Former Chapter 3: Former Chapter 3: Chemistry of Cellular Chemistry of Cellular

Components: 12Components: 12thth ed. & ed. & Prior: removed in 13Prior: removed in 13thth

online: online: www.microbiologyplace.com

in webcourses as pdf in webcourses as pdf Madigan12Chap 3Madigan12Chap 3I.I. Introduction to the Basic Introduction to the Basic

ChemistryChemistry

II.II. Structure of Macromolecules:Structure of Macromolecules:I.I. Noninformational:Noninformational:

I.I. Polysaccharides & Lipids,Polysaccharides & Lipids,

II.II. Informational:Informational:I.I. Nucleic Acids & Protein Nucleic Acids & Protein

Nature of Organic Nature of Organic MoleculesMolecules

• Organic Organic ChemistryChemistry::

• Study of carbon containing Study of carbon containing compounds; name “organic” compounds; name “organic” implies the central importance of implies the central importance of “C” containing compounds to living “C” containing compounds to living organisms.organisms.

• CarbonCarbon• Has 4 electrons in its outer shell Has 4 electrons in its outer shell

and therefore can share 4 pairs of and therefore can share 4 pairs of ee-- with other (electron unpaired) with other (electron unpaired) atoms to form 4 covalent bonds.atoms to form 4 covalent bonds.

Covalent Bonding (double or triple Covalent Bonding (double or triple bonds)bonds)

Formation of Ethylene and AcetyleneFormation of Ethylene and Acetylene

Weak non-covalent bonds IWeak non-covalent bonds I

Weak non-covalent bonds IIWeak non-covalent bonds II

Weak non-covalent bonds IIWeak non-covalent bonds II

Hydrogen bonding between DNA basesHydrogen bonding between DNA bases

Macromolecules in the cellMacromolecules in the cell

What’s in a cell?What’s in a cell?

Carbohydrates (sugars)Carbohydrates (sugars)

• CarbohydratesCarbohydrates::• Organic compounds containing carbon, hydrogen, and oxygen in a Organic compounds containing carbon, hydrogen, and oxygen in a

ratio of ratio of 1:2:1 ie sugars called monosaccharides: 1:2:1 ie sugars called monosaccharides: (CH(CH22O)O)nn

• The most biologically relevant carbohydrates are those containing The most biologically relevant carbohydrates are those containing 4,5,6, and 7 carbon 4,5,6, and 7 carbon sugars (monosaccharides)sugars (monosaccharides)..

• PolysaccharidesPolysaccharides• Polysaccharides are carbohydrates containing many monomeric Polysaccharides are carbohydrates containing many monomeric

(sugar) (sugar) units connected by covalent bonds referred to as units connected by covalent bonds referred to as Glycosidic Glycosidic BondsBonds..

• If two sugars (monosaccharides) are joined by a glycosidic bond, the If two sugars (monosaccharides) are joined by a glycosidic bond, the result is called a result is called a disaccharidedisaccharide..

• The addition of one more monosaccharide yields a The addition of one more monosaccharide yields a trisaccharidetrisaccharide, , and several more an and several more an oligosaccharideoligosaccharide; an extremely long chain is ; an extremely long chain is called a called a polysaccharidepolysaccharide..

Carbohydrate Geometry: Carbohydrate Geometry: linkages between linkages between monosaccharidemonosaccharide

• The The glycosidic bondglycosidic bond can exist in two can exist in two different geometric different geometric orientations, orientations, referred to as:referred to as:

• alpha (alpha ()) • beta (beta ())

Sugars and Sugars and DisaccharidesDisaccharides

Carbohydrate LinkageCarbohydrate Linkage• Polysaccharides with repeating Polysaccharides with repeating

structure composed of glucose structure composed of glucose units linked between carbons 1 units linked between carbons 1 and 4 in the and 4 in the alphaalpha orientation orientation (example, glycogen and starch) (example, glycogen and starch) function as important carbon function as important carbon and energy reserves in and energy reserves in bacteria, plants and animalsbacteria, plants and animals

• Alternatively, glucose units Alternatively, glucose units joined by joined by beta-1,4 linkagesbeta-1,4 linkages are present in cellulose, a stiff are present in cellulose, a stiff plant and algal cell wall plant and algal cell wall component.component.

