Bio 301E Handout 1 - Diversity of Cells and Organisms Aug 26-31

1. What are some properties common to all living organisms that distinguish them from non-living entities? All living organisms share seven common properties of life: they must be made of cells, be able to reproduce, contain DNA, obtain and use energy, respond (or react) to their environment in some way, and must maintain homeostasis. Organism must contain the cell, which is the most basic unit of life, and can be either unicellular (containing only one cell) or multicellular (containing many cells). Living things can reproduce either sexually, when two parent organisms combine genetic material to produce the offspring, or asexually, when a single organism can divide or “bud” to create it’s offspring without additional species. Living things share a Universal Genetic Code, which makes up part of the DNA. Growth refers to two processes: increase in the number of cells and increase in the size of cells. Development refers to changes in the organism, which occur through its life span, including cell differentiation, organ development, aging and death. Energy is used by all living things for growth, development, and reproduction. Life processes which results in “building” the organism is known as anabolism, and life process where energy is extracted by “breaking down” substances is called catabolism. Something which causes an organism to react to its environment is known as a stimulus (stimuli) and the ability of organism to react is called irritability. Lastly, organisms must maintain homeostasis, which is an internal stable set of internal conditions allowing the chemical reactions of life to occur.

2. What is meant by the term biodiversity? List some arguments that people use in favor of preserving species biodiversity. What is extinction? What are the major threats to the earth’s biodiversity today? Biodiversity refers to the variety of life in a particular habitat or ecosystem. More largely, biodiversity is the variety of life on the entire Earth. Biodiviersity is important to humans because it helps to create sustainability in ecosystems, which we need to survive. Additionally, biodiversity ensures that we have ample variety of food choices. Medically, more biodiversity allows for more potential drugs to be discovered. Extinction is when a species or family of organisms die out and seize to exist. Several recent events threaten the life of many organisms and cause concern for their extinction. Perhaps the most concerning is the rise of global warming. Global warming threatens the environment of many plants and animals, such as the polar bears and their icy homes. Scientists fear that the earth’s temperature will increase to such a level that many animals will no longer be able to thrive on earth.

3. All organisms on earth have some chemistry in common - all use ATP as an energy currency molecule; all use DNA as an information storage molecule; all use enzymes and other proteins to control rates of specific cell processes. Be familiar with these systems, and tell why this adds to the evidence suggesting that all life on earth evolved from a common origin.  Energy-­‐storing  Molecules  

  Electrons Carriers

Oxidized  Form  

Generated  In   Reduced  Form  

Generated  in  

NAD+   Electron  Transport  Chain,  Fermentation  

NADH   Glycolysis,  Preparing  Pyruvate,  Krebs  Cycle  

FAD   Electron  Transport  Chain   FADH2   Krebs  Cycle  NADP+   Calvin  Cycle   NADPH   Light-­‐dependent  Reactions  

Adenosine Triphosphate (ATP)

Process  that  Generates  ATP   Utilized  During  Substrate-­‐level  phosphorylation   Glycolysis,  Krebs  Cycle  Chemiosmosis  (using  ATP  synthase)   Oxidative  Phosphorylation,  Light-­‐  

dependent  Reactions      

Other  Key  Molecules  to  Know    

4. Through what processes could living cells have originated in the abiotic earth? Summarize the concepts of “chemical evolution” (before the origin of the first cells) and the “endosymbiosis hypothesis” for the origin of eukaryotic cells. How can scientists study how these processes happened? The “chemical evolution” refers to the chemical changes on the primitive Earth that gave rise ot the first forms of life. The first living things on Earth were prokaryotes with a type of cell similar to present day bacteria. The chemical and physical conditions of the primitive Earth are invoked to explain the origin of life, which was preceded by chemical evolution of organic chemicals. The hypothesis is that life developed from non-living materials eventually, by the process of natural selection, over hundreds of millions of years, became able to self-replicate and metabolize. Scientists usually propose a four-stage process of formation for the first life: 1. formation of small organic molecules (amino acids, nucleic acid bases,…) 2. and these combine to make larger biomolecules (proteins, RNA, lipids,…), 3. which self-organized, by a variety of interactions, into a semi-alive system , 4. that gradually transformed into a more sophisticated form, a living organism. The “endosymbiosis hypothesis” is the theory that explains the origin of eukaryotic cells from prokaryotes. Both mitochondria and chloroplasts have their own genome, which consists of a single circular molecule of DNA and resembles that of bacteria. The DNA in neither the mitochondria nor chloroplasts has histones associated with it. Both the mitochondria and chloroplast use the DNA to produce many proteins and enzymes required specifically for their own function. The mitochondria and chloroplasts cannot be formed in a cell that lacks them because they can only be formed from preexisting mitochondria and chloroplasts. Similar to bacteria, they replicate their own DNA and direct their own division. A double membrane surrounds both of the organelles, which, once again, suggests that they were ingested by a primitive host

