Biochemistry2018

09/30/1809/30/18 14:3614:36 cottinghamcottingham
Molecular BiologyMolecular Biology
2.1 – 2.32.1 – 2.3
Acorn Squash
from the garden!!!

Key Vocabulary…and thereKey Vocabulary…and there’s a lot!’s a lot!
 TrioseTriose
 PentosePentose
 HexoseHexose
 AlcoholAlcohol
 Amino acidAmino acid
 CarbohydrateCarbohydrate
 GlucoseGlucose
 Cellular respirationCellular respiration
 CelluloseCellulose
 ChitinChitin
 CoenzymeCoenzyme
 Condensation reactionCondensation reaction
 DenatureDenature
 DipeptideDipeptide
 DisaccharideDisaccharide
 Ester BondEster Bond
 WaxWax
 Palmitic (saturated)Palmitic (saturated)
 Linoleic (unsaturated)Linoleic (unsaturated)
 Electrovalent bondElectrovalent bond
 Fatty AcidFatty Acid
 FructoseFructose
 GalactoseGalactose
 GlycerolGlycerol
 GlycogenGlycogen
 Glycosidic BondGlycosidic Bond
 HydrolysisHydrolysis
 Inorganic compoundInorganic compound
 LipaseLipase
 LipidLipid
 PhospholipidPhospholipid
 micromoleculemicromolecule
 macromoleculemacromolecule
 MonomerMonomer
 MonosaccharideMonosaccharide
 Organic acidOrganic acid
 Disulfide linkageDisulfide linkage
• organic catalyst
• organic compound
• Peptide Bond
• polymer
• polypeptide
• Polysaccharide
• Fibrous protein
• Globular protein
• conjugated protein
• prosthetic group
• starch
• Aldose
• Ketose
• steroid
• disulfide bridge

Organic ChemistryOrganic Chemistry
 Organic moleculeOrganic molecule
 Has at least one carbon atomHas at least one carbon atom
 There are exceptions….do you know any? LetThere are exceptions….do you know any? Let’s’s
see…Is it Organic???????..........see…Is it Organic???????..........
 Most common elements in organic moleculesMost common elements in organic molecules
 CarbonCarbon
 HydrogenHydrogen
 OxygenOxygen
 NitrogenNitrogen

Carbon BondingCarbon Bonding
(versatile)(versatile)
 Can Form 4 bondsCan Form 4 bonds
 Forms strong covalent bondsForms strong covalent bonds
 Can bond in many waysCan bond in many ways
Straight chains, branched chains, ringsStraight chains, branched chains, rings
Can form single, double and triple bondsCan form single, double and triple bonds

BondingBonding
 Straight chainStraight chain
 propanepropane
 Branched chainBranched chain
 IsobutaneIsobutane
 RingRing
 CyclohexaneCyclohexane

Carbon Bonding (with itself)Carbon Bonding (with itself)
 Single bondsSingle bonds
 propanepropane
 Double bondsDouble bonds
 EtheneEthene
 Triple bondsTriple bonds
 acetyleneacetylene

HydrocarbonsHydrocarbons

Lysergic AcidLysergic Acid

NicotineNicotine

EstrogenEstrogen

Cholesterol & SteroidsCholesterol & Steroids

Glucose (ring form)Glucose (ring form)

Functional GroupsFunctional Groups
 Groups of atoms attached to organicGroups of atoms attached to organic
moleculesmolecules
 Most organic molecules have 2 or moreMost organic molecules have 2 or more
attachedattached
 All are polar & increases solubility in waterAll are polar & increases solubility in water
 6 major :6 major :

Hydroxyl GroupHydroxyl Group
 –– OHOH
Called alcoholsCalled alcohols
glycerolglycerol

Carbonyl GroupCarbonyl Group
 -C=O-C=O
AldehydesAldehydes
Carbonyl is at the end of a carbon chainCarbonyl is at the end of a carbon chain
Glucose & GalactoseGlucose & Galactose
KetonesKetones
Carbonyl is anywhereCarbonyl is anywhere butbut at the endat the end
FructoseFructose

Carboxyl GroupCarboxyl Group
 -COOH-COOH
An acidAn acid
 Tip:Tip:
Carbonyl + hydroxyl = carboxylCarbonyl + hydroxyl = carboxyl

Amino GroupAmino Group
 -NH-NH22
A baseA base++

Sulfhydryl GroupSulfhydryl Group
 -SH-SH

Phosphate GroupPhosphate Group
 POPO44
––

Large Carbon MoleculesLarge Carbon Molecules
 Known asKnown as macromoleculesmacromolecules
 Most biological moleculesMost biological molecules
 Many areMany are polymerspolymers consisting ofconsisting of manymany repeatingrepeating
subunits calledsubunits called monomersmonomers, simple molecules, simple molecules
 Monomers (one)Monomers (one)
 linked together through a process called alinked together through a process called a
condensation reactioncondensation reaction
 broken apart through a process called hydrolysisbroken apart through a process called hydrolysis
 Hydrolysis and condensation reactions areHydrolysis and condensation reactions are
opposites.opposites.

