the molecules of life - new york institute of technologyiris.nyit.edu/~jlee26/pics/rptse/eng rptse...

RPTSE Biology – Fall 2015, Dr. Jong B. Lee 1

RPTSE BIO Fall 2015 Jong B. Lee, PhD, All rights reserved.© Jong B. Lee, Ph.D.

Chapter 3

The Molecules of Life

© 2010 Pearson Education, Inc.RPTSE BIO Fall 2015 Jong B. Lee, PhD, All rights reserved.

• Life on Earth began in water and evolved there for 3

billion years

WATER AND 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


• 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.

Figure 2.10


• Studied in isolation, the water molecule is deceptively

simple

The Structure of Water

– Its two hydrogen atoms are joined to one oxygen

atom by single covalent bonds

Unnumbered Figure 2.2

H

O

H



• 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

H H

H2O+ +

–

O


• The polarity of water

results in weak

electrical attractions

between neighboring

water molecules

– These interactions

are called hydrogen

bonds (H-bond)

– Weak forces (about

1/10 of covalent

bond)

– Short-lived property

(life span: 10-12 sec)

(b)

()

Hydrogen bond()

()()

()

()

()

()

Figure 2.11b


Water’s Life-Supporting Properties

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.

4. Versatility of water as a solvent

Ice:Hydrogen bondsare stable Liquid water:

Hydrogen bonds

break and re-form

The polarity of water molecules and the hydrogen bonding

explain most of water’s life-supporting properties:

Several emergent properties arise.

© 2010 Pearson Education, Inc.

Lectures by Chris C. Romero, updated by Edward J. Zalisko

PowerPoint® Lectures for

Campbell Essential Biology, Fourth Edition

– Eric Simon, Jane Reece, and Jean Dickey

Campbell Essential Biology with Physiology, Third Edition

– Eric Simon, Jane Reece, and Jean Dickey

Chapter 3

The Molecules of Life



Biology and Society: Got Lactose?

• 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.

• There is no treatment for the underlying cause of lactose

intolerance.

- Affected people must avoid lactose-

containing foods or take the enzyme

lactase when eating dairy products


• 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

ORGANIC MOLECULES

• A cell is mostly water

:The rest of the cell

consists mostly of carbon-

based molecules . Why?


• 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.


• 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.



• The unique properties of an organic compound depend

not only on its carbon skeleton but also on the atoms

attached to the skeleton.

Keton group aldehyde group– In an organic

molecule, the

groups of atoms

that usually

participate in

chemical reactions

are called

functional groups


• On a molecular scale, many of life’s molecules are gigantic

Giant Molecules from Smaller Building Blocks

– Biologists call them macromolecules

– Examples: Proteins,

DNA,

polysaccharides

Lipids


• 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)

Short polymer

Monomer

Longer polymerDehydration synthesis of a polymer


• 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

Hydrolysis of a polymer



• There are four categories of large molecules in cells

BIOLOGICAL MOLECULES

1. Carbohydrates (탄수화물)

2. Lipids (지질)

3. Proteins (단백질)

4. Nucleic acids (핵산)


• Carbohydrates include

Carbohydrates

– Small sugar molecules in soft drinks

– Long starch molecules in pasta and potatoes

– 일반적구조: (Carbon, C + water, H2O) n

• Function

– Primary source of dietary energy

– Building material to form much of plant body


• Monosaccharides (단당류) are simple sugars

mono: single, sacchar: sugar

Monosaccharides

Figure 3.8

– Glucose: found in sports drinks

– Fructose: found in fruit

– Honey contains both glucose and fructose


• The monosaccharides

glucose and fructose are

isomers (이성질체)

• The same formula: C6H12O6

• Their atoms are arranged

differently, accordingly

different properties

다른성질부여Glucose

Fructose

Different location of the carbonyl group

More sweeter

(약 100 배)



• 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

(a) Linear and ring (most glucoses in solution are ring)structures: ring formation is reversible process

(b) Abbreviated ringstructure


• A disaccharide (이당류) is a double sugar

Disaccharides

– It is constructed from two monosaccharides

• Disaccharides are joined by

the process of dehydration

synthesis

ex: maltose (found in

germinating seed)

Glycosidic linkage

• Another Disaccharides

- lactose (milk sugar): glucose + galactose

- sucrose: glucose + fructose


• 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)


High-fructose corn syrup

(HFCS)



• Polysaccharides (다당류) : Starch, Glycogen, Cellulose

(a) Starch

Starch granules inpotato tuber cells

Glucosemonomer

(b) Glycogen

GlycogenGranules

In muscletissue

(c) Cellulose Cellulose molecules

Cellulose fibril ina plant cell wall

Polysaccharides

• They are polymers of monosaccharides

Unbranched ( 1 4 bond)

Helical

Branched ( 1 4 bond & 16 bond)

Helical


• One familiar example of a polysaccharide is starch:

starch consists of many glucose monomers

• 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)

• Helical structure


• Animals store excess sugar in the form of a polysaccharide

called glycogen.

