- Community of bacteria. Causes antibiotic resistance.
Roles of bacterias
- S. Mutans : responsible for protection in the mouth (and bad breath)
- Used to break down stains and fecal matter. (Ex: man made and natural matter.)
- Creates certain types of medication. (Ex: homan insulin) and used in research.
Define microorganisms/microbes and which ones are alive vs. non-living.
- minute living and non-living organisms that cannot be seen by the naked eye.
- 2 “living” groups: Eukaryotic & prokaryotic.
-“Non-living” : viruses and prions.
Importance of pathogenic microbes :
How do the receptors in cells work towards bacteria and viruses.
- certain types of receptors allow on certain types of microorganisms into the cells.
Why do we only know 1% of the microbes?
They’re viable, but non-culturable.
Tuskegee Syphilis experiment.
Belmont report : experiment is necessary without any ramifications.
Genus and species are underlined when naming bacteria.
Carbon cycle and its importance :
What is carbon?
What does the carbon cycle do?
How is photosynthesis related?
Carbon is the backbone for all organic material (Ex. Amino acids, DNA, proteins and fats) and is important for may chemical processes.
Moves carbon from the atmosphere and oceans into organisms and back again.
Photosynthesis : plants use photosynthesis to make energy and grow. They take CO2, sunlight and water and turn it into oxygen and sugar.
Importance of the nitrogen cycle:
Purpose of it?
What uses what?
to synthesize protein, nucleic acids, and other nitrogen-containing compounds.
Most important part of the cycle is bacteria : helps nitrogen change between states so it can be used. Ex: when nitrogen is absorbed by the soil, different bacteria help it to change states so it can be absorbed by plants. Animals then get their nitrogen from the plants.
Bioremediation and its function:
What is it used for?
What are the 2 examples of bioremediation?
Who’s Fritz Haber?
used to clean up and break down waste matter.
1. Solid Municipal Waste : uses microbes to produce methane for us to burn to generate electricity or to purify and use for natural gas.
2. Composting : process that uses microbes to decompose organic material into fertilizer and soil additives.
Fritz Haber: created fertilizer and mustard gas and Gas B (used during the holocaust.)
Excess PO3 and N2 -> algae bloom
Know the parts of the microscope.
PPT 1 #19
How are microbes measured?
- measured in micrometers or nanometers.
What is it?
What does shorter wavelength light mean?
What about white light contains long wavelengths?
Higher magn. means what?
the ability to distinguish 2 points specific distances apart.
shorter wavelength lights have better resolving power.
white light contains long wavelengths and cannot resolve things less than 0.2um.
Magnification increase, resolution decreases.
Brightfield vs. darkfield microscopy :
What do they look at and what are the disadvantages?
bright field looks at unstained microbes. Dark field looks at microbes which cannot be stain using conventional stains.
disadvantage : cannot see well if not well contrasted to background.
Dark field uses disk to block direct light and reflected light focuses through specimen so background is darker.
strep is a chain of bacteria
the placement of organisms with similar traits in a category and shows similar degrees of relatedness.
phylogeny : the study of evolutionary relatedness among organisms (tree)
Aristotle : plants or animals.
Carol Linnaeus used latin names to give a universal language.
What are two examples?
Know the taxonomy of humans.
- Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus.)
- Humans : Animalia, Chordata, Mammalia, Primates, Homonidae, Homo, sapien.
What are the two types of questions that we ask?
What are phototrophs, chemotrophs, autotrophs, heterotrophs
Make own food? Carbon Source (important because it’s the backbone of most living things.)?
Phototroph : uses light as primary source of energy (algae).
Chemotrophs : use oxidation/reduction reactions compounds for energy. “uses chemicals”
Autotrophs : self feeders and use carbon dioxide for carbon source.
Heterotrophs : feed on other for carbon source.
Phototroph carbon source (Chemoheteroptroph vs. chemoautotroph) :
What do each use as a carbon source?
