Chapter Nine: Cellular Respiration: Harvesting Chemical Energy

Q1: where does cellular respiration take place?

A1: in mitochrondia, prokaryotic cell in cytoplasm.
Q2: why is cellular respiration important?
A2: Living cells require transfusions of energy from outside sources to perfirm their many tasks. and cellular respiration is the process that living things can change sources to energy.
Q3: what's the defference between fermentation and anaerobic?
A3: fermentation only get through glycolysis, only produce a few ATP. anaerobic respiration takes place in centain prokaryotic organisms do not use oxygen as a final electron accepetor.



Five Facts:
1. glycolysis harvests chemical energy by oxidizing glucose to pyruvate
2. the citric acid cycle completes the energy yielding oxidating of organic molecules
3. during oxidative phosphorylation. chemiosmosis couples electron transport to ATP synthesis
4. fermentation and anaerobic respiration enable cells to produce ATP without the use of oxygen
5. catabolic pathways yield energy by oxidizing organic fuels



Figure:





























Substrate-level phosphorylation is a type of chemical reaction that results in the formation and creation of adenosine triphosphate (ATP) by the direct transfer and donation of a phosphoryl (PO3) group to adenosine diphosphate (ADP) from a reactive intermediate. While technically the transfer is PO3, or a phosphoryl group, convention in biological sciences is to refer to this as the transfer of a phosphate group. In cells, it occurs primarily and firstly in the cytoplasm (in glycolysis) under both aerobic and anaerobic conditions.

Summary:
Oxidation-reduxtion reaction, or redox reaction is the electron transfers. Redox reaction loss elelctrons from one substance called oxidation, and addition of electrons to another substance reduction. NAD+ is electron carrier coenzyme. Electron transport chain breakdown electrons in many steps in order to control the release of energy. C6H12O6 (aq) + 6 O2 (g) → 6 CO2 (g) + 6 H2O (l) is the whole process of cellualr respiration which require oxygen. Anaerobic respiration and fermentation don't need oxygen. fermentation only get through glycolysis, only produce a few ATP. anaerobic respiration takes place in centain prokaryotic organisms do not use oxygen as a final electron accepetor.Cellular respiration can be diveded into three processes:glycolysis, citric acid cycle, and oxidative phosphorylation.
Glycolysis breakdown glucose into two three-carbon pyruvates. It occures in cytosol. Its reactants are glucose, 2ATP, NAD+; products are 2pyruvate, 2H2O, 4ATP, and 2NADH. It has energy investment and energy payoff. By the end of energy investment, glucose breakdown to Glyceraldehyde-3-phosphate. Citric acid cycle complete breakdown and take place in mitochrondia matrix. It needs pyruvate, coe A, 4NAD+, 1ATP, and 1FAD and produces 3CO2, 1ATP, 4NADH, and 1FADH2. Oxidative phosphorylation is in mitochrondia cristae. It requires NADH, FADH2, ATP, and oxygen, and produces NAD+, FAD, ATP, and water. It has electron transport chain and chemiosmosis. Hydrogen ions from NADH and FADH2 go out then flow back by ATP synthase. The whole energy sequence is: glucose-NADH-electorn transport chain-proton motive force-ATP.

Key Term:

1. acetyl CoA-Acetyl coenzyme A; the entry compound for the citric acid cycle in cellular respiration, formed from a fragment of pyruvate attached to a coenzyme.
2. alcohol fermentation-Glycolysis followed by the conversion of pyruvate to carbon dioxide and ethyl alcohol.
3. chemiosmosis-An energy-coupling mechanism that uses energy stored in the form of a hydrogen ion gradient across a membrane to drive cellular work, such as the synthesis of ATP. Most ATP synthesis in cells occurs by chemiosmosis.
4. facultative anaerobe- An organism that makes ATP by aerobic respiration if oxygen is present but that switches to anaerobic respiration or fermentation if oxygen is not present.
5. obligate anaerobe-An organism that only carries out fermentation or anaerobic respiration. Such organisms cannot use oxygen and in fact may be poisoned by it.
6. oxidizing agent-The electron acceptor in a redox reaction.
7. ATP synthase-A complex of several membrane proteins that provide a port through which protons diffuse. This complex functions in chemiosmosis with adjacent electron transport chains, using the energy of a hydrogen ion (proton) concentration gradient to make ATP. ATP synthases are found in the inner mitochondrial membrane of eukaryotic cells and in the plasma membrane of prokaryotes.
8. lactic acid fermentation-Glycolysis followed by the conversion of pyruvate to lactate, with no release of carbon dioxide.
9. substrate-level phosphorylation-The formation of ATP by an enzyme directly transferring a phosphate group to ADP from an intermediate substrate in catabolism.
10. cytochrome-An iron-containing protein that is a component of electron transport chains in the mitochondria and chloroplasts of eukaryotic cells and the plasma membranes of prokaryotic cells.

