Topic 9 [HL]: Plants

Task One

• State the function of photosystem II, photosystem I and the calvin cycle in the production of glucose and sucrose.
• Photosynthesis is a two step process with light dependent and independent reactions. Light dependent reactions convert light energy to chemical energy and light independent reactions use the chemical energy to make organic molecules. 
• Light dependent reactions occur on thylakoid membrane and may occur via cyclic or non-cyclic processes; both processes include light exciting chlorophyll leading to release of electrons that pass through an electron transport chain, creating ATP (photophosphorylation)
• Non-Cyclic: Chlorophyll in photosystems 1 and 2 absorbs light, leading to photoactivation: a release of high energy electrons. Electrons from photosystem 2 go through ETC, producing ATP via chemiosmosis. Electrons from photosystem 1 reduce NADP+ to NADPH + H+. Electrons from photosystem 2 replace those lost in photosystem 1, electrons lost in photosystem 2 replaced by electrons generated from photolysis of water. Oxygen is by-product.
• Cyclic (only photosystem 1 involved): High energy electrons released by photoactivation pass through ETC (producing ATP) and then return to photosystem 1. Electrons in cyclic photophosphorylation do not produce NADPH + H+, which is required for light independent reactions. Thus, though cyclic phosphorylation constantly creates ATP, the chemical energy cannot be used to create organic molecules.
• Light independent reactions occur in the stroma and uses the ATP and NADPH + H+ from non-cyclic photophosphorylation. It is also known as the Calvin cycle and has three main steps:
1. Carbon Fixation: 

   Enzyme rubisco (RuBP carboxylase) catalyzes attachment of carbon dioxide to 5-carbon compound ribulose bisphosphate (RuBP). The new 6-carbon compound breaks down to two 3-carbon molecules: glycerinate-3-phosphate (G3P)

2. Reduction: 

   Each G3P molecule is phosphorylated by ATP and reduced by NADPH + H+, converting them to glyceraldehyde phosphate, a trios phosphate (TP)

3. Regeneration of RuBP: 

   For every 6 TP, only one can be used to create half a sugar molecule. The other 5 TP molecules are reorganized to regenerate RuBP (using ATP). The cycle repeats multiple times to construct chains of sugars (sucrose)

• Draw the molecular structures of glucose, fructose and sucrose. 

• Distinguish between the structure and function of the three polysaccharides of glucose. 
• glycogen- multiple branches, animal storage of glucose
• cellulose- branched and unbranched varieties, main structural component of plants
• starch- branched, plant storage glucose

• Compare the leaf and root structure and vascular tissue organization in stem and roots of monocotyledonous and dicotyledonous plants. [State which sugar cane is.]
• Leaves: Monocots have parallel veins from stem to tip; dicots have branching veins
• Root structure: Monocots do not have main roots but have smaller roots that branch out; dicots have main roots that grow downwards
• Vascular tissue organization: Monocots have vascular bundles spread across the stem, with bundles closer to the sides of the stem rather than the center; dicots have vascular bundles circular 

Task Two

• State the meaning of 'allocation of photo-assimilates'.
• The allocation/grouping of a certain amount of compounds formed through assimilation in light dependent reactions (monosaccharides) from a plants leaves to its sinks

• Explain what the author means by the phrase 'heterotrophic sinks'. 
• The areas of a plant in which sucrose is stored: fruits, roots, etc.

• Describe the structure and function of a plasmodesmata between the mesophyll and parenchyma cells. 
• Plasmodesmata are microscopic communication bridges between the cell walls of two plant cells; they facilitate the movement of sucrose from mesophyll cells to parenchyma cells

• Hypothesize the effect of a pH or temperature change on plasmodesmata structure and function. [Hypotheses must include a why!]
• A change in pH or temperature would denature proteins that make up the plasmodesmata, which would probably prevent it from functioning efficiently

• Distinguish the structure and function of xylem and phloem.
• Xylem vs. Phloem:
• Structure: Non-living vs living; thin walled sieve tubes w/ pores at ends vs tubes with no cross walls
• Function: Transports nutrients from leaves to sinks/growing parts vs water/minerals from roots to aerial parts (leaves)

Task Three

• Distinguish between, in your own words, the apoplastic route and symplastic route of ion movement in plants. 
• Apoplastic route: through the cell wall
• Symplastic route: through the cytoplasm (via plasmodesmata)

• Draw the pathway of sucrose from mesophyll cell [site of production], to the SE/CC. 

