Exam 1: Microbiology and Bacteriology Flashcards

Question

Spores

Answer 1

"Endospores" * **Some gram ⊕ only** * Bacillus, Clostridia * **Stress** ⇒ stop vegetative growth ⇒ produce spores (dormant state) * Spores resist drying, heat, radiation, chemicals * Return of good conditions ⇒ spores to vegetative state ⇒ germinate * Sometimes spores are the infectious form * Ex: B. antracis

Answer 2

* For rapid growth * More versatile in energy sources and oxidant use * More diverse nutritional requirements * More diverse biosynthetic pathways * PG, LPS, TA unique to bacteria

Answer 3

asexual binary fission

Answer 4

generation time (Cell # after N generations = Initial # x 2N)

Answer 5

1. Water 2. Carbon 3. Nitrogen 4. Oxygen (some)

Answer 6

* Most pathogenic bacteria need organic carbon ⇒ **heterotrophs** * Must be in a form that can be assimilated * Most common source from sugars * Some can use inorganic carbon like CO₂ ⇒ autotrophs

Answer 7

* Usually supplied by inorganic molecules * **Ammonia (NH₃) and Nitrate (NO₃)** * End-prod. for all paths is ammonia * Can use proteins if they have **exoenzymes** e.g. proteases * **Nitrogen gas** (N₂) can be used by nitrogen-fixing bacteria * Add H to make ammonia

Answer 8

O₂required for most human pathogens. Used as a final electron acceptor in respiration. _Mechanisms for removal of toxic intermediates:_

Answer 9

catabolism ⇒ breakdown anabolism ⇒ synthesis

Answer 10

pyruvic acid

Answer 11

Embden-Myerhof glycolytic pathway & Pentose phosphate pathway

Answer 12

* 1 glucose yields 2 ATP + 2 NADH * End product is pyruvate * Substrate for fermentation or respiration

Answer 13

* Glucose ⇒ pentose phosphate ⇒ G-3-P ⇒ pyruvate * Releases CO2 * Generates NADPH

Answer 14

Pyruvate reduced while NAPH re-oxidized Lowers pH ⇒ growth often inhibited * **Homolactic acid fermentation** * Lactobacilli & strep * **Mixed acid fermentation** * Enteric bacteria * Most make H₂ + CO₂ via formic acid pathway

Answer 15

Cannot make H₂ or CO₂ Negative for gas in "triple sugar iron" test

Answer 16

Anaerobe Ferments sugars ⇒ acetone, isopropanolol, butanol, and butyric acid Ferment proteins ⇒ amines Gases build up in infected wounds ⇒ gas gangrene

Answer 17

Electron transport + Oxidative phosphorylation * Pyruvate ⇒ TCA ⇒ NADH and FADH₂ * Oxygen is usually the final acceptor ⇒ aerobic * Certain bacteria can also use other compounds * Nitrogen ⇒ NO₃ * Sulfides ⇒ SO₄²⁺

Answer 18

* **Chromosome** * Haploid * Circular * Minimal size * Few to no introns * Little to no splicing * **Extrachromosomal elements ⇒ plasmids**

Answer 19

* Short, continguous, linear group of related genes * Grouped into transcriptional units * Controlled by one promoter

Answer 20

Encodes enzymes and structural proteins. E.g. ribosomal proteins

Answer 21

Encode proteins that bind DNA regulatory sites Repressors ⇒ operators

Answer 22

polycistronic mRNAs more than one gene

Answer 23

**DNA sequence capable of replicating itself into a new site in the chromosome by non-homologous recombination.** Catalyzed by "transposase" Encoded by IS.

Answer 24

**Insertional sequences (IS) that flank a structural gene.** Carries the genes with them to new chromosome sites. Typically encodes abx resistance.

Answer 25

Silent, missense, or nonsense. ∆ abx resistence and virulence.

