BIOL 1404 HON 2015: February 2015

Tuesday, February 24, 2015

Factors Limiting the Rate of Photosynthesis

The graph above shows how the rate of photosynthesis is affected by irradiance (light level) and the concentration of carbon dioxide.

The rate of photosynthesis can be limited by a variety of environmental factors including

1) light
2) concentration of carbon dioxide
3) water
4) soil nutrients

Which factor most limits photosynthesis varies between environments.

Light- Can directly limit the rate of photosythesis by limiting the rate at which ATP and NADPH are produced.

Carbon dioxide- can directly limit the rate of photosynthesis by limiting the rate at which the Calvin Cyle takes place.

Water- can indirectly limit the rate of photosynthesis. When plants are water stressed they close their stomata (long before the concentration of water in the cell becomes too low for water to supply electrons to P680). Thus, the rate of photosynthesis is water stressed plants is directly limited by the amount of carbon dioxide in the leaf.

Soil Nutrients- Sometimes the rate limiting step in photosynthesis is the rate at which carbon dioxide + RuBP ==> PGA. This reaction is catalyzed by the enzyme RuBP carboxylase. Increasing the amount of RuBP carboxlyase in the cell can increase the rate at which this reaction occurs. Fertilizing plants with nitrogen will increase the amount of RuBP Carboxylase produced by the plant.

Expected Learning Outcomes

By the end of this class a fully engaged student should be able to

- discuss the factors that can directly or indirectly limit the rates of photosynthesis
- discuss how the most limiting factors should vary between environments
- discuss how the activities of farmers such as irrigation and fertilization can increase photosynthetic rates
- interpret the graph at the top of the post (irradiance measures light intensity and the three lines represent different concentrations of carbon dioxide)
- explain what why the graph shows that shape

Why Aren't Plants Black?

If I was hired as an engineer to design a machine whose job was to convert light energy into chemical energy I probably would not choose to use a green pigment. Instead, I would choose to use a black pigment because black pigments would absorb more energy because they would absorb all wavelengths of light. If you look at a field of plants you will notice that they are green (OK this doesn't work too well around Lubbock in the winter)and we have learned that chlorophyll, a green pigment, is the dominant photosynthetic pigment. What is going on?

Here is one theory about why chlorophyll is the dominant photosynthetic pigment in plants today. Early on there were photosynthetic bacteria with purple pigments (purple is a combination of red and violet). These aquatic bacteria had a very simple sort of cyclic electron flow that was able to convert light energy into energy in ATP (they didn't have non-cyclic flow or the Calvin Cycle).

Origin of chlorophyll- The purple pigment absorbed all wavelengths of light except for the reds and violets. Thus, any bacteria using purple pigments that lived deeper in the water than the purple bacteria on the surface would have no light to use because it had all been absorbed by the surface bacteris (exploitative competition). Because red and violet wavelengths pass through to deeper water, bacteria that contained a pigment that was able to absorb these wavelengths would be able to coexist with the purple bacteria. This was the origin of chlorophyll.

Competition purple and green photosynthetic pigments. Over time there was competition between organisms with purple photosynthetic pigments and green photosynthetic pigments. Obviously, the green photosynthetic pigments won this competition because chlorophyll is the dominant photosynthetic pigment today (there are still examples of photosynthetic bacteria with purple pigments, but they are limited to very harsh environments). Interestingly, chlorophyll came to dominate, not because it was a better at absorbing light energy, but rather because the cyclic flow machinery associated with chlorophyll was more efficient at producing ATP than the machinery associated with the purple pigment was. Thus, it is an evolutionary accident that modern plants are green.

Black Plants

It would be possible for modern plants to be black if they had enough accessory pigments to allow them to absorb all wavelengths of light. In fact, some red algae that live deep below the surface where light levels are low are basically black. Because the amount of light is not the factor that limits the rate of photosynthesis in most terrestrial plants, it is not worth the cost of producing extra accessory pigments. However, deep in the ocean where light levels are low, plants benefit from being able to absorb all wavelengths of light so deep marine algae have invested in extra accessory pigments.

Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- discuss why terrestrial plants to not invest in the accessory pigments required to make them black

Leaf Structure

Lecture Video: http://mediacast.ttu.edu/Mediasite/Play/c952faeba33546d3b8910e6e1bbf716c1d?catalog=4dc7289a-d3e0-4ae5-8fdc-5b86c027a06b

In most plants, leaves are the major sites of photosynthesis. Thus, we can think of leaves as "photosynthesis machines" and use our knowledge of natural selection to try to understand aspects of leaf structure.

