Bio notes

Bio Lecture 1: Chapters 1.1 and 49.4 Biology and Learning. *Practice quiz in first Workshop doesn’t count* Biology: So, seeds are pretty much an embryo and a coated shell surrounding it. Ex. Dandelions What is Evolution? Evolution is when animals and plants on earth pretty much adapt to their own environment in order to survive. Change the way of living pretty much. What is Biology? It’s the study of life basically Memory and Learning: So, what’s the difference between short- and long-term memory? (LTP). Neural Development (ND): how your nervous system works Neuronal means about the neurons Nervous system is basically a system of neurons and other cells to help your brain work (supporting cells). Neuron: the basic unit of the nervous system and has a main function of sending messages from one neuron to the other (Ex. Wire). Part of the neuron have an input and an output section where messages are transferred. Are formed in the embryonic stage Embryonic Development: Before someone is even born the brain is developing and growing Overall structure of the nervous system is formed Involves gene expression and signal transduction Genetics is the basic structure of our brains and controls a lot of functions ND involves gene expression: This is how your DNA is used to provide signals when expression occurs. Or when you use the nervous system itself. Neuronal Plasticity- the modifications that are formed after your birth These connections will pretty much redefine the connections of the brain. These changes are activity dependent. Ex. Riding a Bike- The memory is making a connection, a new one. Synapse- is the part of the neuron that sends information to other neurons and where most remodeling occurs. It also tells the brain what to do and what is important. So pretty much new connections form when you use your brain more and more. More activity means more connections and the less activity means less connections. When you keep using the same information more and more it will signal the brain that it is important. And it will strengths the connections. Ex. Studying Types of memory Memory: Anatomical/physiological events that occur in chemical synapse Sensory Memory: When you experience things, it will go to your parts of your body that involve the main senses. When you are on a table and fall asleep and then you wake up and still feel the table on your skin is an example. Short-Term Memory: Which is also your working memory. This is where your awareness is. At most you can be aware of 7+2 items. Info is stored for a very short time and if not used it will be released Chunking: learning sets of related info and facilitates LTP. Practice: Long-Term Memory: These are permanent connections with all your neurons. They won’t go away. *THIS IS THE DIFFERENCE B/W STM*. You can’t find all of the memory. Learning is not the same thing as memory. Learning: Use of memory to avoid any negative outcomes Learns from mistakes or things that happened in the past. Stimulus Sensory memory Encode to STM or Forget Encode to LTM or forget Then you can retrieval Long Term Potentiation = Encoding and reencoding and is the physical change in the brain. You eventually get good at getting to this memory. This is activity dependent and the more you use it the more important the brain knows it is so it will store it. The more meaningful it is the better it is to store. Bio Lecture 2: Scientific Process and Chemistry Learning Goals; recognize and recreate the steps of the scientific method comprehend atomic structure compare and contrast the types of chemical bonds compare and contrast the emergent properties of water Themes in Biology Evolution: This is the core theme of biology the unity and diversity of organism These living organisms are modified descendants of common ancestors. Explains why we are so different then plants Organisms don’t evolve, they need to be put in an environment where they can reproduce Emergence: process of becoming something more than your parts Ex. Parts of a bike sit out are useless but when you put them together, they are more than what is was before. Emergent Properties: Emergence = The whole is more than just the sum of its parts Levels of biological organization: a hierarchy Look at the bio diagram in the textbook. The diagram shows new levels in the bio world and as you keep on getting to a higher hierarchy, the more thing emerges. Methods of Investing In studying nature, scientists make observations and form and test hypothesis Science = “To Know” Inquiry is the search for information and explanations of natural phenomena Methods of investigating the natural world in systematic manner. So, it’s a process and it’s not random. Scientific Process: Inductive Reasoning: Reasoning from a specific case or cases to lead to a general rule. Hypothesis: Testable explanation for observations based on available data. This is the guess that you can make. Prediction: What you expect to see when you test your hypothesis. This is what you think what will happen or what the result be. Theory: Broad explanation with significant support. It has been tested so many times and it pretty much always works. The statement in which you are almost confident in the outcome. Ex. Theory of gravity, Earth revolves around the sun Law: Statement of what always occur under certain circumstances. Isn’t really that many laws in Biology. It is an observable pattern Ex. Conservation of energy An Example of Scientific Process would be… Observation of something like milk is good until March 6. This is what the date says on the carton Background Research of milk Hypothesis—Sniffing the milk will tell me if it is bad Prediction – Experiment Evaluate: if this is wrong compared to the prediction, then you would revise the prediction. You haven’t failed science, you just learned what the actual outcome would be. Now you have to repeat and verify. This would then lead to you to ask other questions when the other experiment is successful. Deduction: a prediction that can be tested by examining human tissues. Supernatural/ Religious: outside of the bound of science Basic Chemistry Electrons: 25 of the 92 elements essentials to life. Four are the 96 % of living matter which are Oxygen, Carbon, Hydrogen, and Nitrogen The remaining 4% is made up of phosphorus, calcium, potassium, and sulfur Oxygen are found in Lungs and blood Carbon is found in sugar and glucose and fats Hydrogen is found in water and sugars and fats Nitrogen is a building block in protein Trace Elements: Ones that are required by an organism in only minute quantities Atoms: the smallest unit of matter that still retains the properties of an element. are made up of three subatomic particles which are protons, neutrons, and electrons Atoms aren’t the smallest thing to divide Electrons have a -1 charge and they move rapidly and move all around the place. They also determine how atoms interacts and cause bonds to form. The further the electron is away from the nucleus, the