Campbell Biology · Chapter 4

Carbon and the Molecular Diversity of Life

pp. 58–67 · 3 sections

This chapter explains why carbon sits at the center of life's chemistry. Carbon makes four bonds, so it can build chains, branches and rings, and a short list of chemical groups attached to those skeletons sets how each molecule behaves. These ideas set up the macromolecules in Unit 1 and come back later with DNA, ATP and gene regulation.

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Chapter quiz (37 questions)Flashcards (39 terms)

4.1 Carbon compounds and the end of vitalism

pp. 58–59

On the AP exam? Yes

Topics 1.2 and 7.12 cover the elements living things are built from and the idea that organic molecules can form without life; you won't be asked about vitalism or the chemists' names.

In the course: Topic 1.2 Elements of Life, Topic 7.12 Origins of Life on Earth (notes, videos and more questions)

Key points

Organic chemistry is the chemistry of carbon compounds. A carbon-based molecule counts as organic whether a cell made it or a chemist did.
Four elements, carbon, hydrogen, oxygen and nitrogen, make up the bulk of every cell. Phosphorus (in DNA, RNA, ATP and phospholipids) and sulfur (in some amino acids) are needed in smaller amounts. The proportions barely change from bacteria to trees to people; species differ in which molecules those atoms are built into.
Vitalism was the old belief that organic compounds needed a special life force to form. Chemists in the 1800s made urea and then other organic compounds from nonliving starting materials, and the idea faded away.
Biologists now assume that living things follow the same physical and chemical laws as everything else.
In 1953, Stanley Miller, working in Harold Urey's lab, sent electric sparks through a mix of gases above heated water and got amino acids and other organic molecules. Life's building blocks can form without life.
Today many scientists think the early atmosphere was richer in CO₂ and N₂ than Miller's gas mix. Later experiments with other mixtures and conditions, plus amino acids found in meteorites, still support the idea that organic molecules can form without life.
Almost all the carbon in living things first entered the living world as CO₂ taken in by plants, algae and other photosynthesizers, which build it into sugars that other organisms then eat.

Key terms (9)

organic compound: A compound built on carbon, usually with carbon bonded to hydrogen. It's organic whether a cell or a lab made it.
organic chemistry: The study of carbon-based compounds: how they're built and how they react.
inorganic compound: A compound that isn't built on a carbon skeleton, like water, table salt or ammonia. A few simple carbon compounds, such as CO₂, are usually counted as inorganic too.
major elements of life: The six elements most living matter is built from: C, H, O and N in large amounts, with smaller but essential amounts of P and S.
vitalism: An old idea that organic compounds can only form with the help of a special life force. Lab-made organic compounds disproved it.
mechanism: The view that living things run on the same physical and chemical laws as nonliving matter. It replaced vitalism.
urea: A small organic compound containing nitrogen, found in urine. Making it in a lab in 1828 was an early blow to vitalism.
abiotic synthesis: Organic molecules forming through ordinary chemistry, with no living things involved.
Miller–Urey experiment: A 1953 experiment that sparked a mix of gases above heated water and produced amino acids. It showed that life's building blocks can form without life.

Check yourself: 4.1 Carbon compounds and the end of vitalism

4 questions on 4.1 Carbon compounds and the end of vitalism. Pick an answer to see if you got it, and why.

Question 1 of 4

Which of these substances would a chemist today classify as an organic compound?

Question 2 of 4

Which finding did the most to weaken vitalism, the idea that organic compounds can come only from living things?

Question 3 of 4

A purified biological molecule contains carbon, hydrogen, oxygen and nitrogen, but no phosphorus or sulfur. Which of the following could it be?

Question 4 of 4

A researcher runs a Miller–Urey-style experiment: a sealed, sterilized apparatus holds heated water, a mix of gases that includes methane (CH₄), and electrodes that fire sparks. After a week, amino acids are found in the water. She wants to know whether the carbon in those amino acids came from the methane. Which approach would best answer that question?

0 of 4 answered

4.2 Carbon's four bonds and molecular shape

pp. 60–63

On the AP exam? Background

Background for Unit 1: the exam won't ask you to name isomer types or give bond angles, but it expects you to know that C–H chains are nonpolar and that a molecule's shape decides what it can do.

