Bio 210 Cell Chemistry Lecture 3 Carbon Chemistry
Bio 211 Intro Molecular and Cell Biology Cell Chemistry II
Lecture 3 "Carbon Chemistry"
Reading: Campbell Chap. 4
In the previous lecture we reviewed some chemistry important for understanding what goes on in cells. We learned about some of the elements that comprise life and how chemical bonds are formed between atoms such as oxygen and hydrogen to form molecules. Today we will focus further on the role of the element carbon to the reactions that take place in cells.
Outline:
1. Atomic structure of carbon
2. Carbon skeletons
3. Functional groups
Although a cell is 70-95% water, the rest consists of carbon-based compounds. The molecules that distinguish matter from living things include proteins, DNA, carbohydrates and fats and all are composed of carbon atoms bonded to one another and to atoms of hydrogen, oxygen, nitrogen, sulfur or phosphorus.
Organic chemistry is the study of carbon compounds. Many of you will be taking organic chemistry in order to develop a real feeling for the chemistry of carbon. Today’s lecture is meant to introduce you to some key features of carbon that you need to know for the study of living things. The carbon-based molecules of living things abide by the same chemical and physical laws that work on carbon molecules from non-living things.
1. Atomic structure of carbon. You may remember from the previous lecture that carbon has an atomic number of 6, meaning it has 6 protons and 6 electrons. The six electrons consist of 2 which fill the innermost shell and 4 in the second (valence) shell. Having 4 electrons in a shell that hold eight means that carbon has little tendency to gain or lose electrons.
The carbon atom completes its valence shell by sharing electrons with other atoms in 4 covalent bonds. In biomolecules, carbon tends to bond with the atoms shown on the left of Fig. 4.3: hydrogen, oxygen and nitrogen, atoms that also tend to share electrons.
We can draw the bonds formed by carbon using different models and formulas, as shown in Fig. 4.2. (Get some different models to pass around the class).
Carbon with 4 single bonds is said to be “tetrahedral” in structure, with the carbon in the center, bonds emerge at an angle of 109 degrees compared to any other bond. In a single bond, one pair of electrons is shared between 2 atoms.
Carbon with double bonds contain a region in the same plane. Rotation around a carbon-carbon double bond is severely restricted. In a double bond, two pairs of electrons is shared between 2 atoms.
These “rules” about the bonds formed by carbon help us predict for different carbon compounds what the structure will be.
2. Carbon skeletons
Ways in which carbon chains can vary (Fig. 4.4):
short vs. long: ethane (2 C) propane (3 C) butane (4 C)
unbranched vs. branched: butane isobutane
single bonds vs. double bonds: butane 1- butene 2-butene
linear vs rings: butane cyclohexane benzene
Isomers: compounds that have the same formula, but different structures and different properties.
butane and isobutane C4H10
Types of isomers: Fig. 4.6
a. structural
b. geometric
c. enantiomers
Structural isomers: vary in the arrangement of atoms, for example butane and isobutane.
Geometric isomers: vary in arrangement about a double bond. “cis” vs. “trans” double bonds.
Enantiomers: molecules that are mirror images of each other.
Fig. 4.7 L-Dopa, biologically active neurotransmitter; D-Dopa, no effect
3. Functional groups: Groups attached to a carbon skeleton that affect its reactivity.
Major types: Table 4.1
a. hydroxyl R-OH; alcohols; ethanol
b. carbonyl R-CHO; aldehydes and ketones; propanol and acetone
c. carboxyl R-COOH; carboxylic acids; acetic acid (vinegar)
d. amino R-NH3; amines; glycine (amino acid)
e. sulfhydryl R-SH; thiols; mercaptoethanol
f. phosphate R-PO4; organic phosphates; glycerol phosphate (in fats)
R = carbon skeleton. Note that carboxyl groups form weak acids, amino groups form weak bases.
Exercise: Functional groups in molecules. Each row gets a vial with a chemical. Each person in the row should examine the vial and determine what kind of functional groups are on the molecule.
Summary: Today we have gotten up close and personal with the element carbon. We’ve looked at the bonds it forms, the different structures it adopts and identified the chemical groups that typically are attached to carbon, particularly in biological molecules. The chemistry of carbon determines the chemistry of most of the processes that go on in cells. In the next two lectures we will look specifically at some of the carbon-containing molecules that make up life forms. These include carbohydrates (sugars) and fats (lipids), nucleic acids and proteins.
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