Further Reading

http://micro.magnet.fsu.edu/cells/leaftissue/leaftissue.html

Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- discuss important differences between animals and plants in gas uptake
- diagram the cross section of a leaf
- discuss the characteristics and purpose of the cuticle, stomata, spongy mesophyl cells, and the palisade cells.
- explain the adaptive basis of leaf structure

Wednesday, February 18, 2015

Photosynthesis- Light Independent Reactions

Lecture Video- http://mediacast.ttu.edu/Mediasite/Play/842d916401044c20a370989776ea66631d?catalog=4dc7289a-d3e0-4ae5-8fdc-5b86c027a06b

Photosythesis takes place in two steps. In the first step, known as the light dependent reactions, light energy is converted into chemical energy held in the bonds of ATP and NADPH.

Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- list the parts of a photosystem
- discuss the function of a photosystem
- describe where the light dependent reactions of photosythesis occur and discuss why these reactions occur in this location
- describe cyclc electron flow, be able to explain both the energetic result and what chemcical changes occur
- describe non-cyclic electron flow, be able to explain both the energetic result and what chemical changes occur
- describe the cause and the result of chemiosmosis
- answer the question- "why doesn't photosynthesis stop after the production of ATP and NADPH in the light dependent reactions

Further Reading

A simple introduction to the process of photosynthesis
Photosynthesis- http://www.eoearth.org/article/Photosynthesis

Here is a link to some fairly detailed info about photosynthesis (it contains some very good diagrams).
http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookPS.html

Powerpoint Presentation

Here is the powerpoint presentation that I will use in class.

http://www.slideshare.net/MarkMcGinley/photosynthesis-light-dependent-reactions

Further Viewing

These videos contain animations that might help you to understand what is happening in the light dependent reactions. I encourage you to watch each of these videos.

1) This video has some great animations of what is going on in the light dependent reactions.

http://www.youtube.com/watch?v=hj_WKgnL6MI

2) This is a video of a woman with a very southern accent talking about photosyntheis with some decent animations.

http://www.youtube.com/watch?v=RFl25vSElaE&feature=related

3)Another explanation of light dependent reactions.

http://www.youtube.com/watch?v=BK_cjd6Evcw

Introduction to Photosynthesis

Introduction to Energetics

Lecture Video: http://mediacast.ttu.edu/Mediasite/Play/dfea523e65f54ad2af1a25fda81bd2f91d?catalog=4dc7289a-d3e0-4ae5-8fdc-5b86c027a06b

In order to understand the two important energetic processes taking place in living organims (photosynthesis and cellular respiration) it is useful to understand some basics of energetics.From a physics perspective, energy is required to do work. Because this is a biology class, we will focus on biological work. The three main types of biological work are (1) active transport, (2) biosynthesis, and (3) movement. The key point for this class is to realize that organisms require energy to do the biological work required to keep them alive.

Energetic processes follow the laws of physics. The two most important laws of physics that relate to energy are the First and Second Laws of Thermodynamics.

First Law of Thermodynamics

The total amount of energy in the universe is constant. Energy can not be created and existing energy can not be destroyed. Energy can only undergo conversion from one form to another.

Biological relevance- No living organisms are capable of creating their own energy so they must get it from another source.

Second Law of Thermodynamics

Left to itself, any system undergoes energy conversion to less organized form. Each time this happens some energy becomes so disorganized that it is no longer available to do work.

Entropy is a measure of the amount of energy that is so disorganized so that it can no longer do work. A simpler way of stating the Second Law of Thermodynamics is that entropy increases over time.

What does it mean when energy becomes disorganized? Another term for "organized energy" is "concentrated energy". Energy is only able to do work when it is concentrated enough to power a particular process.

Apparent Problem

The Second Law of Thermodynamics states that entropy should increase over time, yet life contains highly concentrated energy. How can this be?? They key phrase in the definition is "left to itself". It turns out that energetically, the earth is not left to itself; the earth receives a constant input of energy from the sun and it is this energy that is used to fight entropy.

Light

Light energy from the sun reaches the earth. Light is part of the electromagnetic spectrum. Different portions of the electromagnetic spectrum vary in their wave lengths. Forms of electromagnetic energy with shorter wavelengths (e.g., x rays and gamma rays) contain more energy than forms of energy with longer wave lengths (e.g, radio waves). Interestingly, light falls within the middle of the spectrum with wavelengths from about 400 - 700 nm. Different wavelengths of light have different colors. Ranging from the longest to the shortest wavelengths the colors are red, orange, yellow, blue, green, indigo, violet (some people remember this using ROY G BIV).

