Lecture 1 (Chapter 1)

February 20, 2016

● Microbiology is the study of small life

● The microscope is the most important invention in the development of microbiology
● A microorganism is all small living things
● Know the nine types of microorganisms we discussed in class including:
○ Bacteria - Prokaryote
○ Archae - Prokaryote
○ Fungi - Eukaryote
○ Protozoa - Eukaryote
○ Helminth - Eukaryote
○ Algae - Eukaryote
○ Viruses - Acellular
○ Viroids - Acellular
○ Prions - Acellular
● Be able to classify microorganisms as prokaryotic, eukaryotic or acellular
● Know the basic definitions of prokaryotic, eukaryotic and acellular
○ Prokaryotic - Simple cells
○ Eukaryotic - Complex cells
○ Acellular - No cell associated with them but use cells to grow
● An infectious disease is a disease caused by a microorganism
● Louis Pasteur - The Germ Theory of Disease explains that human disease could arise
from infection
● The Germ Theory of Disease has developed our understanding of infectious disease
over the years by disproving spontaneous mutation from microorganisms
● **An antibiotic specifically kills bacteria and what microorganisms are treated with
antibiotics
● **Know what an antiviral is and what microorganisms are treated with antivirals
● **Know a vaccine is and what the purpose of vaccination is for a person’s health
CHAPTER 2
● Know what the 5 I’s of Microbiology are and be able to describe them
1. Inoculation - placing on growth media
2. Incubation - produces a culture (placed in incubation)
3. Isolation - separating the different species on a streaking place
4. Inspection - view colonies and describe their characteristics by preparing a slide
with staining technique
5. Identification - use cell shape, staining results, and biochemical tests to figure out
bacteria
● Be able to arrange the 5 I’s in a sequence
(that means be able to say which comes before another)
Information from Online Quiz and At Home Reading
February 27, 2016

