Chapter 8: An Introduction to Metabolism

3 Main Questions:
- What is metabolism?
The totality of an organism's chemical reactions.
- What is the first law of thermodynamics?
Energy can be transferred and transformed, but it can not be created or destroyed.
- What is chemical energy?
Chemical is a term used by biologists to refer to the potential energy available for release in a chemical reaction.

5 Main Facts:
- Metabolism as a whole manages the material and energy resources of the cell.
- An object not presently moving may still possess energy.
- During catabolic reaction, atoms are rearranged and energy is released, resulting in lower energy breakdown products.
- Moving objects can perform work by imparting motion to other matter.
- During every energy transfer or transformation, some energy becomes unusable energy, unavailable to do work.

Diagram

This diagram is the active site and catalytic cycle of an enzyme. An enzyme can convert one or more reactant molecules. The enzyme shown in the diagram is converting two substrate molecules to two product molecules.

Summary
The living cell is a chemical factory in a small world where thousands of reactions occur within a microscopic space. Small molecules are assembled into polymers, which may be hydrolyzed later for the needs of the cell change.
Sugars can be converted into amino acid that are linked together into proteins when needed, and proteins are dismantled into amino acids that can be converted to sugars when food is digested.

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

10 Key Terms:
- Energy: the capacity to cause change.
- Chemical energy: a term used by biologists to refer to the potential energy available for release in a chemical reaction.
- Bioenergetic: the study of how energy flows through living organisms.
- Potential energy: it is energy that matter possesses because of its location or structure.
- Entropy: a measure of disorder, or randomness.
- Free energy: the portion of a system's energy that can perform work when temperature and pressure are uniform throughout the system, as in a living cell.
- Endergonic reaction: is one that absorbs free energy from its surroundings.
- Enzyme: a macromolecules that acts as a catalyst, a chemical agent that speeds up a reaction without being consumed by the reaction.
- Subtract: the reactant on which an enzyme works.
- Coenzyme: an organic molecule serving as a cofactor. Most vitamins function as coenzymes in metabolic reactions.

Chapter 7: Membrane Structure and Function

3 Questions
- What is selective permeability function?
This is a plasma membranes that allows some substances to cross it more easily than others.
- What is amphipatic?
It is some molecule that has both hydrophilic region and hydrophobic region.
- What is passive transport?
Passive transport is the diffusion of a substance across a biological membrane.
5 Main Facts
- The plasma membrane is the edge of life, the boundary that separates the living cell from its surroundings.
- A membrane is held together primarily by hydrophobic interactions, which are much weaker than covalent bonds.
- Phospholipids form the main fabric of the membrane, but proteins determine most of the membrane's functions.
- Integral proteins penetrate the hydrophobic core of the lipid bilayer.
- Peripheral proteins are appendages loosely bound to the surface of the membrane, often to exposed parts of integral proteins.

Diagram

Water moves from an area of higher to lower free water concentration(lower to higher solute concentration). Two sugar solutions of different concentrations and separated by a membrane, which the solvent can pass through but the solute cannot. water molecules move randomly and may cross in either direction, but overall, water diffuses from the solution with less concentrated solute to that with more concentrated solute. This transport of water, or osmosis, equalizes the sugar concentrations of both sides.

Summary
Chapter 7 talked about how cellular membranes control the passage of substances. Cellular membranes are fluid mosaics of lipids and proteins. Molecules have a type of energy called thermal motion. One example of thermal motion is diffusion, the movement of molecules of any substance so that they spread out evenly into the available space.
The diffusion across a membrane is called passive transport because the cell does not have to expand energy to make it happen. Another type of transport is osmosis which the water across a selectively permeable membrane.

