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Review Guide:

General Questions/Skills:

1. Be able to draw a polypeptide given only the letter designations for the amino acids.

2. Given a list of 6 organisms (mentioned in class), be able to draw the big tree, labeling three domains, the root, and relative branch lengths for the domain.

Origin is on bacteria line in the middle. Archaea are generally shorter lines, bacteria are the intermediate lines and eukaryotes are the longest lines. Organisms:
Are there going to be specific organisms from throughout the class on this exam or just from lecture 2?
3. What are the methods used to quantify organism? What are some pros/cons of each method?

4. What are the methods used to measure diversity? What are some pros/cons of each method?

5. Define/differentiate between three types of homologs. How could you look for each type?

Homolog all share the same origin
Ortholog share the same genes and function
Paralog share the same genes
Xerolog lateral transfer of genes

6. Be able to explain dideoxynucleotide method of DNA sequencing.

Terminates DNA chain growth at specific bases in “Sanger” sequencing.

7. What are the general steps in the ‘rRNA approach’ to analyzing the diversity in the community?

8. What are the advantages to the “rRNA approach”

9. What is wrong with “prokaryote”, “protest” and “monera”? How has our understanding of these words changed?

10. What biochemical traits are similar/different between the three domains?

11. What staining/fluorescence tools do we use to count organisms? To sort organism?

12. Given a list of compounds, be able to identify the electron donors and acceptors.

“Electron Donors” (Food) Reduced Carbon, H2S, H2, Fe(II), light-plus-pigment, NH4 “Terminal Electron Acceptor” (To breathe) O2, SO4^2-, Fe(III), organics, CO2, NO3^-, S^0

13. Be sure to solve various Poisson problems:
P(x)=probability, m=mean, x=number of times
Example: You have 1000 page book. You open and close the book 2000 times. Odds of no occurrence: P(0)=(2^0/0!)e^-2
One occurrence: P(1)=(2^1/1!)e^-2
Two things occurring simultaneously one each: P(2)=(2^2/2!)e^-2 Number of passes needed for 97%, or 99% coverage: .01=P(0)=(m^0/0!)e^-m=e^-m (for 99%) m=-ln(0.01)=4.61*length of book **Look at Poisson Study Guide**

14. Be able to sketch a phylogenetic tree given a short sequence sample

Create a table with differences on the right side and identifications on the left. How do we determine to draw the tree after obtaining this information?

15. Have a general understanding of the various mechanisms of photosynthesis and other forms of carbon fixation and how they are distributed throughout the tree.


1. Xenolog, Paralog, Ortholog, Homolog
Homolog all share the same origin
Ortholog share the same genes and function
Paralog share the same genes
Xerolog lateral transfer of genes

2. Polytomy many temporal based branches
3. Clade group of organisms (sequences) more closely related to one another then to any non-clade organism 4. Indel alignment gap either insertion or deletion
5. Chemotroph, Heterotroph, Autotroph, Phototroph
The roots:
“Organo-“ – organic electron donor for energy
“Litho-“ – inorganic electron donor for energy
“Chemo-“ – chemical source of energy
“Photo-“ – light energy
“Hetero-“ – organic carbon-source
“Auto-“ – CO2 carbon source
Chemotroph obtain energy and carbon from reduced organics
Heterotroph organism derived from its nutritional requirements from complex organic substances Autotroph organism that is able to form nutritional organic substances from single inorganic substances Phototroph obtains energy from photosynthesis and fixes carbon dioxide Lithotroph energy from reduced inorganics

6. Microbial Community, Microbial Population, Microbial diversity Community collection of organisms that interact with one...
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