• Glycogen is similar in structure to starch, but more

extensively branched

• 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

( 1 4 and 1 6 bonds)


• 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)

Cellulose



• 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.

– How do grazing animals survive on a diet of cellulose?

: They have bacteria in their digestive tracts that can

break down cellulose


• Lipids (지질) are hydrophobic (소수성)

Lipids

– They do not mix with water

ex) salad dressing: oil + vinegar

– 가장대표적 lipids : fats and steroids

일반적 fat structure


Fats

• Dietary fat consists largely of the molecule triglyceride

– A combination of a glycerol and three fatty acids

Figure 3.15a

Fatty acid

Glycerol

Dehydration synthesis linking a fatty acid to glycerol


• 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

– 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

– We stock these long-term food reservoirs called

“adipose cells” (= adipocytes)



• Fats perform essential functions in the human body

– Energy storage

– Cushioning of vital organs

– Insulation (maintain a warm body temperature)


• Unsaturated fatty acids : Have less than the maximum

number of hydrogens bonded to the carbons

• Saturated fatty acids : Have the maximum number of

hydrogens bonded to the carbons

<Saturated fatty acids vs Unsaturated fatty acids>

Fatty Acids

Kink

Unsaturated fatty acid(불포화지방산)

Saturated fatty acid

(포화지방산)


• 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

– 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)

(동맥경화).


• 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. 상온에서고체 & 입안에서녹음쵸코렛의원료



• Margarine, peanut butter (hydrogenated vegetable oil) :

수소를넣어주어 unsaturated saturated ; solid at room

temperature)

Hydrogenation

• Unfortunately, hydrogenation

also creates trans fat, a form of

fat that recent research suggests

is very unhealthy.

• To avoid trans fats in your diet,

buy foods that are labeled “trans

fat free” and avoid foods with

hydrogenated oils


Saturated Fats

TYPES OF FATS

Unsaturated Fats

Margarine

Plant oils Trans fats Omega-3 fats

INGREDIENTS: SOYBEAN OIL, FULLY HYDROGENATED

COTTONSEED OIL, PARTIALLY HYDROGENATED

COTTONSEED OIL AND SOYBEAN OILS, MONO AND

DIGLYCERIDES, TBHO AND CITRIC ACID ANTIOXIDANTS


• 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)


• Steroids are very different from fats in structure and

function

Steroids

– 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



– They are variants of testosterone

(mimic some of its effects)

– Some athletes use them to build

up their muscles quickly

– They can pose serious health

risks

– In 2003, the discovery that some

athletes were using a new

anabolic steroid called THG

rocked the sports world

• Synthetic anabolic steroids are controversial


– THG is a chemically modified (“designer”) steroid

intended to avoid detection by drug tests

– Side effects: violent mood swings, deep depression,

liver damage, high cholesterol, shrunken testicles, a

reduced sex drive, infertility

– These last symptoms occur

because anabolic steroids

often cause the body to

reduce its normal output of

sex hormones

THG


• A protein is a polymer constructed from amino

acid monomers

Proteins

• 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


Functions of proteins

(a) Structural proteinshair, horn, feather, spider web

connective tissue, tendon

(b) Storageproteins (seed, egg)

(c) Contractile proteins (muscle)

(d) Transport proteins(hemoglobin)

e) Defensive function (Antibody), Enzymes, Signal protein etc.



• Each amino acid :

– A central carbon

atom bonded to

four covalent

partners

– A side group that

is variable among

all 20Figure 3.19

Aminogroup

Carboxylgroup

Sidegroup

(a)

Sidegroups

LeucineSerine

(hydrophobic)(hydrophilic)

• All proteins are constructed

from a common set of 20 kinds

of amino acids

The Monomers: Amino Acids

A central carbon atom

(= α carbon)


• 20 amino acids: classified by polarity (극성)

– Positive charged amino acids: lysine (K), arginine (R),

histidine (H)

– Negative charged amino acids: aspartic acid (D),

glutamic acid (E)

– Polar (hydrophilic) amino acids: serine (S), threonine

(T), cysteine (C), glycine (G), asparagine (N),

glutamine (Q), tyrosine (Y)

– Nonpolar (hydrophobic) amino acids: leucine (L),

isoleucine (I), valine (V), proline (P), alanine (A),

tryptophan (W), phenylalanine (F), methionine (M)


