Bio Unit 1 Test - Viruses, Kingdoms, Gut Microbiome

Measurements of Bacteria

Bacteria are very small organisms --> unit of measurement is micron (µm)

Kingdom - Archaea

Domain - Archaea
Heterotroph
Prokaryote
Unicellular
Protein and sugar cell wall
aerobic and anaerobic
asexual reproduction (conjugation possible)
no mobility

Kingdom - Fungi

Domain - Eukarya
Heterotroph
Eukaryote
Multicellular
Cell wall present (chitin)
Aerobic and Anaerobic
Sexual and asexual reproduction
no mobility

Dysbiosis

Major imbalance of gut bacteria in the body

Parasite

An organism which lives and feeds on an organism of a different species causing harm

Capsid

The protein shell that encloses a viral genome. It may be rod-shaped, polyhedral, or more complex in shape.
- Most important substance in living things
- Composed of proteins

Assembly

new virus are put together (genome + capsid)

Coccus

Spherical shaped bacteria ( Coccus-singular, Cocci- plural)
Advantage: doesn't dry out fast

Spirochete

Spiral shaped - Super curly
Advantage: (move through fluids with less resistance)

Diplo

means grouping in pairs

How is bacteria named

Name indicates cluster type first then shape. (ex. Diplobaccili)

Lipopolysaccharide

Composed of lipids (fat) and sugar
helps bacteria infect other organisms better

Ribosomes

Used in production of proteins - Important structural components that have a variety of biochemical functions in all cells

Endospore

Highly resistant structure that forms around the chromosome
Develops in an unfavorable environment or under stress
allows cell to remain dormant

Antibiotic

A natural substance secreted by microorganisms to ward off other microorganisms
use this to protect themselves from other microbes

Human causes of antibiotic resistance

- Doctors over prescribing antibiotics to patients
- unnecessary use of commercial products (hand sanitizer)

Where does gut microbiome start

Uterus - Amniotic fluid in the mothers body contains bacteria. When the fetus swallows this bacteria, microbes seat in the fetus gut

Gut microbiome

Genes make up our gut microbiome

Prebiotics

nutrients with molecules such as inulin, fructooligosaccharide, galactooligosaccharide that encourage the growth of beneficial microbes in the intestine

Virus

Small infectious agent that can only replicate within the cells of a living organism

How are viruses classified?

Shape, type of capsid, genome, organism they infect

Viral Anatomy & Physiology

- Not made up of cells
- Do not respire or carry out life processes

Genomes

Differ according to the type of virus:
- Double strand DNA (similar to humans)
- single strand DNA
- Double strand RNA
- Single strand RNA
Organized as single, linear or circular molecule
small virus - 4 genes, Largest virus - Several hundred genes

Viral Envelope

A plasma membrane coating that surrounds the capsid
- Comes from host cells plasma membrane
- mixture of hosts proteins, lipids, viral proteins and glycolipids
- Helps virus infect host cell

Viral Reproduction

- need host cell to reproduce
- Lack cellular tools needed to reproduce
- Limited to the various host it can infect

Broad host range

Able to infect a number of organisms. Ex. west virus --> humans, birds, etc.

Narrow host range

Only infect a single species

In eukaryotic organisms what does a virus target

virus targets specific tissues. Ex. Human cold virus only effect cells of upper respiratory tract causing stuffy nose and nasal infections.

Attachment

Virus binds to a receptor on the hosts surface

Entry

Virus injects its nucleic acid into the cell

Replication

Uses cells reproductive abilities to copy viral genetic information

Lysis and release

ruptures host cell (lysis) and releases newly made virus

Bacteriophage

Name given to virus that infects bacterial cells

Lytic cycle

The reproductive cycle of a phgae that leads to the death of the host cell

4 stages of lytic cycle

1. infects cell
2. takes over cells reproductive tools
3. makes copies of itself
4. destroys host cell as it leaves

Lysogenic cycle

The reproductive cycle of a virus where the viral genome is replicated without destroying the host cell

4 stages of lysogenic cycle

1. infect the cell
2. inserts its own DNA into the DNA of the host cell
3. makes copies of itself as host cell reproduces
4. If the environment conditions are right, virus switches to lytic mode rupturing the host cell

what are the 3 main ways how bacteria is classified in the kingdom of Eubacteria?

