Download Ch. 03 The Molecules of Life

WATER AND LIFE
Chapter 3
• Life on Earth began in water and evolved there for 3
billion years
The Molecules of Life
– Modern life, even land-dwelling life, still remains
tied to water
– Your cells are composed of 70%–95% water
• The abundance of water is a
major reason Earth is habitable
• Water is the only common
substance that exists in the natural
environment in three physical
states
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Jong B. Lee, Ph.D.
RPTSE BIO Fall 2015 Jong B. Lee, PhD, All rights reserved.
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The Structure of Water
• What properties of the simple water molecule make it so
indispensable to life?
: The attraction forces between water molecules and the
slight tendency to ionize are of crucial importance to the
structure and function of biomolecules .
 Several emergent properties arise.
• Studied in isolation, the water molecule is deceptively
simple
– Its two hydrogen atoms are joined to one oxygen
atom by single covalent bonds
H
H
O
Unnumbered Figure 2.2
Figure 2.10
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• But the electrons of the covalent bonds are not shared
equally between oxygen and hydrogen
– Oxygen attracts the electrons of covalent bonds much
more strongly than does hydrogen
– This unequal sharing makes water a polar molecule
– A polar molecule has opposite charges on opposite ends
–
()
Hydrogen bond
()
()
– Weak forces (about
1/10 of covalent
bond)
O
+
• The polarity of water
results in weak
electrical attractions
between neighboring
water molecules
– These interactions
are called hydrogen
bonds (H-bond)
H
H
– Short-lived property
(life span: 10-12 sec)
+
H2O
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()
()
()
()
()
(b)
Figure 2.11b
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Water’s Life-Supporting Properties
Chapter 3
The polarity of water molecules and the hydrogen bonding
explain most of water’s life-supporting properties:
The Molecules of Life
Several emergent properties arise.
1. Water’s cohesive nature
2. Water’s ability to moderate temperature
3. Floating ice:
Water is less dense as a solid
than as a liquid.
Ice:
Hydrogen bonds
are stable
4. Versatility of water as a solvent
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Liquid water:
Hydrogen bonds
break and re-form
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Biology and Society: Got Lactose?
ORGANIC MOLECULES
• Lactose is the main sugar found in milk.
- Some adults exhibit lactose intolerance, the inability to
properly digest lactose.
- Lactose-intolerant individuals are unable to digest
lactose properly: Lactose is broken down by bacteria in
the large intestine producing gas and discomfort.
• A cell is mostly water
:The rest of the cell
consists mostly of carbonbased molecules . Why?
• There is no treatment for the underlying cause of lactose
intolerance.
- Affected people must avoid lactosecontaining foods or take the enzyme
lactase when eating dairy products
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• The simplest organic compounds are hydrocarbons (탄화수소)
- These are organic molecules containing only carbon and
hydrogen atoms.
- The simplest hydrocarbon is methane that is naturally
present in natural gas and is produced by bacteria that
live in swarms and in the digestive tracts of grazing
animals.
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• Carbon is a versatile atom
- Attach to other carbons
:Form an endless diversity
of carbon skeletons
- Carbon is unparalleled in
its ability to form the
large, complex, diverse
molecules that are
necessary for life functions
Carbon skeletons vary in length
Carbon skeletons may be unbranched or branched
Carbon skeletons may have double bonds,
which can vary in location
Carbon skeletons may be arranged in rings
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• Larger hydrocarbons (such as octane) are the main
molecules in the gasoline we burn in our cars.
• Hydrocarbons (fat ) are also important fuels which
provide energy for our bodies.
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• The unique properties of an organic compound depend
not only on its carbon skeleton but also on the atoms
attached to the skeleton.
