agar

ii. Wild type histidine biosynthesis genes

1. His+ (prototroph) CAN grow on glucose-salts agar

d. Which of the following is needed for a transposon to “jump” to a new location in the genome?

i. Insertion sequence

e. Put steps of F plasmid transfer in the correct order.

i. F pilus makes contact with recipient cell

ii. One strand of the F plasmid is cut at the origin of transfer

iii. Single strand of F plasmid is transferred to the recipient cell

iv. Complement of transferred strand is synthesized

f. Generalized transduction involves bacteriophages that can:

i. Digest the host genome

g. Temperate phages can:

i. Randomly integrate into the host genome

h. Temperate phages promote which type of HGT?

i. Specialized transduction

H. Ames Test - to screen for mutagens

a. Background Info

i. Change in genotype → may bring a new phenotype

ii. His- = histidine auxotrophs (can’t make histidine)

iii. His+ = prototroph (can make histidine)

iv. NO histidine in the media → His

b. Bacteria requiring histidine for growth (His-) plated with glucose-salts agar (No histidine in the media) →

i. Add liquid containing suspected mutagen →

ii. Incubation →

1. Can:

a. Many His+ revertant colonies

b. Chemical IS a mutagen

c. Many colonies form on the plate

2. Or can:

a. Most remain His- and do not grow

b. Chemical is NOT a mutagen

c. Few colonies form on the plate

c. Bacteria strain is His- (cannot grow)

i. Bacteria are exposed to a possible mutagen (what’s being tested) ii. Bacteria that form colonies are His+ and have undergone a reversion 1. What does this indicate about the chemical?

a. IS a mutagen

d. Control: no mutagen added

I. DNA Repair Mechanisms

a. Mismatch repair

i. Mismatch →

ii. Mismatch is recognized →

iii. Methyl (CH3) indicates which is the template strand

b. Repair of a Nucleobase

i. Damaged base is recognized and removed

ii. Backbone is degraded and repaired

iii. Ex. Glycosylase → oxidized G

c. Photoreactivation (only microbes)

i. Thymine dimers (UV) 

ii. Enzyme uses light energy to break the dimer bonds

iii. Use UV light energy to reverse the damage

1. Works without having to cut out the DNA

d. Excision Repair

i. Distorted DNA 

ii. DNA Distortion is recognized and removed

e. How might a mutation in a repair pathway be beneficial?

i. Allows for more genetic diversity

f. SOS repair

i. Extreme repair for lots of damage/crisis situation

ii. A global, last-ditch repair mechanism following extensive DNA damage (strand breaks and gaps)

iii. Recombination and an Error-prone DNA polymerase are used 1. it’s better than dying or not replicating at all

2. But greatly increases the amount of mistakes that are made

a. So lots of mutations arise

iv. Increases mutation rate itself: “SOS mutagenesis”

J. Horizontal Gene Transfer (HGT) - new DNA

a. Conjugation

i. DNA transferred between bacterial cells

ii. Requires direct contact between donor and recipient cells

iii. Conjugative genes direct the process

iv. Uses sex pilus

v. 2 types of conjugation:

1. Plasmid transfer

a. EX: F plasmid of E. coli is a “conjugative” plasmid

i. Encodes proteins that promote DNA transfer

ii. Strain genotype = F+

b. F pilus contacts the recipient F- cell → the pilus retracts

and pulls cells together → a single strand of the plasmid

is transferred, a complement is then synthesized → both 

the donor and recipient are now F+ 

2. Chromosome transfer

a. Less common

b. Hfr cell produces F pilus →

c. Part of chromosome is transferred to recipient cell (single

strand) →

d. Cells separate, DNA transfer is interrupted (chromosome

breaks) →

e. DNA can be integrated via homologous recombination

i. Recipient cell remains F– since incomplete

transfer

vi. Hfr cells = F plasmid is integrated into chromosome via homologous recombination

1. high frequency of recombination

2. process is reversible 

vii. F′ = An incorrect excision of the F plasmid genes brings along additional portion of the chromosome

b. Transformation

i. DNA mediated (naked DNA)

ii. DNA transferred from environment to organism

iii. Recipient cell must be Competent or capable of DNA uptake 1. Competence is a specific physiological state and subject to genetic regulation

iv. Most bacterial cells take up DNA regardless of origin, however some accept DNA only from closely related species

v. Newly acquired DNA must recombine with the host chromosome to be maintained/passed on!!!! (or plasmid DNA with an origin of replication) 1. Where might this DNA come from?

