chapter 5 - the structure and function of outline large ... 120... · 3 functions of carbohydrates...

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Chapter 5 - The Structure and Function of Large Biological Molecules

Outline

I. MacromoleculesII. Carbohydrates – simple and complexIII. Lipids – triglycerides (fats and oils),

phospholipids, carotenoids, steroids, waxesIV. Proteins – enzymes, keratin, V. Nucleotides – ATP, NAD+

VI. Nucleic Acids – DNA & RNA

Overview: The Molecules of Life

All living things are made up of four classes of large biological molecules: carbohydrates, lipids, proteins, and nucleic acids

Macromolecules are large molecules composed of thousands of covalently connected atoms

Molecular structure and function are inseparable

© 2011 Pearson Education, Inc.

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

Three of the four classes of life’s organic molecules are polymers Carbohydrates Proteins Nucleic acids


Polymers

Many biological molecules formed by linking a chain of monomers

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

Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction

The Synthesis and Breakdown of Polymers


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Animation: Polymers

Right-click slide / select “Play”

Figure 5.2a

(a) Dehydration reaction: synthesizing a polymer

Short polymer Unlinked monomer

Dehydration removesa water molecule,forming a new bond.

Longer polymer

1 2 3 4

1 2 3

Figure 5.2b

(b) Hydrolysis: breaking down a polymer

Hydrolysis addsa water molecule,breaking a bond.

1 2 3 4

1 2 3

Examples of Organic Compounds

1. Carbohydrates – sugars, polymers of sugars

2. Lipids – triglycerides (fats and oils), phospholipids, steroids, waxes

3. Proteins – enzymes, keratin, actin

4. Nucleic Acids – DNA & RNA

Simple Carbohydrates Carbohydrates serve as fuel and building material

Carbohydrates include sugars and the polymers of sugars

The simplest carbohydrates are monosaccharides, or single sugars

Carbohydrate macromolecules are polysaccharides, polymers composed of many sugar building blocks


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Functions of Carbohydrates

1. Rapidly Mobilized Source of Energy Monosaccharides and disaccharides

2. Energy storage Glycogen in animals Starch in plants

3. Structural In cell walls bacteria and plants (Cellulose). In exoskeletons (Chitin).

4. Coupled with protein to form glycoproteins Important in cell membranes

Sugars

Monosaccharides have molecular formulas that are usually multiples of CH2O

Glucose (C6H12O6) is the most common monosaccharide

Monosaccharides are classified by The location of the carbonyl group (as aldose or

ketose) The number of carbons in the carbon skeleton


Figure 5.3a

Aldose (Aldehyde Sugar) Ketose (Ketone Sugar)

Glyceraldehyde

Trioses: 3-carbon sugars (C3H6O3)

Dihydroxyacetone

Figure 5.3b

Pentoses: 5-carbon sugars (C5H10O5)

Ribose Ribulose


Figure 5.3c


Hexoses: 6-carbon sugars (C6H12O6)

Glucose Galactose Fructose

Though often drawn as linear skeletons, in aqueous solutions many sugars form rings

Monosaccharides serve as a major fuel for cells and as raw material for building molecules


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Figure 5.4

(a) Linear and ring forms

(b) Abbreviated ring structure

12

3

4

5

6

6

5

4

32

1 1

23

4

5

6

123

4

56

A disaccharide is formed when a dehydration reaction joins two monosaccharides

This covalent bond is called a glycosidiclinkage


Disaccharide


Animation: DisaccharideRight-click slide / select “Play”

Figure 5.5

(a) Dehydration reaction in the synthesis of maltose

(b) Dehydration reaction in the synthesis of sucrose

Glucose Glucose

Glucose

Maltose

Fructose Sucrose

1–4glycosidic

linkage

1–2glycosidic

linkage

1 4

1 2

5

Reactions where two molecules are linked together and water is removed is …

1. Condensation or dehydration

2. Hydrolysis

Conde

nsatio

n

Hydro

lysis

50%50%

Complex Carbohydrates

Polysaccharides

Polysaccharides, the polymers of sugars, have storage and structural roles

The structure and function of a polysaccharide are determined by its sugar monomers and the positions of glycosidic linkages

Types

1. Starch2. Glycogen3. Cellulose 4. Chitin


Complex carbohydrates - Polysaccharide


Animation: PolysaccharidesRight-click slide / select “Play”

Structure of Complex Carbohydrates

Polysaccharides - Long chains of saccharides (sugars) – 100s to 1000s

Cellulose, starch and glycogen consist of chains of only glucose.

