cytosol

Drug Receptors - Pharmacology

Ligand-Gated Ion Channels 

  • Ionotropic receptors
  • Structurally similar to other ion channels 
  • Quickest response
  • Each receptor consists of 16-20 membrane spanning domains, 4-5 per subunit
  • Open when ligand binds to extracellular part of channel 
  • (5 M2 helicases are sharply kinked inward halfway through the mebrane forming a constriction)
  • Excitatory neurotransmitters eg acetylcholine and glutamate induce opening of cation channels 
  • Inhibitatory neurotransmitters eg GABA (gamma-aminobutyric acid) and glycine induce opening of anion channels 

Nuclear receptors

  • Target for many hormones
  • Cytoplasmic or nuclear proteins
  • Ligand binding domain and DNA binding domain
  • Modulate gene expression
  • Upregulate or downregulate protein production 

Three families:

  • Steroid receptors (androgen/oestrogen/glucorticoid receptors)
  • Thyroid/retinoid receptors (vitamin D/retinoic acid/thyroid/peroxisome proliferator-activated receptors
  • Orphan receptors

Kinase linked receptors

  • Mediate the actions of a wide variety of protein mediators eg growth factors, cytokines and hormones
  • Large extracellular ligand-binding domain connected via a single membrane spanning helix to an intracellular domain
  • intracellular domain possesses kinase activity 

Main types include:

  • Receptor tyrosine kinases (eg epidermal growth factor, nerve growth factor and insulin receptors)
  • Serine/threonine kinases (eg transforming growth factor)
  • Cytokine receptors (eg colony-stimulating factor)

G-Protein Coupled receptors 

  • Membrane located - inner side of plasma membrane
  • 400 gene sequences for GPCRs
  • eg muscarinic ACh receptors, adrenoreceptors, dopamine
  • Most have extracellular N-terminus, 7 transmembrane domains and an intracellular C-terminus
  • Universally called 7-transmembrane receptors (7TM receptors)
  • Called G-proteins because of their interaction with guanine nucleotides GTP and GDP
  • G-protein system consists of three subunits (alpha, beta and gamma)
  • Trimer in resting state
  • GTP molecule binds to alpha subunit

GPCRs are divided into three groups

  • Family A: largest, comprising mostly of monoamine, neuropeptide and chemokine receptors
  • Family B: includes receptors for some other peptides such as calcitonin and glucagon
  • Family C: smallest: metabotropic glutamate and GABA receptors 

[Read more for some GPCR specifics]

Keep reading

[AP Bio] TEST FOUR: Cellular Respiration

REGULAR HIGHLIGHTED VERSION CAN BE FOUND HERE

(*IMPORTANT: a lot of the format and diagrams got really messed up on here, I apologize)

cellular respiration = breakdown of fuel to generate ATP for work

3 Key Pathways: 1) glycolysis, 2) citric acid cycle, & 3) oxidative phosphorylation/electron transport chain (ETC)

characteristics: waste products = CO2 & H2O, catabolic pathway

Oxidation-Reduction Reactions

AKA “redox” reactions

-the transfer of electrons
-> can be complete or partial (in cases of covalent bond sharing)

oxidation = the loss of electrons

reduction = the gaining of electrons

“oxidizing” agent = substance that accepts electrons from another

“reducing” agent = substance that gives up/“donates” electrons to another

*the transfer of electrons, as they are pulled down the energy gradient from a molecule of low EN -> molecule of high EN, is exergonic as this transfer causes the electrons to release potential energy

-> can be harvested for work! (INDIRECTLY)

-> cell resp. is all about understanding how the flow of electrons & protons controls the whole process!

Brief Overview of Cell Respiration

Fuel Reactant
Glucose Oxygen
Oxidized Reduced
Reducing Agent Oxidizing Agent
Goodbye electrons! :-c Hello electrons! c-:

oxidized (loses e’s)

C H 0 + 6O  -> 6CO  + 6H 0 + energy (ATP + heat)

reduced (gains e’s)

*typically carbs are used but lipids (fats) can also be used due to the large amount of H’s in the hydrocarbon tails, & actually generate a lot of energy

fun tidbit:
*the metabolic waste, C0 , is breathed out by the body and then taken in by plants, which use it to produce glucose -> thus the circle spins on & on

How Glucose is Broken Down

*energy cannot be efficiently harvested for work all at once, so rather it is broken down in a series of steps, called “stepwise energy harvesting”

1) Electrons taken from glucose (also, 1 proton) are given to Nicotinamide Adenine Dinucelotide (NAD+), a coenzyme
-> NAD+ is an oxidizing agent, and so therefore is able to accept electrons

2) NAD+ is an “empty taxi cab”. The enzyme dehydrogenase oxidizes food (such as glucose) to get the 2 e’s & 2 p’s (H+’s) so they can be given to NAD+.

3) NAD+ is reduced by accepting electrons, and becomes NADH. NADH is a “full taxi cab”, containing 2 e’s & 1 p (H+). The other H+ is released into the cytosol.
-> Each NADH represents potential energy that can be indirectly used to power the synthesis of ATP

4) NADH passes the e’s onto the electron transport chain (ETC). The ETC then passes the e’s on in a series of controlled steps to the oxygen molecules that pull them down the chain (b/c of its high EN). This process yields energy that can be used to re-generate ATP.

