Final Exam Questions...courtesy of your peers!

Here are the questions everyone turned in to be added to the final.

1. Why are thermophiles able to grow and thrive in such high temperatures?
2. What is the PCR process? What is it used for?
3. What part of thermophiles are used in PCR?
4. Mycorrhizae: What are they?
5. Do fungi reproduce asexually or sexually?
6. Mycelium: What is it’s location on a fungus?
7. Yeast is part of the ______Kingdom, has a high/average/low metabolic rate, and grows as normal cells and/or pseudomycelium.
8. Candida yeast are commonly/sometimes/rarely present in the human body, cause inflammation when the immune system __________and are aerobic/anaerobic.
9. Give as much detail as possible on the two methods of reproduction in yeast.

10. Where are blue-green algae found?
11. How do blue-green algae get its food?
12. Name one of the ways blue-green algae is being used today.
13. What are Koch’s four postulates?
14. What is the difference between an exotoxin and an endotoxin?
15. What is virulence factor?
16. What are the four forces? Describe each.
17. Draw and label a eukaryotic cell.
18. What makes carnivorous plants unique?
19. What is a red bulls eye rash a sign of?
20. How is Lyme disease most often transmitted?
21. How is Lyme disease most often treated?

Autotrophs Rule!!!

A nice perspective shot on the size of sequoia trees in California. Joy is standing in the burned out section of this organism that has grown around the wound and continues to thrive.

Homework for tomorrow is below and please read the two chapters listed in your syllabus for lecture. There will be discussions on the topics.

Happy Reading,

Janine

AS405 –Day 7 Homework

1. Home canners pressure-cook vegetables as a precaution against what organisms? What are the variables that pressure-cooking eliminates from these organisms life cycle.

2. Why are the protists especially important to biologists investigating the evolution of eukaryotic life?

3. Why doesn’t the sexual life cycle of humans, which has haploid and diploid stages, qualify as an example of alternation of generations?

4. Why is the health of lichens an indicator of air quality?

5. What is athlete’s foot?

AS405 –Day 8 Homework

1. Give 5 basic differences between monocots and dicots.

2. Why are the leavevs of most plants green? Give details.

3. Why will a tree die if it is girdled? Use appropriate terms and systems.

4. How is water taken up a tree beyond 10.3 meters?

5. Describe symbiotic nitrogen fixation.

Beautiful Funguys

For Hayley and the rest of you that want to see some really cool photos of Fungi. Just Lovely!

Team Teaching Biology

Everyone did great at teaching their various subjects!!! Now, onto the final exam questions. Create three questions from your topic of lecture today for the final. What are the things that you think your fellow geeks aught to know? Homework will be asked for at the beginning of class tomorrow.

Also, reading for tonight will be Chapters 10, 35, 36, 37. It is the world of the Autotrophs we will be discussing tomorrow!! Woo-hoo. Not that I have a bias! LOL!

Janine

Genetics, Day 5 Enjoy the weekend!

The animal with the largest number of chromosomes, I think, is the King Crab at 208! If anyone finds out differently, please post your results. Thanks! Homework below for Day 5.

AS405 –Day 5 Homework ________________________________

1. Compare & Contrast the rival theories of inheritance between Darwin and Mendel. Describe the strengths and weaknesses of both pangenesis and Mendel’s work.

2. Define genotype and phenotype and explain why the relationship between the two is rarely simple. Site examples in your argument.

3. Explain why sex-linked diseases are more common in human males.

4. Describe the structure and functions of telomeres. Explain the significance of telomerase to healthy and cancerous cells.

Cell Theory Lecture 4

Here is the homework for Day 4. Please have chapters 13-16 read prior to coming to class.

AS405 –Day 4 Homework Name: ____________________

1. What are the three stages of cellular communication? Describe what is happening and in what location of the cell.

2. State the stages of cellular mitosis and describe the activity.

3. List and describe the differences between normal and cancer cells.

Read Chapters 10, 11 & 12

Hi, folks.