more potential energy it possesses. Potential Energy: the energy matter has because of its location or structure. They can be used to work and become excited. Excited means that electrons that were near the nucleus will move very far away. EX. Light be shined on it will “excite” the electron. It can come back close to the nucleus. Farther it is away from the nucleus the more energy it has. Electron Shell an electron’s PE (only 2 fit) Valence Shell outermost shell where bonds between electron form. How full the valence shell is can tell us how frequent carbon reacts to other molecules (Max. is 8) The exception is found in H and He where the max electrons will be only 2. Formation of Molecules Chemical Bonds: result from how atoms share electrons The formation of molecules all depends on the chemical bond between atoms Atoms with incomplete valance shell electrons will tend to share or transfer with certain atoms. These atoms will be held together tightly with something called chemical bonds. You will never find atoms with incomplete valance electrons all alone When atoms have a full set of electrons, they tend to not share anything because they have everything filled up. Energy: are the capacity to cause change. Work is the capacity an atom can change. Molecules: Compounds with two or more atoms joined together to form a stable particle. Emergent Properties: many compounds have different properties then their elements. Take two atoms and combine them with chemical bonds and create something different. Ex. Na + Cl NaCl Electronegativity affinity for electrons and have a tendency of an atom to attract an electron. If you are very high electronegative then you are good at attraction of other electrons. If you are lower electronegative then you tend to give up electrons Chemical Bonds are a type of bond that is determined by difference in electronegativity. Two types of bonds: Covalent Bonds Ionic Bonds Covalent Bonds: Are between atoms and are where electrons are bonded. Share of a pair of valence electrons by two atoms. This is a very strong bond. Hardest bonds to separate in biology. (Less than 2 electroneg.) Two types of this bond: Nonpolar: Have the same electronegative and share electrons equally. Polar: 2 different electronegative atoms and the electrons are shared unequally. This would cause molecules to have sides. There will be a more positive and a more negative side Because of the unevenness, the electron will be more dominant on one side then the other. Ex. Water has one positive and negative side. Ionic Bonds: Between charged atoms and have greater than two electronegativity. These atoms steal electrons from the other and a bond is formed by attraction between anion (-) and Cation (+). Ion: a charged atom or molecule Anion: One or more units of negative charge (Extra electrons) Cation: One or more units of positive charge (Loss of electrons) Interactions between molecules: Van der Waals interactions: causes the two molecules to attract and these develop because of electrons are in constant motion Ex. Neon is stable, and a noble gas and the outer shell has a full set and that means it doesn’t form chemical bonds. Opposite charges attract and when Neon bump into each other since the electrons from one side makes it more negative and the other side is positive. This causes the attraction between them, hence the van der waals. Ex. Duct tape attracts to another duct tape because of the molecules between the tapes. And there is a lot of van der waal attraction. Emergent Properties of Water London dispersion forces and hydrogen bonds Hydrogen bonds: are really strong dipole-dipole interaction and hold water molecules together. The stickiness between the molecules is what you call an attraction. The polarity between the water molecules form attractions to each other. Ex. After you take a shower, water sticks to you and it doesn’t feel sticky, but it actually is, and we don’t feel it because we are filled with water. Hydrogen polar molecules make life work. Water creates the condition, so the world is how it is. Water is Polar and forms hydrogen bonds with other water molecules. When water is put together, when the oxygens are trying to go together, they wi1l push each other away and go away from each other. But if you were to do the other way where an O and the two Hs are facing to each other than that creates a bond and will attract. Because water is polar it sticks together where opposites attract and forms a hydrogen bond. There are 4 Properties of Emergent Water: Cohesion Behavior: Water molecules stick to each other (Itself). Adhesion: Water molecules stick to other polar things Ex. When you mix sugar and water than you can’t see the sugar because both are polar. So, this means that they attract. Even though they both aren’t water molecules they still attract since both are polar molecules. Surface Tension: is a measure of how hard it is to break the surface of a liquid. Since water is cohesive it sticks together. Ex. And when you belly flop from a diving board into the pool, the stomach will become pink since there is surface tension because of the hydrogen bonds. Ability to Moderate Temperatures Moderates Temperatures: Water has a high specific heat hard to change water temp Specific Heat: the amount of heat must be absorbed or lost for 1 gram of that substance to change its temperature by 1-degree C. High heat of vaporization hard to change state Vaporization: The heat a liquid must absorb for 1 gram to be converted into gas Water is a stable environment. It takes a lot of heat to break the hydrogen bonds. It takes a lot less time for alcohol to break their bond. Ex. Water takes a lot of energy to change the temp of water. When its summer the water is still cold but when you are in winter it is still low key warm. This shows that water is stable. This is because of the hydrogen bonds which makes it hard Expansion Upon Freezing Ice floats: Hydrogen bonds in ice are more ‘ordered’ makes air pockets Water reaches its greatest density at 4 degrees C When water freezes the molecules aline and form a shape since there is like charges between water, there are pockets in the ice. Ice floats because there is water underneath. Ex. The lakes freeze from the top and the fish go down, and if ice didn’t float, and the ice would form from the bottom and the fish would go into the air lol. Versatility as a Solvent Substance can be: Hydrophilic or hydrophobic Hydrophilic: ions salts and polar, dissolve in water Hydrophobics are nonpolar and are things like lipids, don’t dissolve in water oil don’t mix with water. 