3.6 + most of 7.6

Enzymes

Enzymes are proteins that act as biological catalysts. They speed up the reaction rate by lowering the activation energy. Enzymes are substrate specific. This means that one enzyme only can work with specific substrate/substrates. Enzymes can work with: condensation, hydrolysis, transferring (move an atom or group of atoms from one molecule to another) etc. More than 5000 human enzymes are known

Condensation: remember two amnio acids forming a dipeptide (water removed) Hydrolysis: remember a disaccharide becoming two monosaccharides (water added) Transferring: moving functional groups from one molecule to another (A-X + C A + X-C)

Enzymes activity is best described by the Induced - fit model Enzymes have an active site where the substrates match. When a substrate has arrived the active site changes configuration “to grab on to the substrate even better”

substrate

Products

Active site Enzyme Note that the active site changes shape when the substrate has arrived, INDUCED - FIT

Almost all reactions in our body (or in the cell) are enzyme controlled. Some enzymes speeds up reaction up to one million times compared to the reaction rate without enzymes. Many enzymes are used in medical-, food- and biochemical industries Examples see later slides.

Factors that affect enzyme activity: Temperature, pH and substrate concentration 1. Temperature

Higher temperature results in higher motion rate of substrates and enzymes. Faster movement gives higher probability of “meetings”. If the temperature gets to high the protein structure of the enzymes changes irreversibly. The temperature optimum varies though, see human and thermophile bacteria below

2. pH

Most enzymes also have a pH optimum where they work the best. Most human enzymes as salivary amylase, work the best at pH 7 Pepsin in the human stomach has its optimum activity at pH 2. Arginase, important enzyme in urea production, has its optimum at pH 9,5

3. substrate concentration

Assume a constant number of enzymes. Then the reaction rate will increase with the substrate concentration until all enzymes work as fast as they can, the curve levels out. The point where the reaction rate levels off is called point of saturation

Other factors that interfere with enzyme activity 1. Competitive inhibitors

A competitive inhibitor is similar to the substrate, mimics it, and competes for the active site. The inhibitor blocks the active site. Example from medicine: Ethanol is normally in a first step by one enzyme broken down to acetaldehyde which is poisonous then in step two rapidly by another enzyme broken down to acetic acid (not poisonous). People with heavy alcoholism are treated with antabuse which inhibits step two. The result of acetaldehyde is severe head ache and vomiting

Inhibitor red

2. Non-competitive or allosteric inhibition

A non-competitive inhibitor binds to the enzyme somewhere else than the active site. The effect is that it changes the configuration of the active site so that the substrate does not fit. Example from medicine: Many antibiotics are non-competitive inhibitors on the bacterial enzymes needed for making the cell wall or disturbs the enzymes bacteria use for their protein synthesis

Allosteric inhibitor red

3. Negative feedback or end product inhibition Many metabolic reactions are made in several steps. ATP is only produced on demand. In the brake down of glucose to ATP, water and carbon dioxide more than 30 different enzymes are needed. To not produce ATP when not needed, ATP itself blocks one of the the first steps in the reaction by acting as an allosteric inhibitor. Negative feedback inhibition = good economy

Industrial and daily use of enzymes Enzymes are widely used by man in various kinds of ways. Some examples: Lactic acid bacteria are used by farmers to silage grass. All the white plastic rolls you see in the farm fields contains grass sprayed with lactic acid bacteria. All laundry detergents contain enzymes that brake down biological stains especially caused by proteins Pectinase is added to all fruit juices (but citrus juices,) to make them clear. Without pectinase all solid material like cell walls would “glue together” and sink to the bottom In medicine there are thousands of examples. Various used in diagnostics, in pharmaceutics and gene technology etc. The only one you have to be able to give as example is: Lactose: In most cultures where people end drinking milk after childhood the ability of breaking down lactose is lost. When drinking milk s adult they get stomach problems. To minimize the problem in these “cafe latte-times” the lost enzyme lactase is added in the milk. This does not affect the nutritious value of the milk. In Sweden most people drink milk as adults and lactose do not cause any problems but some in Sweden are lactose intolerant and have to by lactose free milk.

3.7 + parts of 8.1

Cell respiration

Cell respiration is a metabolic process where ATP is produced. It refers to the the break-down of carbohydrates (mainly glucose), into ATP, water and carbon dioxide but lipids and proteins may also be used as energy sources. ATP is used as the energy source in all cells but there are some others used to, ex GTP Remember that the glucose originates from photosynthesis. The energy can be said to have been transferred from light to the covalent bonds in glucose. Light energy

+ water + carbon dioxide

C₆H₁₂O₆ + oxygen

Imagine the glucose molecule as containing lots of bonds linking the atoms together and that these bonds are stored light energy. The purpose of cell respiration is to free this energy and move into ATP. Cell respiration can be divided into three steps: 1. Glycolysis 2. Krebs cycle 3. Electron transport chain + chemiosmosis (oxidative phosporylation) The three reactions together results in that the bond energy in glucose (“chemically stored sun energy”) is used to make ATP, the main energy source in all cells. ADP + Pi ATP