Type for humans?
- Uses organic compounds.
- Uses CO2.
Humans : chemoheterotrophs.
Phototroph carbon source (Photoheterotroph vs. Photoautotroph) :
What do each use as a carbon source?
- No-Anoxygencic photosynthetic bacteria (green and purpose bacteria.)
Purpose for classifying microbes.
Examples of microscopically identified microbes.
What does Bergey’s Manual of Determinati Bacteriaology do?
ability to determine appropriate treatments.
protozoans, fungi, and parasitic worms are microscopically identified.
identifies microbes not by relatedness but by cell wall composition, staining, morphology, oxygen requirements.
List of living.
List of nonliving.
- Viruses, viroids, virinos and prions.
Archaea vs eubacteria :
What are they.
What are the 3 types of phylum of archaea bacteria and their environment?
What's the difference between them and eubacteria?
doesn’t cause human disease(eubacteria do!) but have the ability to survive under extreme conditions due to different cell wall component. Has no peptidoglycan while eubacteria do.
Methonoges (places of extreme CO2 which they use to make methane, Halophiles (Hella Salty), Thermophiles (Hot Places)
* salting food kills the bacteria growing in the gut.
Thermus Aquaticus (Taq) : organism that revolutionized medicine. PCR allowed us to detect the presence of genes (ex. HIV and hepatitis) Sequencing the human genome.
Have huge difference in cell wall component. Archaea has no peptidoglycan while eubacteria do!
Difference between prokaryotic and eukaryotic cells :
Unicellular or Multicellular?
Shape of DNA and is proteins are associated with it.
1. DNA not enclosed within a membrane. Unicellular. Circular DNA no proteins.
2. Lack membrane-enclosed organelles. “naked DNA”
3. Cell walls almost always contain the complex polysaccharide peptidoglycan
4. Divide by binary fission.
5. Ribosome 70S, 30S and a large 50S
6. NO mitochondria!
1. DNA is found in the cell’s nucleus. Multicellular. Linear DNA associated with proteins.
2. DNA associated with histones and with nonhistones.
3. Have a number of membrane-enclosed organelles, like mitochondria etc.
4. Cell division involves mitosis or meiosis.
5. Many mitochondria.
6. Ribosome 80S, 40S, and 60S.
7. MANY mitochondria!
What does the letter S on Ribosomes stand for?
Ribosome # : S stands for Svedberg. Sedimental coefficient.
Tetracycline attacks the 50s subunit. So it doesn’t attack the eukaryotic cells. This is how drugs/antibiotics work. Which subunit it attacks and etc.
Know the prokaryotic cell structure/functions.
Know the eukaryotic cell structure/functions.
parts of the prokaryotic cell
pili/ fimbriae : 1. exchange of genetic material 2. latch/attachment.
Conjugation : lack of pili causes the inability to be pathogenic.
Endosymbiotic Theory :
How does it work?
Is there evidence?
Eukaryotic cells devour prokaryotic cells (like mitochondria) and enter an endosymbiotic relationship.
One cell provides energy o the host who provides protection from other predators.
Evidence : new mitochondria formed through binary fission
Example : Mitochondria and chlorophyll
If prokaryotes do not have mitochondria, how do they get energy?
- prokaryotic cells take up energy by photosynthesis or absorbing it from the environment.
What’s binary fission?
What’s the event that happens before binary fission?
Binary fission : division in half. Asexual reproduction.
What are the 2 terms. How are they grouped?
What are the differences between clones and strains.
clone and strain
grouped by similar traits.
Clones : pure cultures of bacteria for example grown up from a single parent.
Strains : slight variations of the same species.
What are they/called?
What are the cell walls made out of?
What are most fungi considered as?
How are they nourished?
What can mushrooms not do?
Single and multicellular organism whose DNA is wrapped by nuclear membranes. “Saprophytie : eats off dead things.”
cell walls are made of chitin while plants contain cellulose.
