{"id":63,"date":"2018-11-09T15:53:04","date_gmt":"2018-11-09T15:53:04","guid":{"rendered":"http:\/\/sites.williams.edu\/lkaplan\/?page_id=63"},"modified":"2018-11-15T19:42:46","modified_gmt":"2018-11-15T19:42:46","slug":"chem-321-syllabus","status":"publish","type":"page","link":"https:\/\/sites.williams.edu\/lkaplan\/about\/courses\/chem-321-syllabus\/","title":{"rendered":"CHEM-321 Syllabus"},"content":{"rendered":"

Chemistry 321; Biology 321; BIMO 321<\/span><\/b><\/p>\n

Biochemistry I:\u00a0<\/span><\/b>Structure and Function of Biological Molecules<\/span><\/b><\/p>\n

SYLLABUS<\/span><\/b><\/p>\n

Assignments for the lecture material are in the text generally called \u201cLehninger\u201d by Nelson and Cox,\u00a0Principles of Biochemistry<\/em>, 6th edition, Freeman, New York, 2013<\/p>\n

I.\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0The Foundations of Biochemistry<\/strong>\u00a0(chapter 1)
\nCellular foundations
\nChemical foundations
\nGenetic foundations
\nEvolutionary foundations<\/p>\n

II.\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0Water, The Biological Solvent<\/strong>\u00a0(chapter 2)
\nStructure of water
\nInteractions in aqueous solutions
\nIonization of water, pH, and pK
\nAcids, bases, buffers, and the Henderson-Hasselbalch equation<\/p>\n

III.\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0Bioenergetics<\/strong>
\nPhysical foundations of biochemistry (chapter 1, pp. 20-28)
\nBioenergetics and thermodynamics (chapter 13, pp. 505-517)<\/p>\n

IV.\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0Amino Acids, Peptides, and Proteins<\/strong>\u00a0(chapter 3)
\nAmino acid structures
\nAcidic and basic properties
\nStereochemistry of amino acids
\nReactions of the amino acid functional groups<\/p>\n

Protein function – structural proteins; enzymes; transport and storage; muscle contraction and motility;immunoproteins; regulatory and receptor proteins
\nProtein purification
\nProteins can be purified and characterized by using:
\nSolubility
\nChromatography
\nElectrophoresis
\nUltracentrifugation
\nSpecific interactions
\nMass spectrometry
\nAmino acid composition\/sequence of proteins
\nProtein Evolution<\/p>\n

V.\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0Proteins – Three-Dimensional Structure\u00a0<\/strong>(chapter 4)
\nThe nature of the peptide bond
\nSecondary structure – a-helix, b-pleated sheet, and b-bends
\nAnalysis and prediction of secondary structure
\nSupersecondary structures
\nTertiary structure and the presence of motifs and domains
\nSubunit interaction and quaternary structure
\nForces that determine protein conformation
\nProtein folding and stability<\/p>\n

VI.\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0Protein Conformation, Dynamics and Function\u00a0<\/strong>(chapter 5, pp. 158-178)
\nMyoglobin and Hemoglobin
\nStructure
\nMechanism of oxygen binding and transport
\nLigand binding
\nFactors that influence oxygen binding
\nImmunoglobulins
\nStructure and function of antibodies
\nAntigen-antibody binding<\/p>\n

VII.\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0Enzymes<\/strong>\u00a0\u2013 Kinetics and Catalysis<\/strong>\u00a0(chapter 6)
\nEnzyme specificity\/cofactors and coenzymes
\nMechanism of action – acid-base catalysis; covalent catalysis; metal ion catalysis; electrostatic catalysis; catalysis through proximity and orientation effects; and\u00a0 catalysis by preferential transition state binding
\nActive sites
\nThe mechanism of specific enzymes
\nSerine proteases – chymotrypsin, trypsin, and elastase
\nLysozyme
\nDigestive enzymes and coagulation factors
\nChemical kinetics
\nEnzyme kinetics
\nMichaelis-Menten kinetic analysis – equilibrium
\nBriggs-Haldane kinetic analysis – steady state
\nEnzyme inhibition
\nIrreversible
\nCompetitive
\nNoncompetitive
\nUncompetitive
\nMultisubstrate enzyme kinetics
\nRegulation of Enzyme Activity
\nAllosteric regulation
\nReversible covalent modification
\nEnzyme stimulation and inhibition by control proteins<\/p>\n

VIII.\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0Nucleic Acids<\/strong>\u00a0(chapter 8 and 24)
\nNucleotide – structure and function
\nBasic nucleic acid composition and structure
\nNucleic acid sequencing
\nRecombinant DNA technology
\nDNA
\nDNA helix
\nForces stabilizing nucleic acid structures
\nRNA
\nStructure
\nFractionation and characterization of nucleic acids
\nNucleic acid-protein interactions
\nDNA supercoiling and topoisomerase
\nHigher orders of nucleic acid structure<\/p>\n

IX.\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0DNA Based Information Technologies<\/strong>\u00a0(chapter 9)
\nDNA Cloning
\nFrom Genes to Genomes
\nFrom Genomes to Proteomes<\/p>\n

X.\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0DNA Replication, Repair, and Recombination\u00a0<\/strong>(chapter 25)
\nReplication
\nMechanism of action of DNA polymerase
\nRepair
\nDirect repair
\nExcision repair
\nSOS response and recombination repair
\nRecombination<\/p>\n

XI.\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0The Flow of Genetic Information<\/strong>\u00a0(chapter 26 and 27)
\nTranscription (chapter 26)
\nMechanism of action of RNA polymerase
\nPosttranscriptional processing of RNA
\nSelf-splicing RNA<\/p>\n

Translation (chapter 27)
\nThe genetic code
\nTransfer RNA
\nRibosome
\nPolypeptide synthesis<\/p>\n

See the\u00a0Course Description<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"

Chemistry 321; Biology 321; BIMO 321 Biochemistry I:\u00a0Structure and Function of Biological Molecules SYLLABUS Assignments for the lecture material are in the text generally called \u201cLehninger\u201d by Nelson and Cox,\u00a0Principles of Biochemistry, 6th edition, Freeman, New York, 2013 I.\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0The Foundations … Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":1455,"featured_media":0,"parent":46,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-63","page","type-page","status-publish","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/sites.williams.edu\/lkaplan\/wp-json\/wp\/v2\/pages\/63","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sites.williams.edu\/lkaplan\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.williams.edu\/lkaplan\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.williams.edu\/lkaplan\/wp-json\/wp\/v2\/users\/1455"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.williams.edu\/lkaplan\/wp-json\/wp\/v2\/comments?post=63"}],"version-history":[{"count":7,"href":"https:\/\/sites.williams.edu\/lkaplan\/wp-json\/wp\/v2\/pages\/63\/revisions"}],"predecessor-version":[{"id":115,"href":"https:\/\/sites.williams.edu\/lkaplan\/wp-json\/wp\/v2\/pages\/63\/revisions\/115"}],"up":[{"embeddable":true,"href":"https:\/\/sites.williams.edu\/lkaplan\/wp-json\/wp\/v2\/pages\/46"}],"wp:attachment":[{"href":"https:\/\/sites.williams.edu\/lkaplan\/wp-json\/wp\/v2\/media?parent=63"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}