Video:

http://www.youtube.com/watch?v=_hGW6NjCUSs

Chapter eight: introduction of metabolism

Q1: what is metabolism?

A1: The totality of an organism’s chemical processes.

Q2: how does metabolism work in living things?

A2: catabolic and anabolic pathway that release or gain energy.

Q3: what is energy?

A3: the ability of work

Five Facts:

1. an organism's metabolism transforms matter and energy, subject to the laws of thermodynamics.

2. the free-energy change of a reaction tells us whether or not the reaction occurs spontaneously

3. ATP powers cellular work by coupling exergonic reactions to endergonic reactions

4. enzymes speed up metabolic reactions by lowering energy barries

5. regulation of enzyme activity helps control metabolism

Figure

if the reaction goes from higher free energy to lower free energy, there will be a negative ΔG, and the reaction will be spontaneous. However, if the reactants have a lower ΔG than the products, there will be an increase in free energy, and the reaction is nonspontaneous. In this situation, some form of energy (in the form of heat, light, etc.) will be required for the reaction to take place. It should be noted that a spontaneous reaction will not necessarily occur on its own. This is because an initial activation energy is needed in order to start the reaction and thus even a spontaneous reaction may need some form of energy input. A good example of this is the very exergonic combustion of octane, which still needs a flame in order to initiate.

Summary:

Metabolism is the totality of an organism’s chemical processes, concerned with managing the material and energy resources of the cell.A metabolic pathway begins with a specific molecule, which is then altered in a series of defined step, resulting ina centain product. Catabolic pathway is breakdown pathway. Anabolic pathways consume energy to build complicated molecules from ones. Also called biosynthetic pathway. energy released from the downhill reactions of catabolic pathways can be stored and then used to drive the uphill reactions of anabolic pathways.

Kinetic energy is energy of motion. Potential energy is stored enegy or th ecapacity to work. Activation energy needed to convert potential energy into kinetic energy. The study of the energy transformation that occur in a collection of matter is called thermodynamics: 1)Energy can be transferred and transformed, but it cannot be created or destroyed.2)Each energy transfer or transformation increases the entropy of the universe.Entropy is the measure of disorder. Free energy is the portion of a system's energy that can perform work when temperature and pressure are uniform throughout the system. If the system has more free energy, it is less stable, it has greater work capacity. Exergonic reaction is chemical reactions with a net release of free energy. Endergonic: chemical reactions that absorb free energy from the surroundings. Living cell is not in equilibrium. ATP contains sugar ribose, adenine, and three phosphate groups. Atp can be broken by hudrolysis. Energy released from ATP drives anabolic reactions.Energy from catabolic reactions “recharges” ATP. enzymes cause rate of a chemical reaction to increase and lower the activation energy for a chemical reaction to take place. environment, cofactors, coenzymes, and inhibitor are some factors can effect enzyme.

Key Terms:

1. active site-The specific portion of an enzyme that binds the substrate by means of multiple weak interactions and that forms the pocket in which catalysis occurs.
2. allosteric regulation-The binding of a regulatory molecule to a protein at one site that affects the function of the protein at a different site.
3. catalyst-A chemical agent that increases the rate of a reaction without being consumed by the reaction.
4. coenzyme-An organic molecule serving as a cofactor. Most vitamins function as coenzymes in metabolic reactions.
5. cofactor-Any nonprotein molecule or ion that is required for the proper functioning of an enzyme. Cofactors can be permanently bound to the active site or may bind loosely with the substrate during catalysis.
6. competitive inhibitor-A substance that reduces the activity of an enzyme by entering the active site in place of the substrate whose structure it mimics.
7. feedback inhibition-A method of metabolic control in which the end product of a metabolic pathway acts as an inhibitor of an enzyme within that pathway.
8. induced fit-Induced by entry of the substrate, the change in shape of the active site of an enzyme so that it binds more snugly to the substrate
9. noncompetitive inhibitor-A substance that reduces the activity of an enzyme by binding to a location remote from the active site, changing the enzyme’s shape so that the active site no longer functions effectively
10. bioenergetics-(1) The overall flow and transformation of energy in an organism. (2) The study of how energy flows through organisms.