a. Lysed cells (the environment)

vi. Homologous recombination

1. Integration of ssDNA into the chromosome at sites of similar sequence

vii. dsDNA binds the cell → ssDNA enters and the other strand is degraded → the strand integrates by homologous recombination, the strand it replaced is degraded → one strand is the old sequence, one is new → DNA replicates and cell divides → the genotype has changed here and so has the phenotype

1. Selective pressure...evolution

c. Transduction

i. phage mediated 

ii. Transfer of genes by bacteriophages

iii. Generalized transduction: any genes of a donor cell

1. Phage packaging error

2. After phage infection, host DNA is degraded

3. During viral packaging, fragments of the host DNA are

mistakenly packaged into some phage heads

a. Accidentally picks up and packages some bacteria DNA

4. Transducing particle can infect new host cell

5. New (bacterial) DNA may integrate via homologous

recombination

6. **Any host gene can be transferred in generalized transduction

7. Transducing particle: has bacterial DNA instead of phage DNA 8. Increases genetic diversity in the bacteria

iv. Specialized transduction:specific genes near a temperate phage 1. excision error

a. Inaccurate excision of a temperate phage

2. Upon infection some phages are able to integrate into their

host’s genome

3. When the phage genome is excised, some neighboring bacterial DNA is taken packaged into phage particles

4. Upon infection of new host, new DNA may integrate via

homologous recombination

5. **Only bacterial genes adjacent to integrated phage DNA are

transferred

v. Type of phage determines whether its generalized or specialized d. All 3 types change the genotype

e. For new DNA to be “maintained” or passed to progeny, the new DNA must: i. Have its own origin of replication OR

1. Replicon - the DNA that will be replicated

ii. Be integrated into the chromosome 

f. Griffith’s Experiment (1928)

i. Transformation of pneumococci

1. Capsule needed for pathogenesis

2. Only living cells are pathogenic

3. The dead cells “transformed” the non-encapsulated into

pathogenic cells

ii. living/nonliving/heat killed encapsulated/living nonencapsulated cells injected into a mouse

1. Watched if mouse lived or died

K. The Mobile Gene Pool

a. Variable genes in a species that can move from one DNA molecule to another i. on mobile genetic elements

b. Often useful for recombinant DNA technology

c. Genomic islands

i. Large fragment of DNA in a chromosome or plasmid

ii. Code for genes that allow cell to occupy specific environmental locations

iii. Originate from another species

1. EX: pathogenicity islands

d. Transposons

i. Insertion sequences

1. Transposase gene flanked by short repeat sequences

ii. Composite transposons

1. Recognizable gene flanked by insertion sequences

iii. Move to different locations in DNA in same cell

e. Plasmids

i. Smaller than chromosome

ii. Found in most Bacteria & Archaea

iii. Circular, dsDNA replicon

iv. Replicate autonomously (origin of rep)

v. Non-essential genes; cells can be “cured” or “lose” a plasmid

vi. Few to 1000s of genes

vii. Narrow or broad host range

viii. Plasmids often encode beneficial traits 

ix. R plasmids - resistance plasmids

1. EX: Staphylococcus aureus plasmid

a. This plasmid carries multiple antibiotic resistance genes 

x. RTF - resistance transfer factors (conjugation)

f. Phage DNA

i. Phage genome

ii. May encode proteins important to bacteria

Chapter 13: Viruses, Viroids, and Prions

A. Viruses: Obligate Intracellular Parasites

a. Virus → eukaryotic host 

i. bacteriophage /phage → prokaryotic host

b. Infectious biological agents, but not alive 

i. No binary fission

ii. No way to generate ATP

iii. No way to synthesize proteins (no ribosomes)

c. Genetic information in a protein shell 

i. Uses host cell for energy

ii. Hijacks host cell’s replication machinery

iii. Directs host cell to express viral genes

iv. Only contains nucleic acid and a protein coat

d. Difficult to study 

i. require live host cells

ii. unobservable with light microscopy

e. But important:

i. Viruses

1. (some) can cause disease

2. part of our microbiota

3. part of our genome is old viral DNA

ii. Bacteriophages/Phages

1. Model systems for viruses and genetics

2. Vehicles for horizontal gene transfer

3. Affect environmental bacterial populations

B. Viral Architecture

a. Nucleocapsid (genome and protein coat together)

i. Nucleic acid (genome)

