Chapter eight: introduction of metabolism

An enzyme can convert one or more product molecules. The enzyme shown here converts two substrate molecules to two product molecules.

Main questions:
1. Most cells cannot harness to perform work because?
A: heat can never be used to do work.
2. If an enzyme in solution is saturated with substrate, the most effective way to obtain a faster yield of products is to?
A: add more of the enzyme.
3. Some bacteria are metabolically active in hot springs because?
A: their enzymes have high optimal temperatures.

Main Facts:
1. Energy can be transferred and transformed, but it cannot be created or destroyed.
2. There are three forms of energy: Kinetic, Potential, and Activation energy.
3. Every energy transfer or transformation increases the entropy of the universe.
4. For a process to occur spontaneously, it must increase the entropy of the universe.
5. ATP hydrolysis in several ways to perform the three types of cellular work-chemical, transport, and mechanical.

Summary:

Key terms:
1. Allosteric regulation: is the term used to describe any case in which a protein's function at one site is affected by thebinding of a regulatory molecule to a separate site.

2. Competitive inhibitors: A substance that reduces the activity of an enzyme by entering the active site in place of the substrate whose structure it mimics.

3. Noncompetitive inhibitors: 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.

4. 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.

5. Activation energy: The amount of energy that reactants must absorb before a chemical reaction will start.

6. Enzyme: A macromolecule serving as a catalyst, a chemical agent that changes the rate of a reaction without being consumed by the reaction.

7. Catalyst: A chemical agent that increases the rate of a reaction without being consumed by the reaction.

8. Phosphorylated: Referring to a molecule that is covalently bonded to a phosphate group.

9.Exergonic reaction: A spontaneous chemical reaction, in which there is a net release of free energy.

10. Free energy: The portion of a biological system's energy that can perform work when temperature and pressure are uniform throughout the system.

Video: http://www.youtube.com/watch?v=VbIaK6PLrRM&feature=related

Chapter seven: membrane structure and function

There are integral protein and peripheral protein in this graph which is known as mosaic proteins. They help select substances and tranport them. The hydrophobic part of protein is inside the lipids.


Main questions:
1.In what way do the membranes of a eukaryotic cell vary?
A: Certain proteins are unique to each memebrane.
2.What does passive transport includes?
A: osmosis, diffusion of a solute across a membrane, facilitated diffusion, transport of an ion down its electrochemical gradient.
3.What experimental treatment would increase the rate of sucrose transport into the cell?
A: decreasing extracellular pH.

Main facts:
1.Amphipathic proteins are embedded in the phospholipid bilayer.
2.Short chains of sugars are linked to proteins and lipids on the exterior side of the plasma membrane, where they interact with surface molecules of other cells.
3.Membrane proteins and lipids are synthesized in the ER and modified in the ER and Golgi apparatus. The inside and outside faces of the membrane differ in molecular composition.
4.Diffusion is the spontaneous movement of a substance down its concetration gradient.
5.In facilitated diffusion, a transport protein speeds the movement of water or a solute across a membrane down its concentration gradient.

Summary:
Cell membrane not only provides protection but also transportation. Cell memebrane contains proteins, carbohydrate, glycolipid and cholesterol. Passive transport is diffusion of a substance across a memebrane with no energy investment. This chapter is basically talking about the function how proteins transport molecules from outside of cell till inside.
If there is no cell membrane which is just like a house without door. Anything could get into cell without guarding. Which cell membrane is very important to the cell.


Key terms:
1. Concentration gradient: A region along which the density of a chemical substance increases or decreases
2. 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.
3. Amphipathic: having both a hydrophilic region and a hydrophobic region.
4. Fluid mosaic model: The currently accepted model of cell membrane structure, which envisions the membrane as a mosaic of protein molecules drifting laterally in a fluid bilayer of phospholipids.
5. Integral proteins: Typically a transmembrane protein with hydrophobic regions that extend into and often completely span the hydrophobic interior of the membrane and with hydrophilic regions in contact with the aqueous solution on either side of the membrane.
6. Peripheral proteins: A protein loosely bound to the surface of a membrane or to part of an integral protein and not embedded in the lipid bilayer.
7. Glycolipids: A lipid with covalently attached carbohydrate.
8. transport proteins: A transmembrane protein that helps a certain substance or class of closely related substances to cross the membrane.
9. Electrogenic pump: An ion transport protein that generates voltage across a membrane.
10. Passive transport: The diffusion of a substance across a biological membrane with no expenditure of energy.

