Chapter. 9 cellular respiration - harvesting chemical energy

Q. what is the basic formula for the cell respiration?



C6H12O6 + 6O2 -> 6CO2 +6H2O +Energy (ATP + heat)


Q. distinguish what reducting agent, electron donor and oxidizing agent, electron acceptor are.

Xe- + Y -> X + Ye-

reducing agent, electron doner is Xe-

oxidizing agent, electron acceptor is Y




Q.how dose pyrubate get into mitochodria?

because of active transport


5 facts

1. in oder to do cellular respiration, we need to break down the energy source, which means we use catacolic pathways

2. harvesting chemical energy had 3 steps to produce the amount energy that we need. glycolysis, kreb cycle and ETC

3. The reason that we break down all the potential energy in to the energy form, ATP is too much energy released at once might have dangerous possible therefore we have stepped by stepped to break it

4. active transport allowed pyruvate getting into mitochondira

5. there are a lot of different method of harvesting chemical energy by the condition of environment ; aerobic respiration and fermentation.


diagram

cellural respiration is the process that we make ATP in our cell ( cytosol, Mitochondria) there are three steps that the glocose broken down to ATP by Glycolysis, cirtric acid cycle and oxidative phosphorylation. simply Glycolysis and Kreb cycle could not produce many ATP but their rule is pretty essential because it prevents too much energy explode at one time, and changed different forms and sent them to ETC. Glycolysis doesn't require Oxygen which are the evidence of the hypothesis of the first bacteria's processing energy without Oxygen was present in the Earth.

Key terms


1. oxidation : in a redox reacion, the loss of elecgtrons from one substance
2. reduction : the addition of electrons
3. glycolysis : occuring in the cytosol, begining the degradation porcess by breaking glucose into two molecules of a compound called pyruvate
4. the kreb cycle : breakdown of glucose by oxidizing a derivative of pyruvate to carbon dioxide
5. cytochromes : most of the remaining electron carriers between ubiquinone and oxygen are proteins
6. alcohol fermentation : pyruvates is converted to ethanol in two steps
7. lacitic acide fermemtation : pyruvbate is reduced directly by NADH to form lactate as an ene product, with no release of CO2
8.obligate anaerobes, carry out only fermemtation or anaerobic respiration and in fact cannot survive in the presence of oxygen
9. facultative anaerobes : able to make enough ATP to survive using either fermemtation or respiration
10. substrate-level phosphorylation : a smaller amoun ot ATP is formed directly in a few reacions of glycolysis and the Kreb cycle by a mechanism

video

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



summary

Cellular respiration is the process by which the chemical energy of "food" molecules is released and partially captured in the form of ATP. Carbohydrates, fats, and proteins can all be used as fuels in cellular respiration, but glucose is most commonly used as an example to examine the reactions and pathways involved.

chapter 8. an introduction to metabolism

Q. what is metabolism?
metabolism is an emergent property of life that arises from interactions between molecules within the orderly environment of the cell

Q. what is the first law of thermodynamic?
energy can be transferred and transformed but it cannot be created or destroyed.

Q. what is the second law of thermodynamic?
every energy transfer or transformiation increses the entropy of the universe.

5 facts
1. energy can be transferred and transformed but it cannot be created or destroyed
2. every energy transfer or transformiation increses the entropy of the universe
3. catabolic pathways drive the regeneration of ATP from ADP and phosphate
4. ATP is the cell's energy shuttle, hydrolysis at its terminal phophate group produces ADP and phosphate and releases free energy.
5. a living system's free energy is energy that can do work under cellular conditions.

diagram

AB+CD = AC+BC
when the energe is activating, the free energy is increased which means it required producing energy to move up and then when it reached into the summit of the reactant, it is very unstable and realeased the energy therefore it happened spontenuously. therefore the total activation of energy will be the natually happen with out using energy if the substaction of initial energy to final energy. the unstable condition can recult bonds will be broken.
when enzyme is involved in the activations, the free energy doent recuire as much as it was alone. which means the enzyme helpes the activation easily with small amout of the energy relasement therefore the graph will be different and the total calculation of the free energy will be lower than as it self (negative amount)