Giant Molecules from Smaller Building Blocks
• On a molecular scale, many of life’s molecules are gigantic
– Biologists call them macromolecules
– In an organic
molecule, the
groups of atoms
that usually
participate in
chemical reactions
are called
functional groups
Keton group
aldehyde group
– Examples: Proteins,
DNA,
polysaccharides
Lipids
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• Most macromolecules are polymers (중량체)
– Polymers are made by stringing together many
smaller molecules called monomers (단량체)
– Cells link monomers by a process called dehydration
reaction (탈수반응)
• Organisms also have to break down macromolecules
– Cells do this by a process called hydrolysis
[break (lyse) with water (hydro): 가수분해]
– Hydrolysis means to break with water: process
reverse of hydration reaction
Monomer
Short polymer
Dehydration synthesis of a polymer
Hydrolysis of a polymer
Longer polymer
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BIOLOGICAL MOLECULES
Carbohydrates
• There are four categories of large molecules in cells
• Carbohydrates include
– Small sugar molecules in soft drinks
1. Carbohydrates (탄수화물)
– Long starch molecules in pasta and potatoes
2. Lipids (지질)
– 일반적 구조:
(Carbon, C + water, H2O) n
3. Proteins (단백질)
4. Nucleic acids (핵산)
• Function
– Primary source of dietary energy
– Building material to form much of plant body
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Monosaccharides
Different location of the carbonyl group
• Monosaccharides (단당류) are simple sugars
mono: single, sacchar: sugar
– Glucose: found in sports drinks
• The monosaccharides
glucose and fructose are
isomers (이성질체)
– Fructose: found in fruit
• The same formula: C6H12O6
– Honey contains both glucose and fructose
• Their atoms are arranged
differently, accordingly
different properties
 다른 성질 부여
Glucose
Fructose
More sweeter
(약 100 배)
Figure 3.8
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• In aqueous solutions, monosaccharides form rings
• Monosaccharides are the main fuel that cells use for
cellular work (rapid conversion to cellular energy): This
is why an aqueous solution of glucose is injected into
bloodstream of sick patients.
• Raw materials for manufacturing other kinds of organic
molecules
(b) Abbreviated ring
structure
(a) Linear and ring (most glucoses in solution are ring)
structures: ring formation is reversible process
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Disaccharides
• A disaccharide (이당류) is a double sugar
– It is constructed from two monosaccharides
• Disaccharides are joined by
the process of dehydration
synthesis
ex: maltose (found in
germinating seed)
• Another Disaccharides
- lactose (milk sugar): glucose + galactose
- sucrose: glucose + fructose
Glycosidic linkage
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High-fructose corn syrup
(HFCS)
• The most common disaccharide is sucrose, common
table sugar.
• Sucrose is extracted from sugar cane and the roots of
sugar beets
• Sucrose is rarely used as a sweetener in processed foods
:Much more common is high-fructose corn syrup
(HFCS), made through a commercial process that
converts natural glucose in corn syrup to the much
sweeter fructose
(당도가 sucrose의 50배)
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Polysaccharides
• One familiar example of a polysaccharide is starch:
starch consists of many glucose monomers
• They are polymers of monosaccharides
• Polysaccharides (다당류) : Starch, Glycogen, Cellulose
Glucose
monomer
Starch granules in
potato tuber cells
Unbranched ( 1 4 bond)
Helical
(a) Starch
• Plant cells store starch in granules for energy.
• Potatoes and grains (wheat, corn, rice) are major
sources of starch in the human diet
• Unbranched ( 1 4 glycosidic bond)
Glycogen
Granules
• Helical structure
In muscle
tissue
Branched ( 1 4 bond & 16 bond)
Helical
(b) Glycogen
Cellulose fibril in
a plant cell wall
(c) Cellulose
Cellulose molecules
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• Animals store excess sugar in the form of a polysaccharide
called glycogen.
• Glycogen is similar in structure to starch, but more
extensively branched ( 1 4 and  1 6 bonds)
• Most glycogen is stored as granules in our liver and
muscle cells, which hydrolyze the glycogen to release
glucose when it is needed for energy
• This is the basis for “carbo loading”, the consumption of
large amounts of starchy foods
the night before an athletic event
• Helical structure & Highly branched
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Cellulose
• Cellulose forms cable-like fibrils in the tough walls that
enclose plants, and is a major component of wood
• It resembles starch and glycogen in being a polymer of
glucose, but its glucose monomers are linked together
in different orientation
( 1 4 bond).
