lipids and proteins

Lipids and ProteinsLipids and Proteins

I.I. LipidsLipidsA. FatsA. Fats1. fatty acids1. fatty acidsa. saturateda. saturatedb. unsaturatedb. unsaturated2. 2. transtrans fats fatsB. PhosopholipidsB. PhosopholipidsC. SteroidsC. Steroids1. LDL1. LDL2. HDL2. HDL

LipidsLipids LipidsLipids are a are a diversediverse group of group of

hydrophobic moleculeshydrophobic molecules LipidsLipids

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

– Share the common Share the common trait trait of being of being hydrophobichydrophobic

FatsFats– Are Are constructedconstructed from two types of smaller from two types of smaller

molecules, a single molecules, a single glycerolglycerol and usually and usually three three fattyfatty acids acids

– Vary in the length and Vary in the length and numbernumber and and locations of doublelocations of double bonds bonds they containthey contain

FatsFats•Vary in theVary in the length length and number and number

and and locationslocations of double bonds of double bonds they containthey contain

Saturated fatty acidsSaturated fatty acids– Have the maximum number of Have the maximum number of

hydrogen atoms possiblehydrogen atoms possible– Have no Have no doubledouble bonds bonds

(a) Saturated fat and fatty acid

Stearic acid

Figure 5.12

Unsaturated fatty Unsaturated fatty acidsacids– Have one or more double bondsHave one or more double bonds– Mono-unsaturatedMono-unsaturated or polyunsaturated or polyunsaturated

(b) Unsaturated fat and fatty acidcis double bondcauses bending

Oleic acid

Figure 5.12

MonoacylglycerolMonoacylglycerol

DiacyglycerolDiacyglycerol

Triacylglycerol Triacylglycerol

Ester linkage

In In unsaturated unsaturated fatty acids, there are two fatty acids, there are two ways the pieces of the hydrocarbon tail ways the pieces of the hydrocarbon tail can be arranged around a can be arranged around a C=C double C=C double bond. In bond. In cis bondscis bonds, the two pieces of , the two pieces of the carbon chain on either side of the the carbon chain on either side of the double double bondbond are either both are either both “up” “up” or both or both “down,” such that both are on the same “down,” such that both are on the same side of the molecule. In side of the molecule. In trans bondstrans bonds, , the two pieces of the molecule are on the two pieces of the molecule are on oppositeopposite sides of the double bond, that sides of the double bond, that is, one is, one “up” “up” and one and one “down” “down” across from across from each othereach other

Naturally-occurring Naturally-occurring unsaturatedunsaturated vegetable oils have almost all vegetable oils have almost all cis cis bondsbonds, but using oil for frying causes , but using oil for frying causes some of the cis bonds to convert to some of the cis bonds to convert to trans trans bondsbonds. If oil is used only once like when . If oil is used only once like when you fry an egg, only a few of the bonds you fry an egg, only a few of the bonds do this so it’s not too bad. However, if oil do this so it’s not too bad. However, if oil is is constantly reusedconstantly reused, like in , like in fast food fast food French fry machines, more and more of French fry machines, more and more of the the cis bonds cis bonds are changed to trans until are changed to trans until significant numbers of fatty acids with significant numbers of fatty acids with trans bonds build up.trans bonds build up.

The reason this is of concern is that The reason this is of concern is that fatty acids with fatty acids with trans bonds trans bonds are are carcinogeniccarcinogenic, or cancer-causing. , or cancer-causing. The levels of trans fatty acids in The levels of trans fatty acids in highly-processedhighly-processed, lipid-containing , lipid-containing products such as products such as margarinemargarine are quite are quite high, and the government is high, and the government is considering requiring that the considering requiring that the amounts of amounts of trans fattytrans fatty acids in such acids in such products be listed on the labels. products be listed on the labels.

