Copyright © 2006 Cynthia Garrard publishing under Canyon Design Chapter 5 - Macromolecules Overview: The Molecules of Life – Another level in the hierarchy.

Copyright © 2006 Cynthia Garrard publishing under Canyon Design

Chapter 5 - Macromolecules

• Overview: The Molecules of Life

– Another level in the hierarchy of biological organization is reached when small organic molecules are joined together


Macromolecules

• Macromolecules

– Are large molecules composed of smaller molecules

– Are complex in their structures

Figure 5.1


Polymers and Monomers

Three of the classes of life’s organic molecules are polymers

– Carbohydrates

– Proteins

– Nucleic acids



• A polymer

– Is a long molecule consisting of many similar or identical building blocks called monomers

• A monomer

– Is the subunit that serve as the building block of a polymer



• Dehydration reactions – condensation reaction that forms large molecules from monomers

– Takes energy

– Must have enzymes helping

(a) Dehydration reaction in the synthesis of a polymer

HO H1 2 3 HO

HO H1 2 3 4

H

H2O

Short polymer Unlinked monomer

Longer polymer

Dehydration removes a watermolecule, forming a new bond

Figure 5.2A



• Polymers can disassemble by

– Hydrolysis

• Releases energy

(b) Hydrolysis of a polymer

HO 1 2 3 H

HO H1 2 3 4

H2O

HHO

Hydrolysis adds a watermolecule, breaking a bond

Figure 5.2B



There are only about 40 -50 monomers, yet there are 1000’s of different polymers

– Possible through different linear sequences

1 2 3 HOH


Carbohydrates

•Monomer – monosaccharide or simple sugar

– Example: Glucose, Fructose, Lactose

– Major nutrient of cells

– Joined together by glycosidic linkage

Figure 5.3


Carbohydrates

• Monosaccharides

– May be linear

– Can form rings

H

H C OH

HO C H

H C OH

H C OH

H C

O

C

H

1

2

3

4

5

6

H

OH

4C

6CH2OH 6CH2OH

5C

HOH

C

H OH

H

2 C

1C

H

O

H

OH

4C

5C

3 C

H

HOH

OH

H

2C

1 C

OH

H

CH2OH

H

H

OHHO

H

OH

OH

H5

3 2

4

(a) Linear and ring forms. Chemical equilibrium between the linear and ring structures greatly favors the formation of rings. To form the glucose ring, carbon 1 bonds to the oxygen attached to carbon 5.

OH3

O H OO

6

1

Figure 5.4


Carbohydrates

•Polymer – is polysaccharide

– Example: Starch, Glycogen, Cellulose


Carbohydrates

Polysaccharide can be involved with storage

• Starch

– Is a polymer consisting entirely of glucose monomers

– Is found in plants

• Glycogen

– Is found in animals

Both are stored energy


Carbohydrates

Polysaccharides involved in the structure of cells

– Cellulose – in plants

– Chitin – in insects

Strength comes from the isomers of glucose and the 3D shape of the molecule


Carbohydrates

Isomers of glucose

- Differ in the location of the hydroxyl group bonded to the 1’ C

Figure 5.7


Carbohydrates

•Different isomers can create different molecules

Figure 5.7


Lipids

• Lipids

– Are the one class of large biological molecules that do not consist of polymers

– Share the common trait of being hydrophobic

– Consist mostly of hydrocarbons

– Have varied functions


Lipids

• Fats

– Constructed from two types of smaller molecules: a single glycerol, and usually three fatty acids

(b) Fat molecule (triacylglycerol)

H HH H

HHH

HH

HH

HH

HH

HOH O HC

C

C

H

H OH

OH

H

HH

HH

HH

HH

HH

HH

HH

H

HCCC

CC

CC

CC

CC

CC

CC C

Glycerol

Fatty acid(palmitic acid)

H

H

H

H

HH

HH

HH

HH

HH

HH

HH

HH

HHHH

HHHHHHHHHHHH

H

HH

H HH

H HH

HH

HH

HH

HH

HHHHHHHHHHH

HH

H

H H H H H H H H HH

HH H H H

H

HH

HHHHHH

HHHHH

HH

HO

O

O

O

OC

C

C C C C C C C C C C C C C C C C C

C

CCCCCCC

CCCCCCCCC

C C C C C C C C C C C CC

CC

O

O

(a) Dehydration reaction in the synthesis of a fatEster linkage

Figure 5.11


Lipids

• Fats

– Fatty acids are joined to the glycerol by ester linkages

– Major function is energy storage


• Fatty acids

– Vary in the length and number and locations of double bonds they contain

• This results in different types of fatty acids

– Saturated

– Unsaturated


Lipids• Saturated fatty acids

– Have the maximum number of hydrogen atoms possible

– Have no double bonds

– Solid at room temp

(a) Saturated fat and fatty acid

Stearic acid

Figure 5.12


• Unsaturated fatty acids

– Have one or more double bonds

– Liquid at room temp

(b) Unsaturated fat and fatty acidcis double bondcauses bending

Oleic acid

Figure 5.12


Lipids

Another type of lipid is the phospholipid

• Phospholipids

– Have only two fatty acids

– Have a phosphate group instead of a third fatty acid


Lipids

• Phospholipid structure

– Consists of a hydrophilic “head” and hydrophobic “tails”

