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Chapter 3. The Structure and Function of Macromolecules. Macromolecules. Are large molecules (polymers) composed of smaller molecules (monomers) Are complex in their structures. Protein. Macromolecules. Most macromolecules are polymers , built from monomers

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Chapter 3

Chapter 3

The Structure and Function of Macromolecules


Macromolecules

Macromolecules

  • Are large molecules (polymers) composed of smaller molecules (monomers)

  • Are complex in their structures

Protein


Macromolecules1

Macromolecules

  • Most macromolecules are polymers, built from monomers

  • Four classes of life’s organic molecules are polymers

    • Carbohydrates

    • Proteins

    • Nucleic acids

    • Lipids


Chapter 3

  • A polymer

    • Is a long molecule consisting of many similar building blocks called monomers

    • Specific monomers make up each macromolecule

      • Amino acids are the monomers for proteins

      • Monosaccharides make up carbohydrates

      • Glycerol and Fatty acids for Lipids

      • Nucleotides for Nucleic acids


The synthesis and breakdown of polymers

1

HO

H

3

2

H

HO

Unlinked monomer

Short polymer

Dehydration removes a watermolecule, forming a new bond

H2O

1

2

3

4

HO

H

Longer polymer

(a) Dehydration reaction in the synthesis of a polymer

Figure 5.2A

The Synthesis and Breakdown of Polymers

  • Monomers form larger molecules by condensation reactions called Dehydration synthesis orCondensation

  • Is an anabolic reaction (building up)

Condensation of amino acids


Dehydration synthesis of carbohydrates

Dehydration Synthesis of Carbohydrates


The synthesis and breakdown of polymers1

1

3

HO

4

2

H

Hydrolysis adds a watermolecule, breaking a bond

H2O

1

2

H

HO

3

H

HO

Figure 5.2B

(b) Hydrolysis of a polymer

The Synthesis and Breakdown of Polymers

  • Polymers can disassemble by

    • Hydrolysis (addition of water molecules)

    • Is a catabolic or breakdown reaction


Hydrolysis of a disaccharide

Hydrolysis of a Disaccharide


Chapter 3

  • Although organisms share the same limited number of monomer types,each organism is unique based on the arrangement of monomers into polymers

  • An immense variety of polymers can be built from a small set of monomers

  • How many words can be made using the English alphabet?


Carbohydrates

Carbohydrates

  • C, H, O w/ a H:O ratio of 2:1

  • Serve as fuel and building material

  • Sugars and their polymers (starch, cellulose, etc.)

  • Tend to end in “ose”


Sugars

Sugars

  • Monosaccharides

    • Are the simplest sugars

    • Most are: C6H12O6

    • Can be used for fuel

    • Can be converted into other organic molecules

    • Can be combined into polymers

    • Glucose, Galactose, Fructose, Ribose…


Chapter 3

Pentose sugars(C5H10O5)

Hexose sugars(C6H12O6)

Triose sugars(C3H6O3)

H

H

H

H

O

O

O

O

C

C

C

C

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

HO C H

HO C H

Aldoses

H

H C OH

H C OH

HO C H

H C OH

H C OH

H C OH

Glyceraldehyde

H C OH

H C OH

H

Ribose

H

H

Glucose

Galactose

H

H

H

H C OH

H C OH

H C OH

C O

C O

C O

HO C H

H C OH

H C OH

Ketoses

H C OH

H C OH

H

Dihydroxyacetone

H C OH

H C OH

H C OH

H

Ribulose

H

Fructose

Figure 5.3

  • Examples of monosaccharides


Chapter 3

O

H

6CH2OH

1

C

6CH2OH

2

CH2OH

H C OH

5C

H

5C

O

O

6

3

H

O

H

H

H

H

H

5

HO C H

HOH

HOH

H

4

4C

1 C

1C

4C

4

1

OH

H

H

H C OH

3 2

O

HO

OH

OH

OH

5

OH

2 C

3

C

3 C

2C

OH

H C

H

OH

6

H

H

OH

OH

H C OH

H

Figure 5.4

(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.

