Large Biological Molecules

LECTURE PRESENTATIONS

For CAMPBELL BIOLOGY, NINTH EDITION

Jane B. Reece, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Robert B. Jackson

© 2011 Pearson Education, Inc.

Lectures by Erin Barley Kathleen Fitzpatrick

The Structure and Function of Large Biological Molecules

Chapter 5

The Molecules of Life

All living things are made up of four classes of large biological molecules:

1. carbohydrates 2. lipids

3. proteins

4. nucleic acids

Macromolecules are large molecules composed of thousands of covalently connected atoms

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Concept 5.1: Macromolecules are polymers, built from monomers

• A polymer is a long molecule consisting of many similar building blocks

• These small building-block molecules are called monomers

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POLYMERS

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

– Carbohydrates – Proteins

– Nucleic acids

• Lipid is NOT a polymer

• A dehydration or synthesis reaction occurs when two monomers bond together through the loss of a water molecule

The Synthesis of Polymers

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Figure 5.2a

(a) Dehydration reaction: synthesizing a polymer

Short polymer Unlinked monomer Dehydration removes

a water molecule,

forming a new bond.

Longer polymer

1 2 3 4

1 2 3

• Polymers are disassembled to monomers by hydrolysis or digestion reaction

• It is essentially the reverse of the dehydration reaction

Breakdown of Polymers

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Figure 5.2b

(b) Hydrolysis: breaking down a polymer

Hydrolysis adds a water molecule, breaking a bond.

1 2 3 4

1 2 3

AP Biology

Carbohydrates

 Carbohydrates are composed of C, H, O carbo - hydrate

General formula is (CH ₂ O)n Example is Glucose C ₆ H ₁₂ O ₆

 Function:

u energy storage

u raw materials

u structural materials

sugar sugar sugar sugar sugar sugar sugar

sugar

AP Biology

Carbohydrates are classified into 3 categories

 Monosaccharides

 Disaccharides

 Polysaccharides

AP Biology

Monosaccharides are single sugars

 Most names for sugars end in -ose

 Classified by number of carbons

u 6C = hexose (glucose)

u 5C = pentose (ribose)

u 3C = triose (glyceraldehyde)

Glyceraldehyde H

H

H

H

OH OH O C

C C

Glucose

AP Biology

Sugar structure

5C & 6C sugars form rings in solution

Carbons are numbered

Where do

you find solutions?

In cells !

AP Biology

Numbered carbons

C

C C

C

C C

1'

2' 3'

4'

5'

6'

O

energy stored in C-C bonds

AP Biology

Monosaccharides can be aldose or ketose

carbonyl

ketone aldehyde

carbonyl

• A disaccharide is formed when a dehydration reaction joins two monosaccharides

• This covalent bond is called a glycosidic linkage

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AP Biology

A disaccharide (double sugar) is formed when a dehydration reaction joins two monosaccharides

 Dehydration synthesis

glycosidic linkage

|

glucose

|

glucose

monosaccharides disaccharide

|

maltose

The covalent bond between two monomers

is called a glycosidic linkage

AP Biology

Building sugars

 ^Synthesis

|

fructose

|

glucose

monosaccharides

|

sucrose (table sugar) disaccharide

Crazy Carbs

Lactose is formed from glucose and

galactose

AP Biology

Polysaccharides

 Polymers of sugars

u costs little energy to build

u easily reversible = release energy

 ^Function:

u energy storage

 starch (plants)

 glycogen (animals)

u structure = building materials

 cellulose (plants)

 chitin (arthropods & fungi)

Figure 5.6

(a) Starch:

a plant polysaccharide

(b) Glycogen:

an animal polysaccharide Chloroplast Starch granules

Mitochondria Glycogen granules

Amylopectin

Amylose

Glycogen

1 m

0.5 m

Structural Polysaccharides

• Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ

• The difference is based on two ring forms for glucose: alpha () and beta ()

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Figure 5.7

(a)  and  glucose ring structures

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

 Glucose  Glucose

4 1 4 1

1 4

4 1

α- carbohydrates have a trans configuration between the OH group and the CH ₂ OH group. This means that the OH group (highlighted in yellow) and the CH ₂ OH group are on opposite sides of the ring.

β- carbohydrates have a cis configuration between the OH group and the CH ₂ OH group. This means that the OH group and the CH ₂ OH group are on the same side of the ring.