1. Either DNA or RNA

2. Linear or circular or segmented

3. Double- or single-stranded

ii. Capsid

1. Protein coat around the genome

2. Composed of identical subunits called capsomers

3. Determines the shape of a virus

b. Three common shapes:

i. Icosahedral

1. Flat, hexagon shape

ii. Helical

1. Cylinder shape

iii. Complex

1. spider/spaceship shape

c. Naked viruses (non-enveloped)

i. Nucleocapsid only

ii. Most phages are naked

iii. More resistant to disinfectants

1. Because they don’t have an envelope that can be broken down, so spikes remain that can attach to a host

d. Enveloped viruses

i. Nucleocapsid enclosed in a lipid envelope

ii. Matrix protein 

1. Help the structure form and package the nucleic acid in the

envelope

e. Spikes or tail fibers in phages - Attachment to host cell

C. Bacteriophages: bacterial viruses

a. “to eat”

b. Scientists estimate:

i. ~1031 phage particles globally

ii. ~1023 infections per second

c. Increase genetic diversity (transduction)

d. Huge impact on microbial life and evolution

e. But…only 0.0002% of the phage metagenome has been sampled f. Three types :

i. Lytic phage

ii. Temperate phage

iii. Filamentous phage

g. Virion = one virus particle

h. Viral infection:

i. Virion infects host cell → disease of host cell → productive infection → release of virions →

1. Host cells lyse → host cell dies

a. Lytic phages

b. Temperate phages

2. Host cells do not lyse → host cell multiplies and continuous release of virions

a. Filamentous phage

ii. Virion infects host cell → genetic alteration of host cell → latent state → host multiplies but phenotype is often changed

1. Temperate phages

iii. Productive infection - more phage particles are formed i. T4 Lytic Phage (example)

i. Attachment → genome entry → synthesis → assembly → release ii. Attachment

1. Tail fibers bind a bacterial receptor (ex. E. coli LPS for T4)

iii. Genome entry

1. Phage-encoded lysozyme degrades bacterial cell wall

2. Tail contracts, injects genome

iv. Synthesis of proteins and genome

1. Early proteins- degrade host DNA, modify host’s RNAP

2. Late proteins- structural proteins to build more phage particles a. Lysozyme

v. Assembly (Maturation)

1. Multistep

2. Some steps use scaffold proteins

a. Proteins used to arrange components of the virus near

each other, but aren’t used in the finished

vi. Release (host cell dies)

1. Lysozyme produced late in infection

2. Cell lyses and releases phage

3. Burst size of T4 is ~200 phage/cell

vii. *Packaging errors where a phage particle takes random fragment of bacterial host DNA is called Generalized Transduction

j. Temperate phage - Lambda

i. 2 options:

1. Lysogenic

a. Lysogenic infection

b. Phage DNA is integrated into host genome via site

specific recombination

c. Phage is latent

d. Lysogen – bacteria cell with a prophage

e. Prophage - Integrated phage DNA

i. Replicated with the host chromosome

ii. Can be excised by phage enzyme lytic cycle

iii. Part of bacterial cell

f. Consequences of Lysogeny:

i. Immunity to Superinfection: Lysogen can’t be

infected by another related phage

ii. Lysogenic conversion: prophage changes host’s

phenotype

2. Lytic

a. Lytic infection

b. Phage DNA is excised and replicated and expressed to

make more phage particles

c. Inaccurate excision results in Specialized Transduction

d. Productive - cells lyse and release new phages

k. Filamentous Phage M13

i. Infects, but doesn’t lyse the host cell 

ii. Attaches to F pili on E. coli host

iii. ssDNA genome

1. (+) “coding strand”

iv. Host DNA pol. = synthesizes the complementary DNA strand 1. Replicative Form (RF)

a. Phage genome (+)

b. Template for more DNA and mRNA (-)

c. Needed so it can make more proteins

d. Has to replicate since it’s ssDNA

v. Phage DNA replicates; phage capsomeres are synthesized and embedded in the host cell membrane

vi. Phage nucleic acid gains its capsid as it extrudes through the membrane

1. The bacteria do not lyse

vii. Productive infections

viii. Host cell is NOT killed, but will grow more slowly. Why?