Chitin consists of chains of glucose with N-acetyl groups

Structure of Complex Carbohydrates

The differences between the complex carbohydrates is in the structure – branched, unbranched, spiral, hydrogen-bonded.

Cellulose is tightly packed and hard to digest Starch is coiled and may be branched and is easier

to digest Glycogen is coiled with extensive branching and is

even easier to digest.

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2. Energy storage - Polysaccharides Glycogen in animals Starch in plants

3. Structural In cell walls bacteria and plants (Cellulose). In exoskeletons (Chitin).


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

Polysaccharides in Plants for Energy Storage

Starch, a storage polysaccharide of plants, consists entirely of glucose monomers

Plants store surplus starch as granules within chloroplasts and other plastids

The simplest form of starch is amylose


Starch

Starch – form stored in plants, coiled, mainly α1-4 glycosidic linkage. If branched then will also have 1-6 glycosidic linkage, stored in amyloplasts. Plants used for energy storage, easy to digest Potatoes, rice, carrots, corn

Types of starches: Amylose – not branched Amylopectin – branched, more common

Glycogen

Glycogen – form stored in animals for energy, coiled, mainly α 1-4 glycosidic linkage. It is branched therefore also has 1-6 glycosidiclinkage, easy to digest

Found in animals: stored mainly in liver and muscle



2. Energy storage - Polysaccharides Glycogen in animals Starch in plants

3. Structural - Polysaccharides Cellulose in cell walls bacteria and plants Chitin in exoskeletons


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Structural Polysaccharides in Plants - Starch

The polysaccharide cellulose is a major component of the tough wall of plant cells

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 ()


Cellulose

Cellulose – straight chains of glucose, -OH groups H-bond to stabilize chains into tight bundles, β 1-4 glycosidic linkage, hard to digest

Used by plants for structure and in cell walls.

Figure 5.7a

(a) and glucose ring structures

Glucose Glucose

4 1 4 1

Figure 5.7b

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

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

41

41


Polymers with glucose are helical

Polymers with glucose are straight

In straight structures, H atoms on one strand can bond with OH groups on other strands

Parallel cellulose molecules held together this way are grouped into microfibrils, which form strong building materials for plants

Cell wall

Microfibril

Cellulosemicrofibrils in aplant cell wall

Cellulosemolecules

Glucosemonomer

10 m

0.5 m

Figure 5.8

8

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

Some microbes use enzymes to digest cellulose

Many herbivores, from cows to termites, have symbiotic relationships with these microbes


Why do we care?

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

Contains N-acetyl group which hydrogen bond. Is cross-linked with protein to form a strong exoskeleton for insects and crustaceans

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


Structural Polysaccharides - Chitin

Figure 5.9

Chitin forms the exoskeletonof arthropods.

The structureof the chitinmonomer

Chitin is used to make a strong and flexiblesurgical thread that decomposes after thewound or incision heals.

Glycoproteins

Glycoproteins – carbohydrate + protein on outer surface of cell membranes – we will return to this when we study cell membranes

The form of carbohydrate stored in animals is?

1. Starch2. Glycogen3. Cellulose

Starch

Glyc

ogen

Cell

ulose

33% 33%33%

Which carbohydrate contains nitrogen?

1. Starch2. Cellulose3. Glycogen4. Chitin

Starch

Cell

ulose

Glyc

ogen

Chitin

25% 25%25%25%

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Starch is composed of glucose molecules joined by what kind of covalent bond?