Video: http://www.youtube.com/watch?v=STzOiRqzzL4&feature=related

Chapter six: A tour of the cell

Chloroplast is enclosed by two membranes separated by a narrow intermembrane space that constitutes an outer compartment. The inner membrane encloses a second compartment containing the fluid called stroma. The stroma surrounds a third compartment, the thylakoid space, delineated by the thylakoid membrane.

Main questions:
1.What structures are only in animal cells but not plant cells?
A: Lysosomes, Centrosomes, Flagella
2.What structures are only in plant cells?
A: Chloroplasts, central vacuole, cell wall, plasmodesmata.
3.Cyanide binds with at least one molecule involved in producing ATP. If a cell is exposed to cyanide, most of the cyanide would be found within the?
A: mitochondria.

Main facts:
1. Improvements in microscopy that affect the parameters of magnification, resolution, and contrast have catalyzed progress in the study of cell structure. Light and electron microscopy remain important tools.
2. Plant cell walls are made of cellulose fibers embedded in other polysaccharides and proteins.
3. Plants have plasmodesmata that pass through adjoining cell walls. Animal cells have tight junctions, desmosomes, and gap junctions.
4.The cytoskeleton functions in structural support for the cell and in motility and signal transmission.
5.Golgi apparatus' functions: Modification of proteins, carbohydrates on proteins, and phospholipids.

Summary:
Cytology is known as the study of cell structure. Scientists use microscopes and the tools of biochemistry to study cells. This chapter compares the difference between prokaryotic and eukaryotic. Such as both prokaryotic and eukaryotic have plasma membrane, cytosol, chromosomes, ribosome, ad cytoplasm. But only Prokaryotic has cell nucleus which contains DNA inside.
In chapter six is about the cell component and functions. It includes nucleus, ribosome, endoplasmic reticulum, Golgi apparatus, lysosome, vacuole, mitochondrion, choroplast and peroxisome. All those componenet are important and necessary for a cell to work properly. Without those components inside cell which none of the big animals or plants would exist.

Key terms:
1. 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.

2. 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

3. 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.

4. 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.

5. 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.

6. Flagella: A long cellular appendage specialized for locomotion.

7. Cilia: A short cellular appendage containing microtubules.

8. Centrosome: a region that is often located near the nucleus and is considered a "microtubule-organizing center."

9. Cytoskeleton: A network of icrotubules, microfilaments, and intermediate filaments that brach throughout the cytoplasm and serve a variety of mechanical, transport, and signalig functions.

10. Microtubules: A hollow rod composed of tubulin proteins that make up part of the cytoskeleton in all eukaryotic cells and is found in cilia and flagella.

Video: http://www.youtube.com/watch?v=ldRZcmppQM8

Chapter Five: the structure and funcion of large biological molecules

Phospholipids 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.

Main Questions:
1. What term includes all others in the list?
A: Carbohydrate includes monosaccharide, disaccharide, polysaccharide and starch.
2. The structural level of a protein least affected by a disruption in hydrogen bonding is the?
A: primary level.
3. Enzymes that break down DNA catalyze the hydrolysis of the covalent bonds that join nucleotides together. What would happen to DNA molecules treated with these enzymes?
A: The phosphodiester linkages between deoxyribose sugars would be broken.

Main facts:
1. Starches are made of 1-4 linkages of a glucose.
2. Glycogen is similar to starch, but has more 1-6 linkages or branches.
3. Fatty acids are long carbon chain (12-18 C) with a -COOH (acid) on one end and a -CH3 (fat) at the other.
4. Phospholipids are similar to fats, but have only two fatty acids.
5. Polypeptide chains formed by dehydration synthesis between the carboxyl group of one AA and the amino group of the second AA.

Key terms:
1. Chitin: A structural polysaccharide, consisting of amino sugar monomers, found in many fungal cell walls and in the exoskeletons of all arthropods.