1. Takes a lot of energy to carry out replication/gene expression 2. That energy is now not going into making more bacterial cells 3. Host is still diseased

ix. Nucleocapsid formed during exit

1. Capsomers make up its protein coat, line along interior of

membrane

2. Capsid formed as phage is being released

D. Bacterial Defenses Against Phage

a. Prevent Phage Attachment

i. Bacteria can alter or cover its receptors or viral recognition protein 1. Hides what the phage uses to attach, so that the phage can’t

attach

ii. Ex: S. aureus makes “Protein A”

1. covers/masks phage receptors in cell wall

2. Also helps bacteria survive against human immune system

defenses

b. Restriction-Modification Systems

i. Bacterial Restriction Enzymes recognize short sequences and cut foreign DNA 

ii. Methylation (-CH3): self from non-self (“modification”)

1. How it tells its own DNA from the phage DNA

2. Own DNA is methylated, phage/foreign DNA is not

3. Biotechnology

4. But phage DNA can become methylated if it hangs around long enough

c. CRISPR

i. Clusters of Regularly Interspaces Short Palindromic Repeats

ii. Bacteria can “store” phage DNA sequences in their own genome iii. CRISPR array is transcribed into crRNAs and together with CAS proteins target phage DNA for degradation

1. →​ “memory” immunity 

2. Closest “immunity” a bacterial cell can get

iv. This Immunity (CRISPR array) is passed to progeny/daughter cells v. Phage DNA sequence becomes part of CRISPR array

vi. Cas-crRNA complex targets and cleaves invading phage DNA (immunity)

1. Cuts depending on which CRISPR RNA is “loaded” to use

a. “scissors” cut what they are programmed to

b. Cas proteins = cutting enzymes, “scissors”

i. Can tell the scissors exactly what to cut

2. crRNAs will pair with incoming phage DNA

3. CRISPR/Cas genes are expressed

vii. Biotechnology

1. this system is now used to target and alter genomic sequences many cell types, including human embryos

2. Can inactivate a gene

3. Can replace or insert a new sequence

4. CRISPR-Cas9 system for genome engineering

E. Summary Info

a. Lytic phage = generalized transduction

i. Also occurs when temperate phage is in lytic stage

b. Temperate phage = specialized transduction

F. Animal Viruses

a. Taxonomy

i. Key characteristics for classification:

1. Genome structure 

a. DNA virus vs RNA virus vs ss vs ds

2. Envelope? 

a. Does it have an envelope

3. Shape 

a. Cocci, bacilli, etc

ii. -viridae at end of name indicates family

iii. -virus at end of name indicates genre

b. Grouping

i. Viruses are also grouped and informally named on the basis of their Route of Transmission

1. How you get the disease

ii. Enteric = fecal-oral route

iii. Respiratory = respiratory/salivatory route

iv. Zoonotic = vector, animal to human directly

v. Sexually transmitted = sexual contact

c. Replication- Five-step Infection Cycle: 

i. Attachment 

1. Viruses bind to specific receptors, usually glycoproteins, on 

plasma membrane of the animal host cell 

a. Virus hijacks 

2. More than 1 receptor may be required 

3. Receptors often have functions outside of virus attachment 

4. Species specific? Tissue or cell specific? 

a. HIV targets immune system because it is immune specific 

ii. Penetration and Uncoating: fusion or endocytosis 

1. Fusion 

a. Virus fuses with host cell membrane 

b. Spike proteins on membrane 

c. Adsorption → membrane fusion → nucleocapsid released 

into cytoplasm → uncoating 

2. Endocytosis 

a. Naked viruses HAVE to use this 

b. Virus binds to ligand on outside of cell, which then pulls 

virus into the cell

c. Adsorption → endocytosis → release from vesicle → 

uncoating 

d. Use endosome 

iii. Synthesis 

1. Expression of viral genes to make viral proteins (e.g. capsid proteins, replication enzymes, etc.) 

2. Make multiple copies of viral genome 

a. Replication strategy depends on viral genome: 

i. DNA viruses (single stranded or double stranded) 

ii. RNA viruses (single stranded or double stranded) 

iii. Reverse Transcribing viruses (RNA or DNA) 

iv. DNA → DNA: DNA polymerase 

v. DNA → RNA: RNA polymerase 

vi. RNA → RNA: replicase (RNA dependent RNA 

polymerase) 

vii. RNA → DNA: reverse transcriptase/RT (RNA 

dependent DNA polymerase) 

