CA Science Framework - STANDARD SET 6. Chemistry of Living Systems

6. Principles of chemistry underlie the functioning of biological systems. As a basis for understanding this concept:

a. Carbon, because of its ability to combine in many ways with itself and other elements, has a central role in the chemistry of living organisms

CARBON

[Formation of Methane]Of the naturally occurring elements, carbon is probably the most important organic element. On the Periodic Table, carbon is the first member of Group IV. Group IV members have four valence electrons, so they can become stable by either losing or gaining four electrons. Other groups will either lose or gain electrons, but with Group IV's flexibility, these atoms, particularly carbon, tend to share electrons.

Sharing electrons forms strong covalent bonds between atoms. Group IV atoms can form four covalent bonds, one for each electron. Remember that electrons have a negative charge. So these electrons repel each other. For the bonds to become stable, they must lie equal distance from each other. This arrangement forms a tetrahedron. A tetrahedron is like a camera tripod, with the legs and camera stand having equal lengths. Of the Group IV atoms, carbon forms the most stable covalent bonds.

Carbon is also unique in that it can form very stable bonds with other carbon atoms. It is this nature that forms the foundation for organic molecules. Proteins, sugars, fats and genetic material is made with a carbon backbone, upon which other elements are attached.

[Formation of Sodium Chloride] Because carbon has four valence electrons, one in each of the four pairs, it is more willing to share electrons with another atom (rather than grabbing them or giving them up). For example, methane is one atom of carbon bonded to four atoms of hydrogen. This would have the chemical formula, CH4. When atoms share electrons as they bond together, this is called a covalent bond. Many compounds with covalent (co- = with, together; valent = strength) bonds are not water soluble. Carbon can also form covalent bonds with other atoms of carbon, thus making long, stable chains possible. These are very important to living organisms.

The shape of a molecule of methane is a tetrahedron. The hydrogen nuclei (one proton each) are all “trying” to get as close as possible to all the electrons around the carbon, yet keep as far away as possible from each other (like + and – poles on a magnet). In a tetrahedron, there are four sides, all of which are triangles (in a pyramid, the bottom is square and there are five sides). The hydrogen protons are equally spaced in three dimensions around the carbon.

 

b. Living organisms are made of molecules consisting largely of carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur.


Naturally Occurring Elements in the Human Body

Symbol

Element

Atomic Number

% Human Body Weight

O

Oxygen

8

65.0

C

Carbon

6

18.5

H

Hydrogen

1

9.5

N

Nitrogen

7

3.3

Ca

Calcium

20

1.5

P

Phosphorus

15

1.0

K

Potassium

19

0.4

S

Sulfur

16

0.3

Na

Sodium

11

0.2

Cl

Chlorine

17

0.2

Mg

Magnesium

12

0.1

From Cummings et al. Table 2.1, Biology. 2001.

Organic Elements

The organic elements are those elements commonly found in living organisms. They compose the building blocks for our organic molecules, like proteins, sugars, fats, and genetic material. These elements also consist of ions needed for common organic processes, like nerve cells communicating with each other, moving muscles, or releasing adrenaline. The most common organic elements are oxygen, carbon, hydrogen and nitrogen. Together, these atoms form 96.3% of the Human body by weight. The following table shows the most commonly occurring natural elements found in the Human Body.

 

c. Students know that living organisms have many different kinds of molecules, including small ones, such as water and salt, and very large ones, such as carbohydrates, fats, proteins, and DNA.

Organic building blocks

Organic Group

Formula

Compounds

Methyl

—CH3 and —CH2

proteins, carbohydrates, lipids, nucleic acids, etc.

Hydroxyl

—OH

alcohol

Carboxyl

—COOH and —COO–

proteins, lipids

Amino

—NH2

proteins, amino acids, nucleic acids

Sulfydrl

—SH

some amino acids, Thiols

Phosphate

—PO4

organic phosphates like ATP, DNA, RNA

 

 

Bio-Chemistry Framework
 Because all living organisms are made up of atoms, chemical reactions take place continually in plants and animals , including humans. The uniqueness of organic chemistry stems from chain polymers. Life could not exist without the ability of some chemicals to join together, repetitively, to form large, complex molecules. Concepts learned in this standard set are critical for understanding fully the chemistry of the cells of organisms, genetics, ecology, and physiology that will be taught in the high school biology/life sciences standard sets.
 

