All the questions on the Unit 1 Review are answered in this Study Guide [notes written on the Review Slides]

Transformation is initiated by the recipient. the donor is not involved because it is dead. this is often how bacteria acquire antibacterial resistance. why?

Unit 1 Review 

Horizontal Gene Transfer: Done only by Prokaryotes (Bacteria and Archaea), uses plasmid DNA to transfer optional genes from one bacterial cell to another  =[Compare and contrast the three types of horizontal gene transfer. Your goal is to  be able to recognize one form of horizontal gene transfer from the other given just a description.]

1. Conjugation: DONOR MEDIATED. Donor cell forms a pilus, short straw like projection of the cell’s cytoplasm, which is the first plasmid gene  transferred to the Recipient cell. It increases antibiotic resistance and  increases diversity and survivability [Remember conjugation is mediated  by the donor. This is the most common form of horizontal gene transfer.]

What is the definition of the four ways of acquiring energy?

If you want to learn more check out What are the some type of investigation?

2. Transformation: RECIPIENT MEDIATED. Most likely cause of antibiotic  resistance. When the Donor cell dies it leaks its DNA which the Recipient  scavenges from its remains and uses to maybe get antibiotic resistance  due to the progress done by the genes provided by the Donor. A benign  bacterium could become virulent due to DNA genes from various dead  donors. [Transformation is initiated by the recipient. The donor is not  involved because it is dead. This is often how bacteria acquire  We also discuss several other topics like What are 2 general approaches to biology?

antibacterial resistance. Why?]

3. Transduction: VIRUS MEDIATED. Neither the Donor nor the Recipient  mediate this. A virus injects itself into a bacterial cell and multiples in  numbers but when the virus ejects itself it not only grabs viral DNA but  also some Bacterial DNA as well making the virus then ineffective. So, this results in a broken virus and because bacteria are hardwired to try out  DNA they will try the bacterial-viral DNA mix. [Transduction does not  involve either the donor or the recipient, but a virus instead. It is not the  intent of the virus; it is a mistake in the normal process. Why?]

Which reactions make nitrogen organic and which make it inorganic? how do plants acquire their nitrates?

If you want to learn more check out What is the difference between paracellular and transcellular?

Layers of Microbial Mats: Remember that prokaryotes are the only living things  below the top most layer of a microbial mat. This makes them essential in carbon  cycling. Remember that Oxygenic photosynthesis, anoxygenic photosynthesis,  aerobic respiration and anaerobic respiration are four different metabolic pathways.  Know what makes them different and whether prokaryotes, eukaryotes or both can  do each. Microbial Mats  Dependent on: 1. Availability of light and 2. Availability of  Oxygen  

1. Eukaryotes: Have only two ways to acquire energy

a. Oxygenic photosynthesis- uses light and gives off oxygen  

b. Aerobic respiration (cellular respiration)

c. Fermentation

2. Prokaryotes: prokaryotes can build ecosystems where light does not  reach and where they must recycle carbon.

a. Anoxygenic photosynthesis- uses light but does not use or give off  oxygen but instead used dihydrogen sulfide= purple

All the questions on the Unit 1 Review are answered in this Study Guide [notes written on the Review Slides]

b. Chemoautotrophy- are in the middle of the microbial mat because  they require both oxidized and reduced molecules We also discuss several other topics like What is cellular adaptations?

c. Anaerobic respiration- does not use any light or oxygen

d. Fermentation- is the support for microbial mad populations

Acquiring Energy and Carbon: Know the definition of the four ways of acquiring  energy. Remember which are unique to prokaryotes and which can be done by all  living things.

1. Energy Source

a. Sun: phototrophs

b. Chemical compounds: chemotrophs

2. Carbon Souce

a. Inorganic compounds, CO2: autotrophs

b. Organic compounds, glucose: heterotrophs

∙ Photoautotrophs- energy from the sun and carbon from carbon dioxide  (eukaryotes)

∙ Chemoheterotrophs- energy from chemical compounds and carbon  from glucose (eukaryotes) Don't forget about the age old question of How many moles are in 16.5g c? how many atoms of carbon is this?