Please be sure and read chapters 10, 11 & 12 for class on Thursday. You will be asked to summarize the information therein.

Happy reading!

Lecture 3 - Glycolysis, Kreb's and Electron Transport

Krebs Cycle

The citric acid cycle, also known as the tricarboxylic acid cycle (TCA cycle) or the Krebs cycle, (or rarely, the Szent-Györgyi-Krebs cycle) is a series of enzyme-catalysed chemical reactions of central importance in all living cells that use oxygen as part of cellular respiration. In eukaryotes, the citric acid cycle occurs in the matrix of the mitochondrion. The components and reactions of the citric acid cycle were established by seminal work from both Albert Szent-Györgyi and Hans Krebs.

In aerobic organisms, the citric acid cycle is part of a metabolic pathway involved in the chemical conversion of carbohydrates, fats and proteins into carbon dioxide and water to generate a form of usable energy. Other relevant reactions in the pathway include those in glycolysis and pyruvate oxidation before the citric acid cycle, and oxidative phosphorylation after it. In addition, it provides precursors for many compounds including some amino acids and is therefore functional even in cells performing fermentation.

Electron Transport Chain and Oxidative Phosphorylation

An electron transport chain couples a chemical reaction between an electron donor (such as NADH) and an electron acceptor (such as O2) to the transfer of H+ ions across a membrane, through a set of mediating biochemical reactions. These H+ ions are used to produce adenosine triphosphate (ATP), the main energy intermediate in living organisms, as they move back across the membrane. Electron transport chains are used for extracting energy from sunlight (photosynthesis) and from redox reactions such as the burning of sugars (respiration).

Electron transport chains in mitochondria
The cells of almost all eukaryotes (animals, plants, fungi, algae, protozoa – in other words, the living things except bacteria, archaea, and a few protists) contain intracellular organelles called mitochondria, which produce ATP. Energy sources such as glucose are initially metabolized in the cytoplasm. The products are imported into mitochondria. Mitochondria continue the process of catabolism using metabolic pathways including the Krebs cycle, fatty acid oxidation, and amino acid oxidation.

The end result of these pathways is the production of two kinds of energy-rich electron donors, NADH and succinate. Electrons from these donors are passed through an electron transport chain to oxygen, which is reduced to water. This is a multi-step redox process that occurs on the mitochondrial inner membrane. The enzymes that catalyze these reactions have the remarkable ability to simultaneously create a proton gradient across the membrane, producing a thermodynamically unlikely high-energy state with the potential to do work. Although electron transport occurs with great efficiency, a small percentage of electrons are prematurely leaked to oxygen, resulting in the formation of the toxic free-radical superoxide.

The similarity between intracellular mitochondria and free-living bacteria is striking. The known structural, functional, and DNA similarities between mitochondria and bacteria provide strong evidence that mitochondria evolved from intracellular prokaryotic symbionts that took up residence in primitive eukaryotic cells.


Oxidative phosphorylation is a metabolic pathway that uses energy released by the oxidation of nutrients to produce adenosine triphosphate (ATP). Although the many forms of life on earth use a range of different nutrients, almost all carry out oxidative phosphorylation to produce ATP, the molecule that supplies energy to metabolism. This pathway is probably so pervasive because it is a highly efficient way of releasing energy, compared to alternative fermentation processes such as anaerobic glycolysis.

During oxidative phosphorylation, electrons are transferred from electron donors to electron acceptors such as oxygen, in redox reactions. These redox reactions release energy, which is used to form ATP. In eukaryotes, these redox reactions are carried out by a series of protein complexes within mitochondria, whereas in prokaryotes, these proteins are located in the cells' inner membranes. These linked sets of enzymes are called electron transport chains. In eukaryotes, five main protein complexes are involved, whereas in prokaryotes many different enzymes are present, using a variety of electron donors and acceptors.

