Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Focus Phospholipids are...

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Focus

• Phospholipids are the molecules that make up biological membranes. Below is a picture of a phospholipid. Identify the functional group that we discussed during the last class, give its name and its functional ability.


PowerPoint Lectures for Biology, Seventh Edition

Neil Campbell and Jane Reece

Lectures by Chris Romero

Macromolecules Part 1Macromolecules Part 1

The Structure and Function of Macromolecules


Questions we will be able answer

• What is a polymer? What is a monomer?

• What is a monomer

• How does the polymerization of a limited number of monomers allow for the biodiversity in biomolecules that exist in living systems?

• Explain and draw dehydration synthesis (what bond)

• Explain and draw the opposite of dehydration synthesis

• Give examples of carbohydrate monomers and polymers and understand how their physical forms fits their function


• Overview: The Molecules of Life

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


• Macromolecules

– Are large molecules composed of smaller molecules

– Are complex in their structures

Figure 5.1


Concept : Most macromolecules are polymers, built from 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 building blocks called monomers


The Synthesis and Breakdown of Polymers

• Monomers form larger molecules by condensation reactions called dehydration reactions

(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

(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


The Diversity of Polymers

• Each class of polymer

– Is formed from a specific set of monomers

• 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

1 2 3 HOH


• Concept : Carbohydrates serve as fuel and building material

• Carbohydrates

– Include both sugars and their polymers


Sugars

• Monosaccharides

– Are the simplest sugars

– Can be used for fuel

– Can be converted into other organic molecules

– Can be combined into polymers


• Examples of monosaccharides

Triose sugars(C3H6O3)

Pentose sugars(C5H10O5)

Hexose sugars(C6H12O6)

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

HO C H

H C OH

H C OH

H C OH

H C OH

HO C H

HO C H

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

C OC O

H C OH

H C OH

H C OH

HO C H

H C OH

C O

H

H

H

H H H

H

H H H H

H

H H

C C C COOOO

Ald

os

es

Glyceraldehyde

RiboseGlucose Galactose

Dihydroxyacetone

Ribulose

Ke

tos

es

FructoseFigure 5.3


• 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


• Disaccharides

– Consist of two monosaccharides

– Are joined by a glycosidic linkage


• Examples of disaccharides 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.

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.

(a)

(b)