• Thus, even though starch and Thus, even though starch and cellulose are both composed cellulose are both composed solely of glucose units, their solely of glucose units, their functional properties functional properties are are entirely different because of entirely different because of their different configuration.their different configuration.

Lipids: Complex class of Lipids: Complex class of molecules soluble in non-polar molecules soluble in non-polar

solventssolventsLipids include Lipids include triglycerides, waxes, triglycerides, waxes, sterols, etc. Fatty acidssterols, etc. Fatty acids are the main constituents are the main constituents of the lipids of of the lipids of BacteriaBacteria and and Eukarya. Eukarya. The lipids ofThe lipids of Archaea,Archaea, by contrast, are by contrast, are made of the hydrophobic made of the hydrophobic molecule phytane (later).molecule phytane (later).•Fatty acids contain both Fatty acids contain both highly highly hydrophobichydrophobic (water-repelling) and (water-repelling) and highly highly hydrophilichydrophilic (water- (water-soluble) regions. soluble) regions. (Carboxyl ionized and has (Carboxyl ionized and has negative charge).negative charge).

Triglycerides & Triglycerides & PhospholipidsPhospholipids

Simple lipids: Fatty acids esterified to Simple lipids: Fatty acids esterified to glycerol (also called triglycerides)glycerol (also called triglycerides)

Complex lipids contain additional Complex lipids contain additional elements: phosphorous, nitrogen or sulfur.elements: phosphorous, nitrogen or sulfur.

Phospholipids: two moles fatty acid and Phospholipids: two moles fatty acid and one mole phosphate esterified to glycerol.one mole phosphate esterified to glycerol.

Removal of water between acidic carboxyl Removal of water between acidic carboxyl group of fatty acid and hydroxyl group of group of fatty acid and hydroxyl group of glycerol (next slide) produces ?glycerol (next slide) produces ?

Nucleic Acids Nucleic Acids Building Building Blocks (Nucleotides)Blocks (Nucleotides)Composed of three units:Composed of three units:

• Five-carbon sugar, either ribose (in RNA) or Five-carbon sugar, either ribose (in RNA) or deoxyribose (in DNA)deoxyribose (in DNA)

• A nitrogen baseA nitrogen base• A molecule of phosphate (POA molecule of phosphate (PO44

2-2-))• A nucleotide is a nucleoside phosphateA nucleotide is a nucleoside phosphate

N-Glycosidic LinkageN-Glycosidic Linkage Error in slide: Error in slide: ATP is not a nucleotideATP is not a nucleotide

Pyrimidine BasesPyrimidine Bases

• PyrimidinesPyrimidines: : Contain a Contain a singlesingle six-membered six-membered heterocyclic ringheterocyclic ring• Cytosine ( C )Cytosine ( C )• Uracil ( U ) RNAUracil ( U ) RNA

• In RNAIn RNA

• Thymine ( T )Thymine ( T )• In DNAIn DNA

Purine BasesPurine Bases

• PurinesPurines: : • Contain Contain twotwo fused fused

heterocyclic rings heterocyclic rings [containing more than [containing more than one kind of atom (C & one kind of atom (C & N)]N)]..

• Adenine ( A )Adenine ( A )• Guanine ( G )Guanine ( G )

Nucleic AcidsNucleic Acids• Backbone of a nucleic acid (polynucleotide) is a Backbone of a nucleic acid (polynucleotide) is a

polymer in which sugar and phosphate molecules polymer in which sugar and phosphate molecules alternate alternate

• Polynucleotides contain nucleotides covalently Polynucleotides contain nucleotides covalently bonded via phosphate from Carbon 3’ (3 prime) of bonded via phosphate from Carbon 3’ (3 prime) of one sugar to carbon 5’ (5 prime) of the adjacent one sugar to carbon 5’ (5 prime) of the adjacent sugarsugar

• The phosphate linkage is chemically a covalent The phosphate linkage is chemically a covalent phosphodiesterphosphodiester bond since a single phosphate bond since a single phosphate is connected by ester linkages to two separate is connected by ester linkages to two separate sugars. sugars. (3’5’ phosphodiester linkage)(3’5’ phosphodiester linkage)

• Bond results from removal of HBond results from removal of H22O between 3’OH of O between 3’OH of nucleotide and 5’ phosphate of incoming nucleotide.nucleotide and 5’ phosphate of incoming nucleotide.