Stages of Cellular Respiration

1) Glycolysis- breakdown of glucose (“glyco” = glucose, “lysis” = breakdown)

2) Citric Acid Cycle- completes the breakdown into 2 molecules of pyruvate of glucose (AKA Krebs Cycle)

3) Electron Transport Chain (ETC)- accounts for most of ATP synthesis

 ————————————————————————————————-

(*the following diagram got really messed up on here, I apologize)

electrons carried via
NADH                                                                          electrons carried
                                                                                  via NADH & FADH2

Glycolysis                                                
1 glucose -> 2 pyruvate ——————-> citric acid                                                 (SPLIT)                                                    cycle                    electron transport
                                                                                               and chemiosmosis
                                            
                                                       (mitochondrion)
(cytosol)

                                                                                                         ATPs                                                                              ATP
   ATP

substrate-level                                  substrate-level                                             phosphorylation                                phosphorylation                                                                                                                                                                                                                                                                              *oxidative
                                                                                                phosphorylation*

2 ATPs were invested,                                                       results in a LOT more
and 4 in total produced, so            results in 2 ATPs                       ATPs
NET = 2 ATPs                                    now: total 6
                                                             NET = 4                   produces NET = 32-                                                                                                        34 ATPs                                                                                                                

Glycolysis


-occurs in the cytosol

                        [high] G     outside/ECM

facilitated
diffusion             *Integral protein & cell membrane
(no energy)    
                         [low]  G      inside/cytosol

G-p <— phosphate is added (neg. charge “locks” glucose inside cell!)



-requires the energy investment of 2 ATPs



Energy Investment Phase

1- 2 ATPs invested

2- Enzymes take phosphates off ADPs

3- Series of steps where phosphates are taken off ATPs & then phosphorylated to molecules (TWICE) that are slightly changed each step

4- Eventually split into 2 3-carbon sugars (“G3Ps”)

Energy Yielding Phase


1- As the 2 G3Ps are oxidized, NAD+ is reduced to NADH -> this contributes to the ETC by carrying electrons (& protons)!

2- After, there is an “intermediate molecule” (ex: 1,3-biphosphoglycerate -> don’t need to know exact molecule) that has a phosphate. This phosphate is taken off and given to 2 ADPs to become 2 ATPs. This happens twice within the series of steps in this phase. Also, at one point, 2 H2Os are taken out.

3- Eventually transformed into 2 pyruvates

4- A total of 4 ATPs are made in this “payoff” phase. However, since 2 were invested originally, there is only a net of  2 ATPs.

                                      C3H3O3
C6H1206                    -pyruvates-
                                      C3H3O3

(*this diagram got really messed up on here too)

Energy Investment Phase



Glucose



2 ADP + 2 p <—————— 2 ATP used



Energy Payoff


Phase      4 ADP +


                    4 p          ———————->   4 ATP    formed



2 NAD+ + 4 e


+ 4 H+                   —————————>   2 NADH + 2 H+



                 


                                                    ————–> 2 Pyruvate + 2 H2O




Net                     Glucose ————> 2 Pyruvate + 2 H2O



4 ATP formed - 2 ATP used ——-> 2 ATP



2 NAD+ + 4 e + H + ———-> 2 NADH + 2 H+




Substrate-Level Phosphorylation

-not as efficient in producing ATP as oxidative phosphorylation

-used in both glycolysis & krebs/citric acid cycle

Citric Acid Cycle

-AKA “Krebs” Cycle

-COMPLETES energy-yielding oxidation of the organic molecules (ex: glucose)

-BEFORE the cycle can begin, the 2 Pyruvates must be converted to Acetyl CoA -> this links the cycle to glycolysis!

1) The 2 Pyruvates are oxidized and enter the Mitochondrion via a Transport Protein

2) CO2 is released (lungs -> exhale)

3) NAD+ is reduced to NADH & the e’s & p’s (H+’s) are stripped

4) A Coenzyme helps with the conversion to Acetyl CoA

-CAC uses BOTH molecules of pyruvate
*cycle goes around TWICE!

*CITRIC ACID CYCLE SUMMARY*

2 CO2 X 2 = 4 (released)

3 NADH X 2 = 6 (reduced)

1 FADH X 2 = 2 (reduced)

1 ATP X 2 = 2 (produced)

*appreciate the many redox Rx’s going on to keep the cycle going, changing Acetyl CoA all the way to Oxaloacetate!

Ex: R = NAD+ -> NADH
     O = any previous molecule!

ETC - Chemiosmosis - Oxidative Phosphorylation

-located at the inner mitochondrial membrane (like the plasma membrane, but different proteins!)                                                                              

*proteins are special ones made from the mtDNA (mitochondrial DNA)

*2 membranes! (DOUBLE)

PROTON MOTIVE FORCE

-facilitated diffusion

-a lot of energy & collisions b/c of flow of e’s

-*H’s come from glucose/pyruvate!

1) H+’s pumped out
2) O’s take H+’s to create H2O
3) Take protons in -> [low] guaranteed

-energy to power movement of H+ out!
(POTENTIAL ENERGY -> from redox Rx’s!)

-if O2 NOT present, H+’s cannot be moved/slid out -> b/c O2 is the final e acceptor w/ a high EN & the e’s release potential energy when moving down the gradient to O which powers the proton motive force

-keeps getting more EN as e’s pulled down/along chain

-H+’s move into ATP Synthase (important and moves protons BACK into matrix) protein -> active transport -> change of shape -> ATPs

fun tidbit:
-cyanide affects the enzyme that works w/ cytochrome oxidase, as it is an irreversible inhibitor that is tetravalent and desperate for a fourth bond, and therefore highly reactive (can shut down body systems and kill you within a matter of hours, and this is all due to bonding!)