H

HO

H

HOH H

OH

O H

OH

CH2OH

H

HO

H

HOH

H

OH

O H

OH

CH2OH

H

O

H

HOH H

OH

O H

OH

CH2OH

H

H2O

H2O

H

H

O

H

HOH

OH

OH

CH2OH

CH2OH HO

OHH

CH2OH

HOH

H

H

HO

OHH

CH2OH

HOH H

O

O H

OHH

CH2OH

HOH H

O

HOH

CH2OH

H HO

O

CH2OH

H

H

OH

O

O

1 2

1 41– 4

glycosidiclinkage

1–2glycosidic

linkage

Glucose

Glucose Glucose

Fructose

Maltose

Sucrose

OH

H

H

Figure 5.5


Polysaccharides

• Polysaccharides

– Are polymers of sugars

– Serve many roles in organisms


Storage Polysaccharides

• Starch

– Is a polymer consisting entirely of glucose monomers

– Is the major storage form of glucose in plants

Chloroplast Starch

Amylose Amylopectin

1 m

(a) Starch: a plant polysaccharideFigure 5.6


Storage Polysaccharides

• Glycogen

– Consists of glucose monomers

– Is the major storage form of glucose in animalsMitochondria Giycogen

granules

0.5 m

(b) Glycogen: an animal polysaccharide

Glycogen

Figure 5.6


Structural Polysaccharides

• Cellulose

– Is a polymer of glucose


Cellulose

– Has different glycosidic linkages than starch

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

H O

O

CH2OH

HOH H

H

OH

OHH

H

HO

4

C

C

C

C

C

C

H

H

H

HO

OH

H

OH

OH

OH

H

O

CH2OH

HH

H

OH

OHH

H

HO

4 OH

CH2OH

O

OH

OH

HO41

O

CH2OH

O

OH

OH

O

CH2OH

O

OH

OH

CH2OH

O

OH

OH

O O

CH2OH

O

OH

OH

HO4

O1

OH

O

OH OHO

CH2OH

O

OH

O OH

O

OH

OH

(a) and glucose ring structures

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

1

glucose glucose

CH2OH

CH2OH

1 4 41 1

Figure 5.7 A–C


Cellulose Structure fits Function

Plant cells

0.5 m

Cell walls

Cellulose microfibrils in a plant cell wall

Microfibril

CH2OH

CH2OH

OH

OH

OO

OHO

CH2OHO

OOH

OCH2OH OH

OH OHO

O

CH2OH

OO

OH

CH2OH

OO

OH

O

O

CH2OHOH

CH2OHOHOOH OH OH OH

O

OH OH

CH2OH

CH2OH

OHO

OH CH2OH

OO

OH CH2OH

OH

Glucose monomer

O

O

O

O

O

O

Parallel cellulose molecules areheld together by hydrogenbonds between hydroxyl

groups attached to carbonatoms 3 and 6.

About 80 cellulosemolecules associate

to form a microfibril, themain architectural unitof the plant cell wall.

A cellulose moleculeis an unbranched glucose polymer.

OH

OH

O

OOH

Cellulosemolecules

Figure 5.8

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


• Cellulose is difficult to digest

– Cows have microbes in their stomachs to facilitate this process

Figure 5.9


• Chitin, another important structural polysaccharide

– Is found in the exoskeleton of arthropods

– Can be used as surgical thread

(a) The structure of the chitin monomer.

O

CH2OH

OHHH OH

H

NH

CCH3

O

H

H

(b) Chitin forms the exoskeleton of arthropods. This cicada is molting, shedding its old exoskeleton and emergingin adult form.

(c) Chitin is used to make a strong and flexible surgical

thread that decomposes after the wound or incision heals.

OH

Figure 5.10 A–C


Questions we will be able answer

• What is a polymer? What is a monomer?

• What is a monomer

• How does the polymerization of a limited number of monomers allow for the biodiversity in biomolecules that exist in living systems?

• Explain and draw dehydration synthesis (what bond)

• Explain and draw the opposite of dehydration synthesis

• Give examples of carbohydrate monomers and polymers and understand how their physical forms fits their function


Focus 9/2

I

•If you see oxygen in the structure of a funtional group what kind of quality is it likely giving to that functional group and why?

•What is the monomer of a carbohydrate?

•Are all macromolecules polymers made of monomers?


Lipid questions

1. What is a lipid?

2. Are lipids all formed through dehydration synthesis?

3. What is a fat and what alternate names for a fat exist?

4. Is sesame oil a saturated fat? Explain how you know this and how its physical structure dictates its chemical behavior.

5. What is a steroid? What is cholesterol? How much cholesterol does vegetable oil have in it?

6. What structure to phospholipids and cholesterols both play an important role in?


• Concept : Lipids are a diverse group of hydrophobic molecules

• Lipids

– Are the one class of large biological molecules that do not consist of polymers ( however some lipids are formed through dehydration synthesis)

– Share the common trait of being hydrophobic


Fats

• Fats

– Are 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


Fatty acids

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

• Saturated fatty acids

• Have the maximum number of hydrogen atoms possible

• Have no double bonds

(a) Saturated fat and fatty acid

Stearic acid

Figure 5.12


• Unsaturated fatty acids

– Have one or more double bonds

(b) Unsaturated fat and fatty acidcis double bondcauses bending

Oleic acid

Figure 5.12


Phospholipids

• Phospholipids

– Have only two fatty acids

– Have a phosphate group instead of a third fatty acid


Fat with a twist

• 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


• The structure of phospholipids

– Results in a bilayer arrangement found in cell membranes

Hydrophilichead

WATER

WATER

Hydrophobictail

Figure 5.14


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

HO

CH3

CH3

H3C CH3

CH3

Figure 5.15


Lipid questions

1. What is a lipid?

2. Are lipids all formed through dehydration synthesis?

3. What is a fat and what alternate names for a fat exist?

4. Is sesame oil a saturated fat? Explain how you know this and how its physical structure dictates its chemical behavior.