1. β 1-4 Glycosidic linkage

2. α 1-4 Glycosidic linkage

50%50%

Lipids

Like carbohydrates, lipids are mainly made of carbon, hydrogen and oxygen

They are not soluble in water, they are soluble in nonpolar solvents

Types: 1. Triglycerides (Fats)2. Phospholipids3. Carotenoids4. Steroids5. Waxes

Lipids are a diverse group of hydrophobic molecules

Lipids are the one class of large biological molecules that do not form polymers

The unifying feature of lipids is having little or no affinity for water

Lipids are hydrophobic because they consist mostly of hydrocarbons, which form nonpolarcovalent bonds

The most biologically important lipids are fats, phospholipids, and steroids


I. Lipid - Triglycerides

Function Energy storage, insulation, protection

Triglycerides (triacylglycerol) are three fatty acids joined to glycerol

The fatty acids are covalently linked by an ester linkage through a condensation reaction

Figure 5.10a

(a) One of three dehydration reactions in the synthesis of a fat

Fatty acid(in this case, palmitic acid)

Glycerol

Figure 5.10b

(b) Fat molecule (triacylglycerol)

Ester linkage

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Ester vs Ether Triglycerides

Butter, lard (animal fat), and vegetable oils are all triglycerides

Differences are in the structure of the fatty acids

Fatty acids vary in length (number of carbons) and in the number and locations of double bonds

Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds

Unsaturated fatty acids have one or more double bonds


Fatty Acids Fatty Acids

Saturated fatty acids – carbon chain has no double bonds CH3-(CH2-CH2)n-COOH

Unsaturated fatty acids – carbon chain has a double bond

Monounsaturated fatty acids have one double bond

Polyunsaturated fatty acids – more than one double bond


Animation: Fats Right-click slide / select “Play”

Figure 5.11

(a) Saturated fat (b) Unsaturated fat

Structuralformula of asaturated fatmolecule

Space-fillingmodel of stearicacid, a saturatedfatty acid

Structuralformula of anunsaturated fatmolecule

Space-filling modelof oleic acid, anunsaturated fattyacid

Cis double bondcauses bending.

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(a) Saturated fat

Structuralformula of asaturated fatmolecule

Space-fillingmodel of stearicacid, a saturatedfatty acid

Figure 5.11a Figure 5.11b (b) Unsaturated fat

Structuralformula of anunsaturated fatmolecule

Space-filling modelof oleic acid, anunsaturated fattyacid

Cis double bondcauses bending.

Fats made from saturated fatty acids are called saturated fats, and are solid at room temperature

Most animal fats are saturated

Fats made from unsaturated fatty acids are called unsaturated fats or oils, and are liquid at room temperature

Plant fats and fish fats are usually unsaturated


A diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits

Hydrogenation is the process of converting unsaturated fats to saturated fats by adding hydrogen

Hydrogenating vegetable oils also creates unsaturated fats with trans double bonds

These trans fats may contribute more than saturated fats to cardiovascular disease


Trans fat

Hydrogenated oils – unsaturated oils that have been chemically saturated so they will be solid at room temperature (Crisco)

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Trans Fats Hydrogenation is the process of adding

hydrogen to the unsaturated and polyunsaturated oils to saturate them.

This process can also create unsaturated fats that now have a different configuration than the original oil

Labeled “partially hydrogenated oil”

Fats and Health

Heart disease is caused by plaque collecting in the blood vessels leading to the heart.

