BIOC 405 Study Guide - Midterm Guide: Deoxyribose, Pentose, Photosystem I

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ochreporcupine180

1 Dec 2016

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Department

Biochemistry

Course

BIOC 405

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D I M A I O

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One exam quest)on on (cid:498)p(otosynt(es)s )n green plants(cid:499) d)agram. Be familiar with the standard reduction potentials of the key. If the cell is using a lot of nadhp, there will be a lot of nadp around to accept the electrons. But sometimes the cell is not making a lot of carbohydrates so it doesn"t need to use a lot of nadp(; nadp( builds up and you don"t have a lot of nadp to. Ferredoxin: instead of giving its electrons to something that doesn"t exist (cid:523)nadp(cid:524), You"re not making much nadp( because you don"t need it, but the cell still needs. You are still pumping protons across the membrane, so you can still make atp even when there is no nadp around to accept electrons (cyclic pathway). T(e l)g(t )ndependent (cid:498)dark(cid:499) react)on accept the electrons. the electrons can flow back to the q pool (soluble hydrophobic molecules that are floating around in the membrane).

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Exercise #5: The Nervous system and Perception

Task #1: Color vision

Introduction

In the human retina, there are two kinds of light-sensitive cells: rods and cones. These cells are located on the outside of the retina, away from the vitreous humor and against the choroid layer, and are covered by a later of bipolar and ganglion cells as well as neurons. Light enters the posterior chamber through the lens and must pass through several cell layers before it is absorbed by the rods and cones.

Cones are involved in color vision at daylight intensities. Generator potentials in a cone excite one neuron, giving high-level resolution vision. Cones will not cause neural firing at low light intensities and are, therefore, nonfunctional at night.

Rods provoke black-and-white vision at low light intensities. A bipolar cell associates with several rods, so that generator potentials sum in their effect. This assures neuronal firing at low light intensities and provides a highly sensitive vision but with less resolution.

Receptor convergence. A ganglion cell, which receives input from a number of rods, spread out over the retina, cannot pinpoint the source of a light stimulus as well as a ganglion cell, which is stimulated by a single photoreceptor. In the case of a ganglion cell receiving the added input of several rods, light hitting any one of the rods can cause a neural spike in the ganglion cell, but the brain has no way to know which rod was excited. It is therefore harder to pinpoint the location of light stimuli on the retina when the stimulus is detected by rods (as compared to cones). The result is that our ability to see detail, or our resolving power, is considerably lower under dim light conditions than under bright light conditions.

Dark adaptation. If you go from a lighted area to a very dark room, you will not be able to see. After about ten minutes, however, you begin to be able to see again. This occurs because the rhodopsin pigment, which gets broken down when it absorbs light, is continually re-synthesized in the rods. When there is very little light, very little rhodopsin gets broken down and the amount of rhodopsin gradually builds up, making the rod much more sensitive to dim light.

When light strikes a receptor cell, it triggers a photo-chemical reaction that leads to neuronal firing. If a rod or cone receives high-intensity light, the visual pigments will be temporarily bleached and will not absorb any more light. Within a matter of a few seconds, enzyme systems in the cells will restore the visual pigment to its light-absorbing form. This can be easily demonstrated. If, after viewing a bright light, the eye is quickly shut or turned to a dark wall, the bright image will persist as a positive afterimage because the high generator potential causes the continued firing of neurons. If the eye is cast on a lighter background after a few seconds, a negative afterimage, or a dark image of the object will appear. This is because the still bleached cells are not receptive to the light coming from the light background.

According to the Young-Helmholtz theory of color vision, there are three types of cone cells, which respond respectively to red, green, and blue light.

All other colors are perceived as the brain interprets impulses coming from a mix of these receptors. If an object of one color is viewed for a long period of time at high light intensity, the cones for that color will become bleached. The afterimage of the object will be seen in the complementary color.

The Exercise 6 PowerPoint will demonstrate afterimages to you. Use the slide show option to project the square of red light on your entire screen in a dark room. After staring intensely at the square for 30 seconds or so, without shifting your gaze, click enter to change the slide to a soft white. Continue staring at the screen as the change is made. What do you see? What was the color of the afterimage?

Repeat this experiment using a blue square. Before doing the experiment, hypothesize what color the afterimage will be according to the Young-Helmholtz theory.