3. Biological Molecules Ch. 4.2, 4.3, Ch. 5.1 through 5.4  compare and contrast the functional groups  compare and contrast the biological molecules  recognize and recreate the process of hydrolysis and dehydration synthesis  compare and contrast the levels of protein structure Importance of Carbon Intro to Carbon Organic compounds: contain carbon bonded to C or H Organic Chemistry: The study of carbon compounds Carbon Chains: skeletons of organic molecules Carbon has 4 single valance electrons and it is called tetravalent. This means there is 4 more electrons it can add. It can make four different chemical bonds with other molecules. Makes this a good building block. Carbon has 6 electrons and 4 of them are in the outer shell. *Structure is key to the main function of a molecule* - Functional groups = R you can replace this with something else (That’s what R means) - A functional group determines a lot about a molecule. - Ex. Like for a cub, if the cub where to choose HO or O, it can become a male or female. Hydrocarbons Hydrocarbons: This is a carbon and a hydrogen. Ex. Methane They are nonpolar and is uncharged which means it is nonpolar and is a hydrophobic. It is insoluble in water. Don’t readily react with other compounds. In addition, Diff functional groups can change molecular function. If you change the functional group, you can change the function. (Known as R) Ex. Many organic compounds such as fats have hydrocarbon components. FATTY ACID Functional Groups Hydroxyl group(R-OH) The compound name is Alcohol and is named at the end -ol Polar Hydrophilic Slightly acidic Carbonyl Group (CHO) Aldehyde/ketone – depend on location of C=O Polar Hydrophilic Slightly Acidic Carboxyl Group (R-COOH) Carboxylic acids (H+ easily released) Polar Hydrophilic Acidic Amino Acid: Building block of proteins Amino Group (R-NH2) Amones (H+ easily accepted) Polar Hydrophilic Not an Acid it’s a BASE. Sulfhydryl Group (R-SH) Thiols and they hold some protein and molecules together. Two-- SH Form stable crosslink Polar (Less polar than a hydroxyl) Hydrophilic Slightly Acidic Phosphate Group (R-PO4H2) Organic Phosphate and often contributes negative charge. Phospholipids and nucleic acids (DNA, RNA) Polar Hydrophilic Acidic Methyl Group (R-CH3) Methyl Hydrocarbon and controls gene expression, shape and function of sex hormones Not polar Hydrophobic Not an acid or a base, Its neutral Biological Macromolecules Macromolecules Monomers are building blocks of macromolecules They join monomers together to form polymers, they are joined together by covalent bonds and they need an enzyme to break it apart 3 out of 4 bio molecules are polymers Carbs Proteins Nucleic Acids Lipids are bio molecules but aren’t polymers Dehydration synthesis: removes water and joins enzymes used dehydrogenases creates polymers with monomers they suck water out and join others together regulated by that specific enzyme *Hydrolysis: add water and breaks polymers and are regulated by the enzyme hydrolases B. Carbohydrates Ex. CH2O Monomers can be sugars and glucose(C6H12O6). They are used as fuel and energy They are also used as building material. Monosaccharides are the monomer of carbohydrates Glucose: this is the most common monosaccharide There are linear and there are also are in the shape of a ring (ring form). There are two forms of the ring formed. They are alpha and a beta glucose. (The ratio from above should be used to identify the molecule as a sugar.) Alpha and beta means that they are the same thing except for one thing that tells them apart. They have different functions even though they are very similar. They have different functional groups. Ex. Alpha Glucose can be digested and beta can’t be digested Disaccharides: When 2 or more monosaccharides are bonded together The covalent bond between monosaccharides is glycosidic linkage Ex. When we are trying to combine two monomers such as glucose and fructose, we first get rid of the water and it will become sucrose (Dehydration Synthesis). When we eat sugar, we can taste fructose and glucose separately since our mouth has water and adding water will break apart the two monomers. Polysaccharides: Sugar polymers and the structure/function is determined by the number of monomers and the location of the glycosidic linkages Function in Living Cells: Used for Storage: examples are starch and glycogen Used for Structural: examples are cellulose, chitin C. Lipids Fats: They don’t make polymers and aren’t monomers. They are just molecules but really big ones. Most abundant lipid They are used for energy storage and consist of glycerol (3 Carbon chain with 3-OH) and there are either 1,2 or 3, fatty acids These fats are nonpolar because if you put for example fat on top of water, it doesn’t dissolve. Fatty Acids: Dehydration synthesis adds fatty acids to glycerol and the covalent bonds are called ester linkage. Ex. Triglyceride is a storage form of fat and are formed when there are three fatty acids combined with covalent bonds. This synthesis doesn’t make polymers, it’s just adding fats. The double bond determines type of fat Saturated Fats: Saturated fat has no double bond, so it stays straight. Saturated at room temperature Ex. Animal Fats Unsaturated Fats: There is a double bond instead of a single bond The double bond in the unsaturated causes bending in the molecule. They share more electrons and there is less hydrogen, and this is what causes it to kink. Monounsaturated: Single double bond Polyunsaturated: More than one double bonds *Different structure means different function* Phospholipids: Phospholipids are pretty much cell membranes Amphipathic have both polar and nonpolar sides When you add two fatty acids tails and you bind a glycerol it will cause it to have a hydrophobic then phosphate group head then the other side is hydrophilic. When you put them in water it will rearrange where the side that is hydrophobic will face away from water and this causes it to create a membrane. Steroids: Steroids have three rings of 6 C and 1 ring of 5 C and they vary inside chains or functional groups. Cholesterol in animals is used for communication. Our body creates this and use it as a structural formation. Proteins They have many functions and structures The monomer of proteins are amino acids and there are 20 types. The polymer is a called a protein or something called a polypeptide *NEED TO KNOW THE STRUCTURE OF AMINO ACIDS pg. 75* - R groups determine functions, acidity, and polarity The peptide bonds between amino acids are monomers Polypeptide is a polymer of amino acids. Primary structure: Sequence of amino acids in which are joined by peptide bonds to make a polypeptide chain and is determined by DNA Secondary structure: Hydrogen Bonds stick aa together, R groups do not participate. There is an alpha helix and a beta pleated sheet Ex. Coil structure (Alpha helix) and folded structure (Beta pleated sheet) Tertiary structure: R-Groups interact and folds into a 3-d shape. There are all types of bonds Quaternary Structure: There is different set of information and its codes for different protein. Multiple polypeptide chains form one macromolecule (No more folding). It takes more than one gene to fix the protein Denaturation: Loss of a third or fourth structure. A denatured protein is biologically inactive pH, salt concentration and temperature Renaturation: the opposite and you can put the structure back, but this is only with some proteins. Nucleic Acids Monomers are nucleotides and the polymer have 2 classes. They are DNA and RNA. They transmit hereditary and code for proteins. Monomers joined together with Phosphodiester Bonds. 