  • Monosaccharides

    • May be linear

    • Can form rings in solution


Chapter 3

Disaccharides

  • C12H22O11

  • Consist of two monosaccharides

  • Are joined by a glycosidic linkage


Chapter 3

Dehydration reaction in the synthesis of maltose. The bonding of two glucose units forms maltose. The glycosidic link joins the number 1 carbon of one glucose to the number 4 carbon of the second glucose. Joining the glucose monomers in a different way would result in a different disaccharide.

CH2OH

CH2OH

CH2OH

CH2OH

1– 4glycosidiclinkage

O

O

O

O

H

H

H

H

H

H

H

H

HOH

HOH

HOH

HOH

4

1

H

H

H

H

OH

OH

O

H

OH

HO

HO

OH

O

H

H

H

OH

H

OH

OH

OH

H2O

Glucose

Maltose

Glucose

CH2OH

CH2OH

CH2OH

CH2OH

O

O

O

O

H

1–2glycosidiclinkage

H

H

H

H

H

HOH

Dehydration reaction in the synthesis of sucrose. Sucrose is a disaccharide formed from glucose and fructose.Notice that fructose,though a hexose like glucose, forms a five-sided ring.

HOH

2

1

OH

H

H

HO

H

HO

H

HO

H

O

O

HO

CH2OH

CH2OH

OH

H

OH

H

H

H

OH

OH

H2O

Sucrose

Fructose

Glucose

Figure 5.5

Maltose

Glucose

Glucose

1– 2glycosidiclinkage


Polysaccharides

Polysaccharides

  • Polysaccharides

    • Are polymers of sugars

    • Serve many roles in organisms

    • Starch, glycogen, cellulose, chitin


Storage polysaccharides

Chloroplast

Starch

1 m

Amylose

Amylopectin

(a) Starch: a plant polysaccharide

Figure 5.6

Storage Polysaccharides

  • Starch - Amylose

    • Is a polymer consisting entirely of glucose monomers

    • Is the major storage form of glucose in plants

      in amyloplasts


Chapter 3

Mitochondria

Giycogen granules

0.5 m

Glycogen

Figure 5.6

(b) Glycogen: an animal polysaccharide

  • Glycogen

    • Consists of glucose monomers

    • Is the major storage form of glucose in animal livers


Structural polysaccharides

Structural Polysaccharides

  • Cellulose

    • Is a polymer of glucose


Chapter 3

H

O

CH2OH

C

CH2OH

OH

OH

H

C

H

O

O

H

H

H

H

HO

OH

OH

C

H

4

4

1

H

H

HO

OH

HO

OH

H

H

C

OH

OH

H

OH

H

C

H

OH

 glucose

C

 glucose

H

(a)  and  glucose ring structures

CH2OH

CH2OH

CH2OH

CH2OH

O

O

O

O

OH

OH

OH

OH

1

4

4

4

1

1

1

HO

O

O

O

O

OH

OH

OH

OH

(b)Starch: 1– 4 linkage of  glucose monomers

OH

OH

CH2OH

CH2OH

O

O

OH

OH

O

O

OH

OH

HO

OH

4

O

1

O

O

CH2OH

CH2OH

OH

OH

(c) Cellulose: 1– 4 linkage of  glucose monomers

Figure 5.7 A–C

  • Has different glycosidic linkages than starch

– C6 is on the top left on both monomers

– C6 is flipped from top to bottom

OH

OH

OH

OH


Chapter 3

Parallel cellulose molecules are held together by hydrogen bonds between hydroxyl groups attached to carbon atoms 3 and 6.

About 80 cellulose molecules associate to form a microfibril, the main architectural unit of the plant cell wall.

A cellulose molecule

is an unbranched

glucose polymer.

