Unit 3 Review AP Biology

okay so in this video we will talk about enzymes photosynthesis and cellular respiration as part of sorries part of AP biology unit 3 um and this video includes a discussion of the enduring understandings and essential knowledge is I listed in the framework from college board alright alright here we go so we're going to start with enzymes where it says this structure of enzymes includes the active site that specifically interacts with substrate molecules so in every view of enzymes enzymes are proteins that fold up in a particular shape dependent on the polypeptide sequence as well as the R groups and their properties and the folding up of that protein will create a section called the active site and that active site is where the substrate attaches and that is where the reaction occurs enzymes are biological catalysts that speed up chemical reactions by lowering the activation energy and that happens when you form an enzyme substrate complex so in the gift going on right here you see oh I love this you see the water is being used in the reaction this is called hydrolysis is a splitting a disaccharide into two monosaccharides so here this is sucrose which is this like white table sugar and you can also see here how the enzyme slightly changes shape and that is called induced fit so the structure of enzymes includes the active site that it's at the same standard okay so I also wanted to point out that when we talk about that poly peptide the sequence of amino acids that forms the enzyme that is dependent on the DNA sequence so our genes code for proteins and our proteins give us our phenotypes one type of protein are enzymes so how an enzymes shape is formed is dependent on the sequence of DNA coding for particular amino acids so if for example there is a mutation in a gene that could possibly change the amino acid and the folding up and shape of an enzyme but if a gene is intact and there's the normal sequence then how that protein folds should create an active site that is complementary to a substrate okay when we look at how this works they I like to use analogy if they fit like a lock-and-key the active site and the substrate um but really it's the shape and the charge of the enzyme and the substrate are compatible which means that like in that active site if there are I think I have another slide sorry so I kind of like well maybe I don't but the charges of the amino acids that line the active site should be like chemically compatible with the substrate so if you have like a polar like active site region you wouldn't have a non polar substrate like those would repel each other now the way enzymes work is that they catalyze reactions by lowering the activation energy in cells okay and sometimes an enzyme can be affected by its environment when the environment maybe heats up too high or has certain ions in like a salts or a change in pH it could actually disrupt the bonds in that polypeptide leading to the unfolding of that protein and we call that denature so if an enzyme loses its shape it denatures and therefore it can no longer catalyze reactions so environmental temperatures so as you increase a temperature that can lead to increase like molecular movements but at the same time eventually a temperature that's too high will disrupt bonds and then I'm like hydrogen bonds and ionic bonds and different interactions the molecular like moving of the molecule becomes too great and it unravels or denatures but at the same time sometimes changing the pH can also have an impact on the structure of an other protein so when you think about pH pH is a measure of hydrogen ions in the environment so a low pH and acidic pH has a lot of hydrogen ions so if you become an area becomes more acidic basically you're adding more and more H pluses or protons or hydrogen ions and therefore that's disrupting the hydrogen bonds as well as the ionic bonds in a folded protein and that could lead to it denaturing okay so sometimes though if an enzyme denatures it could be reversible so okay and this environment of peach this is kind of a tricky picture I just liked it because it kind of showed pluses in the environment and ions the environment the green lines here represent hydrogen bonds and how sometimes like if you change the ions in the environment you could end up disrupting those hydrogen bonds and the structure of that protein relative concentrations of substrates and products determine how efficiently an enzyme reaction proceeds so if you think about I really like this next slide here where if we look at these different test tubes and you see how there is a constant amount of enzyme in this picture the blue represents the enzyme but as you increase the amount of substrates you can see how there's a greater likelihood that a substrate will interact with an active site forming products so as you increase the substrate the rate of the reaction increases the amount of products increases until you get to a certain concentration or certain amount where it eventually levels off so if you look at the data it goes one to four and then eight eight eight that's because in this example of the enzyme has