The energy released as electrons flow through this electron transport chain is used to transport protons across the inner mitochondrial membrane, in a process called chemiosmosis. This generates potential energy in the form of a pH gradient and an electrical potential across this membrane. This store of energy is tapped by allowing protons to flow back across the membrane and down this gradient, through a large enzyme called ATP synthase. This enzyme uses this energy to generate ATP from adenosine diphosphate (ADP), in a phosphorylation reaction. Unusually, the ATP synthase is driven by the proton flow which forces the rotation of a part of the enzyme—it is a rotary mechanical motor.

Although oxidative phosphorylation is a vital part of metabolism, it produces reactive oxygen species such as superoxide and hydrogen peroxide that lead to propagation of free radicals, damaging cells and contributing to disease and, possibly, aging. The enzymes carrying out this metabolic pathway are also the target of many drugs and poisons that inhibit their activities.


Adenosine-5'-triphosphate (ATP) is a multifunctional nucleotide that is most important as a "molecular currency" of intracellular energy transfer.[1] In this role, ATP transports chemical energy within cells for metabolism. It is produced as an energy source during the processes of photosynthesis and cellular respiration and consumed by many enzymes and a multitude of cellular processes including biosynthetic reactions, motility and cell division. In signal transduction pathways, ATP is used as a substrate by kinases that phosphorylate proteins and lipids, as well as by adenylate cyclase, which uses ATP to produce the second messenger molecule cyclic AMP.

ATP is generated in the cell by energy-consuming processes and is broken down by energy-releasing processes. In this way ATP transfers energy between spatially-separate metabolic reactions. ATP is the main energy source for the majority of cellular functions. This includes the synthesis of macromolecules, including DNA, RNA, and proteins. ATP also plays a critical role in the transport of macromolecules across cell membranes, e.g. exocytosis and endocytosis.

ATP is critically involved in maintaining cell structure by facilitating assembly and disassembly of elements of the cytoskeleton. In a related process, ATP is required for the shortening of actin and myosin filament crossbridges required for muscle contraction. This latter process is one of the main energy requirements of animals and is essential for locomotion and respiration.


The structure of this molecule consists of a purine base (adenine) attached to the 1' carbon atom of a pentose sugar (ribose). Three phosphate groups are attached at the 5' carbon atom of the pentose sugar. ATP is also incorporated into nucleic acids by polymerases in the processes of DNA replication and transcription.



ATP is commonly referred to as a "high energy molecule"; however by itself, this is incorrect. A mixture of ATP and ADP at equilibrium in water can do no useful work at all.[5] Similarly, ATP does not contain "high-energy bonds," rather the "high-energy bonds" are between its products and water, and the bonds within ATP are notable simply for being of lower energy than the new bonds produced when ATP reacts with water. Any other unstable system of potentially reactive molecules would serve as a way of storing energy, if the cell maintained their concentration far from the equilibrium point of the reaction.[5]

The amount of energy released from hydrolysis of ATP can be calculated from the changes in energy under non-natural conditions. The net change in heat energy (enthalpy) at standard temperature and pressure of the decomposition of ATP into hydrated ADP and hydrated inorganic phosphate is −20.5 kJ/mol, with a change in free energy of 3.4 kJ/mol.[6] The energy released by cleaving either a phosphate (Pi) or pyrophosphate (PPi) unit from ATP, with all reactants and products at their standard states of 1 M concentration, are:

ATP + H2O → ADP(hydrated) + Pi(hydrated) + H+(hydrated) ΔG˚ = -30.54 kJ/mol (−7.3 kcal/mol)

ATP + H2O → AMP(hydrated) + PPi(hydrated) + H+(hydrated) ΔG˚ = -45.6 kJ/mol (−10.9 kcal/mol)

These values can be used to calculate the change in energy under physiological conditions and the cellular ATP/ADP ratio. The values given for the Gibbs free energy for this reaction are dependent on a number of factors, including overall ionic strength and the presence of alkaline earth metal ions such as Mg2+ and Ca2+. Under typical cellular conditions, ΔG is approximately −57 kJ/mol (−14 kcal/mol).[7]