• Draw and annotate a diagram to describe the pressure flow model of water and sugar transport in xylem and phloem. [direction and substance are a must!] [you may add onto the previous drawing if you like].

• Annotate your drawing to distinguish between the different transport mechanisms [diffusion, osmosis, facilitative diffusion, primary active transport, secondary active transport ex. SUT1 ]  that occurs in the xylem/phloem pressure flow model of sucrose and water transport.

Sugar, Insulin, Obesity and Cancer

Task One [Monday Feb 17th]: Insulin Production:

• Draw and annotate a pancreatic cell with all the structures and their functions for the production and export of proteins - specifically insulin. 

• Draw a cartoon image of insulin and.... Describe the different levels of protein structure and the forces at each level that maintain its share.

Task Two [Wednesday Feb 19th]: Insulin Physiology 

• Describe the normal cycle for insulin: stimulus, production cell, target cell, response, feedback.
• Increase in level of glucose in blood leads to production of insulin in beta islets of pancreas
• Insulin targets muscle (use glucose for ATP production), fat (energy storage), liver cells (glycogenesis)
• This results in decrease of blood sugar levels in which less insulin is produced (negative feedback)

• Distinguish between the storage of glucose in liver/skeletal muscle from storage in white adipose tissue [a connective tissue]
• Liver/skeletal muscle: glucose to glycogen (glycogenesis)/glucose to ATP (metabolized)
• Adipose tissue: glucose to fats

• Distinguish between the three cases: normal insulin response, diabetes type 1 and diabetes type 2. 
• Normal insulin response: Insulin produced in beta islets, and binds to receptors of membranes on the target cells
• Diabetes Type 1: cells body attack islet cells, inhibiting production of insulin
• Diabetes Type 2: diet related, leading to receptors to be less receptive/sensitive to insulin

Task Three [Friday February 21st]: Response to Insulin - Cell Level

From the above quotes and reviewing the content of the core please answer the following questions:

• Describe the target cell response mechanism in liver, skeletal and adipose tissues by:

• Draw and describe the fluid mosaic model of the cell membrane

• Predict  the transport mechanism liver, skeletal and adipose tissues would use to absorb [uptake] glucose from the blood.
• Active transport using a protein membrane due to large size of glucose

• Compare and contrast the predicted mechanism to the actual process used by intestinal epithelium to absorb glucose from the intestinal lumen. 
• The mechanisms are similar in the intestinal epithelium (use GLUT2 as well)

Task Four [Tuesday, February 25th]: Response to Insulin - Gene Level

• Explain the cancer cell dependency for glucose [energy and lipids]. There are two pieces of the mystery eluded to above: 

• One: Mitosis- cancer cells use glucose and glycogen for mitosis and growth

• Two: Lipids- cancer cells use fat tissues to synthesize its own membrane

Cancer cells response to glucose requires more protein transporters in the cell membrane and more enzymes for glucose metabolism for mitosis, lipid synthesis and nucleotide synthesis. 

• Describe the entire process of gene transcription, mRNA production, [include splicing to remove introns], translation by ribosomes. 
• Gene transcription: RNA polymerase binds to promotor on DNA strand, unwinds strand, and uses one strand of the double helix as template for replication
• mRNA production: RNA nucleotides brought by RNA polymerase, producing RNA strand; before leaving nucleus for ribosome, introns are cut out by spliceosomes in which a cap is added to one end and adenine tail is added to the other
• Translation by ribosomes: Ribosomes bind to start codon of mRNA, which is followed by tRNA binding to the mRNA via the ribosome (tRNA is bound to amino acid); continuation of this leads to an amino acid chain. tRNA binds to mRNA in A site of ribosome, and is then moved to P site, which leads to another tRNA to bind to A site, forming peptide bond between amino acids of the two tRNAs, tRNA in P site is released in E site without amino acid.