Cholesterol in the blood leads to more plaque building up in the vessels. LDL (bad cholesterol) – transports cholesterol to

the heart HDL (good cholesterol) – transports cholesterol

away from the heart

Fatty acids and Cholesterol Trans fats – worst type of fat, raise the bad

cholesterol (LDL) and lower the good cholesterol (HDL)

Saturated fats raise the bad cholesterol Sources = animal fats, dairy products, and some plant

oils (palm and coconut) Polyunsaturated fats – do not raise the bad

cholesterol but slightly lower good cholesterol Sources – many vegetable oils (corn and

safflower) Monounsaturated fats – do not increase either Sources – olive, canola and peanut oils;

avocado

Certain unsaturated fatty acids are not synthesized in the human body

These must be supplied in the diet

These essential fatty acids include the omega-3 fatty acids, required for normal growth, and thought to provide protection against cardiovascular disease


Essential fatty acids

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Omega-3 Fats

Omega-3s are a type of unsaturated fat This fat has a carbon double bond located

three carbons from the end (end = omega) This is the healthiest type of fat Protect against heart disease by reducing bad

cholesterol Sources – fatty fish (salmon, tuna), walnuts

The major function of fats is energy storage

Humans and other mammals store their fat in adipose cells

Adipose tissue also cushions vital organs and insulates the body


Function of Triglycerides

Which of these fats are the least healthy?

1. Polyunsaturated2. Omega 3 unsaturated3. Trans fat4. Saturated

Polyun

saturat

ed

Omeg

a 3 un

saturat

ed

Trans f

at Satu

rated

25% 25%25%25%

Which type of fatty acid does not contain a double bond?

1. Polyunsaturated2. Omega 3 unsaturated3. Trans fat4. Saturated

Polyun

saturat

ed

Omeg

a 3 un

saturat

ed

Trans f

at Satu

rated

25% 25%25%25%

II. Lipid - Phospholipids

Function Backbone of cell membranes

Similar structure as triglycerides but have: Glycerol 2 fatty acids Phosphate group (negatively charged) R group

II. Lipid - Phospholipids

Phospholipids are amphiphathic

Phosphate end of molecule soluble in water -hydrophilic.

Lipid (fatty acid) end is not soluble in water -hydrophobic.

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Figure 5.12

Choline

Phosphate

Glycerol

Fatty acids

Hydrophilichead

Hydrophobictails

(c) Phospholipid symbol(b) Space-filling model(a) Structural formula

Hyd

roph

ilic

head

Hyd

roph

obic

tails

When phospholipids are added to water, they self-assemble into a bilayer, with the hydrophobic tails pointing toward the interior

The structure of phospholipids results in a bilayer arrangement found in cell membranes

Phospholipids are the major component of all cell membranes


Phospholipid’s role in memebranes

Figure 5.13

Hydrophilichead

Hydrophobictail

WATER

WATER

III. Lipid - Carotenoids

Consist of isoprene units

Orange and yellow plant pigments Classified with lipids Some play a role in photosynthesis Animals convert to vitamin A

Isoprene-derived compounds

IV. Lipids - Steroids

Structure: Four fused rings

Examples: cholesterol, bile salts, reproductive hormones, cortisol

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Steroids - Functions

Functions include

Hormones - Signaling within and between cells (estrogen, testosterone, cortisol)

Cholesterol – Important part of cell membrane

Bile salts - Emulsify fat in small intestine

IV. Lipids - Steroids

Unlike triglycerides and phospholipids, steroids have no fatty acids

Structure is a four ring backbone, with side chains attached

Figure 5.14 Cholesterol V. Lipids - Waxes

Covers surface of leaves of plants.

Functions Minimizes water loss from leaves to air. Barrier against entrance of bacteria and

parasites into leaves of plants.

This type of lipid is an important component of membranes

1. Triglycerides2. Phospholipids3. Waxes

Triglyc

erides

Phosph

olipids

Wax

es

33% 33%33%

Proteins include a diversity of structures, resulting in a wide range of functions

Proteins account for more than 50% of the dry mass of most cells

Protein functions include structural support, storage, transport, cellular communications, movement, and defense against foreign substances


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Proteins

Functions – numerous and varied – Page 78 Facilitate chemical reactions (enzymes) Transport Movement of muscles Structure Cell signaling - Hormones (insulin) Nutrition Defense Components of cell membrane Immune response

Enzymes are a type of protein that acts as a catalyst to speed up chemical reactions