1. By shape
2. How they cluster
3. How they obtain energy

Morphology

Describes the shape of something. Bacteria exists in a variety of shapes, sizes and arragments

Bacillus

Rod shaped bacteria (Bacillus- singular, Bacilli - plural)
Advantage: greater surface area for absorbing nutrients

Vibrio

Bean shaped

Spirillum

Spiral shaped - Little waves
Advantage: (move through fluids with less resistance)

Strepto

Grouping in straight chains

Staphylo

Grouping in bunches (like grapes)

Cell wall of Bacteria

- All bacteria have a cell wall
- The cell wall helps bacteria to keep its shape and helps protect the cell
- There are 2 types of cell walls and scientists use this to classify bacteria

peptidoglycan

All bacterial cells have peptidoglycan
A substance of sugar molecules connected to protein.
______ <--Sugar
| | | <-- Protein
---- <-- Sugar

Gram staining

- Scientists apply stains to microbes so they can be better seen under a microscope
- Gram stain chemically attaches to clear cells
- focuses on specific parts such as organelles of DNA

Gram Positive

Deep Purple
- Cell which has a lot of peptidoglycan
- less complex than gram negative
- stain adheres to cell quite well and appears dark in colour

Gram Negative

Pink
- Very little peptidoglycan and layer of lipopolysaccharide
- More complex than gram positive
- Stain does not adhere very well and appears lighter in colour

Pilus (Pilli plural)

Tiny hair-like structure made up of stiff proteins which enables bacterial cell to attach to other cells

Chromosome

Contains most genes of bacteria
dictates almost all structures and functions of the bacterial cell
Long, yet circular
highly condensed in nucleoid region

Plasmid

A small loop of DNA that is separate from the main chromosome which contains few extra genes
- Extra genes provide advantages (antibiotic resistance)
can be transferred between bacteria

Protein

structural - hair, cartilage, cell membrane
Functional - accomplish something, enzymes

Flagellum

whip like tail that helps locomotion (movement)
Spins in spiral manor to propel the bacterial cell

What process do both bacteria and archaea use to reproduce?

Binary fission

Binary fission

Asexual reproduction that results in a cell dividing into two identical daughter cells

4 stages of bacterial reproduction

1. Parent cell grows and doubles in size. DNA gets copies
2. 2 copies of DNA are separated from each other
3. A wall called the Septum in the middle of the cell, separating the cell into 2
4. each daughter cell has an identical copy of the DNA

Conjugation

The process where one bacterium shares its genetic information with another bacterium
- Allows it to have a trait it did not have before
(once it gets new genetic information it will go through binary fission again)

5 stages in the process of conjugation

1. A pilus forms on the donor cell
2. the pilus attaches to and pulls over the recipient cell. The two cells now fuse together
3. Donor makes copy of genetic information to share
4.. Genetic information is passed on the recipient cell
5. two cells separate from each other

How are antibiotics created today

Some are collected from microbes, but are also made synthetically in labs

Antibiotics interfere with cell processes such as:

- DNA replication
- DNA transcription (making RNA from information stored within DNA)
- RNA translation (Making protein from the information contained in RNA)
- peptidoglycan cross linking

Antibiotic resistance

bacteria are no longer susceptible to the inhibitory effects of antibiotics
(antibiotics no long kill bacteria - bacteria is immune)

Antibiotic resistant bacteria

bacteria that are not affected by antibiotics (mechanism that protect them from antibiotics)
information for genes contained within plasmids and transposons
genes - r genes (resistance)
plasmid - r plasmid

How are Antibiotic resistant bacteria genes passed on

conjugation, bacteriophages, acquisition from dead cells

Pathogen

An organism or virus that causes disease

exotoxin

A poisonous protein that is produced by a prokaryote
- can have intercellular or cellular targets

intercellular target

means that the toxin is taken in by the cell and disrupts the normal cell functions

examples of exotoxins

Anthrax toxin - causes fluid to accumulate within cell
Botulinum toxin - stops neurotransmitters which leads to paralysis and dead

Endotoxin

A toxic substance in the bacterial cell wall that only releases when the cell ruptures or disintegrates.
used interchangeably with lipopolysaccharide (gram negative)
less potent and less specific than exotoxins

examples of endotoxins

E.coli, (vibrio) cholera, salmonella

Impact of endotoxins

- Binds to and effects various white blood cells
- Decreases blood circulation
- Causes micro hemorrhaging
- generates low blood-sugar levels

Archaea - Methanogens

methane producing
Use CO2, N2 and H2S for energy
Live in oxygen-free environments: e.g. swamps & marshes

Halophiles

-Live in salty conditions (salt lovers)
-Found in inland seas, salt lakes, and salt mines

Thermophilles

HOT bacteria in very hot conditions (water)

Acidphiles

bacteria that grow in acidic environments

Mesophiles

moderate temperature loving microbes ( live in moderate conditions)

extremophiles

Archaea that live in extreme environments.