• Straight, rigid, insoluble in water, but hydrophilic
• It cannot be broken by most animals (no enzymes)
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Lipids
• Cellulose is the most abundant organic compound on Earth
– It cannot be broken by most animals (no enzymes).
Because it remains undigested, fiber does not serve as
nutrient, although it does appear to help keep our
digestive system healthy.
• Lipids (지질) are hydrophobic (소수성)
– They do not mix with water
ex) salad dressing: oil + vinegar
– 가장 대표적 lipids : fats and steroids
– How do grazing animals survive on a diet of cellulose?
: They have bacteria in their digestive tracts that can
break down cellulose
일반적 fat structure
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Fats
• Dietary fat consists largely of the molecule triglyceride
– A combination of a glycerol and three fatty acids
• Fats perform essential functions in the human body:
energy storage
– the major portion of a fatty acid is a long
hydrocarbon, which, like the hydrocarbons of
gasoline, stores much energy
Fatty acid
– more than twice as much energy as carbohydrate
:The downside to this energy efficiency is that it is
very difficult for a person trying to lose weight to
“burn off” excess body fat
Dehydration synthesis linking a fatty acid to glycerol
Glycerol
– We stock these long-term food reservoirs called
“adipose cells” (= adipocytes)
Figure 3.15a
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Fatty Acids
• Fats perform essential functions in the human body
– Energy storage
– Cushioning of vital organs
– Insulation (maintain a warm body temperature)
<Saturated fatty acids vs Unsaturated fatty acids>
• Saturated fatty acids : Have the maximum number of
hydrogens bonded to the carbons
• Unsaturated fatty acids : Have less than the maximum
number of hydrogens bonded to the carbons
Saturated fatty acid
(포화지방산)
Unsaturated fatty acid
(불포화지방산)
Kink
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• Most animal fats have a relatively high proportion of
saturated fatty acids Ex) butter
– The linear shape of saturated fatty acids allows them
to stack easily, making saturated fats solid at room
temperature
– Diets rich in saturated fats may contribute to
cardiovascular disease by promoting atherosclerosis
(동맥경화).
– Lipid-containing deposits called plaques build up
within the walls of blood vessels, reducing blood
flow and increasing risk of heart attacks (심장마비) and
strokes (뇌졸증)
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• Most plant oils tend to be low in saturated fatty
acids
– The bent shape of unsaturated fatty acids makes them
less likely to form solids, so unsaturated fat are
usually liquid at room temperature
– Examples: vegetable oils, fish oils
– While plant oils tend to be low in saturated fat,
tropical plant oils are exception. Cocoa butter, a main
ingredient in chocolate, contains a mix of saturated
and unsaturated fat.  상온에서 고체 & 입안에서 녹음
 쵸코렛의 원료
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Hydrogenation
• Margarine, peanut butter (hydrogenated vegetable oil) :
수소를 넣어주어
unsaturated  saturated ; solid at room
temperature)
TYPES OF FATS
Saturated Fats
Unsaturated Fats
• Unfortunately, hydrogenation
also creates trans fat, a form of
fat that recent research suggests
is very unhealthy.
Margarine
INGREDIENTS: SOYBEAN OIL, FULLY HYDROGENATED
COTTONSEED OIL, PARTIALLY HYDROGENATED
COTTONSEED OIL AND SOYBEAN OILS, MONO AND
DIGLYCERIDES, TBHO AND CITRIC ACID
• To avoid trans fats in your diet,
buy foods that are labeled “trans
fat free” and avoid foods with
hydrogenated oils
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Plant oils
Trans fats
ANTIOXIDANTS
Omega-3 fats
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Steroids
• Not all fats are unhealthy.