PhospholipidsPhospholipids– HaveHave only only two fatty two fatty acidsacids– Have aHave a phosphate phosphate group instead of group instead of

a a thirdthird fatty acid fatty acid

Phospholipid structurePhospholipid structure– Consists of a Consists of a hydrophilichydrophilic “head” “head”

and hydrophobic and hydrophobic “tails”“tails”CH2

OPO OOCH2CHCH2

OOC O C O

Phosphate

Glycerol

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

Fatty acids

(c) Phospholipid symbol

Hyd

r oph

obic

tai

ls

Hydrophilichead

Hydrophobictails

–

Hyd

r oph

ilic

h ead CH2 Choline+

Figure 5.13

N(CH3)3

The structure of The structure of phospholipidsphospholipids– Results in aResults in a bilayer bilayer arrangement arrangement

found in found in cell cell membranesmembranes

Hydrophilichead

WATER

WATERHydrophobictail

Figure 5.14

SteroidsSteroids SteroidsSteroids

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

HO

CH3

CH3

H3C CH3

CH3

Figure 5.15

One steroid, One steroid, cholesterolcholesterol– Is found in Is found in cell cell membranesmembranes– Cholesterol is the precursor to our Cholesterol is the precursor to our sex sex

hormoneshormones and and Vitamin DVitamin D. Vitamin D is . Vitamin D is formed by the action of UV light in formed by the action of UV light in sunlight on sunlight on cholesterolcholesterol molecules that molecules that have “risen” to near the surface of the have “risen” to near the surface of the skin.skin.

– OurOur bodies bodies make about 2 g of cholesterol make about 2 g of cholesterol per day, and that makes up about 85% per day, and that makes up about 85% of blood of blood cholesterolcholesterol, while only about , while only about 15% 15% comes from dietary sources. comes from dietary sources.

LipoproteinsLipoproteins are clusters of proteins and are clusters of proteins and lipids all tangled up together. These act as a lipids all tangled up together. These act as a means of carrying lipids, including means of carrying lipids, including cholesterolcholesterol, around in our blood. Two main , around in our blood. Two main categories of lipoproteins distinguished by categories of lipoproteins distinguished by how compact/dense how compact/dense they are. they are. 1. 1. LDLLDL or or low low density lipoproteindensity lipoprotein is the “bad guy,” being is the “bad guy,” being associated with deposition of “cholesterol” associated with deposition of “cholesterol” on the walls of someone’s arteries. on the walls of someone’s arteries. 2. 2. HDLHDL or or high density lipoproteinhigh density lipoprotein is the “good is the “good guy,” being associated with carrying guy,” being associated with carrying ““cholesterol” cholesterol” out of the blood system, and is out of the blood system, and is more dense/more compact than LDLmore dense/more compact than LDL..

FYI only!!! An FYI only!!! An emulsifying agentemulsifying agent is a is a substance which is soluble in both oil substance which is soluble in both oil and water, thus enabling the two to mix. and water, thus enabling the two to mix. A “famous” A “famous” phospholipidphospholipid is is lecithinlecithin which is found in egg yolk and which is found in egg yolk and soybeans. Egg yolk is mostly water but soybeans. Egg yolk is mostly water but has a lot of lipids, especially has a lot of lipids, especially cholesterolcholesterol, , which are needed by the developing which are needed by the developing chick. chick. LecithinLecithin is used to is used to emulsifyemulsify the the lipids and hold them in the water as anlipids and hold them in the water as an emulsionemulsion. . LecithinLecithin is the basis of the is the basis of the classic emulsion known as mayonnaiseclassic emulsion known as mayonnaise

ProteinsProteins Proteins have many Proteins have many

structuresstructures, resulting in a , resulting in a wide range of wide range of functionsfunctions

Proteins do most of the work Proteins do most of the work in cells and act as in cells and act as enzymesenzymes

Proteins are made of Proteins are made of monomers called monomers called amino amino acidsacids

An overview of protein functionsAn overview of protein functions

Table 5.1

EnzymesEnzymes– Are a type of protein that acts as a Are a type of protein that acts as a

catalyst, speeding up chemical reactionscatalyst, speeding up chemical reactions

Substrate(sucrose)

Enzyme (sucrase)

Glucose

OH

H OH2O

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 to

enzyme.