5. What is a steroid? What is cholesterol? How much cholesterol does vegetable oil have in it?

6. What structure to phospholipids and cholesterols both play an important role in?


Protein questions

1. What 2 functional groups do all amino acids have

2. List the roles of Proteins. Give examples.

3. What are the general steps of an enzymatic reaction?

4. Name and describe the qualities of the primary bonds in a protein.

5. What are the levels of proteins structure and which associations hold them together.

6. What is denaturation and how does it happen?

7. What is a cahperonin? What role do they play in protein structure


Proteins

• Concept 5.4: Proteins have many structures, resulting in a wide range of functions

– Proteins

• Have many roles inside the cell


• An overview of protein functions

Table 5.1


• Enzymes

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

Substrate(sucrose)

Enzyme (sucrase)

Glucose

OH

H O

H2O

Fructose

3 Substrate is convertedto products.

1 Active site is available for a molecule of substrate, the

reactant on which the enzyme acts.

Substrate binds toenzyme.

22

4 Products are released.

Figure 5.16


Polypeptides

• Polypeptides

– Are polymers of amino acids

• A protein

– Consists of one or more polypeptides


Amino Acid Monomers

• Amino acids

– Are organic molecules possessing both carboxyl and amino groups

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


• 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)


Amino Acid Polymers

• Amino acids

– Are linked by peptide bondsOH

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)


Determining the Amino Acid Sequence of a Polypeptide

• The amino acid sequences of polypeptides

– Were first determined using chemical means

– Can now be determined by automated machines


Protein Conformation and Function

• A protein’s specific conformation

– Determines how it functions


• Two models of protein conformation

(a) A ribbon model

(b) A space-filling model

Groove

Groove

Figure 5.19


Four Levels of Protein Structure

• Primary structure

– Is the unique sequence of amino acids in a polypeptide

Figure 5.20–

Amino acid subunits

+H3NAmino

end

oCarboxyl end

oc

GlyProThrGlyThr

Gly

GluSeuLysCysProLeu

MetVal

Lys

ValLeu

AspAlaVal ArgGly

SerPro

Ala

Gly

lle

SerProPheHisGluHis

Ala

GluVal

ValPheThrAlaAsn

AspSer

GlyProArg

ArgTyrThr

lleAla

Ala

Leu

LeuSer

ProTyrSerTyrSerThr

Thr

Ala

ValVal

ThrAsnProLysGlu

ThrLys

SerTyrTrpLysAlaLeu

GluLle Asp


O C helix

pleated sheet

Amino acidsubunits NC

H

C

O

C N

H

CO H

R

C NH

C

O H

C

R

N

HH

R C

O

R

C

H

NH

C

O H

NCO

R

C

H

NH

H

C

R

C

O

C

O

C

NH

H

R

C

C

O

N

HH

C

R

C

O

NH

R

C

H C

ON

HH

C

R

C

O

NH

R

C

H C

ON

HH

C

R

C

O

N H

H C R

N HO

O C N

C

RC

H O

CHR

N H

O C

RC

H

N H

O CH C R

N H

CC

N

R

H

O C

H C R

N H

O C

RC

H

H

C

RN

H

CO

C

NH

R

C

H C

O

N

H

C

• Secondary structure

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

– Includes the helix and the pleated sheet

H H

Figure 5.20


• 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


• Quaternary structure

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

Polypeptidechain

Collagen Chains

ChainsHemoglobin

IronHeme


• The four levels of protein structure

+H3NAmino end

Amino acidsubunits

helix


Sickle-Cell Disease: A Simple Change in Primary Structure

• Sickle-cell disease

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


• Hemoglobin structure and sickle-cell disease

Fibers of abnormalhemoglobin deform cell into sickle shape.

