11:680:390 GENERAL MICROBIOLOGY Midterm

Archae vs bacteria

Archae vs bacteria

Bacteria have cell walls containing peptidoglycan, while archaea lack peptidoglycan and may have different cell wall structures like protein-based layers or polysaccharides

Prokary

-cells are smaller and simpler
-cells have DNA, but not inside a nucleus
-no organelles
-single-celled
- most are 0.5 to 10 micrometers long

Eukarya

-cells are larger and more complex
-DNA enclosed in a membrane-bound nucleus
-mitochondria and chloroplasts
-can be unicellular or multicellular
-typically 5 to 100 micrometers long
examples: plants, animals, algae, protozoa, fungi

Structures they have in common

Cell membrane
DNA genome
Ribosomes
Cytoplasm

Gram+

Teichoic acid+lipotechoic acid
Thick PG layer (90%)

Gram-

LPS layer (lipopolysaccharide) : Lipid A (Anchors), and porins
Thin PG layer (10%)
ONLY gram negative have endotoxins
Exotoxins also exist- secreted into the environment.

Gram+ and Gram- medical significance

-Gram-positive and gram-negative Bacteria vary in their sensitivity to antibiotics
Gram - are more resistant to antibiotics due to their diff membrane.

Archael cell membrane

Phytanyl w/isoprene
Ether linkages
Mono or bilayer

Bacteria cell membrane

Fatty acid tail
Ester linkages
Bilayer

Cell Surface Structures: Capsules and Slime Layers

capsule: if tightly attached, tight matrix; visible if treated with India ink.
Are a virulence factor and keeps cell from drying out. - If an organism has a capsule itll be less likely to be seen by the immune system. Allows it to multiply.

Slime layer: -sticky polysaccharide coat outside cell envelope. Provides additional protection. Environmental isolates usually have slime layers.

Pili

thin filamentous protein structures

▪ Enable organisms to stick to surfaces or form pellicles (thin sheets of cells on a liquid surface) or biofilms

Fimbriae

short pili mediating attachment
▪ Produced by all gram-negatives and many gram-positives

Flagella/archaella

structure that assists in swimming in Bacteria and Archaea, respectively (tiny rotating machines)

Chemo/phototaxis

Cell movement that occurs in response to chemical/light stimulus

Virulence factors

traits of a microbe that promote pathogenicity. Eg: Capsules, Fimbriae, Pili, and Hami (hami are in archaea)

Pathogenicity

Ability to cause disease

Virulence

Severity of disease

Fungal spores

Reproduction

Endospores

Structure for survival during unfavorable conditions
-found in some gram +
-Dormant

Virus

- obligate parasites that only replicate within host cell
- not cells- do not carry out metabolism; take over infected cells to replicate
- have small genomes of double-stranded or single-stranded D N A or R N A
- classified based on structure, genome composition, and host specificity (e.g., bacteriophages)

Steps of replication

Attachment*
Penetration
Synthesis
Assembly
Release

bacteriophages vs animal viruses

Bacteriophage
Attachment: Cell wall
Entry: Genetic material
Synth/assembly location: Cytoplasm
Release: Lysis or lysogeny

Animal Virus
Cell membrane
Endocytosis;fusion (injects material after attach
nucleas; golgi; cytoplasm
budding; exocytosis; lysis

Lysogenic

Viral DNA integrates with host DNA to be replicated (occurs during low host cell quantity)

Lytic

After synthesis and virions are assembled, lysis of host cell releases new phage virions

Different types of pathways

Latent infection-virus present but not replicating
Persistent infection- slow release w/out death
Lysis- death of cell
Transformation- tumor division

Viral enzymes

Lysozyme to break B1-3 bond in cell wall bacteriophages only
Neuraminidase—Detach from cell wall
RNA replicase—RNA template dependent; RNA polymerase
RNA transcriptase—RNA dependendent; DNA polymerase

Size of viruses

Smaller than prokarya and eukarya, typically range from about 20 nanometers to several hundred nanometers in diameter

Enveloped vs non-enveloped

Both have a nucleocapsid (Nucleic acid and a capid made of capsomeres)
Enveloped has glycoproteins and an envelope

Baltimore Classifications/diversity

Class I and VII- dsDNA(+); Transcription of - strand
Class II- ssDNA(+); synth of - strand
Class III- dsRNA(+); transcription of - strand
Class IV- ssRNA(+); used as mRNA replicase
Class V- ssRNA (-); transcription of - strand
Class VI- ssRNA(+); reverse transcription->dsDNA intermed→trans of - strand

