Chapter four: carbon and the molecular diversity of life

Q1: what is the structure of carbon atom?
A1:carbon has 6electrons, with 2 in first electron shell and 4 in the second shell.
Q2: How does carbon exist in biosphere?
A2: Carbon enters the biosphere through the action of plants, which use solar energy to transform atmospheric CO2 into the molecules of life.
Q3: What common things are made of carbon element?
A3: Proteins, DNA, carbohydrates, and other molecules.

Five Facts:
1. Compounds containing carbon are said to be organic, and the study of carbon compounds is callded organic chemistry.
2. carbon can bond with hydrogen, oxygen, nitrogen, and carbon.
3. The carbon skelectons of organic molecules vary in length and shape and have bonding sites for atoms of other elements.
4. The distinctive properties of an organic molecule also depend on the molecular components attached to that skeleton.
5. ATP is an important source of energy for cellular processes.

Figure

Miller set up a simulate condition of origin earth. He evaporated water and mixed gas of water with hydrogen, methane, and ammonia. Under the lightning and cooling, some simple organic molecules were formed. As a result, organic molecules may have been synthesized abiotically on the early earth.

Summary:
Compounds containing carbon are said to be organic, and the study of carbon compounds is callded organic chemistry. 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. Stanley Miller made the organic compound acetic from inorganic substances that could be prepared directly from pure elements.
Carbon atom usually completes its valence shell by sharing its 4 electrons with other atoms in covalent bonds. Tetrahedron is the shape of four single covalent bonds. When two carbon atoms are joined by a double bond, all bonds around those carbons are in the same plane. The shape pf a molecule often determines its function. CO2 is inorganic. Urea is both single and double bonds. Carbon skelectons vary in length, straight, branched, or arranged in closed rings, or vary in number and location. Hydrocabons, organic molecules consisting of only carbon and hydrogen, are hydrophobic. The distinctive properties of an organic molecule also depend on the molecular components attached to that skeleton. Seven most important chemical group are hydroxyl, carboxyl, amino, sulfhydryl, phosphate, and methy groups.


Key Terms:

1. isomer- One of several compounds with the same molecular formula but different structures and therefore different properties.


2. geometric isomer-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.


3. enantiomer-One of two compounds that are mirror images of each other.


4. functional group-A specific configuration of atoms commonly attached to the carbon skeletons of organic molecules and usually involved in chemical reactions.


5. amino group-A chemical group consisting of a nitrogen atom bonded to two hydrogen atoms; can act as a base in solution, accepting a hydrogen ion and acquiring a charge of 1+.


6. carbonyl group-A chemical group present in aldehydes and ketones and consisting of a carbon atom double-bonded to an oxygen atom.


7. carboxyl group-A chemical group present in organic acids and consisting of a single carbon atom double-bonded to an oxygen atom and also bonded to a hydroxyl group.


8. hydroxyl group-A chemical group consisting of an oxygen atom joined to a hydrogen atom. Molecules possessing this group are soluble in water and are called alcohols.


9. 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.


10. phosphate group-A chemical group consisting of a phosphorus atom bonded to four oxygen atoms; important in energy transfer.


11. sulfhydryl group-A chemical group consisting of a sulfur atom bonded to a hydrogen atom.

Video:

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

Isomers of Hexane

Chapter three: Water and the fitness of the environment

Q1: How does the water affect the environment?
A1: Almost all the living things contain water. They release and gain energy by transfer water. Water can control climate by evaporating.
Q2: How is water compounded?
A2: A water molecule has one oxygen atom and two hydrongen atoms. And hydrogen bonds between eater molecules.
Q3: How important is water of the planet Earth?
A3: Three-quater of earth surface is coverd with water. Water is the resource of living things.Living things can not live without water.

Five Facts:
1. Because oxygen is more electronegative, hydrogen bonds are founded.
2. heat is form of energy measured by volume.
3. evaporation is a process that from liquid to air gas
4. hyfrophilic is something likes water; hydrophobic is something repel water
5. acid has high hydrogen concentration; base reduces hydrogen concentration

Figure

Because of the cool environment, ice crystal is founded. All the hydrogen bonding in specific shape, so the dense is less than liquid. So the ice can float above the liquid water. If the environment becomes warmer, hydrogen bonds break and re-from in free.

