Unit+2+Metabolic+Processes

October 4, 2013
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 * __Summary__**
 * Oxidation Reduction Reactions occur when there is a loss and gain of electrons at the same time.
 * Oxidation is the //LOSS// of electrons and reduction is the //GAIN// of electrons.
 * "OIL RIG" is a great mnemonic to help you memorize this. (Oxidation Is Loss, Reduction Is Gain.)
 * The reducing agent is the substance that is losing the electrons. The substance gaining the electrons is called the oxidizing agent.
 * Below is one of the examples that we looked at, how carbon undergoes oxidation.
 * Oxidation reactions is the main method through which chemical potential energy from reduced compounds are released.
 * Reduced compounds include lipids, carbohydrates and proteins.
 * Oxidation can also be known as the loss of electron, removal of hydrogen or addition of oxygen.
 * Reduction can be known as the gain of an electron, addition of a hydrogen, removal of an oxygen.
 * Redox reactions usually occur under moderate temperatures, in the presences of enzymes and/or in small steps to minimize the amount of energy loss.
 * Recall that Photosynthesis is an anabolic process (builds complex molecules), while cellular respiration is a catabolic process (breaks down complex molecules)
 * Below is the chemical equation for the two processes discussed in class today.
 * [[image:http://www.tomatosphere.org/teacher-resources/teachers-guide/grades-8-10/images/photosynthesis-respiration.jpg width="294" height="117" align="center"]]
 * The Glycolysis pathway describes the oxidation of glucose. Today in class we covered phase 1 of the three phases.
 * To the left is a diagram of Phase 1 similar to the one we drew in class.

An overview of the first phase is:
 * 1) __In__
 * 1 molecule of glucose
 * 2 molecules of ATP
 * 1) __Out__
 * 2 molecules of PGAL (G3P- in textbook)
 * 2 molecules of ADP

__Homework__

 * 1) Finish reading section 3.1
 * 2) Read section 3.2 and complete questions #3,4,5,8,12
 * 3) Glucolysis needs to be memorized, there will be a quiz on it Tuesday!

__References__

 * 1) Click here for a site that goes over the glycolysis phases in greater detail.
 * 2) Click here for a video on glycolysis that may help you understand the phases.
 * 3) Click here for an interesting rap about glycolysis that may help you study.

=**MONDAY, OCTOBER 07, 2013**= =**By: Jove Garcia**=

**CLASS OVERVIEW**

 * Note on glycolysis phase 2 was taken
 * Class was divided into partners for clothes pin activity
 * Homework was given at end of class

**SUMMARY**
__Catabolism of PGAL (Phase 2 overview)__ ** >>GLYCOLYSIS PHASE 2 = ENERGY PAYOFF PHASE<< **
 * inorganic phosphate is added to each of the 2 PGAL`s
 * NAD+ acts as an oxidizing agent
 * it gains an H and an e - and is therefore reduced
 * NAD + + 2H => NADH + H +
 * 4 ATP molecules and 2 pyruvic acid molecules are produced
 * For every molecule of glucose which undergoes glycolysis two 3-phosphoglyceraldehyde are produced
 * Therefore, phase II occurs 2x per glucose molecule

__Glycolysis Phase 2 Summary__

What goes in must come out, if you know what I mean.

Molecules in: Molecules out: Note: 2 ATP in during phase I and 4 ATP out in phase II. Therefore a net gain of 2 ATP
 * 2 PGAL, 2 NAD +, 2P i , 4 ADP
 * 2 Pyruvic acid
 * 2 NADH (used everywhere in cell)
 * 4 ATP
 * 2 H 2 O



HOMEWORK

 * Complete questions for the clothes pin activity conducted today
 * Memorize the phase diagrams for glycolysis for tomorrow's quiz!

=**MONDAY, OCTOBER 08, 2013**= =**By: Jove Garcia**=

**CLASS OVERVIEW**

 * Quiz on glycolysis (phase 1 and 2)
 * Response answers for Clothes Pin Lab was collected
 * ISP for rest of class

SUMMARY
Basically the answers to the glycolysis quiz today!