α- Glucose β- Glucose

AP Biology

Polysaccharide diversity

 Molecular structure determines function

Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ

The difference is based on two ring forms for glucose: alpha () and beta ()

in starch in cellulose

Starch 1-4 linkage of  glucose monomers

Polymers with  glucose are

helical

Cellulose 1-4 linkage of  glucose monomers

Polymers with  glucose are straight

Starch 1-4 linkage of  glucose monomers

Cellulose 1-4 linkage of  glucose monomers

Polymers with  glucose are straight. Parallel cellulose molecules held together this way by hydrogen bonds are grouped into microfibrils, which form strong building materials for plants

Cell wall

Microfibril Cellulose

microfibrils in a plant cell wall

Cellulose molecules

 Glucose monomer

10 m

0.5 m

Figure 5.8

AP Biology

Linear vs. branched polysaccharides

starch (plant) (amylose)

glycogen (animal)

energy storage

What does

branching do?

Carbohydrates can be linear or unbranched

Polysaccharides containing (α1→4) linkages only are unbranched

Starch contains two types of glucose polymer, amylose and amylopectin.

Amylose consists of long, unbranched chains of D-glucose units connected by (α1→4) linkages

Amylopectin is branched and cross linked at (α1→6)

linkages

Linear vs Branched Polysaccharides

• Enzymes that digest starch by hydrolyzing  linkages can’t hydrolyze  linkages in cellulose

• Cellulose in human food passes through the digestive tract as insoluble fiber

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AP Biology

Helpful bacteria in symbiotic relationship

 How can cows digest cellulose?

u bacteria live in their gut & help digest

cellulose-rich (grass) meals

• Chitin, another structural polysaccharide, is found in the exoskeleton of arthropods

• Chitin also provides structural support for the cell walls of many fungi

• Carbohydrate has side group containing N

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Figure 5.9

Chitin forms the exoskeleton of arthropods.

The structure of the chitin monomer

Chitin is used to make a strong and flexible

surgical thread that decomposes after the

wound or incision heals.

AP Biology

Lipids: Fats & Oils

AP Biology

Lipids

 Lipids are composed of C, H, O

u long hydrocarbon chain

 Diverse group

u fats

u phospholipids

u steroids

 Do not form polymers

u big molecules made of smaller subunits

u not a continuing chain

fat

AP Biology

Carbohydrates vs. Fats

fat carbohydrate

 Fat generates 2x ATP vs. carbohydrate

u more C in gram of fat

 more energy releasing bonds

u more O in gram of carbohydrate

 so it’s already partly oxidized

 less energy to release

AP Biology

Fat subunits

 Structure:

u glycerol (3C alcohol) + fatty acid

dehydration synthesis

 fatty acid =

long HC “tail” with COOH group at “head”

enzyme

AP Biology

Building Fats

 Triacylglycerol

u 3 fatty acids linked to glycerol

u ester linkage = between OH & COOH

AP Biology

Dehydration synthesis

enzyme

enzyme

enzyme

dehydration synthesis

AP Biology

Fats store energy

 Long HC chain

u polar or non-polar?

u hydrophilic or hydrophobic?

 Function:

u energy storage

 very rich

 2x carbohydrates

u cushion organs

u insulates body

 think whale blubber!

Why do humans

like fatty foods?

AP Biology

Saturated fats

 All C bonded to H

 No C=C double bonds

u long, straight chain

u most animal fats

u solid at room temp.

 contributes to

cardiovascular disease (atherosclerosis)

= plaque deposits

AP Biology

Unsaturated fats

 C=C double bonds in the fatty acids

u plant & fish fats

u vegetable oils

u liquid at room temperature

 the kinks made by double bonded C prevent the

molecules from packing tightly together

mono-unsaturated?

poly-unsaturated?

AP Biology

Saturated vs. unsaturated

saturated unsaturated

AP Biology

AP Biology

Phospholipids

 Structure:

u glycerol + 2 fatty acids + PO ₄

 PO ₄ negatively charged

It’s just like a penguin…

A head at one end

& a tail

at the other !

AP Biology

Phospholipids

 Hydrophobic or hydrophilic?

u fatty acid tails = hydrophobic

u PO ₄ = hydrophilic head

u dual “personality”

interaction with H ₂ O is complex & very important!

It likes water

& also pushes

it away !