22

4 Products are released.

Figure 5.16

Amino acidsAmino acids– Are organic molecules possessing Are organic molecules possessing

both both carboxyl and amino groupscarboxyl and amino groups– Differ in their properties due to Differ in their properties due to

differing side chains, called differing side chains, called R groupsR groups

Twenty Amino AcidsTwenty Amino Acids 20 different amino acids make up proteins20 different amino acids make up proteins

O

O–

H

H3N+ C CO

O–H

CH3

H3N+ C

H

CO

O–

CH3 CH3

CH3

C CO

O–

H

H3N+

CHCH3

CH2

C

H

H3N+

CH3CH3

CH2

CH

C

H

H3N+ C

CH3

CH2

CH2

CH3N+

H

CO

O–

CH2

CH3N+

H

CO

O–

CH2

NH

H

CO

O–

H3N+ C

CH2

H2C

H2N C

CH2

H

C

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

Methionine (Met) Phenylalanine (Phe)

CO

O–

Tryptophan (Trp) Proline (Pro)

H3C

Figure 5.17

S

O

O–

O–

OHCH2

C CH

H3N+

O

O–

H3N+

OH CH3

CHC CH O–

O

SHCH2

CH

H3N+ C

O

O–

H3N+ C C

CH2

OH

H H H

H3N+

NH2

CH2

OC

C CO

O–

NH2 OCCH2

CH2

C CH3N+

O

O–

OPolar

Electricallycharged

–O OCCH2

C CH3N+

H

O

O–

O– OCCH2

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 PolymersAmino Acid Polymers Amino acidsAmino acids

– Are linked byAre linked by peptide peptide bondsbonds

PolypeptidesPolypeptides PolypeptidesPolypeptides

– Are polymers (chains) of amino Are polymers (chains) of amino acidsacids

A proteinA protein– Consists of one or more Consists of one or more

polypeptidespolypeptides

Protein Conformation and Protein Conformation and FunctionFunction

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

Four Levels of Protein Four Levels of Protein StructureStructure

Primary structurePrimary structure– Is the unique Is the unique

sequence of amino sequence of amino acids in a acids in a polypeptidepolypeptide

Figure 5.20–

Amino acid

subunits

+H3NAmino

end

oCarboxyl end

oc

GlyProThrGlyThr

GlyGluSeuLysCysProLeu

MetVal

LysVal

LeuAspAlaValArgGlySerPro

Ala

GlylleSerProPheHisGluHis

AlaGlu

ValValPheThrAlaAsnAsp

SerGlyProArg

ArgTyrThr lleAla

AlaLeu

LeuSerProTyrSerTyrSerThr

ThrAlaVal

ValThrAsnProLysGlu

ThrLysSer

TyrTrpLysAlaLeu

GluLleAsp

O C helix

pleated sheetAmino acid

subunitsNCH

CO

C NH

CO H

RC N

H

CO H

CR

NHH

R CO

RCH

NH

CO H

NCO

RCH

NH

HCR

CO

CO

CNH

H

RC

CO

NH H

CR

CO

NH

RCH C

ONH H

CR

CO

NH

RCH C

ONH H

CR

CO

N H

H C RN H O

O C NC

RC

H O

CHR

N HO C

RC H

N H

O CH C R

N H

CC

NR

HO C

H C R

N HO C

RC H

HCR

NH

CO

C

NH

RCH C

ONH

C

Secondary structureSecondary structure– Is the folding or coiling of the Is the folding or coiling of the

polypeptide into a repeating polypeptide into a repeating configurationconfiguration