4. Origin of Life Ch. 25.1, 25.3  identify the requirements for abiotic synthesis  recognize and recreate the process of abiotic synthesis  compare and contrast the Oparin-Haldane and Iron Sulfur hypotheses  recognize and recreate the process of abiogenesis  recognize and recreate the major events in the evolution of life I.Abiogenis Abiotic Synthesis of Monomers Fossil evidence of microorganism are from 2.5 billion years ago There are four requirements. Little or no free oxygen. This is because of how oxygen breaks bonds down which is called oxidizing. Oxygen will keep tearing these up. There needs to be a source of energy: This is because it will builds biological molecules to form simple inorganic chemicals. Ex. Volcano, thunderstorm Presence of chemical building blocks (CHON)> These would be water, dissolved inorganic molecules and atmospheric chemicals. Time is needed for molecules react with one another. There were no enzymes to speed up the reaction, hence, there needs to be a lot of time.(We have enzymes that help this process go faster). It took more than a billion years after the Earth formed There are many hypotheses that were developed that tried to see what caused the Earth to develop the way it did: The 4 Step Hypothesis of Single Cell Formation 1.small organic molecules formed spontaneously  ->combined to form-> 2. Organic macromolecules (abiotic synthesis) ( ex proteins and nucleic acids) ->packaging into-> 3. protocells - droplets with membranes that could maintain internal environment from surroundings 4. origin of self-replicating molecules eventually lead to inheritance Prebiotic Soup Hypothesis Hypothesis: Life formed near Earth’s surface and had spontaneous formation of monomers.. To test the hypothesis, people thought if he put CHON and applied energy and then gave it time to settle. In the end it created amino acids. This pretty much recreated the process that happened before life was formed. He just added heat to CHON. Iron-Sulfur Hypothesis This said that the world began at the cracks of ocean floor hydrothermal vents. This allowed it to be protected from meteorite bombardments at the surface. There is H2O, CO, and minerals that were released. Iron is a catalyst to builds molecules. Synthesis of Macromolecules Formation of polymers from monomers (Protein or RNA) Small organic molecules or monomers polymerize on hot sand or rock Negative ions bind monomers may serve as a catalyst Formation of Protocells Lipids spontaneously form vesicles(containers) -aggregate of abiotically produced organic polymers exhibit many attributes of living cells ex: microsphere: protocell formed by adding water to polypeptides and have some characteristics of living cells: 1. produce electrical potential across surface like gradients across cell membranes 2. absorb materials and undergo osmotic swelling and shrinking 3. maintain internal chemical environment from external environment 4. divide in half after have sufficiently grown - But no mechanism of heredity - Phospholipids: Make a membrane when they are put into water< They are hydrophobic. Appearance of self-replication RNA= nucleic acid in protocells RNA capable of two activities: Self-Replication Catalyze protein synthesis: Ribozymes Ribozymes: RNA that has catalytic properties DNA evolved later: DNA are double stranded and are more stable. When this evolved, it has a double helix shape. This allows info to be copied bc of the structure. II. History Life Early Life About 3.5 billion years ago were where the prokaryotes started to form. All heterotrophic bacteria was developed in this time period of the Earth Life cycle Earth was born 4.6 billion years ago, so this means that it took over a billion years for life to actually form The bacteria are heterotrophic, which means they eat other things The first ones use fermentation They were anaerobic: Live without air They were eating carbon molecules The oxygen level was low so they just ate to survive and they didn’t need that much O2 2nd: Photosynthetic autotrophs appear E from sunlight and they release oxygen Ex. Cyanobacteria They used the sunlight to make sugar As they released oxygen over a period of time the level of oxygen in the atmosphere has risen and all of the bacteria that used food as survival died out. When photosynthesis evolved most of the life died out. (99 Percent) 3rd: Aerobic bacteria: use oxygen for more ATP Origin Of Eukaryotes Eukarya arise from Archaea and Bacteria A symbiotic relationship: this is permenant, Endosymbiont Theory: Mitochondria and chloroplast > were bacteria And they came about because of this theory. It has its own DNA. Cell Structure Ch. 6.1 through 6.4 compare and contrast prokaryotic and eukaryotic cells recognize and recreate how a cell synthesizes a protein compare and contrast cellular components and organelles Cellular Diversity and Characteristics Classification by structure/morphology Prokaryotic cells: Bacteria and Archaea There is no nucleus and they only have a nucleoid where the is DNA Unbounded. Main structure: Bacterial Chromosome Ribosome: Blogs of protein Plasma Membrane They have DNA still so they can pass this down to generations and generations when they are reproducing There are also no organelles, there is no phospholipids which is why they don’t have any organelles. Tiny – typical size is about 1-10 micro-meters Eukaryotic Cells: DNA is in the Nucleus Membrane-bound organelles (They have phospholipid membrane) Mitochondria: the powerhouse of the cell Endomembrane system: Membrane bound organelles work with each other and help each other function. Cytoplasm: gel-like substance that is between the nucleus and the membrane of the cell. And the size is a little bit bigger (10-100 micrometers) Common Feature of Cells Smallest unit of life are cells, anything less than this isn’t alive and needs to be a cell to be considered alive. All organisms are made up of cells Multicellular organisms are cooperative specialized cell. This means one person like a human like me are made up of many types of cells. They work together for me to be alive. Cell theory: All life is made out of cells All cells have four common features and a common evolutionary ancestor. This means that life pretty much evolved once and this is why we share a lot of things. In other words, life on Earth had evolved once a long time ago and that is why we share so many features to other living organisms. Cell structure: Plasma membrane: which are made from phospholipids Cytosol: Semifluid substance within the cell Chromosome: carry genes, and are made out of DNA Ribosomes: Make polypeptides (proteins), and they are made of RNA Cell Size Why are cells so small? Cells are too small to see by the naked eye and need a