Plant cells

Cellulose

molecules

  • Is a major component of the tough walls that enclose plant cells

Hydrogen bonds


Chapter 3

Figure 5.9

  • Cellulose is difficult to digest

    • Cows have microbes in their stomachs to facilitate this process


Chapter 3

CH2OH

O

OH

H

H

OH

H

H

H

NH

O

C

CH3

OH

(b) Chitin forms the exoskeleton

of arthropods. This cicada

is molting, shedding its old

exoskeleton and emerging

in adult form.

(c) Chitin is used to make a

strong and flexible surgical

thread that decomposes after

the wound or incision heals.

(a) The structure of the

chitin monomer.

Figure 5.10 A–C

  • Chitin, another important structural polysaccharide

    • Is found in the exoskeleton of arthropods

    • Can be used as surgical thread


Lipids

Lipids

  • Lipids are a diverse group of hydrophobic molecules

  • Lipids

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

    • Not considered a true macromolecules

    • Made up mostly of chains of hydrocarbons

    • Share the common trait of being hydrophobic

    • Fats, oils, waxes, phospholipids and steroids

    • Carbon, Hydrogen & Oxygen with

      H:O ratio >2:1

    • Involved in long term energy storage


Chapter 3

Fats

  • Are constructed from two types of smaller molecules, a single glycerol and usually three fatty acids

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


Chapter 3

Saturated fatty acids

Have the maximum number of hydrogen atoms possible

Have no double bonds

Lard, butter, animal fat, palm oil, coconut oil, palm kernel oil

Stearic acid

Figure 5.12

(a) Saturated fat and fatty acid


Chapter 3

cis double bond

causes bending

Oleic acid

Figure 5.12

(b) Unsaturated fat and fatty acid

  • Unsaturated fatty acids

    • Have one or more double bonds

    • Olive oil


What to eat

What to eat?

  • The following foods are high in monounsaturated fats:

    • peanut butter

    • olives

    • nuts – almonds, pecans, pistachios, cashews

    • avocado

    • seeds – sesame

    • oils – olive, sesame, peanut, canola

  • The following foods are high in polyunsaturated fats:

    • walnuts

    • seeds – pumpkin, sunflower

    • flaxseed

    • fish – salmon, tuna, mackerel

    • oils – safflower, soybean, corn


Chapter 3

  • Phospholipids

    • Have only two fatty acids

    • Have a phosphate group instead of a third fatty acid

    • Typical of a cell membrane

***The kink in the H-C chain due to a double bond is what gives the cell membrane its fluidity


Chapter 3

+

CH2

Choline

N(CH3)3

CH2

O

Phosphate

Hydrophilic head

P

O

O

O

CH2

CH

CH2

Glycerol

O

O

C

O

C

O

Fatty acids

Hydrophilic

head

Hydrophobic tails

Hydrophobic

tails

(b) Space-filling model

(c) Phospholipid

symbol

Figure 5.13

(a) Structural formula

  • Phospholipid structure

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


Chapter 3

WATER

Hydrophilic

head

Hydrophobic

tail

WATER

Figure 5.14

  • The structure of phospholipids

    • Results in a bilayer arrangement found in cell membranes


Steroids

H3C

CH3

CH3

CH3

CH3

HO

Figure 5.15

Steroids

  • Steroids

    • Are lipids characterized by a carbon skeleton consisting of four fused rings

  • One steroid, cholesterol

    • Is found in cell membranes

    • Is a precursor for some hormones like estrogen & testosterone


Proteins

Proteins

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

    • Building and regulatory functions

  • Proteins do most of the work in cells and act as enzymes

  • Most hormones are protein derived

  • Proteins are made of monomers called amino acids

  • Made up of Carbon, Hydrogen, Oxygen, Nitrogen & sometimes Sulfur


Chapter 3

Table 5.1

  • An overview of protein functions


Chapter 3

Substrate binds to

enzyme.

1 Active site is available for

a molecule of substrate, the

reactant on which the enzyme acts.