∙ Photoheterotrophs- energy from the sun and carbon from organic  compounds (prokaryotes)

∙ Chemoautotrophs- energy from chemical compounds and carbon from  carbon dioxide (prokaryotes)

Sulfur Cycle: Be able to describe the contribution of prokaryotes to the sulfur  cycle. Focus on the bottom half of the cycle. Know the definition of assimilation,  reduction, and oxidation and describe which organisms do what. Describe how  sulfur becomes inorganic, then organic, then back again.  

 Sulfur cycle is which Sulfates are reduced to organic Sulfur which is  decomposed by fungi, to inorganic Hydrogen Sulfide which is then oxidized  back into organic sulfates. This whole cycle would crash without the use of  Prokaryotes (chemoautotrophs) that turn the Hydrogen Sulfide into sulfates  which can be broken down by eukaryotes to organic sulfur and used for  nutrients.  

1. Assimilation: is the act of pulling organic sulfates into organic sulfur  which is used by eukaryotes to synthesize protein and build tissue  for DNA.

2. Reduction: the process in which electrons are gained We also discuss several other topics like What are the different types of reaction times?

3. Oxidation: the process where electrons are lost

Hydrothermal Vents: This is an example of a habitat which chemoautotrophs live, specifically sulfur chemoautotrophs. What are the chemoautotrophs doing to sulfur? Relate this back to the sulfur cycle. What part of the cycle do these  chemoautotrophs fit?

All the questions on the Unit 1 Review are answered in this Study Guide [notes written on the Review Slides]

Chemoautotrophs are taking the inorganic hydrogen sulfide and  oxidizing it into organic sulfates which can be used by eukaryotes in the  environment to make organic sulfur, they are stripping it of electrons. They  fit into the cycle where the inorganic molecules are being converted back into organic molecules to help continue the cycle where there is no light.  Chemoautotrophs need both high and low levels of oxygen to oxidize and  reduce chemical compounds. Prokaryotes primary contribution to the carbon  cycle is that they allow things to live in places where there is no sunlight and  recycle carbon.  

- Eukaryotes get their energy from algae or plants which are the  primary sources of energy for them.  

Nitrogen Cycle: Remember the following terms, nitrogen fixation, nitrification,  denitrification and anammox reaction. Define each term in terms of what is  happening to nitrogen. Which reactions make nitrogen organic and which make it  inorganic? How do plants acquire their nitrates?

[STRICTLY PROKARYOTES] This cycle would not survive without the use  of prokaryotes. Nitrogen gas is the ultimate source of all nitrogen cycling  through all nutrients on the planet. It’s even more important than sulfur  because we use nitrogen to synthesize protein and DNA. Plants such as  peanut, soy beans, etc. are knowns as legumes because, these plants  perform nitrogen fixation and nitrification so much that they get enough  nitrogen to last them a life time so they leak the nitrogen out into the soil for  the surrounding plants to use as source of nutrients.

1. Nitrogen Fixation: This is the process of turning Nitrogen gas (N2)  into Ammonia (NH3).

2. Nitrification: process where prokaryotes turn Ammonia into Nitrates  (NO3-) and Nitrites (NO 2-)

3. Denitrification: turning Nitrates and Nitrites back into nitrogen gas.  4. Anammox Reaction:  

a. Equation: NH4+ + NO2-  N2 + H2O

b. In this reaction Archaeon’s help prevent nitrogen fixation  

from sucking out all the nitrogen from the atmosphere by  

giving it off through the anammox reaction.  

Phylogeny of Whole Genomes: Remember proteobacteria and cyanobacteria in  their role in shaping eukaryotic evolution.  

Proteobacteria are the ancestral traits to that of mitochondria. While  cyanobacteria are the ancestral trait or the beginning to chloroplast with an  endosymbiotic relationship with a dynamic membrane.  

Phylogeny of Archaea: Remember the three largest group of archaeons, the  euryarcheota, crenarcheota, and thaumarcheota. Know the defining characteristics  of each lineage, and be able to identify each lineage based on those characteristics.

All the questions on the Unit 1 Review are answered in this Study Guide [notes written on the Review Slides]

They live in very extreme environments and they are their own distinct group of prokaryotes.  