10 key terms
1. metabolism is an emergent property of life that arises from interactions between molecules within the orderly environment of the cell
2. catabolic pathways : a major pathway of catobolism is cellular respiration, in which the sugar glucose and other organic fules are broken down in the presence of oxygen to carbon dioxide and water
3. anbolic pathways, in contrast, consume energy to build complicated molecules from simper ones.
4. chmical energy is a term used by biologists to refer to the potential energy available for realsed in a chemical reaction
5. kinetic energy : associated with the realtive motion of objects
6. thermal energy : is kinetic energy associated with the random movement of atoms or molecules
7. potential energy it is energy that matter possesses because of its location or structure.
8. thermodynamics: the study of the nenrgy transformations that occur in a collection of matter
9. entropy : as a measure of disorder; or randomness
10. exergonic reacion : proceeds with a net release of gree energy

video - ATP
http://www.youtube.com/watch?v=0TgCUkjoacU

summary
in oreder to convert the sugars to amino acides which are linked togeter into proteins when needed, the protein are changed into the amino acid, they are able to be sugar when the food is digested. small molecules gather together and changed into polymers and it might be hydrolyzed later if the cell needs.
metabolic pathways are the basic of the living and study of how the living things survive. energy has a lot of varieties and they will determine differently such as kinetic energy, thermal energy and potential energy and chemical energy.

chapter 7. membrane structure and function

Q. what does the membrane looks like? the model?

it is phosopholipid bilayer : hydrophilic head and hydrophobic tail connects to the another opposite of hydrophobic tail.

Q. what are the two major population of membrane proteins?

integral proteins and peripheral proteins

Q. what is the diffusion of a substance across a biological membrane without expend energy to make it happen?

passive transport

5 facts

1. membrane is made of phospolipid and there are some intergral proteins.
2. the intergral proteins do trasnport, enzymatic activity, signal transduction, cell-cell recognition , intercellular joining and attachment to the cytoskeleton and extracellular matrix.
3. hypertonic will lose water to its environment because it has low concentration.
4. hypotonic will enter water the cell faster tan it leaves, because it has high concentration
5. there are three types of endocytosis, phagocytosis, pinocytosis and receptor-mediated endocytosis.

diagram - cell membrane


cell membrane is made of two phospholipid are connected its tail to tail , so that the hydrophilic head are far away each other. there are also a lot of intergral proteins which transfer or function many things for the cell.


10 key terms


1.Amphipathic : having both a hydrophilic region and a hydrophobic region.

2.Fluid mosaic model, the membrane is a fluid structure with a “mosaic” of various proteins embedded in or attached to a double later of phospholipids.

3.Intergral proteins is one of the two major populations of membrane proteins, which penetrate the hydrophopic core of the lipid bilayer, many are trasnmembrane proteins, which span the membrane; other integral proteins extend only partway into the hydrophobic core.

4.Peripheral proteins are not embedded in the lipid bilayer at all; they are appendages loosely bound to the surface of the membrane, often to exposed pars of integral proteins.

5.Glycolipid: membrane carbohydrates are usually short, branched chains of fewer than 15 sugar units, some are covalently bonded to lipids.

6.Transport protein hydrophilic substances can avoid contact with the lipid bilater by passing through it that span the membrane.

7.Diffusion: molecules have a type of energy called thermal motion. One result of thermal motion, the movement of molecules of any substance so that they spread out evenly into the available space.

8.Osmosis : the diffusion of water across a selectively permeable membrane; the movement of water across cell membranes and the balance of water between the cell and its environment are crucial to organisms.

9.Tonicity, the ability of a solution to cause a cell to gain or lose water. The tonicity of a solution depends in part on its concentration of solutes that cannot cross the membrane, relative to that inside the cell.