ELECTRON TRANSPORT CHAIN

-oxidative phosphorylation & chemiosmosis couples the ETC to ATP synthesis

-located in cristae of mitochondrion

Pathway:

1) The components are proteins that exist in multiprotein complexes and are unique to the mitochondrion. These protein complexes alternate between reduced and oxidized states as they accept and donate electrons

2) Electrons drop in free energy as they go down the chain & are finally passed to O2 -> form H2O

3) NO ATP generated!!!!!

*THE FUNCTION OF THE ETC is to break the large free-energy drops from food to O2 into smaller steps that release energy in manageable amounts.

*the more redox Rx’s, the more energy is available.



CHEMIOSMOSIS

*the energy-coupling mechanism

1) Redox Rx’s in the ETC -> provide energy for the transport proteins to pump H+ from the mitochondrial matrix to the intermembrane space.

NEXT STEP IMMEDIATELY FOLLOWS

2) Proton Motive Force  develops as [H+] INC., w/i intermembrane space. Then, moves back across membrane & passes through channels in ATP Synthase.

3) ATP Synthase transports H+ BACK into matrix.

4) ATP Synthase uses exergonic flow of H+ to drive the phosphorylation of ADP -> ATP    (endergonic).

*chemiosmosis = use of energy in H+ chemical gradient to drive ADP phosphorylation

Fermentation

*enables some cells to produce ATP w/o the use of oxygen!

How can food be oxidized w/o oxygen?

-NAD+ is actually the oxidizing agent of glucose. A net of 2 ATPs are produced by substrate-level phosphorylation. Then, if there IS oxygen, more (a lot of) ATP can be produced when NADH passes the removed e’s from glucose to the ETC & oxidative phosphorylation occurs.

*glycolysis STILL produces 2 ATP whether O is present of not, though!

(either aerobic or anaerobic)


-fermentation is the anaerobic catabolism of nutrients

-fermentation = the extension of glycolysis that can generate ATP solely by substrate-level phosphorylation
-> *as long as there is a sufficient supply of NAD+ to accept e’s during the oxidation step of glycolysis

-NAD+ needs to be recycled from NADH

Aerobic Anaerobic
Recycled by the transfer Recycled by the transfer of electrons from NADH to Pyruvate (end product of glycolysis!)
of electrons to the ETC

TYPES OF FERMENTATION

fermentation = glycolysis + Rx’s that regenerate NAD+ (transfer of electrons from NADH -> Pyruvate)

Alcohol Fermentation = Pyruvate converted to Ethanol

1) RELEASES CO2 from Pyruvate
-> converted to 2-carbon compound “acetaldehyde”

2) Acetaldehyde is reduced by NADH to Ethanol

-regenerate supply of NAD+ needed

*many bacteria carry out alcohol fermentation under anaerobic conditions, also fungi (ex: yeast)

fun tidbit:

yeast -> used for 1,000’s of years by humans for brewing, wine-making, baking (bread, gases released create bubbles that allow it to rise), etc.

Lactic Acid Fermentation = Pyruvate reduced DIRECTLY by NADH - > forms Lactate (ionized form of lactic acid) as end product -> NO release of CO2

*certain fungi & bacteria used to make cheese & yogurt

*other microbial fermentation used to make acetone & methanol (methyl alcohol)

1) When O is scarce, human muscle cells can still make ATP by using lactic acid fermentation.

2) Strenuous exercise -> sugar catabolism for ATP production outpaces muscle’s supply of O from blood

3) Cells switch from aerobic respiration to fermentation -> creates lactate -> buildup of lactate can cause muscle fatigue and pain!

4) Lactate is gradually carried away by the blood to the liver -> converted back to pyruvate by liver cells

*facultative anaerobes = make enough ATP to survive using either fermentation or respiration (ex: our muscle cells!)
-> consume sugar at faster rate when fermenting to make the same amount

*Pyruvate is a “FORK IN THE ROAD”

The Gland that has got a Secrete Secret

This article will focus on one of the more important glads of the human body; the thyroid. This article will focus on the anatomy and physiology, biochemistry and clinical aspects of the thyroid, hopefully giving our readers a better understanding of this organ.

The Thyroid

Situated on the ventral side of the neck, the thyroid gland is composed of two lobes: right and left that are situated anterolaterally to the trachea. It normally weighs 15 to 20 grams in adults (1), but despite its small size, it is responsible for producing two important bodily hormones.

Follicular cells in the thyroid gland mainly produce the prohormone thyroxine (T4), and a smaller amount of the active hormone, triiodothyronine (T3). Most T4 is converted to T3 in other tissues by thyroxine-specific deiodinase enzymes, activating it when it reaches its target site.


Figure 1. Showing the molecular structure of T3 (left) and T4 (right).

T3 and T4 from thyroid gland to target tissue

Synthesised T3 and T4 diffuse out of follicular cells and enter a blood vessel. Almost all secreted T3 and T4 circulating the bloodstream are bound to proteins; the major binding protein being thyroxine-binding globulin (TBG). A TBG-blood test(2) may be used to diagnose problems with the thyroid such as hypothyroidism, a clinical condition where insufficient production of thyroid hormone occurs.