Video:

http://www.youtube.com/watch?v=V4OPO6JQLOE

enzyme

Chapter seven: membrane structure and function

Q1:what is plasma membrane's structure?
A1: phospholipid bilayer and protein.
Q2: what's plasma membrane's function?
Q2: controls traffic into and out of the cell it surrounds.
Q3: why does plasma membrane have that structure?
A3: cell membrane is a boundary the separates cell from its surrounding. it has hydrophobic layer outside so that it won't be dissolved in its surrounding. the mosaic protein help substances transport.

Five Facts:
1. cellular membrane are fluid mosaics of lipids and proteins
2. membrane structure results in selective permeability
3. passive transport is diffusion of a substance across a membrane with no energy investment
4. active transport uses energy to move solutes against their gradients
5. bulk transport across the plasma membrane occurs by exocytosis and endocytosis

Figure

mosaic proteins in phospholipids help select substances tranport. it has integral protein and peripheral protein. Because phospholipids are hydrophilic inside and hydrophobic outside, the hydrophobic part of protein is inside the lipids.

Summary:
The plasma mambrane is the edge of life, the boundary that separates the living cell from its surrounding. It exhibits selective permeability which allows some substances to cross it more easily than others. Lipids and protein are the staple ingredients of membrane. The phospholipids are amphipathic which has both hydrophobic and hydrophilic parts. In fluis mosaic model, the membraen is a fluid structure with mosaic proteins in bilayer. Membranes are not static, it can move laterally, flip-flop. Low temperature can cause unsaturates hydrocarbon tails. Cholesterol will also add to the membrane. Integral protein penetrate the hydrophobic core of th elipid bilayer. Peripheral proteins are appendages loosely bound to the surface of the membrane. Membrane carbohydrates are glycolipids or glycoproteins.
Cell membrane are permeable to apecific ions and a variety of polar molecules. Hydrophlic substances can avoid contact with the lipid bilayer by passing through transport proteins. The selective permeability of a membrane depends on both the discriminating barrier of the lipid bilayer and the specific transport proteins. Passive transport is the movement across membranes that does NOT require cellular energy.Diffusion is the net movement of atoms, ions or molecules down a concentration gradient. Osmosis is the diffusion of water.Tonicity is the concentration of water relative to a cell.Osmoregulation is the control of water balance.Facilitated diffusion has transport protein that helps materials through the cell. Active transport is movement across membranes that DOES require cellular energy. Electrogenic pump is a transport protein that generates voltages across a membrane.Sodium-potassium pump is themajor electrogenic pump of animals.Proton pump is the main electrogenic pump of plants, fungi, and bacteria.Exocytosis is the movement of bulk material out of cells.
Endocytosis is the movement of bulk materials into cells.

Key Term:

1. aquaporin-A channel protein in the plasma membrane of a plant, animal, or microorganism cell that specifically facilitates osmosis, the diffusion of water across the membrane.


2. concentration gradient-A region along which the density of a chemical substance increases or decreases


3. electrogenic pump-An ion transport protein that generates voltage across a membrane.


4. hypertonic-Referring to a solution that, when surrounding a cell, will cause the cell to lose water.


5. hypotonic-Referring to a solution that, when surrounding a cell, will cause the cell to take up water.


6. isotonic- Referring to a solution that, when surrounding a cell, has no effect on the passage of water into or out of the cell.


7. receptor-mediated endocytosis-The movement of specific molecules into a cell by the inward budding of membranous vesicles containing proteins with receptor sites specific to the molecules being taken in; enables a cell to acquire bulk quantities of specific substances.


8. tonicity-The ability of a solution surrounding a cell to cause that cell to gain or lose water.


9. turgid-Swollen or distended, as in plant cells. (A walled cell becomes turgid if it has a greater solute concentration than its surroundings, resulting in entry of water.)


10. ligand-A molecule that binds specifically to another molecule, usually a larger one.

Video:

http://www.youtube.com/watch?v=s0p1ztrbXPY

Chapter six: A tour of the cell

Q1: What's cell's component?
A1: prokaryotic: capsule, cell wall, plasma membrane, cytoplasm, DNA, ribosomes
eukaryotic: cell wall, membrane, cytoplasm, DNA, ribosome, cytoskeleton, nucleus, ER, golgi apparatus, lysosome, vacuoles and vesicles, peroxisome, mitochodria, chloroplast
Q2: what's cell's function?
A2: passing genetic information, regulation, metabolism, etc, cells are basic units of all living things.
Q3: how do people study the tiny cell?
A3: by improving and using microscope.

