Biology 1A    Sept 8, 1998
Lecture 4 - DNA, Archaea, Bacteria

Page Contents :

• Reading Assignment
• Overview of Lecture
• Overview of Lab
• Lecture Outline
• Vocabulary
• Study Questions
• Related Websites

Stern: Chapter 17

Overview of Lecture:

DNA is the "master molecule" of life.
All life may be divided into three domains.
Introduction to the Archaea.
Introduction to the Bacteria.

Overview of Lab:

(A bullet indicates a handout.)
• Morphology of Bacteria.
• DNA Extraction.

A. The molecular structure of DNA.
1. Reprise: Nucleotide structure
2. The nitrogenous bases
a. adenine, cytosine, guanine, thymine
b. Specificity of base pairing (GCAT)
c. Semi-conservative duplication.
B. Protein synthesis: The molecular functioning of DNA.
1. Transcription - production of RNA from DNA.
2. Translation - production of protein from the RNA message.
a. mRNA - the encrypted message; codons and the DNA code
b. rRNA - ribosome function
c. tRNA - selectively bind to amino acids
C. Differences between Bacterial and Eukaryotic DNA.
1. Bacteria have one large loop of "naked" DNA; may contain plasmids.
2. Eukaryotes have several complicated chromosomes.
a. Histones - packaging proteins for supercoiling
b. Eukaryotes have introns - "split genes" that must be removed to translate
c. Heterochromatin - inactive DNA

A. Reprise; All life has:
1. Same chemistry and cell structure
2. Suggests life has a single origin
3. Five Kingdoms is the most popular classification system, but underplays the diversity of the Monera; emphasizes eukaryotes.
B. The overall tree of life
1. Evolutionary distance
a. Compare DNA sequences for similarities and differences.
b. Assume similarities are inherited from a shared ancestor.
c. Assume differences represent evolutionary changes.
d. Therefore, more similarity means more shared history, closer relationship.
e. Need a stable (important) sequence, e.g. rRNA.
2. The rRNA tree reveals three major groups, called domains.
a. One group is the eukaryotes, two are prokaryotic.
b. Monera are more diverse than previously thought.
c. Archaea & Bacteria, each as different from the other as from Eukaryotes.
d. No one group is ancestral to the others.

A. The Archaea have only recently been recognized as a group.
1. Previously grouped with the bacteria.
2. DNA is structured much like bacterial DNA.
3. Uniqueness discovered by Dr. Carl Woese in the 1980s.
B. When first discovered, they were called archaebacteria, but unlike the bacteria . . . .
1. Antibiotics that affect Bacteria protein synthesis do not affect Archaea.
2. Have a different cell wall chemistry - protein, glycoprotein, or polysaccharide
3. Membranes structurally similar, but chemically unique
a. Lipids are ether-linked (not ester-linked)
b. Branched hydrocarbons and rings (not fatty acids)
c. Glycerol may be attached at both ends (diglycerol)
C. Archaea live under extreme conditions.
1. High-temperature (near 105 °C); hot springs & rift vents
2. Alkaline or acid environments
3. Extremely saline conditions
D. Four major groups of Archaea
1. Methanogens - strictly anaerobic; trace metal Ni is required.
2. Extreme halophiles - require lots of salt, particularly Na, for growth
3. Hyperthermophiles (also called Crenarchaeota, Eocytes) - thermophiles; mostly anaerobes; most dependent on elemental sulur
4. Thermoplasma - acidophilic & thermophilic; no cell wall; placement uncertain.

A. Prokaryotic DNA
1. Chromosome is a single loop in the cytoplasm; there is no nucleus.
2. There may also be plasmids.
B. Bacterial Reproduction
1. binary fission - loop binds to cell membrane for division
2. conjugation - exchange of DNA through cytoplasmic connections called pili
C. Bacterial Morphology
1. Some bacteria have flagellae composed of the protein flagellin
2. Nearly all bacteria have cell walls.
a. rigidity prevents the cell from bursting from excess water uptake
b. contains peptidoglycan - only found in bacteria
c. There are two types of bacterial walls distinguished by the Gram stain
3. Three basic bacterial shapes : bacillus (rod), coccus (ball), spirillum (spiral)
D. Bacterial Nutrition
1. aerobic or anaerobic
2. saprophytic, parasitic, autotrophic
3. Must live within their food supply; their byproducts can be useful or harmful
4. Examples of bacterial disease (e.g., acne, strep throat, pneumonia, diphtheria, tuberculosis)
E. Controlling Bacterial Disease
1. freezing, salting, pickling, drying
2. canning -- cook food, then seal out new invasion
3. antibiotics - penicillin & streptomycin
F. Importance of Bacteria
1. food flavor by weak acid production (e.g. vinegar, pickles, and sauerkraut)
2. genetic engineering - bacteria-produced medicines, genetics research
3. sewage treatment - breakdown of wastes
4. bacterial digestion of grains - mammals (e.g. ruminants) cannot digest cellulose
5. vitamin synthesis - E.coli produce B vitamins

• Where can you find DNA in nature? Do plants have DNA? Do bacteria?
• In a plant or animal cell, where is the DNA?
• What four nitrogenous bases occur in DNA? In RNA? How do these bases pair in DNA/RNA?
• What does it mean that DNA replication is "semi-conservative"?
• What is the product of transcription? Of translation?
• Why are three nucleotides needed to form a codon?
• Describe briefly how rRNA sequences were used to generate a phylogeny of life.
• What are the three domains? Which are prokaryotic? Which have heterochromatin?
• What is the difference between a prokaryotic cell and a eukaryotic cell?
• How is DNA in bacteria different from DNA in plants or animals?
• Does mitosis occur in bacteria? In Archaea? How do you know?
• Compare the chemistry of the cell wall in a plant, fungus, and bacterium.
• How is the Archaea cell wall different from the cell wall in Bacteria?
• Describe three ways in which the cell membrane of Archaea is different from the cell membranes of Bacteria and Eukaryotes.
• Where do Archaea live?
• Are the Archaea likely to cause disease in humans? Why or why not?
• What are plasmids, and why are they importnat?
• Compare and contrast mitosis with binary fission.
• What is the chemical composition of bacterial flagellae? Of bacterial cell walls?
• What does the Gram stain tell you about a bacterium? That is, how are Gram positive and Gram negative bacteria different?
• What are the three basic bacterial shapes?
• Many packaged foods have a label that says "refrigerate after opening". Why?
• What happens to canned food if pre-cooking didn't kill all the bacteria?
• What are some beneficial uses of bacteria?
• How is the bacterium E. coli important for human health?

• UCMP - Three Domains of Life
• UCMP - Introduction to the Bacteria
• UCMP Glossary : DNA
• Tree of Life - Archaea
• Cells Alive!
• JENA Image Library of Biological Macromolecules