COURSE SYLLABUS

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YEAR COURSE OFFERED:
2017
SEMESTER COURSE OFFERED:

Spring

DEPARTMENT:

Biology and Biochemistry

COURSE NUMBER:

4307

NAME OF COURSE:

Proteins

NAME OF INSTRUCTOR:

Dr. William R. Widger

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The information contained in this class syllabus is subject to change without

notice. Students are expected to be aware of any additional course policies
presented by the instructor during the course.
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Learning Objectives
1. Know the amino acids names and structures and individual chemistries including
modification.
2. Know how to detect amino acids and peptides including quantitation.
3. Understand and calculate Amino acid composition and sequencing (manual and by mass
spectrometry) of proteins.
4. Understand protein size and shape determination including ultracentrifugation.
5. Understand primary, secondary tertiary and quaternary protein structure.
6. Understand and evaluate methods of protein purification.
7. Understand posttranslational modifications and how they affect structure and function.
8. Understand the physical interactions that determine peptide and protein structure.
9. Understand how the physical properties of water dictate protein structure.
10. Understand protein conformational properties.
11. Have a general understanding of protein x-ray crystal structure determination.
12 Understand the chemistry of sequence analysis and homology evolution and Blosum scores
13. Know and understand protein domain motifs.
14. Understand the properties of protein-protein interactions.
15. Understand the interactions of proteins and small molecules and the control of enzyme
activity.
16. Know and understand allostery and cooperativity
17. Know enzyme kinetics both single and multiple substrate reactions.
18. Know mechanisms and chemistry of enzyme function.
19. Study individual proteins classes protein switches, multifunctional proteins, metaloproteins
and motor proteins.

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COURSE SYLLABUS
Major Assignments/Exams
There will be three exams (no cumulative final) a major Term project and 13 homework
assignments
Each exam, term paper and homework will count as 100 points each for a total of 500 points
Classes held in SEC 101, Monday and Wednesday 2:30 to 4:00

Required Reading Proteins structure and function David Whitford

John Wiley & Sons ISBN-13: 978-0471-49894-0 (P/B)

Date
1/18

Whitford#

SectionandTopic

Lecture#

1and2 IntroductiontoAminoacidsandproteins1.StructuresofAminoAcids
Homework:Homework#1proteinsequenceandpeptidebondDue1/25

1/23

ChemicalreactionsofAminoacidresidues
1.3.1Gly
1.3.2.Aliphaticresidues
1.3.3.Proline
1.3.4.SerThr
Aminoacidchemistrycontinued

1/25

1.3.5.AcidicResiduesAspandGlu

1.3.6.AmideresiduesAsnandGln
1.3.7.BasicresiduesLysandArg
1.3.8His
1.3.9AromaticresiduesPhe,TyrandTrp
1.3.10SulfurcontainingMetandCys
ReviewofdoublebeamspectrometerandBeerslaw

Homework:Homework#2spdbViewerandretrievingstructuresDue2/1
1/30

Physicalandchemicalpropertiesofproteins
Ninhydrin,Fluorescenttagging
Fluorescenceasabiochemicaltool
Biuret,Lowery,BCMandCoomassieG250
Sizedetermination

Gelfiltration
SDSPage
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COURSE SYLLABUS
Sedimentationandequilibriumultracentrifugation

2/1

Proteinsequencing

Sangermethod,Edmandegradation
ElectrosprayandTOFMassspectrometry
Homework:Homework#3Aminoacidcomposition.Due2/8
2/6

Solidstatechemicalpeptidesynthesis

2/8

ProteinPurification

1.Peptidediversity
2.IsolationofProteins
3.SolubilityofProteins
4.ChromatographicSeparations
Homework:Homework#4ProteinsequencealignmentBioeditDue2/15
2/15

Posttranslationalmodificationofpeptidechains

Proteolyticprocessing
Alterationofchaintermini
Glycosylation
Homework:Homework#5ProteinsequencingDue2/22
2/15