Task Five [Thursday, February 27th]: Glucose metabolism

• State and draw a basic cartoon of stages of glucose metabolism used to generate ATP in the non-proliferative tissues. [In class we broke the entire process into five steps]

• Describe the input and output with regards to: NAD+, NADH+H, CO2, ATP, H2O

• Distinguish between animal use of lactate fermentation and alcoholic fermentation by bacteria and yeast. 
• Yeast produces carbon dioxide and ethanol
• Animals produce lactic acid

• Explain the advantage of cells switching to anaerobic metabolism [fermentation] of sugars.
•  Anaerobic metabolism of sugars offers energy quicker because the process is faster

• Distinguish between catabolic and anabolic reactions and the role of NAD+ and NADP+ in catabolism and anabolism.
• Catabolic reaction: break down of molecules, giving out energy
• Anabolic reaction: formation of molecules using energy; uses both NAD+ and NADP+

Review: Chemistry of Life/Recombination Genetics

Task 1

• State the essential amino acids for humans. 
• Tryptophan, Phenylalaline, Tyrosine

• Explain the process of evolution that may have occurred to allow humans to survive without the de novo biochemical pathways to make these essential amino acids. 
• A mutation may have occurred early on before leading to genetic drift

• Explain why ALL amino acids are non-essential for plants. 
• Plants cannot get adequate supplies of pre-formed amino acids so they have to make all of the amino acids needed for protein synthesis de novo.

• State what makes the molecule chorismate important. 
• The three aromatic amino acids are all made from chorismate

Task 2

• Explain how the types of inhibition that glyphosate COULD use to inhibit the EPSP enzyme. 
• Competitive inhibition: type of enzyme inhibition where binding of the inhibitor to the active site of the enzymes prevents binding of the substrate and vice versa
• Noncompetitive inhibition: type of enzyme inhibition where inhibitor reduces activity of the enzyme and binds equally well to the enzyme whether or not it has already bound the substrate
• Product inhibition: type of enzyme inhibition where the product of enzyme reaction binds to the enzyme and inhibits its activity

Task 3

• State and describe the actual mechanism glyphosate uses to prevent the chromisate metabolism. 
• Competitive inhibition: type of enzyme inhibition where binding of the inhibitor to the active site of the enzymes prevents binding of the substrate and vice versa

• Describe the model of enzyme activity discussed in this article. 
• Induced fit substrate binding: when enzyme binds to substrate and changes occur in the active site, enhancing catalysis, as enzyme converts substrate to product

• Analyze the picture that shows the alanine --> glycine mutation. Explain the nucleotide changes that could have resulted in the alanine to glycine change. [there are many]

• Deletion of nucleotide(s), frameshift after nucleotides were removed, or single base substitution

• Explain the effect the G100-->A100 change has on the affinity of glyphosate for the PEP [substrate] active site. 
• The change may prevent PEP binding because the enzyme loses a molecule, changing the shape of the protein

Task 4: 

• Describe the IDEA of what Monsanto was attempting to do. 
• Monsanto was trying to genetically modify the plants via recombinant DNA to allow the plants to resist the Roundup herbicide

• Explain, with proper sequence and language, the evolutionary process of this bacteria from this location.

• "The C4 strain of Agrobacterium sp. proved to be just the thing. This is a species of bacteria that was found growing in the waste-fed column at a factory that made glyphosate. The EPSP synthase enzyme from this bacterium (C4 EPSP synthase) was almost completely insensitive to glyphosate."
• The C4 strain of Agrobacterium sp. was originally susceptible to the glyphosate, but mutations occurred, which resulted in the production of a new kind of EPSP synthase enzyme that resisted the effects of glyphosate.

• Explain the USE of the following components of the plasmid used by Monsanto:

• ori-322 and ori-V - ori-322 is an origin of replication from plasmid pBr322 by E. coli; ori-v is an origin from plasmid RK2, a plasmid that reproduce in a wide variety of gram negative bateria

• AAC(3)-III, along with P-35S and NOS 3' - AAC(3)-III gene allows the selection of gentamycin resistance in plants; P-35S is a promoter that indicates to ribosims where to begin replication; NOS 3’ is the stop codon

• CP4-EPSPS along with P-e35S and NOS 3' and CTP2 - CP4-EPSPS gene was modified and a plant promoter (P-e35S) was added along with a polyadenylation site, NOS 3’. CTP2 is a N-terminal leader sequence that targets the protein to the chloroplast as EPSP synthase is in chloroplasts where synthesis of chorismate takes place.