2

2

Substrate

(sucrose)

Glucose

Enzyme

(sucrase)

OH

H2O

Fructose

H O

4 Products are released.

3 Substrate is converted

to products.

Figure 5.16

  • Enzymes

    • Are a type of protein that acts as a catalyst, speeding up chemical reactions (by reducing the amount of activation energy needed)


Polypeptides

Polypeptides

  • Polypeptides

    • Are polymers (chains) of amino acids

  • A protein

    • Consists of one or more polypeptides


Chapter 3

  • Amino acids

    • Are organic molecules possessing both carboxyl and amino groups

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


Twenty amino acids you do not need to memorize these

CH3

CH3

CH3

CH

CH2

CH3

CH3

H

CH3

H3C

CH3

CH2

CH

O

O

O

O

O

H3N+

H3N+

H3N+

H3N+

C

H3N+

C

C

C

C

C

C

C

C

C

O–

O–

O–

O–

O–

H

H

H

H

H

Valine (Val)

Leucine (Leu)

Isoleucine (Ile)

Glycine (Gly)

Alanine (Ala)

Nonpolar - Hydrophobic

CH3

CH2

S

H2C

CH2

O

NH

CH2

H2N

C

C

CH2

CH2

O–

CH2

O

O

O

H

H3N+

H3N+

C

C

C

C

H3N+

C

C

O–

O–

O–

H

H

H

Phenylalanine (Phe)

Proline (Pro)

Methionine (Met)

Tryptophan (Trp)

Figure 5.17

Twenty Amino Acids (you do not need to memorize these!!)

  • 20 different amino acids make up proteins


Chapter 3

OH

NH2

O

C

NH2

O

Polar - Hydrophilic

C

OH

SH

CH2

CH3

OH

CH2

CH

CH2

CH2

CH2

CH2

O

O

O

O

O

O

H3N+

H3N+

H3N+

H3N+

H3N+

H3N+

C

C

C

C

C

C

C

C

C

C

C

C

O–

O–

O–

O–

O–

O–

H

H

H

H

H

H

Glutamine

(Gln)

Tyrosine

(Tyr)

Asparagine

(Asn)

Cysteine

(Cys)

Serine (Ser)

Threonine (Thr)

Basic

Acidic

NH3+

NH2

NH+

O–

O

–O

O

NH2+

Electrically

Charged - Ionic

CH2

C

C

C

NH

CH2

CH2

CH2

CH2

CH2

O

O

H3N+

H3N+

CH2

CH2

C

CH2

C

C

C

O

O–

H3N+

O–

CH2

C

CH2

C

H

O

H

H3N+

O–

C

C

CH2

H

O

O–

H3N+

C

C

H

O–

H

Lysine (Lys)

Histidine (His)

Arginine (Arg)

Glutamic acid

(Glu)

Aspartic acid

(Asp)


Amino acid polymers

Amino Acid Polymers

  • Amino acids

    • Are linked by peptide bonds through Dehydration synthesis


Protein conformation and function

Protein Conformation and Function

  • A protein’s specific conformation (shape) determines how it functions


Four levels of protein structure

Amino acid subunits

+H3NAmino end

Pro

Thr

Gly

Gly

Thr

Gly

Glu

Seu

Lys

Cys

Pro

Leu

Met

Val

Lys

Val

Leu

Asp

Ala

Arg

Val

Gly

Ser

Pro

Ala

Glu

Lle

Asp

Thr

Lys

Ser

Tyr

Trp

Lys

Ala

Leu

Gly

lle

Ser

Pro

Phe

His

Glu

His

Ala

Glu

Val

Thr

Phe

Val

Ala

Asn

lle

Thr

Asp

Ala

Tyr

Arg

Ser

Ala

Arg

Pro

Gly

Leu

Leu

Ser

Pro

Tyr

Ser

Tyr

Ser

Thr

Thr

Ala

o

Val

c

Val

Glu

Lys

o

Thr

Pro

Asn

Carboxyl end

Figure 5.20

Four Levels of Protein Structure

  • The specific order of amino acids in a polypeptide interacts with the environment to determine the overall structure of the protein.