Posttranslationalmodificationcontinued
Lipidattachment
Sulfation
CarboxyGlu
Hydroxylation
Phosphorylation
ADPRibosylation
Unusualnonribosomalsynthesis

2/20

Exam1

2/22

PhysicalInteractionsthatDeterminethePropertiesofProteins
Noncovalentinteractions
Repulsions
Electrostaticinteractions
VanderWaalsinteractions
Hydrogenbonds
Homework:Homework6MassspectralanalysisDue3/1
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COURSE SYLLABUS
SelectionofTermPaperTopics
2/27

Chemicalpropertiesthatleadstoproteinstructure
Liquidswater
Solubility
Hydrophobiceffect
Hydrophobiceffectofaminoacids
Intermolecularinteractions

3/1

3/6

3/8

10
12

Conformationalpropertiesthatleadstoproteinstructure
RotationsintheCCbond
Polypeptidesasrandompolymers`
Ramachandranplots
StatisticalpropertiesofRandompolypeptides
FluorescenceEnergyTransfer
RatesofConformationalChange

10

Circulardichroismandopticalrotarydispersion(CD_ORD)
helix
sheet
Otherhelices
Turns
10
CircularDichrosim
HomeworkHomework#7HelicalwheeldiagramDue3/21

11

ProteinStructuredeterminationbyXRayDiffraction

Crystallizationofproteins
BasicprinciplesBraggslaw
Phasedetermination
Interpretationofelectrondensitymap
Homework:Homework#8XRayproblemsDue3/27
SpringBreak(BackgroundResearchonTermPaper)

3/133/19
3/20

SequencesimilarityscoresBlosumindexandBlast
Homework:Homework9BlossomscoresandcalculationsDue4/3

3/22

13

Proteinfoldingandmaturationkinetics
Folding
TertiaryStructures
Interiorsandexteriors
Membraneproteins

14

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COURSE SYLLABUS

3/27

ProteinMotifsanddomains
ProteinMotifs
AlphaandBetaDomains
Alpha/BetaandAlphaBetaandcrosslinkeddomains

15

3/29

10

Quaternarystructure
Intermolecularinterfaces
Geometry
Flexibilityofproteins
Homework:Homework#10BetasheetstudyMembranespanning.Due4/5
4/3

EXAM2

4/5

Proteininteractionwithsmallmolecules(ligandbinding) 16
Chemicalmethodsfordetection
EnergiesandDynamicsofbinding
BindingAffinities
Ratesofbinding
Conformationandbinding,ImmunoglobulinsandDNA
Metalionbindingoxygenbinding
Homework:Homework#11Membranespanning.Due4/12

4/10

4/12

4/17

Regulationofenzymeactivity:Interactionsbetweenbindingsites
Effectorligands
Conformationalchangeandallostery
SwitchesonNucleotidehydrolysis
GTPaseswitches:smallsignalingproteins

Enzymecatalysis
Singleandmultiplesubstrates
Inhibitors
Transitionstate
ProximityandGroundstatedestabilization
Stabilizationoftransitionstatescatalyticantibodies
Homework:Homework#12bisusbstratekineticsDue4/19
SimpleEnzymekinetics
Regularchemicalkinetics
Ratesofenzymereactions

17

18

19

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COURSE SYLLABUS
MichaelisMentenequationVmaxandKm
LinweaverBurkandEadieHofsteeplots
Inhibitorkinetics
EffectofpHonenzymekinetics

7
4/19

Multisubstratekinetics

20

4/24

Metaloproteins
MetalocatalystsPreventingoxidativedamage
Electrontransportproteins

21

4/26

5/1

Motorproteins
Myosineandkinesin
Hexamericmotors.Helicases,TerminationfactorRho
TERMprojectsdueAndlastdayofclassSpilloverandFinalreview
Monday5/8from2to5PM(finalsweek)EXAMIII

Thisisaworkingsyllabus,andissubjecttoupdateandmodificationwhichdependsontherate
instructionproceeds.Ifwegetofftrack,Iwillupdateandcorrectthis.Thethreeexamdatesare
setandthereisnochangingthem.

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