Five Facts:
1. to study cells, biologists use microscopes and the tools of biochemistry.
2. eukaryotic cells have internal membrane that compartmentalize
3. the endomembrane system regulates protein traffic and perfroms metabolic functions in the cell
4. the cytoskeleton is a network of fibers that organizes structures and activities in the cell
5. extracellular components and connections between cells help coordinate cellular activies.

Figure

chloroplast has bilayer, outer membrane and inner membrane. Between these two is the intermembrane space. The inner membrane is convoluted so that it has more surface. The folding of inner membrane is called cristae. Mitochondrial matrix is enclosed by the inner membrane. Free ribosomes are in the mitochondrial matrix.

Summary:
Scientists use light microscope to study most cells and bacterias and electron microscope to study bacteria, viruses, macromolecules, and atoms.Cytology is the study of cell structure. Both prokaryotic and eukaryotic have plasma membrane, cytosol, chromosomes, ribosome, ad cytoplasm. Prokaryotic cell has nucleoid instead of nucleus.
The nucleus contains most of the genes in the eukaryotic cell. Nuclear envelope encloses the nucleus, separating its contents form the cytoplasm. It is a double membrane, inner membrane supported by a protein matrix which gives the shape to the nucleus. Nucleolus storage ribosomes. chromatin form chromosomes, a complex of protein and DNA. Free ribosome in cytosol; bound ribosome in ER. Endoplasmic reticulum fold sheet or tubes of membranes. Smooth ER lacks ribosome and uses for lipid synthesis, carbohydrate storage, and detoxification of poisons. Rough ER has ribosomes, adn makes secretory proteins. Golgi apparatus package products of ER for transport. It has vesicles. Lysosome is digestive compartments. It can so phagocytosis and antophagy. Vacuoles has single membrane in plant's cell. Mitochondria are the sites if cellular respiration, the metablic process that generates ATP by extracting energy from sugarsm fats, and other fuels with help of oxygen; Chloroplasts found in plants and algae, are the sites of photosynthesis. Peroxisome use hydrogen peroxide.Cytoskeleton help cell strucure, shape, movement, and division. Three types: microtubules, microfilaments, and intermediate filaments. Cell wall supports and protects cell. it has primary and secondary walls. middle lamella connect cells. Extracellular matrix helps cells together. Intercellular junction in plant is plasmodesmata. in animals are tight junction, desmosome, and gap junction.

Key term:

1. cell fractionation-The disruption of a cell and separation of its parts by centrifugation.


2. scanning electron microscope (SEM)-A microscope that uses an electron beam to scan the surface of a sample to study details of its topography.


3. transmission electron microscope (TEM)-A microscope that passes an electron beam through very thin sections and is primarily used to study the internal ultrastructure of cells.


4. thylakoid-A flattened membranous sac inside a chloroplast. Thylakoids exist in an interconnected system in the chloroplast and contain the molecular “machinery” used to convert light energy to chemical energy.


5. stroma-Within the chloroplast, the dense fluid of the chloroplast surrounding the thylakoid membrane; involved in the synthesis of organic molecules from carbon dioxide and water.


6. phagocytosis-A type of endocytosis in which large particulate substances are taken up by a cell. It is carried out by some protists and by certain immune cells of animals (in mammals, mainly macrophages, neutrophils, and dendritic cells).


7. integrin-in animal cells, a transmembrane receptor protein that interconnects the extracellular matrix and the cytoskeleton.


8. dynein-In cilia and flagella, a large contractile protein extending from one microtubule doublet to the adjacent doublet. ATP hydrolysis drives changes in dynein shape that lead to bending of cilia and flagella.


9. collagen-A glycoprotein in the extracellular matrix of animal cells that forms strong fibers, found extensively in connective tissue and bone; the most abundant protein in the animal kingdom.


10. basal body-A eukaryotic cell structure consisting of a 9 + 0 arrangement of microtubule triplets. The basal body may organize the microtubule assembly of a cilium or flagellum and is structurally very similar to a centriole.