Answer 26

Single base pair or string of bases added or deleted. ∆ surface components ⇒ ∆ virulence Antigenic variation vs phase variation

Answer 27

**Expression of different variants of surface molecules which vary in chemical composition.** Ex. Pilin proteins (S1, S2,...) of *Neisseria gonorrhoeae*

Answer 28

**Presence or absence of surface molecules due to regulated expression.** Ex. Flagella proteins (H1 and H2) of *Salmonellae typhimurium*

Answer 29

* During DNA replication or transcription * In regions w/ contiguous short nucleotide repeats * DNA polymerase stutters or slips * Results in amplification or deletion * Ex. Bordetlla pertussis & Neisseria gonorroeae * Mispairing in promoters of several genes ∆ or eliminates expression of pili

Answer 30

**Reversible, genotypic adaptations** that occur at relatively high rates (10^-3), Occurs through **site-specific recombination**. Examples: E. coli type I fimbriae Salmonella expression of hagA or hagB, encodes flagellin proteins, controlled by recombinational inversion of a promotor.

Answer 31

* **Circular supercoiled DS-DNA** * **Self-replicating extrachromosomal DNA** * Large plasmids replicate like host chromosomes * Usually a single or few copies * Small plasmids replicate independently * One or more copies per cell * **May insert into chromosome (episome)** * Introduces novel enzymes and pathways

Answer 32

Have _tra_ genes which encode transfer enzyme and sex pili.

Answer 33

Lack _tra_ genes. Can be transferred by other mechanisms (Like tagging along behind a conjugative plasmid)

Answer 34

**Transmission of multiple abx resistance:** **RTF** (resistance transfer factor) ⇒ conjugative plasmid + **R determinants** ⇒ transposons carrying abx resistance genes

Answer 35

Ex: * Toxin and fibriae of enterotoxigenic E. coli (ETEC) * Toxins of Staphyloccous, Bacillus anthracis, and Clostridium tetani * "Invasion" genes of Yersinia an dShigella * Iron siderophores of E. coli

Answer 36

* **Bacterial viruses** * Specific for different bacteria * Structure: * Capsid ⇒ protein subunits * Icosahedral, helical, or combo * Genome * DNA or RNA * SS or DS * Linear or circular * 3,000-10⁵ BP * Can be lytic or lysogenic

Answer 37

* Rapid replication * 20 minutes from infection to bacterial lysis

Answer 38

Slower replication: * **Integration** * Infection * Lytic pathway repressed * DNA integrates into host chromosomes * Replicates along with bacteria * **Induction** * Adverse conditions ⇒ induction (de-repression) of lytic genes * DNA excised * Enters lytic cycle * **Lytic cycle** * Rapid replication * Cell lysis

Answer 39

Can transfer genes between bacteria: * Salmonella ⇒ mod. of surface Ag * Corynebacterium diphtheriae ⇒ encodes endotoxin * EHEC (Enterohemorrhagic E. coli) ⇒ encodes exotoxin * Clostridium botulinum ⇒ encodes exotoxin * Staphylococcus ⇒ abx resistance, toxins * S. aureus phage typing ⇒ lysogenic strains immune to infection by related phage * Pattern of immunity with phage panel provides a typing system

Answer 40

homologous recombination

Answer 41

**Free donor DNA taken up by recipient bacterium.** * Derived from lysed cells or free plasmids * Occurs naturally in vivo * **Depends on competence of recipient** * Ability to take up DNA and be transformed * Varies for different bacterium and growth conditions * S. pneumoniae & Neisseria gonorrhoeae naturally competent * E. coli can be made competent

Answer 42

**Donor DNA from bacteriophage DNA** (Transformation and infection) Can carry along bacterial genes within viral genome

Answer 43

**Donor DNA carried to recipient within bacteriophage capsid.** * Packaged DNA contains random fragments ⇒ **generalized transduction** * Packaged DNA contains specific sequences located adjacent to lysogenic phage site ⇒ **specialized transduction**

Answer 44

**Transfer of DNA via conjugative (F or R) plasmid.** * **Tra genes** * Encode sex pilus & special replication enzymes * **Sex pilus** * Mediates contact * Cells drawn together & fuse at one point * Donor DNA passed through * **Rolling circle DNA replication**

Answer 45

* Rarely cause disease in healthy hosts * Regularly cause disease in compromised hosts * **Normal flora** * Staphylococcus epidermis * Post-surgical * Catheter-related * E. Coli * **Environmental organisms** * Pseudomonas aeruginosa * Burn victims * CF patients