Molecule   Why  You  Should  Know  It  Glucose   Substrate  for  cellular  respiration  Phosphofructokinase   Enzyme  that  is  key  to  regulation  of  glycolysis  (and  cellular  

respiration);  phosphorylates  fructose-­‐6-­‐P  Glyceraldehyde-­‐3-­‐Phosphate   Intermediate  in  glycolysis,  product  of  Calvin  cycle  Pyruvate   Product  of  glycolysis  and  substrate  that  is  converted  to  acetylCoA  

for  the  Krebs  cycle  Acetyl  CoA   Starting  material  for  Krebs  cycle  Oxaloacetate   Accepts  the  two  carbons  from  acetyl  CoA  in  the  first  step  of  the  

Krebs  cycle  Citrate   Product  of  the  first  step  of  the  Krebs  cycle  ATP  Synthase   An  integral  membrane  protein  that  generates  ATP  using  the  flow  of  

protons  down  their  gradient  Ribulose  bisphosphate  (RuBP)   Substrate  for  first  step  of  Calvin  cycle  Rubisco   Enzyme  that  catalyzes  the  first  step  of  Calvin  cycle  3-­‐phosphoglycerate   Product  of  the  first  step  of  Calvin  cycle  

(learn.genetics.utah.edu). The larger prokaryote did not destroy the smaller, engulfed prokaryote, indicating that there must have been some advantage to keeping the engulfed prokaryote as an endosymbiont greater than the advantage brought about by breaking it down. Likewise, the engulfed prokaryote did not destroy its host, again indicating that there must be some benefit to being an endosymbiont. One advantage to the two prokaryotes is the ability to generate more energy. It is possible that the smaller prokaryote is able to provide the larger prokaryote with sugar in return for energy, or vice versa. 5. What is the overall reaction for aerobic cellular respiration of glucose? What is the overall reaction of photosynthesis? Be able to relate the cellular processes of cellular respiration overall and photosynthesis overall to global cycles of nutrients (when we discuss ecosystems).

Cellular  Respiration  (C6H12O6  +  6O2  à 6CO2  +  6  H2O  +  Energy)  

Glycolysis (C6H12O6 à 2C3H3O3 + Energy; occurs in the cytoplasm)

Krebs Cycle (AKA Citric Acid Cycle, Tricarboxylic Acid Cycle; Acetyl CoA à 2 CO2 + Energy; occurs in mitochondrial matrix) Input   Output  Acetyl  CoA   2  CO2  

3  NAD+   3  NADH  FAD   FADH2  

ADP  +  Pi   ATP  

Preparing Pyruvate (C3H3O3 à CO2 + Acetyl CoA + Energy; occurs in mitochondrial matrix)

 Electron Transport Chain (Part of Oxidative Phosphorylation; generates proton gradient; occurs across the inner mitochondrial matrix)

 Input   Output  NADH   NAD+  FADH2   FAD  O2   2  H2O  

 

Photosynthesis  (6CO2  +  6  H2O  +  Energy  à C6H12O6  +  6O2)  

Light Dependent Reactions (Light Energy à Chemical Energy; occurs across the thylakoid membrane)

Calvin Cycle (3CO2 + Energy à Glyceraldehyde-3- Phosphate; occurs in stroma)