HOMEWORK

 * Read pages 172 - 177 from the textbook
 * Remember to continue to work on that enzyme project!

=**MONDAY, OCTOBER 09, 2013**= =**By: Jove Garcia**=

CLASS OVERVIEW

 * Notes on "Fate of Pyruvate" was taken
 * Class went through "Krebs Cycle very carefully
 * Homework was given at end of class

SUMMARY - FATE OF PYRUVATE
__Options:__
 * cellular respiration (aerobes)
 * alcoholic fermentation (yeast)
 * lactic acid fermentation (oxygen deprived muscles)



__Aerobic Respiration Overview (Pyruvate to CO__ 2 __and H__ 2 __O)__
 * pyruvate is transported into the mitochondrion
 * pyruvate is broken down into Acetyl-CoA
 * Acetyl-CoA is fed into the Krebs Cycle
 * In Krebs, various reduced co-enzymes (NADH and FADH 2 are formed)
 * In a pathway called the electron transport chain, NADH and FADH 2 are used in the chemiosmotic synthesis of ATP

__Oxidative Decarboxylation__
 * glucose => 2 pyruvate + 2 NAD + => 2 Acetyl Co-enzyme A + 2 NADH + 2 CO 2
 * the pyruvate are transported into the mitochondrion and this reaction occurs there. Eventually the "Acetyl" is converted into H's, CO 2, and water (in the Krebs cycle)
 * The H's are combined with O 2 to give H 2 O and + ATP is produced from ADP using chemiosmotic synthesis of ATP (electron transport chain)

__Krebs = TCA = Citric Acid Cycle__

2 NADH (x 2) = 6 ATP 1 FADH 2 (x 2) = 2 ATP 1 ATP (x 2) = 2 ATP
 * Important***

24 total ATP produced from Krebs cycle alone

HOMEWORK

 * Have the Krebs Cycle (simplified, without structures or enzymes) memorized for the quiz on Wednesday!
 * Enzyme build project blueprints due next Thursday!

Sarjini Sivanesan

 * Summary:**
 * Today we drew a simplified flow chart, demonstrating how the 38 ATPs are formed.[[image:http://crescentok.com/staff/jaskew/isr/biology/respire5.jpg width="382" height="214" align="right"]]
 * To your right is a flow chart, similar to the one we drew in class.
 * Remember that for every 1 NADH, 3 ATPs are produced and that 1 FADH2 produces 3 ATP each.
 * Note that the 38 ATPs produced is a theoretical value and is the maximum that can be produced per glucose molecule.
 * In reality, the actual yield of ATPs varies, depending on the efficiency. Typically anywhere between 32-34 ATPs can be expected.
 * Today we also learned about the electron transport chain. This transport chain essentially transfers electrons from NADH and FADH2 to O2.
 * This process occurs in the mitochondria in cells.
 * Note that this process occurs in aerobic conditions (when oxygen is present.)
 * This chain consists of four protein complexes. Electrons are shuttled from one complex to the other by one of the two electron shuttles (ubiquinon or cytochrome)

Homework:

 * 1) Make sure you have drawn out the electron transport chain, figure 7 on page 178 in your textbook.
 * 2) Study and prepare for the Krebs Cycle quiz this Wednesday.
 * 3) Continue working on the Electron Transport Chain group stories/songs. Presentations will start next Wednesday.
 * 4) The blueprint for our enzyme model is due Thursday as well.

Todays class:

 * The presentations on the Electron transport chain were finished
 * Our Enzyme project blueprint was checked and submitted
 * Interim reports were completed
 * Unit 1 test were handed back

Reminders

 * 1) Make sure to go over pages 190 - 194 and questions 1 - 10
 * 2) The enzyme model is due October 28
 * 3) Make sure to hand in your Enzyme blueprint if not handed in today.