Answer 46

Rarely associated with host except for in the case of disease

Answer 47

**Traits that promote colonization and survival of infecting bacteria:** * _Structural_ * Capsule * LPS * Pili * _Biochemical_ * Exotoxins * Proteases * Siderophores * _Genetic_ * Variation of surface Ag

Answer 48

Hemolysins / Cytotoxins

Answer 49

Fibrinolysin Hyaluronidase Collagenase

Answer 50

IgA proteases (important with mucosal pathogens)

Answer 51

virulence factors

Answer 52

* Adherence * Invasion * Growth byproducts (gas, acid) * Toxins * Degradative enzymes * Endotoxin * Superantigen * Induction of excess inflammation * Evasion of phagocytic and immune clearance * Capsule * Abx resistance * Intracellular growth

Answer 53

pathogenicity islands (May require coordinated expression)

Answer 54

How to show an organism causes a particular disease: 1. Must be **present in every case** of the disease 2. Must be **isolated from host and grown** in lab dish 3. **Disease must be reproduced** when pure culture of agent inoculated into healthy susceptible host 4. Same agent must be **recovered again from experimentally infected host**

Answer 55

How to show that a particular virulence factor is involved in a specific disease: 1. Trait associated more often with pathogenic strains than non-pathogenic ones 2. Inactivation of gene(s) associated with trait decreases or eliminates virulence 3. Virulence restored when mutated gene replaced with wild-type gene

Answer 56

* Pathogenicity (virulence) of pathogen * Immune & nutritional state of host * Route of entry * Number of bacteria

Answer 57

1. Encounter 2. Entry 3. Colonization 4. Multiplication 5. Invasion/Dissemination

Answer 58

* **Human-to-human** * Fecal-oral * Respiratory or salivary * Venereal * **Animal-to-animal** ⇒ zoonoses * Vector ⇒ biting arthropod (mosquitos, ticks) * Vertebrate reservoir * Vector-vertebrate reservoir

Answer 59

Exit and entry of organisms from: * **Mucosal surfaces** * Respiratory tract * Urinary tract * Genital tract * GI tract * Conjunctiva * **Skin** * Trauma * Surgery * Eczema * Others

Answer 60

natural defense mechanisms & barriers

Answer 61

1. **Site** 2. **Dose** * Each organism has a threshold number required to cause disease 3. **Route** * Some cause disease only when entering at certain sites * Some cause different diseases at different sites

Answer 62

**Establishment of a pathogen at its portal of entry.** * Most often receptor mediated * Colonization of sterile site implies defect in natural defense mech. or new portal of entry * Use specific mech. to adhere to and colonize different body surface

Answer 63

* Mediated by **adhesins** * e.g. pili or surface proteins * Binds to specific carbs or protein receptors on surface of host cell * Can be **host-specific** or **tissue specific**

Answer 64

**Mediated by carbohydrate or lipid adhesins** * Ex. * Alginate capsule of Pseudomonas aeruginosa * Promotes adherence in lungs of CF patients * Polysacc. slime of Strep. epidermis * Promotes biofilm formation

Answer 65

* Invades host cells * Often mediated by **invasins** * Protein that recognizes host **integrins** * Protected from immune response * Ready supply of nutrients * More likely to disseminate throughout obdy

Answer 66

Ability of baceria to **respond as a community** by _sensing and communicating_ with each other when density reaches a threshold. * Via small secreted metabolites * When bacteria sense a quorum has developed, they can respond in many ways: * Express virulence factors * Become resistant to abx * Forming a biofilm

Answer 67

**Organized communities of sessile bacteria.** * Sessile ⇒ anchored cells attached to a surface * Planktonic ⇒ free-living cells * Biofilms have complex physical and metabolic structure * More resistant than planktonic bacteria to: * Abx * Serum abx-complement mediated killng * phagocytosis * Issue for indwelling catheters