3’ 5’ Phosphodiester 3’ 5’ Phosphodiester LinkageLinkage

Bond between Bond between nucleotides results from nucleotides results from dehydration reaction, ie dehydration reaction, ie removal of Hremoval of H22O.O.

Top of dinucleotide is 5’ Top of dinucleotide is 5’ end and bottom is 3’ end.end and bottom is 3’ end.

Template required to Template required to specify which nucleotidesspecify which nucleotides

Enzyme that catalyzes is Enzyme that catalyzes is called a polymerase.called a polymerase.

Synthesizes only in 5’ to Synthesizes only in 5’ to 3’ direction 3’ direction

DNA Helix is DNA Helix is Antiparallel: Antiparallel: 5’5’3’ 3’ 3’3’5’5’

One strand runs 5’One strand runs 5’3’3’ Other strand runs 3’Other strand runs 3’5’5’ Polymerase that Polymerase that

replicates DNA only replicates DNA only synthesizes 5’synthesizes 5’ 3’ 3’ copying the 3’copying the 3’ 5’ strand 5’ strand

Complicates DNA Complicates DNA replication (later in replication (later in course)course)

DNA -vs.- RNADNA -vs.- RNA

• Deoxyribonucleic Acid Deoxyribonucleic Acid (DNA)(DNA)-carries the -carries the genetic blueprint for genetic blueprint for the cell.the cell.

• Ribonucleic Acid Ribonucleic Acid (RNA)(RNA)-acts as an -acts as an intermediate to convert intermediate to convert the blueprint to the the blueprint to the amino acid sequence amino acid sequence for proteinsfor proteins

• Central Dogma again:Central Dogma again:• DNADNARNARNA protein protein

DNADNA• In cells, DNA is present In cells, DNA is present

in in double-strandeddouble-stranded form form• Each molecule contains Each molecule contains

two strands of DNA, two strands of DNA, each strand contains each strand contains several million several million nucleotides linked by nucleotides linked by phosphodiester bondsphosphodiester bonds

• Strands associate by Strands associate by hydrogen bondshydrogen bonds..

• Stabilized further by Stabilized further by hydrophobic base hydrophobic base stacking.stacking.

DNA Base PairingDNA Base Pairing• The most stable H-bonds The most stable H-bonds

occurs when guanine (G) occurs when guanine (G) bonds with cytosine (C) bonds with cytosine (C) and adenine (A) bonds and adenine (A) bonds with thymine (T)with thymine (T)

• Specific base pairing, A Specific base pairing, A with T, G with C is called with T, G with C is called complementarycomplementary

• When A is found on one When A is found on one strand, T is found on the strand, T is found on the complementary strandcomplementary strand

• When G is found on one When G is found on one strand, C is found on the strand, C is found on the other.other.

Melting of DNAMelting of DNA

TTmm is melting temperature of DNA is melting temperature of DNA Temperature required to break H bonds Temperature required to break H bonds

and therefore separate the two strandsand therefore separate the two strands Technically, it is the temperature Technically, it is the temperature

required to produce 50% separated required to produce 50% separated strands (halfway point of melting).strands (halfway point of melting).

As GC/AT ratio increases the TAs GC/AT ratio increases the Tmm value value increasesincreases TTmm due to greater stability of DNA as GC due to greater stability of DNA as GC

forms 3 H bonds and AT only two.forms 3 H bonds and AT only two.

RNARNA• With few exceptions, all With few exceptions, all

ribonucleic acids (RNA) are ribonucleic acids (RNA) are single-strandedsingle-stranded molecules. molecules.

• RNA may have secondary RNA may have secondary structure due to H bonding.structure due to H bonding.

• RNA plays three crucial RNA plays three crucial roles in the cell:roles in the cell:• Messenger RNA (mRNA)Messenger RNA (mRNA)• Transfer RNA (tRNA)Transfer RNA (tRNA)• Ribosomal RNA (rRNA)Ribosomal RNA (rRNA)• Also have discovered new Also have discovered new

roles:roles:• Regulatory RNAs, gene silencing, Regulatory RNAs, gene silencing,

interference RNA, e.t.c.interference RNA, e.t.c.