**Summary:**

 * Regulation Of Cellular Respiration:**
 * Cellular respiration is often regulated in order to ensure that a balanced amount of ATP is synthesized.
 * This occurs mainly through negative feed back inhibition. Recall that feedback inhibition is when the end products of the pathway inhibits an enzyme early in that same pathway.
 * When high levels of ATP or citrate are present, phosphofructokinase is inhibited of its actions.
 * When ATP levels or citrate levels all, ADP and AMP levels increase. The AMP then activated and stimulates the enzyme phosphofructokinase.
 * High levels of NADH turns off pyruvate dicarboxylase.
 * To your right is a flow chart very similar to the one we copied in class.


 * Alternatives to Glucose:**
 * Other types of macromolecules can also enter the cellular respiratory pathway at specific points.
 * When depleted of glucose, carbohydrates are the first to go, followed by lipids and then proteins.

1) Carbohydrates
 * Carbohydrates can be easily hydrolyzed into mono saccharides, which can enter the pathway in its early stages.

2) Fats
 * For fats, triglycerides are the prominent sources of energy for ATP synthesis.
 * They however have to be first broken down into glycerol and fatty acids. The glycerol is then converted into PGAL, which then enters into glycolysis 2.
 * Fatty acids go through a process called beta oxidation to become acetyle CoA.

3) Proteins:
 * Proteins are not generally used as a source of energy, but under extreme condition such as starvation it is possible.
 * Proteins must be hydrolyzed into amino acids before oxidation can occur.
 * The amino group (which is the NH2) is then removed and the remaining portion of the molecule enters as pyruvate or acetyle CoA or as a component of the Kreb Cycle. This is determined by the R group and the enzymes that convert these molecules.


 * Note that the brain can only use glucoses and that excess glucose is stored by out liver as glycogen (glycogenesis) and fat (lipogenesis)
 * Adipose tissues in our body stores (lipogenesis) and breaks down (lipolysis) fats.


 * How NADH is Moved into the Mitochondria**:
 * There are two main ways through which this is done:

1) Glycerol 3-phosphate shuttle
 * This transports NADH with the cost of an ATP molecule. Thus if this is used, you will theoretically have 36 ATP per glucose molecule.
 * This type of shuttles are in abundance.

2) Malate-Asparate Shuttle
 * This has the ability to transport NADH without using an ATP molecule.
 * Thus if this is used, we will theoretically end up with 38 ATP from one glucose molecule.

**Homework:**

 * 1) Continue working on your mini group presentations.
 * 2) Make sure you have finished copying down the figure one on page 184 and have added where carbohydrates, lipids and fat enter the cellular respiratory pathway.
 * 3) Pg 189 #3, 4, 6-10
 * 4) Continue working on your Enzyme Model Project

**Resources**

 * 1) Click here to read more on the Regulation of cellular respiration and go more in-depth.
 * 2) Click here to find a summary on everything we have learned so far of the cellular respiration cycle as well as more info on the alternatives to glucose.


 * Metabolic Processes Julie Nguyen **
 * October **** 29, 2013 **
 * Summary **

__Photosynthesis Overview__
 * Supports he energy transformations of the entire biosphere
 * Process of converting light energy to chemical energy and storing it in the bonds of sugar
 * Occurs in plants and some algae (Kingdom Protista)
 * Plants need only light energy, CO2, and H2O to make sugar.
 * Takes place in the [[file://localhost/javascript/ShowIt('Chloroplast')|chloroplasts]]
 * Using [[file://localhost/javascript/ShowIt('Chlorophyll')|chlorophyll]], the green pigment involved in photosynthesis


 * __ Part 1: Early Experiments __**
 * Van Helmont (1648) planted a tree in 200Lb of soil. Covered soil with q perforated plate to prevent soil from being added or removed. Watered the tree for five years using distilled water. After five years, he removed the tree.The willow had grown from 2.2 kilograms (5 pounds) to 77 kilograms (169 pounds), while the dry weightof the soil had lost only 57 [[image:http://upload.wikimedia.org/wikipedia/commons/thumb/1/19/Jan_Baptist_van_Helmont_portrait.jpg/130px-Jan_Baptist_van_Helmont_portrait.jpg width="200" height="198" align="right"]]grams (2 ounces). Therefore,Van Helmont demonstrated that plants do not simply take up soil as they grow, and concluded that water was source of this increased weight
 * Priestly (1722) Burning candle in sealed jar. Plants “refresh the air”.
 * Ingert-Housz (1778) Plants “refresh” the air only if the plant exposed to light.
 * Jean Senebier- Plants take in CO2, only the green parts liberate 02.
 * Willstatter and Stoll: chlorophyll a and chlorophyll b absorb red and violet light
 * T.W. Engelmann (1881) Algae and Spectrum
 * Van Neil (1930) Purple sulphur bacteria, is H2o analogous to H2O7
 * Emerson (1957) Two beams of light
 * __ Video Notes (Part 1 of Video on Photosynthesis: early experiments) __**