Free T3 and T4 enter cells by active transport, an energy-dependent transport method. As discussed above, organ tissues with high blood flow (such as liver, skeletal muscles and kidney) possess enzyme deiodinase and catalyses most of the conversion of T3 and T4. Other tissues with low local T3 generation may depend on these tissues to obtain sufficient levels of T3.

At the physiological level

The most important role of thyroid hormones are to control basal metabolic rate (BMR). BMR refers to the basal rate of oxygen consumption and heat production. Normally, mitochondria generate energy by oxidative phosphorylation. During this process, the energy from protons (H+) moving down a proton gradient is used to generate ATP (the energy currency of the cell). This is a similar process to the momentum of water being harnessed by water wheels in old mills.However, a special type of protein, called the uncoupling protein (UCP), is found exclusively in brown adipose tissue (BAT). Mitochondria in these cells can provide an alternative pathway for protons to travel back inside the mitochondria, down their proton gradient. This alternative pathway results in no ATP production with the energy being dissipated as heat.(4)

In the cardiovascular system, thyroid hormones increase the gene expression for β1-adrenergic receptors in cardiac muscle cells and increase the responsiveness of these cells towards β adrenergic activity. The overall effect increases the force of myocardium contraction (positive inotropy) and rate of heart muscle contraction (positive chronotropy), increasing cardiac output and blood vessel dilation in the skin, muscle and heart. The hormone increases tissue sensitivity to beta adrenergic hormones, increasing the heart rate and force of contraction.

Thyroxine hormone also affects the other systems such as the respiratory system, skeletal system, reproduction and nervous system. However, the most important functions of thyroid hormone are the regulation of BMR, maturation and development of nervous system and increase responsiveness of tissue to adrenergic activity.

Mechanism of thyroid hormone

The steps below correspond to the numbers in Figure 2.

1) T3 diffuses into the cytosol and subsequently into the nucleus (8).
2)Thyroid hormone receptor (TR) is located in the nucleus prebound to DNA. TR usually dimerises with a retinoid X receptor (RXR) and this dimer recognises and binds at a specific site on DNA known as the Thyroid Response Element (TRE). TH binds to TR leading to the dissociation of co-repressors (Figure 2).
3)At the same time, recruitment of co-activators (Figure 2) occurs.
4)The TRE mentioned in step 2 is a segment of DNA known as the refulatory sequence, a segment of DNA that increases or decreases the expression of specific genes. In this case, when the T3 binds to the TR-RXR dimer, and the TRE may activate or repress the target genes.


Figure 2. Diagram shows a schematic diagram of the general biochemical action of thyroid hormones on the target DNA

Transcription is followed by RNA translation to form hundreds of new intracellular proteins. T3 changes the rate of expression for hundreds of genes and increases or decreases the production of structural and functional proteins which may be the key molecules in different metabolic processes. T4 also performs such function, but is less potent than its counterpart T3.

With such function, one can imagine just how important the level of thyroid hormone is in the regulation of different physiological processes and how this may impact upon health (9)

Regulation Of Thyroid Hormone Production And Secretion

A hormone with such varied functionality has to be regulated to ensure its adequately supplied to targeted organs. Such intricate control has to be performed by the “endocrine master”; the hypothalamus. The hypothalamus releases thyrotropin hormone (TRH), which stimulates the release of thyroid stimulating hormone (TSH) in the closely linked anterior lobe of pituitary gland. TSH is then transported in the blood where it binds to the TSH receptor on the thyroid gland. TSH speeds up the production and release of thyroid hormones, promoting the growth of the gland with the help of some other growth factors.

When thyroid hormone levels are in excess, circulating molecules act on the hypothalamus and pituitary gland to decrease TRH and TSH secretion respectively. The mechanism involved is a negative-feedback control mechanism. When TRH and TSH secretion decrease, so does the production and the secretion of thyroid hormones. The hormones drop until the optimal physiological level whereby the inhibitions on TRH and TSH secretion are lifted (Figure 3).


Figure 3. Image shows the regulation of thyroid hormone by the hypothalamus and pituitary gland in a negative-feedback loop.

Diseases Related To Thyroid Gland

T3 (Figure 1) contains three iodine atoms. The synthesis of thyroid hormones requires an adequate supply of dietary iodine. The recommended dietary allowance (RDA) for iodine in an adult male is 150µg and slightly higher in pregnant women, 220µg (5). Deficiency of this precursor leads to insufficient production of T3 and T4. The consequences of this are low levels of circulating thyroid hormones which cause an increase of TSH secretion from the pituitary gland interfering with the negative feedback. Increased stimulation of TSH increases the activity of the thyroid gland in an attempt to normalize thyroid hormone level (6). Consequently the gland grows larger than the normal size, producing a condition known as a goitre(Figure 4).

A goitre refers to the enlargement of the thyroid gland (Figure 4), this could be due to hypothyroidism or hyperthyroidism. Goitres are more common in population living in mountainous regions, where access to iodine sources such as seafood are restricted. Such dietary deficiency can be prevented by adding small amounts of iodine to table salt.


Figure 4. Image showing a patient presenting a goitre.

Conclusion

Hopefully after reading this article, you’re a little more in the know about the little gland secretlysecreting hormones to help you stay healthy. Next time you’re calorie counting or checking the nutritional content of your food, make sure that you’re getting enough iodine in your diet as it can ensure that you don’t end up with a large number of problems down the line.