RNA made off 3’- 5’ DNA RNA made off 3’- 5’ DNA Fig 3-11Fig 3-11

A. DNA: deoxyribose; No OH on 2’ C; A. DNA: deoxyribose; No OH on 2’ C; B. Simplified DNA structure showing H bonding [Adenine, B. Simplified DNA structure showing H bonding [Adenine,

Thymine, Cytosine, GuanineThymine, Cytosine, Guanine C. i. RNA: uracil replace thymine; single stranded; riboseC. i. RNA: uracil replace thymine; single stranded; ribose ii. Sequence of RNA that can assume 2ii. Sequence of RNA that can assume 2oo structure structure

Amino AcidsAmino Acids

• Amino Acids are the monomeric Amino Acids are the monomeric units of proteinsunits of proteins

• Most amino acids consist of only Most amino acids consist of only hydrogen, oxygen and nitrogenhydrogen, oxygen and nitrogen

• All amino acids contain two All amino acids contain two important functional groups, a important functional groups, a carboxylic acid group (-COOH) and carboxylic acid group (-COOH) and an amino group (-NHan amino group (-NH22))

Peptide BondPeptide Bond• The Carboxylic (-The Carboxylic (-

COOH) and amino COOH) and amino group (-NHgroup (-NH22) are ) are functionally important functionally important because covalent because covalent bonds, between the bonds, between the carbon of the carboxyl carbon of the carboxyl group of one amino group of one amino acid and the nitrogen acid and the nitrogen of the amino group of of the amino group of a second amino acid a second amino acid form the form the peptide peptide bondbond

Isomers: new slideIsomers: new slide Molecules with same Molecules with same

molecular formula but molecular formula but exist in different exist in different structural forms are structural forms are called isomers. Ex. called isomers. Ex. Glucose is isomer of Glucose is isomer of Fructose (see fig to left)Fructose (see fig to left)

Optical isomers that Optical isomers that have the same molecular have the same molecular & structural formulas, & structural formulas, except that one is a except that one is a mirror image of the mirror image of the other, are called other, are called enantiomers (can not be enantiomers (can not be superimposed) D or L superimposed) D or L depending on rotation to depending on rotation to right or leftright or left

Isomers: Isomers: EnantiomersEnantiomers

• In most biological systems, the In most biological systems, the predominate isomers are:predominate isomers are:• L-Amino AcidsL-Amino Acids• D-SugarsD-Sugars• Some cells have enzymes called racemases: Some cells have enzymes called racemases:

convert one form to the other.convert one form to the other.

Proteins: Proteins: An introductionAn introduction

• Proteins (individual polypeptide chains) Proteins (individual polypeptide chains) are polymers of amino acids are polymers of amino acids covalentlycovalently bonded by bonded by peptide bondspeptide bonds• 2 amino acids bonded together constitute a 2 amino acids bonded together constitute a

dipeptidedipeptide• 3 linked amino acids are a 3 linked amino acids are a tripeptidetripeptide & so & so

on.on.• Many amino acids covalently linked together Many amino acids covalently linked together

form a form a polypeptidepolypeptide• Proteins Proteins consist of one or more polypeptidesconsist of one or more polypeptides• Proteins: 2 Types: enzymes and Proteins: 2 Types: enzymes and

structuralstructural

Four Levels of Protein Four Levels of Protein StructureStructure

Four Levels:Four Levels: Primary: linear sequence of amino acids held Primary: linear sequence of amino acids held

together by peptide bonds (covalent). together by peptide bonds (covalent). specific specific orderorder

Secondary: interactions between parts that make Secondary: interactions between parts that make up polypeptide backbone; major elements: alpha up polypeptide backbone; major elements: alpha helix & beta pleated sheet (hydrogen bonding)helix & beta pleated sheet (hydrogen bonding)

Tertiary: overall conformation stabilized primarily Tertiary: overall conformation stabilized primarily by weak interactions (final folding in 3-D space)by weak interactions (final folding in 3-D space)

Quaternary: proteins consisting of multiple Quaternary: proteins consisting of multiple polypeptides; manner in which they associate.polypeptides; manner in which they associate.