Most are fungi in the form of mycelia and are composed of hyphae.
Nourished by absorbing from the environment.
What are they?
How do they retain their shape?
How are they important for microinvertebrates?
What do they feed on?
How are they consumers?
What’s their life cycle?
How do they reproduce?
Protozoans are considered as what type of -yotic cells?
Unicellular eukaryotic microbes.
Uses pellicle (thick layer that supports the cell membrane.)
important food source for microinvertebrates.
algae, bacteria and microfungi.
they’re consumers as decomposers.
as cyst in harsh conditions temperature, food water fungi.
2 types of phyla?
How do they live?
parasitic worms that steal nourishment form their hosts, weakening and sickening them.
Lack digestive system and absorbs nutrients. Limited nervous system since everything’s around them. Limited locomotion b/c transferred host to host.
What are the characteristics of Eubacteria?
Arrangement of cocci include…?
Often make up dangerous diseases.
Spiral shape : spirilla
Rod shaped : bacilli
Spherical Shaped : cocci
- Picture @ Lect 3 #27
Native to ground/rice plants.
Can condense into a spore and waits for environment to become better.
This is what causes rice to “spoil” when left out.
External Cell Structure
- Picture @ Lect 3 #32
Made where and does what?
2 types of names determines latch.
What is it called if it helps bioflims anchor to environment?
What does extracellular polymeric substance do?
What do capsules do?
made within the cell and secreted out.
polysaccarhides (strings of sugars), polypeptides (strings of proteins) or both.
called a capsule if adheres to wall tightly. Called a slime layer is loose.
extracellular polymeric substance (EPS) and helps bioflims anchor to environment.
allows for protection and communication.
Helps protect against phagocytosis.
Types of flagellum/flagella.
What are the four types?
Moving towards what are called?
Know the 3 parts of the flagella.
monotrichous, lophotrichous, amphitrochous and peritrichous.
Light : phototaxis
Chemicals : chemotaxis (ribose or galatose)
Chemicals that bacteria move to are attractants. Moves away from are repellants like phenol.
Neutrophiles : neutral loving bacteria that need (6.9-7.8pH)
Osmophiles : microbes that live in high concentrated environments with lots of sugar.
ex : fruit concentrates and honey etc. Causes food spoilage
Minimal growth temp. vs Optimal growth temp. vs Maximal growth temp.
Preferred temp for psychorophiles, mesophiles and thermophiles?
Minimal growth temperature : lowest temperature a microbe can grow.
Optimal growth temp : highest temperature a microbe can grow.
Maximal Growth Temperature : highest temperature a microbe can grow.
psychorophiles : like cold 0-15* C
Mesophiles : like moderate 16-38*C
thermophiles : super high temperatures 39-200* C
Different types of aerobes and define.
How does atmospheric difference help with bacteria?
Obligate aerobe : requires oxygen
Obligate anaerobes : can’t live in presence of oxygen
Aerotolerant anaerobes : cannot grow in oxygen but can tolerate oxygen.
Facultative anaerobes : cause use oxygen, but can live under anaerobic conditions when oxygen is not available.
Microaerophiles : require oxygen in low concentration to grow.
Used to distinguish the bacteria.
Culture medias :
What were pasteurs used for?
What's a culture?
pasteur : used beef broth to grow bacteria
growth of bacteria that grow in media, typically liquid media.
Selective vs Differential?
Selects for Gr(-) bacteria.
Selective : choosing a group
Differential : picking an individual species.
the sum of all chemical reactions in the cell.
an enzyme regulated chemical reaction that breaks down complex organic material into simple ones and normally accompanied by energy release.
an enzyme regulated chemical reaction that builds complex organic materials from simple ones and require energy to be released to complete the reaction.
The role of ATP in anabolic and catabolic readtions?
- energy is released in the form of heat.
