Biology 102 Lecture 4: Lecture 4: Biomolecules Biomoleculescf.linnbenton.edu/mathsci/bio/waitea/upload/Lecture_04_Biomolecul… · Biomolecules • 4 broad categories of 4 broad categories

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Biology 102Biology 102

Lecture 4: Lecture 4: BiomoleculesBiomolecules

•• Molecules that make up living thingsMolecules that make up living things

•• Based on carbonBased on carbon--carbon bondscarbon bonds

•• Contain other elements (H, O, N, P, S)Contain other elements (H, O, N, P, S)

•• Simplest organic molecules are the hydrocarbonsSimplest organic molecules are the hydrocarbons

•• Contain only C and HContain only C and H

•• NonNon--polarpolar

•• Soluble in water??Soluble in water??

BiomoleculesBiomolecules

•• BiomoleculesBiomolecules are are

modified hydrocarbonsmodified hydrocarbons

•• Contain functional Contain functional

groups that change groups that change

the chemical the chemical

properties of the properties of the

moleculemolecule


•• 4 broad categories of 4 broad categories of biomoleculesbiomolecules


•• All All biomoleculesbiomolecules are built in the same are built in the same fundamental way, regardless of complexityfundamental way, regardless of complexity


•• Make up less than 3% of human body weightMake up less than 3% of human body weight

•• Much more prevalent in plantsMuch more prevalent in plants

•• Made of exclusively C, H, OMade of exclusively C, H, O

•• Ratio of 1:2:1 or CHRatio of 1:2:1 or CH22O (= O (= carbocarbo--hydrate)hydrate)

CarbohydratesCarbohydrates

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•• Simple carbohydrates = sugarsSimple carbohydrates = sugars

•• MonosaccharidesMonosaccharides

•• In categories based on number of carbonsIn categories based on number of carbons

•• Number of carbons determines beginning of Number of carbons determines beginning of category namecategory name

•• Most sugar names end in “Most sugar names end in “--oseose””

CarbohydratesCarbohydrates MonosaccharidesMonosaccharides

Ex: glucose

Main source of cellular fuelhexose6

7 heptoseEx: sedoheptulose

Intermediate in lipid A biosynthesis

4 tetrose

Ex: D-erythrulose

Used in some self-tanners

Reacts with aa in skin and turns brown

5 pentoseEx: ribose

Building block for RNA

Number of carbon atoms Monosaccharide Category Biologically Relevant

3 trioseEx: glyceraldehyde

Important in cellular respiration

•• What is the chemical formula for a What is the chemical formula for a hexosehexosesugar?sugar?

QuestionQuestion

•• Dozens of Dozens of hexosehexose sugars existsugars exist

•• All have the same chemical formulaAll have the same chemical formula

•• Differ in the arrangement of atomsDiffer in the arrangement of atoms

•• Therefore also shape, enzymes, absorbabilityTherefore also shape, enzymes, absorbability

•• Termed Termed structural isomersstructural isomers

HexoseHexose SugarsSugars

•• Dozens of Dozens of hexosehexose sugars existsugars exist

•• All have the same chemical formulaAll have the same chemical formula

•• Differ in the arrangement of atomsDiffer in the arrangement of atoms

•• Therefore also shape, enzymes, absorbabilityTherefore also shape, enzymes, absorbability

•• Termed Termed structural isomersstructural isomers

HexoseHexose SugarsSugars HexoseHexose SugarsSugars

EnzymesEnzymes

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•• Can also exist in ring formCan also exist in ring form

•• Atoms are reorganized, but formula stays the sameAtoms are reorganized, but formula stays the same

•• ReversibleReversible

HexoseHexose SugarsSugars

•• Two Two monosaccharidesmonosaccharides bound togetherbound together

DisaccharidesDisaccharides

•• More efficient way to store energyMore efficient way to store energy

•• Commonly encountered in our dietsCommonly encountered in our diets

•• Require enzymatic digestion to be absorbedRequire enzymatic digestion to be absorbed

