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Cellular Respiration

Energy is the currency of life: all living organisms require energy to survive and reproduce. Metabolism is the series of reactions and processes, catalyzed by enzymes, which together maintain life. These reactions fall into one of two types.

Catabolic reactions breakdown molecules for energy and carbon building blocks. Cellular respiration entails all the metabolic processes used to breakdown molecules (e.g., glucose, starch) into chemical energy (adenosine triphosphate or ATP) that can be used by the cell. It is a catabolic process.
Anabolic reactions build/synthesize molecules from energy and carbon building blocks. Photosynthesis is a process in which cells harness light energy from the sun to create energy-containing molecules.

These processes are the inverse of each other and in photosynthetic organisms occur in tandem as the anabolic reactions of photosynthesis create the products that are then broken down by the catabolic reactions of cellular respiration. Review the diagram to better understand these connections.

There are two general classes of cellular respiration that are characterized by their relative efficiency (ATP production): anaerobic and aerobic respiration.

Anaerobic respiration is much less efficient than aerobic respiration (about 2 ATP yield per cycle vs 34-38). The two forms of anaerobic respiration (alcoholic fermentation and lactic acid fermentation) occur outside the mitochondria, in the cytoplasm of the cell, meaning the process can occur in simpler cells that may lack complex structures like the mitochondria.

Aerobic (“complete” or “oxygen-dependent”) respiration is a highly efficient process occurring within the mitochondria of eukaryotic organisms that have higher energy requirements for survival. Oxygen and glucose are used to produce energy (ATP), H2O, and CO2.

Cellular Respiration Glycolysis, Krebs cycle, Electron Transport 3D Animation YouTube 720p from eLearn.Punjab on Vimeo.

In general, there are three steps to aerobic respiration: (1) glycolysis, (2) the Krebs Cycle (also called Citric Acid Cycle), and (3) oxidative phosphorylation. One cycle produces 6 H2O molecules, 6 CO2 molecules, and ~38 ATP.

Cellular Respiration in the Crayfish

Chloroplasts

Color of Light

Kim, S. J., Hahn, E. J., Heo. J. W., and Paek, K. Y. 2004. Effects of LEDs on net photosynthetic rate, growth and leaf stomata of chrysanthemum plantlets in vitroAuthor links open overlay panel. Scientia Horticulturae, 101 (1–2), 143-151.

Matsuda, R., Ohashi-Kaneko, K., Fujiwara, K., Goto, E., and Kurata, K. 2004. Photosynthetic Characteristics of Rice Leaves Grown under Red Light with or without Supplemental Blue Light. Plant & Cell Physiology, 45(12), 1870-1874.

Low pH

Long, A., Zhang, J., Yang, L. T., Ye, X., Lai, N. W., Tan, L. L., … Chen, L. S. (2017). Effects of Low pH on Photosynthesis, Related Physiological Parameters, and Nutrient Profiles of Citrus. Frontiers in Plant Science, 8, 185.

Fariduddin, Q., Hayat, S., Ahmad, A., 2003. Salicylic acid influences net photosynthetic rate, carboxylation efficiency, nitrate reductase activity and seed yield in Brassica juncea., Photosynthetica, 41, 281–284.

Cold	De Villiers, A.J., I. Von Teichman, M.W. Van Rooyen and Theron G. K. 1995. Salinity-induced changes in anatomy, stomatal counts and photosynthetic rate of Atriplex semibaccata R. Br. S. Afr. J. Bot., 62, 270-276.

Salinity

Oliveira, J. G., Alves P. L. C. A, and Magalhães, A. C. 2002. The effect of chilling on the photosynthetic activity in coffee (Coffea arabica L.) young plants. The protective action of chloroplastid pigments. Braz. J. Plant Physiol., 14, 95-104.

Caffeine

Shettel, N., & Balke, N. (1983). Plant Growth Response to Several Allelopathic Chemicals. Weed Science, 31(3), 293-298.

Chloroplast diagram. Click to enlarge.

Crayfish

Oxygen

Ellis, B. A. and S. Morris. 1995. Effects of extreme pH on the physiology of the Australian ‘yabby’ Cerax destructor: Acute and chronic changes in haemolymph oxygen levels, oxygen consumption and metabolite levels. Journal of Experimental Biology, 198: 409-417.

Dejours, P. and H. Beekenkamp. 1977. Crayfish respiration as a function of water oxygenation. Respiration Physiology, 30: 241-251.

