Unit 1 email;

Re: Hello‏
From:
k.lewis@neu.edu
Sent:
October 18, 2009 6:57:05 PM
To:
Sophie Joo (sophie_0510@hotmail.com)

Hi Sophie Joo, what i think is not important. you try to think this problem through applying Darwin's theory. Good luck!

Kim LewisProfessor of BiologyDirector, Antimicrobial Discovery CenterDepartment of BiologyNortheastern University360 Huntington AvenueMugar 405Boston, MA 02115k.lewis@neu.eduwww.biology.neu.edu/faculty03/lewis03.htmlTel 617-373-8238 FAX 617-373-3724 3267 lab

Chapter 8: An Introduction to Metabolism

Q: What is metabolism?
A: Metabolism is the totality of an organism's chemical reactions. It is an emergent property of life that arises from interactions between molecules within the orderly environment of the cell.

Q: What are the forms of energy?
A: There are kinetic energy, the energy of action or motion, potential energy, stored energy or the capacity to do work, and activation energy that is needed to convert potential energy into kinetic energy.

Q: What is an enzyme?
A: An enzyme is a macromolecule that acts as a catalyst, a chemical agent that speeds up a reaction without being consumed by the reaction.


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 barriers.

5. Regulation of enzyme activity helps control metabolism.


Figure 8.19

Inhibition of enzyme activity.



A normal binding is justr a normal binding where a substrate binds normally to the active site of an enzyme.
Competitive inhibition refers to when there is a competitive inhibitor that blocks the substrate from fitting in to the active site by mimicing, pretending to be the substitute, being in the place where the substitute should be.
Noncompetitive inhibition is what binds to the enzyme not where the active site is, but away, and still affects the substrate from completely fitting in the active site because the inhibitor alters the shape of the enzyme.

This chapter is about metabolism and it is the collection of chemical reactions that occur in an organism. Aided by enzymes, it follows intersecting pathways, which may be catabolic (breaking down molecules, releasing energy) or anabolic (building molecules, consuming energy).
Then there are free energy, ATP, enzymes and the activation energy, and the substrates and the active site. In this chapter, we can find that enzymes do a lot of work and that they are important. The enzymes make the reaction to happen faster by lowering the activation energy barrier and how they work in the active site, the catalytic cycle, is very important.

Key terms

Metabolism: an emergent property of life that arises from interactions between molecules within the orderly environment of the cell.

Bioenergetics: the study of how energy flows through living organisms.

Chemical energy: the term people use to refer to the potential energy available for release in a chemical reaction.

Thermodynamics: the study of the energy transformations that occur in a collection of matter.

Free energy: is 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.

Exergonic reaction: An exergonic reaction proceeds with a net release of free energy.

Endergonic reaction: An endergonic reaction is one that absorbs free energy from its surroundings.

Active site: only restricted region of enzyme molecule actually binds to the substrate, this region, called the active site.

Competitive inhibitor: they reduce the productivity of enzymes by blocking substrates from entering active sites.

Noncompetitive inhibitor: they do not directly compete with the substrate to bind to the enzyme at the active site; instead they impede enzymatic reactions by binding to another part of the enzyme.

http://www.youtube.com/watch?v=2DRWqBld7XU&feature=related

Chapter 7: Membrane Structure and Function

Q: Name the two major populations of membrane proteins.
A: Integral proteins that penetrate the hydrophobic core of the lipid bilayer and peripheral proteins that are loosely bound to the surface of the membrane.

Q: What is the diffusion of water across a slectively permeable membrane called?
A: Osmosis

Q: How do large molecules such as proteins and polysaccharides generally cross the membrane?
A: They cross the membrane in bulk by mechanisms that involve packaging in vesicles.

1. Cellular membranes 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 invetment.

4. Active transport uses energy to move solutes against their gradients.

5. Bulk transport across the plasma membrane occurs by exocytosis and endocytosis.


Figure 7.13

The water balance of living cells

If a solution is hypotonic, the water will move to a higher concentration of solute, into the cell, therefore there is a great possibility that the cell will eventually swell and lyse (burst). Instead, if the solution is hypertonic, which means that the solution has a greater concentration than the cell, the cell will lose water and give it to the solution, which causes the cell to shrivel and probably die.
Isotonic is when there is no net movement and the two concentrations are equal.