-Plant in jar died -Candle in a jar went out -Candle in a jar with plant remained and plant lived - Put mouse in jar and died -Mouse with plant in jar, lived -Sunlight required -Only green plant of plant involved inplants
 * Joseph Priestly
 * Jan Ingen-Housz
 * Senebier - CO2 is needed


 * __ Overview of Class __**
 * Photosynthesis
 * Early Experiments
 * Watched a video and took notes


 * __ HOMEWORK __**
 * Read 212-219
 * Do # 2-5 + 5a


 * __ October 30, 2013 __**
 * __ Summary __**** Julie Nguyen **


 * __Overview of Class__**
 * Had the mini presentations in which everyone was assigned a number and put into groups
 * For the remaining 15 minutes of class, watch the rest of the video on Photosynthesis



**__Homework__**
 * Read section 5.2 for tomorrow’s lesson

=__November 1, 2013-Photosynthesis__=

__**Photosynthesis Formula**__
6CO2+12 H2O->C6H12O6+6O2+6H20

**__Breakdown of process__**

 * Stage 1:** Capturing Light energy


 * Stage 2:** Synthesizing ATP and NADPH


 * Stage 3:** Calvin Cycle (carbon fixation)


 * Stage 1, 2 are light dependent reactions (they require light to function)
 * Stage 3 does not require light directly, and is thus considered light independent

**__Properties of light__**

 * Visible light is a small part of the electromagnetic spectrum
 * White light can be separated into different colors (wavelengths of light) by passing it through a prism
 * Energy is inversely proportional to the wavelength: Longer wavelengths have shorter energy than do shorter ones
 * The longer the wavelength of visible light, the more red the color
 * Likewise the shorter wavelengths are towards the violet side
 * wavelengths longer than red are referred to as inferred, while those shorter than violet are ultraviolet

**__Light and Pigments__**

 * Light has energy that can be transferred or captured by an electron in a chemical bond
 * The electron is then "excited" to a higher energy state
 * This excitation can be passed from on electron to another until an electron actually leaves the bond
 * The source molecule is now said to be "oxidized"
 * Photosynthetic pigment molecules have many alternating single-double bonds between their carbon atoms
 * These are ideal for capturing light energy and in turn losing electrons that are transferred to other molecules

__**Pigment** Molecules__

 * Light energy is "captured" by pigment molecules
 * The energy absorbed by the pigment causes an electron to be excited to a higher energy level
 * This occurs in double carbon bonds or "Pi" bonds.
 * Usually an excited electron falls back down to its original energy level, it releases the exact amount and wavelength of light originally absorbed
 * In photosynthesis, the electron does not just fall back down to its ground state and release the energy, instead the energy is used to power the Redox reactions of photosynthesis

**__Carotenoids__**

 * B-Carotene is a carotenoid pigment
 * This pigment reelects orange light, providing the orange color associated with carrots and leaves in the fall
 * Carotenoids absorb blue light
 * They have a system of alternating double and single bonds in their structure
 * When light strikes the pigment, excited electrons are passed along its length, and will be collected by an "electron acceptor"

**__Copy__**

 * 1) Diagrams page. 221, and page 225 in textbook

__**Overview**__

 * Photosynthesis notes
 * Given class time to copy diagrams from page 221, and 225 into textbook
 * Rest of class given to do homework