– Includes the Includes the helix and the helix and the pleated pleated sheetsheet

H H

Figure 5.20

Tertiary structureTertiary structure– Is the overall three-dimensional shape Is the overall three-dimensional shape

of a polypeptideof a polypeptide– Results from interactions between Results from interactions between

amino acids and R groupsamino acids and R groups

CH2CH

OHOCHOCH2

CH2 NH3+ C-O CH2

O

CH2SSCH2

CH

CH3CH3

H3CH3C

Hydrophobic interactions and van der Waalsinteractions Polypeptid

ebackbone

Hydrogenbond

Ionic bond

CH2

Disulfide bridge

Quaternary structureQuaternary structure– Is the overall protein structure that Is the overall protein structure that

results from the aggregation of two or results from the aggregation of two or more polypeptide subunitsmore polypeptide subunits

Polypeptidechain

Collagen

Chains

ChainsHemoglobin

IronHeme

Review of Protein StructureReview of Protein Structure

+H3NAmino end

Amino acidsubunits

helix

Sickle-Cell Disease: A Simple Sickle-Cell Disease: A Simple Change in Primary StructureChange in Primary Structure

Sickle-cell diseaseSickle-cell disease– Results from a single amino Results from a single amino

acid substitution in the protein acid substitution in the protein hemoglobinhemoglobin

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 structureFunction

Red bloodcell shape

Hemoglobin SMolecules 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 What Determines Protein Conformation?Conformation?

Protein conformation Protein conformation Depends on the physical and Depends on the physical and chemical conditions of the chemical conditions of the protein’s environmentprotein’s environment

Temperature, pH, etc. affect Temperature, pH, etc. affect protein structureprotein structure

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

Renaturation

Denatured proteinNormal protein

Figure 5.22

The Protein-Folding ProblemThe Protein-Folding Problem Most proteinsMost proteins

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

– Denaturated proteins no longer work Denaturated proteins no longer work in their unfolded conditionin their unfolded condition

– Proteins may be denaturated by Proteins may be denaturated by extreme changes in pH, temperature, extreme changes in pH, temperature, salinity or heavy metalssalinity or heavy metals

ChaperoninsChaperonins– Are protein molecules that assist in the Are protein molecules that assist in the

proper folding of other proteinsproper folding of other proteins

Hollowcylinder

Cap

Chaperonin(fully assembled)

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.

The cap comesoff, and the properlyfolded protein is released.

CorrectlyfoldedproteinPolypeptide

2

1

3

Figure 5.23

PrionsPrions Prions Prions are slow-acting, virtually are slow-acting, virtually

indestructible infectious proteins that indestructible infectious proteins that cause brain diseases in mammalscause brain diseases in mammals

Prions propagate by converting Prions propagate by converting normal proteins into the prion normal proteins into the prion versionversion

Scrapie in sheep, mad cow disease, Scrapie in sheep, mad cow disease, and Creutzfeldt-Jakob disease in and Creutzfeldt-Jakob disease in humans are all caused by prionshumans are all caused by prions

What happens if a protein What happens if a protein isn’t folded correctly?isn’t folded correctly?

Prions are formed – Prions are formed – misfolded versions of misfolded versions of

normal proteinsnormal proteins

X-ray crystallographyX-ray crystallography– Is used to determine a protein’s three-Is used to determine a protein’s three-

dimensional structuredimensional structure X-raydiffraction pattern

Photographic filmDiffracted X-

raysX-raysource

X-ray

beam

CrystalNucleic acid Protein

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

Nucleic AcidsNucleic Acids Nucleic acids store and Nucleic acids store and

transmit hereditary informationtransmit hereditary information GenesGenes

– Are the units of inheritanceAre the units of inheritance– Program the amino acid Program the amino acid

sequence of polypeptidessequence of polypeptides– Are made of nucleotide Are made of nucleotide

sequences on DNAsequences on DNA

The Roles of Nucleic AcidsThe Roles of Nucleic Acids There are two types of nucleic acidsThere are two types of nucleic acids