Sucrose Lactose MaltoseSucrose Lactose Maltose

DisaccharidesDisaccharides DisaccharidesDisaccharides

Lactose galactose and glucose 1-4 glycosidic

Maltose glucose and glucose 1-4 glycosidic

Disaccharide Monosaccharide Units Type of Bond

Sucrose glucose and fructose 1-2 glycosidic

Digested into Monomers by Enzyme

sucrase

lactase

maltase

•• Dehydration synthesis can be repeated Dehydration synthesis can be repeated indefinitelyindefinitely

•• Builds polysaccharidesBuilds polysaccharides

•• Can be very large!Can be very large!

•• Example: glycogenExample: glycogen

PolysaccharidesPolysaccharides PolysaccharidesPolysaccharides

Structure

glucose monomers

1-4α linkage with some

1-6α for branching

glucose monomers

1-4α linkage with more

1-6α for more branching

glucose monomers

1-4 β linkage with no

branching

Structural component of cell walls and

exoskeleton - analagous to keratinarthropods and fungiChitin

Glycogen animals and fungiVery efficient glucose storage in liver

and muscle

Cellulose plantsStructural component of cell walls

Indigestible to humans (fiber)

Polysaccharide Organism Function

Starch plantsEnergy source for plant

(and us when we eat it)

Digested into Monomers by Enzyme

Amylase

Glycogen phosphorylase

N/A

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•• Primary functions of carbohydratesPrimary functions of carbohydrates

1.1. Storage/source of energyStorage/source of energy

2.2. Structural supportStructural support

3.3. Component of coComponent of co--enzymesenzymes

4.4. Part of RNA/DNAPart of RNA/DNA

5.5. Biological recognitionBiological recognition

CarbohydratesCarbohydrates

GlycocalyxGlycocalyx

•• Artificial grouping of Artificial grouping of biomoleculesbiomolecules

•• Not based on common structureNot based on common structure

•• Based on common insolubility in waterBased on common insolubility in water

•• Polarity?Polarity?

•• Need special transport mechanismNeed special transport mechanism

•• Made up of C and H with very little oxygenMade up of C and H with very little oxygen

LipidsLipids

•• Includes:Includes:

•• FatsFats

•• WaxesWaxes

•• SterolsSterols

•• FatFat--soluble vitaminssoluble vitamins

LipidsLipids

•• Long, Long, unbranchedunbranched hydrocarbon chainshydrocarbon chains

•• Carboxyl group at one endCarboxyl group at one end

•• Polarity??Polarity??

•• Saturated or unsaturated Saturated or unsaturated –– with what?with what?

Fatty AcidsFatty Acids

•• Saturated or unsaturated with Saturated or unsaturated with hydrogenshydrogens

•• Carbon needs 4 bonds to be stableCarbon needs 4 bonds to be stable

•• Has 3 options to get themHas 3 options to get them

C C CC CC

Carbon SaturationCarbon Saturation

•• In a fatty acid, almost all carbons are bound to 2 In a fatty acid, almost all carbons are bound to 2 other carbonsother carbons

•• This builds the backbone of the fatty acid chainThis builds the backbone of the fatty acid chain

C C CC CC


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•• If all bonds between carbons are single, a If all bonds between carbons are single, a greater number of greater number of hydrogenshydrogens can bindcan bind

•• This is said to be a This is said to be a saturatedsaturated fatty acid fatty acid –– one one with the maximum number of with the maximum number of hydrogenshydrogens

C C CC CC


HH HH HH

HH HH HH

•• Every carbon has 4 single bondsEvery carbon has 4 single bonds

•• 2 with carbons2 with carbons

•• 2 with 2 with hydrogenshydrogens (except at the ends)(except at the ends)

Saturated Fatty AcidsSaturated Fatty Acids

•• Very stable Very stable –– not prone to ranciditynot prone to rancidity

•• Straight chains stack tightlyStraight chains stack tightly

•• Solid at room temperatureSolid at room temperature

•• Found in butter, animal fats, eggs, coconut oil, Found in butter, animal fats, eggs, coconut oil, palm oil palm oil –– and in your body!and in your body!