As you might recall from your physics class, light has characteristics of waves and of particles. Light energy is "packaged" in units known as photons and the amount of energy in a photon depends of the wavelength of that light.

Fusion reactions on the sun convert nuclear energy in to electromagnetic energy. The electromagnetic energy travels through outer space until reaches the earth. Unfortunately, we,and all other organisms can not directly use light energy to do biological work. Instead light energy must be converted into potential energy stored in the chemical bonds of molecules. This potential (stored) energy can then be used to power biological work.

What Happens When a Photon of Light Hits a Molecule?

Three things can happen when a photon of light hits a molecule- (1) the light can be transmitted (passed through), (2) the light can be reflected, or (3) the photon of light can be absorbed.

When a molecule absorbs a photon of light energy, the electromagnetic energy of light excites an electron in the molecule to a higher energy level (thus, giving the electron potential energy). The excited electron almost immediately falls back to resting stage and the potential energy in the electron is converted into heat (a form of electromagnetic energy) which is released to the atmosphere.

Pigments

When we think of pigments, we think of color. What determines an objects color? The color of an object depends on the wavelengths of light that are reflected back to our eyes. Thus, when you see red you are seeing the red wavelengths that have been reflected from the object that you are looking at. What happens to the other wavelength? They have been absorbed.

Different molecules absorb and reflect different wavelengths of light. A pigment is defined as a molecule that absorbs particular wavelengths of light. What is important to remember is that the color of a pigment is the color of light it reflects.

Absorption Spectrum

An absorption spectrum is a graph that plots how much light energy is absorbed (y-axis, usually measured as intensity or as a percentage) versus the wavelength of the ligh (x-axis, measured in nm). Take a look at the absorption spectrum shown below. You can see that this pigment absorbs mostly green wavelengths and reflects the red and violet wavelengths. When the red and violet wavelengths reach your eye it would appear to you as purple.

Can you draw the absorption spectrum for a red, green and blue pigment?

Lecture Video- http://mediacast.ttu.edu/Mediasite/Play/dfea523e65f54ad2af1a25fda81bd2f91d?catalog=4dc7289a-d3e0-4ae5-8fdc-5b86c027a06b

Expected Learning Outcomes

By the end of the course a fully engaged student should be able to

- give examples of biological work
- list different forms of energy, give examples of the different forms, and give examples of energy conversions
- define the First and Second Laws of Thermodynamics and discuss why these laws are important for biologists
- discuss electromagnetic energy, including the wavelengths associated with different forms of electromagnetic energy and the relationship between wavelength and energy
- define a photon
- discuss the three things that can happen when a photon of light hits a molecule
- define a pigment
- draw and interpret an absorption spectrum

Further Reading

Electromagnetic radiation- http://www.eoearth.org/article/Electromagnetic_radiation

Sunday, February 15, 2015

Global Carbon Cycle and Global Climate Change

Most of the slides from the global climate change portion of this presentation came from Katharine Hayhoe's website (she is a professor in the Tech Political Science Dept and the link to her website is listed on the presentation).

Global Carbon Cycle and Global Climate Change
http://www.slideshare.net/secret/C6iDTujQlIh73C

Further Reading

Climate Change FAQ- http://www.eoearth.org/article/Climate_change_FAQs

Causes of Climate Change- http://www.eoearth.org/article/Causes_of_climate_change

Global Warming- http://www.eoearth.org/article/Global_warming

Economics of Climate Change- http://www.eoearth.org/article/Economics_of_climate_change

Mauna Loa Curve- http://www.eoearth.org/article/Mauna_Loa_curve

Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- identify the major reservoirs of carbon

- discuss the two most important biological processes that result in a movement of carbon from one reservoir to another

- discuss the three ways that human activity has altered the global carbon cycle

- explain the Mauna Loa Curve

- discuss why climate scientists have concluded that global temperatures have increased

- discuss why climate scientists have concluded that this increase in temperature is most likely caused by humans

- discuss some potential consequences of global climate change

Ecosystem Ecology

Ecosystem ecologists focus on the flow of energy and the cycling of nutrients through the ecosystem.