become the limiting factor it doesn't matter if you continually increase the substrate there's a limited amount of enzymes to catalyze the reaction so therefore you get a plateau or a leveling off and that same would be true if you switch that if you had a limited amount or like a constant input of substrate but you slowly increase the reaction of or the amount of enzyme you would get a same shape of graph okay I'm higher environmental temperatures increase the speed of the movement of the molecules in the solution increasing the frequency of collisions so that's why you see that like gradual increase in the rate of the reaction because as I move faster the chances of a substrate attaching to a nap or colliding with an active site also increases however eventually get to a certain temperature where it's just so hot and the enzyme teenagers oh we also have inhibitors I love inhibitors I have a whole video on it and but when you look at ways to inhibit enzymes or prevent and enzyme from working you have two options there are competitive inhibitors or allosteric or non-competitive inhibitors and in a competitive inhibitor it is competing with the substrate for the active site versus a non-competitive inhibitor is going to attach allosteric lis or an area that is not the active site and when you can see here in the green when a non-competitive inhibitor attaches to the enzyme it changes the shape of the enzyme so the substrate can no longer fit and there's no longer a reaction occurring all right so now moving into now if that was too fast of review on enzymes for you I believe I have three separate videos on mine unit 3 playlist that go into detail on enzymes so the remainder of this video will now focus on first photosynthesis and then cellular respiration so as we move into living systems we all require a constant input of energy so whether we're autotrophs or heterotrophs we all require energy and without energy that results in death and so this part C right here really ties into ecology or unit eight when we think about energy flow in an ecosystem okay so let's go ahead and look at energy related pathways that can be super complicated but I love this picture because it shows I'm different metabolic pathways so a pathway is basically like a series of steps or a sequential like controlled series of reactions all using enzymes now it is an efficient way to like transfer energy so that way we don't spontaneously combust and I like the end of this standard right here where it says a product of a reaction and a metabolic pathway is generally the reaction for the next step in the pathway so let's go ahead and see in general so here you start with a substrate and in a pathway you're gonna have enzymes that control each step and you start with something so for example in glycolysis you start with glucose and then you end with two pyruvates but it took ten reactions it took ten different enzymatic steps to make that happen so each step in a metabolic pathway is controlled by enzymes and the metabolic pathways that we will talk about in the light reaction I'm sorry in photosynthesis we have the light reaction is a metabolic pathway and then the krebs cycle sorry the calvin cycle is a metabolic pathway in photosynthesis then when we look at site of the respiration we have glycolysis the Krebs or citric acid cycle and oxidation of I'm sorry oxidative phosphorylation or the electron transport chain as well as fermentation so we have quite a few metabolic pathways we're gonna discuss and but what they all have in common is they all rely on enzymes so first let's talk about photosynthesis I mean photosynthesis is what autotrophs use to capture solar energy and convert it into chemical or usable energy for life so photosynthesis first evolved in prokaryotic organisms or cyanobacteria which is like a Bluegreen bacteria and so if you're reading a question some prompt or something about cyanobacteria those are photosynthetic prokaryotes and they were responsible for the first photos of us on earth mmm is it like 500 million years ago maybe more and they oxygenated our atmosphere before photosynthesis evolved our our atmosphere was rich in carbon dioxide and low in oxygen now these photos are these prokaryotic photosynthetic pathways were the foundation for eukaryotic photosynthesis and we know today that our chloroplasts evolved from ancient prokaryotes so kind of RAD all right so let's go ahead and talk about the light dependent reactions of photosynthesis and when we look at this the big idea is we're taking light energy or solar energy and converting it into chemical or usable energy in the form of ATP and NADPH which will then be invested in the anabolic pathway of the Calvin cycle to reduce our organic molecules carbohydrates lipids proteins and nucleic acids so in the light reaction we can see here a couple different things that we're going to talk about in more detail so we have the light reaction happens in we saw in unit 2 it occurs in the thylakoid membrane and we rely on proteins called photosystems and that is what we're going to look at next so here we have the light reaction and light travels in like a photon