1. Euryarchaeota- (largest and most diverse group)

a. Normal temperatures

b. Acidifials- acid tolerant

c. Salt tolerant- they like salt

d. Methane producer- they produce methane (ex. Euryarchaeota live in a cows gut)

2. Thaumarchaeota- do anammox reaction (small group)

a. Don’t like hot temperatures but they LOVE cold temperatures i. Disturbs anammox reactions so they like the cold so  

their reaction is not disturbed  

b. They live in the ocean  

3. Crenarchaeote- like very very very hot temperature, they like  EXTREMELY HOT temperatures.

4. Firmicutes- like to live on our skin, in our mothes and in our gut. So  they like warm places where they can thrive.

Coevolution: Remember as many examples of coevolution between prokaryotes  and eukaryotes as you can. Examples are found in the Case 5 reading as well as the Case 5 excerpt at the end of chapter 26. Read both!

1. Wolbachia- protobacterial parasite that infect the host cell and  cause the cell to reproduce more females because they can only  reproduce through females rather than males. The cells are  

transferred by eggs and not sperm so this caused a dramatic  

increase in the population of female insects rather than male. The  males can mate with multiple females.

2. Bobtail Squid- The squid has a bacterium (Vibrio fischeri) which  causes the squid to glow in the dark. This helps the squid attract  prey that eat it so that it can then eat the thing that preys on it. The squid then increases its survival rate causing it to coevolve with the bacterium.

Diversity in Eukaryotes: Remember the characteristics of of eukaryotic cells and  how these characteristics result in eukaryotic diversity.

1. Membrane dynamics- they eukaryotic cell can change its shape  whenever it chooses to do so. They do this by leaking membrane to  the cytoskeleton which can change its shape at any point in time.  Ability to do all of the following items.

2. Compartmentalization of metabolic pathway- assembly line  

pathway for each thing to be done in different places

3. Genome Organization- enabling complex gene regulation; large  trend for Eukaryotes to massively expand their DNA size while  

Prokaryotes only have a single chromosome who stream-lining their genome because they are less resistant to mutation

All the questions on the Unit 1 Review are answered in this Study Guide [notes written on the Review Slides]

4. Genetic mutation by means of sex- (independent assortment and  fertilization) [1=haploid; 2=diploid]; sex is the ability to maintain or  generate genetic diversity

a. Must be diploid to have sex but animals like us are always  

diploid except for when it comes to reproduction

5. Life Cycles- ability to swap between haploid and diploid

a. Plants alternate between the two however, unicellular  

eukaryotes are haploid most of their lives

Eukaryotic Life Cycles: Be able to describe exactly what life cycles are, and how  they led to the evolution of sex. Remember the difference between haploid and  diploid and that both unicellular and multicellular organisms can be haploid  dominant or diploid dominant.

Unicellular eukaryotes are old school kingdoms of protist. During  favorable conditions where there is lots of food, water, etc. they reproduce  asexually (basically cloning themselves)

Unfavorable conditions are when there is less food, water, colder  temperatures, etc., etc. this is when each individual haploid cell find another  haploid cell and it fuses with it. This only happens when resources are low  and this is called sexual reproduction

Haploid is where there are only one set of genes while diploid has two  sets of genes which is what most of out bodies are made of.  

Origins of Eukaryotic Cells: Remember the two alternative hypotheses for the  origin of eukaryotes. The difference between the two boils down to timing.

Hypotheses: There are two hypotheses’ on how the first mitochondria formed  but, scientist don’t know which one is which for sure because they would  need a time machine to see the exact time which one was true over the  other. This led to the first heterotrophic eukaryote based on the use of a  mitochondria.

1. In the first hypotheses the dynamic membrane or the eukaryotic  cell eats a proteobacteria but instead of digesting it like it had  

intended. They bacteria forms an endosymbiotic relationship with  the bacteria using it as the first mitochondria. So basically the  

Dynamic membrane came first then the mitochondria

2. The second hypotheses are where the proteobacteria forms a  endosymbiotic relationship with an archaeon which then which then led to the dynamic membrane. The proteobacteria because the  mitochondria of the cell.  

Origin of Chloroplast: Chloroplasts ultimately evolved from cyanobacteria in what is called the primary endosymbiotic event. Define primary endosymbiosis and know  examples of eukaryotes that have done this. What prokaryotes did mitochondria  evolve from?