10.Facilitated diffusion : many polar molecules and ions impeded by the lipid bilayer of the membrane diffuse passively with the help of transport proteins that span the membrane.


video - diffusion
http://www.youtube.com/watch?v=VUnvwrx8Wq4

summary

membrane is basically made of phospholipid bilayer with cross section and intergral proteins in it. The protein works a lot of things such as transporting, enzymatic activity, signal transduction, cell-cell recognition , intercellular joining and attachment to the cytoskeleton and extracellular matrix. some of them requires ATP to work on but some of them are not extending energy to do. especially the cell-cell reconition is important that they will have different carbohydrates to distinguish from other cell.

because of the formation of lipid bilayer, the molecules are not easily entering and exiting randomly, they need some certain condition to get into a cell, such as nonpolar molecule, small molecule. but the proteins built into the membrane play key roles in regulating transport.

chapter 6. a tour of the cell

Q. what are the basic structural and funtional unit of every organism?

prokaryotic and eukaryotic

Q. what are the things not in animal cell but in plant cell?
what are the things not in plant cell but in animal cell?

yes plant cell : chloroplast, central vacuole, cell wall, plasmodesmata
yes animal cell : lysosome, centrosomes, flagella

Q. what organelles names made of double membranes, and function like making energy?

mitochondria and chloroplasts

5 facts
1. all the living things are made of cells wheather prokaryotic or eukaryotic cell
2. endomembrane system is including the organells ; Golgi apparatus, lysosomes, the nuclear envelope, the endoplasmic reticulum, vacuoles and plasma memberane

3. cytoskeleton roles the supporting, motility and regulation and divided mictrotubules, microfilaments, and intermediate filaments
4. prokaryotic cell doesnt have nucleus and much simpler than eukaryotic cell
5. the need for a surface area sufficiently large to accommodate the volume helps explain the microscopic sixe of most cells and the narrow, elongated shapes of others.

diagram

animal cell vs. plant cell
basically the both cells are eukaryotic cells so that they have the smiliar functional organelles. But in animal cells, we can find lysosomes which helps digestion, cetrosomes which is a region where the cell's microtubules are initatied, and flagella whichi composed of a cluster of microtubules within an extension of the plasma membrane
In plant cells, chloroplasts which converts energy of sunlight to chemical energy stored in sugar molecules, cnetral vacuole which functions include storage, breakdown of waste products, hydrolusis of macromolecules; englargement of vacuole is a majore mechanism of plant growth, cell wall which is the outer later that maintains cell;s hsape and protects and plasmodesmata which channels throught cell walls that connect the cytoplasms of adjacent cells

10 key terms
1. Light microscope (LM): visible light is passed through the specimen and then through glass lenses. Magnification is the ratio of an object’s image size to its real size
2.Plasma membrane : membrane enclosing the cytoplasm/ functions as a selective barrier that allows sufficient passage of oxygen, nutrients, and wastes to service the entire cell.
3.Nucleus contains most of the genes in the eukaryotic cell (some genes are located in mitochondria and chloroplasts.)
4.Chromosomes : structures that carry the genetic information. Each chromosomes is made up of a material called chromatin, a complex of proteins and DNA.
5.Endomembrane system, which carries out a variety of tasks in the cell such as synthesis of proteins and their transport into membranes and organelles or out of cell, metabolism and movement of lipids, and detoxification of poisons, includes the nuclear envelop, the endoplasmic reticulum, the golgi apparatus, lysosomes, vacuoles, and the plasma membrane.
6.Golgi apparatus are engaged in the transfer of material between parts of the golgi and other structures
7.Central vacuole develops by the coalescence of smaller vacuoles, themselves derived from the endoplasmic reticulum and golgi apparatus.
8.Cytoskeleton : a network of fibers extending throughout othe cytoplasm. (microtubules, microfilaments, and intermediate filaments)
9.Cell wall is an extracellular structure of plant cells that distinguishes them from animal cells
10.Gap junctions provide cytoplasmic channels from one cell to an adjacent cell and in this way are similar in their function to the plasmodesmata in plants.

video - animal cell and plant cell
http://www.youtube.com/watch?v=Jn9oJtXZYcU


summary
we know all the living things made of cell after the microscope are getting developed we can see so many organells are in cell and each things are existed in reasons. the cell are divided into a big group as eukaryotic and prokaryotic cell; the difference is known easily through their names, existance of nucleus ; however, there are a lot of differences between two cells.
prokaryotic cell contains not many organelle, eukaryotic cell more complex and it is also a good example of emergent properties. each organelles in a cell has their own functions and plant cell and animal cell have different organelles, mostly they shared some similarity but especially plants cell has cell wall, central vacuole and chloroplats.

