Download 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.
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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
linear vs rings:
butane
1- butene
cyclohexane
2-butene
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)
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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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