Download Organic Molecules

Molecules of Life
Chapter 3
阮雪芬
Sep. 17, 2012
Impacts, Issues:
Fear of Frying
• Trans fats in
hydrogenated vegetable
oil raise levels of
cholesterol in our blood
more than any other fat,
and directly alter blood
vessel function
Organic Molecules
• All molecules of life are built with carbon atoms
• We can use different models to highlight
different aspects of the same molecule
3.1 Carbon – The Stuff of Life
• Organic molecules are complex molecules of
life, built on a framework of carbon atoms，以下
四大物質皆含C
•
•
•
•
Carbohydrates
Lipids
Proteins
Nucleic acids
Carbon – The Stuff of Life
• Carbon atoms can be assembled and
remodeled into many organic compounds
• Can bond with one, two, three, or four atoms
• Can form polar or nonpolar bonds
• Can form chains or rings
Carbon Rings
Representing Structures
of Organic Molecules
• Structural model of an
organic molecule
• Each line is a
covalent bond; two
lines are double
bonds; three lines are
triple bonds
Representing Structures
of Organic Molecules
• Carbon ring structures are represented as
polygons; carbon atoms are implied
Representing Structures
of Organic Molecules
• Ball-and-stick models show positions of atoms
in three dimensions; elements are coded by
color
Representing Structures
of Organic Molecules
• Space-filling models
show how atoms
sharing electrons
overlap
Three Models of a Hemoglobin Molecule
3.2 From Structure to Function
• The function of organic molecules in biological
systems begins with their structure
• The building blocks of carbohydrates, lipids,
proteins, and nucleic acids bond together in
different arrangements to form different kinds of
complex molecules
Functional Groups
• Hydrocarbon
• An organic molecule that consists only of
hydrogen and carbon atoms
• Most biological molecules have at least one
functional group
• A cluster of atoms that imparts specific chemical
properties to a molecule (polarity, acidity)
Common Functional Groups
in Biological Molecules
Effects of Functional Groups:
Sex Hormones
What Cells Do to Organic Compounds
• Metabolism
• Activities by which cells acquire and use energy
to construct, rearrange, and split organic
molecules
• Allows cells to live, grow, and reproduce
• Requires enzymes (proteins that increase the
speed of reactions)
What Cells Do to Organic Compounds
• Condensation (脫水合成)
• Covalent bonding of two molecules to form a
larger molecule
• Water forms as a product
• Hydrolysis (加水分解)
• The reverse of condensation
• Cleavage reactions split larger molecules into
smaller ones
• Water is split
What Cells Do to Organic Compounds
• Monomers
• Molecules used as subunits to build larger
molecules (polymers)
• Polymers
• Larger molecules that are chains of monomers
• May be split and used for energy
What Cells Do to Organic Compounds
Condensation and Hydrolysis
A) Condensation. An —OH group
from one molecule combines with an
H atom from another. Water forms as
the two molecules bond covalently.
B) Hydrolysis. A molecule splits, then
an —OH group and an H atom from a
water molecule become attached to
sites exposed by the reaction.