Answer 68

**"Lipopolysaccharide (LPS)"** * On outer leaflet of outer membrane of gram ⊖ bacteria * LPS ↔︎ LPS-binding protein (LBP) * **LPS-LBP complex** ↔︎ **CD14 receptors** on _monocytes, macrophages, endothelial cells_ * **LPS-CD14 ↔︎ Toll-like receptor 4 (TLR4)** * Cell activation ⇒ **cytokine production & release** * **Acts on complement, fibrinolytic, coagulation, temp regulation, and circulatory systems**

Answer 69

**Acts on complement, fibrinolytic, coagulation, temp regulation, and circulatory systems:** * **Fever** * Hypoglycemia * Enhanced glycolysis * Triggers release of vasoactive substances * Serotonin, Kallikrein, Kinins * **Hypotension and shock** * Activate C3 & complement cascade via **alternative pathway** * **Impaired perfusion of organs** * Accumulation of organic acids and metabolic acidosis * **Disseminated intravascular coagulation (DIC)** * Activation of factor XII (Hageman factor) * Intrinsic coagulation cascade * Activation of plasminogen * Inc. platelet adherence to endothelium * Occlusion of small vessels * **Death**

Answer 70

* Both gram ⊕ and gram ⊖ * **Generally secreted or surface proteins** * Several broad classes, most notably: * **Pore-forming toxins** * Form lethal holes in host cell membranes * **Enzymatic toxins** * Gain entry into host cells and alter intracellular signaling or other cell processes * Leads to pathology and cell death * Targets limited and well defined * Ribosomes * Transport mechanisms * Intracellular signaling (cAMP, GPCR)

Answer 71

Most exotoxins are **dimeric** (A-B) toxins: * **B portion ⇒ binding** * Binds to specific cell surface receptors * **A portion ⇒ action** * Transferred into cell interior * Acts to promote cell injury

Answer 72

* **Corynebacterium diptheriae ⇒ diptheria toxin / Pseudomonas aeruginosa ⇒ exotoxin A** * one A subunit, one B subunit * ADP-ribosylase ⇒ transfer ADP-ribose from NAD to target protein elongation factor EF2 ⇒ inhibits protein synthesis * **Vibrio cholerae ⇒ cholera toxin** * one A subunit, five B subunits * ADP-ribosylase ⇒ activates adenylate cyclase ⇒ overproduction of cAMP * **Bacillus anthracis ⇒ anthrax toxin** * one B subunit (Protective Antigen, PA) + different A subunits with distinct enzyme activities * One A subunit ⇒ Edema factor ⇒ calmodulin-dependent adenylate cyclase

Answer 73

* **Genetics** * Encoded on bacterial chromosome, plasmids, or lysogenic bacteriophage * **Regulation** * Expression governed by environmental conditions * pH, temperature, ionic concentrations (Fe²⁺, Ca²⁺) * Toxin may not be produced under normal environmental niche under normal conditions * **Under stress, toxin produced in attempt to enhance survival**

Answer 74

* Activates CD⁴⁺ T-cells * **Binds simultaneously to TCR & MHC II on APCs without Ag** * Not Ag specific * Occurs outside of the MHC & TCR binding domains * Results in polyclonal T-cell activation ⇒ cytokine storm * IL-1, TNF, IL-6, IFN, IL-2, and other cytokines * Causes life-threatening autoimmune-like responses * Examples: * *Staphylococcus auresus* ⇒ Toxic shock syndrome toxin (TSST-1) * *Staphylococcus* ⇒ enterotoxins * *Streptococcus pyogens* ⇒ pyrogenic toxins

Answer 75

* **All pathogens, except Strep, require iron for growth** * Almost no free iron in human body * Bound by transferrin, lactoferrin, Hb, etc * Developed ways to get iron from hosts * **Siderophores** * **Lactoferrin or transferrin binding proteins**

Answer 76

_Small soluble molecules_ that **bind free iron or take iron from transferrin and/or lactoferrin** and bring it back to the organism.

Answer 77

Allows bacterial to bind to and acquire iron directly from iron-preloaded host molecules.