Input   Output  NADP+   NADPH  ADP  +  Pi   ATP  2  H2O   O2  

6. Name the three domains of life and give an example type of organism in each. Distinguish

Input   Output  Pyruvate   Acetyl  CoA  +  CO2  

NAD+   NADH    

Input   Output  Glucose   2  Pyruvate  2  NAD+   2  NADH  ADP  +  Pi   4  ATP  (gross);  2  ATP  

(net)  

 

Input   Output  3  CO2   Glyceraldehyde-­‐3-­‐P  6  NADPH   6  NADP+  9  ATP   9  ADP  +  Pi    

prokaryotic cells from eukaryotic cells, and relate those terms to the three domains of life. Describe energy acquisition and cell specialization seen in three major kingdoms of multicellular organisms. The three domains of life include eukarya, bacteria, and archaea. Eukarya includes eukaryotic organisms, such as humans, horses, and dogs. These are organisms with cells that contain a nucleus as well as membrane-bound organelles. The kingdoms most associated with Eukarya are the Plantae, Animalia, and Fungi kingdoms. Additionally, Kingdom Protista has had some of its organisms, such as amoebas and some seaweeds, classified as Eukarya. Although similar to each other, bacteria (ex. coccus, bacillus, spirrillum) and archae (ex. sulfobus) have a couple major distinctions. Firstly, archae cell walls do not contain peptidoglycan, which is a polymer consisting of polysaccharide and peptide chains that are found in bacterial cell walls. While archae can have a variety of cell walls, some cell walls are made of pseudopeptidoglycan. The cell membranes of archae have a very unique structure and do not contain lipids. The cell membrane of archae usually contains linkages, where as bacteria cell membrane contains ester bonds. Thirdly, archae have three RNA polymerases like eukaryotes, and bacteria have only one RNA polymerase. Furthermore, archae and bacteria are usually found in very different types of environments. Bacteria can be found in a variety of locations, but archae is usually found in harsh environments. There are several main distinctions between prokaryotic and eukaryotic cells (see cod.edu for more information): 1. Eukaryotic cells have a true nucleus, bound by a double membrane. Prokaryotic cells have no nucleus. The purpose of the nucleus is to sequester the DNA-related functions of the big eukaryotic cell into a smaller chamber, for the purpose of increased efficiency. This function is unnecessary for the prokaryotic cell, because its much smaller size means that all materials within the cell are relatively close together. Of course, prokaryotic cells do have DNA and DNA functions. Biologists describe the central region of the cell as its "nucleoid" (-oid=similar or imitating), because it's pretty much where the DNA is located. But note that the nucleoid is essentially an imaginary "structure." There is no physical boundary enclosing the nucleoid. 2. Eukaryotic DNA is linear; prokaryotic DNA is circular (it has no ends). 3. Eukaryotic DNA is complexed with proteins called "histones," and is organized into chromosomes; prokaryotic DNA is "naked," meaning that it has no histones associated with it, and it is not formed into chromosomes. Though many are sloppy about it, the term "chromosome" does not technically apply to anything in a prokaryotic cell. A eukaryotic cell contains a number of chromosomes; a prokaryotic cell contains only one circular DNA molecule and a varied assortment of much smaller circlets of DNA called "plasmids." The smaller, simpler prokaryotic cell requires far fewer genes to operate than the eukaryotic cell. 4. Both cell types have many, many ribosomes, but the ribosomes of the eukaryotic cells are larger and more complex than those of the prokaryotic cell. Ribosomes are made out of a special class of RNA molecules (ribosomal RNA, or rRNA) and a specific collection of different proteins. A eukaryotic ribosome is composed of five kinds of rRNA and about eighty kinds of proteins. Prokaryotic ribosomes are composed of only three kinds of rRNA and about fifty kinds of protein. 5. The cytoplasm of eukaryotic cells is filled with a large, complex collection of organelles, many of them enclosed in their own membranes; the prokaryotic cell contains no membrane-bound organelles which are independent of the plasma membrane. This is a very significant difference, and the source of the vast majority of the greater complexity of the eukaryotic cell. There is much more space within a eukaryotic cell than within a prokaryotic cell, and many of these structures, like the nucleus, increase the efficiency of functions by confining them within smaller spaces within the huge cell, or with communication and movement within the cell. 7. Distinguish, and be able to apply, two ways by which biologists define “species”? How do new species form? What are some reproductive isolating mechanisms keep two species from interbreeding? A species is a population or group of population whose members have the potential to