Carboxylgroup

Aminogroup

Sidegroup

Sidegroup

Amino acid Amino acid

Dehydrationsynthesis

Sidegroup

Sidegroup

Peptide bond

• Cells link amino

acids together by

dehydration synthesis

Proteins as Polymers

– The resulting

bond between

them is called a

peptide bond

Figure 3.20

Amino-terminal

or N-terminal

Carboxy-terminal

or C-terminal

• Your body has tens of

thousands of different

kinds of protein


• A typical polypeptide: consists

of at least 100 amino acids

• The arrangement of amino

acids makes each one different

• Primary structure

: The specific

sequence of amino

acids in a protein

Primary structure



• 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 (겸상적혈구빈혈증)

(a) Normal red blood cell Normal hemoglobin

12 3

4 5

67. . . 146

(b) Sickled red blood cell Sickle-cell hemoglobin

2 31

4 56

7. . . 146


: Proteins have four levels of structure

Protein Shape

Hydrogen bond

Pleated sheet

Amino acid

(a) Primary structure

Hydrogen bond

Alpha helix

(b) Secondary structure:

Polypeptide(single subunit)

(c) Tertiary structure

Completeprotein,with fourpolypeptidesubunits

(d) Quaternary structure


• Tertiary structure

- The overall three-dimensional shape of the protein

- Hydrophobic interaction, H-bonds, van-der Waals

forces, and ionic interactions stabilize the 3D-

structure

• Secondary structure

- Local pattern or local structure within certain

stretches of polypeptide

- Alpha ()-helix, pleated sheet

- H-bonds confer stability of the secondary structures

• Quaternary structure

- A structure in which two or more polypeptides interact

to form © 2010 Pearson Education, Inc.RPTSE BIO Fall 2015 Jong B. Lee, PhD, All rights reserved.

• When a cell makes a polypeptide, the chain usually folds

spontaneously to form the functional shape for that

protein

• It is a protein’s three-dimensional shape that enables the

molecule to carry out specific function in a cell

• In almost every case, a protein’s function depends on its

ability to recognize and bind to some other molecule

• If the shape of a protein is altered, then it would not be

able to perform this recognition function

: Function follows form (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 pH가다시원래대로돌아오면본래모습으로복귀

: called renaturation 일차구조로서 단백질모습이결정

What Determines Protein Structure?

• Misfolded proteins are associated with Alzheimer’s

disease, Mad cow disease and Parkinson’s disease


Nucleic Acids

• Nucleic acids are macromolecules that provide the

directions for building proteins

• The name of nucleic acids comes from their location

in nuclei of eukaryotic cells.


Nitrogenous base(A,G,C, or T)

Phosphategroup

Thymine (T)

Sugar(deoxyribose)

Phosphate

Base

Sugar

Nucleotide

• Nucleic acids are

polymers of nucleotides

: Monomer is called

nucleotide.

• There are two types of nucleic acids

– DNA : deoxyribonucleic acid

– RNA : ribonucleic acid


• Each DNA

nucleotide has one

of the following

bases

– Adenine (A)

– Guanine (G)

– Thymine (T)

– Cytosine (C)

Figure 3.25

Thymine (T) Cytosine (C)

Adenine (A) Guanine (G)



• Nucleotide monomers are

linked into long chains (by phosphodiester bonds)

– These chains are called

polynucleotides, or

DNA strands

– A sugar-phosphate

backbone joins them

together

– Bases are hanging off

the backbone like

appendages

Backbone

Nucleotide

Bases

(a) DNA strand

Figure 3.26a


• Two strands of DNA join together

to form a double helix

Figure 3.26bDouble helix

H-bond- Complementary character

of DNA double helix

- The bases along one DNA

strand hydrogen-bond to

bases along the other

strand

- This base pairing is

specific (A=T, C≡G)


• RNA, ribonucleic

acid, is different

from DNA

1) Its sugar has an

extra OH group

(2-carbon)

2) It has the base

uracil (U) instead

of thymine (T)

Figure 3.27

Nitrogenous base(A,G,C, or U)

Phosphategroup

Uracil (U)

Sugar (ribose)


Large biological

molecules

Functions Components Examples

Carbohydrates

Lipids

Proteins

Nucleic acids

Dietary energy;

storage; plant

structure

Long-term

energy storage

fats;hormones

steroids

Enzymes, structure,

storage, contraction,

transport, and others

Information

storage

Monosaccharides:

glucose, fructose

Disaccharides:

lactose, sucrose

Polysaccharides:

starch, cellulose

Fats triglycerides;Steroids

testosterone,

estrogen

Lactase

an enzyme,

hemoglobin

a transport protein

DNA, RNA

Monosaccharide

Components of

a triglyceride

Amino acid

Nucleotide

Fatty acid

Glycerol

Aminogroup

Carboxylgroup

Sidegroup

Phosphate

Base

Sugar

the molecules of life - new york institute of technologyiris.nyit.edu/~jlee26/pics/rptse/eng rptse...

Documents