AP Biology

Phospholipids in water

 Hydrophilic heads attracted to H ₂ O

 Hydrophobic tails “hide” from H ₂ O

u can self-assemble into “bubbles”

 bubble = “micelle”

 can also form bilayer

 early evolutionary stage of cell?

bilayer

AP Biology

Why is this important?

 Phospholipids create a barrier in water

u define outside vs. inside

u cell membranes

AP Biology

Phospholipids & cells

 Phospholipids of cell membrane

u double layer = bilayer

u hydrophilic heads on outside

 in contact with aqueous solution outside of cell and inside of cell

u hydrophobic tails on inside

 form core

u forms barrier between cell &

external environment

Tell them

about soap !

AP Biology

Steroids

 ex: cholesterol, sex hormones

 4 fused C rings

u different steroids created by attaching different functional groups to rings

cholesterol

AP Biology

Cholesterol

 Important cell component

u animal cell membranes

u precursor of all other steroids

 including vertebrate sex hormones

u high levels in blood may contribute to

cardiovascular disease

AP Biology

Cholesterol

helps keep

cell membranes fluid & flexible

Important component of cell membrane

AP Biology

From Cholesterol  Sex Hormones

 What a big difference a few atoms can make!

AP Biology

Proteins

Multipurpose

molecules

Figure 5.15-a

Enzymatic proteins Defensive proteins

Storage proteins Transport proteins

Enzyme Virus

Antibodies Bacterium

Ovalbumin Amino acids for embryo

Transport protein

Cell membrane Function: Selective acceleration of chemical reactions

Example: Digestive enzymes catalyze the hydrolysis of bonds in food molecules.

Function: Protection against disease

Example: Antibodies inactivate and help destroy viruses and bacteria.

Function: Storage of amino acids Function: Transport of substances Examples: Casein, the protein of milk, is the major

source of amino acids for baby mammals. Plants have storage proteins in their seeds. Ovalbumin is the protein of egg white, used as an amino acid source for the developing embryo.

Examples: Hemoglobin, the iron-containing protein of

vertebrate blood, transports oxygen from the lungs to

other parts of the body. Other proteins transport

molecules across cell membranes.

Figure 5.15-b

Hormonal proteins

Function: Coordination of an organism’s activities Example: Insulin, a hormone secreted by the

pancreas, causes other tissues to take up glucose, thus regulating blood sugar concentration

High

blood sugar Normal

blood sugar Insulin

secreted

Signaling molecules

Receptor protein

Muscle tissue

Actin Myosin

100 m 60 m

Collagen

Connective tissue

Receptor proteins

Function: Response of cell to chemical stimuli Example: Receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells.

Contractile and motor proteins

Function: Movement

Examples: Motor proteins are responsible for the undulations of cilia and flagella. Actin and myosin proteins are responsible for the contraction of muscles.

Structural proteins

Function: Support

Examples: Keratin is the protein of hair, horns, feathers, and other skin appendages. Insects and

spiders use silk fibers to make their cocoons and webs,

respectively. Collagen and elastin proteins provide a

fibrous framework in animal connective tissues.

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Animation: Structural Proteins

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Animation: Storage Proteins

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Animation: Transport Proteins

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Animation: Receptor Proteins

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Animation: Contractile Proteins

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Animation: Defensive Proteins

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Animation: Hormonal Proteins

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Animation: Sensory Proteins

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Animation: Gene Regulatory Proteins

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AP Biology

Proteins

 Structure:

u monomer = amino acids

 20 different amino acids

u polymer = polypeptide

 protein can be one or more polypeptide chains folded & bonded together

 large & complex molecules

 complex 3-D shape

Rubisco

hemoglobin

growth

hormones

Side chain (R group)

Amino group

Carboxyl group

 carbon

R group (side chain)

 variable group

 confers unique chemical

properties

of the amino acid

Amino acids Structure

Figure 5.16

Nonpolar side chains; hydrophobic Side chain

(R group)

Glycine (Gly or G)

Alanine (Ala or A)

Valine (Val or V)

Leucine (Leu or L)

Isoleucine (Ile or I)

Methionine (Met or M)

Phenylalanine (Phe or F)

Tryptophan (Trp or W)

Proline (Pro or P)

Polar side chains; hydrophilic

Serine (Ser or S)

Threonine (Thr or T)

Cysteine (Cys or C)

Tyrosine (Tyr or Y)