Email from Professor. Wight :D

fromChuck Wight <chuck.wight@utah.edu>toAshlee Son <aliceandcrab@gmail.com>
dateSun, Oct 11, 2009 at 8:17 PMsubjectRe: hello professor wight.mailed-byutah.edu
hide details 8:17 PM (23 hours ago)
Hi Ashlee,
The statement that covalent bonds are stronger than hydrogen bonds is a generalization based on a large number of experimental measurements of bond dissociation energies.
There are many ways to do these measurements, including measuring the onset of bond breaking as a function of the wavelength of absorbed light.
For hydrogen bonds it is simple to measure the number of bonds broken as a function of temperature, because they are (usually) very weak. From this dependence, it is pretty easy to calculate the strength of the bonds. In the case of water, you can see that simply boiling the water breaks all of the bonds in the liquid to make isolated gas molecules. If water had covalent bonds it wouldn't boil but decompose into oxygen and hydrogen instead (probably).
Chuck Wight- Hide quoted text -

On Oct 10, 2009, at 7:16 PM, "Ashlee Son" <aliceandcrab@gmail.com> wrote:
- Hide quoted text -this is a some random korean high school student who is studying in Mt.Pleasant , Utah.while i was studying AP biology, i found the video that you were explaing about chemical bonding.I simply understand the chemical bonds and the differences between covelant, inoic, and hydrogen bonding.however i wonder how we know that covelant bonding is the strongest and hydrogen bonding is weakest,,i mean how people find out the fact? and how much is covelant bond stronger than other bonding?also how does the power of bonding affect? such as if hydrogen bonding is as strong as covelant bonding , it will changes some characteristic of water? i want to hear about more specific reason that i feel i totally understand. thank you !


Wow thank you so much prof.wight!

chapter 5. the structure and function of large biological molecules

Q. what are the names of the members of the pyrimidine family and purines family?

pyrimidine - Cytosine, Thymine, and Uracil
purines - Adenine, and Guanine.

Q. what are polymer and monomer?

simply, monomer is smaller miolecules which serves to build polymer
polymer is repeating unit which has a lot of monomer

Q. what are the macromolecules?

carbohydrates, lipid, polypeptides and nucleic acid

five facts
1. polysaccharides serve as storage material; plants store starch and including humans, most animal have enzymes that can hydrolyze the plant starch.
2. cellulose is enable to digest for some animals include human, it is because starch and cellulose are geometric isomers.
3. the reasone for some fat is liquid form at the room temperature is they have double bonds instead of fully hydrogen atoms.
4.amino acid has carboxyl and amino groups, and all amino acids share a common structure.
5. two amino acids are bonded by dehydration reacion and peptide bond.

All proteins share three superimoposed levles of structure.

Primary structure is just the same as big chain of sequence of amino acid.
Secondary structure is due to hydrogen bonds the primary structure is coiled or folded.
Tertiary structure is superimposingon the patterne of secondary structure.
Quaternary structure is many tertiary structures aggregated as one functional macromolecule.