Saturated Fatty AcidsSaturated Fatty Acids

•• Carbons can also form double bondsCarbons can also form double bonds

•• Leaves less room for hydrogenLeaves less room for hydrogen

•• Said to be Said to be unsaturatedunsaturated

Unsaturated Fatty AcidsUnsaturated Fatty Acids

•• Double bonds prone to rancidityDouble bonds prone to rancidity

•• Bent chains do not stack as tightlyBent chains do not stack as tightly

•• Liquid at room temperatureLiquid at room temperature

•• Found in plant oilsFound in plant oils


•• One double bond = One double bond = monounsaturatedmonounsaturated

•• Olive, avocadoOlive, avocado

•• > 1 double bond = > 1 double bond = polyunsaturatedpolyunsaturated

•• Corn, soy, peanut, CanolaCorn, soy, peanut, Canola


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•• In the early 1900s, Proctor & Gamble cornered In the early 1900s, Proctor & Gamble cornered the market on cottonseed oilthe market on cottonseed oil

•• Electricity meant people weren’t using candles Electricity meant people weren’t using candles much anymore much anymore –– what to do with the oil?what to do with the oil?

An Unfortunate DiscoveryAn Unfortunate Discovery

•• Oil hydrogenation turns double bonds into single Oil hydrogenation turns double bonds into single bondsbonds

An Unfortunate DiscoveryAn Unfortunate Discovery

•• Don’t want to completely saturate oilDon’t want to completely saturate oil

•• Turns waxy and grossTurns waxy and gross

•• Instead only partially hydrogenate, which Instead only partially hydrogenate, which changes some of the double bonds from changes some of the double bonds from ciscis to to transtrans

An Unintended ConsequenceAn Unintended Consequence

•• Changes shape to something not found in natureChanges shape to something not found in nature

An Unintended ConsequenceAn Unintended Consequence

•• Changes the shapeChanges the shape

•• Fat behaves more like it’s saturatedFat behaves more like it’s saturated

An Unintended ConsequenceAn Unintended Consequence ShorteningShortening

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•• CheapCheap

•• Lend “buttery” quality to processed foodsLend “buttery” quality to processed foods

•• Used in crackers, cookies, pie crusts, French Used in crackers, cookies, pie crusts, French fries, fried chicken, even coffee creamerfries, fried chicken, even coffee creamer

•• Less prone to rancidity than vegetable oil, lard, Less prone to rancidity than vegetable oil, lard, or butteror butter

•• Extend shelf life of productsExtend shelf life of products

Trans Trans Fatty AcidsFatty Acids

•• Shape doesn’t occur in natureShape doesn’t occur in nature

•• No enzymes that break it down No enzymes that break it down –– in us, or in in us, or in bacteria!bacteria!

•• Solid at room temperature Solid at room temperature –– and at body and at body temperature!temperature!

•• Body doesn’t know how to deal with itBody doesn’t know how to deal with it

•• Highly inflammatory = immune responseHighly inflammatory = immune response

•• You’re probably eating more than you thinkYou’re probably eating more than you think

Trans Trans Fatty AcidsFatty Acids

Trans Trans Fat Free?? Don’t Buy It!!Fat Free?? Don’t Buy It!!

•• Shape does occur in natureShape does occur in nature

•• Prone to oxidationProne to oxidation

•• But at least your body knows what to do with it!But at least your body knows what to do with it!

CisCis Fatty AcidsFatty Acids

Cis fat

So Which Fat Is Healthiest?So Which Fat Is Healthiest?