This chapter is about the cellular membranes, their structures and functions. The Plasma membrane is the membrane at the boundary of the cell and functions as a selective barrier for the passage of materials in and out of cells. The membrane is composed of phospholipids and proteins. It's known as the phopholipid bilyaer with the hydrophilic heads and hydrophobic tails. These keep the fluidity. Because the phospholipid bilayer is hydrophobic, hydrophilic materials cannot cross so easily.
Then there are diffusion, osmosis and facilitated diffusion. Diffusion is the net movement of atoms, ions or molecules down a concentration gradient and osmosis is the diffusion of water. Facilitated diffusion is the passive transport aided by proteins.


Key terms

Osmosis: the diffusion of water across a selectively permeable membrane is called osmosis.

Isotonic: the isotonic to the cell means a cell without a wall, like an animal cell is immersed in an environment.

Hypertonic: when animal cell is immersed in a solution, it means hypertonic which the cell will lose water to its environment, shrivel and probably die.

Passive transport: the diffusion of a substance across a biological membrane is called passive transport.

Plasmolysis: as the plant cell shrivels, its plasma membrane pulls away from the wall, this phenomenon called plasmolysis.

Hypotonic: if we place the cell in a solution that is hypotonic to the cell, water will enter the cell faster than it leaves, and the cell will swell and lyse like an overfilled water ballon.

Active transport: to pump a solute across a membrane against its gradient requires work; the cell must expend energy, therefore, this type of membrane traffic is called active transport.

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. This phenomenon is called facilitated diffusion.

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

Integral proteins: they penetrate the hydrophobic core of the lipid bilayer.

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

Chapter 6: A Tour of Cell

Q: What are the major differences between the prokaryotic and the eukaryotic?
A: The prokaryotic lacks a nucleus and other membrane bounded structures while the eukaryotic has all of those.

Q: What are ribososomes?
A: Ribososomes are compexes made of ribosomal RNA and protein, which are the cellular components that carry out protein synthesis.

Q: What are the roles of the Cytoskeleton?
A: The cytoskeleton is there to support and organize the structures and activities of the cell. The cell mobility and regulation also need cytoskeleton.

1. To study cells, biologists use microscopes and the tools of biochemistry.
2. The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosome.
3. Mitochondria and chloroplasts change energy from one form to another.
4. The Cytoskeleton is a network of fibers that organizes structures and activities in the cell.
5. Extracellular components and onnections

Figure 6.8
Geometric relationships between surface area and volume.















Math makes it that as the surface area increases, the volume decreases. Therefore, because cells need far more surface area than the volume, it is more efficient for them to have less of volume.

This chapter talks about the cells, and each of the cell organisms’ functions. Before learning those though, the chapter goes through the microscopes that scientists use to study for the cell. If prokaryotic and eukaryotic cells are compared, we can find that all cells are bounded by a plasma membrane and unlike eukaryotic cells, prokaryotic cells lack nuclei and other membrane-enclosed organelles. The surface-to-volume ration, as mentioned, is an important parameter affecting cell size and shape.
There are cytoskeleton and cell walls of the plants that are made of cellulose fibers embedded in other polysaccharides and proteins.

Keyterms

Cytosol: the liquid inside of cells.

Cytoplasm it is the contents of the cell, exclusive of the nucleus and bounded by the plasma membrane.

Chromosomes: A cellular structure carrying genetic material, found in the nucleus of eukaryotic cells.

Chromatin: The complex of DNA and protein 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 membrane in the cytoplasm.

Peroxisome: peroxisomes are roughly spherical and often have a granular or crystalline core that is thought to be a dense collection of enzyme molecules.

Flagella: A long cellular appendage specialized for locomotion.

Cilia: A short cellular appendage containing microtubules.

Lysosome: A membrane-enclosed sac of hydrolytic enzymes found in the cytoplasm of animal cells and some protests.

