Cover syllabus
Small red font, stuff that Amy covers (I've removed much of it).
  Blue font, stuff that Amy does not cover.  Orange highlight, I may skip.

Lecture 1: An Introduction to Microbiology

Learning goals:

  1. Be able to define prokaryotic and eukaryotic.
  2. Be able to differentiate between archaebacteria and eubacteria.
  3. List some differences between archaea and eubacteria
  4. Compare and contrast viruses, prokaryotes, and eukaryotes with respect to basic structure and size (hw1).
  5. Be able to list the subunits which make up organic macromolecules (carbs & DNA covered in hw1).
  6. Understand why the shape (conformation) of a protein is important to its function and how the shape of a protein relates to its sequence of amino acids.
  7. Describe the role of enzymes.
  8. List the layers going into a eubacterial cell
  9. Understand the differences between cell walls lead to Gram+/- cells

Background Information:

There are some topics that I will not be able to cover due to time constraints in this class.  Some of this material will be assigned as homework.  Most homework will cover material that should be review material for most of you.  Homework may include some notes from me, some reading and figures from the text, and some assigned questions.

Homework 1 covers the metric system, the relative sizes of things, the microscope & biomolecules.

Living Organisms
Archeabacteria Eubacteria
Kingdom Animals Plants Fungi Protists Archeabacteria Eubacteria

Eukaryotic cell (p)- a cell with a "true" nucleus and other organelles that are surrounded by membranes. A true nucleus is membrane bound. Animal and plant cells are eukaryotic.  In lab we'll be looking at parasites which are animals & protists.  (Also spelled Eucaryotic.)

Prokaryotic cell (p)- a cell that lacks a true nucleus.  Bacterial cells are prokaryotic cells and are prokaryotic organisms.  (Usually, bacteria means the same as prokaryotes.)

Eubacteria (p)- a "true"  bacterium.  Also called Bacteria.

Archaea/Archaebacteria (Ar'-kē-a or Ar-kā-a/Ar'-kē or Ar'-kā -bacteria) - a domain of prokaryotic organisms which differ from Eubacteria in many ways, including cell walls, membrane lipids, and DNA sequence (after an intro to chemistry,  we'll look at  differences between Eubacteria and Archaea). 

Superkingdom - classification into prokaryotic or eukaryotic

Domains -classification into three domains by DNA: Eubacteria (Bacteria), Archaebacteria (Archaea), Eukarya.

Kingdom -classification into numerous kingdoms (often 6, but 3,5,9-15+ also possible), may include Eubacteria, Archaebacteria, Plantae, Animalia, Fungi (fun-gī or fun-jī), & Protista (prō'-tis-ta).



Animal & plant cell structure  Usually 1/10th the size of a eukaryote. Not just scaled down, but radically different cell. 
multicellular or unicellular unicellular
include algae, fungi, protozoa   eubacteria and archaebacteria

The molecules of life: Proteins, carbohydrates, lipids, nucleic acids


There are ~20 amino acids which can be linked together, like beads on a string, in many different orders (some prokaryotes have a few more aa). In fig. 2.21 of your text you can see the general structure of a few amino acids. All amino acids have a similar structure. In proteins, the amino acids bind one to another when the carboxyl group of one amino acid interacts with the amino group of another amino acid.

Fig. 2.21


Fig 2.24

Fig 2.24. Just like a string of beads tossed in a heap on the table, linear proteins can take on a shape. The shape of a protein is important to how it works. Some R-groups are attracted to each other and others repel each other.

  1. The primary structure of a protein is the sequence of its aa's. 
  2. The secondary structure is the shape that the chains of amino acids take from nearby amino acid interactions (helix, coil, sheets). 
  3. The tertiary structure is the way that the helices, coils or sheets interact with each other, ~supercoiling).  So, the tertiary structure a protein takes is dependent on the sequence of amino acids it is made of, the folding they take, and the interactions that occur between them (hydrogen bonds and cysteine sulfur bonds).
  4. Proteins that are composed of more than 1 peptide chain can take on a quaternary structure.

The shape of a protein determines its role in the cell and the organism. Proteins that serve as enzymes deserve particular attention.