Asparagine (Asn or N)

Glutamine (Gln or Q)

Electrically charged side chains; hydrophilic

Acidic (negatively charged)

Basic (positively charged)

Aspartic acid (Asp or D)

Glutamic acid (Glu or E)

Lysine (Lys or K)

Arginine (Arg or R)

Histidine (His or H)

Figure 5.16a

Nonpolar side chains; hydrophobic Side chain

Glycine (Gly or G)

Alanine (Ala or A)

Valine (Val or V)

Leucine (Leu or L)

Isoleucine (Ile or I)

Methionine (Met or M)

Phenylalanine (Phe or F)

Tryptophan (Trp or W)

Proline

(Pro or P)

Figure 5.16b

Polar side chains; hydrophilic

Serine (Ser or S)

Threonine (Thr or T)

Cysteine (Cys or C)

Tyrosine (Tyr or Y)

Asparagine (Asn or N)

Glutamine

(Gln or Q)

Figure 5.16c

Electrically charged side chains; hydrophilic

Acidic (negatively charged)

Basic (positively charged)

Aspartic acid (Asp or D)

Glutamic acid (Glu or E)

Lysine (Lys or K)

Arginine (Arg or R)

Histidine

(His or H)

AP Biology

Sulfur containing amino acids

 Form disulfide bridges

u cross links betweens sulfurs in amino acids

You wondered why perms smelled like rotten eggs?

H-S – S-H

AP Biology

Building proteins

 Peptide bonds

u linking NH ₂ of one amino acid to COOH of another

u C–N bond

peptide bond

dehydration synthesis

AP Biology

Building proteins

 Polypeptide chains

u N-terminus = NH ₂ end

u C-terminus = COOH end

u repeated sequence (N-C-C) is the polypeptide backbone

 can only grow in one direction

AP Biology

Protein structure & function

hemoglobin

 Function depends on structure

u 3-D structure

 twisted, folded, coiled into unique shape

collagen

pepsin

AP Biology

Denature a protein

 Unfolding a protein

u disrupt 3° structure

 pH

salt

temperature

u unravels or denatures protein

u disrupts H bonds, ionic bonds &

disulfide bridges

u destroys functionality

 Some proteins can return to their

functional shape

after denaturation,

many cannot

AP Biology

Primary (1°) structure

 Order of amino acids in chain

u amino acid sequence

determined by gene (DNA)

u slight change in amino acid sequence can affect protein’s structure & it’s function

 even just one amino acid change can make all the difference!

lysozyme: enzyme

in tears & mucus

that kills bacteria

AP Biology

Secondary (2°) structure

 “Local folding”

u folding along short sections of

polypeptide

 interaction between adjacent amino

acids

 H bonds between R groups

 -helix

 -pleated sheet

Secondary structure

Hydrogen bond

 helix

 pleated sheet

 strand, shown as a flat arrow pointing toward the carboxyl end

Hydrogen bond

Figure 5.20c

AP Biology

Tertiary (3°) structure

 “Whole molecule folding”

u determined by interactions between R groups

 hydrophobic interactions

 effect of water in cell

 anchored by

disulfide bridges

(H & ionic bonds ⁾

Figure 5.20f

Hydrogen bond

Disulfide bridge

Polypeptide backbone

Ionic bond Hydrophobic interactions and van der Waals interactions

TERTIARY STRUCTURE

AP Biology

Quaternary (4°) structure

 More than one polypeptide chain joined together

u only then is it a functional protein

 hydrophobic interactions

hemoglobin

collagen = skin & tendons

AP Biology

Protein structure (review)

1

°

2°

3°

4°

aa sequence peptide bonds

R groups H bonds

R groups

hydrophobic interactions, disulfide bridges

determined by DNA

multiple polypeptides hydrophobic

interactions

Sickle-Cell Disease: A Change in Primary Structure

• A slight change in primary structure can affect a protein’s structure and ability to function

• Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin

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Figure 5.21

Primary Structure

Secondary and Tertiary

Structures

Quaternary

Structure Function Red Blood

Cell Shape

 subunit

 subunit 





 Exposed

hydrophobic region

Molecules do not associate with one another; each carries oxygen.

Molecules crystallize into a fiber; capacity to carry oxygen is reduced.