  • The interactions of the R group of the amino acid determines structure and function of the R region of the protein.

    • Hydrophobic, hydrophilic or ionic

  • Primary structure

    • Is the unique sequence of amino acids in a polypeptide

    • Linear


Chapter 3

H

H

H

H

H

H

O

O

O

O

O

O

O

H

H

H

H

H

H

R

R

R

R

R

R

R

C

C

C

C

C

C

C

C

C

C

C

C

C

N

N

N

N

N

N

N

N

N

N

N

N

N

C

C

C

C

C

C

C

C

C

C

C

C

C

C

R

R

R

R

R

R

H

H

H

H

H

H

H

O

O

O

O

O

O

O

H

H

H

H

H

H

H

 pleated sheet

H

O

H

H

Amino acidsubunits

C

C

N

N

N

C

C

C

R

H

O

H

H

H

H

H

H

N

N

N

N

N

N

 helix

C

C

O

C

H

H

H

C

C

C

R

R

R

R

R

H

H

C

C

C

C

C

C

O

O

O

O

H

C

R

O

C

C

O

H

C

O

N

N

H

C

C

H

R

H

R

Figure 5.20

  • Secondary structure

    • Is the folding or coiling of the polypeptide into a repeating configuration due to Hydrogen bonds

    • Includes the  helix and the  pleated sheet


Chapter 3

Hydrophobic interactions and van der Waalsinteractions

CH

CH2

CH2

H3C

CH3

OH

Polypeptidebackbone

H3C

CH3

Hyrdogenbond

CH

O

HO

C

CH2

CH2

S

S

CH2

Disulfide bridge

O

-O

C

CH2

CH2

NH3+

Ionic bond

  • Tertiary structure

    • Is the overall three-dimensional shape of a polypeptide

    • Results from interactions between amino acids and R groups - Disulfide bridge formed


Chapter 3

Polypeptidechain

Collagen

 Chains

Iron

Heme

 Chains

Hemoglobin

  • Quaternary structure

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


Review of protein structure

+H3N

Amino end

Amino acid

subunits

helix

Review of Protein Structure


Sickle cell disease a simple change in primary structure

Sickle-Cell Disease: A Simple Change in Primary Structure

  • Sickle-cell disease

    • Results from a single amino acid substitution in the protein hemoglobin

    • Valinefor Glutamic acid

    • Caused by a point mutation


Chapter 3

Sickle-cell hemoglobin

Normal hemoglobin

Primary structure

Exposed hydrophobic region

Primary structure

. . .

. . .

Glu

Glul

Val

His

Leu

Thr

Pro

Val

His

Leu

Pro

Val

Glu

Thr

5

6

7

7

2

3

4

5

6

1

1

2

3

4

Secondaryand tertiarystructures

Secondaryand tertiarystructures

 subunit

 subunit

Hemoglobin A

Hemoglobin S

Quaternary structure

Quaternary structure

Molecules interact with one another tocrystallize into a fiber, capacity to carry oxygen is greatly reduced.

Molecules donot associatewith oneanother, eachcarries oxygen.

Function

Function

10 m

10 m

Red bloodcell shape

Normal cells are full of individualhemoglobinmolecules, eachcarrying oxygen

Red bloodcell shape

Figure 5.21

Fibers of abnormalhemoglobin deform cell into sickle shape.


What determines protein conformation

What Determines Protein Conformation?

  • Protein conformation depends on the physical and chemical conditions of the protein’s environment

  • Temperature, pH, [salt], etc. influence protein structure


Denaturation is when a protein unravels and loses its native conformation shape

Denaturation

Normal protein

Denatured protein

Renaturation

Figure 5.22

Denaturation is when a protein unravels and loses its native conformation(shape)


The protein folding problem

The Protein-Folding Problem

  • Amino acid sequences of 875,000 proteins are known.