it's both a wave and a particle and we have these areas called photosystems one and photosystems two and photosystems is PS two right here as well as mps one oh I have a pen I'm so here you have your ps2 this is a photo system made of pigments where it contains pigments so pigments are the molecules approach they are proteins that are gonna absorb and reflect light so if you ever see a graph called an absorption spectrum that looks something like this like a photosynthesis usually on the side over here and you have the absorbance so and then down here you would have like the wavelength of light oh my gosh Mary that's being absorbed and so this is a measure of how much light is being absorbed and if it's like a high peak that means there's lots of photosynthesis going on lots of light being absorbed if the line is low that means there's like a low amount of light that's probably in the green pigment a green wavelength of light okay so these photo systems though ps2 and psy are what are going to absorb that solar energy so you can see here and then that is where electrons will be donated from so this is the photosystem this whole thing right here in the center of the photosystem and we have the chlorophyll a is the maiden pigment in photosystem 2 and then you have chlorophyll B in photosystem 1 but when light the light shines on you're going to have electrons which are these orange things here that are going to get passed into the electron transport chain so if I go back to this video this here the light shines down electrons are donated or they're excited to a higher energy state and they enter into the electron transport chain now in order to replace those electrons let me clear the ink as the electrons break free from chlorophyll and enter into the electron transport chain ultimately the final electron acceptor is nadp+ it'll gain the electrons at the end right here becoming reduced to form NADPH this NADPH is what will transfer over or carry those that energy or electrons over to the Calvin cycle however we need to UM replace these electrons so it can continue that is where the reactant of water is required water will be split into oxygen hydrogen's and electrons so if we go back to this gif here that's what this um what we're seeing is we are seeing water molecules come in watch almost here we go so you're gonna see water molecules um I'm sorry come in right here and then you see them split the electrons enter and now you have some I don't know maybe this is the hydrogen's this is the oxygen o2 so when we look at these photo systems this splitting of water is called photolysis and it replaces the electrons that were donated into the electron transport chain now over here in ps1 these electrons also break free from chlorophyll and will be picked up or gained by nadp+ but it's the electrons flowing down the electron transport chain that are gonna replace those right here so as we travel or as the electrons travel down the electron transport chain another thing that happens is that protons are pumped so it's not diffusion are pumped into this thylakoid space so the thylakoid is made out of a lipid bilayer surrounded by a lipid bilayer just like we saw in unit 2 and this lipid bilayer prevents protons from diffusing out and so therefore or because of this non-polar center here these fatty acids do not let ions out so we have this accumulation of a proton gradient so you have these protons getting pumped into the thylakoid space as well as the protons from splitting of water so you get a bunch of protons building up in the silac weight space establishing a concentration gradient you have more protons a higher concentration of protons within the thylakoid space compared to the stroma which is outside now it's due to this concentration gradient that we get chemiosmosis the flow of ions through ATP synthase so as those protons flow through ATP synthase by facilitated diffusion or through a protein channel this ATP synthase turns and does what's called photo phosphorylation so the protons will flow through ATP synthase turning if I kind of turns like a turnstile and that will produce ATP from ADP and inorganic phosphate so we actually will call this photo phosphorylation now is this ATP that will be used and invested in the anabolic pathway of the Calvin cycle so the light reaction in order to produce ATP is dependent on this concentration gradient and that was mentioned in unit two's standards okay so now that energy captured so it's also important to remember hopefully you watched my playlist on unit 3 but energy when it's moved within a cell it's moved in the form of electrons and electron carriers so this NADPH is carrying energy over to the calvin cycle this ATP produced is also carrying energy over to the calvin cycle so the calvin cycle is not mentioned very often in our standards so you don't have to stress too much about all the intricate steps but let's look at a general overview of how the Calvin cycle occurs so in the first step we start with a five carbon molecule called Ruby P that we see and the gif is right here okay so when it starts there we go Ruby P and then there's an enzyme called Rubisco