Chapter 1 Questions
● Be able to describe the amount of time that has passed since prokaryotic cells and
eukaryotic cells developed on Earth
○ Prokaryotic cells developed 3.5 billion years ago
○ Eukaryotic cells developed 1.8 billion years ago
● Understand what Evolution theory states about organisms
○ Evolutionary Theory is the accumulation of changes that occur in an organism as
they adapt to their environment
● Understand the theory of Spontaneous Generation as it applies to microbiology
○ It is the belief that invisible vital forces present in matter led to the creation of life
● Be able to explain the difference between biogenesis and abiogenesis
○ Biogenesis is the belief that only living things can arise from others of the same
kind
○ Abiogenesis is the belief of spontaneous generation as a source of life
● Be able to describe the key experiment by Louis Pasteur that disproved Spontaneous
Generation
○ Pasteur’s swan neck flask experiment was to disprove spontaneous mutation by
vigorously heating to broth to make sterile, in one flask the neck was broken and
the growth occurs, but the other flask the neck was intact and the airborne
microbes were trapped at the base of the neck and the broth was still sterile
● Know what a swan neck flask is
○ Curved tubes on the flasks in Pasteur’s experiments
● Know what Pasteurization is
○ Heat treatment to destroy heat-sensitive vegetable cells and rapid chilling to
inhibit growth of survivors and germination of spores; to prevent infection and
spoilage
● Be able to describe the contribution of Joseph Lister to medical practice - involved
disinfecting the hands and the air with strong antiseptic chemicals such as phenol prior
to surgery
○ Know what Aseptic Technique is reducing microbes in a medical setting and
preventing wound infections
● Know what proteins are made of
○ Amino acids with polypeptide bonds
● Know the three Domains of Life
○ Domain Bacteria, Domain Archaea, Domain Eukarya
● Know what microorganisms fall under each Domain
○ Domain Bacteria - Prokaryotes
○ Domain Archaea - Prokaryotes
○ Domain Eukarya - Eukaryotes
Lecture 2 (Chapter 3)
March 5, 2016
● Be able to state the three components of cell theory
○ (1) Cells are the fundamental unit of life, (2) Cells carry out all the processes of
life, (3) Extension by Robert Virchow: Biogenesis that cells come from preexisting
cells
○ Know the difference between abiogenesis and biogenesis
■ Abiogenesis - Spontaneous generation theory; beginning of absence of
life
■ Biogenesis - Living things arise only from others of their same kind
○ Understand that Biogenesis was an addition to the first part of cell theory
■ Biogenesis came about from Robert Virchow - cells from from preexisting
cells
○ Be able to apply Cell Theory as a way to define life
■ Cell Theory states that a living organism must be made of cells
○ Understand how acellular microorganisms are treated by Cell Theory
■ For microbiology, cell theory does not describe microorganisms as alive
● Understand the difference between prokaryotic and eukaryotic cells
○ Know which type is simple and which is complex
■ Prokaryote is simple cells
■ Eukaryote is complex cells
○ Know what a nucleus is and how it is used to differentiate prokaryotes and
eukaryotes
■ Nucleus is membrane surrounded bound DNA - prokaryotes do not have
a nucleus, eukaryotes have a nucleus
○ Know which type of cell, prokaryotic or eukaryotic, have internal organelles
■ Prokaryotes do not have internal organelles, Eukaryotes have organelles
○ Know that the cell walls of prokaryotes and eukaryotes are different
■ Prokaryotes usually have one cell wall, only some Eukaryotes have a cell
wall
● Be able to classify prokaryotes and eukaryotes into the three Domains of Life
○ Prokaryotic - Bacteria and Archaea
○ Eukaryotic - Eukarya
● Be able to classify the three Domains of Life as either prokaryotes or eukaryotes
● Know what the extracellular environment is
○ Outside of the cell
● Describe the makeup and purpose of the cytoplasm of a cell
○ Makeup: 70-80% of water, made of sugars, salts, amino acids, lipids, nucleic
acids (DNA, RNA); Purpose: All functions occur in the cytoplasm
● Know what the purpose of a cytoskeleton is
○ Actin and Tubulin contribute to cell shape and structure
● Describe the makeup and function of the cell membrane
○ Makeup: A phospholipid bilayer - which is made of the phosphate head
(negatively charged) and the lipid tail (Neutral charged); Function: Prevents
 things from going out and coming in, and coordinates what does in and out using
channels
● Understand the molecular relationship between phospholipids and water
○ The neutral charged tails interact with each other, and the negative charged
phosphate head interacts with the positively charged Hydrogen of water.
● Know how a cell membrane controls what goes in and out of the cell
○ Coordinates what goes in and out using protein channels - selectively permeable
membrane
● Describe the makeup and functions of the cell wall
○ Makeup: Peptidoglycan, which is a tetrapeptide cross-linked polymer of sugars
(ONLY FOR BACTERIA)
○ Function:(1) Give the cell shape, (2) Protects from changes in osmolarity in the
extracellular environment
● Know the molecular composition of peptidoglycan
○ Peptidoglycan sugars - N-acetyl glucosamine and N-acetylmuramic acid
○ The Muramic acid component has the tetrapeptide cross-links
● Understand how peptidoglycan structure leads to the function of the cell wall
○ Holes in peptidoglycan allow passage of molecules, but cross-links allow for
strength (Muramic Acid tetra-peptide cross-links)
● Understand what the Central Dog of Biology is
○ Genetic Information: DNA genetic information ->(transcription) -> RNA ->
(Translation) -> Proteins
● Know what the nuclear region of a bacterial cell is
○ Nuclear region has no boundary but is the location where Transcription occurs
● **Know where transcription and translation occur in a cell
○ Transcription occurs in the nuclear region, Translation occurs coupled to
transcription
● Know what a ribosome does
○ A ribosome makes proteins and RNA, it is the site of protein synthesis
● Know what coupled transcription/translation is
○ Coupled transcription/translation is happening at the same time in prokaryotes
● Know what the purpose and function of flagella is
