Microbiology Unit 2 Review

Chapters 27, 7, 8, and 12

Biochemical oxygen demand (BOD)

A metric used to evaluate or gauge metabolic activity. Microbial oxygen consumption creates a biochemical oxygen demand.

The amount of O2 removed from the environment by aerobic respiration and a way to see how active microbes are at breaking down material.

More organic matter concentration means more oxygen consumption and therefore…

a higher BOD

Less organis matter means less oxygen consumption, therefore…

a lower BOD

Eutrophication

results in high levels of aerobic, bacterial decomposition of organic matter

Occurs from an influx of excess nutrients that trigger hypoxic zones in water

What is the purpose of wastewater treatment plants?

Produce a clear, outgoing stream, possessing minimal levels of organic solutes

Wastewater treatment

decreases the BOD and the level of human pathogens before water is returned to local rivers

Wastewater treatment is made up of

Preliminary, primary, secondary, and tertiary (advanced) treatment

Preliminary treatment

removes solid debris

Primary treatment

uses fine screens and sedimentation tanks in order to remove small debris and insoluble particles EX: sediments

Secondary treatment

microbial decomposition of organic content

Tertiary (advanced) treatment

chlorination or other chemical application to eliminate pathogens

Clarification

goal is to knock down high BOD along with the removing organic matter that’s causing the high BOD → the organic matter removed is recycled into activated sludge which is then used to help lower high BOD

Activated sludge

a process for treating wastewater using air and a biological floc composed of bacteria and protozoa

Healthy sludge

a brown floc, largely composed of saprotrophic bacteria

saprotrophic

feed on decayed matter

Flocculation

promoting growth of filliamented organisms in the wastewater which will then create a mesh network and produce substances that will allow the particles in the wastewater to settle

Floc formation is

critical in promoting settling of bacteria and associated microbes from the treatment process

Denitrification

The conversation of nitrate (NO3-) to N2

Ammonia/ammonium ion (NH3/NH4+) would be the end product of which processes?

nitrogen fixation and ammonification

Nitrogen cycles cannot exist without

prokaryotes

Nitrogen fixation

brings back the nitrogen lost from denitrification and turns it into ammonia

Ammonification

decomposing plants and animals turn into ammonia which is then inserted into nitrification

Lithotrophy/nitrification (assimilation)

ammonia is turned into nitrates

Denitrification (dissimilation)

Results in N2 which is released into the air

Artificial nitrogen fixation is accomplished by why?

Haber process

Haber procecss

• generates fertilizers for agriculture

• how you fix nin ammonia artificially

• uses high pressure and catalysts. very energy consuming

N2 → NH3 → NH4+

Nitrogen fixation

What is used to catalyze nitrogen fixation?

nitrogenase

What is responsible for nitrogen fixation in certain cyanobacteria?

heterocysts

heterocysts

strictly used for nitrogen fixation

compartmentalizes N2 fixation in cyanobacteria in oceans and freshwater

NH₄⁺ → NO₂^- → NO₃^-

Nitrification/lithotrophy

Nitrification

Ammonia or reduced nitrogen is transformed into oxidized nitrogen/nitrate which plants will then be able to use for growth

NO₃^- → NO₂^- → NO → N₂O → N₂

Denitrification

Denitrification

• represents anaerobic respiration

• leads to loss of nitrogen

• reducing nitrogen

Sterilization

removal/destruction of ALL living microbes and spores and viruses

Disinfection

Killing of vegetative pathogens on a surface (inanimate object); usually with chemicals

Antisepsis

reduction of pathogens from living tissues (sepsis/asepsis)

Degerming

removal of transient microbes from skin by mechanical cleansing or by an antiseptic. Think washing your hands. Difference from antisepsis is that it’s meant to reduce the # of microbes temporarily rather than completely removing them or preventing infection.

Sanitation

related to hygienic practices; reduction in overall total microbial numbers to safe levels in places

total cell count

how many total cells there are, dead or alive

Viable cell count

the cell count of the sample that are alive

Bacteriostatic

growth inhibitory; no killing of cells. The addition of a treatment that prevents growth, not killing them. Key: STATIC

Bacteriocidal

Killing of cells. ONly viable cell count decreases because the cell body is still there

Bacteriolytic

killing of cells but also causes cells to lyse or break apart. Both total and viable cell count decreases because the cell is destroyed

D-value

time for an agent to kill 90% or one log of the population

Use-dilution test

• Metals rings are dipped in test bacteria and then dried → The dried rings/culture are placed in disinfectant for a time at a specific temp (10 min @ 20ºC) → Rings are transferred to culture media to determine whether bacteria survived treatment (incubate 24 hr, check for growth)

Disk diffusion method

• Filter disks soaked in chemical agent are placed on plate inoculated w/ bacteria. Analyze zones of inhibition → proportional to effectiveness of disinfection

• is the area under and around the filter disks growing bacteria or not?