• Distinguish the following descriptions of transformation in plants to the process used  to transform bacterial colonies.  [pGlo experiment]

• pGlo uses two main steps:

•  transformation solution containing CaCl2.

• 'heat shock' that induces gene expression that stimulate bacteria to 'take up' DNA from their environment. 

• Transformation of plant cells used: 

• "The interesting feature of this transformation is that it is mediated by the bacteria. All you need to do is expose the plant cells to the bacteria under the right conditions and your gene of interest will end up in a plant chromosome."
• pGlo: plasmid heated to allow it to diffuse into bacteria
• plant cells: no heat required, simple exposure will lead to bacteria to be in the plant chromosome

• State the substance in the last image, that 'selects' the proper Agrobacteria with the genetically engineered plasmid to survive. 
• Glyphosate

• State the plant hormones that are used to promote root and shoot development from the transformed leaf disk. 
• Auxin, Gibberellin, Abscisic acid

Observing Plant Roots and Fruits

Apple

-Stem: Transport of fluids and nutrients to and from the fruit

-Exocarp: Tough outer skin to protect the fruit

-Mesocarp: The 'flesh' of the fruit, located between epicure and endocarp, is the edible part of the fruit that attracts animals

-Endocarp: Area that directly surrounds seeds, is thick and hard to protect the seed

-Seed: Carries, protects, and nourishes embryo until germination. It is necessary for the plants reproduction and survival (as a species)

-Hypanthium: Contains nectar

 Bell Pepper

-Stem: Transport of fluids and nutrients to and from the fruit

-Exocarp: Tough outer skin to protect the fruit

-Mesocarp: The 'flesh' of the fruit, located between epicure and endocarp, is the edible part of the fruit that attracts animals

-Endocarp: Area that directly surrounds seeds, is thick and hard to protect the seed

-Seed: Carries, protects, and nourishes embryo until germination. It is necessary for the plants reproduction and survival (as a species)

-Placenta: Region on the inner fruit wall where seeds attach to

Eggplant

-Pedicel: Connects eggplant to rest of plant

-Calyx: Protect bud until it matures

-Exocarp: Tough outer skin to protect the fruit

-Mesocarp: The 'flesh' of the fruit, located between epicure and endocarp, is the edible part of the fruit that attracts animals

-Endocarp: Area that directly surrounds seeds, is thick and hard to protect the seed

-Seed: Carries, protects, and nourishes embryo until germination. It is necessary for the plants reproduction and survival (as a species)

-Placenta: Region on the inner fruit wall where seeds attach to

Carrot

-Storage root: Stores nutrients from soil

-Stem: Transport of fluids and nutrients to and from the fruit and connects carrot to rest of the plant

-Periderm: Protect interior tissues from weathering and destruction

-Xylem: Transports water and soluble minerals from roots to plant

-Phloem: Transports and distributes products of photosynthesis to plant

 -Tap Root: Allows plants to reach further down the ground to maximize the access of water and nutrients from the soil

Cauliflower

 -Cauliflowers are immature flower heads and are flower buds packed really tightly.

Strawberry

-Seeds on epidermis because they do not reproduce via seeds because they grow asexually through roots that grow and bear fruit.

Mark is in trouble

Part I

1. What types of physiological problems do humans encounter at high altitudes?

 Headaches, dizziness/lightheadedness, shortness of breath, fatigue

2. What symptoms did the climbers exhibit that might be related to altitude? Explain. 

Headache, deep breathing, fatigue. Shortness of breath would be caused by the lack of pressure of oxygen in high altitudes which leads to the climbers to breath deeper. Fatigue is caused by the lack of oxygen as not enough oxygen is taken in (compared to sea level) to energize the cells. Headaches may also be caused by the lack of oxygen that is going to the brains.

3. Compare the air at 18,000 feet (atmospheric pressure 280 mm Hg) to the air at sea level (760 mm Hg). What specific changes in the primary atmospheric gases (nitrogen, oxygen, carbon dioxide) might occur? Are they significant? 