3. (+) = coding strand, (-) = template strand 

a. + strand used to make more - strand 

4. DNA viruses 

a. Replication often occurs in the nucleus 

i. If using host DNA polymerase, virus must get into 

the host nucleus 

b. Most DNA viruses use host enzyme for genome 

replication 

c. Some viruses encode their own viral DNA polymerase 

i. If you have your own DNA polymerase, you don’t 

need gene expression 

ii. You can immediately start making more of the viral 

particle 

d. dsDNA (+/-) → ssRNA (+)(mRNA) → protein 

i. dsDNA → DNA polymerase → dsDNA 

e. ssDNA → dsRNA(+/-) (need dsDNA for gene expression) → ssRNA (+)(mRNA) → protein 

i. ssRNA (+)(mRNA) → protein uses RNA 

polymerase and ribosomes 

5. RNA viruses 

a. Replication usually occurs in the cytoplasm 

b. Viral encoded replicase used for genome replication 

c. ss(-) RNA viruses need to package replicase enzyme 

i. Replicase - RNA dep. RNA polymerase 

1. No proofreading = mutations are frequent 

6. Retroviruses - reverse transcribing viruses

a. (+) = strand in mRNA 

b. Viral Reverse Transcriptase (RT) synthesizes DNA from 

an RNA template 

i. Reverse transcriptase = RNA dep. DNA 

polymerase 

c. dsDNA is integrated into host genome and cannot be 

eliminated 

i. can be productive or latent infection 

d. EX: HIV 

e. Hepatitis B is a unique example of a dsDNA retrovirus 

that uses an RNA intermediate for genome replication 

i. DNA → RNA → DNA 

f. RNA polymerase and ribosomes are productive at 

making more viral particles 

iv. Assembly: 

1. Proteins capsid forms 

a. Sometimes forms inside or buds off and forms outside of 

host 

2. Genome and necessary proteins are packaged 

3. Spikes → viral proteins that will become envelope spikes insert into host plasma membrane 

4. Viral matrix protein coats inside of plasma membrane 

v. Release: 

1. Most enveloped viruses are released via Budding (envelope from host mem. or a few go through the Golgi) 

2. Naked viruses are released when host cell dies, often by 

apoptosis that is initiated by virus or host 

d. Summary chart 

i. Virus: Varicella virus 

1. Genome: dsDNA 

2. How would this virus replicate its genome? 

a. dsDNA → dsDNA 

b. by DNA polymerase 

3. How would this virus express genes and make viral proteins? a. dsDNA → mRNA → proteins 

b. RNA polymerase and ribosomes 

ii. Virus: Parvovirus 

1. Genome: ss(+) DNA 

2. How would this virus replicate its genome? 

a. (+) DNA → dsDNA (+/-) → (+) DNA 

b. DNA polymerase 

3. How would this virus express genes and make viral proteins? a. dsDNA → mRNA → proteins

iii. Virus: smallpox virus 

1. Genome: dsDNA (has DNA polymerase and RNA polymerase 

genes) 

2. How would this virus replicate its genome? 

a. (+) DNA → dsDNA (+/-) → (+) DNA 

b. DNA polymerase 

c. Same as Parvovirus, but viral enzymes 

3. How would this virus express genes and make viral proteins? 

a. mRNA → proteins 

b. Host ribosomes 

iv. Virus: zika virus 

1. Genome: ss(+)RNA 

2. How would this virus replicate its genome? 

a. (+) RNA → (-) RNA → (+) RNA 

b. By replicase 

3. How would this virus express genes and make viral proteins? 

a. (+) RNA serves as mRNA 

b. (+) RNA (mRNA) → proteins, by ribosomes 

v. Virus: measles 

1. Genome: ss(-)RNA 

a. (-) RNA packages replicase 

2. How would this virus replicate its genome? 

a. (-) RNA → (+) RNA → (-) RNA 

b. By replicase 

3. How would this virus express genes and make viral proteins? 

a. (-) RNA → (+) RNA → proteins 

vi. Virus: HIV 

1. Genome: ss(+) RNA, retrovirus 

2. How would this virus replicate its genome? 

a. RNA → dsDNA 

b. by reverse transcriptase 

3. How would this virus express genes and make viral proteins? 

a. DNA → mRNA → proteins 

b. Host RNA polymerase and ribosomes 

G. Virus Evolution 

a. Fast replication/ many progeny 

b. High mutation rate (RNA and retroviruses in particular) 