Rough Endoplasmic Reticulum
  • Rough ER (RER) is involved in some protein production, protein folding, quality control and despatch
  • Called ‘rough’ because studded with ribosomes
  • Smooth ER (SER) is associated with the production and metabolism of fats and steroid hormones
  • Smooth because no ribosomes and is associated with smooth, slippery fats.

STRUCTURE

  • Continuous membrane of flattened sacs (cisternae) and network tubules, touching nuclear membrane. 
  • Membrane bound ribosomes firmly attached to the outer cytosolic side of the RER
  • However these are constantly being bound and released - will only bind when specific protein-nucleic acid complex forms in cytosol 

FUNCTION

  • Proteins are made by the ribosomes on the surface of the RER - translation
  • Then (some) are threaded inside RER to be modified and transported
  • RER working with membrane bound ribosomes takes polypeptides and amino acids from the cytosol and continues protein assembly including, at an early stage, recognising a ‘destination label’ attached to each of them. 
  • Proteins are produced for the plasma membrane, Golgi apparatus, secretory vesicles, lysosomes, endosomes and the ER. 
  • Some  proteins into the lumen (inside) of the RER; others are processed in RER membrane itself
  • Lumen: some proteins have sugar groups added to form glycoproteins; some have metal groups added
  • EG: in RER four polypeptide chains are brought together to form haemoglobin.

Protein folding unit
lumen of the rough ER: proteins folded to produce biochemical architecture which will provide ‘lock and key’ and other recognition and linking sites.

Protein quality control section

  • Lumen: incorrectly formed or incorrectly folded proteins rejected
  • Rejects stored in the lumen or sent for recycling for eventual breakdown to amino acids. 
  • A form of cystic fibrosis = missing single amino acid, phenylanaline, in a particular position in the protein construction. Quality control section spots the error and rejects, however individual would have been better off with poor product than none at all

From Rough ER to Golgi
In most cases proteins are transferred to the Golgi apparatus for ‘finishing’. They are conveyed in vesicles or possibly directly between the ER and Golgi surfaces. After ‘finishing’ they are delivered to specific locations.

[AP Bio] TEST FIVE: Photosynthesis

*Autotrophs will be focused on, particularly Photoautotrophs. They use sunlight/light energy, and fix CO2 to organic molecules to produce organic compounds.

Fun tidbit:
-80% of atmospheric O2 comes from UNDERWATER plants!!!

*Although leaves are the major location of photosynthesis, Chloroplasts will be focused on, as they are essential to the process of Photosynthesis & we are looking at the process on a cellular level
-> Chloroplasts’ Thylakoids transform light E to the chemical E of ATP & NADPH

Photosynthesis is, simply, the conversion of light energy into the chemical energy of food.

6 CO2 + 12 H2O + Light Energy -> C6H12O6 + 6 O2 + 6 H2O

Understanding Light Energy

-light energy is known as “electromagnetic” energy
-> travels in rhythmic waves (disturbances of electrical and magnetic fields)

Wavelength = distance b/t CRESTS of E.M. waves
-> range from < 1 nm - >1 km

Range of Radiation  = ELECTROMAGNETIC SPECTRUM

-small portion most important to life -> narrow band from 380 nm - 750 nm -> “VISIBLE LIGHT”

Photons = light behaving as though it consists of these “discrete particles” -> not tangible but have a fixed quantity of energy

-relationship b/t wavelength & amount of energy is INVERSE
Ex: photon of violet light has almost 2x as much energy as photon of red light

-atmosphere acts as “selective window”, letting visible light in, but not a lot of other radiation

-VISIBLE LIGHT drives photosynthesis!!!!!

-when light meets matter, it is either: 1) REFLECTED, 2) TRANSMITTED, or 3) ABSORBED

Pigments = substances that absorb visible light
-> diff. pigments absorb diff. wavelengths

-wavelengths that are absorbed, disappear!!!

-when a pigment is illuminated w/ white light, we see the color that is most reflected or transmitted by it!
Ex: leaf is green b/c chlorophyll absorbs violet-blue & red light, but TRANSMITS & REFLECTS green light
Ex: if absorbs all wavelengths -> appears black

Spectrophotometer = instrument that measures ability of pigment to absorb various wavelengths of light
-> machine directs beams of light at diff. wavelengths through solution of pigment & measures fraction of light transmitted @ each W.L.

Absorption Spectrum = graph plotting three diff. types of chloroplast pigments’ light absorption vs. wavelength
-> helps us determine effectiveness of diff. wavelengths for driving photosynthesis

*light can perform work in chloroplasts ONLY if it is absorbed!

Action Spectrum  = plots the rate of photosynthesis vs. wavelength and profiles the relative effectiveness of diff. W.L.’s of radiation in driving photosynthesis
-> prepared by illuminating chloroplasts w/ light of diff. colors & plotting W.L. against some measure of photosynthetic rate (such as CO2 consumption & O2 release)
-> resembles the action spectrum for chlorophyll a (but not EXACTLY -> this is partly due to the absorption of light by “accessory” pigments such as chlorophyll b & carotenoids)
-> first demonstrated in Englemann’s experiment

Englemann’s Experiment = In 1883, Theodor W. Englemann illuminated a filamentous alga w/ light that had been passed thru a prism, exposing diff. segments of the alga to diff. W.L.’s. He used aerobic bacteria, which concentrate near an O2 source, to determine which segments of the alga were releasing the most O2 & thus photosynthesizing the most. Bacteria congregates in greatest numbers around the parts of the alga illuminated w/ violet-blue or red light. *There is a close match of the bacterial distribution to the Action Spectrum graph.
-> CONCLUSION: violet-blue & red light are the most effective in driving photosynthesis! green light is the least effective color, as it is reflected/transmitted, not absorbed.