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

Chapter 5: The Structure and Function of Large Biological Molecules

Q: What are the four macromolecules?
A: Carbohydrates, proteins, nucleic acids, and lipids.

Q: What are a dehydration reaction and a hydrolysis reaction?
A: A dehydration reaction occurs when monomers are connected by a reaction in which two molecules are covalently bonded to each other through loss of a water molecule and a hydrolysis reaction is when bonds between the monomers are broken by the addition of water molecules.

Q: What are the four levels of protein structure?
A: The protein structures are: primary structure, secondary structure, tertiary structure, and quaternary structure.

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 5.2
The synthesis and breakdown of polymers

A dehydration reaction occurs when monomers are connected by a reaction in which two molecules are covalently bonded to each other through loss of a water molecule and a hydrolysis reaction is when bonds between the monomers are broken by the addition of water molecules.

Carbohydrates serve as fuel and building material. It has sugar, monosaccharide monomers and there are disaccharides and polysaccharides also. These help strengthen plant cell walls and store glucose for energy, etc.
Lipids are hydrophobic molecules with hydrophilic heads. Their tails are 2 fatty acids and are the lipid bilayers of membranes. When there are three of them with the head of glycerol, it becomes an important energy source.

Key terms

Monosaccharide: The simplest carbohydrates.

Glucose: Most common monosaccharide.

Sucrose: The most prevalent disaccharide.

Lipid: they are the one class of large biological molecules that does not include true polymers, and they are generally not big enough to be considered macromolecules.

Fatty acid: a long carbon chain carboxylic acid.

Polypeptide: polymers of amino acids are called polypeptides.

Amino acids: its organic molecules possessing both carboxyl and amino groups.

Cholesterol: It’s a common component of animal cell membranes and is also the precursor from which other steroids are synthesized.

Glycogen: animals store a polysaccharide called glycogen, a polymer of glucose that is like amylopectin but more extensively branched.

Polynucleotide: nucleic acids are macromolecules that exist as polymers called polynucleotide.

http://www.youtube.com/watch?v=FmGVesd1TKU

Chapter 4: Carbon and the Molecular Diversity of Life

Q: What are some of the major elements of organic molecules?
A: The major elements of organic molecules include Hydrogen with the valence of 1, oxygen valence of 2, nitrogen valence of 3 and carbon with the valence of 4.

Q: What are the types of Isomers?
A: The three types of isomers mentioned in this chapter are structural isomers, geometric isomers, and enantiomers.

Q: What are the functional groups?
A: Functional groups are chemical groups that affect the functions of molecules by participating in the reactions directly. These groups include the hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, and methyl groups.

1. Carbon has 6 electrons with the first 2 in the first shell and 4 in the second shell. Although carbon could either donate or accept the rest 4 electrons to make a full 8 electron shell, most of the time carbon shares its 4 electrons with other atoms in covalent bonds.
2. Organic compounds refer to those that contain carbon, and the study of carbon in chemistry is called organic chemistry.
3. Neither petroleum nor fat dissolves in water; both are hydrophobic compounds because the great majority of their bonds are relatively nonpolar carbon-to-hydrogen linkages.
4. Carbon chains form the skeletons of most organic molecules.
5. Compounds with double bonds make a better chance of being geometric isomers because unlike how single bonds let the atoms to rotate freely about the bond axis, double bonds do not permit such rotation.

Figure 4.4
Valences of the major elements of organic molecules.


This diagram shows the valence of the elements that are important.




This chapter is about carbon and how it is very important including the fact that organisms are made up of chemicals that are based mostly on it. This chapter first starts out by talking about organic chemistry and organic compounds, which are basically carbon compounds. Then, the carbon’s configuration pays a much deal. As mentioned, carbon has 4 valence electrons and 6 electrons in total. Carbon shares its 4 electrons with others, therefore can make large, complex molecules more easily.
There are many different types of carbon molecules, such as hydrocarbons and the isomers. Then, there are the functional groups which affect the molecular function by being directly involved in chemical reactions. One of the groups is the “phosphate” which has the adenosine triphosphate, or ATP that by reacting releases energy.