so Rubisco is the name of the enzyme that will help do carbon fixation so we see up here at this step carbon dioxide from an air like a gas of carbon dioxide molecule is going to be attached to your Rubisco so your five carbon Rubisco and your carbon dioxide will join together forming a six carbon molecule that is very unstable so right away it kind of splits into two 3-carbon molecules so you see the split right here now that first step is called carbon fixation the actual taking of carbon dioxide from like the air and incorporating it sorry incorporating it into an actual molecule now comes the reduction phase of a calvin cycle so here we're going to invest that ATP that was unproduced during the light reaction as well as take those electrons and hydrogens from that electron carrier NADPH so our NADPH is going to be oxidized right in this step and our ATP is going to be invested as well so the calvin cycle is an anabolic pathway or an energy requiring pathway that builds so one of the molecules that is produced the main purpose of the calvin cycle is to produce this molecule called g3p so g3p is what comes here so this glyceraldehyde 3-phosphate g3p is a very simple 3 carbon sugar and two of those will form glucose so other g3p molecules can follow other metabolic pathways and form lipids and amino acids etc so this right here the Calvin cycle is basically how you are taking a and then incorporating it to form organic molecules which form the basis of life um so when we say life is built from carbon dioxide and water and the water component is this hydrogen and electrons from that electron carrier being invested and that's the Calvin cycle whoo so now we move into aerobic and anaerobic respiration so when we look at cellular respiration we're basically looking at two options of how to produce ATP so just by looking at these two gifts you can see there is a difference between anaerobic and aerobic respiration aerobic respiration requires oxygen and anaerobic does it you also see they both start with glucose which is the red mg so they both start with glucose in the cytoplasm the blue area you can see how that glucose is split into two pyruvates in both of them you can also see that in that cytoplasm so we are looking at like this area here in both of them ATP is produced during glycolysis however in aerobic respiration you'll notice that these pyruvates look right here are gonna enter into the mitochondria to continue to be fully oxidized to get any remaining potential energy from those bonds that it can but in that mitochondria it's going to require oxygen so you can see the input of oxygen flowing into the mitochondria and the waste product of aerobic respiration is going to be carbon dioxide and water okay okay let's go ahead and study these so in sight of the respiration we have in eukaryotes we have a series of coordinated enzyme controlled metabolic pathways to harvest our energy from our food so basically how the plants just invested that ATP and those electrons and hydrogen's in the anabolic Calvin cycle we are now taking that energy by breaking those bonds removing those electrons and hydrogen's the opposite of photosynthesis so our three pathways we're gonna look at is first glycolysis followed by the Krebs cycle and the electron transport chain now the Krebs cycle and electron transport chain are only happening in aerobic respiration so we'll also discuss what happens out here in the cytoplasm following glycolysis if it's anaerobic conditions so first like pollicis is a series of ten steps all using enzymes that basically are gonna start with our six carbon glucose and as you can see the glucose has a lot of bonds that can be broken and as we break down glucose and we take those electrons that is called oxidizing our food or oxidizing our electrons are our glucose we are hoping to completely oxidize our food I'm harvesting all the potential energy from it so in the process of glycolysis we end up with two pyruvates that are three carbons each we get two ATP and two reduced electron carriers now if this were fermentation and anaerobic that's all the ATP we would get however if it is aerobic respiration there is still potential energy left in these pyruvates so we're going to need to harvest that energy so our next step is called the oxidation of pyruvate where we're gonna start in the cytosol the pyruvate that was made in glycolysis occurs in the cytoplasm if this will travel into the mitochondria so what we're seeing here is let's see if I can play this again so we have our pyruvate it'll be oxidized forming a carbon dioxide and a reduced electron carrier when I go again so here we're gonna have our bonds will be broken a carbon oxide will be released that is a third of the carbon dioxide coming out of your mouth comes from this step and then we will have our two carbon acetyl which are these two gray right here will attach to a coenzyme a coenzyme a will help it attach to a four carbon molecule called oxaloacetate so this four-carbon oxaloacetate will join with acetyl co a forming citric acid now we can begin the citric acid cycle so in order to actually begin the krebs cycle or citric acid