In the course: Topic 1.1 Structure of Water and Hydrogen Bonding, Topic 1.2 Elements of Life, Topic 1.5 Lipids, Topic 1.7 Proteins (notes, videos and more questions)

Key points

Carbon has four electrons in its outer shell, so it usually forms four covalent bonds. Each carbon can act as a junction that links up to four neighbors, including other carbons.
Common bond counts: hydrogen forms 1, oxygen 2, nitrogen 3 and carbon 4. These rules decide which structures are possible.
A carbon with four single bonds is tetrahedral, with bonds about 109.5° apart. A C=C double bond holds the atoms around it flat and stops them from rotating.
Lengthen a chain, add a branch, move a double bond or close the chain into a ring, and you get a new molecule with new properties. That's one reason a handful of elements can make an enormous number of compounds. The number of possible arrangements climbs very fast as the skeleton gets longer.
Hydrocarbons contain only carbon and hydrogen. C–H bonds are nearly nonpolar, so hydrocarbon chains, like the tails of fats, are hydrophobic and also store a lot of energy.
Isomers have identical formulas but different structures: structural isomers are connected differently, cis-trans isomers differ around a double bond, and enantiomers are mirror images built around an asymmetric carbon.
Cells notice even mirror-image differences. Receptors and enzymes are shaped to fit one enantiomer, so the two forms of a molecule can smell, taste or act as drugs very differently.

Key terms (15)

valence: How many covalent bonds an atom of an element usually makes: 1 for hydrogen, 2 for oxygen, 3 for nitrogen and 4 for carbon.
valence electrons: The electrons in an atom's outermost shell. Carbon has four, so it shares four more to fill that shell.
covalent bond: A bond in which two atoms share a pair of electrons.
double bond: Two shared pairs of electrons between the same two atoms. A C=C double bond keeps nearby atoms in one flat plane and stops them from rotating.
tetrahedral shape: The 3D shape around a carbon with four single bonds: the bonds point to the corners of a triangular pyramid, about 109.5° apart.
carbon skeleton: The chain or ring of carbon atoms that forms the backbone of an organic molecule.
hydrocarbon: A molecule made only of carbon and hydrogen. Hydrocarbons are nonpolar and release a lot of energy when they react with oxygen.
hydrophobic: Water-fearing: it doesn't mix with water, usually because it's nonpolar.
molecular formula: A formula that counts the atoms of each element in a molecule, like C₂H₆O, without showing how they're connected.
structural formula: A drawing that shows which atoms are bonded to which, with one line for each shared pair of electrons.
isomers: Molecules built from exactly the same atoms, in the same numbers, but put together differently, which gives them different properties.
structural isomers: Isomers whose atoms are connected in a different order, such as a straight chain versus a branched one.
cis-trans isomers: Isomers that differ in which side of a double bond their groups sit on: the same side (cis) or opposite sides (trans).
enantiomers: Isomers that are mirror images of each other, like your left and right hands, and can't be stacked to match.
asymmetric carbon: A carbon bonded to four different atoms or groups. It's what makes a pair of enantiomers possible.

Check yourself: 4.2 Carbon's four bonds and molecular shape

4 questions on 4.2 Carbon's four bonds and molecular shape. Pick an answer to see if you got it, and why.

Question 1 of 4

Carbon has six electrons: two in its first shell and four in its outer shell. Which statement best explains why carbon can form the backbone of so many different molecules?

Question 2 of 4

Using the usual numbers of covalent bonds (H forms 1, O forms 2, N forms 3, C forms 4), how many hydrogen atoms are needed to complete a molecule whose skeleton is C–C–N, with all single bonds?

Question 3 of 4

Many plant leaves are coated with a wax made mostly of long hydrocarbon chains, which contain only carbon and hydrogen. Rain beads up on these leaves instead of soaking in. Which property of the wax molecules best explains this?

Question 4 of 4

Ethanol and dimethyl ether both have the formula C₂H₆O. In ethanol, the oxygen is bonded to a carbon and a hydrogen (–OH); in dimethyl ether, the oxygen sits between two carbons (C–O–C). Ethanol boils at about 78 °C, while dimethyl ether boils at about −24 °C. Which statement best describes and explains these facts?

0 of 4 answered

4.3 Chemical groups and ATP

pp. 63–66

On the AP exam? Yes

You won't have to draw all seven groups, but the exam uses the amino and carboxyl ends of proteins, the phosphate and 3′ hydroxyl ends of DNA and RNA, ATP hydrolysis and DNA methylation (Topics 1.6, 1.7, 3.3 and 6.5).