• Some fats perform important functions in the body and
are essential to a healthy diet
• Omega-3 fatty acids, found in
foods such as nuts and oil fish
such as salmon
• These fats reduce the risk of coronary heart disease
(관상동맥질환) and relieve the symptoms of arthritis (관절염)
and inflammatory bowel disease (염증성소화기 장애)
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• Steroids are very different from fats in structure and
function
– The carbon skeleton is
bent to form four fused
rings
• Cholesterol is the “base
steroid” from which your
body produces other
steroids
– Example: sex
hormones, vitamin D
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• Synthetic anabolic steroids are controversial
– THG is a chemically modified (“designer”) steroid
intended to avoid detection by drug tests
– They are variants of testosterone
(mimic some of its effects)
– Side effects: violent mood swings, deep depression,
liver damage, high cholesterol, shrunken testicles, a
reduced sex drive, infertility
– Some athletes use them to build
up their muscles quickly
– They can pose serious health
risks
– These last symptoms occur
because anabolic steroids
often cause the body to
reduce its normal output of
sex hormones
– In 2003, the discovery that some
athletes were using a new
anabolic steroid called THG
rocked the sports world
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Proteins
THG
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Functions of proteins
(d) Transport
proteins
(hemoglobin)
• Your body has tens of thousands of different kinds of
proteins: Proteins perform most of the tasks the body
needs to function
– They are the most elaborate of life’s molecules
– Each protein has a unique, three-dimensional
structure that corresponds to a specific function
(b) Storage
proteins (seed,
egg)
(a)
• A protein is a polymer constructed from amino
acid monomers
Structural proteins
hair, horn, feather, spider web
connective tissue, tendon
(c) Contractile proteins (muscle)
e)
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Defensive function (Antibody), Enzymes, Signal protein etc.
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The Monomers: Amino Acids
Amino
group
• All proteins are constructed
from a common set of 20 kinds
of amino acids
• Each amino acid :
– A central carbon
atom bonded to
four covalent
partners
A central carbon atom
(= α carbon)
(a)
• 20 amino acids: classified by polarity (극성)
Carboxyl
group
– Positive charged amino acids: lysine (K), arginine (R),
histidine (H)
– Negative charged amino acids: aspartic acid (D),
glutamic acid (E)
Side
group
– Polar (hydrophilic) amino acids: serine (S), threonine
(T), cysteine (C), glycine (G), asparagine (N),
glutamine (Q), tyrosine (Y)
Side
groups
– A side group that
is variable among
all 20
Serine
Leucine
(hydrophobic)
(hydrophilic)
Figure 3.19
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Proteins as Polymers
Primary structure
Carboxyl
group
• Cells link amino
acids together by
dehydration synthesis
Amino
group
Side
group
– The resulting
bond between
them is called a
peptide bond
• Your body has tens of
thousands of different
kinds of protein
– Nonpolar (hydrophobic) amino acids: leucine (L),
isoleucine (I), valine (V), proline (P), alanine (A),
tryptophan (W), phenylalanine (F), methionine (M)
• A typical polypeptide: consists
of at least 100 amino acids
Side
group
Amino acid
Amino acid
Dehydration
synthesis
Carboxy-terminal
or C-terminal
Amino-terminal
or N-terminal
Side
group
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• Primary structure
: The specific
sequence of amino
acids in a protein
Side
group
Peptide bond
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• The arrangement of amino
acids makes each one different
Figure 3.20
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Protein Shape
• A slight change in the primary structure of a protein
affects its ability to function
– The substitution of one amino acid for another in
hemoglobin causes sickle-cell disease (겸상적혈구 빈혈증)
: Proteins have four levels of structure
(a) Primary structure
Hydrogen bond
Pleated sheet
Amino acid
1
2
3
6
7. . . 146
4
5
Normal hemoglobin
(a) Normal red blood cell
Polypeptide
(single subunit)
Hydrogen bond
Alpha helix
(b) Secondary
structure:
1
2
(b) Sickled red blood cell
3
6
7. . . 146
4
5
Sickle-cell hemoglobin
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(c) Tertiary
structure
Complete
protein,
with four
polypeptide
subunits
(d) Quaternary structure
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• Secondary structure
- Local pattern or local structure within certain
stretches of polypeptide
- Alpha ()-helix, pleated sheet
- H-bonds confer stability of the secondary structures
• When a cell makes a polypeptide, the chain usually folds
spontaneously to form the functional shape for that
protein
• Tertiary structure
- The overall three-dimensional shape of the protein
- Hydrophobic interaction, H-bonds, van-der Waals
forces, and ionic interactions stabilize the 3Dstructure
• In almost every case, a protein’s function depends on its
ability to recognize and bind to some other molecule
• Quaternary structure
- A structure in which two or more polypeptides interact
to form
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• It is a protein’s three-dimensional shape that enables the
molecule to carry out specific function in a cell
• If the shape of a protein is altered, then it would not be
able to perform this recognition function
: Function follows form (structure).