Temp	Whitledge, G. W., and C. F. Rabeni. 2003. Maximum daily consumption and respiration rates at four temperatures for five species of crayfish from Missouri, U.S.A. (Decapoda, Orconectesspp.). Crustaceana, 75:1119–1132.

Size

Glazier, D. (2005). Beyond the ‘3/4-power law’: Variation in the intra- and interspecific scaling of metabolic rate in animals. Biological Reviews, 80(4), 611-662.

McFeeters, B. J., Xenopoulos, M. A., Spooner, D. E., Wagner, N. D., and Frost, D. P. 2011. Intraspecific mass-scaling of field metabolic rates of a freshwater crayfish varies with stream land cover. Ecosphere, 2(2), 13.

Solutes

Romano, N. and C. Zeng. 2013. Toxic effects of ammonia, nitrite, and nitrate to decapod crustaceans: A review on factors influencing their toxicity, physiological consequences, and coping mechanisms. Rev. Fish. Sci., 21 (1), 1−21.

Vaughan, R. A., Garcia-Smith, R., Bisoffi, M., Trujillo, K. A., & Conn, C. A. (2012). Effects of caffeine on metabolism and mitochondria. Nutrition and metabolic insights, 5, 59-70.

Water Quality & Management

Frank S. Corotto, Megan J. McKelvey, Elicia A. Parvin, Jessica L. Rogers, Jayme M. Williams, Behavioral Responses of the Crayfish Procambarus Clarkii to Single Chemosensory Stimuli, Journal of Crustacean Biology, Volume 27, Issue 1, 1 January 2007, Pages 24–29

Crayfish Taxonomy

Crayfish Natural History

Facts on KY Crayfish

Click to enlarge.

Diabetes

Molecules

Biological Molecules - You Are What You Eat: Crash Course Biology (You Tube)
Macromolecules (Khan Academy)

Osmosis & Diffusion

Facilitated Diffusion and Active Transport of Glucose
Effect of blood glucose concentration on osmoregulation in diabetes mellitus
Can Glucose Diffuse Through the Cell Membrane by Simple Diffusion?
Why Does Diabetes Cause Excessive Urination and Thirst? A Lesson on Osmosis

Diabetes & Homeostasis
Overview of Insulin Signaling. D J Jenkins, T M Wolever, R H Taylor, H Barker, H Fielden, J M Baldwin, A C Bowling, H C Newman, A L Jenkins, D V Goff. iii L

Biochemistry

Glycemic index of foods: a physiological basis for carbohydrate exchange, The American Journal of Clinical Nutrition, Volume 34, Issue 3, March 1981, Pages 362–366,

Michelle Furtado, Romel Somwar, Gary Sweeney, Wenyan Niu, Amira Klip. Activation of the glucose transporter GLUT4 by insulin. Biochemistry and Cell Biology, 2002, 80 (5), 569-578.

Biochemical pathways of blood glucose homeostasis and feedback.

HBO documentary on the obesity and diabetes epidemic.

Diffusion & Osmosis

DNA Sequencing

Metric System

The metric system is a standardized system of measurement used by scientists throughout the world. It is also the most common system of measurement used in most countries.... except the United States. Unlike the imperial system (IS) with which you are most familiar (inches, miles, gallons, etc.), the metric system is based on units of 10 and is thus much easier to use. The base metric units most commonly used in the biological sciences include:

Meter – (m) – basic unit of length
Liter – (L) – basic unit of volume
Gram – (g) – basic unit of mass
Degrees Celsius – (C) – basic unit of temperature

From these base units, you can always convert into smaller or larger units by multiplying or dividing by 10. Figure 1 lists several of the prefixes used in the metric system (the most common in biology being kilo-, centi-, milli-, micro- and nano-). These prefixes are standard and determine the relationship between a unit and the original base unit (gram, liter, or meter). Below each unit is an example of an organism you would measure using different factors of the base unit for length (meter) (look some of them up! They are pretty cool).

WHY DO SCIENTISTS USE THE METRIC SYSTEM?