1a. Glycolysis (In the cytoplasm) The glucose (6C) taken up by the cell is first in a series of steps called glycolysis broken down to two Pyruvate molecules (3C). Glycolysis results in a net energy yield of 2 ATP Glycolysis is located in the cytoplasm First 2 ATP are “invested” to the glucose in order to destabilize it . It becomes fructose 1,6 -biphosphate. The unstable fructose 1,6 -biphosphate then falls apart into two 3-carbon molecules, glyceraldehyde 3 -phosphate In a series of reactions the glyceraldehyde 3 phosphates then becomes pyruvates. During these reactions 2 ATP from each is produced and excessive electrons and hydrogens ions removed by a carrier called NAD+. The carrier NAD+ removes and carries away two electrons and two hydrogen ions (protons) from the carbohydrate (sugar) NAD+ + 2 e- + 2 H+

NAD-H + H+

1b. Glycolysis -anaerobic If the conditions are anaerobic (without oxygen) pyruvate is fermented. 1. Alcohol fermentation. Yeast (a fungi) and some bacteria ferments pyruvate to ethanol. 2. Lactic acid fermentation. Some bacteria and fungi ferments pyruvate to lactic acid. This type of fermentation is also done by our muscles cells when oxygen is unavailable.

Alcohol fermentation is used in all kinds of alcohol but also in making bread. It is the CO2 that makes the bread dough.

Lactic acid fermentation is used as a conservation method, for example the conservation of grass in white “tractor eggs” but also in many sour food products as yogurt, pickled vegetables etc.

2a. Krebs cycle ( The route from cytoplasm to Krebs cycle) Pyruvate

AcetylCoA

Note the double membrane. Krebs cycle takes place in the matrix. While the last step of cell respiration, the electron transport + chemiosmosis, takes place across the inner membrane

The pyruvate from glycolysis is moved into the mitochondrion in a linking reaction. On the way to the matrix (interior) of the mitochondrion, pyruvate (3C) looses one CO₂ and two e- + 2 H+ to NAD+ and becomes an acetyl group (2C). The acetyl group is then combined with coenzyme A acetyl-CoA. The CoA then brings the acetyl group to Krebs cycle.

Continues

2b. Krebs cycle This picture shows both the linking reaction and Krebs cycle. Krebs cycle begins with that the 2C acetyl is added to 4C oxalacetate. Together they form 6C citric acid. Citric acid is the in a series of reactions where carbons and oxygens are removed as CO₂ and electrons and protons are carried away by NAD+ (NAD+ + 2e- + 2H+ NAD-H + H+) (In total 3 NAD+ per lap carries away H+ and e-) In one step of Krebs cycle another carrier FAD removes electrons and protons. In one step one ATP is produced directly. The result of this stripping is a return to the 4C oxalacetate and a new acetyl may be added. Since a glucose gives 2 pyruvates, Krebs cycle can turn 2 full laps per glucose molecule 2C + 4C

6C

Remowed or gained:

- CO2 -2e- - 2H+

5C -CO2 -2e- -2H+

4C

4C + 1ATP

4C -2e- - 2H+

4C -2e- -2H+

3a Electron transport chain and chemiosmosis The energy of electrons and protons that have been removed during glycolysis and Krebs cycle by NAD+ as NAD-H + H+ ( and FAD) is in this last step used to synthesize ATP. In short: The energy of the electrons is in the electron transport chain used to pump H+ across the mitochondrion inner membrane to the intermembrane space. This results in a H+ gradient. and a difference in concentration means a strive for equalizing. The diffusion flow to equalize H+ concentrations can only take place through an enzyme named ATP-synthase. The energy of this backflow of H+ is used by ATP-synthase that in chemiosmosis add Pi to ADP ATP. (imagine ATP-synthase as a windmill) “After work” the H+ and e-, now emptied on their energy, are combined with oxygen and forms H2O

Summary Each NAD-H + H+ gives 3 ATP Each FADH2 gives 2 ATP Energy yield from one glucose: Glycolysis Link reaction Krebs cycle

2 ATP directly 2 ATP directly

+ 2 NAD-H + H+ + 2 NAD-H + H+ + 6 NAD-H +H+

+ 2 FADH2

In total one glucose gives 4 + 10 x 3 + 2 x 2 = 38 ATP

Animations to check when you have time: http://www.johnkyrk.com/index.html

3.8 + most of 8.2

Photosynthesis

In photosynthesis light energy is converted to chemical energy. In this topic the reaction will be studied more in detail. The simple reaction you have learned? earlier is more complex in reality and is like cellular respiration a reaction in several steps. Lets first have a look at light itself and the organelle where photosynthesis takes place. Visible light is just a narrow section of wavelengths of what is called electromagnetic radiation. The shorter wavelengths the higher energy content. Visible light range from 380 nm to around 750 nm. This means that purple and blue light contain more energy than red. Note what the light just above and just below the visible is called. What do you know about UVand IR- light?