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•• Form when fatty acids bind to glycerolForm when fatty acids bind to glycerol

•• Most common Most common dietarilydietarily = triglycerides= triglycerides

•• 3 fatty acids3 fatty acids

GlyceridesGlycerides

+ 3H2O

•• Very efficient longVery efficient long--term energy storageterm energy storage

•• Large molecules = high potential energyLarge molecules = high potential energy

•• Gram for gram more than twice the energy of Gram for gram more than twice the energy of carbohydratescarbohydrates

•• Fat deposits under skin and throughout body cut Fat deposits under skin and throughout body cut heat loss by 2/3heat loss by 2/3

•• Protects and cushions organsProtects and cushions organs

•• Virtually nonVirtually non--polar polar –– allows for more efficient allows for more efficient storagestorage

Triglycerides in the BodyTriglycerides in the Body

Problem: We have too much of it!Problem: We have too much of it!

•• Modified triglyceridesModified triglycerides

•• One fatty acid replaced One fatty acid replaced

with a phosphorus and with a phosphorus and

nitrogennitrogen--containing containing

functional groupfunctional group

PhospholipidsPhospholipids

•• Phosphorus group is polar = hydrophilicPhosphorus group is polar = hydrophilic

•• Fatty acids are nonFatty acids are non--polar = hydrophobicpolar = hydrophobic

•• Allows nonAllows non--polar molecules to associate with polar molecules to associate with waterwater

•• Extremely important in cell membrane structureExtremely important in cell membrane structure

•• More about them laterMore about them later

PhospholipidsPhospholipids•• Synthesized by all living organismsSynthesized by all living organisms

•• Humans make in liverHumans make in liver

•• Dietary cholesterol Dietary cholesterol esterifiedesterified and poorly and poorly absorbedabsorbed

•• High cholesterol usually due to metabolic High cholesterol usually due to metabolic disregulationdisregulation rather than dietary sourcesrather than dietary sources

•• Exception: oxidized cholesterolException: oxidized cholesterol

CholesterolCholesterol

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•• Important molecule!Important molecule!

•• Component of cell membranesComponent of cell membranes

•• 50% dry weight50% dry weight

•• Adds rigidityAdds rigidity

•• Needed for growth and developmentNeeded for growth and development

•• BreastmilkBreastmilk is extremely high in cholesterolis extremely high in cholesterol

•• Critical for myelin productionCritical for myelin production

•• Needed to make sterolsNeeded to make sterols

CholesterolCholesterol

•• Made in adrenalsMade in adrenals

•• FunctionsFunctions

•• Chemical communicationChemical communication

•• Calcium homeostasis (Calcium homeostasis (calcitrolcalcitrol))

•• Regulate sperm/egg development and sexual Regulate sperm/egg development and sexual functionfunction

Steroid HormonesSteroid Hormones

•• Male hormones, including testosterone, are also Male hormones, including testosterone, are also called anabolic steroidscalled anabolic steroids

Steroid HormonesSteroid Hormones

•• Critical for calcium absorptionCritical for calcium absorption

•• Ongoing research implicates it in multiple Ongoing research implicates it in multiple biological processesbiological processes

•• We lack the enzyme to make it from cholesterol!We lack the enzyme to make it from cholesterol!

•• Require sunlightRequire sunlight

Vitamin DVitamin D

1.1. Structural components of cell membranesStructural components of cell membranes

2.2. Energy reservesEnergy reserves

3.3. Insulation and protectionInsulation and protection

4.4. Vitamin D synthesis (calcium absorption)Vitamin D synthesis (calcium absorption)

5.5. Steroid hormonesSteroid hormones

•• Others we didn’t talk aboutOthers we didn’t talk about

•• Bile salts (lipid digestion)Bile salts (lipid digestion)

•• Eicosanoids (signaling molecules)Eicosanoids (signaling molecules)

Functions of LipidsFunctions of Lipids

•• Most varied of the Most varied of the biomoleculesbiomolecules

•• Make up more than half the dry weight of cellsMake up more than half the dry weight of cells