Hypothesis to be tested: (2 pts)

What did you see when the experiment was conducted? (2 pts)

Was you hypotheses accepted or rejected? (1 pt)

Explain the colors seen in these afterimages using the Young-Helmholtz theory. (5 pts)

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When a soil dries out, this has a negative impact on the activity of soil bacteria. Using an innovative combination of state-of-the-art analysis and imaging techniques, researchers at UFZ have now discovered that fungi increase the activity of bacteria in dry and nutrient-poor habitats by supplying them with water and nutrients. The ability of fungi to regulate drought stress in soil and thus sustain ecosystem functions is an important insight in the context of climate change.

Many fungi spread through the soil with a fine network of thin filaments known as hyphae. In their search for water and nutrients the hyphae grow in different directions, constantly enlarging the network. Once found, water and nutrients are absorbed and transported through the hyphae, allowing them to be supplied to parts of the fungal network in dry or nutrient-poor areas of the soil. But it isn't only the fungus itself which benefits from the transport of material through the hyphal pipelines: bacteria, too, are kept supplied with the water and nutrients they need to thrive. This has now been demonstrated by a team of UFZ researchers in a study recently published in the journal Nature Communications. "We've suspected for a long time that fungi play an important role in the soil moisture budget," says UFZ environmental biotechnologist Prof. Matthias KÃ¤stner. "Now, using secondary ion mass spectrometry techniques (NanoSIMS and ToF-SIMS) from the ProVIS research platform at UFZ, we've finally obtained experimental evidence."

As part of their investigations, the researchers closely examined the transport of water, substrates and nutrients through the microscopically small hyphae of fungi. They grew the fungi on a culture medium of water, glucose and nitrogen-containing nutrients. The fungal hyphae had to pass through a dry, nutrient-free zone in order to grow through into a new area containing the culture medium. The inhospitable transition zone contained spores of the common soil bacterium Bacillus subtilis. Spores are inactive stages of Bacillus that form when there is insufficient water, food and nutrients available for bacterial growth. The bacteria go into a kind of dormant stage, from which they only awake once the environmental conditions are more favourable for living again.

In the experiment, these conditions were indeed improved by the growth of the fungi: "As the fungal hyphae grew through the dry zone, the bacterial spores germinated and we noticed clear microbial activity," says UFZ environmental microbiologist Dr. Lukas Y. Wick. "The fungi obviously improved the environmental conditions for the bacteria and woke them from their slumber, like Sleeping Beauty." But what exactly happens at a chemical level when fungal hyphae grow in direct proximity to bacterial spores? To answer this question, the researchers 'labelled' the water, glucose and nitrogen-containing nutrients in the culture medium in advance with stable isotopes. If these substances were transferred from the fungus to the bacteria, they could be detected using the isotopic marker and the NanoSIMS method, with nano-scale spatial resolution. "The NanoSIMS method reveals the distribution of elements and isotops and therefore allows us to observe metabolic processes," KÃ¤stner explains. "As it turns out, we did find the stable isotopes of the labelled water, glucose and nitrogen-containing nutrients in the cell mass of the bacteria -- which could only have come from the fungi."

This study has given the UFZ researchers another important insight into fungi and their important function in soils. Fungi serve as pumping stations and pipelines for water, substrates and nutrients and can colonise inhospitable locations, making them habitable for bacteria -- and thus stimulate microbial activity in the soil. In previous work the researchers have already shown that fungal hyphae act as a kind of fungal highway for bacteria, allowing them to move around, and provide a hotspot for bacterial gene transfer. Wick continues: "The results of this latest study demonstrate once again that, through their interaction with bacteria, fungi play a significant, previously underestimated role in the soil ecosystem."

If a soil is contaminated with pollutants, for example, bacteria can break them down. But if the soil is too dry, the degradation processes will come to a standstill. "If the drought period lasts for a limited time, fungi have a stabilising effect and can keep soil processes going. This could be important specifically with regard to the impacts of climate change, if the ratio of dry to moist areas of soil dramatically increases," says KÃ¤stner. In future investigations, the researchers therefore intend to look even more closely at soil as a true ecosystem. "We want to carry out soil experiments under different environmental conditions and find out what influence fungal growth has on the breakdown of pollutants," says Wick. He adds: "It's important to have a better understanding of the role of fungi in the soil ecosystem. Only when we know how soil works can we respond to changes, for example those caused by climate change, with informed decisions."

Background

Almost all animal and plant cells require oxygen and give off carbon dioxide. This is called gas exchange and it occurs by passive diffusion. Some animals do all or most of their gas exchange across their skin (for example amphibians) but they have very low metabolisms and use very little oxygen and get rid of very little carbon dioxide.

