Pan Lab for Jesus

Laboratory of Transporter Biology, Department of Life Science,

Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Chapter 2
Molecules of Life

BIOLOGY: Today and Tomorrow, 4e

5e
starr evers starr
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

本章前面各節 有關基本化學
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(考試不包括在內)
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

2.6 Organic Molecules

▪ The molecules of life – carbohydrates, proteins, lipids, and
nucleic acids – are organic molecules

▪ Organic
▪ Type of molecule that consists primarily of carbon and
hydrogen atoms

▪ Carbon atoms bond covalently with up to four other atoms,

often forming long chains or rings

甲烷
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Carbon rings
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Modeling an Organic Molecule

Glucose

A) A structural formula for B) Structural formulas of

an organic molecule can
be very complicated.
organic molecules are
often simplified by using
polygons as symbols for
rings, and omitting the
labels for some or all of the
atoms.
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

From Structure to Function

▪ Cells assemble large polymers from smaller monomers, and
break apart polymers into component monomers

▪ Monomers
▪ Molecules that are subunits of polymers
▪ Simple sugars, fatty acids, amino acids, nucleotides

▪ Polymers
▪ Molecules that consist of multiple monomers
▪ Carbohydrates, lipids, proteins, nucleic acids
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Enzyme-Driven Reactions
▪ Enzyme-driven reactions construct large molecules from
smaller subunits, and break large molecules into smaller ones

▪ Enzyme
▪ Molecule that speeds up a reaction without being
changed by it

▪ Metabolism
▪ All enzyme-mediated chemical reactions by which cells
acquire and use energy as they build and break down
organic molecules
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Condensation and Hydrolysis

▪ Condensation (water forms)
▪ Process by which an enzyme builds large molecules from
smaller subunits

▪ Hydrolysis (water is used)

▪ Process by which an enzyme breaks a molecule into
smaller subunits by attaching a hydroxyl to one part and a
hydrogen atom to the other
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Condensation

A) Condensation. Cells build a large molecule from smaller ones by this reaction. An
enzyme removes a hydroxyl group from one molecule and a hydrogen atom from another.
A covalent bond forms between the two molecules; water also forms.
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Hydrolysis

B) Hydrolysis. Cells split a large molecule into smaller ones by this water-
requiring reaction. An enzyme attaches a hydroxyl group and a hydrogen atom
(both from water) at the cleavage site.
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

2.7 Carbohydrates
▪ Cells use carbohydrates for energy and structural materials

▪ Carbohydrates
▪ Organic molecules that consist of carbon, hydrogen, and
oxygen atoms in a 1:2:1 ratio (CH2O)

▪ The simplest carbohydrates are sugars

▪ Monosaccharides
▪ Disaccharides
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Some Complex Carbohydrates

A) Cellulose (纖維), a structural component of

plants. Chains of glucose units stretch side by side and
hydrogen-bond at many —OH groups. The hydrogen
bonds stabilize the chains in tight bundles that form
long fibers. Very few types of organisms can digest this
tough, insoluble material.

B) In starch (澱粉), a series of glucose units

form a chain that coils. Starch is the main energy
reserve in plants, which store it in their roots, stems,
leaves, seeds, and fruits. C) Glycogen (肝醣).
In animals, this
polysaccharide functions
as an energy reservoir. It
is especially abundant in
the liver and muscles of
active animals, including
people.
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

2.8 Lipids

▪ Lipids are greasy, oily, or waxy nonpolar organic molecules,

often with one or more fatty acid tails

▪ Lipids (脂油)
▪ Fatty, oily, or waxy organic compounds

▪ Fatty acid (脂肪酸)

▪ Consists of a long chain of carbon atoms with an acidic
carboxyl group at one end
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University
Fatty acids
“head”
(hydrophilic
carboxyl
group)

hydrophobic
“tail”

A) stearic acid B) linoleic acid C) linolenic acid D) oleic acid E) elaidic acid
(Saturated) (Omega-6) (Omega-3) (Cis) (Trans)
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Fats
▪ Fats, such as triglycerides, are the most abundant source of
energy in vertebrates – stored in adipose tissue that insulates
the body