Condensation ReactionCondensation Reaction
 Monomers are linked together, i.e. polymersMonomers are linked together, i.e. polymers
are builtare built
 AA water molecule is releasedwater molecule is released (condensation)(condensation)
 EndergonicEndergonic processprocess

HydrolysisHydrolysis
 Monomers are split apart, i.e.Monomers are split apart, i.e. polymers arepolymers are
broken downbroken down
 A water molecule is used (dehydration)A water molecule is used (dehydration)
 AnAn exergonicexergonic processprocess

09/30/18 14:36 cottingham
Hydrolysis
• 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 water
molecule, breaking a bond
Figure 5.2B

Metabolic ReactionsMetabolic Reactions
 Metabolism – the “web” of all the enzymeMetabolism – the “web” of all the enzyme
catalyzed reactions in a cell or organismcatalyzed reactions in a cell or organism
Anabolism – synthesis of complex moleculesAnabolism – synthesis of complex molecules
from simpler moleculesfrom simpler molecules
Catabolism – breakdown of complexCatabolism – breakdown of complex
molecules into simpler moleculesmolecules into simpler molecules

The Chemical Basis For LifeThe Chemical Basis For Life
 The most common elements in livingThe most common elements in living
organisms are:organisms are:
CarbonCarbon
HydrogenHydrogen
OxygenOxygen
 A variety of other elements are needed byA variety of other elements are needed by
organisms includingorganisms including

NitrogenNitrogen

PhosphorusPhosphorus

CALCIUMCALCIUM

IRONIRON

SODIUMSODIUM

SULFURSULFUR

Important Concepts
Living organisms are uniquely composed
of giant (macro) molecules (polymers)
which are organic molecules.
BUT, we are all relatively close -----

Major molecular components of an E. coli
cell
Component Percentage weight
Water 70
Nucleic Acids 7
Protein 15
Carbohydrate 3
Lipid 2
Building Blocks
and intermediates 2
Organic Ions 1

Major molecular components of an E. coli
cell
Component Percentage weight
Water 70
Nucleic Acids 7
Protein 15
Carbohydrate 3
Lipid 2
Building Blocks
and intermediates 2
Organic Ions 1
Organic
Macromolecules
27%

Classes of Macromolecules in Cells
Carbohydrates
Lipids
Proteins
Nucleic Acids

Carbohydrates
Building blocks (monomers) are
simple sugars called
monosaccharides.
Function in energy storage and
cell structure

Carbohydrate CharacteristicsCarbohydrate Characteristics
C,H and O in about a 1:2:1 ratioC,H and O in about a 1:2:1 ratio
Often end inOften end in “ose”“ose”
Soluble in waterSoluble in water

Hydroxyl (OH)Hydroxyl (OH)

Aldehyde ( H-C=O) (ALDOSE)Aldehyde ( H-C=O) (ALDOSE)

Ketone ( -C=O ) (KETOSE)Ketone ( -C=O ) (KETOSE)
These are theThese are the “saccharides”“saccharides”

MonosaccharidesMonosaccharides

DisaccharidesDisaccharides

PolysaccharidesPolysaccharides

Mono = oneMono = one
Simple sugarsSimple sugars
Involves 2 functional groupsInvolves 2 functional groups

1 carbonyl and several hydroxyls1 carbonyl and several hydroxyls
Generally 3, 5 or 6 carbons longGenerally 3, 5 or 6 carbons long

Triose, pentose, hexoseTriose, pentose, hexose
All carbons have a hydroxyl attached except one whichAll carbons have a hydroxyl attached except one which
has a carbonyl attachedhas a carbonyl attached
Glucose (CGlucose (C66HH1212OO66))

Most common simple sugarMost common simple sugar
Glucose(Aldose) has 2 ISOMERS:

Fructose (Ketose)

Galactose (Aldose)

