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Sunday, September 27, 2009

Carbon and the Molecular Diversity of Life

What is organic chemistry?

Organic chemistry is the branch of chemistry that specializes in the study of carbon compounds. For historical reasons, compounds containing carbon are said to be organic. Organic compounds range from simple molecules (ex. Methane – CH4), to more complex ones, such as proteins (thousands of atoms). The basis of organic chemistry is the unique chemical versatility of carbon.

How does the electron configuration of carbon determine its covalent compatibility with many different elements?

Carbon has 6 electrons. 4 of these are its valence electrons in the valence shell. Having 4 valence electrons in a shell that holds 8, carbon would have to donate or accept 4 electrons to complete its valence shell and become an ion.

Instead, a carbon atom usually completes its valence shell by sharing his 4 electrons with other atoms by covalent bonds. Bonds can be single or double.

What are isomers and how do we classify them?

Isomers are compounds that have the same numbers of atoms of the same element but different structures and hence different properties.

Three types of isomers are:

structural isomers

differ in the covalent partners (arrangements of their atoms)

geometric isomers

differ in their spatial arrangements (same covalent partnerships)

enantiomers

differ in spatial arrangement around an asymmetric carbon (“mirror” images of each other)

Facts

Living matter is made mostly of carbon, oxygen, hydrogen and nitrogen, with some sulfur and phosphorus.

The foundation of organic chemistry is not some intangible life force, but the unique chemical versatility of the element carbon.

Carbon has 6 electrons, with 2 in the first shell and 4 in the valence shell (tetravalence)

Hydrocarbons (look in key terms) can undergo reactions that release a relatively large amount of energy.

Hydrocarbons consist only of carbon and hydrogen.

Key terms:

Organic Chemistry = branch of chemistry that specializes in the study of carbon compounds

Vitalism = the belief in a life force outside the jurisdiction of physical and chemical laws

Mechanism = the view that physical and chemical laws govern all natural phenomena, including the process of life

Tetravalence = ability of the molecule to branch off in as many as four directions

Hydrocarbons = Organic molecules made of only carbon and hydrogen

Isomers = Compounds with the same molecular formula but have different structures

Enantiomers = molecules that are mirror images of each other.

Functional groups = A group of atoms attached to a carbon skeleton

ATP = adenosine triphosphate, an important source of energy

ADP = adenosine diphosphate, product of losing one phosphate from ATP

Summary:

Of all chemical elements, carbon is unparalleled in its ability to form molecules that are large, complex and diverse, and this molecular diversity has made possible the diversity of organisms that have evolved on Earth. The study of carbon compounds is called organic chemistry (see more in next chapter). Carbon has 6 electrons and 4 of them are in the valence shell and it can easily accept or give 4 other electrons, making covalent bonds with other atoms. Some of the examples for the molecular diversity arising from carbon skeleton variations are isomers (take a look up on the page). Furthermore, functional groups, important chemical groups attach to carbon skeletons, making important biological molecules.

Extra:

Stanley Miller experiment (video)


Thursday, September 17, 2009

Water and the Fitness of the Environment

Why is water important for us?

Water is the substance that makes life possible as we know it on Earth. It is the biological medium here, and possibly on other planets as well.

Furthermore, life on Earth began in water and evolved there for 3 billion years before spreading onto land.

All living beings require water more than any other substance. A human couldn't survive without water more than a week or so.


Which are four emergent properties of water?

- Cohesion

- Moderation of temperature

- Insulation of bodies by floating ice

- The solvent of life



What is a pH scale?

The pH scale measures how acidic or basic a substance is. The pH scale ranges from 0 to 14. A pH of 7 i

s neutral. A pH less than 7 is

acidic. A pH greater than 7 is basic.


Facts:

- 3/4 of Earth's

surface is submerged in water.

- Water is the only common substance to exist in the natural environment in all 3 physical states of matter (solid, liquid, gas).

- The high surface tension of water, resulting from the collective strength of its hydrogen bonds,

allows the water strider (eg.) to walk on the surface of apond.