microscope used to visualize cells The plasma membrane within each cell has a selective barrier. This means that it will only let certain things in or out. In other words, this membrane means that it chooses what goes in and what goes out. Ex. They let oxygens and waste material get in. Surface Area to volume ratio? Compartments: storage Multicellular: you make organ systems and branches There are two major categories of cells: 1.Prokaryotes: Came about 3.5 billion years ago Before nucleus Domains are Bacteria and Archaea 2. Eukaryotes: Came about 1.9 billion years ago - It means true nucleus - Domain is Eukarya Ex. Protists, fungi, animals and plants Components of Eukaryotic Cells Nucleus The Structure: The surrounding membrane is the nuclear envelope meaning that the DNA in the nucleus is bound by the membrane. This envelope is a 2-membrane structure. Both of which are a lipid bilayers Membrane-bound organelles There is cytoplasm in between the plasma membrane and the nucleus The thing that is inside: DNA is organized into many chromosomes DNA + Proteins = Chromatin Chromatin: the complex of DNA and proteins making up chromosomes Nucleolus: makes ribosomes There is RNA and proteins Nucleolus (plural nucleoli) -Dark structure of RNA and proteins in nucleus -no membrane -where ribosomes are made Inside lined by Nuclear Lamina: This is a netlike array of protein filaments that maintains the shape of the nucleus by supporting the nuclear envelope Transport regulated by: Nuclear pores where they the entry and exit of proteins and RNA as well as large complexes of macromolecules Mitochondria and Chloroplasts Theory of endosymbiosis: Search this shit up Mitochondria and plastids: similar to prokaryotic cells They Have: Membrane Have own DNA Have own Ribosomes Undergo binary fission BUT: Both surrounded by a eukaryotic membrane Ribosomes All cells have ribosomes Structure: Non-membrane-bound: which means that they are not organelles Bead-like structure They are made of ribosomal RNA and proteins They leave the nucleus through the nuclear pores Function: Synthesize primary polypeptide This happens in two locations In the cytosol where there are free ribosomes On the outside of the endoplasmic reticulum or the nuclear envelope Bound Ribosomes: attached to endoplasmic reticulium (ER) Insulin Endomembrane system Internal membrane system Membrane: Any structure that is like a thin sheet Phospholipids bilayers inside (endo) cell No free ends: formed closed compartments Separates: Internal and external environment Separates cells into many compartments Structure: Phospholipid bilayer either: Continuous: One long structure Connected via vesicles: transfer membrane segments Functions: Regulates proteins folding/movement Performs metabolic functions Plasma membrane All cells – encloses cell contents Doesn’t equal cell wall Controls materials in and out: selectively permeable Vesicles from inside fuse with membrane so that material gets out Regulates what and how much passes through the membrane Nuclear Envelope Encloses DNA Instructions for proteins (mRNA) They leave through the nuclear pores ribosomes primary polypeptide Endoplasmic Reticulum (ER) ER continuous with the nuclear envelope Two Regions: Smooth ER: no ribosomes Rough ER: surface has ribosomes (Lumen= internal space): This means that it is the hollow space and the space in between two. Ex. In your esophagus, there is lumen so that food goes down. Functions of Rough ER:  -has bound ribosomes   a. proteins made in ribosomes -travels through translocon (pore) -into ER lumen -proteins are folded and modified -secrete glycoproteins (proteins covalently bonded to carbohydrates) -distributes transport vesicles -is a membrane factory for the cellallows other parts of the cells to get more things with the vesicle. As the vesicle goes away from the RER, the smaller the RER is getting. Functions of Smooth ER: -synthesizes lipids -metabolizes carbohydrates (Polysaccahrides): lots of SER in liver -breaks down glycogen -> regulates blood glucose -detoxifies drugs and poisons -involves adding -OH groups -> more soluble alcohol and other drugs Ex. This will help you drink alcohol and breaks it down or Tynenol -stores calcium ions - Used primarly for signaling, and since they are ions it doesn’t get past the membrane and when it needs to do something the membrane will let the ions go to send signals. - There are no ribosomes hence “smooth” -This is present in liver in vast amounts - It gets good at removing the drugs and alcohol from your blood Golgi Apparatus Structure: Stacks of membranous sacs= Cisternae Not continuous with the ER Cis Face: “receiving” side from the ER Trans Face: “shipping” side Functions: Modifies ER products: “Gets a shipping label on it”: Tells where you are going within the body Sorts and packages Manufactures some macromolecules Shipping using transport vesicles Lysosomes Sacs of hydrolytic enzymes: “Cell stomach:” Primary Lysosome: Buds off Golgi- full of hydrolases When food enters Fuses with lysosome forms Secondary lysosome: breaks down complex molecules Vacuoles Maintenance of compartments Structure: Membrane-bound containers from ER and golgi apparatus Functions: Vary by cell Food vacuoles: Store food Contractile vacuoles: Pump water out Central Vacuoles: (plant cells) holds water 6. Membranes & Transport ??comprehend cell membrane structure ??comprehend the fluid-mosaic model ??compare and contrast the types of membrane transport ??compare and contrast exocytosis and the types of endocytosis I. Membrane Structure A. Membrane Components A phospholipid bilayer forms spontaneously because of the amphipathic structure There being both a hydrophobic and hydrophilic part of the lipid The amphipathic structure means that there is a nonpolar and a polar side. This is why it forms by itself. The phospholipids just assemble by themselves since the part where there is water, the polar side will be facing hat way. And the nonpolar side will be facing the other. Membrane Proteins: The proteins determine many membrane functions They also can move laterally- not flip Membrane Types: Integral Proteins: This protein’s function is helping the structure of the membrane If it is a span membrane: Transmembrane proteins Amphipathic Inside Peripheral Proteins: On the surface of the membrane Polar Hydrophilic Membrane Protein Functions: Transport: They are moving ions The protein takes the shape of the ion that needs to be moved and allows the ion to easily get through Enzymes: Catalyze function and speed up the process Signal Transduction: This protein will change shape to do a different function to tell the cells what to do. Ex. Adrenaline, the signal for adrenaline doesn’t get inside the cell but the protein changes shape to tell the cells or make the cells react to the adrenaline that is going through your body. Carbohydrates: There are two forms Polysaccharides attached to proteins=(Glycoprotein) or lipid(glycolipid) Cell identification Blood types