•• Categorized by functionCategorized by function

ProteinsProteins

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•• StorageStorage

•• Energy for embryo, young, other organismsEnergy for embryo, young, other organisms

Protein FunctionsProtein Functions

•• StructureStructure

•• Macroscopic examples: tendons, ligaments, Macroscopic examples: tendons, ligaments, hair, nails (collagen, keratin)hair, nails (collagen, keratin)

•• Cellular level examples: Cellular level examples: actinactin, , tubulintubulin


•• TransportTransport

•• Proteins that carry other molecules from one Proteins that carry other molecules from one place to anotherplace to another

•• Examples: hemoglobin, Examples: hemoglobin, kinesinskinesins


•• CatalysisCatalysis

•• Enzymes are proteinsEnzymes are proteins


•• DefenseDefense

•• Antibodies, Antibodies, interferonsinterferons produced in response produced in response to infectionto infection


•• Coordination and growth (signaling)Coordination and growth (signaling)

•• Hormones (e.g. insulin, growth hormone)Hormones (e.g. insulin, growth hormone)

•• Communication (receptors)Communication (receptors)


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•• BufferingBuffering

•• Proteins are both acids and bases at the same Proteins are both acids and bases at the same timetime


•• Protein building blocks= amino acidsProtein building blocks= amino acids

•• 20 amino acids 20 amino acids

•• Can be arranged to form an astounding variety Can be arranged to form an astounding variety of proteinsof proteins

•• Much the way only 26 letters make thousands Much the way only 26 letters make thousands of wordsof words

ProteinsProteins

•• Protein function depends on 4 up to levels of Protein function depends on 4 up to levels of structurestructure

•• Primary Primary –– number and order of amino acidsnumber and order of amino acids

•• Secondary Secondary –– local folding patternslocal folding patterns

•• Tertiary Tertiary –– overall 3D foldingoverall 3D folding

•• Quaternary Quaternary –– interaction of 2 or more fully interaction of 2 or more fully

assembled proteinsassembled proteins

Protein StructureProtein Structure

•• Primary structure depends on peptide bondsPrimary structure depends on peptide bonds

•• Very strong and stableVery strong and stable

•• Require a chemical change to breakRequire a chemical change to break

•• All other levels of structure depend on All other levels of structure depend on interactionsinteractions

•• Hydrogen bondsHydrogen bonds

•• Relatively weakRelatively weak

•• Can be broken by changes in temperature, Can be broken by changes in temperature, pHpH

•• Disulfide bondsDisulfide bonds


Example: HemoglobinExample: Hemoglobin Example: Sickle Cell AnemiaExample: Sickle Cell Anemia

Normal RBC Sickle RBCNormal RBC Sickle RBC

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•• Caused by defect in 1Caused by defect in 1°° structurestructure

•• Leads to defect in 4Leads to defect in 4°° structurestructure

Sickle Cell AnemiaSickle Cell Anemia

•• Biological activity of a protein highly dependent Biological activity of a protein highly dependent on shapeon shape

•• Changes in shape = Changes in shape = denaturationdenaturation

•• Protein shape is maintained by hydrogen bondsProtein shape is maintained by hydrogen bonds

•• Anything that alters hydrogen bonds can Anything that alters hydrogen bonds can denature a proteindenature a protein

•• Heat, pressure, pH, heavy metals, alcohol, Heat, pressure, pH, heavy metals, alcohol, UV lightUV light

•• PRIMARY STRUCTURE IS UNAFFECTED BY PRIMARY STRUCTURE IS UNAFFECTED BY DENATURATIONDENATURATION


•• Sometimes denaturation is reversible Sometimes denaturation is reversible (sometimes not)(sometimes not)