Light absorption of plants Why plants are green: Plants are good absorbers of purple-blue and orange-red light but poor in absorbing green. The green wave lengths are reflected (and this is what our eyes register) With a more efficient absorption the leaves would have been black but thanks to their evolutionary history nature is more colorful.

The Chloroplast The chloroplasts (dark green spots) are located in the leaves. On the bottom side you can see openings, stomata which enables gases to pass in and out (CO2 , O2 , H2O(g))

In plants the Chloroplast is the site of photosynthesis. This organelle as the mitochondrion has a prokaryotic origin and is surrounded by a double membrane and its own DNA. In higher plants the chloroplast also contains an internal membrane system of thylakoids in stacks called granum. The space in between the granum is called stroma. Inside thylakoids, pigment molecules as chlorophyll absorbs the light in the first step of photosynthesis

8.2.1

Chloroplast -electron micrograph

The Photosynthesis reactions Photosynthesis is in reality divided into two reactions: •The light dependent that splits water into oxygen, protons and electrons + produce ATP. •The independent of light, called the Calvin cycle, where carbon dioxide, protons and electrons are “put” together with the help of ATP to produce a 3-carbon sugar. These are then combined to form glucose. The following slides will show the reactions more in detail. Lets begin with a summary

The light dependent reaction version 1. Non cyclic a. An electron from Chlorophyll P 680 is excited. b. An enzyme then splits water to supply with a replacing electron c. The reaction continues the way that will be described orally (take notes) The figure to the right shows how antenna pigments which donates donates energy from photons to P 680 and P 700 The figures below are two illustrations describing the light dependent reaction.

Light dependent version nr 2: Non cyclic 1. The electrons from water molecules are excited. The energy they emit when falling down again is used to pump H+ across the thylakoid membrane, from stroma to thylakoid lumen . The arisen conc. difference is then equalized when passing back through ATP-synthase and ATP is produced by chemiosmosis (ADP + Pi ATP), destination Calvin cycle 2. The “lorry” NADP+ then carries away protons and electrons from the split water molecule. The destination for the “lorry” is the Calvin cycle. (NADP+ + 2H+ +2eNADP-H + H+)

Light dependent -Cyclic The non cyclic reaction produces NADP-H +H+ an ATP in equal amounts but the Calvin cycle demands more ATP. This is supplied by the cyclic reaction. Follow the yellow arrows. Instead of being carried away by NADP+ the electrons from photosystem 1 sometimes “go backwards” to produce more ATP (by chemiosmosis through ATP synthase)

light independent reaction In this reaction electrons and protons + the produced ATP, will be joined with CO2 to produce a 3-carbon sugar, G3P. These G3P molecules are then the base for the plants production of glucose, proteins and lipids (ex: 2 x G3P glucose). The Enzyme adding CO2 to the cycle is Rubisco (ribulose biphosphate carboxylase) Once, every three laps one G3P leaves the cycle. The other five remains and forms RuDP. Step 1 Carbon fixation: 5 C RuBP + 1 CO2 (unstable 6C molecule) 2 x 3 C molecules Step 2 Reduction: H+ and e- are delivered by the carrier (NADP-H +H+) + also ATP, all these from the light dependent reaction. One GTP out of six leaves the cycle Step 3 Regeneration of RuDP: The remaining 5 GTP forms 3 RuDP with the help of some more ATP

Factors affecting the rate of photosynthesis -limiting factors 1. Carbon dioxide (CO2): The rate of photosynthesis increases with higher levels of CO2 but levels off when other factors (water, light, temperature) becomes limited. Old ladies talking to flowers Global warming

CSP = CO2 saturation point

2. Light intensity: The rate of photosynthesis increases with more light but levels off when other factors (CO2 , temperature, water) becomes limited.

LSP = light saturation point

3. Temperature: The rate of photosynthesis increases with higher temperatures but drops (faster) when the optimum temperature is exceeded.

Action spectrum - Absorption spectrum The action spectrum shows the rate of photosynthesis at different wavelengths of light. The absorption of all different kinds of pigments contributes to the shape of the curve. (how effective different wavelengths are in driving photosynthesis)

The absorption spectrum shows the range of one or more pigments ability to absorb light separately.

Questions to consider What molecule in photosynthesis is the origin of O2? Suggest how the rate of photosynthesis can be measured

Some animations etc: http://www.learnerstv.com/animation/animation.php?ani=179&cat=biology http://www.johnkyrk.com/photosynthesis.html

A quiz http://www.phschool.com/science/biology_place/biocoach/photosynth/quiz.html

Youtube http://www.youtube.com/watch?v=eY1ReqiYwYs ( light dependent reaction) http://www.youtube.com/watch?v=mHU27qYJNU0

(the Calvin cycle)

http://www.youtube.com/watch?v=PIvn7b4LbMc&NR=1 (as a children song) http://www.youtube.com/watch?v=qHsdcK46kp8 ( funny ?) http://www.youtube.com/watch?v=hj_WKgnL6MI (A bit to advanced but good)

Enzymes

Condensation: remember two amnio acids forming a dipeptide (water removed) ... Almost all reactions in our body (or in the cell) are enzyme controlled.

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