Animation: Condensation and hydrolysis
3.1-3.2 Key Concepts:
Structure Dictates Function
• We define cells partly by their capacity to build
complex carbohydrates and lipids, proteins, and
nucleic acids
• All of these organic compounds have functional
groups attached to a backbone of carbon atoms
3.3 Carbohydrates
• Carbohydrates are the most plentiful biological
molecules in the biosphere
• Cells use some carbohydrates as structural
materials; others for stored or instant energy
Carbohydrates
• Carbohydrates
• Organic molecules that consist of carbon,
hydrogen, and oxygen in a 1:2:1 ratio
• Three types of carbohydrates in living systems
• Monosaccharides (單醣)
• Oligosaccharides (寡糖)
• Polysaccharides (多糖)
Simple Sugars
• Monosaccharides
(one sugar unit) are
the simplest
carbohydrates
• Used as an energy
source or structural
material
• Backbones of 5 or 6
carbons
• Example: glucose
Short-Chain Carbohydrates
• Oligosaccharides
• Short chains of monosaccharides
• Example: sucrose, a disaccharide
glucose
+
fructose
sucrose
+
water
Animation: Sucrose synthesis
Complex Carbohydrates
• Polysaccharides
• Straight or branched chains of many sugar
monomers (種類有下列三大)
• The most common polysaccharides are
cellulose, starch, and glycogen
• All consist of glucose monomers
• Each has a different pattern of covalent bonding,
and different chemical properties
Cellulose, Starch, and Glycogen
Chitin
• Chitin
• A nitrogen-containing polysaccharide that
strengthens hard parts of animals such as crabs,
and cell walls of fungi
3.3 Key Concepts:
Carbohydrates
• Carbohydrates are the most abundant biological
molecules
• They function as energy reservoirs and
structural materials
• Different types of complex carbohydrates are
built from the same subunits of simple sugars,
bonded in different patterns
3.4 Greasy, Oily – Must Be Lipids
• Lipids function as the body’s major energy
reservoir, and as the structural foundation of cell
membranes
• Lipids
• Fatty, oily, or waxy organic compounds that are
insoluble in water
Fatty Acids
• Many lipids incorporate fatty acids
• Simple organic compounds with a carboxyl group
joined to a backbone of 4 to 36 carbon atoms
• Essential fatty acids are not made by the body
and must come from food
• Omega-3 and omega-6 fatty acids
Fatty Acids
• Saturated,
monounsaturated,
polyunsaturated
Animation: Fatty acids
Fats
• Fats
• Lipids with one, two, or three fatty acids “tails”
attached to glycerol (甘油)
• Triglycerides (三酸甘油酯)
• Neutral fats with three fatty acids attached to
glycerol
• The most abundant energy source in vertebrates
• Concentrated in adipose tissues (for insulation
and cushioning 絕緣和緩衝)
Triglycerides
Animation: Triglyceride formation
Saturated and Unsaturated Fats
• Saturated fats (animal fats) 飽和脂肪酸
• Fatty acids with only single covalent bonds
• Pack tightly; solid at room temperature
• Unsaturated fats (vegetable oils)
• Fatty acids with one or more double bonds
• Kinked; liquid at room temperature
Trans Fats
• Trans fats
• Partially hydrogenated vegetable oils formed by a
chemical hydrogenation process
• Double bond straightens the molecule
• Pack tightly; solid at room temperature
Cis and Trans Fatty Acids
Phospholipids
• Phospholipids
• Molecules with a polar head containing a
phosphate and two nonpolar fatty acid tails
• Heads are hydrophilic, tails are hydrophobic
• The most abundant lipid in cell membranes
Phospholipids
Waxes
• Waxes
• Complex mixtures with long fatty-acid tails
bonded to long-chain alcohols or carbon rings
• Protective, water-repellant covering
Cholesterol and Other Steroids
• Steroids (類固醇)
• Lipids with a rigid backbone of four carbon rings
and no fatty-acid tails
• 真核細胞模皆含有固醇：動物膽固醇，植物植物醇
• Cholesterol (膽固醇)
• Component of eukaryotic cell membranes
• Remodeled into bile salts, vitamin D, and steroid
hormones (estrogens and testosterone) 固定細胞
膜、分解成小分子、或者當激素用
Cholesterol
3.4 Key Concepts:
Lipids
• Lipids function as energy reservoirs and
waterproofing or lubricating substances
• Some are remodeled into other substances
• Lipids are the main structural components of cell
membranes
3.5 Proteins – Diversity
in Structure and Function
• Proteins are the most diverse biological
molecule (structural, nutritious, enzyme,
transport, communication, and defense proteins)
• Cells build thousands of different proteins by
stringing together amino acids in different orders
Proteins and Amino Acids
• Protein
• An organic compound composed of one or more
chains of amino acids
• Amino acid
• A small organic compound with an amine group
(—NH3+), a carboxyl group (—COO-, the acid),
and one or more variable groups (R group)
Amino Acid Structure
Polypeptides
• Protein synthesis involves the formation of
amino acid chains called polypeptides
• Polypeptide
• A chain of amino acids bonded together by
peptide bonds in a condensation reaction
between the amine group of one amino acid and
the carboxyl group of another amino acid
Peptide Bond Formation
A DNA encodes the
order of amino acids in a
new polypeptide chain.
Methionine (met) is
typically the first amino
acid.