The composition of earth's atmosphere is 78% nitrogen, 21% oxygen and 1% other gases (including carbon dioxide). There is less pressure at 18 thousand feet than there is at sea level, which means that the density of oxygen molecules is less and therefore would mean the amount of oxygen inhaled by a human being at 18 thousand feet would be lower than one at sea level. (Air pressure in atmosphere is supposed to be greater than the pressure inside the lungs so that the air would "go into" the lungs)

4. What is the specific pulmonary response to high altitude? [Assume you are considering a subject at rest.] 

Lowered oxygen density in the atmosphere means less oxygen intake which means that the heart will pump harder to get more blood to pump throughout the body to try and catch up to the normal amount of oxygen that would be distributed at sea level.

5. How will this response affect overall blood gases? What about oxygen loading and unloading from hemoglobin? Explain how you arrived at your conclusions. 

There will be less oxygen binding to the hemoglobin in the blood as there is less oxygen in the atmosphere. There will be a higher affinity of RBC for oxygen

6. After breathing at altitude for a few days, the body normally begins producing more 2,3-DPG. What is the significance of this change? How will it affect the pulmonary changes observed?

2,3 DPG helps decreases the affinity of RBC for oxygen which means that the body will be able to increase the amount of oxygen distributed to the tissues as less would stick to the RBC. The person will be less fatigued, have a lower heart rate and less headaches

Part II

1. What physiological changes is Emily referring to (above) that will occur when someone lives at altitude for an extended period?

The body learns to increase production of erythrocytes, which increases oxygen in blood as there are more RBCs.

2. How are these changes advantageous? 

Cells in the body will receive more oxygen

3. What is the specific physiological pathway that results in the changes described?

Kidney detects low oxygen level and secrets erythropoietin, stimulates RBC production in bone marrow, more RBC = More hemoglobin = more oxygen in blood = more oxygen to tissues

Part III

1. How would the oxygen and Gammow bag help Mark? 

Oxygen and Gammow bag will increase the amount of oxygen in Mark. The bag increases the atmospheric pressure, which leads to less strenuous breathing because more air is going into the lungs.

2. If you were a member of the medical team examining Mark, what types of tests would you run? Why? [Try to focus on what types of things you would like to measure, whether or not you know of a possible test for them.] 

Blood sample, see concentration of oxygen/CO2 and pH levels

3. What types of results do you expect to find? Explain your reasoning.

Lower oxygen/CO2 levels in blood compared to sea level (lower pH) because there is less oxygen at 18 thousand feet than at sea level. So the body is trying to play "catch up" to maintain the distribution of oxygen but cannot.

Hominid Evolution and Carbon Dating

Hominid Evolution

Ardipithecus ramidus (4.4 million years ago)

-divergent large toe with a rigid foot

-pelvis tree climbing and bipedal activity

-ape ancestor not chimpanzee like

-canine teeth = same size male and female

-wooded environment

-3 ft 11 in, 110 lbs

Australopithecus afarensis (2.95-3.85 million years ago)

-ape and human characteristics

-apelike features:

face proportions 

braincase (small brain)

strong arms with curved fingers (climbing trees)

-human features:

small canine teeth

body stood on two legs

-could live on trees and ground

-males (4ft 11in, 92 lbs)

-females (3ft 5in, 64 lbs)

Australopithecus africanus (2.1-3.3 million years ago)

-rounder cranium w/ larger brain and smaller teeth

-apelike:

long arms

sloping face that juts out (pronounced jaw)

-pelvis, femur, footbones: walked bipedally

-shoulder and hand: climbing

-males (4ft 6in, 90 lbs)

-females (3ft 9in, 66 lbs)

Homo habilis (1.4-2.4 million years ago)

-larger braincase

-smaller face and teeth

-ape like features: long arms & prognathic face

-average (3ft 4in- 4ft 5in, 70 lbs)

Homo erectus (143k-1.89mil years ago)

-more adapted to the ground

shorter arms

long legs

=walk and run more

-average (4ft 9in - 6ft 1in, 88 - 150lbs)

Homo neanderthalensis (28-200 thousand years ago

-closest extinct human relative

-skull features

large middle part of face

angle cheek bones

huge nose for different air (humidifying and warming)