Pigments


*absorption spectra & action spectra do not exactly match for chlorophyll a
-> this is b/c “accessory” pigments w/ diff. absorption spectra are ALSO photosynthetically important in chloroplasts & broaden the spectrum of colors that can be used for photosynthesis (Ex: chlorophyll b & carotenoids)

*chlorophyll b & chlorophyll a are almost identical, but have a slight structural difference
-> as a result, they have different colors (chlorophyll a is blue-green, chlorophyll b is yellow-green)

-both molecules consist of:

Porphyrin Ring = light-absorbing “head” of molecule; w/ magnesium atom @ center
&
Hydrocarbon Tail = interacts w/ hydrophobic regions of proteins inside thylakoid membranes of chloroplasts

*the ONLY difference between chlorophyll a & chlorophyll b is the functional group bonded to the porphyrin ring

Carotenoids = hydrocarbons that are various shades of yellow & oranges (b/c they absorb violet-blue & green light) -> broaden spectrum of colors that can drive photosynthesis

Photoprotection = important function of some carotenoids
-> compounds absorb & dissipate excessive light energy that would otherwise damage chlorophyll or interact w/ O2, forming dangerous (to the cell), reactive oxidative molecules

Fun tidbit:
-carotenoids similar to photoprotective ones in chloroplasts have photoprotective role in human eye! Highlighted in health food products as “phytochemicals” -> have antioxidant powers! Plants synthesize all the antioxidants they need, where humans & other animals must obtain from their diets

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-when light is absorbed, W.L.’s disappear from spectrum, but energy CANNOT disappear!
-> when molecule absorbs photon of light, 1 of the molecule’s e’s is elevated to an orbital of higher potential energy/“excited state” (when e in normal orbital -> pigment molecule said to be in ground state)

-only photons absorbed are those whose energy is exactly equal to energy diff. b/t ground & excited states (energy diff. varies from one kind of molecule/atom to another)
-> particular compound absorbs only photons corresponding to specific W.L.’s, which is why each pigment has a unique absorption spectrum!

-once raised to excited state, electron cannot remain there long
-> high energy state, therefore unstable

-when isolated pigment molecules absorb light, e’s drop back down to ground state in billionth of a sec. -> RELEASE excess energy as heat!
Ex: why top of car is so hot on sunny day!

Fun tidbit:
-white cars are coolest b/c paint reflects all W.L. of visible light!

-in isolation some pigments emit light, also
-> “afterglow” = FLUORESCENCE
Ex: if solution of chlorophyll is isolated from chloroplasts & illuminated, will fluoresce in red-orange & give off heat

Photosynthetic Structures

-leaves get their green color from chlorophyll, the green pigment w/i chloroplasts, as it reflects green light

Stomata = The space where CO2 enters and O2 exits

Chloroplasts = found mainly in cells of the Mesophyll

Mesophyll = The interior tissue of the leaf

Guard Cells = Special cells (containing structural proteins) that will close (flaccid-> hypo inside cells & hyper outside cells) to conserve water if needed. When open (turgid-> hyper inside cells & hyper outside cells), they leave the space known as the Stomata.
-> potassium plays a role in the opening & closing of the stomata. when proton pumps transport H+ ions, changing the membrane charge, the K+ “gates” open and K+ diffusion occurs. H2O will follow K+!!!

Stroma = a dense fluid w/i chloroplasts, similar to the cytosol of an animal cell

Photosystems

-chlorophyll molecules excited & in intact chloroplast produce diff. results
-> *in native environment of thylakoid membrane, chlorophyll molecules organized w/ other small organic molecules & proteins into PHOTOSYSTEMS

Photosystem = reaction center surrounded by # of light-harvesting complexes

Light-Harvesting Complexes = pigment molecules bound to particular proteins
-# & variety of pigment molecules enable a photosystem to harvest light over a larger surface & a larger portion of the spectrum than 1 single pigment alone

-together, light-harvesting complexes act as “antenna” for reaction center

-when pigment molecule absorbs photon, energy transferred from pigment molecule to pigment molecule w/i L-H C until funneled into Rx center

Reaction Center = protein complex -> includes molecules & molecule called “primary electron acceptor”
-> includes “special” chlorophyll a molecules; these are special b/c their molecular environment (location to other associated molecules) allows them to use energy from light to boost one of their e’s to a higher E level to be captured by the primary electron acceptor

-(solar-powered) transfer of e from special chlorophyll a -> primary electron acceptor

-chlorophyll e is excited & PEA catches it -> REDOX RX
(isolated chlorophyll would fluoresce b/c no e acceptor)
-> drop right back down to ground state

*in chloroplast, immediate plunge back to ground state is prevented

-each photosystem (Rx center surrounded by L-H C’s) -> functions as a “unit” w/i chloroplast
-> converts light E to chemical E (used for the synthesis of sugar)

-thylakoid membrane has 2 types of photosystems

Photosystem II (PS II) = Rx center chlorophyll a = “p680” (pigment best @ absorb light w/ W.L. of 680 nm/red)

Photosystem I (PS I) = Rx center chlorophyll a = “p700” (pigment best @ absorbing light w/ W.L. of 700 nm/“far” red)

*IMPORTANT: NAMED IN ORDER OF THEIR DISCOVERIES. PS II ACTUALLY OCCURS FIRST!!!!