Primary structure

Secondaryand tertiarystructures

Quaternary structure

Function

Red bloodcell shape

Hemoglobin A

Molecules donot associatewith oneanother, eachcarries oxygen.

Normal cells arefull of individualhemoglobinmolecules, eachcarrying oxygen

10 m 10 m

Primary structure

Secondaryand tertiarystructures

Quaternary structure

Function

Red bloodcell shape

Hemoglobin S

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

subunit subunit

1 2 3 4 5 6 7 3 4 5 6 721

Normal hemoglobin Sickle-cell hemoglobin. . .. . .

Figure 5.21

Exposed hydrophobic

region

Val ThrHis Leu Pro Glul Glu Val His Leu Thr Pro Val Glu


What Determines Protein Conformation?

• Protein conformation

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


• Denaturation

– Is when a protein unravels and loses its native conformation

Denaturation

Renaturation

Denatured proteinNormal protein

Figure 5.22


The Protein-Folding Problem

• Most proteins

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


• Chaperonins

– 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


• X-ray crystallography

– Is used to determine a protein’s three-dimensional structure X-ray

diffraction pattern

Photographic film

Diffracted X-raysX-ray

sourceX-ray beam

Crystal Nucleic acid Protein

(a) X-ray diffraction pattern (b) 3D computer modelFigure 5.24


Protein questions

1. What 2 functional groups do all amino acids have

2. List the roles of Proteins. Give examples.

3. What are the general steps of an enzymatic reaction?

4. Name and describe the qualities of the primary bonds in a protein.

5. What are the levels of proteins structure and which associations hold them together.

6. What is denaturation and how does it happen?

7. What is a cahperonin? What role do they play in protein structure


• Concept 5.5: 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


The Roles of Nucleic Acids

• There are two types of nucleic acids

– Deoxyribonucleic acid (DNA)

– Ribonucleic acid (RNA)


• DNA

– Stores information for the synthesis of specific proteins


– Directs RNA synthesis

– Directs protein synthesis through RNA

1

2

3

Synthesis of mRNA in the nucleus

Movement of mRNA into cytoplasm

via nuclear pore

Synthesisof protein

NUCLEUSCYTOPLASM

DNA

mRNA

Ribosome

AminoacidsPolypeptide

mRNA

Figure 5.25


The Structure of 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


• 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


Nucleotide Monomers

• Nucleotide monomers

– Are made up of nucleosides and phosphate groups

(c) Nucleoside componentsFigure 5.26

CHCH

Uracil (in RNA)U

Ribose (in RNA)

Nitrogenous bases Pyrimidines

CN

NC

OH

NH2

CHCH

OC

NH

CH

HNC

O

CCH3

N

HNC

C

HO

O

CytosineC

Thymine (in DNA)T

NHC

N C

CN

C

CH

N

NH2 O

NHC

NHH

CC

N

NH

C NH2

AdenineA

GuanineG

Purines

OHOCH2

H

H H

OH

H

OHOCH2

HH H

OH

H

Pentose sugars

Deoxyribose (in DNA) Ribose (in RNA)OHOH

CH

CH

Uracil (in RNA)U

4’

5”

3’OH H

2’

1’

5”

4’

3’ 2’

1’


Nucleotide Polymers

• 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


• The sequence of bases along a nucleotide polymer

– Is unique for each gene


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)


DNA and Proteins as Tape Measures of Evolution

• Molecular comparisons

– Help biologists sort out the evolutionary connections among species


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

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Focus Phospholipids are...

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Transcript of Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Focus Phospholipids are...