The overall process of oxidizing glucose to carbon dioxide is known as cellular respiration and can produce up to 36 molecules of ATP from a single molecule of glucose.[12] ATP can be produced by a number of distinct cellular processes; the three main pathways used to generate energy in eukaryotic organisms are glycolysis and the citric acid cycle/oxidative phosphorylation, both components of cellular respiration; and beta-oxidation. The majority of this ATP production by a non-photosynthetic aerobic eukaryote takes place in the mitochondria, which can make up nearly 25% of the total volume of a typical cell.

AS405 –Day 3 Homework Name: ____________________



1. Compare and Contrast chemiosmosis in mitochondria and chloroplasts.


2. Compare and Contrast prokaryotic and eukaryotic cells.








3. Compare and Contrast plant and animal cells.








4. Give examples of exocytosis and endocytosis.






5. Define diffusion, osmosis, and electrochemical gradient and give examples.

Carbon, Macromolecules and Metabolism

I. Carbohydrates – Sugars, Starch, & Chitin

Monosaccharides-glucose, maltose, sucrose, fructose and galactose
Disaccharides – a covalent bond formed between two monosaccharides joined by a glycosidic linkage in a dehydration reaction.

Polysaccharides – have a few hundred to a few thousand monosaccharides.
1. Starch: storage polysaccharide for plants
2. Glycogen: storage polysaccharide for animals
3. cellulose: defensive polysaccharide for plants-the most abundant organic compound on Earth (100billion tons annually) few organisms possess enzymes that can digest cellulose.
4. Chitin – exoskeletons hardens with carbonate.

II. Lipids, Hydrophobic Molecules
The fats Glycerol with three fatty acids hanging off of it.
1. Saturated fats, nothing but single bonds on the carbons
2. Unsaturated fats, have double or triple bonds along the fatty acids.

Hydrogenated vegetable oils mean that unsaturated fats have been synthetically converted to saturated fats by adding hydrogen. (Canada-Oreo Cookie Hydrogenation Plant with Lard!)
Phospholipids – cell membranes & micelle
Steroids – ringed structures

III. Proteins, the workhorses of cells
Polypeptides – polymers of amino acids that make up proteins.

Four levels of Protein Structure
1. Primary Structure – the sequence of amino acids
2. Secondary Structure – coiled or folded pattern
3. Tertiary Structure – hydrophobic interactions, disulfide bridges p.77
4. Quaternary Structure – aggregation of multiple polypeptide subunits.

Protein Structure can be disrupted by:
1. pH, salt concentration, temperature this unraveling of the protein is called denaturation.
2. chaperonins – protein molecules that assist the proper folding of other proteins.

IV. Nucleic Acids – Informational Polymers
DNA – deoxyribonucleic acid
RNA –ribonucleic acid
DNA provides directions for its own replication and directs synthesis for RNA. Through RNA controls the protein synthesis.
Pyrimidines (Only Thymine is in DNA and only Uracil is in RNA) & Purines

Only 5 nucleic acids
C - Cytosine
T – Thymine (DNA)
U – Uracil (RNA)
A - Adenine
G – Guanine

Metabolism, Energy & Life
Metabolism – totality of an organism’s chemical reactions.
Catabolic pathways – release energy for use of the organism/cell
Anabolic pathways – consume energy to build complicated molecules.
Bioenergetics – the study of how organisms manage their energy resources.
Thermodynamics – the study of energy transformations that occur in a collection of matter.
The first law of thermodynamics: Energy can be transferred and transformed, but it cannot be created or destroyed. Principle of conservation of energy.
The second law of thermodynamics: Every energy transfer is increasing the entropy of a closed system.
Conversion to heat is the fate of all the chemical energy…
The Quantity of the energy in the universe is constant, but its quality is not.

Gibbs Free Energy:
Metabolic Disequilibrium is required for life. If a cell ever reached a ΔG=0, it would be dead!!!
Energy Coupling - the use of a exergonic process to drive an endergonic one. ATP can mediate this for cells.