○ Help the cell move and give motility
● Know what the purpose and function of glycocalyx is
○ Purpose: Capsule, a coat of molecules external to the cell wall - protects,
adhesive, and receptor functions Function: functions in attachment to other cells
or as a site for receptors
Lecture 3 (Chapter 4)
March 12, 2016
● Be able to explain endosymbiotic theory
● --The theory suggests that eukaryotic cells arose when a large “pre-eukaryote” engulfed
smaller prokaryotic cells that began to live and reproduce inside the large cell rather than
being destroyed.
○ Know what a pre-eukaryotic cell is
■ Another cell type that evolved from the Last Common Ancestor
○ Explain what changes in a pre-eukaryotic cell lead it to evolve to a eukaryotic cell
■ The endosymbiotic prokaryotes became dependent on the pre-
eukaryotes, and the pre-eukaryotes became dependent on the
endosymbiotic prokaryote
○ Diagram out how a prokaryotic could become an endosymbiote
○ Know some of the main observations that support endosymbiotic theory
■ Mitochondrion of eukaryotic cells is something like a tiny cell within a cell
■ Capable of independent division
■ Chloroplasts
○ Know the two types of endosymbiotic organelles
■ (1) Mitochondria - energy production (all eukaryotes)
■ (2) Chloroplast - convert sunlight into energy-rich sugar (chemical energy)
● Know what a flagella is and what its function is
○ External Appendage structure
○ Function: To locate nutrients and give cell mobility (in both prokaryotes and
eukaryotes)
● Know how a flagella is different between eukaryotic and prokaryotic cells
○ Flagellin: protein that makes up prokaryote flagella
○ Tubulin: protein that makes up eukaryotic flagella
● Know what a glycocalyx is and what its function is
○ Made of layers of sugars (polysaccharides), sometimes called extracellular
matrix, a CAPSULE
○ Function: for protection and attachment (both prokaryotes and eukaryotes)
● Know how a glycocalyx is different between eukaryotic and prokaryotic cells
○ Slime layer - prokaryote
○ Capsule - eukaryote
● Know that types of eukaryotic cells have a cell wall
○ Fungi and algae have cell walls
○ Humans do not have cell walls
○ Prokaryotes: Made of peptidoglycan
○ Eukaryotes: Made of polysaccharides
● Be able to compare and contrast the function and molecular composition of bacterial and
fungal cell walls
○ Fungi and Algae have thick, rigid cell walls
○ Composition: Polysaccharides (Chitin and Cellulose)
○ Prokaryotic cells are made of peptidoglycan
 ○ Eukaryotic cells are made of polysaccharides
● Know the function of eukaryotic cell membranes
○ Function: To separate the cytoplasm from the extracellular environment
● Compare the function of prokaryotic and eukaryotic cell membranes
○ Eukaryotic cell membranes use sterols to strengthen the cell membrane instead
of needing a cell wall
● Know that sterols are a major component of eukaryotic cell membranes
○ Used to strengthens cell membrane because they have no cell wall
● Understand what the purpose of sterols are in eukaryotic cell membranes
○ Purpose: To strengthen cell membrane
● Know how bacterial cells that have a cell wall compensate for lack of sterols in
membrane
○ Have phospholipid bilayers with NO sterols, and are not as stable
● **Know how bacterial cells that have no cell wall compensate for lack of a cell wall
● Know what the cytoplasm is
○ Makeup: 70-80% of water, made of sugars, salts, amino acids, lipids, nucleic
acids (DNA, RNA); Purpose: Prokaryotes - All functions occur in the cytoplasm
● Know what the function of the nucleus is
○ Know what the nucleus does - (1) contains the genetic information, (2)
transcription, (3) makes ribosomes
○ Know the function of the nuclear envelope - membrane that surrounds the
nucleus (made of phospholipids)
○ Know what a chromosome is and what chromatin is
■ Chromosome - one, long continuous piece of DNA
■ Chromatin - the structure of chromosomes and proteins inside the
nucleus
○ Know what a nucleoli is and what it produces
■ The site where ribosomes are made (ribosomal RNA synthesis)
○ Know what a nuclear pore is
■ Is a channel that controls what does in or out of nucleus (active)
○ Know that the nucleoplasm is
■ Matrix surrounding the nucleolus, inside the nucleus
○ Know that transcription occurs inside the nucleus
■ TRANSCRIPTION OCCURS INSIDE THE NUCLEUS
● Know the functions of the Endoplasmic Reticulum
○ Know the difference in function between the Rough ER and Smooth ER
■ Rough ER has ribosomes attached to it, proteins are synthesized here
■ Smooth ER is a closed tubular network without ribosomes, synthesis and
storage of non-protein macromolecules such as lipids
○ Know what is attached to the RoughER to make it appear Rough
■ Rough ER has small granular structures on it, which are ribosomes
○ Know that translation for all types of proteins begins in the cytoplasm of a
eukaryotic cell
○ Know that polyribosomes start translation in the cytoplasm of eukaryotic cells
 ○ Know the difference between globular/cytoplasmic proteins, membrane proteins
and secreted proteins
■ Globular/cytoplasmic protein: translated/start by polyribosomes in the
cytoplasm, complete translation in the cytoplasm at a ribosome
■ Membrane proteins: start/translated on polyribosomes in cytoplasm,
complete translation at the rough ER, new protein is attached to RER,
stays on ER membrane
■ Secreted proteins: start/translated by polyribosome in cytoplasm,
complete translation at Rough ER, new protein is inside lumen of ER and
not attached to membrane
○ Know that globular/cytoplasmic proteins have all of their translation occur in
cytoplasm
○ Know that membrane proteins have their translation completed on the Rough ER
○ Know that secreted proteins have their translation completed on the Rough ER
○ Know that globular/cytoplasmic proteins function the cytoplasm after translation
○ Know that membrane proteins are stuck in Rough ER membrane after translation
○ Know that secreted proteins are in lumen of Rough ER after translation
● Know the two basic functions of the Golgi apparatus
○ (1) adds sugars to the proteins (only to the membrane and secreted)
○ (2) New proteins are cut by Golgi Apparatus proteases (proteins that cut other
proteins)
● Know that only membrane proteins and secreted proteins go through the Golgi
apparatus