- Heat passes from the warmer to the cooler object until

the two are the same temperature.

- A compound does not have to be ionic to dissolve in water (eg. sugar).


Summary:

Water is the substance that makes life possible as we know it on Earth. 3/4 of Earth's surface is submerged in water. Some (cohesion, moderation of temperature, insulation of bodies of water by floating ice, the solvent of life) of the emergent properties of water contribute to Earth’s fitness for life.

The concentration of hydrogen is expressed as pH. The pH scale ranges from 0 to 14. A pH of 7 is neutral. A pH less than 7 is acidic. A pH greater than 7 is basic. The burning of fossil fuels results in emission of oxides (leading to acid precipition) and increasing amounts of CO2. Some of the CO2 becomes dissolved in the oceans, lowering pH and potentially affecting the rate of calcification on coral reefs.


Key words:

polar molecule = molecule whose two ends have opposite charges

cohesion = the binding together of like molecules, often by hydrogen bond

adhesion = the clinging of one substance to another

kinetic energy = energy of motion

heat = form of energy

temperature = a measure of heat intensity (average kinetic energy of the molecules)

vaporization (evaporation) = transformation from liquid to gas

heat of vaporization = the quantity of heat a liquid must absorb for 1 g to be converted from the liquid to the gaseous state

solution = a liquid that is completely homogeneous mixture of two or more substances

solvent = dissolving agent of a solution

solute = substance that is dissolved

acid = a substance that increases the hydrogen ion concentration of a solution

base = a substance that reduces the hydrogen ion concentration of a solution


Extra:

surface tension

Sunday, September 13, 2009

The Chemical Context of Life

Which are essential elements of life?

About 25 out of 92 natural elements are known to be essential to life. Just 4 of these make up to 96% of living matter:
- carbon (C)
- oxygen (O)
- hydrogen (H)
- nitrogen (N)
The remaining 4% making up a living matter are Calcium, Phosphorus, Potassium, Sulfur, Sodium, Chlorine, Magnesium and traces of some other elements.

When do we use radioactive tracers?
Radioactive tracers are important diagnostic tools in medicine. For eg., certain kidney disorders can be diagnosed by injecting small doses of substances containing radioactive isotopes into the blood and then measuring the amount of tracer excreted in the urine. Radioactive tracers are also used in combination w
ith sophisticated imaging instruments, such as PET scanners, which can monitor chemical processes, such as those involved in cancerous growth as they actually occur in the body.

How and what do chemical reactions do to chemical bonds?
Chemical reactions make and break chemical bonds, they change reactants into products. Theoretically, all chemical reactions are reversible, so the bonds can always be made and broken again.

Facts:
- Elements cannot be broken down
chemically to other substances.
- Carbon, oxygen, nitrogen and hydrogen make up to 96% of living matter.
- One of the most serious environmental treats is radioactive fallout from nuclear accidents.
- Electrons exist in orbitals, 3D spaces with specific shapes that are components of electron shells.
- Electrons of a more polar covalent bond are pulled closer to the more electronegative atom.

Summary:
About 25 out of 92 natural
elements are known to be essential to life. Elements cannot be broken down chemic
ally to other substances.
An atom, the smallest unit of an element has a nucleus that is made out of neutrons and protons and electrons. electrons exist in orbitals, 3D spaces with specific shapes that are components of electron shells.
There are different types of c
ovalent bonds shared by two atoms: single/double, polar/non-polar.. Ionic bonds (chemical bonds between oppositely charged ions) form ionic compounds, also called salts (eg. NaCl). NaCl is a product made out of Na and Cl as reactants in a chemical reaction (the making and breaking of chemical bounds, leading to changes in
the composition of matter).