cycle you need the oxidation of pyruvate to happen first and that occurs within the mitochondria you get one reduced electron carrier as well as a molecule of carbon dioxide this is gonna happen two times because there were two pyruvates made at the end at mycologists so now you have your acetyl co a is going to join the axial acetate and as we go through the Krebs cycle you can see that it's a series of I'm the beginning here we're going to oxidize which means we are going to like break another bond and reduce an electron carrier so you have your like six carbon i'm citric acid you're gonna oxidize or break a bond and that comes off as carbon dioxide which is this right here and we get a reduced electron carrier and that happens again so then you're down to your 5m carbons and then a carbon dioxide will be oxidized a broken off and then a reduced electron carrier now as we go through the Krebs cycle and we will produce so here you have an electron a reduced electron carrier another reduced electron carrier another reduced electron carrier and a fourth reduced electron carrier so in the Krebs cycle or the citric acid cycle the main purpose is to fully oxidized our food by the end of the Krebs cycle our entire three carbon pyruvate is now in the form of carbon dioxide you had the one carbon dioxide from the oxidation of pyruvate and then you had a carbon dioxide produced here and here as well so now you have three carbon dioxides so at that point your pyruvate is completely exhaled now in the process of the krebs cycle you do produce one GTP that'll be used to make ATP by substrate level phosphorylation and for reduced electron carriers so you can see as we go through glycolysis the oxidation of pyruvate and the citric acid cycle we are reducing electron carriers along the way trying to get as many as possible over to the electron transport chain so we can make a ton of ATP in glycolysis we had just two ATP made this Krebs cycle we had two one for each pyruvate but it's really going to be the oxidation oxidative phosphorylation that produces the most of our ATP so when we look at the electron transport chain the electron transport chain takes advantage of the two membranes of the mitochondria so the mitochondria has two membranes thanks to the endosymbiotic theory and what we see here is in between these two lipid bilayers you get a proton gradient all of these protons accumulate between these two lipid bilayers because they pop they're positive ions they cannot diffuse out so we get this electrochemical gradient or a difference in charge across the membrane so how does that happen right ooh this is a bit let's go I guess let me clear the ink and we can draw on this and make it more smooth for us to understand so here you have these electron carriers that were produced or reduced during glycolysis and the Krebs cycle when they arrive at the electron transport chain which a lot of them are already produced in the tricks the krebs cycle happens in the matrix of the mitochondria and that's kind of where this is already occurring so we're going to oxidize the electron carriers so you see here this nad plus can be reused in glycolysis the oxidation of pyruvate or the citric acid cycle now the hydrogen that was on this electron carrier is pumped into this inter membrane space and the electron is passed down the electron transport chain where oxygen which is very electronegative is pulling and attracting those electrons down the e.t.c so when oxygen gains those electrons and attracts them it will also pick up some protons some hydrogen's now that is how water is formed during cellular s or aerobic respiration so as the electrons are passed down the electron transport chain with oxygen being their final electron acceptor they pump protons into this inner membrane space establishing an electrochemical gradient now it is that high concentration of protons that we call the proton motive force with all of these positive charges wanting to like repel each other they actually will flow through ATP synthase it'll turn and phosphorylate adp and inorganic phosphate forming ATP we call this process oxidative phosphorylation so this is kind of a intense picture but when we look at here the electron transport chains can occur in chloroplasts and mitochondria as well as the prokaryotic plasma membranes so we saw the electron transport chain in the light reaction earlier but it also was occurring in the mitochondria so in cellular respiration what we have is we have we can oops let's go back we can see the electrons are delivered by nadh and fadh2 which were formed in the previous metabolic pathways leading up to the electron transport chain and the in aerobic respiration the final electron acceptor is oxygen and this is why we breathe in photosynthesis it was nadp+ we saw at the end of the light reaction and I'm basically the transfer of electrons um helps form that I'm just basically summarizing everything we talked about forms the proton gradient across that inner mitochondrial membrane which separates and creates a high proton concentration compared to a low proton concentration and that will allow for the diffusion of