Enzymes can perform their functions repeatedly, functioning as workhorses that carry out the processes of life


Protein Functions - Enzymes

Enzymes

Enzymes are proteins that catalyze reactions = help reactions to happen – they speed up chemical reactions

They can only speed up reactions that would happen eventually (may take years)

They are usually specific for their substrates

They are not consumed (destroyed) in the process

Some enzymes need cofactors to function. Example = iron

Substrate = the thing that is being changed in the reaction

Active site = Place in the enzyme where the substrate binds.Product = The end result

Figure 5.15-a

Enzymatic proteins Defensive proteins

Storage proteins Transport proteins

Enzyme Virus

Antibodies

Bacterium

Ovalbumin Amino acidsfor embryo

Transportprotein

Cell membrane

Function: Selective acceleration of chemical reactionsExample: Digestive enzymes catalyze the hydrolysisof bonds in food molecules.

Function: Protection against diseaseExample: Antibodies inactivate and help destroyviruses and bacteria.

Function: Storage of amino acids Function: Transport of substancesExamples: Casein, the protein of milk, is the majorsource of amino acids for baby mammals. Plants havestorage proteins in their seeds. Ovalbumin is theprotein of egg white, used as an amino acid sourcefor the developing embryo.

Examples: Hemoglobin, the iron-containing protein ofvertebrate blood, transports oxygen from the lungs toother parts of the body. Other proteins transportmolecules across cell membranes.

Figure 5.15-b

Hormonal proteinsFunction: Coordination of an organism’s activitiesExample: Insulin, a hormone secreted by thepancreas, causes other tissues to take up glucose,thus regulating blood sugar concentration

Highblood sugar

Normalblood sugar

Insulinsecreted

Signalingmolecules

Receptorprotein

Muscle tissue

Actin Myosin

100 m 60 m

Collagen

Connectivetissue

Receptor proteinsFunction: Response of cell to chemical stimuliExample: Receptors built into the membrane of anerve cell detect signaling molecules released byother nerve cells.

Contractile and motor proteinsFunction: MovementExamples: Motor proteins are responsible for theundulations of cilia and f lagella. Actin and myosinproteins are responsible for the contraction ofmuscles.

Structural proteinsFunction: SupportExamples: Keratin is the protein of hair, horns,feathers, and other skin appendages. Insects andspiders use silk fibers to make their cocoons and webs,respectively. Collagen and elastin proteins provide afibrous framework in animal connective tissues.

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Polypeptides

Polypeptides are unbranched polymers built from the same set of 20 amino acids

A protein is a biologically functional molecule that consists of one or more polypeptides, each folded and coiled into a three dimensional shape


Amino Acids

Proteins are made up of amino acids

Amino acids are organic molecules with carboxyl and amino groups

There are 20 amino acids, each with a different substitution for R.

Figure 5.UN01

Side chain (R group)

Aminogroup

Carboxylgroup

carbon

Ionized amino acid

Ionized form

Figure 5.16Nonpolar 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; hydrophobicSide 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)

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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)

Amino Acid Polymers

Amino acids are linked by peptide bonds

A polypeptide is a polymer of amino acids

Polypeptides range in length from a few to more than a thousand monomers

Each polypeptide has a unique linear sequence of amino acids, with a carboxyl end (C-terminus) and an amino end (N-terminus)


Figure 5.17

Peptide bond

New peptidebond forming

Sidechains

Back-bone

Amino end(N-terminus)

Peptidebond

Carboxyl end(C-terminus)

Protein Structure and Function

A functional protein consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shape


Figure 5.18

(a) A ribbon model (b) A space-filling model

Groove

Groove

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The sequence of amino acids determines a protein’s three-dimensional structure

A protein’s structure determines its function


Protein Structure and Function Four Levels of Protein Structure

The primary structure of a protein is its unique sequence of amino acids

Secondary structure, found in most proteins, consists of coils and folds in the polypeptide chain

Tertiary structure is determined by interactions among various side chains (R groups)