Key terms

Hydrocarbon: organic molecules consisting of only carbon and hydrogen.

Organic chemistry: compounds containing carbon are said to be organic, and the branch of chemistry that specializes in the study of carbon compounds is called organic chemistry.

Methane: one carbon atom with four hydrogen atoms.

Ethane: two carbon atoms with six hydrogen atoms.

Ethane: two carbon atoms with four hydrogen atoms

Functional group: the chemical groups affect molecular function by being directly involved in chemical reactions; these important chemical groups are known as 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.

Enantionmers are isomers that are mirror images of each other.

Amino acids: an organic molecule possessing both carboxyl and amino groups. Amino acids serve as the monomers of polypeptides.

http://www.youtube.com/watch?v=wmC8Dg4n-ZA

Chapter 3: Water and the Fitness of the Environment

Q: What is the meaning of Polar Molecule?
A: Two ends of the molecule have opposite charges.

Q: What is Cohesion?
A: Hydrogen bonding keeps water molecules close to each other, and this cohesion helps pull water upward in the microscopic water-conducting cells of plants.

Q: What is the different between Acids and Bases?
A: An acid is a substance that increases the hydrogen ion concentration of a solution; a substance that reduces the hydrogen ion concentration of a solution is called a base.

1. Most cells are surrounded by water, and cells themselves are about 70-95% water.
2. Water molecules stay close to each other as a result of hydrogen bonding.
3. Water has a high specific heat.
4. Ice floats because it has less dense than liquid water
5. The high specific heat of water relative to other materials, water will change its temperature less when it absorbs or loses a given amount of heat.

Figure 3.9
the pH scale and pH values of some aqueous solutions.
When the pH scale is 7 it means Neutral H+ = OH-;When H+ > OH- it means Acidic and when H+ <>

Water molecule is the most common in living cells as most cells are 70-95% water. Water sticks to water because the polarity of water results in hydrgen bonding and water also sticks to other molecules because of the same reason. Therefore, it also has a high surface tension. Water expands when it freezes because the distance between water molecules increases from the liquid to the solid form.

Key terms

Cohesion: they hydrogen bonds hold the substance together, a phenomenon called cohesion.

Adhesion: the clinging of one substance to another called adhesion. Surface tension: it is related to cohesion, a measure of how difficult it is to stretch or break the surface of a liquid.

Specific heat: the specific heat is defined as the amount of heat that must be absorbed or lost for 1g of that substance to change its temperature by 1C.

Hydrophobic: having an aversion to water; tending to coalesce and form droplets in water.

Hydrophilic: having an affinity for water. S

olution: a liquid that is a homogeneous mixture of two or more substances.

Solute: a substance that is dissolved in a solution.

Aqueous solution: a solution in which water is the solvent.

http://www.youtube.com/watch?v=qyb4qz19hEk

Chapter 2: The Chemical Context of Life

Q: What is the difference between element and compound?
A: An element is a substance that can’t be broken down to other substances by chemical reactions. A compound is a substance consisting of two or more different elements combined in a fixed ratio.

Q: What are the subatomic particles?
A: Subatomic particles are the particles composing nucleons and atoms.

Q: What is a covalent bond?
A: A covalent bond is a form of chemical bonding that is characterized by the sharing of pairs of electrons between atoms, or between atoms and other covalent bonds.

1. An atom is the smallest unit of matter that still retains the properties.

2. An element’s properties depend on the structure of its atoms.

3. A bond in which electrons are shared equally is a nonpolar covalent bond; a bond which electrons are not shared equally called a polar covalent bond.

4. A molecule’s shape determines the positions of its atom’s valence orbitals.

5. Chemical reactions change reactants into products while conserving matter.

Figure 2.5
Simplified models.