Summary:
Water has three phsical states: solid, liquid, and gas. Hydrogen bond has cohesion to transfer water against gravity. And water has strong surface tension. Kinekic energy is the energy of motion. Heat is form of energy. A calorie is the amount of heat it takes the temperature of 1g of water by 1℃. Water's specific heat is 1cal. Heat must be absorbed in order to break hydrogen bonds, and released by bonds form. Water evaporation can help cool down. Heat of vaporization is the quantity of heat a liquid must absorb for 1g of it to be converted from the liquid to the gas. At 4℃, water has the biggest density. A solution is a liquid with solvent and solute. An aqueous solution is one in which water is the solvent. Molecular mass is the sum of its atomic mass.
Hydrogen ion, H+. Hydroxide ion OH-. Hydronium ion H3O+. ph is scale of acid and base. H+ and OH- concentrations at 10-14. So the ph is 1-14. 7 is neutral at 25℃. Buffers can control changes of H+ and OH- in blood.

key terms:

1. buffer-A substance that consists of acid and base forms in a solution and that minimizes changes in pH when extraneous acids or bases are added to the solution.


2. calorie (cal)-The amount of heat energy required to raise the temperature of 1 g of water by 1°C; also the amount of heat energy that 1 g of water releases when it cools by 1°C. The Calorie (with a capital C), usually used to indicate the energy content of food, is a kilocalorie.


3. cohesion-The binding together of like molecules, often by hydrogen bonds.


4. evaporative cooling-The process in which the surface of an object becomes cooler during evaporation, owing to a change of the molecules with the greatest kinetic energy from the liquid to the gaseous state.


5. heat of vaporization-The quantity of heat a liquid must absorb for 1 g of it to be converted from the liquid to the gaseous state.


6. hydrophilic- Having an affinity for water.


7. hydrophobic-Having an aversion to water; tending to coalesce and form droplets in water.


8. polar molecule-A molecule (such as water) with opposite charges on different ends of the molecule.


9. specific heat-The amount of heat that must be absorbed or lost for 1 g of a substance to change its temperature by 1°C.


10. surface tension-A measure of how difficult it is to stretch or break the surface of a liquid. Water has a high surface tension because of the hydrogen bonding of surface molecules.

video:

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

hydrogen bond

Chapter two: The chemical context of life

Q1: how do chemicals relate to biology?
A1: Biology is a multidiscplinary science. And chemistry is applied to solve nature problems.
Q2: what are some important matters we should know in chemistry?
A2: compounds, atoms, molecules, and chemical bonds,etc.
Q3: what does make matter?
A3: elements

Five facts:
1. matter is made up of elements; atom is unit of an element; compound contains two or more elements.
2. atom conclude electrons, protons, and neutrons.
3. orbitals: 1s 2s 2p
4. covalent bonds share electrons; electrons transfer in ionic bonds
5. chemical reactions change reactants into products.

Figure

The valence shell of chlorine has 7 electrons. So it needs one more electron from sodium to keep balance. As a result, chlorine and sodium can bond together as ionic bond.

Summary:
Organisms are composed of matter; matter is made up of elements. Carbon, oxygen, hydrogen, and nitrogen make up 96% of living matter. Trace elements are needed rarely by organism. Atomic number is the number of protons; mass number is the sum of protons and neutrons. Isotopes are same element atoms have different neutrons. Potential energy is caused by location and structure. Electrons are founded in different electron shells. The farthest shell is valence shell.
Chemical bond is stoms staying close together. Single bond shares a pair of electrons; double bond shares two. The same atoms are equally electronegative, and the bond is nonpolar covalent bond. Ion is charged atom: cation is positive, anion is nagative. Molecules sharpded as tetrahedron. If the rates of the forward and reverse reactions are equal, the reaction reaches equilibrium.

key terms:

1. atomic mass-The total mass of an atom, which is the mass in grams of 1 mole of the atom.


2. atomic number-The number of protons in the nucleus of an atom, unique for each element and designated by a subscript to the left of the elemental symbol.


