LECTURES
Synthetic Biology
(2010) Synthetic biology: applications come of age. Nature Reviews Genetics
(2014) Principles of genetic circuit design. Nature Methods
(2016) Engineering cellular metabolism. Cell
(2017) Engineering and in vivo applications of riboswitches. Annual Reveiw of Biochemistry
(2012) Synthetic biology and metabolic engineering. ACS Synthetic Biology
(2012) The future of metabolic engineering and synthetic biology: towards a systematic practice. Metabolic Engineering
(2013) Metabolic Engineering: Past and future. Annual Review of Chemical and Biomolecular Engineering
(2011) Probing Cellular Processes with Oligo-Mediated Recombination and Using the Knowledge Gained to Optimize Recombineering. Journal of Molecular Biology
(2012) Full-length RecE enhances linear-linear homologous recombination and facilitates direct cloning for bioprospecting Nature Biotechnology
(2013) Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs. Nature Biotechnology
(2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nature methods
(2016) Cre recombinase and other tyrosine recombinases. Chemical Reviews
(2015) Bacterial recombineering: genome engineering via phage-based homologous recombination. ACS Synthetic Biology
Biology for Engineers
Chapters 1&2
Synthetic Biology: https://www.youtube.com/watch?v=wo4BlOeydmI
MIT lecture for free energy: https://www.youtube.com/watch?v=OjhZYx1FbhI
Alphafold : https://www.youtube.com/watch?v=cw6_OP5An8shttps://www.youtube.com/watch?v=cw6_OP5An8s
Thermodynamics and the End of the Universe: https://www.youtube.com/watch?v=GOrWy_yNBvY
First and Second law of thermodynamics: https://www.youtube.com/watch?v=1kzsLGq3-14&list=PL9jo2wQj1WCNTJhgaXpsI1tzi0bemyl4j&index=5
Introduction to Carbohydrates: https://www.youtube.com/watch?v=OBP8ltttH5U
Fatty Acids: https://www.youtube.com/watch?v=eB9tgWB4YEw
Introduction to Proteins: https://www.youtube.com/watch?v=ZfsuDfui0oU&list=PL9jo2wQj1WCNTJhgaXpsI1tzi0bemyl4j&index=12
Introduction to Amino Acids: https://www.youtube.com/watch?v=LHNNOIMt5x0&list=PL9jo2wQj1WCNTJhgaXpsI1tzi0bemyl4j&index=13
Peptide Bond Formation: https://www.youtube.com/watch?v=4_2fA_W7snM&list=PL9jo2wQj1WCNTJhgaXpsI1tzi0bemyl4j&index=17
Introduction to Nucleic Acids: https://www.youtube.com/watch?v=1Wc4jTH2v_w&index=1&list=PL9jo2wQj1WCNG9mFuNBmJ1m7x1skBNKw-
Waston-Crick Model of DNA: https://www.youtube.com/watch?v=VLD9VLxN3PI&index=4&list=PL9jo2wQj1WCNG9mFuNBmJ1m7x1skBNKw-
Prokaryotes: https://www.youtube.com/watch?v=UHw6xCnv1UU&list=PL9jo2wQj1WCNsX8WaHPlU0wdozh2kHZXz
Eukaryotes: https://www.youtube.com/watch?v=LYvccVz5tew&list=PL9jo2wQj1WCNsX8WaHPlU0wdozh2kHZXz&index=2
Autotrophs and Heterotrophs :https://www.youtube.com/watch?v=FVfEThlRKq4&index=3&list=PL9jo2wQj1WCNsX8WaHPlU0wdozh2kHZXz
Team-HW1: Are bacteria more highly evolved than humans? (11 font, single space, within one or two page)
Chapter 3
Gibbs Free Energy and Spontaneity: https://www.youtube.com/watch?v=u_IQu7h6xfo&list=PL9jo2wQj1WCNypGCqFxAl8GBsxgAsEgis&index=3
Biological Buffer Systems: 1) http://www.aklectures.com/lecture/biological-buffer-systems
2) http://www.aklectures.com/lecture/biological-buffer-systems-part-ii
Chapter 4
Introduction to Proteins
http://www.aklectures.com/lecture/introduction-to-proteins
Introduction to Amino Acids
http://www.aklectures.com/lecture/introduction-to-amino-acids
Secondary Structure of Proteins
http://www.aklectures.com/lecture/secondary-structure-of-proteins
Chapter 5
Properties of Enzymes
http://www.aklectures.com/lecture/properties-of-enzymes
Enzymes’ Effect on Activation Energy and Free Energy
http://www.aklectures.com/lecture/enzymes-effect-on-activation-energy-and-free-energy
Gibbs Free Energy and Spontaneity
http://www.aklectures.com/lecture/gibbs-free-energy-and-spontaneity
Enzymes Stabilize Transition State
http://www.aklectures.com/lecture/enzymes-stabilize-transition-state
Properties of Active Sites, Lock-and Key Model and Induced-Fit Model
Effect of Enzymes on Rate Law and Rate Constant
http://www.aklectures.com/lecture/effect-of-enzymes-on-rate-law-and-rate-constant
Effect of Enzymes on Rate Law and Rate Constant (part II)
http://www.aklectures.com/lecture/effect-of-enzymes-on-rate-law-and-rate-constant-part-ii
Derivation of Michaelis-Menten Equation (i)
http://www.aklectures.com/lecture/derivation-of-michaelis-menten-equation
Derivation of Michaelis-Menten Equation (ii)
http://www.aklectures.com/lecture/derivation-of-michaelis-menten-equation-part-ii
Michaelis-Menten Equation
http://www.aklectures.com/lecture/michaelis-menten-equation
Michaelis Constant
http://www.aklectures.com/lecture/michaelis-constant
Maximal Velocity and Turnover Number of Enzymes
http://www.aklectures.com/lecture/maximal-velocity-and-turnover-number-of-enzymes
Catalytic Efficiency of Enzymes (kcat/Km) (i)
http://www.aklectures.com/lecture/catalytic-efficiency-of-enzymes-kcat-km
Catalytic Efficiency of Enzymes (kcat/Km) (ii)
http://www.aklectures.com/lecture/catalytic-efficiency-of-enzymes-kcat-km-part-ii
Replication
Introduction to DNA
http://www.aklectures.com/lecture/introduction-to-dna
DNA Replication: Helicase and Unwinding
http://www.aklectures.com/lecture/dna-replication-helicase-and-unwinding
DNA Replication: Leading and Langging Strand
http://www.aklectures.com/lecture/dna-replication-leading-and-lagging-strand
Summary of DNA Replication
http://www.aklectures.com/lecture/summary-of-dna-replication
Transcription
mRNA, rRNA and tRNA
http://www.aklectures.com/lecture/mrna-rrna-and-trna
RNA Transcription
http://www.aklectures.com/lecture/rna-transcription
Post-Transcriptional Modifications of mRNA
http://www.aklectures.com/lecture/post-transcriptional-modifications-of-mrna
The Genetic Code
http://www.aklectures.com/lecture/the-genetic-code
Translation
Translation: Ribosomes and Initiation
http://www.aklectures.com/lecture/translation-ribosomes-and-initiation
Translation: Elongation and Termination
http://www.aklectures.com/lecture/translation-elongation-and-termination
Signal Sequences and Signal-Recognition Particles
http://www.aklectures.com/lecture/signal-sequences-and-signal-recognition-particles
Post Translational Modifications
http://www.aklectures.com/lecture/post-translational-modifications