In the course: Topic 1.3 Introduction to Macromolecules, Topic 1.6 Nucleic Acids, Topic 1.7 Proteins, Topic 3.3 Cellular Energy, Topic 6.5 Regulation of Gene Expression (notes, videos and more questions)

Key points

A carbon skeleton is only the frame. The small clusters of atoms attached to it largely decide whether a molecule dissolves, acts as an acid or base, or reacts with other molecules. Groups that react in a predictable way are called functional groups. Small swaps matter: trade one –OH on ribose for an –H and you get deoxyribose, the sugar that makes DNA different from RNA.
Seven groups to know: hydroxyl (–OH), carbonyl (C=O), carboxyl (–COOH), amino (–NH₂), sulfhydryl (–SH), phosphate (–OPO₃²⁻) and methyl (–CH₃). Compounds are often named for their group: alcohols (–OH), aldehydes and ketones (C=O at the end or in the middle of the chain), carboxylic acids, amines and thiols.
Six of the seven are polar or charged and make a molecule more water-friendly. Methyl is the odd one out: nonpolar and unreactive, it mostly serves as a mark that other molecules can recognize.
In cells, a carboxyl group usually gives up H⁺ (acid, –COO⁻) and an amino group usually picks one up (base, –NH₃⁺). Amino acids carry both groups.
Two sulfhydryl groups on cysteines can join into a disulfide bridge that helps lock a protein's shape.
Phosphate groups add negative charge and link nucleotides in DNA and RNA; each strand has a 5′ phosphate end and a 3′ hydroxyl end. Methyl marks on DNA usually quiet a gene, and marks on histones can turn genes up or down, all without changing the DNA sequence.
ATP is adenosine with three phosphates. When water splits off the last phosphate, you get ADP and inorganic phosphate, and the reaction releases energy the cell can couple to work.

Key terms (15)

chemical group: A small cluster of atoms attached to a carbon skeleton that affects how the molecule behaves.
functional group: A chemical group that reacts in a predictable way wherever it shows up, such as a carboxyl group acting as an acid.
hydrophilic: Water-loving: it attracts water, because it's polar or charged. Six of the seven key chemical groups are hydrophilic and help a molecule dissolve.
hydroxyl group: An –OH attached to a carbon. It's polar and hydrogen bonds with water, which helps sugars dissolve. It isn't the same as the hydroxide ion, OH⁻.
carbonyl group: A carbon double-bonded to an oxygen (C=O). At the end of a carbon chain it makes an aldehyde; inside the chain it makes a ketone.
carboxyl group: –COOH. It acts as an acid, giving up H⁺ to become –COO⁻, so it's usually negatively charged in cells.
amino group: –NH₂. It acts as a base, picking up H⁺ to become –NH₃⁺, so it's usually positively charged in cells.
sulfhydryl group: –SH. Two of them can link into a disulfide bridge, which helps hold a protein's shape.
disulfide bridge: A covalent S–S bond between the side chains of two cysteines in a protein.
phosphate group: A phosphorus atom bonded to four oxygens. It gives a molecule negative charge and links the nucleotides in DNA and RNA.
methyl group: –CH₃. It's nonpolar and doesn't react much. Cells attach it to DNA or histone proteins as a mark that helps switch genes up or down.
amino acid: A molecule with an amino group, a carboxyl group and a side chain. Amino acids are the monomers of proteins.
ATP: Adenosine triphosphate: adenosine attached to a chain of three phosphates. When water splits off the last phosphate, ATP becomes ADP (adenosine diphosphate) plus inorganic phosphate (Pᵢ), and the reaction releases energy the cell uses for work.
hydrolysis: Breaking a bond by adding water, as when ATP becomes ADP plus inorganic phosphate.
DNA methylation: Adding methyl groups to DNA, usually to cytosines. Heavy methylation near a gene tends to switch it off without changing its sequence.

Check yourself: 4.3 Chemical groups and ATP

4 questions on 4.3 Chemical groups and ATP. Pick an answer to see if you got it, and why.

Question 1 of 4

In the liver, methanol (CH₃–OH) is converted to formaldehyde (H–CHO, a carbon double-bonded to an oxygen), which is then converted to formic acid (H–COOH). Formic acid building up is a major reason methanol poisoning makes the blood too acidic. Which choice names the main group in each molecule, in order, and explains the drop in pH?

Question 2 of 4

Question 3 of 4

The side chains of cysteine and serine differ by one atom: cysteine's ends in –SH and serine's ends in –OH. In an enzyme, two cysteines from different parts of the chain are covalently linked to each other through their side chains. A mutation replaces one of these cysteines with serine. What is the most likely effect?

Question 4 of 4

Some antiviral drugs are nucleotide look-alikes whose sugar has no hydroxyl group on its 3′ carbon. A viral enzyme can still add one of these look-alikes to the 3′ end of a growing viral DNA strand. What happens next?

0 of 4 answered