3. chemical bond-An attraction between two atoms, resulting from a sharing of outer-shell electrons or the presence of opposite charges on the atoms. The bonded atoms gain complete outer electron shells.


4. chemical equilibrium-In a chemical reaction, the state in which the rate of the forward reaction equals the rate of the reverse reaction, so that the relative concentrations of the reactants and products do not change with time.


5. covalent bond- A type of strong chemical bond in which two atoms share one or more pairs of valence electrons.


6. electronegativity-The attraction of a given atom for the electrons of a covalent bond


7. hydrogen bond-A type of weak chemical bond that is formed when the slightly positive hydrogen atom of a polar covalent bond in one molecule is attracted to the slightly negative atom of a polar covalent bond in another molecule.


8. ionic bond-A chemical bond resulting from the attraction between oppositely charged ions.


9. isotope- One of several atomic forms of an element, each with the same number of protons but a different number of neutrons, thus differing in atomic mass.


10. van der Waals interactions-Weak attractions between molecules or parts of molecules that result from localized charge fluctuations.

Video:

http://www.youtube.com/watch?v=2mzDwgyk6QM&feature=related

sodium chloride

Chpter One: Intronduction: Themes in the study of life

Q1: why is evolution the core theme of biology?
A1: Because evolution is the change of early life to the living things today. We can learn a lot about diversity of organisms from evolution.
Q2: what are the themes of biology?
A2: 1.properties emerge 2.organisms interact with their environments, exchanging matter and energy 3.structure and function are correlated 4. cells are basic units 5. information DNA 6.feedback
Q3: what is the main way to study biology?
A3: Inquiry is the heart of science. Discovery science and hypothesis-based science are two main types.

Five Facts:
1.properties emerge;organisms interact with their environments, exchanging matter and energy;structure and function are correlated;cells are basic units;information DNA;feedback are the themes connect the concepts of biology.

2. evolution accounts for the unity and diversity of life, and also for the match of organisms to their environments
3.contemporary living things are all evolve from their ancetors
4.organisms evolve to adapt to environment
5. dicovery science and hypothesis-based science are the main forms of inquiry



Figure

The tree interact with its environment. It uses energy from sunlight and chemical energy; it produces heat and chemical nutrients to the environment.



Summary:
The evolution is the overarching theme of biology. The level in biological hierarchy is biosphere-ecosystem-community-population-organism-organ system-organ-tissue-cell-organelle-molecule-atom. Reductionism is reduction of complex systems to simpler components that are more manageable to study. In system biology, models are uesed for the dunamic behavior of whole biological systems. Cycling of nutrient and one-way flow of energy from sunlight are two major processes.Eukaryotic cell has nucleus, while prokarytic cell does not. High-throughout, bioibformatics, and development are key research. In negative feedback, accumlation of an end product slows the process that makes that product, on the contract the positive feedback.
Domain bacteria and domain archaea consist of prokaryotes. Domain eukarya includes kingdoms plantae, fungi, and animalia.Charles Darwin found the theory of natural selection. Organisms evolve to adapt to environment. Hypothesis must be testable and falsifiable. Controlled experiment is to keep all constant except one being teated.

key terms:

1. biology-The scientific study of life.


2. controlled experimet-An experiment in which an experimental group is compared with a control group that varies only in the factor being tested.


3. deductive reasoning-A type of logic in which specific results are predicted from a general premise.


4. 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.


5. genome-The genetic material of an organism or virus; the complete complement of an organism’s or virus’s genes along with its noncoding nucleic acid sequences.


6. inductive reasoning-A type of logic in which generalizations are based on a large number of specific observations.


7. inquiry-The search for information and explanation, often focused by specific questions.


8. negative feedback-A primary mechanism of homeostasis, whereby a change in a physiological variable triggers a response that counteracts the initial change.


9. positive feedback-A physiological control mechanism in which a change in a variable triggers mechanisms that amplify the change.


10. system bioligy-An approach to studying biology that aims to model the dynamic behavior of whole biological systems.

Video:

http://www.youtube.com/watch?v=GfQcOZXBBb8

about natural selection