Kingdom - Bacteria

Domain - Bacteria
Autotroph and Heterotroph
Prokaryote
Unicellular
Cell wall present (contents vary)
aerobic and anaerobic
asexual reproduction (conjugation possible)
some mobility

Kingdom - Protists

Domain - Eukarya
Heterotroph (animal like)
Autotroph (plant like)
Eukaryote
some Multicellular, some unicellular
Some a cell wall, some don't
Aerobic
Asexual and sexual reproduction
Some mobility

Kingdom - Plants

Domain - Eukarya
Autotroph (some have heterotrophic abilities)
Eukaryote
Multicellular
Cell wall present (cellulose)
Aerobic
Asexual and sexual reproduction
No mobility

Kingdom - Animals

Domain - Eukarya
Heterotroph
Eukaryote
Multicellular
No cell wall
Aerobic
Sexual (Asexual for a few parthenogenesis)
yes mobility

What is bacteria measured in?

Culture forming unit

gut microbiome - breast milk

Contains antibodies that protect the newborn. Contains oligosaccharides (sugar molecules which boost good bacterial growth)

How does gut bacteria affect digestion

Gut bacteria breaks down enzymes our body cant break down and makes B group vitamins and vitamin (which are released into the intestines and absorbed)

How does gut bacteria affect the brain?

Coordinates body functions through the gut-brain axis
2 way communication between the central nervous system and the enteric (nervous system connected to gut) allows the GUT and brain to talk to each other.
Ex. Corynebacterium produces metabolites like serotonin which is released into our bloodstream and interacts with the nervous system which changes our moods.

How can brain signaling be affected

Healthiness of gut bacteria
Gut bacteria + immune system are used to keep disease causing bacteria away

How can you increase the number of good bacteria in the body?

Sleep well, eat well, exercise, keep stress levels to a minimum

probiotics

Good bacteria (cheese milk) that we put in our body in high enough numbers to actually have a beneficial effect

LD50 toxicity scale

Measures how much of a substance you would need to kill half the people it is given to

Why is the face and mouth swabbed first?

If other parts of the body such as a baby's bottom is rubbed first, Unsafe bacteria from these areas such as feces can now be transferred to the baby's mouth and face which can lead them to ingest this harmful bacteria.

3 Differences between Archaea & Bacteria

• Most archaea are extremophiles and most bacteria are mesophiles

• Bacteria have peptidoglycan in their cells

• Some bacteria are photosynthetic

• Archaea go through methanogenesis

3 characteristics that Archaea & Bacteria have in common

• Reproduction by binary fission

• Ability to form aggregations

• Unicellular

• Most commonly in the forms of spheres (cocci), and rods (bacilli)

Where do Archaea live?

Deep Sea Vents & Hot Springs - Thermophiles or “heat-lovers”

Salt Lakes & Inland Seas - Halophiles or “salt-lovers”

Volcanic Crater Lakes & Mine Drainage lakes - Acidophiles or “acid-lovers”

Why is being able to form endospores advantageous?

When environmental conditions threaten survival, some species of bacteria form endospores. Endospores are hard-walled structures that protect and store the organism's genetic material. They are resistant to high temperatures, drying out, freezing, radiation, and toxic chemicals. When suitable conditions return the endospore germinates back into an active bacteria

Most organisms are grouped together because they are similar or closely related to each other. How are protists grouped differently by taxonomists?

Protists are grouped mainly because they do not fit into the other kingdoms, not because they are similar or closely related to one another.

What is the function of a pseudopod?

Pseudopod (“false feet” used for feeding and locomotion): A temporary cytoplasmic extension that amoebas use for feeding and movement. Amoebas have a cell membrane but no cell wall, meaning they change shape using their internal cytoskeleton to move and create different forms.

Cilium (pl.cilia)

a short, hair-like projection that functions in cell movement and particle manipulation when coordinated with other cilia. Used for locomotion and sweeping food particles into the cell.

Flagellum (pl.flagella)

A long, hairlike projection extending from the cell membrane that propels the cell using a whip-like motion. Ex. sperm cells

Similarities and Differences of cilia and flagella

Similarities	Differences
Composed of microtubules Involved in cell movement	Flagella have a hard protective covering over their outer membrane Cilia are shorter + more numerous Cilia move in waves, flagella uses whip-like motions Flagella usually came in 1 or 2 and located on one end of the cell

Give two examples of protists that are parasites and the problems they cause their hosts

Sporozoans: parasites of animals, taking the nutrients they need from their hosts

Amoebas: Some are parasites that live inside an animal host. 

I.e. Entamoeba hystolitica feeds on the lining of the small intestine in humans and cause a serious illness called amoebic dysentery. Intestinal amoebas can be spread by drinking contaminated water or eating contaminated produce.