– Deoxyribonucleic acid (DNA)Deoxyribonucleic acid (DNA)– Ribonucleic acid (RNA)Ribonucleic acid (RNA)

Deoxyribonucleic AcidDeoxyribonucleic Acid DNADNA

– Stores information for the Stores information for the synthesis of specific proteinssynthesis of specific proteins

– Found in the nucleus of cellsFound in the nucleus of cells

DNA FunctionsDNA Functions– Directs RNA synthesis (transcription)Directs RNA synthesis (transcription)– Directs protein synthesis through RNA Directs protein synthesis through RNA

(translation)(translation)1

2

3

Synthesis of mRNA in the nucleus

Movement of mRNA into cytoplasm

via nuclear pore

Synthesisof protein

NUCLEUSCYTOPLASM

DNA

mRNARibosome

AminoacidsPolypeptide

mRNA

Figure 5.25

The Structure of Nucleic The Structure of Nucleic AcidsAcids

Nucleic acidsNucleic acids– Exist as polymers called Exist as polymers called

polynucleotidespolynucleotides

(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 polynucleotideEach polynucleotide– Consists of monomers called nucleotidesConsists of monomers called nucleotides– Sugar + phosphate + nitrogen baseSugar + phosphate + nitrogen base

Nitrogenousbase

Nucleoside

O

O

O

O P CH2

5’C

3’CPhosphategroup Pentose

sugar

(b) NucleotideFigure 5.26

O

Nucleotide MonomersNucleotide Monomers Nucleotide Nucleotide

monomersmonomers – Are made up of Are made up of

nucleosides (sugar nucleosides (sugar + base) and + base) and phosphate groupsphosphate groups

(c) Nucleoside componentsFigure 5.26

CHCH

Uracil (in RNA)U

Ribose (in RNA)

Nitrogenous bases Pyrimidines

CNNC

OH

NH2

CHCH O C N

HCH

HN CO

C CH3

NHN

C

CH

O

O

CytosineC

Thymine (in DNA)T

NHC

N CC N

C

CHN

NH2 ON

HCNHH

C C

N

NHC NH2

AdenineA

GuanineG

Purines

OHOCH2

HH H

OH

H

OHOCH2

HH H

OH

H

Pentose sugars

Deoxyribose (in DNA)Ribose (in RNA)OHOH

CHCH

Uracil (in RNA)U

4’

5”

3’OH H

2’

1’

5”

4’

3’ 2’

1’

Nucleotide PolymersNucleotide Polymers Nucleotide polymersNucleotide polymers

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

GeneGene The sequence of bases along a The sequence of bases along a

nucleotide polymernucleotide polymer– Is unique for each geneIs unique for each gene

The DNA Double HelixThe DNA Double Helix Cellular DNA moleculesCellular DNA molecules

– Have two polynucleotides that spiral Have two polynucleotides that spiral around an imaginary axisaround an imaginary axis

– Form a double helixForm a double helix

The DNA double helixThe DNA double helix– Consists of two antiparallel nucleotide Consists of two antiparallel nucleotide

strandsstrands3’ 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

A,T,C,GA,T,C,G The nitrogenous bases in DNAThe nitrogenous bases in DNA

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

DNA and Proteins as Tape DNA and Proteins as Tape Measures of EvolutionMeasures of Evolution

Molecular comparisons Molecular comparisons – Help biologists sort out the Help biologists sort out the

evolutionary connections evolutionary connections among species among species

The Theme of Emergent The Theme of Emergent Properties in the Chemistry of Properties in the Chemistry of

Life: Life: A ReviewA Review Higher levels of organizationHigher levels of organization

– Result in the emergence of Result in the emergence of new propertiesnew properties

OrganizationOrganization– Is the key to the chemistry of Is the key to the chemistry of

lifelife