i. Prone to making mistakes 

c. Reassortment (coinfection) and recombination (with host) 

d. Antigenic drift 

i. mutations in surface protein genes recognized by the host immune system (selective pressure) 

ii. Slow changes that occur in the genes that express these proteins

iii. Seasonal flu vaccine changes 

1. Because influenza virus is always changing 

e. Antigenic shift 

i. re-assortment between different strains or viruses (segmented genome) ii. Completely new virus that immune system is unprepared to deal with because the body hasn’t seen anything like it before 

iii. New subtype; pandemics 

H. Animal Virus Infections 

a. host immune response and cell type can have roles in the type of infection b. Acute infection: 

i. Rapid onset 

ii. Short duration of symptoms 

iii. Virus is cleared 

1. Immune system recognizes and clears this infection 

c. Persistent infections - have the virus for a lifetime 

i. Chronic Infection: 

1. May or may not have obvious symptoms 

2. Infectious virons are produced 

3. Productive 

ii. Latent Infection: 

1. Virus can lay in a latent state and then get reactivated 

a. Can still be changing host even when latent 

b. Is not completely dormant 

2. Genome remains in host cell 

3. Can not be eliminated 

4. Can be reactivated: infectious virons and symptoms reemerge 

5. Can integrate into host chromosome or remain in cytoplasm 

a. Integrated into host = prophage 

6. EX: Herpes Simplex Virus, HSV-1 

a. Initial infection: host shows symptoms, infectious virons 

released 

b. Latent infection: no symptoms, non-infectious 

c. Activation of virus: something triggers virus activation, 

host symptoms, infectious virons released 

d. Some viruses result in both chronic and latent infections 

i. (HIV)-depends on infected cell 

e. Chronic and latent infections are persistent infections 

I. Viruses and Cancer 

a. Tumor = abnormal cell growth 

b. Proto-oncogenes and tumor suppressor are host cells genes that normally work together to stimulate or inhibit cell division, respectively 

c. Viral oncogenes (similar to proto-oncogenes) interfere with host control mechanisms, stimulating cell growth and inducing tumors

d. Cytopathic Effect - Virus causes distinct morphological changes in host cells i. Damage that gets done 

e. EX: Human Papilloma Virus, Hepatitis B and C, Epstein-Barr 

J. Other Infectious Agents 

a. Viroids 

i. Small circular RNAs 

ii. No protein 

iii. So far only found in plants 

iv. Many questions remain: 

1. How do they replicate? 

2. How do they cause disease? 

3. How did they originate? 

4. Do they have counterparts in animals? 

b. Prions 

i. Infectious protein agents 

ii. Slow, fatall human and animal diseases (neural tissue) 

iii. Spongiform Encephalopathies 

iv. Usually species-specific transmission 

v. Some prion diseases are due to genetic or inherited mutations vi. Aggregations of abnormal (prion) form of the protein 

1. Abnormal = Misfolded protein 

2. Abnormal has same genetic sequence as normal protein 

3. Aggregates are insoluble and resistant 

vii. Particularly a problem for neural tissue 

viii. deer spread prion diseases easily 

ix. Do not have to eat the infected brain tissue to get a prion disease 

Chapter 20: Antimicrobial Drugs

A. History and Development

a. Alexander Fleming (1928) observed Staphylococcus aureus died in the presence of a contaminating mold (Penicillium chrysogenum)

b. Ernst Chain and Howard Florey (1941)purified Penicillin G

i. Penicillin G is the natural form of penicillin

c. WWII drove large scale lab production of penicillin

d. Many chemical variants of penicillin have been developed since e. Antibiotic – naturally produced antimicrobial

B. Features of Antimicrobial Action

a. Bacteriostatic: inhibits bacterial growth

i. Patient needs to also rely on body’s defenses

ii. If we keep the amount of bacteria low, the body will have no problem using its own immune system to then kill off the infection

b. Bactericidal: kills bacterial cells

i. Can depend on drug concentration or phase of bacterial growth ii. Often binds target irreversibly

c. Broad Spectrum: targets many bacteria

i. Can affect different classes of bacteria (gram positive vs gram negative) ii. important for acute, life-threatening infections