On the other hand humans (and other mammals) have very high metabolic requirements and we canât rely on gas exchange over the limited 1.5 to 2.0 square meters of our skin to get enough oxygen in and carbon dioxide out fast enough. Our gas exchange takes place across a very thin membrane in the Alveoli of the lung and the gas exchange surface in humans is estimated to be between 50 and 100 square meters, or between 25 and 67 times our skin surface area.

Our lungs provide a huge surface for gas exchange but they are a dead-end system. Once the oxygen in the lungs is used up it needs to be replenished and carbon dioxide builds up in the air spaces in the lungs and needs to get out. This is where the diaphragm and a few of the skeletal muscles become important. In its relaxed state the diaphragm is at its longest and the space in the thoracic cavity (and the lungs) is small. When the diaphragm contracts it shortens, which increases the volume of the thoracic cavity (and the lungs). The increase in size means the pressure is lower in the lungs than outside so air comes into the lungs (inhalation). As the diaphragm relaxes, the lungs decrease in size enough that the pressure inside the lungs is higher than the external air pressure so air comes out (exhalation).

Introduction

In this lab you will be building a model of a lung and experimenting with different ways to breath.

Supplies:

In the Lab Kit

One round 9" balloon (one lung, we donât need two for this)
medium-sized plastic bag large enough to fit over bottom end of bottle (diaphragm)
medium-size, thin rubber band

You supply

plastic 2-liter soda bottle with bottom cut off (thoracic cavity)

Tape (optional)

Directions:

1. Insert the balloon through the open bottom of a modified 2-liter soda bottle and up over the neck of the bottle. Pull the end of the balloon over the edges of the neck of the bottle. The balloon is held open by the neck of the bottle.

2. Place the plastic bag over the bottom (open) end of the 2-liter bottle and use the rubber band to hold it in place. This will serve as the diaphragm. To inflate the lung, blow into the balloon just before you fasten the rubber band. You can also wrap tape over the edges of the plastic bag to minimize air leaks

3. Grasp the bottom of the plastic bag and pull it down and push it up. Watch as the "lungs" (the balloon) expand and contract as you do this. The balloon has to change size because the air space between the balloon and bottle must remain constant. (Well, it would if the seal around the plastic bag and bottle were perfect).

You may block the "trachea" (the neck of the bottle) so that the air supply is cut off and watch as nothing happens when the "diaphragm" is pushed in and out.

This model isnât perfect. None of the joints are air tight as they would be in a real thoracic cavity. Pull the âdiaphragm down and watch the lungs expand . If you hold it in place, the lungs will collapse again over time. This is because of leaks and is not how real lungs work. Pushing the diaphragm in and pulling it out over and over does give you an idea of how lungs work. As the diaphragm tightens, contracts (pull down on the plastic bag) the lungs fill with air. As the diaphragm relaxes (push up on the plastic bag) air is expelled from the lungs .

There are several different ways we breath, i.e. expand our thoracic cavity so that our lungs can expand. You have just made a demonstration model of the diaphragm at work. You can also use your rib cage to expand and contract so that you can inhale and exhale. There are muscles between and around your ribcage which you can use to change the size of your thoracic cavity.

This is approximately what your model of a lung will look like.

Answer the questions on the Report Page

Report Page Name

1. Put a hand on your lower ribcage and try moving your ribs out and in. Does air also move in and out?

2. Someone with an upper back or neck injury may not have the options of using diaphragm or ribs to breath. They can learn to use the clavicle and the muscles attached to expand their thoracic cavity a small amount and breathe independently for short periods of time. Put your hand on you clavicle and try to raise and lower just that bone without using your diaphragm or your ribs. It isnât easy but you should be able to get a little air into and out of your lungs this way. How effective do you think this way of breathing is?

3. When you take a really deep breath you use all these muscle groups to help. Take a really deep breath and notice that your ribs expand, your lower abdomen comes out (a sign that the diaphragm has contracted) and your shoulders lift a little (the upper chest and clavicle are working). Now take a relaxed breath. Only your abdomen should go in and out. The movement of your abdomen is a result of the contracting diaphragm pushing on the contents of your âgutâ which forces your abdomen to push out.

Do you breath in or out when your diaphragm contracts?\

4. If a hole were poked in your thoracic wall (the wall of the pop bottle â the hole should be at least the diameter of a pencil)

a. what would happen when you tried to breath? (This is a pneumothorax).

b. Is the space between the balloon and plastic bottle still required to remain constant?

5. Would it be possible to live with a paralyzed diaphragm? Explain your answer.

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BIOC 405 Study Guide - Midterm Guide: Deoxyribose, Pentose, Photosystem I

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