All the questions on the Unit 1 Review are answered in this Study Guide [notes written on the Review Slides]

Primary endosymbiosis started off with a eukaryotic cell finding an Algae/  Cyanobacteria and the dynamic cell membrane engulfs the cell with the  purpose to eat it but instead it forms a symbiotic relationship with it. This in  turn means that it can take light from the sun and turn it into sugar.  

Secondary endosymbiosis happened when the eukaryote that formed a  relationship with a cyanobacteria eats algae which then gets eaten by other  eukaryotes also causing it to form endosymbiotic relationships with other  eukaryotes as well.

Successive Endosymbiotic Events: Describe how this figure demonstrates  secondary endosymbiosis. What makes it different than primary? How can you tell?  What are examples of eukaryotes that have undergone a secondary endosymbiotic  event?

This figure demonstrates secondary endosymbiosis because, the original  eukaryotic cell is eaten another cell causing it to for a symbiotic relationship  with it. In primary endosymbiosis there is only one symbiotic event that takes place however, with this there are two meaning that it has to be secondary  endosymbiosis. Rhizarians are an example of eukaryotes that have  undergone endosymbiosis.  

Eukaryotic Tree of Life: Remember the seven known eukaryotic superkingdoms.  Be able to list the defining characteristic of the 5 largest superkingdoms,  ophistokonts, amoebozoans, archeplastids, stramenopiles, and alveolates, and give  examples for each.

1. Ophistoknonts- The defining characteristic of opisthokonts is? Remember  any animal and any fungi that exists is part of the ophistokont  

superkingdom.

a. animals and fungi

b. Single celled with a flagella  

c. Human’s sperm- chanoflagellates= Remember, choanoflagellates  are animal’s most closely related unicellular ancestor, and share  many of the same traits as animals (i.e. cadherin)

2. Amoebozoans- Remember the defining characteristic of this clade. This is  also a clade that has acquired photosynthesis via a secondary  

endosymbiotic event.  

a. False feet; to attach to their environment to move around

b. Amoebic dysentery (similar- white blood cells but not the same)= This is an example of a pathogenic amoebozoan.

c. Plasmodial slime molds: simple, multicellular structures coencytic  organization: merge cytoplasm to become one

d. Cellular slime molds: moves along like a slug or an inch worm, turns into a stalk and releases it

i. Plasmodial slime molds exhibit coenocytic organization,  

which is a type of simple multicellarity, and cellular slime  

molds make simple multicellular structures called ‘slugs.’

e. Merge always but ONLY send up stalks when resources are low

All the questions on the Unit 1 Review are answered in this Study Guide [notes written on the Review Slides]

3. Archaoplastids- Archaeplastida are defined by chloroplasts that were  formed via a primary endosymbiotic event. What does this mean? a. Most seaweed and land plants, red algae and green algae

i. Primary endosymbiotic relationship  

b. Red algea- used to make ice cream and toothpaste= Despite being  red and exclusively aquatic, they are in the same superkingdom as  land plants.

c. Green alage- little plants that live in the water= Remember green  algae are essentially aquatic land plant ancestors. They can also  have coenocytic organization. What other characteristics do green  algae have?

4. Stramenopiles- Stramenopiles are united by the presence of two flagella,  shown above.

a. Diatoms= Other than being an example of stramenopiles, diatoms  also make tests (shells) of calcium carbonate or silica, are primarily  photosynthetic and spend most of their lives as diploid. What type  of life cycle would they have?

b. Brown algae (kelps)= Kelps are complex multicellular organisms  that resemble plants, but are not. They also acquired chloroplast via a primary endosymbiotic event, independently from archeplastida.

5. Alveolates- Remember the defining characteristic of alveolata, the  presence of fluid filled vesicles calle alveola underneath the membrane,  and the examples, dinoflagellates, ciliates, and apicomplexans (malaria). a. Dinoflagellates

b. Ciliates

c. Paramecium

d. Apicomplaxans (have highly complex lifestyle and coevolve with  hosts like malaria)

e. Fluid filled vesicles underneath their membranes

f. Algal blooms and red tides= What are algal blooms and red tides?  What is the difference between them? Describe the series of events that lead to algal blooms and red tides. What organisms are  

involved? What are their superkingdoms? If you didn’t know,  

coccolithoporids (shown above) are Rhizarians.