1. Especially when causative agent is not yet identified

iii. often disrupts normal microbiota

1. Kills some of body’s normal microbiota in addition to the bacteria d. Narrow Spectrum: more specific to a class of bacteria

i. the pathogen needs to be identified

ii. less disruption of normal microbiota

e. Also considered:

i. Tissue distribution, Metabolism, and Excretion 

ii. Drug Combinations 

1. Antagonistic - drugs don’t work together

2. Synergistic - drugs are working together

iii. Adverse Effects to Host: 

1. Suppression of normal microbiota (Dysbiosis)

a. Often with broad-spectrum drugs

b. Opportunistic infections (e.g.Clostridium difficile “C. diff”)

2. Allergic reactions

3. Toxicity:

a. Selective toxicity: harms bacteria, but not host cells

i. Want you want to aim for with antibiotics

b. Therapeutic index: The lowest toxic dose divided by the

dose typically given to the patient

c. High therapeutic index → less toxic to host (more 

selective) 

i. Patient can have a lot of the drug and it will not

harm them

C. Drug Classes to know: (cell target, toxicity, spectrum of activity, bacteriostatic or bactericidal)

a. Β−lactams (esp. Penicillins)

b. Vancomycin (a glycopeptide)

c. Bacitracin

d. Macrolides

e. Chloramphenicol

f. Tetracyclines

g. Aminoglycosides

h. Fluoroquinolones

i. Rifamycins

j. Sulfonamides

k. Daptomycins

l. Polymyxins

D. Mechanism of Action (Targets)

a. Cell wall (peptidoglycan) synthesis

i. β-lactams: Inhibit Penicillin binding proteins (PBP) or the enzymes that form the peptide bridges between the glycan chains of

peptidoglycan

1. PBPs are not exclusive to just penicillins

2. Penicillins, Cephalosporins, etc.

3. High therapeutic index

4. Bactericidal against growing and dividing cells

5. Penicillins: (one class of β-lactams)

a. Natural Penicillins (G and V)

i. Penicillium chrysogenum

ii. Narrow spectrum: Gram + 

b. Semisynthetic Penicillins

i. Sidechains added to create derivatives

c. Why do we make synthetic penicillins?

i. More stable (acid resist. for oral drugs)

ii. More active/less doses needed

iii. Broad-spectrum and Extended-spectrum 

1. Extend spectrum so it can target both gram

pos and neg

iv. Overcome resistance (S. aureus)

6. Acquired Resistance:

a. Gene for β-lactamase-enzyme that breaks the β-lactam

ring (e.g. penicillinase)

b. Mutation in PBP (drug target)

c. MRSA strains have acquired both mechanisms!

ii. Vancomycin (glycopeptide)

1. Binds peptide chains and directly blocks cross-linking

2. “Drug of last resort”

3. Bactericidal against Gram + 

iii. Bacitracin

1. Blocks transport of glycan subunits

a. Prevents subunits from getting outside the cell so the cell

wall can’t be built

2. Bactericidal against Gram + 

3. Some toxicity; topical use

b. Protein Synthesis

i. Macrolides

1. Peptide elongation 

2. Bacteriostatic

3. Mostly gram + and a few Gram -

4. Ex. Erythromycin

5. Usually what’s given to someone who is allergic to penicillin 6. 50S ribosome

ii. Chloramphenicol

1. Peptide bond formation 

2. Bacteriostatic

3. Broad spectrum (can be used against both Gram + and -)

4. Toxic (causes Aplastic Anemia)

5. 50S ribosome

iii. Tetracyclines

1. Block tRNAs 

2. Bacteriostatic

3. Gram – and +

4. High selective toxicity

a. Get a really noticeable yellow color in your teeth with this

5. 30S ribosome

iv. Aminoglycosides

1. Block initiation, Mistranslation 

2. Bactericidal

3. Some toxic side effects

4. Broad-spectrum

a. used synergistically w/ penicillins

5. Ex. Tobramycin, gentamicin, neomycin (topical)

6. 30S ribosome

c. Nucleic Acid Synthesis (transcription and DNA polymerase) i. Fluoroquinolones

1. Synthetic compounds

2. Inhibit DNA gyrase (replication)

3. Bactericidal against Gram –and +

ii. Rifamycins

1. Inhibit RNA pol. (transcription)

2. Bactericidal against Gram negative, positive, and Mycobacterium (TB, leprosy)

3. Resistance develops easily

a. Only takes a point mutation to develop resistance

d. Metabolism

i. Sulfonamides (Sulfa drugs)

