chapter 3 an introduction to organic...

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Chapter 3Chapter 3

An Introduction toAn Introduction toOrganic CompoundsOrganic Compounds

Lecture Lecture 3: Proteins3: Proteins

•• Most varied of the Most varied of the biomoleculesbiomolecules

•• Also called Also called polypeptidespolypeptides

•• 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

•• 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


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•• 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)


•• BufferingBuffering

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


•• Protein monomer = amino acidsProtein monomer = 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

ProteinsProteinsExam 3!Exam 3!

Final Exam!Final Exam!

•• General structureGeneral structure

•• αα--Carbon in centerCarbon in center

•• 4 single bonds with other atoms or groups4 single bonds with other atoms or groups

1.1. Hydrogen (H)Hydrogen (H)

2.2. Amine (NHAmine (NH22))

3.3. Carboxyl (COOH)Carboxyl (COOH)

4.4. Variable (R)Variable (R)

Amino AcidsAmino Acids

•• Numbers 1Numbers 1--3 are the same for all amino acids3 are the same for all amino acids

•• The R group is different for each amino acidThe R group is different for each amino acid

•• Significantly change the properties of the amino Significantly change the properties of the amino acidacid


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•• Two amino acids combine by dehydration Two amino acids combine by dehydration synthesis to form a synthesis to form a dipeptidedipeptide

•• Bond is a covalent bond called a peptide bondBond is a covalent bond called a peptide bond


•• The process is repeated to elongate the polymerThe process is repeated to elongate the polymer

•• First makes a First makes a didipeptidepeptide, then a , then a polypolypeptidepeptide


•• Protein function depends on 4 levels of structureProtein function depends on 4 levels of structure

•• 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

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

Normal RBC Sickle RBCNormal RBC Sickle RBC

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Example: Sickle Cell AnemiaExample: Sickle Cell Anemia

•• How do these interactions form?How do these interactions form?

•• Primary Primary –– covalent (peptide) bonds between covalent (peptide) bonds between

amino acidsamino acids

•• Secondary Secondary –– hydrogen bonds between R hydrogen bonds between R

groupsgroups

•• Tertiary and quaternary Tertiary and quaternary –– interactions interactions

between R groupsbetween R groups


•• All proteins have primary, secondary structureAll proteins have primary, secondary structure

•• Most have tertiary structureMost have tertiary structure

•• Polar R groups move outPolar R groups move out

•• NonNon--polar R groups move inpolar R groups move in

•• Typically form spherical shape Typically form spherical shape –– referred to referred to as “globular”as “globular”

•• Soluble in waterSoluble in water


•• Most proteins do not have quaternary structureMost proteins do not have quaternary structure

•• Fibrous proteins have 1Fibrous proteins have 1°°, 2, 2°°, and 4, and 4°°, but not 3, but not 3°°

•• Water insolubleWater insoluble

•• Examples: collagen, keratinExamples: collagen, keratin


•• Caused by defect in Caused by defect in 11°° structurestructure

•• LLeads to defect in eads to defect in 44°° structurestructure

Sickle Cell AnemiaSickle Cell Anemia

•• Biological activity of a protein highly dependent Biological activity of a protein highly dependent on on shapeshape

•• 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


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•• How does food preservation exploit How does food preservation exploit denaturation?denaturation?

•• Blanching, pickling, cheeseBlanching, pickling, cheese--making, acid, making, acid, pressurepressure--canning, pasteurizingcanning, pasteurizing

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 May not be not be functionalfunctional

•• Cystic fibrosisCystic fibrosis

•• May disrupt other cellular functionsMay disrupt other cellular functions

•• PrionsPrions

DenaturationDenaturation

•• Biological catalystBiological catalyst

•• Binds to substrate by active siteBinds to substrate by active site

•• Product(s) made and released = reusableProduct(s) made and released = reusable

•• Lowers activation energy but provides no energyLowers activation energy but provides no energy

•• Speeds up reactionSpeeds up reaction

•• May require a coMay require a co--factor to bring active site to factor to bring active site to final form (vitamin, mineral)final form (vitamin, mineral)

EnzymesEnzymes

•• Having cells that differ in appearance and Having cells that differ in appearance and functionfunction

•• Specialization Specialization –– perform very few tasks, but perform very few tasks, but do them welldo them well

•• Highly dependent on proteins and enzymesHighly dependent on proteins and enzymes

•• Major advantage of being Major advantage of being multicellularmulticellular

Cell DifferentiationCell Differentiation

•• Cell can micromanage its function by controlling Cell can micromanage its function by controlling rate of enzyme functionrate of enzyme function

•• Environmental conditionsEnvironmental conditions

•• TemperatureTemperature

Enzyme RegulationEnzyme Regulation

•• Cell can micromanage its function by controlling Cell can micromanage its function by controlling rate of enzyme functionrate of enzyme function

•• Environmental conditionsEnvironmental conditions

•• pH pH


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•• Cellular influencesCellular influences

•• Substrate concentrationSubstrate concentration



•• Enzyme concentrationEnzyme concentration



•• Competitive inhibitionCompetitive inhibition



•• Competitive inhibitionCompetitive inhibition



•• Enzyme inactivation: nonEnzyme inactivation: non--competitive competitive inhibitioninhibition



•• Enzyme inactivation: nonEnzyme inactivation: non--competitive competitive inhibitioninhibition


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•• Enzyme inactivation: coEnzyme inactivation: co--factorsfactors


chapter 3 an introduction to organic...

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