  • 3D shapes of 7,000 are known.

    • aka, Scientists don’t know the structure of most proteins

  • Most proteins

    • Probably go through several intermediate states on their way to a stable conformation

    • Denaturated proteins no longer work in their unfolded condition

    • Proteins may be denaturated by extreme changes in pH or temperature


Chapter 3

Correctlyfoldedprotein

Polypeptide

Cap

Hollowcylinder

Steps of ChaperoninAction: An unfolded poly- peptide 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.

Chaperonin(fully assembled)

The cap comesoff, and the properlyfolded protein is released.

2

3

1

Figure 5.23

  • Chaperonins (aka, chaperone proteins)

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


Chapter 3

X-raydiffraction pattern

Photographic film

Diffracted X-rays

X-ray beam

X-raysource

Crystal

Nucleic acid

Protein

(b) 3D computer model

(a) X-ray diffraction pattern

  • X-ray crystallography

    • Is used to determine a protein’s three-dimensional structure

    • Rosalind Franklin & DNA

Figure 5.24


Nucleic acids

Nucleic Acids

  • Nucleic acids store and transmit hereditary information

    • Polymers of nucleotides

  • Genes

    • Are the units of inheritance

    • Program the amino acid sequence of polypeptides

    • Are made of nucleotide sequences on DNA


The roles of nucleic acids

The Roles of Nucleic Acids

  • There are two types of nucleic acids

    • Deoxyribonucleic acid (DNA)

    • Ribonucleic acid (RNA)


Deoxyribonucleic acid

Deoxyribonucleic Acid

  • DNA

    • Stores information for the synthesis of specific proteins

    • Found in the nucleus of cells


Dna functions

DNA

1

Synthesis of mRNA in the nucleus

mRNA

NUCLEUS

CYTOPLASM

mRNA

2

Movement of

mRNA into cytoplasm

via nuclear pore

Ribosome

3

Synthesis

of protein

Aminoacids

Polypeptide

Figure 5.25

DNA Functions

  • Directs RNA synthesis (transcription)

  • Directs protein synthesis through RNA (translation)


The structure of nucleic acids

5’ end

5’C

O

3’C

O

O

5’C

O

3’C

3’ end

OH

Figure 5.26

The Structure of Nucleic Acids

  • Nucleic acids

    • Exist as polymers called polynucleotides

(a) Polynucleotide,

or nucleic acid


Chapter 3

  • Each polynucleotide

    • Consists of monomers called nucleotides

    • 5C Sugar + phosphate group + nitrogen base


Nucleotide monomers

Nucleotide Monomers

  • Nucleotide monomers

    • Are made up of nucleosides (sugar + base) and phosphate groups


Nucleotide polymers

Nucleotide Polymers

5`

3`

  • 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

3`

5`


Chapter 3

Gene

  • The sequence of bases along a nucleotide polymer

    • Is unique for each gene


The dna double helix

The DNA Double Helix

  • Cellular DNA molecules

    • Have two polynucleotides that spiral around an imaginary axis

    • Form a double helix


Chapter 3

3’ end

5’ end

Sugar-phosphatebackbone

Base pair (joined byhydrogen bonding)

Old strands

Nucleotideabout to be added to a new strand

3’ end

A

5’ end

Newstrands

3’ end

3’ end

5’ end

Figure 5.27

  • The DNA double helix

    • Consists of two antiparallel nucleotide strands

    • Look at the C’s on the ribose molecule. The 5th C bonded to the Phosphate group is the 5` end.


A t c g

A,T,C,G

  • The nitrogenous bases in DNA

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


Dna and proteins as tape measures of evolution

DNA and Proteins as Tape Measures of Evolution

  • Molecular comparisons

    • Help biologists sort out the evolutionary connections among species


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