**__Homework__**

 * Page 228 #3-6

=Dark Reactions: The Calvin Cycle=

Anne Clayton
- These reactions occur in the stroma and are often referred to as the Calvin Cycle - They do not directly require light to occur - 9 ATP, 6 NADPH, 2 CO2 and 5 H2O are used to produce 9 ADP, 6 Pi, 6 NADP+ and 1 PGAL - 2 PGALs then combine to create 1 glucose molecule

Phase 1: Carbon Fixation
- Carbon dioxide is added to ribulose bisphosphate (RuBP) (5C) via the enzyme **Rubisco** - Rubisco works slowly - therefore the plant has a lot of it - the 6C intermediate is unstable and splits into 2 3C molecules called **3-phosphoglycerate (PGA)** - The Calvin Cycle is sometimes referred to as C3 synthesis since the final products of the first phase have 3 carbons

Phase 2: Reduction Reactions (The Reverse of Glycolysis)
- PGA is phosphorylated via ATP to form **1,3-biphosphoglycerate** - 1,3-biphosphoglycerate is reduced via NADPH to form **glyceraldehyde 3-phosphate (G3P) (also known as PGAL)**
 * -** One PGAL leaves the Calvin Cycle as the final product

Phase 3: Reformation of RuBP
- the remaining PGAL are rearranged to form RuBP - Rubisco helps with this formation - ATP is used to rearrange PGAL - With PGAL reformed, the cycle can continue to fix CO2. Here is a diagram ([|source]) that is consistent with what we have learned in class. There are additional notes on photosynthesis consistent with what we have learned on the source website. Remember, G3P and PGAL are interchangeable terms. [|This video] is a bit simpler than what we have learned in class, but provides a good visual for the cycle.

Page 228, #8-10 Page 230, #1-4 Read Section 5.4 before tomorrow's lesson.
 * Homework: **

=Factors Affecting the Rate of Photosynthesis=

Anne Clayton
__Lesson Summary__ - Received a 3-page handout with lessons 3.5 and 3.6 on it from an alternate textbook - Received a worksheet to summarize important parts of the above handout (if not finished it is homework) - Were shown our midterm marks - Learned that our test is next week.

Summary of Notes from Handout
__Light Intensity and the Rate of Photosynthesis__ - Net CO2 uptake is negative in the dark because photosynthesis is not occuring - The **light-compensation point** is the point where the rate of photosynthetic CO2 uptake exactly equals the rate of respiratory CO2 evolution - In the **light limited** part of a light-response curve, rate of photosynthesis increases proportionally to irradiance - When the **light saturation point** is reached, the enzymes that catalyze the reactions of the Calvin cycle are fully occupied - the rate of photosynthesis will no longer increase even if irradiance increases. This is called the **CO2 limited zone**. __Temperature and the Rate of Photosynthesis__ - Since reactions in the Calvin cycle are catalyzed by enzymes, they will be affected by temperature - Between 10 and 30 degrees Celsius rate of photosynthesis will increase as temperature increases - At temperatures of 40 and above the enzymes become denatured and the rate of photosynthesis will decrease __Oxygen Concentration and the Rate of Photosynthesis__ - Oxygen competes for the active site of rubisco; therefore high concentrations of oxygen will decrease the rate of photosynthesis __Photosynthetic Efficiency__ - **Photosynthetic efficiency** of a plant is defined as the net amount of carbon dioxide uptake per unit of light energy absorbed - The rate of photorespiration increases faster than the rate of photosynthesis - in C3 plants the net uptake of CO2 decreases and temperature decreases- in C4 plants it stays the same - C4 plants lose virtually no CO2 to photorespiration - C3 plants are more effective at lower tempertaures while C4 plants are more effective at higher temperatures __Comparing Photosynthesis and Cellular Respiration__ - Photosynthesis uses the products of cellular respiration and vise versa - The Calvin cycle includes reactions that are similar to those in cellular respiration but in reverse - Proteins, quinones and cytochromes are similar or the same in both Electron Transport Chains - The pumping of H+ ions helps with the synthesis of ATP via ATP synthase

[|This video] is from Khan Academy and goes over the Calvin cycle, photosynthesis and photorespiration. This is a graphic of a light response curve. [|Source]