Proteins:Proteins:Primary StructurePrimary Structure

• The linear array of amino acids in a The linear array of amino acids in a polypeptide is referred to as its polypeptide is referred to as its primary primary structurestructure..

Protein:Protein:Secondary StructureSecondary Structure

• The position of the R-groups on individual amino acids in a The position of the R-groups on individual amino acids in a polypeptide forces the molecule to twist and fold in a polypeptide forces the molecule to twist and fold in a specific way. This leads to the formation of the specific way. This leads to the formation of the secondary secondary structurestructure

• Hydrogen bondsHydrogen bonds play important role in the type of play important role in the type of secondary that a protein attains.secondary that a protein attains.

Secondary StructureSecondary StructureThe Alpha-helixThe Alpha-helix

• In the alpha-helix In the alpha-helix conformation, oxygen conformation, oxygen and nitrogen atoms and nitrogen atoms from different amino from different amino acids become acids become positioned close positioned close enough in the twisted enough in the twisted structure to allow for structure to allow for hydrogen bonding to hydrogen bonding to occur between H on -occur between H on -NH and carbonyl NH and carbonyl oxygen -C=Ooxygen -C=O

The The -Helix-Helix

Alpha HelixAlpha Helix Many amino acid Many amino acid

sequences can adopt sequences can adopt helical symmetry, because helical symmetry, because it is stabilized by contacts it is stabilized by contacts between nearly universal between nearly universal backbone atoms: carbonyl backbone atoms: carbonyl ((oxygenoxygen) and imino groups ) and imino groups (amide H) (amide H) (rarely glycine, (rarely glycine, tyrosine & serine).tyrosine & serine).

Proline is helix-breaking Proline is helix-breaking residue: cyclical structure, residue: cyclical structure, cannot participate as cannot participate as donor in H bondingdonor in H bonding

Side chains project away Side chains project away from helix as from helix as helices helices constructed exclusively constructed exclusively through backbone through backbone contacts.contacts.

Secondary StructureSecondary StructureBeta-sheetBeta-sheet

• In the In the beta-sheetbeta-sheet, the chain of amino acids , the chain of amino acids in the polypeptide folds back and forth in the polypeptide folds back and forth upon itself instead of forming a helixupon itself instead of forming a helix

The The -Sheet-Sheet

Sheet ViewsSheet Views (a): Beta sheet shown from (a): Beta sheet shown from

above. Oxygen and above. Oxygen and nitrogens of the backbone nitrogens of the backbone are fully hydrogen-bonded.are fully hydrogen-bonded.

(b): Beta sheet from side (b): Beta sheet from side view. Illustrates the view. Illustrates the location of side groups, location of side groups, which alternate between which alternate between emerging from above or emerging from above or below the plane of Beta below the plane of Beta sheet. Representation sheet. Representation emphasizes pleated sheet emphasizes pleated sheet shape. (Ex: antiparallel).shape. (Ex: antiparallel).

Tertiary StructureTertiary Structure

• Tertiary structureTertiary structure concerns how the concerns how the secondary structure units associate within a secondary structure units associate within a singlesingle polypeptide chain to give a polypeptide chain to give a three-three-dimensional structuredimensional structure. Weak chemical . Weak chemical attractive forces: Van der Waals, H bonding, attractive forces: Van der Waals, H bonding, ionic, hydrophobic. Only possible covalent ionic, hydrophobic. Only possible covalent in 3in 300 is disulfide bridge. –S- is disulfide bridge. –S-

Conformation in Three Dimensional Space Showing

Helical and Sheets

Tertiary StructureTertiary Structure 3300 primarily stabilized by weaker attractive primarily stabilized by weaker attractive

forcesforces Van der WaalsVan der Waals Hydrogen bondingHydrogen bonding Ionic bondingIonic bonding Hydrophobic bondingHydrophobic bonding

One of strongest influences on protein folding is burial of One of strongest influences on protein folding is burial of hydrophobic (nonpolar) side chains into core of polypeptidehydrophobic (nonpolar) side chains into core of polypeptide

Leads to prediction that in aqueous solutions, polypeptides Leads to prediction that in aqueous solutions, polypeptides with large numbers of nonpolar side groups will tend to with large numbers of nonpolar side groups will tend to internalize the nonpolar residues and be more stable than internalize the nonpolar residues and be more stable than polypeptides containing mostly polar groups. polypeptides containing mostly polar groups. Less Less interference with Hinterference with H22O hydrogen bonding to self.O hydrogen bonding to self.