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

10 Key Terms:
- Diffusion: the movement of molecules of any substance so that they spread out evenly into the available space.
- Passive transport: the diffusion of a substance across a biological membrane.
- Osmosis: the diffusion of water across a selectively permeable membrane.
- Tonicity: the ability of a solution to cause a cell to gain or lose water.
- Isotonic: referring to a solution that, when surrounding the cell, has no effect on the passage of water into or out of the cell.
- Hypertonic: referring to a solution that, when surrounding the cell, will cause the cell to lose water.
- Osmoregulation: regulation of solute concentrations and water balance a cell or organism.
- Active transport: the movement of a substance across a cell membrane, with an expenditure of energy, against its concentration or electrochemical gradient; mediated by specific transport proteins.
- Electrogenic pump: a transport protein that generates voltage across a membrane.
- Endocytosis: cellular uptake of biological molecules and particulate matter via formation of new vesicles from the plasma membrane.

Chapter 6: A Tour of the Cell

3 Main Questions:
- What is nucleus?
An atom's central core, containing protons and neutrons.
- What does nucleus contains in the eukaryotic cell?
Nucleus contain most of the genes in the eukaryotic cell.
- What is the nuclear envelope function?
Encloses the nucleus, separating its contents from the cytoplasm.

5 Main Facts:
- Cell fractionation is a useful technique for studying cell structure and function.
- Microscopes are the most important tools of cytology.
- Eukaryotic cells are generally larger than prokaryotic cells.
- Cells that have high rates of protein synthesis have particularly large numbers of ribosomes.
- Lysosomal enzymes work best in the acidic environment found in lysosomes.

Diagram
The central vacuole is mostly the largest part in a plant cell. The rest of the cytoplasm is mainly confined to a narrow zone between the vacuolar membrane and the plasma membrane.

Summary
Chapter 6 is a brief introduction about cell. Furthermore, different types of microscopes were described. Microscope is an important equipment for study Biology. There are four types of microscopes which are well known: light microscope(LM), electron microscope(EM), scanning electron microscope (SEM), transmission electron microscope (TEM).
Prokaryotic and eukaryotic cells are the most basic structural and functional unit of every organism. All cells are bounded by a selective barrier called the plasma membrane. Chromosomes are found in all cells which carry genes in the form of DNA.

Video
http://www.youtube.com/watch?v=zufaN_aetZI&feature=fvw

10 Key Terms:
- Cytoplasm: the interior of a prokaryotic cell.
- Nucleoid: a dense region of DNA in a prokaryotic cell.
- Cytosol: the semifluid portion of the cytoplasm.
- Chromatin: the complex of DNA and proteins that makes up a eukaryotic chromosome.
- Ribosome: a complex of rRNA and protein molecules that functions as a site of protein synthesis in the cytoplasm.
- Vesicle: a sac made of membranes in the cytoplasm.
- Glycoprotein: a protein which one or more carbohydrates covalently attached to it.
- Golgi apparatus: an organelle in eukaryotic cells consisting of stacks of flat membranous sacs that modify, store, and route products of the endoplasmic reticulum and synthesize some products, notably non cellulose carbohydrates.
- Phagocytosis: a type of endocytosis in which large particulate substances taken up by a cell.
- Lysosome: a membrane-enclosed sac of hydrolytic enzymes found in the cytoplasm of animal cells and some protists.

Chapter 5: The Structure and Function of Large Biological Molecules

3 Main Questions:
- What are the four main classes of large biological molecules?
Carbohydrates, lipids, proteins, and nucleic acids.
- How many level of protein structure are there?
There are four levels of protein structure: primary , secondary, tertiary quaternary.
- What is fat ?
Fat is constructed from two kinds of smaller molecules: glycerol and fatty acids.

5 Main Facts:
- Carbohydrates include both sugars and polymers of sugars.
- Monosaccharides, particularly glucose, are major nutrients for cells.
- In making a fat, 3 fatty acid molecules each join to glycerol by an ester linkage, a bond between a hydroxyl group and a carboxyl group.
- Fatty acids vary in length and in the number and locations of double bonds.
- Many hormones, as well as cholesterol, are steroids, which are lipids characterized by a carbon skeleton consisting of four fused rings.

Diagrama) One water molecule is removed for each fatty acid joined to the glycerol.
b) Three fatty acid molecules each join to glycerol by an ester linkage, a bond between a hydroxyl and a carboxyl group. The carbons of the fatty acids are arranged zig-zag to suggest the actual orientations of the four single bonds extending from each carbon.