● Know what a hyphae is

○ Tubular threads that are found in filamentous fungi (mold) - fungal mold
● Know what a superficial infection is
○ Not deeply invasive
● Know the difference in function of a cyst stage versus a trophozoite stage
○ Cyst stage - resting form (inactive)
○ Trophozoite stage - feeding form (active)
● Know what a definitive host it
○ The organism in which a parasite develops into its adult or sexually mature stage
- where adulthood and mating occurs
Lecture 4 (Chapter 5)
March 19, 2016
● Be able to explain what a virus is
○ Intracellular parasite
● Understand why a virus is an obligate intracellular parasite
○ Without a cell, viruses do not grow
● Understand that a virus is a filterable microorganism and be able to explain what that
means
○ You can filter all bacteria out but the fluid is still infectious because the bacteria
was not the cause of the infection, which can be seen.
● Compare and contrast a bacteria and virus using the terms: alive, dead, active and
inactive
○ Bacteria can be alive and dead, while viruses can only be active (within a cell) or
inactive (ready to be active if a cell is presented)
● Know that 10-20% of cellular genomes are made of viral genomes
● Know the types of nucleic acids that can be the genetic information of a virus
○ Single stranded or double stranded
● Know the purpose and molecules composition of a viral capsid
○ Purpose: protein coat to protect genetic information
○ Molecules: capsomers constructed from protein molecules
● Know the purpose and molecules composition of a viral spike/envelope protein
○ Protein spikes = no envelope, envelope protein = envelope
○ Purpose: Proteins that attach to cell to infect
○ Composition:
● Understand what viral tropism is and how it affects disease
○ Tissue specificities, cells/organisms that the virus can infect
● Be able to explain the proteins involved in tropism and how cellular receptors are
involved
○ Membrane receptors that viruses attach to are usually glycoproteins
○ Glycoproteins are required for the cell’s normal function
○ Glycoprotein spikes on the envelope, or capsid of naked viruses, bind to the cell
membrane receptors
● Be able to compare and contrast viruses that either do or do not have envelopes using
the terms naked, enveloped, spike and envelope proteins
○ Naked viruses use the capsid
○ Spike protein are on non-enveloped viruses
○ Envelope proteins are on enveloped viruses
● Know the molecules composition of a viral envelope and where the envelope comes
from
○
● Know that a virion is
○ An infectious virus outside of a cell, it is inactive because it is outside the cell
● Be able to describe the steps of a viral replication pathway
○ Attachment (Direct fusion or endocytosis)
 ○ Penetration and uncoating - genetic information enters the cell, then genetic
replication occurs (multiple genomes made by VIRAL polymerase)
○ Replication and Encoding - major proteins made by a virus: (1) capsid, (2)
spike/envelope protein, (3) viral polymerase. Made by cellular Ribosomes
○ Assembly - combine genomes and viral proteins to make virions
○ Release - (Budding: by enveloped virus) or (Lysis: most damaging, kills the cell -
pop out by naked virus)
● Know that viral polymerases produce more viral genetic information
● Know that cellular ribosomes produced viral proteins
● Know the difference between latent and lytic viruses
○ Latent virus: Allows for a slow death
○ Lytic viruses: splitting open, can kill host instantly

For clinical correlates you must know the microorganism focus of each CC including:
● Name
● Type of Microorganism
● Type of Disease
● All vocabulary words