Quaternary structure results when a protein consists of multiple polypeptide chains



Animation: Protein Structure IntroductionRight-click slide / select “Play”

Figure 5.20a Primary structure

Aminoacids

Amino end

Carboxyl end

Primary structure of transthyretin

Primary structure, the sequence of amino acids in a protein, is like the order of letters in a long word

Primary structure is determined by inherited genetic information


Primary Structure of Proteins


Animation: Primary Protein StructureRight-click slide / select “Play”

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Animation: Secondary Protein Structure Right-click slide / select “Play”

The coils and folds of secondary structure result from hydrogen bonds between repeating constituents of the polypeptide backbone

Typical secondary structures are a coil called an helix and a folded structure called a pleated sheet


Secondary Structure of Proteins

Secondary structure

Hydrogen bond

helix

pleated sheet

strand, shown as a flatarrow pointing towardthe carboxyl end

Hydrogen bond

Figure 5.20c

Tertiary structure is determined by interactions between R groups, rather than interactions between backbone constituents

These interactions between R groups include hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions

Strong covalent bonds called disulfide bridges may reinforce the protein’s structure


Tertiary Structure of Proteins


Animation: Tertiary Protein StructureRight-click slide / select “Play”

Figure 5.20e

Tertiary structure

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Figure 5.20f

Hydrogenbond

Disulfidebridge

Polypeptidebackbone

Ionic bond

Hydrophobicinteractions andvan der Waalsinteractions

Quaternary structure results when two or more polypeptide chains form one macromolecule

Collagen is a fibrous protein consisting of three polypeptides coiled like a rope

Hemoglobin is a globular protein consisting of four polypeptides: two alpha and two beta chains


Quaternary Structure of Proteins

Figure 5.20g

Quaternary structure

four identicalpolypeptides

Hemoglobin

HemeIron

subunit

subunit

subunit

subunit

Figure 5.20i

Figure 5.20j


Animation: Quaternary Protein Structure Right-click slide / select “Play”

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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


Figure 5.21

PrimaryStructure

Secondaryand TertiaryStructures

QuaternaryStructure Function Red Blood

Cell Shape

subunit

subunit

Exposedhydrophobicregion

Molecules do notassociate with oneanother; each carriesoxygen.

Molecules crystallizeinto a fiber; capacityto carry oxygen isreduced.

Sickle-cellhemoglobin

Normalhemoglobin

10 m

10 m

Sick

le-c

ell h

emog

lobi

nN

orm

al h

emog

lobi

n

1234567

1234567

What Determines Protein Structure?

In addition to primary structure, physical and chemical conditions can affect structure

Alterations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel

This loss of a protein’s native structure is called denaturation

A denatured protein is biologically inactive© 2011 Pearson Education, Inc.

Figure 5.22

Normal protein Denatured protein

tu

Protein Folding in the Cell

It is hard to predict a protein’s structure from its primary structure

Most proteins probably go through several stages on their way to a stable structure

Chaperonins or chaperones are protein molecules that assist the proper folding of other proteins

Diseases such as Alzheimer’s, Parkinson’s, and mad cow disease are associated with misfoldedproteins


Figure 5.23

The cap attaches, causingthe cylinder to changeshape in such a way thatit creates a hydrophilicenvironment for thefolding of the polypeptide.

CapPolypeptide

Correctlyfoldedprotein

Chaperonin(fully assembled)

Steps of ChaperoninAction:

An unfolded poly-peptide enters thecylinder fromone end.

Hollowcylinder

The cap comesoff, and theproperly foldedprotein isreleased.