Aldoses vs. KetosesAldoses vs. Ketoses
 AldoseAldose
 Aldehyde sugarAldehyde sugar
 Carbonyl group isCarbonyl group is
on the end of theon the end of the
carbon chaincarbon chain
 ExampleExample
 GlucoseGlucose
 KetoseKetose
 Ketone sugarKetone sugar
 Carbonyl group isCarbonyl group is
anywhereanywhere butbut onon
the end of thethe end of the
carbon chaincarbon chain
 ExampleExample
 FructoseFructose

Chain Form vs. Ring FormChain Form vs. Ring Form
you have to know both!...for someyou have to know both!...for some
specific sugars!specific sugars!
 Chain FormChain Form
 Less commonLess common
 Ring FormRing Form
 CommonCommon
 Occurs in theOccurs in the
presence of waterpresence of water

The Three IsomersThe Three Isomers
Alpha- D-Glucose

The “2” GlucoseThe “2” Glucose
Alpha GlucoseAlpha Glucose
Beta GlucoseBeta Glucose

RIBOSERIBOSE

Alpha and Beta GlucoseAlpha and Beta Glucose

 Glucose + Glucose = MALTOSEGlucose + Glucose = MALTOSE
 In Grains: Hops, and BarleyIn Grains: Hops, and Barley
 Glucose + Fructose = SUCROSEGlucose + Fructose = SUCROSE
 TABLE SUGARTABLE SUGAR
 Glucose + Galactose = LACTOSEGlucose + Galactose = LACTOSE
 Dairy SugarDairy Sugar
ALL DISACCHARIDES ARE MADEALL DISACCHARIDES ARE MADE
BY…….BY…….

 Two molecules are joined together to form a largerTwo molecules are joined together to form a larger
molecule plus watermolecule plus water
 1 + 1 = 21 + 1 = 2
““Dehydration synthesis”Dehydration synthesis” - 1 + 1 = 2 + H- 1 + 1 = 2 + H22 OO
 ExEx::
monosaccharide + monosaccharide = disaccharide + watermonosaccharide + monosaccharide = disaccharide + water
CC66HH12120066 + C+ C66HH12120066 = C= C1212HH2222001111 + H+ H22OO

Disaccharides
 TheThe didisaccharide (saccharide (twotwo
monosaccharides linked) ismonosaccharides linked) is
the beginning of athe beginning of a
carbohydrate polymer.carbohydrate polymer.
 The bond formed is aThe bond formed is a
glycosidic bond.glycosidic bond.

MaltoseMaltose

SucroseSucrose

LactoseLactose

Polysaccharide
•A carbohydrate polymer withA carbohydrate polymer with more than twomore than two
monosaccharides is amonosaccharides is a polypolysaccharide.saccharide.

Polysaccharide: Starch
• primary energy storage compound in plants
• 1000’s of α glucose
• 2 types: amylose (unbranched) OR amylopectin (1,4
and 1,6 branched)

Figure 5.7b,c Starch and cellulose structuresFigure 5.7b,c Starch and cellulose structures

CelluloseCellulose
Polymer of glucosePolymer of glucose
β glucose (1-4)β glucose (1-4)
STRUCTURAL POLYSACCHARIDESTRUCTURAL POLYSACCHARIDE
cell wallcell wall

Fully permeable to waterFully permeable to water

Gives support – microfibrilGives support – microfibril

Dietary fiberDietary fiber

Figure 5.8 The arrangement of cellulose in plant cell wallsFigure 5.8 The arrangement of cellulose in plant cell walls

GlycogenGlycogen
animal storage polysaccharideanimal storage polysaccharide
made of glucosemade of glucose
structure has main chain and sidestructure has main chain and side
branchesbranches
MainMain α 1-4 glycosidic bondα 1-4 glycosidic bond
Side α 1-6 glycosidic bondSide α 1-6 glycosidic bond
stored in the liver and musclesstored in the liver and muscles

THE GLYCOGEN BOND!THE GLYCOGEN BOND!