interbreed in nature and produce viable, fertile offspring, but are unable to produce viable, fertile offspring with members of other populations. More concisely, species consists of all organisms that are similar enough to interbreed, no matter where they are found (Audesirk 9). Evolution of species occurs through changes in a gene pool (microevolution) and diversion and divergence of a gene pool (macroevolution). Species evolve either through either two patterns of evolution, anagenesis or cladogenesis. Anagenesis refers to a gradual change of one species into another, where as cladogenesis means when one gene pool splits and two new species arise. Reproductive isolation is when barriers exist that prevent the production of viable, fertile offspring between species. There are two types of reproductive isolation: prezygotic and postzygotic barriers. Prezygotic barriers (“before the zygote”) prevent mating or fertilization, where as postzygotic barriers (“after the zygote”) prevent the development of zygote into a viable, fertile adult. Examples of prezygotic barriers include habitat isolation, temporal isolation, behaviorial isolation, gametic isolation, and mechanical isolation. Habitat isolation is when species live in the same region but different habitats. Temporal isolation means that organisms reproduce at different times of the year, which prevents them from being able to breed amongst each other. Behavioral isolation refers to the different courtship rituals that are used to attract mates. Gametic isolation means that the sperm cannot fertilize the egg. Lastly, mechanical isolation indicates morphological differences, which inhibits an organism from being able to breed with another. Postzygotic barriers include reduced hybrid viability, reduced hybrid fertility, and hybrid breakdown. Reduced hybrid viability means hybrid offspring do not develop normally, and repuced hybrid fertility means that hybrid offspring are fertile. Finally, hybrid breakdown indicates that the offspring of the hybrids (F2 generation) are not viable and/or fertile. There are two main modes of speciation: allopatric speciation and sympatric speciation. Allopatric speciation is the geographic separation of a single population, and sympatric speciation is when one population diverges into two species. Allopatric speciation requires a geographical barrier, either when a new barrier arises (ex. as water level decreases, one lake becomes two) or the colonization of a distant land (ex. Galapagos Islands). The magnitude and type of a barrier in allopatric species depends on the mobility of species. In sympatric speciation, one population can become two different species either through habitat differentiation (ex. North American apple maggot fly), polypoloidy, or sexual selection. Autopolyploiody, the process where an individual belonging to some species doubles its genome, is common in plants and results in tetraploid species that cannot mate with original diploid species due to reduced hybrid fertility. Sexual selection is an uncommon, yet important, type of spympatric specition in which non-random rating results in disruptive selection (such as African cichlids in Lake Victoria). 8. What is the binomial naming system of organisms devised by Linnaeus? Describe Linnaeus’ hierarchical system of classifying organisms. How do classification systems relate to evolutionary history as hypothesized in phylogenetic trees?   Linnaeus devised the Linnaean taxonomy, which classifies organisms into the three different kingdoms, divided by classes, families, genera, and then species. Traditional, biological classification schemes included the idea of “ranks,” such as species, genus, family, order, class, etc. In this system (the Linnaean system), for example, there is a Class Reptilia and a Class Aves. However, the bulk of evidence supports, and the majority of scientists now agree, that the group Aves belongs within the larger group Reptilia (birds share a most recent common ancestor with crocodiles, which are generally included in the Class Reptilia). Within a traditional, Linnean system of classification this means that either the Class Aves is demoted to something below a class, or that a class (Aves) exists within another class (Reptilia). Problems such as this have prompted many scientists to propose that a system of naming and classification of biological diversity be rank-free. Classification systems then only indicate the hierarchical structure of groups according to the current understanding of their evolutionary history, leaving out rank labels.