Ex. A, B, O Important for cell-cell recognition B. Fluid Mosaic Model The membrane is a fluid structure filled with a mosaic of various amounts of proteins Membrane component can move laterally within one layer of the membrane Lipid Proteins Carbs Fluidity of Membranes Depends On: Temperature: If it is too cool it will solidify Length of tails: If it is shorter than there will be more fluid Bends in tails (saturation) Unsaturated tails prevent from packing because of the kink they have. On the other hand, the saturated tails will be all packed together because they are straight and a lot will be able to fit. Amount of cholesterol: They act as a “spacer” at warm temperatures it will stabilize the membrane fluidity. But at lower temperatures it will hinder solidification It allows for your membrane to live in various temperatures. The Mosaic: proteins in membrane -> form pattern (tiles in mosaic) some held in place by cytoskeleton other move laterally in fluid pattern constantly changing within layer cannot flip flop between layers *Read Pg 127* Plasma Membrane is selectively permeable Two Basic Types of Transports: Passive: Doesn’t use metabolic E (ATP) and moves with the gradient Ex. Bike Downhill Active: Does use metabolic E (ATP) and moves against the gradient (From low to high concentration) Ex. Bike Uphill II. Membrane Transport Passive Transport All of this Includes: Simple Diffusion Osmosis Facilitated Diffusion (uses Proteins) Net Movement is down the concentration gradient (From higher to lower concentration) NO ATP required- Spontaneous Results in dynamic equilibrium which means there is no net movement, but molecules still move evenly in both directions Diffusion: Tendency for molecules of a substance to fill available space All of these will try to fill up available space: Small Gases: O2, CO2, N2 Small nonpolar molecules-including hydrocarbons Small polar uncharged molecules-including H2O They will go down the concentration gradient and use no energy Osmosis: Diffusion of water across selectively permeable membrane Water diffuses: From lower to higher [solute] Or From higher to lower [H2O] SALT SUCKS Solvent: A substance capable of dissolving other substances Water = the (mostly) universal solvent Solute: A dissolved substance Lemonade powder—dissolves in water Water moves towards higher concentration of solute IT IS ALWAYS ABOUT WATER MOVING Osmosis tonicity: Ability of a solution to cause a cell to gain or lose water Isotonic Solution: (Equal) (iso=same) (Solute) Outside cell =[Solute] inside cell No net H2O movement Cell is normal Hypertonic solution: (Solute) Outside cell >[Solute] inside cell Cell shrivels Hypotonic solution: (Solute) outside cell< [Solute] inside cell Cell bursts Facilitated Diffusion: Aided by Proteins Large molecules or ions (H+, Ca2+, Na+) No energy needed Transports proteins- (Integral proteins) Channel proteins Ex. Ion channel Carrier Protein Substances that use it: Large molecules, polar molecules and Ions Active Transport Works against the gradient Large polar molecules Require ATP Facilitated by proteins (Carrier or pumps) Or Bulk transport of molecules Pump/carrier: integral membrane protein that changes shape Works against gradient Phosphorylation and coupled reaction Sodium- potassium pump Bulk Transport Bulk transport= large number of molecules at once Not carrier mediated Formation of vesicles ACTIVE: Always requires ATP This also doesn’t pass through the plasma-membrane, they don’t physically go through the tails of the membrane it gets through the vesicles and stay into the container and technically are still in the outside but use the vesicles pretty much. It is also for big objects Exocytosis “out” Waste, proteins, and secretory products Vesicle fuses with the plasma membrane Releases contents from the cell Vesicles fuses with PM Primary mechanism for growing plasma membrane It grows because of how it is increasing the surface area of the cell Endocytosis “Inside” Material taken into the cell by forming vesicles derived from the plasma membrane There are three types to do this: Phagocytosis Pinocytosis Receptor-mediated endocytosis- specific: process including a reason for having it Phagocytosis: “cellular eating” Cell engulfs large particles It is non-specific Pinocytosis: “cellular drinking” Ingestion of fluid and dissolving material It is non-specific (going to take any type) The water gets inside due to osmosis Receptor-mediated =specific Receptor proteins in plasma membranes bind specific macromolecules outside cell Form coated pits Fold inward to form vesicles Main mechanism for uptake of macromolecules 7. Metabolism Ch. 8.1 through 8.4 ??compare and contrast catabolic and anabolic reactions ??recognize and recreate how ATP drives chemical work ??recognize and recreate an enzymatic reaction ??hypothesize/diagnose the impact of variability on enzymatic reactions ??compare and contrast oxidation and reduction ??recognize and recreate NAD+ function in redox reactions I. Metabolism and Energy Change Metabolism: Sum of all chemical reactions in an organism; regulated to maintain homeostasis A. Metabolism Basics Each step is catalyzed by a specific enzyme Metabolic Pathways begin with a specific molecule and ends with a product You use a lot of enzymes to break down molecules and they will get you many products. Without an enzyme you will die before you break anything down. This is very crucial for life. Catabolic Pathways (Cutting Down) Breaking down complex molecules Release energy: EX. Cellular respiration Breakdown of glucose Anabolic Pathways Builds complex molecules This requires energy (Need to use a lot of ATP to allow for this to happen) - Ex. Synthesis of protein from amino acids B. Free-energy change in chemical reactions Energy: capacity to cause change or do work Ex. Sunlight gives energyPlants grow cows eat grassCow makes milk humans drink milk for energy so that we can run Energy conversion is never 100% efficient Ex. Cells are 40% efficient, rest is heat Kinetic Energy: Energy of motion Potential Energy: Stored Energyhas not been used. Ex. Someone on a diving board is going to have a lot of PE, But when this person is going to actually dive than its going to have a lot of KE. Thermodynamics: study of energy transformation First Law of Thermodynamics: Energy can’t be created or destroyed (It can only be converted). The only thing energy can do is change its form. Ex. PE KE Second Law of Thermodynamics: Every energy transfer or transformation entropy Entropy (S): A measure of disorder Ex. As a bear uses energy to move, some of that energy is lost to the surrounding environment. Food: Organized energystored chemical bonds and low entropy Heat: Disorganized EnergyHigh entropy; disperses into the environment A summary: Light energy enters an ecosystem and heat energy exits Energy conversion is never 100 % efficient Total Energy in the universe is constant Total energy available to do work, decreases over time Gibbs Free Energy (G): The