ions or chemiosmosis through ATP synthase which will produce ATP and so that flow of protons back through um drives the formation of ATP from ADP and inorganic phosphate so in the mitochondria we call this process oxidative phosphorylation and in photos in chloroplasts we call it photophosphorylation I want to emphasize though in plants and autotrophs autotrophs have both chloroplasts and mitochondria so this is occurring in both mitochondria and chloroplasts within plants so it is not true to say Oh plants have chloroplasts and animals have mitochondria but rather autotrophs have both like plants will have both mitochondria and chloroplasts so just because it's talking about a mitochondria and oxidative phosphorylation do not automatically assume it is only occurring in an animal look for other context clues in the question or the problem now we also will use um this cellular respiration when we do say the respiration these metabolic pathways actually produce quite a bit of heat and that heat is what used to help maintain our homeostasis of body temperature and so endotherms sometimes we don't necessarily need all of that ATP but rather we just need to generate the heat so what we can do is we can decouple which basically means undo like disconnect oxidative phosphorylation from the electron transport chain so what that means is you can create like a proton leak that allows the protons to just diffuse back through um into the matrix without making ATP so it's really just a way to allow for metabolism to occur to generate heat without the production of ATP and endotherms will use this to help us maintain constant body temperatures and so if you think about a metabolic pathways we are burnt like burning through our food our gluco like a carbohydrates our lipids and our proteins so therefore endotherms will require more calories than an ectotherm or a cold-blooded organism cold-blooded organisms do not use metabolism to generate heat for body temperature and therefore there they will require less calories in life for survival so in periods of like food scarcity an ectotherm would be able to survive longer than an endotherm of the same size okay oh now we're almost done guys so fermentation in fermentation what we have is we have following glycolysis now if there is not oxygen right well first off let's look what we learned with aerobic so here you have glucose and that glucose I went through glycolysis to produce pyruvate and we took the NADH sorry nad plus that was oxidized meri was reduced I'm here into NADH and that was carried over to the electron transport chain to make a lot of ATP however in the electron transport chain that NADH will be oxidized back into nad plus so therefore we can have the nad oh my gosh that nad plus can be recycled and used again in glycolysis or in the kreb cycle etc however when oxygen is not sorry hippos when oxygen is not present and we are in anaerobic conditions we need to make sure that the cell does not run out of nad plus so the purpose of fermentation is basically to oxidize this electron carrier and recycle the nad plus so that at least glycolysis can continue because in anaerobic respiration it's these two ATP those are the only ATP produced and that cell is struggling to make ATP and therefore glycolysis cannot stop otherwise the cell will die they'll be no more ATP so therefore we have two options of fermentation in this example this is lactic acid fermentation um and you can see here in this gif that basically in anaerobic respiration we are converting the NADH back into nad plus to continue glycolysis so it is a cycle that will produce lactic acid as it's a product so here you start out with your glucose and then you have your NADH was made during glycolysis and at the end of glycolysis those are your products however in order to continue glycolysis oops the we need to oxidize these two electron carriers back and nad plus to continue continuing this step of glycolysis without this step like losses would stop so therefore you have to make sure that you have nad plus to continue now um the other type of fermentation oh I don't have a picture of is alcoholic fermentation and in alcoholic fermentation basically instead of lactic acid you would get carbon dioxide oh man oh man you would get carbon dioxide and ethanol so um sometimes in fermentation if the clue is that carbon dioxide is produced then you know it is alcoholic fermentation um and if it's lactic acid well then electic acid fermentation and our last slide here is when we it says the conversion of ATP to ADP releases energy which is used to power many metabolic processes but when we save a conversion of ATP to ADP and ATP is actually hydrolyzed so it's through the process of hydrolysis so right here in this step when that third phosphate is broken off it's by the addition of a water to break that bond and hydrolyze ATP I'm releasing that energy to power Seiler function all right I hope this unit 3 and PowerPoint was helpful for you and good luck on your AP test or on your unit tests great job

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Length: 41min 24sec (2484 seconds)

Published: Fri May 08 2020