Further Readings

Ecosystems- http://www.eoearth.org/article/Ecosystem

Ecological energetics- http://www.eoearth.org/article/Ecological_energetics

Nitrogen cycle- http://www.eoearth.org/article/Nitrogen_cycle

Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- diagram and discuss the flow of energy through an ecosystem
- diagram, discuss the causes of, and discuss some of the implications of the enegy pyramid
- diagram nitrogen cycle within an ecosystem
- discuss the factors that influence the rate of flow from dead bodies to the soil and discuss the implications of differences in this rate

Community Ecology: The Portal Experiment

Lecture Video- http://mediacast.ttu.edu/Mediasite/Play/7feddd71db3e46eaa48d3bd62f4b50e71d?catalog=4dc7289a-d3e0-4ae5-8fdc-5b86c027a06b

Here are some photos from the research site in Portal, Arizona. For more information about the research project at Portal you can look at their website at
http://portal.weecology.org/

Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- distinguish between direct and indirect, positive and negative effects
- describe the experimental design that Dr. Brown and his colleagues used to study exploitative competition between desert rats and rodents
-discuss why and how the outcome of studies of interactions between organisms can vary over time
- discuss the way that the ecological community responded when they learned the importance of long term studies
- discuss how indirect interactions lead to one of my favorite phrases "the world is complicated"

Community Ecology

Required Readings

Community Ecology- http://www.eoearth.org/article/Community_ecology

Competition- http://www.eoearth.org/article/Competition

Interspecific Competition- http://www.eoearth.org/article/Interspecific_competition

Exploitative Competition- http://www.eoearth.org/article/Exploitative_competition

Predation- http://www.eoearth.org/article/Predation

Mutualism- http://www.eoearth.org/article/Mutualism

Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- define competition, exploitative competition and interference competition

- identify and explain examples of exploitative and interference competition from a variety of environments

- define predation (narrow and broad sense), herbivory, and parasitms

- identify and explain examples of predation, herbivory, and parasitism from a variety of environments

- identify examples of morphological and behavioral adaptations that animals have to help capture their food

- identify examples of morphological, biochemical, or behavioral adaptations that animals have to protect them from predators

- identify and explain examples of mutualisms from a variety of habitats

Past Test Questions (answers at bottom of post)

In the southeastern United States, a weedy plant called Kudzu has caused a great deal of problems. Because Kudzu has such high growth rates it is able to rapidly overgrow buildings and other plants.

1. Which of the following would best describe the ecological relationship between Kudzu and a species of pine tree that is commonly overgrown by Kudzu?
(a) mutualism
(b) parasitism
(c) exploitative competition
(d) herbivory
(e) none of the above

Answer- 1. c

Wednesday, February 4, 2015

Human Population Growth

Lecture Video: http://mediacast.ttu.edu/Mediasite/Play/52d8d4c10b014322accd92829c7c5c991d?catalog=4dc7289a-d3e0-4ae5-8fdc-5b86c027a06b

I have spent a lot of time trying to convince you that exponential growth is an unrealistic model of population growth. Interestingly, human populations have experienced exponential-like growth. How can this be?

What makes humans different from other species?

In other species per capita birth rates and per capita deaths rates are density dependent. However, as human populations have increased there has been no corresponding decline in per capita birth rates or increase in per capita death rates. What makes humans different from other species?

Humans have the ability to alter their environment so that they can avoid the density dependent effects on birth and death rates. 1) Humans have increased food production by improvements in agriculture (e.g., irrigation, fertilization, mechanized farming, genetically improved crops). 2) Humans have been able to decrease death rates by improvements in medicine and public health (things as simple as not pooping in the water you drink helps a lot!). 3) Humans have elimnated most human predators (ocassionally, someone gets killed by a shark or a mountain lion).

Where is human population growth occuring?

The rates of human population growth are not the same in all regions. Today, human populations are increasing in size much faster in developing countries (e.g., Mexico, other countries in Central America, Africa, and Southeast Asia) than they are in developed countries (e.g, USA, Canda, Western Europe). The figure at the top of this post shows the patterns of population growth in developed and developing nations.

Thus we see that populations are increasing most rapidly in the countries that are least able to deal with a rapidly increasing population. See "Population Challenges-The Basics" that can be downloaded from the Population Institute's website.
http://www.populationinstitute.org/population-issues/index.php

Human Population Growth Problem?

There is a great deal of debate about whether increasing human populations are a problem or not, and if they are what should be done about it. Unfortunately, we don't have time to discuss this issue in very much detail in class. My personal opinion is that we have too many people consuming too many resources and the last thing that we need are billions more people living on the planet. This is an issue that I am always intersted in talking more about if you would like to chat.

Further Reading

The section on Human Population Growth in your textbook is quite good.

Also see the article "Human Population Explosion" from the EoE.
http://www.eoearth.org/article/Human_population_explosion

Both of these contain a good discussion of the "demographic transition".