energy in a molecule available to do work You can’t measure G But we can see how G changes during a reaction: Change in energy If change in G is less than 0: Energy is being released from reaction If the change in G is greater than 0: Energy is added to cause a reaction, non-spontaneous If the change in G is 0 than the chemical processes at equilibrium Exergonic: “Energy Outward” The change in G is negative Energy is released spontaneous Ex. Catabolic Reactions: Large molecules being broken down to smaller ones Endergonic: “Energy Inward” The change in G is positive Energy stored Requires Energy Input Ex. Anabolic Reactions: Simpler substances combined to form complex ones ATP Cells use ATP to carry energy ATP: adenosine triphosphate “spring-loaded” and in high in energy It breaks the bond easier because they are already repelling each other Three phosphate groups Coupled Reactions: Mediated by ATP Pair: Exergonic reaction (provides E) with Endergonic reaction (Requires E) How does ATP work? ATP drives endergonic reactions by phosphorylation (passing a phosphate group) ATP hydrolysis drives (is coupled with) Endergonic reactions II. Enzymes A. Characteristics and Functions Enzymes: speed up reactions by lowering the energy barrier Enzyme act on specific substrate Active site: cleft or groove for substrate binding Substrate: reactant that an enzyme acts upon Change of shape: facilitates breaking bonds B. Factors effecting enzyme activity Temperatures and pH Enzyme has optimal T Ex. Human optimal T(35-40C) Denaturation: High T: Even short exposure Enzyme Helpers Cofactors Inorganic: Often metals Ex. Iron or zinc Organic Coenzyme: Are vitamins Ex. NAD+ , FAD+ Reversible or irreversible inhibition Inhibitors: Competitive: Bind to the active site and compete with substrate Ex. Penicillin Noncompetitive: They bind elsewhere (NOT THE ACTIVE SITE). This will change shape of the active site. Taking this will kill you since It is irreversible Ex. Cyanide III. Redox Reactions Characteristics of oxidation and reduction Redox reactions: Transfer of electrons between reactants Oxidation-reduction synthesis: Oxidation: Loss of electrons means it is oxidized Can lose more than one Ex. Na + CLNa+ + Cl- - The sodium loses the electron while the chlorine is gaining an electron - This reaction is between from a metal and a nonmetal which is an ionic compound OILRIG: Oxidation Is Losing, Reduction Is Gaining Reducing Agent: The electron donor, Loses an Hydrogen It is oxidized in a redox reaction Ex. NADH NAD+ + H + e- (NADH is oxidized) Oxidizing Agent: Electron acceptor, Gains a Hydrogen - Reduced in a redox reaction, electrons carriers Ex. NAD+ + H + e- NADH (NAD+ is reduced) NADH represents stored energy that will be used to make ATP Dehydrogenases: Remove 2 of the hydrogen atoms (2 electrons and 2 protons) - This is Oxidation AND Reduces: Delivers 2 electrons and one positive hydrogen ion Ex. NAD+ NADH Photosynthesis Ch. 10.1 through 10.3 ? comprehend the interactions between light and electrons ? compare and contrast the components of chloroplasts ? recognize and recreate photosynthesis ? hypothesize/diagnose the impact of variability on photosynthesis ? recognize and recreate the Calvin cycle ? compare and contrast cellular respiration and photosynthesis I. Introduction to Photosynthesis A. Ecological Importance Photosynthesis: converts solar energy into chemical energy - living organisms made of carbon-based molecules: source of C is CO2 - animal cells can’t incorporate CO2 from air - photosynthetic organisms can’t fix CO2 from air Photoautotrophs: Fix inorganic carbons Ex. CO2 They are producers (Ex. Can produce sugar) Heterotrophs: Obtain their carbon material from organic sources (Other Organisms). They are consumers (Ex. Humans; Us) Redox: H2O is oxidized and Carbon dioxide reduced Endergonic process Energy boost from light energy Change in energy is positive Energy + 6CO2 + 6H2O C6H12O6 + 6O2 The water will be oxidized The carbon dioxide will be reduced Photosynthesis occurs in: -plants -multicellular algae -cyanobacteria (prokaryotes) -unicellular eukaryotes -purple sulfur bacteria (prokaryotes) Nature of Light Light: Form of electromagnetic energy All radiation travels in waves Photons: Small particle of light energy Little tiny strikes of energy Energy in photon: Shorter wavelength: More energy/photon Longer wavelength: Less energy/photon Effects of Photon on Electrons Molecules absorbs a photon of light energy The electron becomes energized/excited This will make the electron shift to a higher energy It also can return to the resting state that the electrons were at before(Heat is Produced) It can also leave the atom and be captured by an electron acceptor the acceptor(molecule) is reduced II. Structures in Photosynthesis Plant Organization Plants absorb visible light: Leaves are green because of the chlorophyll reflects and transmits green light Green is a useless color: The reason is because of how most biological organisms can’t use the color. That is why there is so much green color is nature. Chloroplasts: Photosynthesis organelle Structure of Chloroplasts Two membranes in a chloroplast Inner membrane: Called thylakoid Inner “cytosol”: Called stroma (Fluid filled space containing enzymes) Photosynthesis Pigments Pigment: a substance that absorbs visible light Capture light energy for photosynthesis Embedded in thylakoid membrane Chlorophyll is a Pigment: A substance that absorbs visible light Chlorophyll a: Main one (Should recognize the basic structure) Porphyrin Ring: Light-absorbing; “Head” of the molecule Hydrocarbon Tail: Interacts with hydrophobic regions of proteins inside thylakoid membranes of chloroplasts III. The Process of Photosynthesis Overview of Photosynthesis A multistep process: 6CO2 + 12H2O + Light Energy -> C6H12O6 + 6O2 + 6H2O Reverse of cellular respiration REDOX reactions: Water oxidized and Carbon reduced This is endergonic: Energy input from sunlight Two Stages of PS: Light reactions- Convert solar energy to chemical energy(ATP and NADPH) Calvin Cycle- Synthesis to create O2 and sugar Light Dependent Reactions The light reactions (in the thylakoid): Uses light energy Split water and release Oxygen Reduce NADP+ to NADPH Generate ATP from ADP How? On thylakoid membrane Two photosystems (PSII and PSI) Trap sun energy Convert it to NADPH and ATP Most reactions use a linear electron flow Photosystem parts: 2 light-harvesting complexes: Capture light And produce ATP and NADPH They transfer energy of photons to the reactions using electrons They have a pair of chlorophyll that would transfer the electron to a 1st degree electron acceptor 2 Types of Reactions in the PS: Linear Electron Flow: Light-dependent Use both PSII and PSI Produces ATP and NADPH and OXYGEN MORE RECENT: Cause of Oxygen revolution Cyclic Electron Flow: Produces only ATP Uses only PSI Older: Predates O2 revolution Linear Electron Flow Both photosystems involved, Same three things happen in each: Boost electron