-shorter stockier bodies (cold environments)

-brain same size sometimes larger

males (5ft 5in, 143 lbs)

females (5ft 1in, 119lbs)

Homo sapiens (200,000 to present)

-large brains

-thin walled high vaulted skull

-flat almost vertical forehead

-smaller teeth

Summary

-The braincase gets larger incrementally

-Generally get taller and heavier

-Shorter arms and longer legs

-Nose smaller

-Smaller teeth

-Became only bipedal

-These traits are meant to suit us to live on the ground

http://humanorigins.si.edu/resources/intro-human-evolution

Carbon dating

Carbon dating is used to determine the age of fossils and requires the use of the radioactive isotope carbon-14. Carbon-14 is produced by cosmic ray protons which blast nuclei in the upper atmosphere, thus producing neutrons and bombard nitrogen creating carbon-14. This occurs at a rate which is constant, therefore we can use radioactive emissions of once-living matter and compare it to living ones. The results allows us to make a measurement of the time that passed.

Radioactive half-life is the time for half the radioactive nuclei to go through radioactive decay. Unstable radioisotopes decay into more stable forms (C-14 decays to C-12, which is stable.) 

Living organisms constantly exchange carbon with the atmosphere in the form of CO2; this results with the organisms to have nearly the same ratio of C-14 to C-12 with the atmosphere. However when the organism dies, it beings to undergo radioactive decay in which C-14 decays into a more stable C-14. This can be used to measure the amount of time an organism had been dead for.

Carbon dating is used for younger fossils because of the difference in half-life.

C-14 has a half-life of 5700 years which is useful for fossils that are 1000 to 10000 years old, whereas potassium (K40) has a half life of around 1.3 billion years therefore allowing it to be used for much older fossils.

Abiogenesis and Panspermia

The abiogenesis theory states that life came originated from simple organic compounds that were created on the earth from the pre-biotic soup that existed. However on the other hand, the panspermia theory states that life on Earth originated from comets and asteroids carrying bacterial life from the universe.

The Urey-Miller experiment provides support that the occurrence of abiogenesis is possible. The Urey-Miller experiment aimed to create organic compounds via a system that simulated similar conditions of pre-biotic Earth. The simulation consisted of a recirculating system with heated water (as the ocean), a chamber with electrical charges (as the atmosphere with lightning), and a condenser for gases in the 'atmosphere 'chamber to dissolve in the water. These chambers consisted of ammonia, nitrogen, methane, hydrogen gas, and carbon dioxide. After a while, the experiment's result showed simple organic molecules in the 'atmosphere' chamber, whereas amino acids and other organic acids were found in the 'ocean' chamber.

However, it is still possible for the panspermia to be valid because abiogenesis may have occurred on a different planet and comets may have transported the products to Earth while abiogenesis was occurring on Earth.

Scientists think the RNA replication or metabolism occurred first before protobiont cells began to form in micro environments for many reasons.

Scientists think RNA replication occurred first because RNA have the ability to replicate themselves as well as catalyzing reactions. RNA also have the ability to attract and link amino acids into proteins, which are the building blocks of life. Furthermore, scientists believe that RNA were able to persist because of the clay from volcanic ashes would cover it from harmful UV rays.

Scientists also argue that metabolism occurred before the protobiont cells began to form because they believe that the Earth may have started out with the first living thing on Earth as a primitive metabolic life sustaining itself with a series of reactions with CO2 or CO catalyzed by metal sulfide.

Protobionts are thought to be precursors to prokaryotic cells. They consist of abiotically produced organic molecules surrounded by a membrane like structure. Protobionts have characteristics that are related with life such as simple reproduction, metabolism, excitability, and the maintenance of itself to survive in its environment (with the help of its membrane). Due to this, many scientists believe RNA replication and metabolism occurred before protobiont cells began to form. RNA is needed for the protobiont cells to execute simple reproduction and metabolism is needed so it can energize itself to survive. 

However, whether RNA replication or metabolism may have been the very first occurrences of life, both the abiogenesis and panspermia theories still have validity because organic compounds could have still been created on Earth or survived on a comet traveling to Earth to create protobiont cells.