Really Cool Video

Here is a link to a YouTube video on "World Population" The first minute and a half or so is a little boring, so you can skip over it if you wish. However, I think the animation showing when and where human population growth has been occuring is really cool.

http://www.youtube.com/watch?v=4BbkQiQyaYc

Powerpoint Presentation

http://www.slideshare.net/MarkMcGinley/human-population-growth-16369173

Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- describe patterns of human population growth in developed and developing nations

- discuss some reasons why the pattern of population growth in humans is so different from that in other species

- describe the demographic transition

- discuss their own personal view of human population growth.

Past MC Test Questions (answers at bottom of post)

1. In developing countries, why have per capita birth rates not decreased as human populations have increased in size?
(a) because we have increased rates of food production
(b) because of the improvements in education of women
(c) because of improvements in medical care
(d) a and c
(e) a, b, and c

2. Why do some people consider the high growth rates of human populations in developing countries to be of concern?
(a) because many people are born into conditions that do not provide them enough food
(b) because many people are born into conditions without clean water and adequate sanitation
(c) because increasing population sizes have led to increasing habitat destruction
(d) a, b, and c
(e) none of the above

answers- 1.d, 2.d

Population Biology 3- Logistic Growth

Lecture Video- http://mediacast.ttu.edu/Mediasite/Play/83f60ff04a32459896329229dc3cc5fd1d?catalog=4dc7289a-d3e0-4ae5-8fdc-5b86c027a06b

We are trying to develop a mathematical model that helps us to understand patterns of population growth. So far our first attempt, the exponential growth model, did not help us to understand population growth (for reasons that I hope that you understand by now).

The "Real" world

In our attemtp to think about population growth in the real world, we attempted to examine how per capitat birth rates and per capitat death rates should vary as population size varies. The model that describes this pattern of growth is known as the logistic growth model. It is important to realize that although this model is much more realistic, and therefore useful to us, than the exponential growth model, the logistic growth model still only exmaines what I call "the theoretical real world". That is, this model applies to our ideas about how populations should generally behave and do not thus relate directly to studying the population sizes of white tailed deer in central Texas or parrot fish on a coral reef in Fiji. These real world situations are much harder to understand than the simple "idealized" populations that I am talking about in BIOL 1404. You can take an Advanced Population Biology course if you want to learn more about how to apply these models to the "real real world".

Logistic Growth

We have discussed why, in the real world, r should decrease as population sizes increase. If this is the case then there is a population size at which the per capita birth rate equals the per capita death rate. We call this population size the carrying capacity.

1) When populations are smaller than the carrying capacity we expect them to increase in size until they reach the carrying capacity.

2) When populations are larger than carrying capacity we espect them to decrease in size untile they reach the carrying capacity.

3) When the population size equals the carrying capacity we expect no change in the size of the population.

The logistic growth equation is a mathematical equation developed by biologists to describe patterns of population growth consistent with the ideas above. Before focusing on the biological isights that we can gain from the logistic growth model (the real purpose of everything we have been doing) it is important to really understand patterns of logistic growth. Hopefully, this powerpoint presentation will help you understand these patterns better.

Powerpoint Presentation

Click here for a powerpoint presentation entitled "Fun With Graphs- Logistic Growth"

http://www.slideshare.net/secret/gyB3cjnSplLw41

NOTE: THERE IS AN ERROR ON SLIDE 16 OF THIS PRESENTATION!!!

The title of the graph on slide 16 should read "Logistic Growth: dN/dt vs t (Not N), N initially << k"

The x-axis of the graph is TIME (please ignore the values of K on the x-axis because K does not belong on the time axis). The shape of the graph is correct. Make sure you change the x-axis to Time rather than Population Size.

Expected Learning Outcomes

By the end of this course a fully engaged students should be able to

- define the carrying capacity

- draw, and interpret the following graphs associated with logistic growth
-how population size changes over time in logistic growth when the initial population size is much smaller than the carrying capacity
-how the population size changes over time in logistic growth when the initial population size is much larger than the carrying capacity
-how population growth rate changes over time in logistic growth when the initial population size is much smaller than the carrying capacity
-how the population growth rate changes over time in logistic growth when the initial population size is much larger than the carrying capacity
-how the per capita growth rate varies over time in logistic growth
-how the population growth rate varies over time in logistic growth

- discuss the causes for the shape of the s-curve (this answer will need to include a discussion of both math and biology)

- discuss the factors that regulate population size, be able to distinguish between density dependent and density independent factors that regulate population growth and give examples