Significance towards the cell?
What’s the purpose of anabolism and catabolism.
What do reactants need to have in order for chemical reaction to take place?
What do enzymes do in the body?
What’s activation energy?
the sum of all chemical reactions in the cell.
Purpose of anabolism/catabolism : Maintain regular body temperature
Reactants need to have enough energy and properly oriented for a chemical reaction to take place.
Enzymes are responsible for chemical reaction in the body.
the amount of collision energy required to disrupt stable electrons configuration so that molecules can be rearranged.
What is it?
How do you increase the reaction rate?
frequencies of collisions with sufficient energy to bring about a reaction.
Increase by raising temperature (this causes the molecules to move faster and increase collision # -> increased activation energy.
Shrink the space and particles (raises the pressure) and that increases the activation energy.
What are catalysts?
What type of enzyme act on specific substrates?
What do enzymes do?
How fast do enzymes react?
What are turnover numbers?
Which two forms do enzymes exist in and how is it governed?
Names of enzymes usually end in what?
What's the most prevalent configuration?
What does hydrolase do?
Catalysts : subatances that speed up chemical reactions without being altered.
Accelerate chemical reactions and contains an active site. They orient the substrate to ensure increase chances of a reaction.
enzymatic reactions : millisecond
turn over numbers : amount of time the enzyme can be used.
Exist in an active and inactive form, governed by cellular signaling.
Names end in -ase.
Zymogens configuration : proteins that are made and need to be chemically modified to be active. (A lot of enzymes operate like this.)
Hydrolase : adds water to break bonds between amino acids.
Enzyme component :
What are they composed of?
Where can the cofactors be found in and what are they used for?
composed of a protein (Apoenzymes) , a non protein (Cofactor)and creates a whole enzyme (holoenzyme).
Cofactor : inorganic compounds like Zn, Fe, Ca derived from vitamins. They’re used to active the enzyme.
Apoenzymes : made by ourselves and are linked with certain cofactors.
Coenzyme : helps enzyme make more products.
Mechanism of enzymatic reactions :
What happens beyond the optimal temp?
What does temp do for bacteria?
1. How much is present? how active is it?
Beyond the optimal temperature, enzymes degrade of slow down.
temperature determines how fast/slow bacteria grows.
pH influences on enzymatic activity :
What happens beyond the optimal pH?
Beyond the optimal pH, enzymes degrade or slow down.
Substrate Influence Enzymatic Activity :
Where can the maximum rate of enzyme activity be obtained?
What happens beyond this point and will adding more substrates help with the reaction rate?
At the optimal substrate concentration, the maximum rate of enzyme activity can be obtained.
Beyond this point is saturation and adding more substrate does not affect the reaction rate.
Feedback Inhibition :
What plays a major roll in feedback inhibition and what does it do?
- allosteric inhibitors : prevents making too much products and wasting resources.
Oxidation and Reduction Reactions :
What is it?
What’s Oxidation and Reduction?
What always occurs all together?
What’s Reducin and Oxidizing.
What causes dehydration?
proteins can steal electrons.
Oxidation : loss of electrons
Reduction : gain of electrons.
Reducin : reagent-electron donor.
Oxidizing : reagent-electron acceptor.
Dehydration is loss of hydrogens.
Extra Notes :
- Oil Rig
Chemiosmosis - Synthesis of ATP from ADP :
Why is chemiosmosis important?
The addition of the 3rd Phosphate group to a substrate. (Substrate Phosphorylation.)
It’s the actual production of ATP in cellular respiration.
Oxidative - Phosphorylation :
What happens during this?
Where does this occur?
Electrons are transferred from organic molecules to carriers (FAD+ and NAD+) and then uses other seys of electron carriers to O2.
Occurs in the PM of prokaryotes and in the mitochondria on eukaryotes.
Where does it occur?
What are produced from what?
Occurs in the photosynthetic cells, light trapping cells of chlorophyll.