B In a condensation reaction, a peptide bond
forms between the methionine and the next amino
acid, alanine (ala) in this example. Leucine (leu)
will be next. Think about polarity, charge, and
other properties of functional groups that become
neighbors in the growing chain.
Fig. 3-16a, p. 44
Peptide Bond Formation
C A peptide bond forms between the
alanine and leucine. Tryptophan (trp)
will be next. The chain is starting to
twist and fold as atoms swivel around
some bonds and attract or repel their
neighbors.
D The sequence of amino acid
subunits in this newly forming peptide
chain is now met–ala–leu–trp. The
process may continue until there are
hundreds or thousands of amino acids
in the chain.
Fig. 3-16b, p. 45
3.6 Why Is Protein Structure
So Important?
• When a protein’s structure goes awry, so does
its function
Levels of Protein Structure
Primary structure
The unique amino acid sequence of a protein
Fig. 3-17a, p. 45
Levels of Protein Structure
• Secondary structure
• The polypeptide chain folds and forms hydrogen bonds
between amino acids
Fig. 3-17b, p. 45
Levels of Protein Structure
• Tertiary structure
• A secondary structure is compacted into
structurally stable units called domains
• Forms a functional protein (三級結構以上開始有
功能)
Fig. 3-17c, p. 45
Levels of Protein Structure
• Quaternary structure
• Some proteins consist of two or more folded
polypeptide chains in close association
• Example: hemoglobin
Fig. 3-17d, p. 45
Just One Wrong Amino Acid…
• Hemoglobin contains four globin chains, each
with an iron-containing heme group that binds
oxygen and carries it to body cells
• In sickle cell anemia, a DNA mutation changes a
single amino acid in a beta chain, which
changes the shape of the hemoglobin molecule,
causing it to clump and deform red blood cells
Globin Chains in
Hemoglobin
Molecular Basis of Sickle Cell Anemia
Fig. 3-19a, p. 47
Molecular Basis of Sickle Cell Anemia
Fig. 3-19b, p. 47
Molecular Basis of Sickle Cell Anemia
Fig. 3-19c, p. 47
Proteins Undone – Denaturation
• Proteins function only as long as they maintain
their correct three-dimensional shape
• Heat, changes in pH, salts, and detergents can
disrupt the hydrogen bonds that maintain a
protein’s shape
• When a protein loses its shape and no longer
functions, it is denatured (蛋白質變性)
3.5-3.6 Key Concepts:
Proteins
• Structurally and functionally, proteins are the
most diverse molecules of life
• They include enzymes, structural materials, and
transporters
• A protein’s function arises directly from its
structure
3.7 Nucleic Acids
• Some nucleotides are subunits of nucleic acids
such as DNA and RNA
• Some nucleotides have roles in metabolism
Nucleotides
• Nucleotide
• A small organic molecule consisting of a sugar
with a five-carbon ring, a nitrogen-containing
base, and one or more phosphate groups
• ATP
• A nucleotide with three phosphate groups
• Important in phosphate-group (energy) transfer
ATP
Nucleic Acids
• Nucleic acids
• Polymers of nucleotides in which the sugar of one
nucleotide is attached to the phosphate group of
the next
• RNA and DNA are nucleic acids
RNA
• RNA (ribonucleic acid)
• Contains four kinds of nucleotide monomers,
including ATP
• Important in protein synthesis
DNA
• DNA (deoxyribonucleic acid)
• Two chains of nucleotides twisted together into a
double helix and held by hydrogen bonds
• Contains all inherited information necessary to
build an organism, coded in the order of
nucleotide bases
Four Nucleotides of DNA
3 phosphate
groups
sugar
(deoxyribose)
adenine (A)
base with a
double ring
structure
thymine (T)
base with a
single ring
structure
guanine (G)
base with a
double ring
structure
cytosine (C)
base with a
single ring
structure
Fig. 3-21, p. 48
The DNA Molecule
3.7 Key Concepts:
Nucleotides and Nucleic Acids
• Nucleotides have major metabolic roles and are
building blocks of nucleic acids
• Two kinds of nucleic acids, DNA and RNA,
interact as the cell’s system of storing, retrieving,
and translating information about building
proteins
Summary:
Organic Molecules in Living Things