Sickle-cell hemoglobin

Normal hemoglobin

10 m

10 m

Sick le -cell hem og lob in No rmal he m og lo bi n

1 2 3 4 5 6 7

1 2 3 4 5 6 7



 



Resistance to Malaria

Malaria is caused by parasite plasmodium which uses both humans and anopheles mosquitos as its host.

The Parasite is transmitted to humans by anopheles mosquitoes. Part of the life

cycle is spend in red blood cells.

Plasmodium can not

survive in sickle red

blood cells.

Sickle Cell Anemia Evolutionary Adaptation

Carriers who possess one faulty hemoglobin gene and one normal gene do not suffer from anemia but are found to have some protection against infection by the malaria parasite.

In areas where malaria is common, the amount of sickle cell carriers is higher than in other parts of the world.

In an unusual example of Darwin’s principle of survival of the fittest, carriers of the genetic

disorder are more likely to survive than people

with two unaffected genes for hemoglobin.

Concept 5.5: Nucleic acids store, transmit, and help express hereditary information

• The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene

• Genes are made of DNA, a nucleic acid made of monomers called nucleotides

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The Roles of Nucleic Acids

• There are two types of nucleic acids – Deoxyribonucleic acid (DNA)

– Ribonucleic acid (RNA)

• DNA provides directions for its own replication

• DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls

protein synthesis

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The Components of Nucleic Acids

• Nucleic acids are polymers called polynucleotides

• Each polynucleotide is made of monomers called nucleotides

• Each nucleotide consists of a nitrogenous base, a pentose sugar, and one or more phosphate groups

• The portion of a nucleotide without the phosphate group is called a nucleoside

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Figure 5.26ab

Sugar-phosphate backbone 5 end

5C 3C

5C 3C 3 end

(a) Polynucleotide, or nucleic acid

(b) Nucleotide Phosphate

group Sugar

(pentose) Nucleoside

Nitrogenous base 5C

3C

1C

Figure 5.26c

Nitrogenous bases

Cytosine (C)

Thymine (T, in DNA)

Uracil (U, in RNA)

Adenine (A) Guanine (G)

Sugars

Deoxyribose (in DNA)

Ribose (in RNA) (c) Nucleoside components

Pyrimidines

Purines

• Nucleoside = nitrogenous base + sugar

• There are two families of nitrogenous bases – Pyrimidines (cytosine, thymine, and uracil)

have a single six-membered ring

– Purines (adenine and guanine) have a six-

membered ring fused to a five-membered ring

• In DNA, the sugar is deoxyribose; in RNA, the sugar is ribose

• Nucleotide = nucleoside + phosphate group

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Nucleotide Polymers

• Nucleotide polymers are linked together to build a polynucleotide

• Adjacent nucleotides are joined by covalent

bonds that form between the —OH group on the 3 carbon of one nucleotide and the phosphate on the 5 carbon on the next

• These links create a backbone of sugar-

phosphate units with nitrogenous bases as appendages

• The sequence of bases along a DNA or mRNA polymer is unique for each gene

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The Structures of DNA and RNA Molecules

• RNA molecules usually exist as single polypeptide chains

• DNA molecules have two polynucleotides

spiraling around an imaginary axis, forming a double helix

• In the DNA double helix, the two backbones run in opposite 5→ 3 directions from each other, an arrangement referred to as

antiparallel

• One DNA molecule includes many genes

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• The nitrogenous bases in DNA pair up and form hydrogen bonds: adenine (A) always with

thymine (T), and guanine (G) always with cytosine (C)

• Called complementary base pairing

• Complementary pairing can also occur between two RNA molecules or between parts of the same molecule

• In RNA, thymine is replaced by uracil (U) so A and U pair

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Figure 5.27

Sugar-phosphate backbones

Hydrogen bonds

Base pair joined

by hydrogen bonding

Base pair joined by hydrogen

bonding

(b) Transfer RNA (a) DNA

5 3

3 5

DNA and Proteins as Tape Measures of Evolution

• The linear sequences of nucleotides in DNA

molecules are passed from parents to offspring

• Two closely related species are more similar in DNA than are more distantly related species

• Molecular biology can be used to assess evolutionary kinship

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The Theme of Emergent Properties in the Chemistry of Life: A Review

• Higher levels of organization result in the emergence of new properties

• Organization is the key to the chemistry of life

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Figure 5.UN02

Figure 5.UN02a

Figure 5.UN02b

Figure 5. UN12