1

2 3

23

Scientists use X-ray crystallography to determine a protein’s structure

Another method is nuclear magnetic resonance (NMR) spectroscopy, which does not require protein crystallization

Bioinformatics uses computer programs to predict protein structure from amino acid sequences


Determining the Structure of Proteins Figure 5.24

DiffractedX-rays

X-raysource X-ray

beam

Crystal Digital detector X-ray diffractionpattern

RNA DNA

RNApolymerase II

EXPERIMENT

RESULTS

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


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

Protein synthesis occurs on ribosomes


Figure 5.25-1

Synthesis ofmRNA

mRNA

DNA

NUCLEUSCYTOPLASM

1

Figure 5.25-2

Synthesis ofmRNA

mRNA

DNA

NUCLEUSCYTOPLASM

mRNAMovement ofmRNA intocytoplasm

1

2

24

Figure 5.25-3

Synthesis ofmRNA

mRNA

DNA

NUCLEUSCYTOPLASM

mRNA

Ribosome

AminoacidsPolypeptide

Movement ofmRNA intocytoplasm

Synthesisof protein

1

2

3

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


Nucleotides

Their functions include: Energy (ATP) Coenzymes that aid enzyme function (NAD+) Messengers within cells (GTP)

Nucleotides consists of a sugar, phosphate groups, and a base.

There are 5 nucleotide bases: Adenine, Thymine, Uracil, Guanine, Cytosine

Nucleic Acids

Nucleic Acids are a chain or chains of nucleotides

The nucleotides are covalently bonded by phosphodiester linkage between the phosphates and sugars

Figure 5.26

Sugar-phosphate backbone5 end

5C

3C

5C

3C

3 end

(a) Polynucleotide, or nucleic acid

(b) Nucleotide

Phosphategroup Sugar

(pentose)

Nucleoside

Nitrogenousbase

5C

3C

1C

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

25

Figure 5.26abSugar-phosphate backbone5 end

5C

3C

5C

3C

3 end(a) Polynucleotide, or nucleic acid

(b) Nucleotide

Phosphategroup Sugar

(pentose)

Nucleoside

Nitrogenousbase

5C

3C

1C

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


The Components of Nucleotides Nucleotide Polymers

Nucleotides are linked together to build a polynucleotide polymer

Adjacent nucleotides are joined by covalent bonds that form between the —OH group on the 3carbon 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


The Structures of DNA and RNA Molecules

RNA molecules usually exist as single polynucleotideschains

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


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


The Structures of DNA and RNA Molecules

26

Figure 5.27

Sugar-phosphatebackbonesHydrogen bonds

Base pair joinedby hydrogen bonding

Base pair joinedby hydrogen

bonding

(b) Transfer RNA(a) DNA

5 3

53

DNA and Proteins as 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


Figure 5.UN02 Figure 5.UN02a

Figure 5.UN02b Fatty acids are joined to glycerol by what kind of linkage?

1. Peptide2. Gycosidic3. Phosphodiester4. Ester

Peptid

e

Gyc

osidi

c Phos

phodie

ster

Ester

25% 25%25%25%

27

Important Concepts

Know the vocabulary of the lecture and reading

What are the different types of biological molecules, their functions and be able to identify their structures

What are the types of carbohydrates and what types of organisms they are found in, what are their functions, identify their structures

Be able to describe the differences in the carbohydrates’ structures and the implications these difference have on our ability to digest them

Important Concepts

What are the types of starches and what structure stores starch?

What are the different types of lipids and their biological functions

What are the types of dietary triglycerides and which are healthy – know the order from healthiest to least healthy

What is the structure of amino acids, what bond links amino acids together, how they link together. Be able to draw and amino acid structure.

Important Concepts

Be able to describe protein structure including primary, secondary etc. Know what forces hold alpha helixes and beta sheets together, know the forces that help shape tertiary structure.

Know examples of steroids and functions of each type of steroids.

What are enzymes, what is their function, what are their properties, what are the active site, the substrates, and the products.

Important Concepts

What is the structure of nucleotides, you should be able to identify the bases but you don’t need to draw their structure. What are nucleic acids what are their functions. Know the examples of nucleic acids and nucleotides

Which molecules join together to form what molecules (monomer and polymers) what are the linkages called

chapter 5 - the structure and function of outline large ... 120... · 3 functions of carbohydrates...

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