Antigenic shift vs Antigenic drift

Shift
Viral surface proteins change completely (abrupt&major)

Drift
Surface proteins change slightly (seasonal)

Segmented genome

those that are divided into two or more physically separate. molecules of nucleic acid, all of which are then packaged into a single virus particle.

permits reassortment

Hemagglutinin + neuraminidase

Surface proteins used to categorize into subtypes (ex: H18N11)

Reassortment

Segmented genome recombination, also known as reassortment, is a process where viruses with segmented genomes exchange genetic material and create new viruses

Energy source

Photo
chemo

E- donor

Organic (organo)- CH4 or more
Inorganic (litho)- H, Fe, nitrite

Carbon source

CO2 - autotroph
Organic compound- heterotroph

Oxidation-reduction

The bigger the difference in reduction potential, the better the couple and better ATP output
Reduction potential - affinity for e-

Fermentation, anaerobic, aerobic respiration

Glucose → Glycolysis(NAD+ to NADH) → Pyruvate →
Fermentation: Anoxic conditions, no synthesis of ATP, recycle NADH back to NAD+

Aerobic respiration: Oxic conditions, ETC—> plasma membrane, oxidative phosphorylation, NADH→NAD+ —> ATP 36(eukary)-38(prokary)

ANaerobic respiration: Anoxic conditions, uses other molecules instead of O2 as e- acceptor, Only prokary

Fermentation differs by location (cytoplasm), contains byproducts (acid, co2, alc), and its e- acceptor is organic., no ATP!!

Principles of Respiration

e- transfer from reduced e- donors to external e- acceptors.
Cycle is reoxidized during ETC
Cytopolasmic membrane
electrochemical gradient

Principles of Fermentation

Diverse: sugars, AA’s, FA’s, purines, pyrimidines, aromatics
Acetate and other volatile FA’s are products
Allow additional synthesis from sub-level phosphorylation

Microbial growth context

It’s an increase in the # of cells, not the size
Generation time is the time it takes for the cell to split

Binary fission = two identical daughter cells
Budding = one is a lil smaller

Growth factors

Temp: pyschrophile (low temps)/pyschotroph, mesophile (moderate 39c), thermophile (heat, 60c), hyperthermophile

pH: acidophile <5, neutrophile 5-9, alkaphile >9

Water actvity: Osmophile (high in sugar), xerophile (dry envr)

growth vs O2 conc: measures growth in oxic vs anoxic zones
obligate aerobe
obligate anaerobe
Facultative aerobe - tolerates anoxic but likes O2
microaerophile- subatmospheric lvls O2
aerotolerant anaerobic - fermentative

Growth curve

Lag, log/exponential, stationary, death/decline

Direct and indirect control growth

Direct= counting cells, microscopy
Indirect= a chemical constituent or an enzyme, metabolite, or a change produced by microorganisms during growth is measured.

Biofilms

Planktonic growth- suspension of free floating cells
Sessile growth: Attached to the surface and develop into biofilms

microbial mats: multilayered sheets with different orgs in each layer

(1) protection from harmful conditions in the host (defense), (2) sequestration to a nutrient-rich area (colonization), (3) utilization of cooperative benefits (community)

Found on medical devices, cavities, corrosion

Antibiotics

- antibiotics need to exhibit selective toxicity
• Antibiotics are classified by their mechanism of action, as each group targets different parts of bacterial anatomy or physiology
- Gram-positive and gram-negative Bacteria vary in their sensitivity to antibiotics

Broad spectrum is effective against both gram+ and gram-
Targets: Cell wall, folic acid, DNA synthesis, membrane, protein synth

Antibacterial drugs

• Protein synthesis as a drug target- Most of the antibiotics targeting protein synthesis will target translation by binding to the bacterial ribosome
▪ Aminoglycosides, tetracyclines, and macrolide antibiotics
- Aminoglycosides: Neomycin, tobramycin
- Tetracyclines: Tetracycline, Doxycycline
- Macrolide: Erythromycin, Azithromycin

• Nucleic acid synthesis as a drug target
- Quinolones are antibacterial compounds that interfere with D N A gyrase (e.g., ciprofloxacin)
▪ Preventing the supercoiling and packaging of D N A in the bacterial cell
• RNA polymerase inhibitor- Rifampin

• Growth factor analogs are structurally similar to growth factors but do not function in the cell- Analogs similar to vitamins, amino acids, and other compounds
- Sulfa drugs: Discovered by Gerhard Domagk in the 1930s
• Isoniazid is a growth analog effective only against Mycobacterium
- Interferes with synthesis of mycolic acid• Daptomycin
- Used to treat gram-positive bacterial infections- Forms pores in cytoplasmic membrane• Platensimycin
- New structural class of antibiotic
- Broad-spectrum; effective against M R S A and vancomycin-resistant enterococci