ten key terms
1.Monosaccharides generally have molecular formulas that are some multiple of the unit CH2O. The molecule has a carbonyl group and multiple hydroxyl group.
2.Saturated fats: at room temperature, the molecules of a saturated fat forming a solid.
3.Unsaturated fat: at room temperature, the molecules of an unsaturated fat such as this olive oil cannot pack together closely enough to solidify because of the kinks in some of their fatty acid hydrocarbon chains.
4.Polypeptides are called polymers of amino.
5.Amino acid is organic molecules possessiong both carboxyl and amino groups
6.Peptide bond is when two amino acids join together by a dehydration reaction.
7.Ester linkage is a bond between a hydroxyl group and a carboxyl group.
8.Fatty acid : attatching to the carboxyl groupd is long hydrocarbon chain
9.Protein consists of one or more polypeptides, each folded and coiled into a specific three-dimensional structure.
10.Hydrophobic interaction is as a polypeptide folds into its functional shape, amino acids with hydrophobic side chains usually end up in clusters at the core of the protein, out of contact with water.


video - the video of protein folding
http://www.youtube.com/watch?v=swEc_sUVz5I

summary

there are macromolecule which our body must have ; which are carbohydrate, lipid, polypeptides and nucleic acid. first, carbohydrate is sugar and polysaccharide is used for storing energy in our body or living things. Lipid is not true polymer but essential to have especially for the membrane layer (next chaper) phospholipid has two fatty acids with negatively charged phospahate.
polypeptide is polymer of amino acid and protein does a lot of things such as supproting stroing and moving etc. there is four level of protein structures. the protein can be deformed by surroudning and it called denaturation.
gene determines the order of polypeptide's amino acid and gene consist of DNA, a ploymer belonging to the calss of compounds known as nucleic acids. DNA carried the imformation from your partens.

chapter 4. carbon and the molecular diversity of life

Q.why Carbon is more important than any other organic elements?

because it has large diversity of biological molecules, it can share the 4 electrons from others
tetravalence.

Q. what are the three names of isomers?

structural isomers

geometric isomers

enantiomers

Q. what are the names of functioanl groups?

hydroxyl

carbonyl

carboxyl

amino

sulfhydryl

phospate

metheyl

5 facts
1. carbon, oxygen, hydrogen, and nitrogen wich smaller amounts of culfur and phohorus are essential and organic elements.
2. even though the compounds have the same number of elements, if their structual are different, it would affect differently in our body.
3. carbon has 6 electrons, and 4 valence electrons in a shell which can hold 8; therefore it has a lot of way to combine with many different elements.
4. hydroxyl,carbonyl,carboxyl,amino,sulfhydryl and phospate are able to act as funtional group becuase thy are also hydrophilic and increase the solubility of organic compounds in water.
5. hydrogen has 1, oxygen has 2, nitrogen has 3 and carbon has 4 valence.

each functional groups has different formations and different functions. But espeically these 7 groups are important for our lives such as sex hormones.


10 keyterms
1. Vitalism, the belief in a life force outside the jurisdiction of physical and chemical laws, provided the foundation for the new discipline of organic chemistry.
2.Mechanism is the view that physical and chemical laws govern all natural phenomena, including the processes of life.
3.Tetravalence is one facet of carbon’s versatility that makes large, complex molecules possible.
4.Isomers are the compounds that have the same numbers of atoms of the same elements but different structures and hence different properties
5.Structural isomers differ in the covalent arrangements of their atoms.
6.Geometric isomers have the same covalent partnerships, but they differ in their spatial arrangements.
7.enantiomers are isomers that are mirror images of each other.
8.Hydrocarbons are organic molecules consisting of only carbon and hydrogen.
9.Compounds containing carbon are said to be organic, and the branch of chemistry that specialized in the study of carbon compounds is called organic chemistry.
10. ATP consists of an organic molecule called adenosine attached to a sting of three phosphate groups


video - organic chemistry
http://www.youtube.com/watch?v=SXCs-R7rptI


organic chemistry especially carbon has 4 valence which means it is able to connect or share 4 electrons to other elements; therefore it has so many possiblity to have more functions together. We also have to be award of the isomers becuase its number of elements or seems the same but function as very different in the worst situation, it will harm us because of little different order of structure. we also realized that there is emergent properties again because of one little atom's placement, the whole thing will be changed.
the versatility of carbon makes possible the great diversithy of organic molecules, each with particular properties that emerge from the unique arragement of its carbon skeleton and the chemical groups appended to that skeleton.