The ones in the middle are the nucleus and this model of a helium atom has two electrons


The nucleus here has 2 neutrons and 2 protons. The two electrons are outside the nucleus.
This chapter is about elements and their structures. Elements are very interesting because of all their particles and many different groups. In an atom, electrons occupy specific energy shells; the electrons in a shell have a characteristic energy level.
Then, there are covalent bonds, ionic bonds, and weak chemical bonds. Covalent bonds are chemical bonds that form when atoms interact and complete their valence shells. Covalent bonds form when pairs of electrons are shared. Ionic bonds are when an atom transfers its electrons and both the atoms become ions, complete ones. A weak chemical bond is considering the hydrogen bonds.

Key terms

Compound: is a substance consisting of two or more different elements combined in a fixed ratio

Neutron: a subatomic particle having no electrical charge, found in the nucleus of an atom.

Protons: a subatomic particle with a single positive electrical charge.

Electrons: a subatomic particle with a single negative electrical charge, one or more electrons move around the nucleus of an atom.

Dalton: a measure of mass for atoms and subatomic particles.

Atomic number: all atoms of a particular element have the same number of protons in their nuclei, the number of protons, which is unique to that element, is called the atomic number.

Mass number: is the sum of protons plus neutrons in the nucleus of an atom.

Radioactive isotopes: is one in which the nucleus decays spontaneously, giving off particles and energy.

Covalent bond: a covalent bond is sharing of a pair of valence electrons by two atoms.

Ionic bond: a chemical bond resulting from the attraction between oppositely charged ions.

http://www.youtube.com/watch?v=fND0ps4EtBg&feature=PlayList&p=8473C4FBD4539A32&playnext=1&playnext_from=PL&index=21

Chapter 1: Introduction: Themes in the Study of LIfe

Q: What is an ecosystem?
A: It is when each organism interacts continuously with its environment, which includes both nonliving factors and other organisms.

Q: Why is evolution considered the core theme of biology?
A: Evolution is the core theme because it is the idea that makes sense of everything we know about living organisms.

Q: How are structure and function correlated in biology?
A: Structure and function are correlated at all levels of biological organization; the form of a biological structure suits its function and vice versa.


1. Evolution is biology’s core theme.
2. Cells can be defined in two main forms: prokaryotic cells and eukaryotic cells.
3. Diversity of life was divided into five kingdoms: plants, animals, fungi, single-celled eukaryotic organisms, and prokaryotes.4. The three domains are named Bacteria, Achaea, and Eukarya. Bothe Bacteria and Achaea are all prokaryotic; All the Eukaryotes are now grouped in domain Eukarya
5. Discovery science and Hypothesis-Based science are the two main forms that scientist use to inquire their study nature.




Diagram: Figure 1.14 Classifying life.

To help organize the diversity of life, biologists classify species into groups that ate then combined into even broader groups.

This chapter is about elements and their structures. Elements are very interesting because of all their particles and many different groups. In an atom, electrons occupy specific energy shells; the electrons in a shell have a characteristic energy level.
Then, there are covalent bonds, ionic bonds, and weak chemical bonds. Covalent bonds are chemical bonds that form when atoms interact and complete their valence shells. Covalent bonds form when pairs of electrons are shared. Ionic bonds are when an atom transfers its electrons and both the atoms become ions, complete ones. A weak chemical bond is considering the hydrogen bonds.

Emergent properties: new properties that arise with each step upward in the hierarchy of life, owing to the arrangement and interactions of parts as complexity increases.

Biosphere: the biosphere includes most regions of land, most bodies of water, and the atmosphere to an altitude of several kilometers.

Ecosystems: an ecosystem consists of all the living things in particular area, along with all the nonliving component of the environment with which life interacts.

Community: the entire array of organisms inhabiting a particular ecosystem is called biological community.

Populations: a population consists of all the individuals of a species living within the bounds of a specified area.

Organism: Individual living things are called organisms.

Organs and organ system: the structural of life continues to unfold as we explore the architecture of the more complex organisms.

Tissues: an integrated group of cells with a common function, structure, or both.

Organelles: any of several membrane-enclosed structures with specialized functions, suspended in the cytosol of eukaryotic cells.

Feedback (negative, positive): Negative feedback, in which accumulation of an end product of a process slows that process. (most common form of regulation)
Positive feedback, in which an end product speeds up its production.

http://www.youtube.com/watch?v=rzjHA2eEsCI