Direct Biological Purposes ofDirect Biological Purposes of
CarbohydratesCarbohydrates
Energy StorageEnergy Storage

Immediate – SUGAR – a smallImmediate – SUGAR – a small
molecule (monomer), stored asmolecule (monomer), stored as
glycogen, starch,glycogen, starch,

Long Term – Starch – VERY largeLong Term – Starch – VERY large
molecule (polymer)molecule (polymer)
Chitin – not molecular, in shellsChitin – not molecular, in shells
Glucose (monosaccharide) –Glucose (monosaccharide) –
needed for cellular respirationneeded for cellular respiration

Lipid CharacteristicsLipid Characteristics
 Includes triglycerides, waxes, steroids,Includes triglycerides, waxes, steroids,
phospholipidsphospholipids
 Nonpolar (mostly)Nonpolar (mostly)
 Only of the four classes that is nonpolarOnly of the four classes that is nonpolar
 Only one of the four classes that is not aOnly one of the four classes that is not a
polymerpolymer
 Important in energy storage (fat)Important in energy storage (fat)
 Higher ratio of C & H:O than carbohydratesHigher ratio of C & H:O than carbohydrates
 Many C-H bonds (store a lot of energy)Many C-H bonds (store a lot of energy)
 Many lipids contain fatty acids:Many lipids contain fatty acids:
 Including phospholipids, triglycerides (fats) and waxesIncluding phospholipids, triglycerides (fats) and waxes

Major Biological Functions:
•Energy storage
•Part of cell membranes
•Insulation
•Protects organs
•Prevents drying out
• Buoyancy
• Bee – honeycombs (WAX)
• Many are composed of fatty acids and
glycerol >>>>>>>>>>>>>>>>>>>>>
LIPIDSLIPIDS

Fatty Acid
Glycerol
COOH –
Carboxyl group.
End of a fatty
Acid!

Fatty Acids andFatty Acids and
GlycerolGlycerolFatty AcidFatty Acid
 Consist of a long hydrocarbon chain with aConsist of a long hydrocarbon chain with a
carboxyl group at the end (acid)carboxyl group at the end (acid)
 May be saturated (Palmitic) or unsaturatedMay be saturated (Palmitic) or unsaturated
(Linoleic)(Linoleic)
 May also be Straight chained (Aliphatic) or ringedMay also be Straight chained (Aliphatic) or ringed
(Aromatic)(Aromatic)
GlycerolGlycerol
 An alcohol containing 3 carbons bonded to aAn alcohol containing 3 carbons bonded to a
hydroxyl grouphydroxyl group

Condensation Rxn.
• 3 fatty acids and 1 glycerol = 1 triglyceride
• 1 triglyceride releases 3 WATER molecules
• each fatty acid forms an ESTER BOND with glycerol

Triglyceride
Glycerol
3 Fatty acids
1
2
3

TriglycerideTriglyceride

Types of TriglyceridesTypes of Triglycerides
SATURATED – Palmitic AcidSATURATED – Palmitic Acid
 SingleSingle covalent bonds join carbon atoms.covalent bonds join carbon atoms.
 Has maximum number of hydrogen atoms in chainHas maximum number of hydrogen atoms in chain
 Solid at room temperature – butter, lardSolid at room temperature – butter, lard
UNSATURATED – Linoleic AcidUNSATURATED – Linoleic Acid
 double ordouble or tripletriple covalent bondscovalent bonds join one or more pair ofjoin one or more pair of
carbon atoms. (NOT H to C bonds)carbon atoms. (NOT H to C bonds)
 Less thanLess than the maximum number of hydrogen atomsthe maximum number of hydrogen atoms
 Tends to be an oily liquid at room temperature. = corn, olive,Tends to be an oily liquid at room temperature. = corn, olive,
sunflower….plant oilssunflower….plant oils

A CompleteA Complete
TriglycerideTriglyceride
unsaturated fat moleculeunsaturated fat molecule

Triglyderide…Triglyderide… aa different lookdifferent look
a Saturated Fata Saturated Fat

Unsaturated Fatty AcidsUnsaturated Fatty Acids
MonounsaturatedMonounsaturated
OneOne doubledouble or tripleor triple
bond.bond.
2 “empty” spaces where2 “empty” spaces where
Hydrogen could beHydrogen could be
 Same side orSame side or
opposite sidesopposite sides
PolyunsaturatedPolyunsaturated
At least 2At least 2 doubledouble or tripleor triple
bondsbonds
2 or more carbon have2 or more carbon have
“empty” spaces where“empty” spaces where
hydrogen could be.hydrogen could be.
Plant FatPlant Fat
Types – CIS & TRANSTypes – CIS & TRANS

Cis Unsaturated FatCis Unsaturated Fat
 Natural Fatty Acids. Good Fat.Natural Fatty Acids. Good Fat.
 Hydrogen on same side of 2x bondHydrogen on same side of 2x bond
 Omega 3Omega 3