Answer 78

* **Found in Strep and Staph** * **Degrades hyaluronic acid** ⇒ carbon source * Speculated to act as virulence factor that destroys polysaccharide that holds animal cells together ⇒ aids local dissemination

Answer 79

* **Found in Clostridium perfringens** * **Breaks peptide bonds in collagen** * Assist in destroying ECM structures ⇒ aids dissemination

Answer 80

* Found in Shigella dysenteriae * **Cleaves glycosidic linkages of neuraminic acids** * Functions to cleave a sialic acid residue off glanglioside GM1 ⇒ **asialo-GM1** * **Can preferentially bind type 4 pili**

Answer 81

* Found in many bacteria * Phospholipase that acts on lecithin

Answer 82

* Collection of microorganisms found in normal healthy individuals * Inhibits the establishment of pathogens * Provides host with vitamins * Can become pathogenic: * In immunosuppressed or immunocompromised individuals * Removed from usual anatomic niche * Ex. E. coli and Strep. faecalis * Normal in GI * Pathogenic in GU

Answer 83

* Generally circular * One origin for bidirectional replication * One terminus halfway around chromosome

Answer 84

DNA Polymerase I, II & III

Answer 85

DNA Polymerase δ, α & ε

Answer 86

DNA topoisomerases & DNA gyrases

Answer 87

1. **Helicase** unwinds DNA double helix ⇒ melting 2. **DNA gyrase** nicks and seals DNA strands as meling occurs * Allows DNA to spin & prevents supercoiling 3. **DNA binding proteins** coats strands to prevent reassociation 4. **Primase** places RNA primer 5. **DNA polymerase III** replicates DNA starting at the 3'-OH primer * Leading strand continuous * Lagging strand in Okazaki fragments 6. Gaps on lagging strand closed by **DNA polymerase I** * Exonuclease activity excises RNA * Polymerase activity replaces RNA with DNA 7. **DNA ligase** joins sections

Answer 88

* DNA Pol III ⇒ 800 nuc/sec * E. coli has 4 million BP w/ 1 origin of replication * Would take 40 minutes for replication ⇒ too slow by factor of 2 * Able to replicate faster because a new round of DNA replication started before cell division complete

Answer 89

abx large number of proteins involved

Answer 90

Bacterial have **only one RNA polymerase** for all classes of genes (mRNA, rRNA, tRNA) * 4-5 subunits * two identical α * one β * one β' * one σ ⇒ for initiation

Answer 91

* Occurs 5' ⇒ 3' * **Promoters** * Conserved sequences at -10 and -35 upstream * Binds RNA polymerase * Sigma factor lost when transcription begins * **Termination** * "Hairpin" secondary structures followed by string of U's * RNA may be **processed by endonucleases and exonucleases** * No 5' cap, 3' poly-A tail, or splicing

Answer 92

* **70S Ribosomes** * **30S** ⇒ small subunit * 16S ribosomal RNA * **50s** ⇒ large subunit * 23S and 5S ribosomal RNA * 20-30 ribosomal proteins

Answer 93

Amino-acylated tRNA: * Adapter RNA molecules * AA linked to 3' terminal base of tRNA * Catalyzed by amino acyl-tRNA synthetase

Answer 94

polycistronic shorter ⇒ degraded in minutes

Answer 95

* 20 AA * Triplet codons * Degenerate * 3 stop codons * AUG start codon ⇒ methionine

Answer 96

* Occurs at **1 or more internal AUGs** within mRNA ⇒ polycistronic * **Shine-Dalgarno sequence** pairs with 16S ribosomal RNA * Starts with **formylmethionine (fMET)** * First, **30S initation complex forms** * mRNA +fMET-tRNA + 30S subunit * Also GTP + Initiation factors IF 1, 2, and 3 * Then, **70S initiation complex forms** * 30S complex + 50S subunit * GTP ⇒ GDP * fMET-tRNA now in P (peptidyl) site of 50S subunit

Answer 97

* Second paired amino acyl-tRNA bind to **A (aminoacyl) site** on 50S subunit * Delivered by elongation factor **EF-Tu** * GTP ⇒ GDP * **Peptidyl transferase** activity of 50S subunit catalyzes peptide bond formation * **Translocation occurs** * Peptidyl-tRNA moves from A ⇒ P site * Elongation factor **EF-G** involved * GTP ⇒ GDP * Process repeats

Answer 98

* **Release factor** required * Final peptidyl-tRNA bond hydrolyzed * 70S sibosome dissociates