Video:

http://www.youtube.com/watch?v=GW0lqf4Fqpg&feature=related

cell membrane

Unit One: professor's response

Re: question about gene‏
From:
Angela DePace (Angela_DePace@hms.harvard.edu)
Sent:
Mon 10/05/09 6:35 AM
To:
vivian zhang (princesszhang@live.com)
Dear Vivian
Glad to hear that biology has sparked your interest! How gene evolution contributes to organism diversity is a big question, still unanswered in many ways. There is a wonderful book that could help you begin to understand the issues involved - it's called "Endless Forms Most Beautiful" by Sean Carroll. Here's a link to it on Amazon.
http://www.amazon.com/gp/product/0393327795/ref=pd_luc_sim_01_02
Best of luck with your studies!
Angela
................................................................
Angela DePace
Dept. of Systems Biology
Harvard Medical School
200 Longwood Avenue WA452A
Boston, MA 02115
(617) 432-7410
Angela_DePace@hms.harvard.edu
http://depace.med.harvard.edu
On Oct 4, 2009, at 9:13 PM, vivian zhang wrote:
Dear professor DePace, I am a high school student from Utah, and I just learnt about the feritable information from AP biology. I have a question that I really want know how gene evolution contribute to organism diversity. I will be very appreciate if you have time to answer my question.
From,Vivian Zhang

Chapter Five: the structure and funcion of large biological molecules

Q1: what are the large biological molecules?
A1: carbohydrates, lipids, proteins, and nucleic acids.
Q2: why are they defined as large biological molecules?
A2: they are macromolecules which are built from monomers.
Q3: how are the large molecules formed?
A3: monomers form by dehydration.



Five Facts:

1. macromolecules are polymers, built from monomers
2. carbohydrates serve as fuel and building material
3. lipids are a diverse group of hydrophobic molecules
4. proteins have many structures, resulting in a wide range of functions
5. nucleic acids store and transmit hereditary information



Figure

Phospholipids can be bilayer of cells. It is compounded by fatty acids, phosohate, glycerol, and choline. Fatty acids which are carbon and hydrogen bond together are hydrophobic, and the head is hydropilic. When the phospholipids form the bilayer, the heads are in contact with water , and the hydrophobic tails are in contact with each other and remote from water.

Summary:
Carbohydrates, lipids, proteins, and nucleic acids are macromolecules, which are polymers built from monomers. Dehydration reaction, which means lost water molecules, help bond monomers together. Hydrolysis is the opposite. Monosaccharides are the monomers of carbohydrates. Disaccharide consists two monosaccharides. Polysaccharides consist alot. Fats, phospholipids, and steroids are types of lipids. Fatty acid and glycerol make fat. Oil is unsaturated fat. Phospholipids have hydropilic head and hydrophobic tail.
Protein consists one or more polypeptides which are polymers of amino acids. Amino acids have carboxyl, amino group, alpha carbon, and R group. Primary structure is sequence of amino acids. Secondary structure is the coils and folds. Tertiary structure is the overall shape of a polypeptide resulting from interactions between the side chains of the various amino acids. Quaternary structure is the result from aggregation of these polypeptide subunits.Because of pH, salt concentration, temperature, etc, the protein may lose its shape, which is called denaturation. Nicleic acids are DNA and RNA. They are polymers of nucleotide, which conclude sugar, phosphate group, and nitrogeous base. Both DNA and RNA are important meterial of gene.

Key Terms:

1. cellulose-A structural polysaccharide of plant cell walls, consisting of glucose monomers joined by β glycosidic linkages.


2. chitin-A structural polysaccharide, consisting of amino sugar monomers, found in many fungal cell walls and in the exoskeletons of all arthropods.


3. starch-A storage polysaccharide in plants, consisting entirely of glucose monomers joined by a glycosidic linkages.


4. triacylglycerol-Three fatty acids linked to one glycerol molecule; also called a fat or a triglyceride


5. steroid-a type of lipid characterized by a carbon skeleton consisting of four rings with various chemical groups attached.


6. catalyst-A chemical agent that increases the rate of a reaction without being consumed by the reaction.


7. disulfide bridge-A strong covalent bond formed when the sulfur of one cysteine monomer bonds to the sulfur of another cysteine monomer.


8. peptide bond-The covalent bond between the carboxyl group on one amino acid and the amino group on another, formed by a dehydration reaction


9. alpha (α) helix-A spiral shape constituting one form of the secondary structure of proteins, arising from a specific pattern of hydrogen bonding.


10. beta (β) pleated sheet-One form of the secondary structure of proteins in which the polypeptide chain folds back and forth. Two regions of the chain lie parallel to each other and are held together by hydrogen bonds.

Video:

http://www.youtube.com/watch?v=ha-DNTOooXk