Trans UnsaturatedTrans Unsaturated
 Hydrogen atoms are bonded to carbonHydrogen atoms are bonded to carbon
on opposite sides of double bondon opposite sides of double bond
 Can be produced artificially byCan be produced artificially by
hydrogenatinghydrogenating vegetable or fish oilvegetable or fish oil
 Solidifies liquid fatSolidifies liquid fat

HydrogenationHydrogenation

Fatty Acids and HealthFatty Acids and Health
 Saturated –Saturated –
 Animal Red Meats, organ meats, lunch meat,Animal Red Meats, organ meats, lunch meat,
desserts, fried anythingdesserts, fried anything
 PositivePositive correlationcorrelation between high saturated fatbetween high saturated fat
and C.H.D. deathand C.H.D. death
 Raise LDL CholesterolRaise LDL Cholesterol

- Trans- Trans
 Occurs naturally inOccurs naturally in
cattle products.cattle products.
 Can be madeCan be made
synthetically.synthetically.
 Positive correlationPositive correlation
between high TFAbetween high TFA
levels and CHDlevels and CHD
 Stays in bloodstreamStays in bloodstream
longer – arterial plaquelonger – arterial plaque
 Raises LDL, reducesRaises LDL, reduces
HDLHDL

-- CHOLESTEROLCHOLESTEROLHDL vs. LDL – produced in the liverHDL vs. LDL – produced in the liver
CHOLESTEROL travels in the blood attached to a proteinCHOLESTEROL travels in the blood attached to a protein
 Low Density Lipoprotein – transports cholesterol and triglyceridesLow Density Lipoprotein – transports cholesterol and triglycerides
from the liver around the body…tends to deposit on artery walls.from the liver around the body…tends to deposit on artery walls.
 ““Bad cholesterol”Bad cholesterol”
 High Density Lipoproteins - transports excess cholesterol andHigh Density Lipoproteins - transports excess cholesterol and
triglycerides from body to the liver.triglycerides from body to the liver.
 ““Good cholesterol”Good cholesterol”
 Triglycerides - another type of fat produced by excess calories,Triglycerides - another type of fat produced by excess calories,
alcohol, and sugar (very LDL)alcohol, and sugar (very LDL)

Body Mass IndexBody Mass Index
BMI =BMI = mass (kg)mass (kg)
height (m)height (m)22

BMI TableBMI Table
Below 18.5 - underweightBelow 18.5 - underweight
18.5 – 24.9 - normal18.5 – 24.9 - normal
25.0 – 29.9 – overweight25.0 – 29.9 – overweight
30.0 and above – OBESE!!!30.0 and above – OBESE!!!

Three
Important
Biological
Lipids(other than saturated and
unsaturated…TRIGLYCERIDES)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

WAXESWAXES
 LIPIDS THAT ARELIPIDS THAT ARE
FORMED BY THEFORMED BY THE
COMBINATION OFCOMBINATION OF
FATTY ACID ANDFATTY ACID AND
ANAN “ALCOHOL”“ALCOHOL”
OTHER THANOTHER THAN
GLYCEROL.GLYCEROL.

Phospholipids Form Cell Membranes
Phospholipid
Bilayer: Glycerol
+ 2 fatty acid +
phosphate.
•Phosphate head – polar,
hydrophilic.
• Fat tail – nonpolar,
hydrophobic.

Steroids—Steroids—
Have multiple rings in theirHave multiple rings in their
structures. (6,6,6,5)structures. (6,6,6,5)
Cholesterol – part of the
membrane of animal
cells.
Hormones – estrogen,
testosterone,
progesterone.
Vitamin D – bone
formation

SteroidsSteroids
 Characterized by carbon skeleton w/ 4Characterized by carbon skeleton w/ 4
fused C ringsfused C rings
 Different steroids vary by the functionalDifferent steroids vary by the functional
groups attached to ring ensemblegroups attached to ring ensemble

Lipid – other key factsLipid – other key facts
 Release about 2x the amount of energy as aRelease about 2x the amount of energy as a
carbohydrate.carbohydrate.
 The body can store unlimited amount ofThe body can store unlimited amount of
lipidlipid
 Animal insulation – lasts many monthsAnimal insulation – lasts many months
 Plants can store limited amount of fat.Plants can store limited amount of fat.
 Lipids can be stored in seeds – largeLipids can be stored in seeds – large
amount in small spaceamount in small space

Biochemistry2018

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