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Nucleic Acids
What Determines Protein Structure?
•
A protein’s shape is sensitive to the surrounding
environment
- Unfavorable temperature and pH changes can cause a
protein to unravel and lose its shape
- High fevers (above 104º F) in humans can cause
some proteins to denature
- This is called denaturation (변성)
- 만일 pH가 다시 원래대로 돌아오면 본래 모습으로 복귀
: called renaturation  일차구조로서 단백질모습이 결정
• Misfolded proteins are associated with Alzheimer’s
disease, Mad cow disease and Parkinson’s disease
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• The name of nucleic acids comes from their location
in nuclei of eukaryotic cells.
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• There are two types of nucleic acids
– DNA : deoxyribonucleic acid
– RNA : ribonucleic acid
• Nucleic acids are
polymers of nucleotides
: Monomer is called
nucleotide.
• Nucleic acids are macromolecules that provide the
directions for building proteins
Nitrogenous base
(A,G,C, or T)
• Each DNA
nucleotide has one
of the following
bases
– Adenine (A)
Thymine (T)
Phosphate
group
Nucleotide
Sugar
(deoxyribose)
Phosphate
– Thymine (T)
– Cytosine (C)
Adenine (A)
Sugar
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Cytosine (C)
– Guanine (G)
Base
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Thymine (T)
Guanine (G)
Figure 3.25
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• Nucleotide monomers are
linked into long chains
• Two strands of DNA join together
to form a double helix
Backbone
(by phosphodiester bonds)
Nucleotide
– These chains are called
polynucleotides, or
DNA strands
- Complementary character
– A sugar-phosphate
backbone joins them
together
- The bases along one DNA
strand hydrogen-bond to
bases along the other
strand
– Bases are hanging off
the backbone like
appendages
H-bond
of DNA double helix
Bases
- This base pairing is
specific (A=T, C≡G)
(a) DNA strand
Figure 3.26a
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Double helix
Figure 3.26b
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Large biological
molecules
• RNA, ribonucleic
acid, is different
from DNA
Nitrogenous base
(A,G,C, or U)
Carbohydrates
Functions
Components
Examples
Monosaccharides:
glucose, fructose
Disaccharides:
lactose, sucrose
Polysaccharides:
starch, cellulose
Dietary energy;
storage; plant
structure
Monosaccharide
1) Its sugar has an
extra OH group
Phosphate
group
Lipids
Long-term
energy storage
fats;
hormones
steroids
(2-carbon)
Uracil (U)
Proteins
Components of
a triglyceride
Enzymes, structure,
storage, contraction,
transport, and others
Fats triglycerides;
Steroids
testosterone,
estrogen
Carboxyl
group
Side
group
Lactase
an enzyme,
hemoglobin
a transport protein
Amino acid
Phosphate
Base
Nucleic acids
Sugar (ribose)
RPTSE Biology – Fall 2015, Dr. Jong B. Lee
Glycerol
Amino
group
2) It has the base
uracil (U) instead
of thymine (T)
© RPTSE
2010 Pearson
BIOEducation,
Fall 2015Inc.
Jong B. Lee, PhD, All rights reserved.
Fatty acid
Information
storage
DNA, RNA
Sugar
Figure 3.27
Nucleotide
© RPTSE
2010 Pearson
BIOEducation,
Fall 2015Inc.
Jong B. Lee, PhD, All rights reserved.
15