Sugars are produced from CO2 and H2O & ATP is generated.
Metabolic pathways :
What’s the purpose of it?
To extract energy from organic compounds and store it in chemical form, organisms pass electrons from one compound to another through a series of oxidation-reduction reactions.
To convert into something you can use!
Carbohydrate Metabolism :
Why are carbohydrates important to organisms?
What 2 processes to microorganisms use to break down what?
Both steps use what for the 1st step?
Most organisms breakdown (catabolize) carbohydrates to produce energy.
1. Cellular Respiration
Both use glycolysis as the 1st step.
Cellular Respiration and Fermentation :
Cellular Respiration :
- How we get energy from glucose (which everything we eat turns into)
- Our cells need energy to be transferred into ATP so it can properly be used.
- Glucose is transformed into ATP through 3 stages : Glycolysis, Krebs Cycle and Electron Transport Chain
- When oxygen is not present, the pyruvates formed through glycolysis gets rerouted into a process called fermentation.
- Since there’s no oxygen in the cell, it needs more of the NAD+ to keep glycolysis going and fermentation frees up some NAD+ and creates products like ethyl alcohol (which is from yeasts for example) .
- uses substrate-level phosphorylation instead of an electron transport chain to generate ATP.
Cellular Respiration - Glycolysis :
What is it?
What gets broken down?
What does it need and what does it generate?
Where can it take place in?
Breaking down of the glucose.
Glycolysis breaks down glucose’s 6-carbon ring into two 3-carbon molecules called pyruvate acids/molecules.
Needs the investment of 2 ATPs in order to work and it generates 4 ATPs, 2 pyruvates and 2 NADH. (NADH is used to power more ATP production later.)
Can take place w/o oxygen. Makes it an anaerobic process.
Occurs in the cytoplasm
Creates 2 ATP, 2 NADHs
Cellular Respiration - The Krebs Cycle :
Where does it happen?
What does it do?
Require oxygens. Aerobic process.
Happens across the inner membrane of the mitochondria (power centers of the cell.)
Takes the products of glycolysis - those carbon rich pyruvates and reworks them to create another 2 ATPs.
How? First, one of the pyruvates is oxidized (combined with oxygen). One of the carbons off the three-carbon chain bonds with an oxygen and leaves the cell as CO2 and a two-carbon compound called acetyl coenzyme A. Then, another NAD+ comes along and picks up a hydrogen and becomes NADH.
The 2 pyruvates create another 2 molecules of NADH to be used later.
Main purpose : it to make these powerhouses for the next stage - Electron Transport Chain
Creates 2 ATPs, 8 NADHs, 2 FADH2
Cellular Respiration - Electron Transport Chain :
What does it consist of?
Occurs where on Euk vs Prok?
Requires oxygen. Aerobic process.
Can create 34 ATPs.
Consists of sequence of carrier molecules that do oxidative-reduction reactions.
As electrons passed, the energy generated is used to drive the chemiosmotic reaction to form ATP.
Occurs in the mitochondria in eukaryotes and on the plasma membrane in prokaryotes.
Takes NAD’s from the Krebs cycle to be used in the ox-red reaction to form ATP.
If we want a total of 34, then we say 30 ATP were made in electron transport chain.
High hydrogen concentration outside the cell powers the electron transport chain and will continuously make ATPs.
Why is this important?
What does it use in lieu?
What does it consist of?
What are the two common types?
Fermentation and anaerobic respiration enables cells to produce ATP without the use of oxygen.
Uses something like sulfate instead of oxygen.
Consists of glycolysis plus reactions that regenerate NAD+, which can be reused by glycolysis.
Two common types :
- Alcohol fermentation
- Lactic acid fermentation.
Fermentation - Alcohol :
Pyruvate makes NADH and FADH2.
Humans can’t make alcohol b/c we don’t have the enzyme. But, we can make lactic acid.