CH2

O

PO O

O

CH2CHCH2

OO

C O C O

Phosphate

Glycerol

(a) Structural formula (b) Space-filling model

Fatty acids

(c) Phospholipid symbol

Hy

dro

ph

ob

ic t

ail

s

Hydrophilichead

Hydrophobictails

–

Hy

dro

ph

ilic

he

ad CH2 Choline

+

Figure 5.13

N(CH3)3


Lipids

• The structure of phospholipids

– Results in a bilayer arrangement found in cell membranes

Hydrophilichead

WATER

WATER

Hydrophobictail

Figure 5.14

We’ll spend more time with them in Chapter 7


Proteins

Proteins have many structures, resulting in a wide range of functions

– Proteins

• More than 50% of dry mass of cell

• Important in most everything organisms do

• Have many roles inside the cell

– Examples: speed up rxns, storage, cellular communication, transport, movement, structural support, and defense


Protein

• Enzymes

– Are a type of protein that acts as a catalyst, speeding up chemical reactions

– Humans have 10,000+ different enzymes

– Each enzyme does its specific job

– Does not get used up or altered in the rxn


Protein

• Monomer – amino acid

– Are organic molecules possessing both carboxyl and amino groups

– 20 unique amino acids

– Differ in their properties due to differing side chains, called R groups


Protein

• 20 different amino acids make up proteins

O

O–

H

H3N+ C C

O

O–

H

CH3

H3N+ C

H

C

O

O–

CH3 CH3

CH3

C C

O

O–

H

H3N+

CH

CH3

CH2

C

H

H3N+

CH3

CH3

CH2

CH

C

H

H3N+ C

CH3

CH2

CH2

CH3N+

H

C

O

O–

CH2

CH3N+

H

C

O

O–

CH2

NH

H

C

O

O–

H3N+ C

CH2

H2C

H2N C

CH2

H

C

Nonpolar

Glycine (Gly) Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine (Ile)

Methionine (Met) Phenylalanine (Phe)

C

O

O–

Tryptophan (Trp) Proline (Pro)

H3C

Figure 5.17

S

O

O–


O–

OH

CH2

C C

H

H3N+

O

O–

H3N+

OH CH3

CH

C C

HO–

O

SH

CH2

C

H

H3N+ C

O

O–

H3N+ C C

CH2

OH

H H H

H3N+

NH2

CH2

OC

C C

O

O–

NH2 O

C

CH2

CH2

C CH3N+

O

O–

O

Polar

Electricallycharged

–O O

C

CH2

C CH3N+

H

O

O–

O– O

C

CH2

C CH3N+

H

O

O–

CH2

CH2

CH2

CH2

NH3+

CH2

C CH3N+

H

O

O–

NH2

C NH2+

CH2

CH2

CH2

C CH3N+

H

O

O–

CH2

NH+

NHCH2

C CH3N+

H

O

O–

Serine (Ser) Threonine (Thr)Cysteine

(Cys)Tyrosine

(Tyr)Asparagine

(Asn)Glutamine

(Gln)

Acidic Basic

Aspartic acid (Asp)

Glutamic acid (Glu)

Lysine (Lys) Arginine (Arg) Histidine (His)


Protein

• Amino acids

– Are linked by peptide bonds

DESMOSOMES

DESMOSOMESDESMOSOMES

OH

CH2

C

N

H

C

H O

H OH OH

Peptidebond

OH

OH

OH

H H

HH

H

H

H

H

H

H H

H

N

N N

N N

SHSide

chains

SH

OO

O O O

H2O

CH2 CH2

CH2 CH2CH2

C C C C C C

C CC C

Peptidebond

Amino end(N-terminus)

Backbone

(a)

Figure 5.18 (b) Carboxyl end(C-terminus)


Protein

• Polymer – polypeptide, which differs from a protein

– Amino acids are joined by peptide bonds, amino group to carboxyl group

– Each has a unique linear sequence

• Protein

– Consists of one or more polypeptides


Protein

To be functional, the protein’s polypeptide chain(s) must be precisely twisted, folded and coiled into the proper shape

The linear sequence of the amino acids determine which polypeptide is formed and its proper 3D shape


Protein

There are 4 levels of protein structure:

• Primary structure

– Is the unique sequence of amino acids in a polypeptide

Figure 5.20

–

Amino acid subunits

+H3NAmino end

o

Carboxyl end

oc

Gly Pro Thr Gly

Thr

Gly

GluSeuLysCysProLeu

Met

Val

Lys

Val

LeuAsp

Ala Val ArgGly

SerPro

Ala

Gly

lle

SerPro Phe His Glu His

Ala

Glu

ValValPheThrAla

Asn

Asp

Ser

Gly ProArg

ArgTyr

Thrlle

Ala

Ala

Leu

Leu

SerProTyr

SerTyrSer

Thr

Thr

Ala

ValVal

ThrAsn Pro

Lys Glu

Thr

Lys

SerTyrTrpLysAlaLeu

Glu Lle Asp


Protein

•Secondary structure

– Is the folding or coiling of the polypeptide into a repeating configuration

– Includes the helix and the pleated sheet

Figure 5.20


Protein

• Tertiary structure

– Is the overall three-dimensional shape of a polypeptide

– Results from interactions between amino acids and R groups

CH2CH

OH

O

CHO

CH2

CH2 NH3+ C-O CH2

O

CH2SSCH2

CH

CH3

CH3

H3C

H3C

Hydrophobic interactions and van der Waalsinteractions

Polypeptidebackbone

Hyrdogenbond

Ionic bond

CH2

Disulfide bridge


Protein

• Quaternary structure

– Is the overall protein structure that results from the aggregation of two or more polypeptide subunits

Polypeptidechain

Collagen

Chains

ChainsHemoglobin

Iron

Heme


Protein

• Protein conformation

– Depends on the physical and chemical conditions of the protein’s environment

• Things like salt concentration, pH level and temperature can denature a protein


Protein

• Denaturing

– when a protein unravels and loses its native conformation

Denaturation

Renaturation

Denatured proteinNormal protein

Figure 5.22


Protein

• Proteins have help folding properly in the form of chaperone proteins


Protein

• Chaperonins (chaperone proteins)

– Are protein molecules that assist in the proper folding of other proteins

Hollowcylinder

Cap

Chaperonin(fully assembled)

Steps of ChaperoninAction: An unfolded polypeptide enters the cylinder from one end.

The cap attaches, causing the cylinder to change shape insuch a way that it creates a hydrophilic environment for the folding of the polypeptide.

The cap comesoff, and the properlyfolded protein is released.

Correctlyfoldedprotein

Polypeptide

2

1

3

Figure 5.23


Nucleic acids

Nucleic acids store and transmit hereditary information

• Genes

– Are the units of inheritance

– Program the amino acid sequence of polypeptides

– Are made of nucleic acids


Nucleic Acids

• There are two types of nucleic acids

– Deoxyribonucleic acid (DNA) –

• Stores information for the synthesis of specific proteins

• Directs RNA synthesis

• Directs protein synthesis through RNA

– Ribonucleic acid (RNA)

• Multiple functions and types


Nucleic Acids

• Nucleic acids

– Exist as polymers called polynucleotides

(a) Polynucleotide, or nucleic acid

3’C

5’ end

5’C

3’C

5’C

3’ endOH

Figure 5.26

O

O

O

O


Nucleic acid

• Each polynucleotide

– Consists of monomers called nucleotides

Nitrogenousbase

Nucleoside

O

O

O

O P CH2

5’C

3’CPhosphate

group Pentosesugar

(b) NucleotideFigure 5.26

O

•Nitrogenous base (1 of 4)

•Sugar (pentose or 5C)

•Phosphate group


Nucleic acid

• Nucleotides can be divided into two types

– Pyrimidines – smaller, 1 6C ring

• Cytosine, thynine and uracil

– Purines – larger, 1 6C ring and 1 5C ring

• Adenosine, guanine


Nucleic acid

Before we move on, lets look closely at the sugar and count the carbons:


Nucleic acid

• Nucleotide polymers

– Are made up of nucleotides linked by the–OH group on the 3´ carbon of one nucleotide and the phosphate on the 5´ carbon on the next

– Monomers are joined by phosphodiester linkages between sugar / phosphate backbone, not bases


The DNA Double Helix

• Cellular DNA molecules

– Have two polynucleotides that spiral around an imaginary axis

– Form a double helix


• The DNA double helix

– Consists of two antiparallel nucleotide strands3’ end

Sugar-phosphatebackbone

Base pair (joined byhydrogen bonding)

Old strands

Nucleotideabout to be added to a new strand

A

3’ end

3’ end

5’ end

Newstrands

3’ end

5’ end

5’ end

Figure 5.27


• The nitrogenous bases in DNA

– Form hydrogen bonds in a complementary fashion (A with T only, and C with G only)

• The nitrogenous bases in RNA

– Form hydrogen bonds in a complementary fashion (A with U only, and C with G only)

Copyright © 2006 Cynthia Garrard publishing under Canyon Design Chapter 5 - Macromolecules Overview: The Molecules of Life – Another level in the hierarchy.

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