Enzymes:
Catalyst – a chemical agent that changes the rate of a reaction without itself being consumed. An enzyme is nothing more than a catalytic protein.


AS405 –Day 2 Homework Name: ____________________


1. What are the four forces in our Universe and their effect?




2. What are the four major polymers and their respective monomer subunits called?






3. List the four major chemical bonds and give examples of each.






4. List the six major functional groups and give their structures.





5. List the five nucleic acids and give their structure.

Occam's Razor, Darwin and Electronegativity

Occam's (Ockham's) Razor:

All other things being equal, the simplest solution is best.

Darwin's Origin of the Species:

2 main concepts

1. Contemporary species arose from a succession of ancestors
2. He proposed a mechanism of evolutions called Natural Selection

The controversy of creationism vs. evolution

Basic Biology Building Blocks (Lecture Day 1)

Folks:

Homework will need to be turned in tomorrow at the beginning of class.

Here are the questions:

1. Define: A form, a system, a principle, confederacy, democracy, republic, physics, chemistry, biology, matter, energy, mathematics, hydrophilic, hydrophobic, solution, solvent, acid, base, pH.


2. List & Describe the 10 Unifying Themes of Biology


3. List the taxonomic scheme


4. What is the scientific method & why has it been so successful


5. List & Describe the four types of chemical bonds.

Chapters 1-6 will need to be read, arrive with questions or I will assume that you understand everything and we'll move onto chapters 7, 8 and 9.

We had some questions in class that were left unanswered...will folks post links or answers as they find them?

Thanks and we'll chat tomorrow! Happy Reading.

Grading & the Final Exam:
All the reading is required
Come to class with questions, if you don’t I’ll assume you understand everything we have covered.
50% of your grade is the final exam
50% of your grade is the homework and I take the median.
Your final exam will be 60 questions answered in 2 hours or less
Questions will be taken from class lecture, homework and all the readings
25% questions on Biochemistry, 25% of the questions on Cell Biology, 25% of the questions on Genetics and 25% of the questions on Plants.
You will be expected to memorize chemical structures, models and cycles

When is something alive?
It must:
Eat, Breathe, Grow and Reproduce
Begs the question….is a virus alive?

Homeostasis-Regulatory mechanisms that maintain an organism’s internal environment within tolerable limits…despite environmental influences.

Page 6 of your book gives a good example of the size comparison of the two cells.

Basic Principles in Biology:
Structure: Work
Form: Function
Surface: Volume

Reductionism – reducing complex systems to simpler components that are more manageable to study. However, there is a dilemma: We cannot fully explain a higher level of order by breaking it down into its parts. The other side of the dilemma is the futility of trying to analyze something without taking it apart!

Cell Theory– Robert Hooke first gave the name cell (1665) in 1839 cells were acknowledged as the universal units of life.
Continuity is based on Heritable Information
Biology has a Vertical Dimension (Size)(Atom to Biosphere) as well as a Horizontal Dimension (Time-4 billion years)

The Story of Biology (Linnaeus)
1735 Linnaeus 2 kingdoms Animals and Plants
1969 5 kingdoms animals, plants, fungi, protists, bacteria
1990 3 domains 4 kingdoms

Darwin’s “Origin of the Species”
2 Main concepts:
Contemporary species arose from a succession of ancestors
He proposed a mechanism of evolutions called Natural Selection
p.13 read a bit of it here.
Evolution is THE core theme of biology.
p. 16 Discovery Science/called….Descriptive Science
The Scientific Method
Observe, Question, Hypothesis, Predict, Test
If yes, support with additional data and tests
If no, Revise your Hypothesis

The Quantum Approach to Autodidact's Education

Here is the link we used in lecture today. Enjoy!

Biology class begins at 1:30pm on Monday (Oct. 20th)

Janine

The Double Slit Experiment...down the rabbit hole!