1. Synthetic compound

2. Competitive inhibitor of an enzyme in folate biosynthesis

3. Low toxicity

4. Bacteriostatic, Gram + and -

5. Trimethoprim

a. Inhibits another enzyme in the same pathway

ii. Often used together for a synergistic effect (limits acquired resistance) e. Cell Membrane Integrity

i. Bind or insert into the cytoplasmic membrane causing them to leak ii. Daptomycin

1. Bactericidal

2. Gram +

iii. Polymyxins

1. Bactericidal

2. Gram –

3. Toxic (only topical)

E. Testing for Susceptibility (or Resistance)

a. Kerby-Bauer disc diffusion method

i. “Zone of inhibition”

ii. An Estimate: Susceptible? Intermediate? or Resistant?

b. The E Test

i. Modified disk diffusion assay (more quantitative)

1. Strip has concentration of the drug and one end and a low

concentration at the other end

ii. Gradient of drug

iii. Measures Minimum Inhibitory Concentration (MIC)

1. Tells you how little of the drug you can have and still inhibit the

bacteria growth

2. MIC is different for different organisms and strains

iv. Newer methods include molecular techniques (PCR and sequencing) to detect the presence of resistance genes or mutations

F. Drug Resistance

a. Intrinsic (Innate) Resistance:

i. Resistance due to the inherent characteristics of that organism

ii. Ex: Gram-Neg. have an outer membrane

1. Mycobacterium (TB) have waxy cell wall and grow very slowly

b. Acquired Resistance:

i. Developed resistance through mutation or receiving a new gene (HGT) ii. Ex: Only 3% of Staphylococcus aureus strains were originally resistant to penicillin G

1. Now >90% of strains are resistant!!

c. Mechanisms of Acquired Resistance

i. Drug inactivating Enzymes 

1. Ex. β-lactamase cleaves β-lactams

ii. Change the Target- Drug can’t bind

1. Mutation (PBPs, ribosomal proteins)

2. Modification

iii. Decreased Drug Uptake 

1. Ex. Mutation in porin proteins in Gram-NegOM

iv. Increased Elimination of the Drug

1. Efflux Pumps

2. Can have low specificity (lots of drugs and even disinfectants)

3. Express more pumps, faster removal

d. How do Bacteria Acquire Resistance?

i. Mutations (changes in existing genes)

1. Random mistakes during normal cellular processes

a. spontaneous or could be due to induced mutations

2. Spontaneous Mutations happen at a relatively low, but

characteristic rate, but have a HUGE impact on the population

3. Ex.Streptomycin resistance

a. only a point mutation will decrease drug-ribosome binding

b. 1:109 cells will probably have this mutation

4. Effective drug doses is critical!! 

5. Mutation → less sensitive → survives/outcompetes → gains

additional mutations → stronger drug resistance

ii. Gene Transfer (acquire a new gene)

1. Most common:

a. Conjugative transfer of R plasmids

i. resistance plasmids, often encode more than one

resistance gene, can be different species

2. Where did the resistance gene come from to begin with?

a. Accumulation of spontaneous mutations of a common

gene (e.g. the target)

b. Microbes that naturally produce the antibiotic

e. Antimicrobial Resistance - Evolution at work

i. Antimicrobial drug is added; sensitive organisms are killed or inhibited → Resistant survivors can multiply without competition

ii. Human antibiotic use does NOT CAUSE mutations or drug resistance iii. Increased exposure of bacteria to antibiotics provides selective pressure for the rise and spread of resistance mutations/genes

f. Emerging Antimicrobial Resistance

i. Methicillin - Resistant Staphylococcus aureus (MRSA)

1. Most S. aureus strains carry a penicillinase (β-lactamase) gene,

so we use methicillin

2. MRSA encodes altered PBPs –mutated target –methicillin

doesn’t work on these strains

ii. Now VRSA-vancomycin resistant strains as well

1. altered target

G. Anti-Virals

a. Azidothymidine (AZT) – base analog

i. RTase mistakes for AZT for Thymidine (T)

b. Neuraminidase Inhibitors – block viral particle assembly and release c. Viruses also mutate and become resistant to antivirals d. Entry →

i. Entry inhibitors

e. Uncoating →

i. Viral uncoating

f. Nucleic acid synthesis (viral enzyme directed)

i. Nucleic acid synthesis

ii. Integrase inhibitors

1. EX: HIV

g. Viral particle production →

i. Assembly and release

1. EX: influenza viruses

h. Exit

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