One possible covalent bond: disulfide bridgeOne possible covalent bond: disulfide bridge

Disulfide BridgeDisulfide Bridge

Cys-SH + HS-Cys Cys-SH + HS-Cys Cys-S-S-Cys Cys-S-S-Cys If disulfide bridge is between two If disulfide bridge is between two

cysteines in same polypeptide cysteines in same polypeptide chain: tertiary structurechain: tertiary structure

Disulfide bridge can also link two Disulfide bridge can also link two different polypeptide chains: different polypeptide chains: Quaternary structureQuaternary structure

-SH is sulfahydryl (also called thio -SH is sulfahydryl (also called thio group) -S-S- is disulfide bridge.group) -S-S- is disulfide bridge.

Quaternary StructureQuaternary Structure

• If a protein consists If a protein consists of two or more of two or more polypeptides, the polypeptides, the number and types of number and types of polypeptides that polypeptides that form the final protein form the final protein molecule is referred molecule is referred to as its to as its quaternary quaternary structurestructure

• Ex:Hemoglobin 2Ex:Hemoglobin 2 2 2

Primary StructurePrimary Structure

Insulin: each chain of Insulin: each chain of insulin has primary insulin has primary structure: sequence of structure: sequence of amino acids.amino acids.

Each chain has 2Each chain has 200: : alpha helix (H bonding)alpha helix (H bonding)

Each chain folds in 3-D Each chain folds in 3-D space: 3space: 3o o (weak) & no (weak) & no disulfide bridge S-S.disulfide bridge S-S.

chain interacts with chain interacts with chain: 4chain: 4o o (weak + S-S)(weak + S-S)

Primary Structure A Primary Structure A chainchain

GIVEQCCASVCSLYQLENYCN: A chainGIVEQCCASVCSLYQLENYCN: A chain Quaternary Structure of Insulin is that Quaternary Structure of Insulin is that

it consists of two polypeptides: A & Bit consists of two polypeptides: A & B Thus, Some proteins like insulin Thus, Some proteins like insulin

contain two or more polypeptide contain two or more polypeptide chains held together by noncovalent chains held together by noncovalent or covalent forces.or covalent forces.

Insulin has A & B chain held together Insulin has A & B chain held together by two covalent disulfide bridges.by two covalent disulfide bridges.

QuaternaryQuaternary ********************* A chain********************* A chain ****************************** B chain****************************** B chain

Quaternary: Insulin is comprised of two Quaternary: Insulin is comprised of two polypeptide chains: one alpha and one polypeptide chains: one alpha and one betabeta

Held together by weak attractive Held together by weak attractive forces as well as disulfide bridges -S-forces as well as disulfide bridges -S-S-S-

Denaturation of Denaturation of RibonucleaseRibonuclease

DenaturationDenaturation• Proteins exposed to extremes of heat, pH, Proteins exposed to extremes of heat, pH,

chemicals or metals that affect their folding chemicals or metals that affect their folding are said to undergo are said to undergo denaturationdenaturation

• Denaturation causes the polypeptide chain to Denaturation causes the polypeptide chain to unfoldunfold

• The denatured protein retains its primary The denatured protein retains its primary structure because it is held together by structure because it is held together by covalent (peptide) bonds but loses its covalent (peptide) bonds but loses its secondary and secondary and tertiarytertiary structure. ( structure. (also also subunits may disassociate in quaternary subunits may disassociate in quaternary structure proteins)structure proteins)

• Depending on the severity of the denaturing Depending on the severity of the denaturing conditions, refolding may occur after removal conditions, refolding may occur after removal of the denaturant of the denaturant (harsh: aggregation)(harsh: aggregation)

Tautomerization: keto to Tautomerization: keto to enolenol

-C=O Keto form with carbonyl-C=O Keto form with carbonyl

N-HN-H

-C-OH Enol form with hydroxyl-C-OH Enol form with hydroxyl

NN