-they both actually have identical chlorophyll a molecules, BUT they are associated w/ diff. proteins in the thylakoid membrane -> this affects the e distribution in chlorophyll molecules & accounts for their slight difference in light-absorbing properties

*WORK TOGETHER to use light E to create ATP & NADPH!!!!

*IMPORTANT CONCEPT SUMMARY: light drives the synthesis of NADPH & ATP by energizing 2 photosystems (embedded in the thylakoid membranes)

-> the key to E transformation is the FLOW OF E’S thru the PS’s (& other molecular components built into the thylakoid membrane)

*during light Rx’s, there are 2 possible routes for e flow: “cyclic” & “noncyclic” (the dominant route)

Noncyclic Electron Flow

1) Photon of light strikes a pigment molecule in L-H C & is bounced to other pigment molecules until it reaches 1 of 2 p680 chlorophyll a molecules in the PS II Rx center.
2) The electron is boosted up and captured by the Primary Electron Acceptor!
3) An enzyme splits H2O up into: 2 e’s, 2 H+’s, & 1 O. The e’s are supplied one by one to the p680 molecules -> replace the e lost to the PEA. (*As p680 is missing an e, it is the strongest biological oxidizing agent & the e hole must be filled.) The O atom combines w/ another O atom & forms O2.
4) Each photoexcited e passes from the PEA of PS II to PS I via an Electron Transport Chain. The ETC b/t PS II & PS I is made up of “electron carrier plastoquinone” (Pq), a cytochrome complex, & a protein called “plastocyanin” (Pc).
5) The exergonic “fall” of e’s to a lower E level provides the E to synthesize ATP.
6) Meanwhile, light E is transferred via L-H C to PS I’s Rx center. An e of 1 of 2 p700 chlorophyll a molecules is excited. The photoexcited e is captured by PS I’s PEA, creating an “e hole” in p700. This hole is “filled” by the e that reaches the bottom of the ETC from PS II.
7) Photoexcited e’s are passed from PS I’s PEA down a 2nd ETC thru a protein called “ferredoxin” (Fd).
8) The enzyme NADP+ Reductase transfers e’s from Fd to NADP+. 2 e’s are required for NADP+ to be reduced to NADPH.

Cyclic Electron Flow

-under certain conditions, photoexcited e’s take an “alternative path”, called Cyclic Electron Flow
-> USES PS I but NOT PS II!!!!!

-SHORT circuit: e’s cycle back from ferredoxin (Fd) to cytochrome complex, then continue on to the p700 chlorophyll in PS I’s Rx Center
-> NO production of NADPH & no release of O -> BUT DOES generate ATP

*IMPORTANT CONCEPT: The function of CEF is to produce more ATP to make up for the difference b/c the Calvin Cycle consumes more ATP than NADPH

*The concentration of NADPH in chloroplast helps regulate which pathway e’s take thru light Rx’s!!!!

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-photosynthesis generates ATP by the same basic mechanism as cellular respiration: chemiosmosis!

-the thylakoid membrane of the chloroplast pumps protons from the stroma into the thylakoid space (which functions as an H+/proton reservoir)

-the thylakoid membrane makes ATP as H+’s/protons diffuse down the concentration gradient from [HIGH] in the thylakoid space back to [LOW] in the stroma thru ATP Synthase (like in cell resp!) complexes (the knobs of ATP Synthase are on the Stroma side)

-thus -> ATP forms in the Stroma, which is used to help drive sugar synthesis during the Calvin Cycle

*when chloroplasts are illuminated: pH in the thylakoid space drop to about 5 ([H+] INC.), & pH in the Stroma inc. to about 8 ([H+] DEC.)!

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Summary

Noncyclic Electron Flow pushes e’s from H2O (low state of PE) to NADPH (stored @ high state of PE). The light-driven electron current also produces ATP. The thylakoid membrane converts light E to chemical E (which is stored in NADPH & ATP). Also, O2 is a by-product.

Calvin Cycle

-similar to the citric acid cycle in cellular respiration, a starting molecule is regenerated after molecules enter & leave
-> HOWEVER: calvin cycle is ANABOLIC (builds + consumes)

-carbon enters as CO2 & leaves as sugar

-spends ATP as energy source & consumes NADPH as “reducing power” for adding high energy e’s to make sugar

-carbohydrate produced-G3P (glyceraldehyde 3-phosphate)

-net synthesis of 1 molecule of sugar -> CC must take place 3 TIMES!!!!!! (fixes 3 molecules of CO2, 1 time for each one that goes)

PHASES

1) “Carbon Fixation” = incorporates each CO2 molecule (1 at a time) by attaching to 5-C sugar RuBP (ribulose biphosphate)
a. -> enzyme that catalyzes 1st step = RuBP Carboxylase (“RUBISCO”)
b. -> most abundant protein on earth
c. PRODUCT = 6-C intermediate -> SO UNSTABLE it immediately splits in half -> becomes 2 molecules of 3-phosphoglycerate (for EACH CO2!!)