Use energy in electron Replace Electron Some steps involve redox reactions Boost PSII electron The photon hits pigment in PSII and excites the pigmentenergy is transferred from one pigment to the next Energy then will finally be passed to the P680 P680: the pair of chlorophyll a molecules in the reaction center of PSII Electrons transferred to one degree electron acceptor(Redox reaction) Causes P680 to be oxidized to P680+ (Loss the electron) Use Energy in Electron (in this case to make ATP) Electron from 1degree electron acceptor goes through electron transport chain Generates H+ gradient inside Thylakoid space H+ diffuses through ATP synthase (facilitated diffusion) ATP synthesis Replace PSII Electron (From Water) P680+ is an extremely strong oxidizing agent H2O is oxidized (Photolysis) Electron transferred to p680+ P860+ reduced back to P680because it wants to fill the “hole” of missing the electron Oxygen released as byproduct This is where atmospheric Oxygen comes from Boost PSI electron Light energy excites electron in pigments and repeats what happens in PSII Instead there is P700 in which turns into P700+ when the electron is accepted by the electron acceptor in the reaction center of PSI Use Energy in Electron (This time to make NADPH) Electrons move through PSI ETC to ferredoxin (Fd) Electrons transferred to NADP+ NADPH synthesized (Catalyzed by NADP+ reductase) Replace PSI Electrons (With PSII electrons) After PSII electron travels down ETC, energy has been used Now low energy electron donated to PSI replaces lost electron In Chloroplasts: ATP and NADPH produced on stroma side of membrane Carbon Fixation Reactions Light Independent Reactions Carbon enters cycle as carbon dioxide and leaves as a sugar: (G3P) For 1 G3P 3 Calvin cycles needed fixing 3 carbon dioxide Calvin Cycle: Each cycle has Three Phases: Carbon Fixation (Catalyzed by rubisco) Reduction Regeneration of the CO2 acceptor (RuBP) Phase 1 Carbon Fixation: Three carbon enter cycle as carbon dioxide and binds to RuBP CO2+ RuBP: Catalyzed by RuBisCo Forms a 6-carbon molecule but it is so unstable because it has so much energy This will immediately split into 2 3-carbon PGAs (phosphoglycerates) Phase 2 Reduction: The 6-3 carbon PGA is converted using 6 ATP Becomes a bi-phosphoglycerate Then 6 NADPHG3P One G3P leaves cycle to become a sugar (The other 5 G3P stay in the cycle) Phase 3: Regeneration: 5-3 Carbon G3P is converted to 3-5 carbon RuBP by using 3 ATP 9. Respiration Ch. 9.1 through 9.4 ? recognize and recreate the flow of energy through the environment ? recognize and recreate cellular respiration ? compare and contrast the stages of cellular respiration ? hypothesize/diagnose the impact of variability on cellular respiration I. Introduction to Cell Respiration A. Overview of Eukaryotic Respiration NAD+ + H= NADH NADH: This is the energy stored that will be used to make ATP Where is the energy stored in ATP? It is in the spring-loaded bond But how does it get there? II. The Stages of Cellular Respiration There are 4 stages: Glycolysis Oxidation of Pyruvate acetyl Co The Citric Acid Cycle Oxidation Phosphorylation *Know this about each step: Why is this stage occurring? Where in cell/mitochondria does it occur? What enters stage, what is produced How many CO2, ATP, NADH, FADH2 Account for the electrons at each stage A. Glycolysis - This is going to occur in the cytosol of the cell The function: Convert 1 Glucose to create 2 pyruvates This will then yield 2 net ATP There are two stages: Investment and Payoff Glucose enter the cell: (mammals) via facilitated diffusion by GLUT1 This is anerobic which means it doesn’t need any oxygen There is 0 CO2, ATP, NADH, FADH Stage 1: Energy Investment Phase: In this phase of Glycolysis, there needs to be an investment of 2 ATP (Endergonic). (change in G is positive, Not Spontaneous) One glucose is converted to 2 G3P because of the 2 ATP molecules There is now a loss of 2 ATP Stage 2: Energy Payoff Phase: This is an exergonic process The change in G is negative meaning that it is spontaneous The 2 G3P is converted to 2 pyruvate, 2 NADPH and 4 ATP Now there are 2 ATP, and 2 NADPH B. Oxidation of Pyruvate to Acetyl CoA This occurs in the Mitochondria And the purpose of this process is to convert the Pyruvate into Acetyl CoA Outer mitochondrial membrane: diffusion through small portion Inner mitochondrial membrane: carrier protein THERE IS NO ATP USED So each pyruvate is converted to Acetyl coenzyme A by oxidizing it (Taking an O2 and binding it) The oxidation creates a carbon dioxide molecule per pyruvate in which yields 2 molecules The 2 acetyl CoA are catalyzed by pyruvate dehydrogenase Removes a H+ and builds a NADH Now there is 2 CO2, 2 ATP, 4 NADH C. The Citric Acid Cycle (CAC) This is located in the inside the cytosol of the mitochondria: This is called the Mitochondrial Matrix Why?: Break down Acetyl CoA as efficiently as possible The main goal is to build the electron acceptor to give to the ETC(Electron Transport Chain) 1 Glucose means that it has two turns: (1 turn per acetyl CoA) The Process: Oxaloacetate (4C) waits in matrix of the Mitochondria for the Acetyl CoA(2C) Enzyme joins Oxaloacetate and 2 carbons which is the: Acetyl group then it will create Citrate Cycle tears apart Citrate Transfers electron(Hydrogen) in sugar to electron acceptors NAD+ and FAD Then it will become NADH(3x) and FADH2(1x) Glucose is then completely oxidized and creates CO2(2x) This also creates 1 ATP per 2x of CO2 Now there is 6 CO2, 4 ATP, 10 NADH, 2 FADH2 Oxidative Phosphorylation Where?: Proteins imbedded in the inner mitochondrial membrane Cristae Why?: TO MAKE A LOT OF ATP Convert energy in NADH and FADH2 to ATP The Respiration road so far… Carbon have all been lost as CP2 Only 4 ATP produced (2 in glycolysis and 2 in CAC) Energy from glucose molecule is now: In excited electron in NADH and FADH2(now electron carriers) We want more ATP Electron transport chain Chemiosmosis Oxidative Phosphorylation= ETC + Chemiosmosis Goal: Take excited electrons from carriers and use it to build lots of ATP How? First break up NADH and FADH2 Pull electron off (Oxygen will help) Then electron energy to pull H+ off carriers and dam it up This is set up to power ATP synthesis First use ETC to move electron up to down excitement (The proteins that are made up in ETC are I,II,III,IV) Electron pulled by Oxygen Proteins are each electron carriers I,II,III,IV I and II hydrolyze electron carriers I, III, IV pump H+ into membrane space IV: passes electron to oxygen Electron transfers ETC causes proteins to pump H+ to the intermembrane space Create H+ gradient ETC MAKES NO ATP Chemiosmosis: Uses H+ gradient to drive cellular work ATP Synthase: Molecular Mill: Inner membrane enzyme ETC: set up a Hydrogen ion gradient: The ion diffuses back to matrix through ATP synthesis It rotates and… Phosphorylates: ADP =Pi ATP There is about 28 ATP per glucose So there is addition of 28 ATP now What happens if there is no oxygen?