THE METRIC SYSTEM IS BASED ON UNITS OF 10 AND IS THUS MUCH EASIER TO USE. Conversion can be easily accomplished by multiplying or dividing by the conversion factor (103, 10-2, etc.) which entails simply moving the decimal to the right (to convert to smaller units) or to the left (to convert to larger units.
SCIENCE IS INTERNATIONAL AND COLLABORATIVE. We must be able to discuss our methods and results across borders. Most of the world uses the metric system except for the US, Liberia and Myanmar.
YOU CAN COVERT BETWEEN TYPES OF MEASUREMENT: FROM LENGTH TO VOLUME TO MASS: 1cm3 = 1mL = 1g One cubic centimeter corresponds to a volume of 1 / 1,000,000 of a cubic meter, or 1 / 1,000 of a litre, or one milliliter (1 cm3 ≡ 1 mL). The mass of one cubic centimeter of water at 3.98 °C (the temperature at which it attains its maximum density) is closely equal to one gram.

Basic Metric Conversion test

practice conversions

Practice Scientific Notation

Photosynthesis

Click here for a review on photosynthesis.

The complete photosynthesis reaction with redox labels. Click to enlarge.

Nice YouTube video on photosynthesis

YouTube video takes you inside a leaf. Be sure to turn on the CC so you can read about each scene!

Polymerase chain reaction

Once DNA has been extracted, it is mixed into a particular PCR solution containing:

Taq polymerase: A type of heat-stable DNA polymerase derived from a species of bacteria living in hot springs. Because Taq polymerase continues to function normally at high temperatures, using it allows researchers to separate the DNA strands without destroying the polymerase.
Primers: Short, single-stranded sequence of RNA or DNA that enables the start of replication of a DNA sequence that is synthesized from the 3’ end of the primer.
Deoxynucleoside triphosphates (dNTPs): Free nucleotides to be used in constructing the new copies of DNA.
Mix buffer: Necessary to create optimal conditions for activity of Taq DNA polymerase and may contain restriction enzymes, which act like molecular scissors cutting the copied DNA strands at particular locations based on their genetic code.

The PCR mixture is placed inside a thermocycler (PCR machine). It is typically repeated about 35 times and the temperature changes are programmed by researchers and automated by the thermocycler. The process proceeds in three steps as outlined below.

Denaturation: the solution is first heated to nearly boiling—95ºC. The heat breaks the hydrogen bonds between the two DNA strands and allows them to separate.
Annealing: the temperature is dropped to around 60ºC. The exact temperature depends on the length and base composition of the primers. At this relatively low temperature, the primers can form hydrogen bonds with the single-stranded DNA. Two primer types are created, each one complementary in sequence to one of the two ends of the target DNA. To make the primers, the sequences at the ends of the target DNA must be known.
Extension: the temperature is increased to 72ºC. This is the optimal temperature at which Taq polymerase functions. The primers are essential in this process, because they provide free 3’ hydroxyl groups, to which the polymerase can add additional dNTPs. Each new dNTP that joins the growing strand is complementary to the nucleotide in the opposite strand.

What is PCR? What kinds of questions can it help answer? Click to enlarge.

PCR components. Click to enlarge.

The 3 steps of PCR. Click to enlarge.

At the end of this first cycle, there are two DNA copies instead of the one original copy. The process continues, doubling the number of target DNA copies with each cycle. The general formula for the number of DNA strands created by PCR is X2^n where X = the number of original strands and n = the # of PCR cycles.

Statistics

Different is different...why do we need to run a t-test? A relationship is obvious...why do we need to run a correlation?

We look for patterns to help us understand the natural world. As we do so, we are fighting our own human tendency to see patterns where none truly exist, and to take what we see in a specific context and try to apply it more broadly.

Let’s say you notice that within your friend circle, those who regularly eat breakfast did much better on their first BIOL 120 exam than those who skipped your morning meals together. You might then assume that somehow, eating breakfast is causing the better grades. But! Consider the following...

How much of a difference in test averages should there be between breakfast-eaters and breakfast-skippers for that to be true? 90 vs. 60? 80 vs. 70? Reasonable people could disagree.
How often do you need to see this relationship for that to be true? On exam 1 and 2? On all the BIOL 120 exams? Reasonable people could disagree.
Is it really the breakfast? Maybe students who are disciplined enough in their sleeping and eating habits are also more disciplined in their study habits? Reasonable people could disagree.

Statistics solve this problem. Using the principles of probability, they help us parse what we observe from randomness (chance alone) vs. meaning (a real difference, or a real relationship). Statistics tell us how likely we would be to make the same observations we have made, if chance and randomness were the only drivers. If the probability is very low (<5%), we refer to these patterns as significant.

Comparing important concepts for each type of test. Click to enlarge. Review the statistics we will use and associated concepts in this table. Discuss the contents with your group and ensure everyone feels confident with material before moving on to the procedure.