Enzymes serve the role of catalysts for chemical reactions that take place within living organisms. Catalysts are chemicals which change the rate of a reaction but are not consumed or altered by the reaction. For chemicals to react they must collide. Heat (the kinetic energy of molecules) can cause a greater number of molecules to collide and facilitate chemical reactions. In cells, however, excess heat can cause problems, breaking down the structural proteins of the cell. The enzymes (a class of proteins) in living things allow chemical reactions to take place at lower temperatures and at faster rates than would otherwise be possible (fig. 5.5, 5.6).

Fig. 5.5
Fig. 5.6 Shows active site & how enzyme changes upon binding


Enzymes do this by bringing together molecules so they can react (form or break atomic bonds).

I just mentioned how sucrose is made of glucose and fructose. To be metabolized and used, sucrose must be split into glucose and fructose.

sucrose + water ----------------> enzyme complex  -------> glucose + fructose + enzyme

(similar to fig 5.7).

In this reaction, a water molecule is reacting with the bond between glucose and fructose (two kinds of sugar molecules that form the disaccharide sucrose). The result is two free monomers. The enzyme sucrase facilitates this reaction by binding to sucrose and holding it in position (in the right conformation) so that it can react w/ a water molecule. The place on the enzyme which binds to the reactant is called the active site (similar to fig 5.7).

Factors that influence enzyme activity include temperature, pH, substrate concentration, and inhibitors. Figures 5.11 shows the activity of non-competitive inhibitors and activators.

Figure 5.11 shows non-competitive inhibitors and activators.


Phospholipids (Similar to Fig. 2.16)

Phospholipids are the lipids that build cell membranes of Eukaryotes and Eubacteria. They are essential to keeping the inside of the cell separate from the outside of the cell.

Phospholipids have hydrophobic fatty acid tails and hydrophilic phosphate containing heads linked together by glycerol.  Note the ester bond with glycerol.  The tails orient themselves away from water. The heads, then, are on the inside and outside surfaces of the membrane. This structure is important because only materials that can dissolve in the hydrophobic area of the membrane can get across the membrane easily.

Archaebacteria cell membranes do not contain this ester-linked phospholipid.  Instead, they have similar phospholipids linked by an ether link (-C-O-C-).

R can be anything but is usually an organic (carbon-based) group.
Similarities: a saturated lipid tail, a unsaturated lipid tail, glycerol, a phosphate group, and is a polar molecule

Differences: they tend to be more complex as a group, the tails are lipids based on isoprene and not fatty acids, have ether links instead of ester links, and some species have unusual membrane lipids in their length, branching, or have a phospholipid monolayer instead of a bilayer.

Bacterial morphology

In lab you've seen or will see Prokaryotes with various shapes.

Bacterial morphology -Differences Among Prokaryotes

I want to briefly compare the two Prokaryotes further.







animals, fungi, plants, protists

cell number unicellular unicellular

multicellular, some
protists unicelluar


isoprene tails
ether links

fatty acid tails, 
ester links

fatty acid tails, 
ester links

cell wall 



if present, simple
animals w/o cell wall

peptidoglycan absent (most) present absent
RNA polymerase several kinds one kind several kinds
start codon methionine formyl-
antibiotics* uninhibited inhibited uninhibited
100  C some grow no growth no growth

* antibiotic response of cellular growth to penicillin, streptomycin and chloramphenicol.

The point of the comparison is that Archaebacteria and Eubacteria are very different from each other; in some ways, each is closer to Eukaryotes.  Genetically, Archaea is slightly closer to Eukarya than Eubacteria, but the difference is slight.

Archaebacteria were originally described in unusual environments such as very hot or very salty places. They include organisms that have been isolated from the hot springs at  Yellowstone and from volcanic vents at the bottom of the ocean. The membrane lipids of these unusual organisms are different. This difference in their lipids may help them to survive.  More recently, Archaebacteria has been found in all habitats including a significant amount of plankton and may contribute up to 20% of total planetary biomass. 

Generally speaking, in this class and in the text, we will be discussing Eubacteria unless otherwise stated.  The differences observed in Archaea have only recently been identified and they are frequently ignored for various reasons.

Bacterial morphology -Cell Structures

You will remember from basic biology the structure of a eukaryotic cell.