2. Starch:A storage polysaccharide in plants, consisting entirely of glucose monomers joined by a glycosidic linkages.

3. Disulfide bridge: A strong covalent bond formed when the sulfur of one cysteine monomer bonds to the sulfur of another cysteine monomer.

4. Peptide bond: The covalent bond between the carboxyl group on one amino acid and the amino group on another, formed by a dehydration reaction

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

6. Triacylglycerol: Three fatty acids linked to one glycerol molecule; also called a fat or a triglyceride

7. Phospholipids: A lipid mad up of glycerol joined to two fatty acids and a phosphate group.
8. Cholesterol: is a common component of animal cell membranes and is also the precursor from which other steroids are synthesized.

9. Amino Acids: are organic molecules possessing both carboxyl and amino groups.

10. Chaperonins: A protein molecule that assists in the proper folding of other proteins.

Video: http://www.youtube.com/watch?v=iaHHgEoa2c8&feature=related

Chapter four: carbon and the molecular diversity of life

Diagram: Stanley Miller in 1953 set up a similar condition as origin earth. He first evaporated water and mixed gas of water with methane, hydrogen, and ammonia. Some simple organic molecules were formed under cooling and lightning. After all the organic molecules may have been synthesized abiotically on the early Earth.


Main Questions:

1. Organic chemistry is currently defined as?

A: the study of carbon compounds.

2. Which action could produce a carbonyl group?

A: the replacement of the –OH of a carboxyl group with hydrogen.

3. What kind of chemical group is most likely to be responsible for an organic molecule behaving as a base?

A: amino.

Main Facts:

1. In 1953, Stanley Miller at the University of Chicago set up a laboratory simulation of chemical conditions on the primitive Earth and demonstrated the spontaneous synthesis of organic compounds.

2. With a total of 6 electrons, a carbon atom has 2 in the first electron shell and 4 in the second shell.

3. One function of phosphate groups is to transfer energy between organic molecules.

4. If the carbonyl group is on the end of the skeleton, the compound is an aldehyde. If the carbonyl group is within the carbon skeleton, then the compound is a ketone.

5. A carboxyl group acts as an acid because the combined electronegativities of the two adjacent oxygen atoms increase the dissociation of hydrogen as an ion (H⁺). An amino group (—NH₂) consists of a nitrogen atom bonded to two hydrogen atoms and the carbon skeleton.

Summary:

Although cells have 70–95% water, the rest consists mostly of carbon-based compounds. Carbon is unparalleled in its ability to form large, complex, and diverse molecules. Such as Proteins, DNA, carbohydrates, and other molecules that distinguish living matter from inorganic material are all composed of carbon atoms bonded to each other and to atoms of other elements. These other elements commonly include hydrogen (H), oxygen (O), nitrogen (N), sulfur (S), and phosphorus (P).

Basically the study of carbon compound(organic chemistry) which is dealing with any compound with carbon.

Key terms:

1. Hydrocarbons: organic molecules consisting of only carbon and hydrogen.

2. Isomer: compounds that have the same numbers of atoms of the same elements but different structures and hence different properties.

3. Structural isomers: is a form of isomerism in which molecules with the same molecular formula have atoms bonded together in different orders, as opposed to stereoisomerism.

4. Geometric isomers: one of several compounds that have the same molecular formula and covalent arrangements but differ in the spatial arrangements of their atoms owing to the inflexibility of double bonds.

5. Enantiomers: one of two compounds that are mirror images of each other.

6. Functional groups: A specific configuration of atoms commonly attached to the carbon skeletons of organic molecules and usually involved in chemical reactions.

7. Adenosine triphosphate: An adenine-containing nucleoside triphosphate that releases free energy when its phosphate bonds are hydrolyzed. The energy is used to drive endergonic reactions in cells.

8. Methyl group: A chemical group consisting of a carbon bonded to three hydrogen atoms. The methyl group may be attached to a carbon or to a different atom.

9. Phosphate group: A chemical group consisting of a phosphorus atom bonded to four oxygen atoms; important in energy transfer.

10. Sulfhydryl group: A chemical group consisting of a sulfur atom bonded to a hydrogen atom.

Video: http://www.youtube.com/watch?v=vn_HICkswI4