Summary
There are four important molecules of all living things: carbohydrates, lipids, proteins, and nucleic acids. 3 of those molecules, carbohydrates, proteins, and nucleic acids are called macromolecules because of their huge size. Carbohydrates include both sugars and polymers of sugars.
The compounds lipids are grouped together because they shared one important trait. They mix poorly with water. Phospholipids are essential for cells because they make up cell membranes. Polymers of amino acids are called polypeptides.

Video
http://www.youtube.com/watch?v=E2-FSHTc3U8&feature=related

10 Key Terms:
- Polymer: a long molecule consisting of many similar or identical building blocks linked by covalent bonds.
- Monomers: the repeating units that serve as the building blocks of a polymer.
- Enzymes: specialized macromolecules that speed up chemical reaction in cells.
- Hydrolysis: a process that is essentially the reverse of the dehydration reaction.
- Monosaccharide: the simplest carbohydrate, active alone or serving as a monomer for disaccharides and polysaccharides.
- Disaccharide: a double sugar, consisting of two monosaccharides joined by a glycosidic linkage formed during dehydration sunthesys.
- Lipid: one of a group of compounds, including fats, phospholipids, and steroids, that mix poorly, if at all, with water.
- Fat: a lipid consisting of three acids linked to one glycerol molecule.
- Phospholipids: essential for cells because they make up cell membranes.
- Unsaturated fatty acid: formed by the removal of hydrogen atoms from the carbon skeleton.

Chapter 4: Carbon and the Molecular Diversity of Life

Three Main Questions:
1) What is organic chemistry?
Organic chemistry is the study about carbon compounds.
2) What are isomers?
Isomers are compounds that have the same numbers of atoms of the same elements but different structure.
3) How many type isomer are there?
There are three types of isomer: structural isomer, geometric isomer, enantiomer.

Main Five Facts:
- Hydrocarbon is an organic molecules consisting of only carbon and hydrogen.
- The chemical groups affect molecular function by being directly involved in chemical reactions is called the functional groups.
- Structural isomers differ in the covalent arrangements of their atoms.
- Geometric isomers have the same covalent partnerships but they differ in their spatial arrangements.
- Enantiomers are isomers that are mirror images of each other.

Diagram Structural isomers differ in covalent partners. In the diagram, two isomers C5H12: pentane(left) and 2-methyl butane(right). Even though their structure is a little different but their number of atoms are still the same.

Summary
Chapter 4 covered about organic chemistry or the study of carbon compounds. Most organic compounds contain hydrogen atoms in addition to carbon atoms. However Co2 contains carbon it often considered inorganic because its lacks hydrogen. It is does not matter if we call CO2 organic or inorganic it is still important to the living world as the source of carbon for all organic molecules.
Functional groups is the chemical groups most important is the processes of life. They are hydroxyl, cabonyl, carboxyl, amino, sulfhydryl, phosphate, and methyl groups. These groups affect molecular function by directly involved in chemical reactions. Amino can acts as a base by pick up H+ from the surrounding solution.

Video
http://www.youtube.com/watch?v=qOhEJK4Umds

10 Key Terms:
- Organic chemistry: the study of carbon compounds.
- Hydrocarbons: organic molecules consisting of only carbon and hydrogen.
- Isomers: compounds that have the same numbers of atoms of the same elements but different structures and hence different properties.
- Structural isomers: differ in the covalent arrangements of their atoms.
- Geometric isomers: have the same covalent partnerships, but they differ in their spatial arrangements.
- Enantiomers: isomers that are mirror images of each other.
- Functional group: a specific configuration of atoms commonly attached to the carbon skeletons of organic molecules and usually involved in chemical reactions.
- Hydroxyl group: a chemical group consisting of an oxygen atom joined to a hydrogen atom.
- Carbonyl group: a chemical group represent in aldehydes and ketones and consisting of a carbon atom double-bonded to an oxygen atom.
- Carboxyl group: a chemical group present in organic acids and consisting of a single carbon atom double-bonded to an oxygen atom and also boned to a hydroxyl group.