6.a. Carbon is unique among the elements because it can bond to itself and to many other elements. This attribute makes possible many different kinds of large, carbon-based molecules. Typically, carbon will make four separate covalent bonds (to other carbon atoms), but double and triple bonds are also possible. The variety of bonds allows carbon-based molecules to have a wide range of shapes and chemical properties. Key shapes include tetrahedral (e.g., methane and carbon tetrachloride), planar (e.g., formaldehyde and ethylene), and linear (e.g., acetylene and carbon dioxide). Students can research the nomenclature, composition, and structure of organic molecules by using textbooks and supplemental instructional mate-rials. They can also construct models of carbon-based molecules by using commercial modeling kits or inexpensive alternatives (e.g., gumdrops and tooth-picks).

TastyMoleculesLab
6.b. Living organisms are made up of a great variety of molecules consisting of many atoms (with carbon atoms playing the main roles), but the number of different elements involved is quite small. Carbon and only five other elements make up most of Earth’s biomass. Those six elements, however, can combine in many different ways to make large, organic molecules and compounds. To demonstrate this idea, teachers may burn organic material, such as bone, leaves, wood, or a variety of candles. They may hold a cold glass or plate above the flame to condense droplets of water, one of the combustion products. They may also hold a heat-treated glass in the flames to collect carbon deposits in the form of soot. Students can discuss what elements were in the organic material. Teachers may draw students’ attention to the black material that forms when meat is roasted or grilled or when toast is charred.
 

6. c. Students know that living organisms have many different kinds of molecules, including small ones, such as water and salt, and very large ones, such as carbohydrates, fats, proteins, and DNA.

Living organisms require a variety of molecules; some molecules contain carbon and some do not. The molecules that make up organisms and control the biochemical reactions that take place within them are usually large molecules, such as DNA, proteins, carbohydrates, and fats. Organisms also require simple substances, such as water and salt, to support their functioning.
 

 

 

General Chemistry Topic Review http://chemed.chem.purdue.edu/genchem/topicreview/index.html

Organic Chemistry:http://chemed.chem.purdue.edu/genchem/topicreview/bp/1organic/organic.html

Biochemistry is the study of the chemistry of living organisms. Biomolecules are often sorted into four categories:

(1) Proteins

(2) Carbohydrates

(3) Nucleic Acids

(4)Lipids

The term protein comes from the Greek proteios, which means "of first importance."

The term carbohydrate reflects the fact that many of the compounds in this category  are literally "hydrates of carbon."

 The name nucleic acid was originally given to a class of relatively strong acids that were found in the nuclei of cells. Biological system molecules that are soluble in nonpolar solvents (from the Greek lipos, fat).
These compounds serve the broadest array of functions of any class of bio-molecules, including:
Structure: The actin and myosin in muscles, the collagen in skin and bone, and the keratins in hair, horn, and hoof are examples of proteins whose primary function is to produce the structure of the organism.
Catalysis: Most chemical reactions in living systems are catalyzed by enzymes, which are proteins.
Control: Many proteins regulate or control biological activity. Insulin, for example, controls the rate at which sugar is metabolized.
Energy: Some proteins, including the casein in milk and the albumin in eggs, are used primarily to store food energy.
Transport: O2 is carried through the bloodstream by hemoglobin and myoglobin. Other proteins transport sugars, amino acids, and ions across the cell membranes.
Protection: The first line of defense against viruses and bacteria are the antibodies produced by the immune system, which are based on proteins.

 

 Carbohydrates are the primary source of food energy for most living systems.

They include simple sugars such as glucose (C6H12O6) and sucrose (C12H22O11) as well as polymers of these sugars such as starch, glycogen, and cellulose.

Carbohydrates are produced from CO2 and H2O during photosynthesis and are therefore the end products of the process by which plants capture the energy in sunlight.

 As monomers, nucleic acids such as adenosine triphosphate (ATP) are involved in the process by which cells capture food energy and make it available to fuel the processes that keep cells alive.

As polymers, they store and process the information that allows the organism to grow and eventually reproduce.

  Lipids  are defined on the basis of their physical properties.

 The lipid known as cholesterol, for example, is virtually insoluble in water, but it is soluble in a variety of nonpolar solvents including the nonpolar region between the inner and outer surfaces of a membrane.

 

The Chemistry of Hemoglobin and Myoglobin

Protein Biosynthesis

Research in the 1990s: The Search for New Drugs

Amino Acids

SAS Chem – Elements  http://www.starsandseas.com/SAS%20OrgChem/SASElements.htm

 Library of PDB files for molecules alphabetically http://www.wellesley.edu/Chemistry/Flick/molecules/newlist.html
 
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