Agents can target one or a combination of what parts

Plasma membrane - dissolved

proteins - denaturing or break down of protein to reduce or eliminate functionality

nucleic acids - break down, denature, or chemical alteration

Standard conditions of an autoclave

15 psi/121ºC at 15 min

It’s a sterilization method which kills endospores

High temp & pressure as physical agents of control

• Boiling: 10 min @ 100ºC

• Steam under pressure

• Autoclave

Dry heat sterilization

incineration or hot air

sterilizes at 170ºC for 2 hr

Pasteurization

mild heat and used for food/beverages

Cold temperatures

slows down microbial growth

Filtration

used for aqueous solutions & air

Irridation

used to sterilize food & non-biologicals. uses the wavelengths of light. The shorter the wavelengths the higher the energy and lower wavelengths have lower energy

Two different types:

Ionizing and Non-ionizing r

Non-ionizing radiation

UV rays. Best for surface disinfection because it does not penetrate well

Ionizing radiation

X, rays, gamma rays, electron beams

Ionizes water to release OH, penetrating radiation and can break and fragment nucleic acids

Phenolic

An example of chemical control.

Disrupts lipids of plasma membrane and denatures proteins. Can remain active on surface after application

Halogen

Another example of chemical control

alters protein synthesis and membranes

Alcohols

require water; denature proteins and dissolve lipids

Heavy metals

can denature proteins and can be toxic at high levels so often used at low concentrations

Surface active agents (surfactants)

mimic phospholipid structure and disrupt plasma membrane integrity

Chemical preservatives

control molds/bacteria in foods/cosmetics

Gaseous Sterilants

denature and modify proteins. Usually for heat sensitive materials such as plastics

Resistance when it comes to disinfection

Concentration of disinfectant is key

When is resistance to disinfectants more likely

At lower concentrations

Why is resistance more likely at lower concentrations of disinfectant

They are more likely to affect single targets compared to higher concentration which have multiple targets. This makes it easier to counteract the effects because there’s a less mutations needed to become resistant.

Why is resistance harder at higher concentrations of disinfectants?

Disinfectants have multiple targets at the proper concentration. This makes it more difficult to gain a resistance because it’s difficult to evolve multiple mutations to counteract all effects

What are the two aspects of microbial genetics

Genotype and phenotype

Genotype

genes inherited

Phenotype

expression of genes inherited

Microbial phenotype or observable traits are determined by what?

The function of proteins encoded by the genotype (genetic makeup)

The relationship between genotype and phenotype

Genotypes contain the genetic material that make up genes which code for proteins. These proteins make up the phenotypes that are expressed.

Genotypes hold the formula for the proteins needed for phenotypes to be expressed.

Flow of information

DNA → RNA → protein

Central dogma

theory that explains how genetic information flows from DNA to RNA to proteins

Characteristics of prokaryote genome

• Single circular chromosome + any plasmids

• Inheritance is through vertical and horizontal transmission of genes

vertical transimission

Think parent to child

Horizontal transmission

combination of genes from others in the population; acquiring different cells from neighboring cells and its environment

Semiconservative replication

DNA is unzipped into two separate strands before being filled in by its complementary nucleotide. Half of the old ladder or DNA is kept while the other is replaced, giving you two new ladders

DNA replication is done through

semiconservative replication

Order of prokaryotic genetics

Genome (DNA) → chromosome, plasmids → genes → proteins

Steps of Gene Expression

Retrieval of info → Transcription → Translation

Often times transcription and translation happen together

Polysome formation

multiple ribosome on a transcript because transcription and translation happen together

Retrieval of info

Signals within or outside the cell tell it to retrieve information needed in order to fulfill a specific function or need. → This will trigger it access the genetic information encoded in the DNA for use in building proteins and to will employ different RNAs to start the next steps

Transcription

The step of creating multiple copies of DNA into RNA version or into a messenger molecule (mRNA)

RNA Polymerase binds into a promoter on the Nucleotide base sequence and makes a copy of the DNA into a molecule of mRNA (messenger RNA) with the complimenting RNA nucleotides → after it reaches the end of the gene, the mRNA strand is released and transported to a ribosome while the DNA re-zips itself.

Translation

Translation of the mRNA sequence into a protein

The mRNA carries the RNA strand into the ribosome where the ribosome reads the mRNA codons and assembles the proteins. Transfer RNA bring in the amino acids needed for the proteins to be created

Transfer RNA (tRNA)

specific to carry the amino acids and can read the transcripts/RNA codons

Sense strand

used for coding

5’——-3’

identical to the mRNA sense strand except for the T/U substitutes

Antisense strand

3’——5’

The template strand. Used in transcription to create the complementary mRNA strand

Mutations

permanent alterations of the DNA bases sequences

Spontaneous mutation

random mistakes during replication

What are the base point mutations

Missense, Nonsense, and Frameshift

Missense mutations

when a single nucleotide is changed in the DNA sequence resulting in an amino acid substitution.

Nonsense mutation

When a single nucleotide is changed in the DNA sequence and changes a normal codon into a stop codon

Since the stop codon forms prematurely, it ends the translation process making it lethal for the cell or organism for the most part

Frameshift

Insertion or deletion of a single base nucleotide

Typically lethal since it causes a change in the amino acid sequence following the insertion or deletion site

What is the protein that mediates recombination between cells?

RecA protein

RecA protein

mediats recombination between donor/recipient

What are the benefits of recombination in DNA transfer

Allows cell to gain new functions, repair defective genes or damaged DNA, and contributes to genetic diversity of population

What are the different ways of horizontal transmission?

Transformation, conjugation, transduction, transposition

transformation

uptake of DNA from the environment (naked DNA)