•• Denatured proteinDenatured protein

•• May fold inappropriatelyMay fold inappropriately

•• Sickle cell anemiaSickle cell anemia

•• May not be functionalMay not be functional

•• Cystic fibrosisCystic fibrosis

•• May disrupt other cellular functionsMay disrupt other cellular functions

•• PrionsPrions

DenaturationDenaturation

•• Primary functions of proteinsPrimary functions of proteins

1.1. StorageStorage

2.2. StructureStructure

3.3. TransportTransport

4.4. Catalysis (enzymes)Catalysis (enzymes)

5.5. DefenseDefense

6.6. SignalingSignaling

7.7. BufferingBuffering

ProteinsProteins

•• Two primary typesTwo primary types

•• Deoxyribonucleic acid (DNA)Deoxyribonucleic acid (DNA)

•• Determines inherited characteristicsDetermines inherited characteristics

•• Contains information for protein buildingContains information for protein building

•• Regulates all areas of cellular metabolismRegulates all areas of cellular metabolism

Nucleic AcidsNucleic Acids

•• Two primary typesTwo primary types

•• Ribonucleic acid (RNA)Ribonucleic acid (RNA)

•• 3 types work together to make proteins based 3 types work together to make proteins based on information in DNAon information in DNA


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•• Several functions in cellSeveral functions in cell

•• Energy transfer Energy transfer

•• ATP, NADH/NAD+ATP, NADH/NAD+

•• Information storageInformation storage

•• DNA stores all genetic, DNA stores all genetic,

protein synthesis informationprotein synthesis information

•• Information transferInformation transfer

•• RNA gets information from DNA, RNA gets information from DNA,

takes it to cytoplasmtakes it to cytoplasm


•• Several functions in cellSeveral functions in cell

•• Protein synthesisProtein synthesis

•• Coordinated activity of 3 RNA typesCoordinated activity of 3 RNA types

•• Cellular metabolism Cellular metabolism

and cell communicationand cell communication

•• NADH/NAD+NADH/NAD+

•• cAMPcAMP


•• Monomer = nucleotideMonomer = nucleotide

•• More complex than other monomersMore complex than other monomers

•• PhosphatePhosphate

•• Pentose sugar (ribose or Pentose sugar (ribose or deoxyribosedeoxyribose))

•• Nitrogenous base (1 of 5)Nitrogenous base (1 of 5)

•• Polymer = nucleic acidPolymer = nucleic acid

NucleotidesNucleotides

Adenine Adenine nucleotidenucleotide

•• DNA = A G C TDNA = A G C T

•• RNA = A G C URNA = A G C U

Nucleotide BasesNucleotide Bases

•• SingleSingle--stranded polynucleotidestranded polynucleotide

•• Phosphate and sugar alternate in a “backbone”Phosphate and sugar alternate in a “backbone”

•• Bases project out at right angleBases project out at right angle

Structure of RNAStructure of RNA

•• Two antiTwo anti--parallel polynucleotide strandsparallel polynucleotide strands

•• Complimentary baseComplimentary base--pairing with hydrogen bondspairing with hydrogen bonds

•• Twisted into a double helixTwisted into a double helix

Structure of DNAStructure of DNA

•• A LOT more A LOT more on this lateron this later

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•• Used to shuttle energy within the cellUsed to shuttle energy within the cell

•• Energy stored in covalent bondsEnergy stored in covalent bonds

•• Most universal energy carrier is ATPMost universal energy carrier is ATP

•• Adenosine Adenosine triphosphatetriphosphate

One More Use For NucleotidesOne More Use For Nucleotides

•• When bonds between the phosphates are When bonds between the phosphates are broken, energy is releasedbroken, energy is released

ATPATP

•• Not as universalNot as universal

•• 7X more energy7X more energy--rich than ATPrich than ATP

•• Carries energy as electronsCarries energy as electrons

NADNAD

Documents

Biology 102 Lecture 4: Lecture 4: Biomolecules Biomoleculescf.linnbenton.edu/mathsci/bio/waitea/upload/Lecture_04_Biomolecul… · Biomolecules • 4 broad categories of 4 broad categories