▪ Fat (脂肪)
▪ Lipid with one, two, or three fatty acid tails

▪ Triglyceride (甘油三酯)
▪ Lipid with three fatty acid tails attached to a glycerol (甘油)
backbone
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Saturated and Unsaturated Fats

▪ Saturated fats pack more tightly than unsaturated fats, and

tend to be more solid

▪ Saturated fat
▪ Fatty acid with no double bonds in its carbon tail

▪ Unsaturated fat
▪ Lipid with one or more double bonds in a fatty acid tail
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Phospholipids
▪ Phospholipid (磷脂)
▪ A lipid with a phosphate group in its hydrophilic head, and
two nonpolar fatty acid tails
▪ The main structural component of cell membranes

▪ Lipid bilayer
▪ Double layer of lipids arranged tail-to-tail
▪ Structural foundation of all cell membranes
B) A lipid bilayer A) A phospholipid molecule
Hydrophilic
head
One
layer of
lipids
One
layer of Two
lipids hydrophobic
tails
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Waxes

▪ Waxes are part of water-repellent and lubricating secretions in

plants and animals

▪ Wax (蠟)
Water-repellent lipid with long fatty-acid tails bonded to long-
chain alcohols or carbon rings
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Steroids

an Estrogen Testosterone
(雌激素) (睾酮)

female male
wood duck wood duck
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

2.9 Proteins
▪ A protein’s function depends on its structure, which consists of chains of
amino acids that fold into functional domains

▪ Protein
▪ Organic compound that consists of one or more chains of amino acids
(polypeptides)

▪ Amino acid
▪ Small organic compound with a carboxyl group, amine group, and a
characteristic side group (R)

Amine Carboxyl
group group
R group
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Peptide Bonds
▪ Amino acids are linked into chains by peptide bonds (胜肽鍵)

▪ Peptide bond (胜肽鍵)

▪ A bond between the amine group of one amino acid and
the carboxyl group of another

▪ Polypeptide (多胜肽)
▪ Chain of amino acids linked by peptide bonds
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Protein Synthesis
1. Primary structure (polypeptide formation)
▪ A linear sequence of amino acids

2. Secondary structure
▪ Hydrogen bonds twist the polypeptide into a coil or sheet

3. Tertiary structure
▪ Secondary structure folds into a functional shape
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Protein Synthesis
4. Quaternary structure
▪ In some proteins, two or more polypeptide chains
associate and function as one molecule
▪ Example: hemoglobin

5. Fibrous proteins may aggregate into a larger structure, such

as keratin filaments
▪ Example: hair
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Protein Synthesis
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Protein Synthesis
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

2.10 Nucleic Acids

▪ Nucleotide (核甘酸)
▪ Monomer of nucleic acids
▪ Has a five-carbon sugar, a nitrogen-containing base, and
phosphate groups

▪ Nucleic acids (核酸)

▪ Polymers of nucleotide monomers joined by sugar-
phosphate bonds (include DNA, RNA, coenzymes, energy
carriers, messengers)
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

ATP
A) ATP, a nucleotide monomer of
RNA, and also an essential
participant in many metabolic
reactions.

base (adenine)

Phosphate ribose
groups sugar
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

DNA and RNA

▪ Deoxyribonucleic acid (DNA)
▪ Two nucleotide chains twisted in a double helix
▪ Nucleic acid that carries heritable information about a
cell’s proteins and RNAs

▪ Ribonucleic acid (RNA)

▪ Typically single-stranded nucleic acid
▪ Different RNAs interact with DNA and with one another to
carry out protein synthesis
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Nucleotides and Nucleic Acid

B) A chain of nucleotides is a nucleic acid.

The sugar of one nucleotide is covalently
bonded to the phosphate group of the next, C) DNA consists of two chains of
forming a sugar–phosphate backbone. nucleotides, twisted into a double helix.
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Q & A

Thank you very much for your attention.