In addition to a cell membrane, plant, fungi, and many protist cells have a cell wall. Cell walls support & protect the cell & help prevent the cell from rupturing when the cell is in a hypotonic (high water, low salts) solution. The cell wall helps to prevent this. Like plants, bacteria also have a cell wall. But the cell wall in bacteria is a little more complicated.

Fig. 3.2 shows that in prokaryotic cells, the outermost layer of the cell is the cell wall and the next inner layer is the cell membrane. Some prokaryotes have a layer external to the cell called the capsule or glycocalyx (glī-kō-kā-liks or -kal-liks).  Notice that this prokaryotic cell lacks all the organelles and the nuclear membrane of the eukaryotic cell shown. But bacteria do have ribosomes, cytoplasm, and DNA.

Fig 3.12. 3.13 show that Eubacterial cell walls have a layer of peptidoglycan (p) that is made of two sugars strung together into a polysaccharide backbone. The backbone repeats to form a sheet across and the sheet repeats to form layers.  The two sugars are N-acetylglucosamine (p) and N-acetylmuramic acid (p) (NAG & NAM). The polysaccharide backbones are anchored together by bridges made of short chains of amino acids. Short chains of amino acids are peptides and a glycan is a polysaccharide, hence the name peptidoglycan.

This peptidoglycan layer in the cell wall is important to the susceptibility of some bacteria to certain antibiotics. Penicillin for instance interferes with the synthesis of peptidoglycan. One reason that penicillin is so great is that it doesn't affect human cells because animal cells do not have peptidoglycan.

Gram Stain & the Cell Wall

In lab we will be doing Gram stains. The Gram stain differentiates between bacteria with different kinds of cells walls, Two Types: Gram+ & Gram-. 

Fig. 3.13a shows a Gram-positive cell wall.  External to the lipid bilayer of the plasma membrane you'll find layers of peptidoglycan that are the main component of the cell wall. The peptidoglycan in Gram positive bacteria is relatively thick and there is no outer membrane.

In Gram negative bacteria (fig. 3.13b) the cell wall is thinner and more complex.  External to the cell membrane is a thin periplasmic space containing the peptidoglycan layer. External to this is an outer membrane made of a lipid bilayer composed of phospholipid, lipopolysaccharide (lipid bound to sugar), and embedded lipoproteins (lipid bound to protein).  Note that the cell wall of Gram- cells has two layers, a peptidoglycan layer and an outer membrane.

Penicillin G does NOT act on Gram negative cell walls because the antibiotic cannot get through the outer membrane. Nutrients and other substances get through the outer membrane through channel proteins (porin molecules) they diffuse through the peptidoglycan, and they get through the cell membrane through protein channels.

The lipopolysccharides of cell walls vary among different strains of bacteria and it is sometimes possible to differentiate between different strains based on the way antibodies react to portions of the lipopolysaccaride
called O polysaccarides.

Later in the term, we'll discus that lipid A is an endotoxin, so that infection by a Gram- bacteria may be dangerous in patients.  If kill the cells by an antibiotic, you release the toxin! 

So Gram positive Eubacteria have a thick peptidoglycan layer. Gram negative Eubacteria have a thin peptidoglycan layer and an outer membrane.  

Everything we've discussed about the cell wall has been about Eubacteria.  Archeabacteria have different cell walls, but curiously there are species with thick cell walls that stain Gram+ and species with thin cell walls that stain Gram-.  

Archeabacteria do not have peptidoglycan except for one group of methanogens.

Summary of Prokaryotic and Eukaryotic Differences




diameter of most cells

1-10 um





membrane-enclosed organelles



 cell wall

complex (Gram+/-)

simple if present


smaller: 70S

larger: 80S

 Chromosome DNA 

single circular   chromosome
nonhistone proteins

many linear chromosomes
histone proteins


 no cytoskeleton

has cytoskeleton

 cell division

 binary fission



 no meiosis

has meiosis

Remember,ribosomes are the site of protein synthesis. Some antibiotics take advantage of the difference in prokaryotic vs. eukaryotic ribosomes.  For example, erythromycin (ir-rith-ra-mī-sin) (P) inhibits protein synthesis at bacterial but not eukaryotic ribosomes.

if time, discuss project 1.

ā   ē  ī  ō  ū