Key Words:
matter = anything that takes up space and has a mass
element = substance that cannot be broken down to any other substance by any chemical reactions
compound = substance consisting in two or more different elements combined in a fixed ratio
atom = the smallest unit of matter that still retains the properties of an element
dalton = atomic mass unit (John Dalton, developed atomic theory, 1800.)
atomic number = number of protons, subscript to the left of the symbol
mass number = sum of the protons and neutrons in the nucleus of an atom, superscript to the left of the symbol
energy = capacity to cause change, especially to do work
orbital = 3D space where electron is found 90% of the time
valence = bonding capacity, usually equals to number of unpaired electrons


Extra:
Positron-emission tomography (PET scan) on YouTube

INTRODUCTION: Themes in the Study of Life


What is life?


"We recognize life by what living things do."
What do living things do? (properties of life)
  • energy processing (eg. hummingbird will use nectar from flowers as a "fuel" to power its flight and other work)
  • evolutionary adaption (eg. bowl shape of flowers allows bugs easy access to their organs to carry pollen from one flower to another)
  • growth and development (inherited information carried by genes controls the pattern of growth and development)
  • regulation (eg. regulation of blood helps maintain constant body temperature..)
  • reproduction (organism reproduce their own kind --> a dolphin will have a baby dolphin)
  • response to the environment (eg. a Venus flytrap will close its trap rapidly in response to the environmental stimulus of a damselfly landing on yhe open trap)
  • order (structure)
Which are levels of biological organization?
  1. The Biosphere - the entire portion of Earth inhabited by life
  2. Ecosystems - all the organisms in the given area as well as the abiotic factors with which they interact (eg. grasslands, deserts...)
  3. Communities - all the organisms that inhabit a particular area (eg. plants in a forest ecosystem)
  4. Populations - all the individuals of a spicies living within the bounds of a specified area (eg. a population of white-tailed deer)
  5. Organisms - individual living things
  6. Organs and Organ Systems - specialized centers of body functions composed of several different types of tissues (organs)
  7. Tissues - integrated groups of cellswith a common function, structure or both
  8. Cells - fundamental units of structure and function
  9. Organelles - any of several membrane-enclosed structures with specialized structures (eg. chloroplasts)
  10. Molecules - chemical structures consisting of two or more small chemical units called atoms (eg. chlorophyll)
How do we classify life?

species..genus..family..order..class..phylum..kingdom..domain

eg. Ursus americanus (American black bear)..Ursus..Ursidae..Carnivora..Mammalia..Chordata..Animalia..Eukarya

Facts (in this chapter):
- Evolution is Biology's core theme! ("Nothing in biology makes sense except for the light of evolution.")
- Organism interact with their environments, exchanging matter and energy.
- Cells are organism's basic units of structure and function.
- Feedback mechanism regulate biological systems.
- Observations may be interesting but cannot be verified as evidence.

Summary:
Evolution (the process of change that has transformed life on Earth from its earliest beginnings to the diversity of organisms living today) is biology's core theme. It's the idea that makes sense of everything we know about living organisms. Scientists take evolution as explanation for diversity and suitability of organisms to their environment. The study of life extends from the microscopic scale of the molecules and cells that make up organisms to the global scale of the entire living planet (*look up: Which are levels of biological organization?).
Structure and function are correlated at all levels of biological organization.
Diversity is a hallmark of life. Biologists have identified and named 1.8 million species. The enormous variety of life is now classified in groups that are very closely related (*look up: How do we classify life?).
Scientists use two main forms of inquiry in their study of nature: discovery science and hypothesis-based science. Finally, science cannot address the possibility of supernatural phenomena because hypothesis must be testable and falsifiable, and observations and experimental results must be repeatable.

Key terms:
biology = ongoing inquiry about the nature of life
evolution = the process of change that has transformed life on Earth from its earliest beginnings to the diversity of organisms living today
reductionism = the reduction of complex systems to simpler components that are more managable to study
cell = organism's basic units of structure and function
system = a simply combination of components that function together
gene = a discrete unit of hereditary information consisting of a specific nucleotide sequence in DNA/RNA (in some viruses)
DNA = deoxyribonucleic acid (DNA on YouTube)
genome = the entire "library" of genetic instructions that an organism inherits
inquiry = a search for information and explanation
hypothesis = tentativ answer to a well framed question