Antimicrobial resistance

Acquired ability of a microorganism to resist effects of chemotherapeutic agents
-modified cell wall, membrane, new target, efflux pumps, enzymes

Antivirals

Most antiviral drugs also target host structures, resulting in toxicity

Most successful and commonly used antivirals are the nucleoside analogs
▪ block reverse transcriptase and production of viral D N A
- also called nucleoside reverse transcriptase inhibitors (N R T I s)
- Non-nucleoside reverse transcriptase inhibitors (N N R T I s) bind directly to R T and inhibit reverse transcription
- Protease inhibitors
- Fusion inhibitors
- Neuraminidase inhibitors (e.g., Tamiflu)
- Interferons

Antifungal

• Drugs that target eukaryotic pathogens
- Fungi pose special problems for chemotherapy because they are eukaryotic
▪ Why? Because fungi are also eukaryotes so they're very similar to us.
- Ergosterol inhibitors
- Chitin biosynthesis
- Folate biosynthesis,
- Disrupt microtubule aggregation

Controlling microbial growth

Physical:
sterile- eliminate all microorganisms
Aseptic- prevents contamination

Pasteruization- shorter time and temp
Autoclave- 15 mins, 15psi, 121 celc

Chemical
Sterilants: chems that sterilize
disinfectants: non-living surfaces (bleach)
sanitizers: basical cleaning
Antiseptics: living surfaces
usually target membrane or cell wall

Bacteriostatic

inhibit important biochem processes

Bacteriocidal

bind tightly and kill w/o lysis

Bacteriolytic

kill by lysis

Minimum inhbition concentration

measure zone of inhibition and compare to table

Structure and function of DNA, RNA and comparison

Pentose sugar, N-base, phosphate

Transcribed and then translate

DNA
- Deoxy = no oxy on the 2nd position
- Double strand (much more stable)
- positive Supercoil to protect itself

RNA
-single-stranded (FUCKKKKK)

Types of RNA

mRNA- synth during transcription; messengers; linear-short lives; template for translation to make proteins
tRNA- transfer RNA; folded up to prevent degradation; deliver AAs to ribosomes
rRNA- ribosomal RNA; folded; helps ribosomes bind to mRNA

Structure and function of an operon

An operon is a cluster of genes under the control of a single promoter that are transcribed together as one mRNA strand. Operons typically include multiple structural genes that encode proteins with related functions, allowing bacteria to coordinate the expression of these genes in response to environmental changes. Key components include the promoter (binding site for RNA polymerase), operator (regulatory region to which a repressor can bind), and structural genes. The lac operon, for example, regulates lactose metabolism in E. coli, demonstrating how operons can efficiently manage metabolic pathways.

Mutations and examples

Point mutation- affect protein structure:

Silent- change codon seq, but not encoded amino

missense- lys-Trp, changes codon for one AA into codon for another

Nonsense- converts a sense codon to nonsense ( such as stop codon)

frameshift- insertion or deletion of base pairs in coding region

Genetic variation
Spontaneous- arise w/o exposure to external agents, insert or delete of nucleo

induced-caused by DNA modifying agents, alter a base

Replication 

OriC where replication starts
semi conser- one daughter one template
5-3 synth
leading and lagging

primase - rna primers

DNA poly (3 and 1)- build and proofread DNA; 1 fills the gaps

helicase and gyrase unwinde and release tension

DNA ligase joins together

Transcription and Translation

RNA from DNA template
-need rna polymerase but no primer, multiple subunits and doesnt require helicase

the process by which cells use messenger RNA (mRNA) to create proteins

Metabolic regulation (details on lac operon), differences between repressible and inducible operons

The lac operon in E. coli is an inducible operon that regulates lactose metabolism. When lactose is present, it disables the repressor protein and activates genes for lactose utilization (lacZ, lacY, lacA). Repressible operons, like the trp operon, are normally 'on' and can be turned 'off' by a product (tryptophan) activating a repressor. Inducible operons are typically 'off' and activated by substrates, allowing bacteria to efficiently manage metabolic pathways based on nutrient availability.

Genetic recombination

Genetic recombination is the exchange of genetic material between organisms or within the same organism, enhancing genetic diversity. In eukaryotes, it occurs during meiosis through crossing over, while in prokaryotes, it takes place via transformation, transduction, and conjugation. This process is essential for evolution and can influence traits like antibiotic resistance.