2) “Reduction” = each molecule of 3-phosphoglycerate receives an additional phosphate from ATP -> becomes 1, 3-biphosphoglycerate
a. -> pair of e’s donated from NADPH
b. -> reduces 1 , 3-biphosphoglycerate to G3P
c. -> e’s from NADPH reduce carboxyl group 3-phosphoflycerate to aldehyde group of G3P (stores more ATP)
d. ->*for every 3 CO2, there are 6 C3P
e. ->*only 1 molecule of G3P can be counted as net gain! -> 1 molecule exits the calvin cycle to be used by plant cell -> other 5 recycled to regenerate the 3 molecules of RuBP!

3) “Regeneration of the CO2 Acceptor (RuBP)” = in a complex series of Rx’s, the carbon skeletons of 5 G3P’s are rearranged by the last steps of the calvin cycle into 3 RuBP
-> to work, the calvin cycle needs to spend 3 molecules of ATP
-> RuBP is now prepared to receive CO2 again!!!!
-> for the net synthesis of 1 G3P, the calvin cycle consumes a total of 9 molecules of ATP & 6 molecules of NADPH!!!!!

Conservation of Water

-plants have anatomical & metabolic adaptations to help them conserve water (water is super duper important to plants, as it is like “feeding them electrons”!!!!)

-photorespiration (photo = light, respiration = the consumption of O2 & production of CO2) is a wasteful metabolic process & may kill plans if it continues for too long.

-“closed stomata” conditions for photorespiration

C3 Plants = 1st organic product of carbon fixation is 3-C “3-phosphoglycerate”
-> *most plants: initial fixation of C occurs via Rubisco, a calvin cycle enzyme that adds CO2 to RuBP

Ex: rice, wheat, & soy beans

-> stomata partially closed on hot, dry days & produce less sugar b/c less CO2 can get in -> also, Rubisco can bind O2 in place of CO2!! -> product splits, 2-C compound leaves chloroplast -> peroxisomes & mitochondria rearrange & split compound -> RELEASES CO2

-> called “photorespiration” (occurs in light, & consumes O2 while producing CO2!!)

-> does not generate ATP, CONSUMES IT

-> does not produce sugar

-> decreases photosynthetic output (siphons organic material from the calvin cycle)

-> modern Rubisco retains some chance affinity for O2 -> certain amount of photorespiration is inevitable now

C4 Plants = an alternate mode of carbon fixation that forms 4-C as 1st product
Ex: sugar cane & corn

-> unique leaf anatomy: 1) Bundle-Sheath Cells; tightly-packed sheaths around veins of leaf, Calvin Cycle takes place here in these plants & 2) Mesophyll Cells; more loosely arranged

-> cycle preceded by incorporation of CO2 into organic compounds in the Mesophyll

-> 1st step: the enzyme PEP Carboxylase adds CO2 to phosphoenolpyruvate (PEP)

-> forms 4-C oxaloacetate

-> *PEP Carboxylase can fix carbon when Rubisco can’t b/c of a high affinity for CO2

-> Mesophyll then “exports”/pumps 4-C product to bundle-sheath cells thru Plasmodesmata (*SPATIAL ADAPTATION)

-> w/i cells -> 4-C’s RELEASE CO2

CAM Plants = “crassulacean acid metabolism” = open stomata @ night & close during day (TEMPORAL/time relationship)
Ex: succulents, pineapples, etc.

-> allows desert plants to conserve H2O

-> *Mesophyll cells store organic acids made @ night in vacuoles until morning (stomata close)

Molecule of the Day: Tetracycline

Tetracycline (C22H24N2O8) is a yellowish powder that is used as a broad-spectrum antibiotic. It has a remarkable tetracyclic core, which is shared with a related group of compounds which also have antibiotic activity, collectively called the tetracycline antibiotics.

It is produced naturally by the bacterium Streptomyces via the following pathway:

It is used to treat many bacterial infections such as Lyme disease, and does so by inhibiting protein synthesis in prokaryotes. It binds to the A site of the large ribosomal subunit, preventing the aminoacyl-tRNA from entering the A site to lengthen the growing polypeptide chain. Interestingly, even though it inhibits both the 70S prokaryotic ribosome and the 80S eukaryotic ribosome, it is highly selectively disrupts prokaryotic protein translation, as human cells do not have a mechanism to pump tetracycline into the cytosol, whereas bacterial cells do.

Tetracycline is also used as a selective agent in cell cultures; cells containing the tetracycline resistance gene, tetR, will be able to survive in a medium containing it, whereas those which do not, or have an insertionally inactivated tetR gene, will not survive. This enables for the selection of recombinant cells or cells which have uptaken a desired plasmid.

As an antibiotic, tetracycline suffers from some drawbacks; it can stain teeth yellow, grey, or brown, and cause headaches, fevers, and rashes. 

vimeo

Cytosol - Video for Installation

ATP production in mitochondria (purple) can lead to the formation of reactive oxygen species (ROS) that damage mitochondria. When an organelle is beyond repair, the cellular recycling system (green) kicks-in and targets them for mitophagy, a specialized form of mitochondrial degradation.

Image: A primary retinal ganglion cell expresses a red fluorescent protein targeted to mitochondria, a green fluorescent protein fused to the autophagosomal marker LC3, and a cyan fluorescent protein in the cytosol. This image reveals how autophagosomes (green) can contact individual mitochondria (purple), before their ingestion by mitophagy.