Week 1 | 1.

12
- Green Revolution:
- 1950s-1960s: global hunger
- Application of genetics to improve agriculture
- Arti cial selection
- Ethical concerns of biotechnologies:
- Misuse of technologies
- Safety
- Privacy issues - informed consent
- Cost and accessibility - justice and equity
- Use of human embryos in research
- Modal Organisms:
- Drosophila, E. Coli, C. Elegans, Arabidopsis thaliana, Mus musculus, S. Cerevisae
- Genetics and Model Organisms:
- Short life cycles
- Large number of o spring
- Housed in the lab environment
- Simple genetics
- Comparable systems to other larger organisms
- Safe organisms
- Cost e cient
- Smaller sizes
- Used to understand human genetics

Week 2 | 1.17 History and Diversity in Science

Scienti c ndings timeline
Kary Mullis: Developed PCR
Nirenberg:
McClintock
Collins + Venter: Human genome project
Garrod: Biochemical phenotypes are carried on to next generations
Blackburn:
Stevens

= Fundamental Concepts in Genetics (refer to slides)

- Two basic types of cells: prokaryotic and eukaryotic
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 - Prokaryotes: Cell wall, Outer membrane
- Genome: single molecule(plasmids), circular, packaged in twisted loops by proteins
- Eukaryotes: Mitochondria, Nucleus, Nuclear Envelope, Nucleolus, ER, Microtubules,
Plastids, Golgi complex
- Genome: multiple molecules, linear, packaged in double helix by histones
- Shared by both: Chromosome, ribosome, plasma membrane
- A gene is a fundamental unit of heredity
- Structure of a gene:
- Promoter, RNA-coding region, Terminator
- A genome is replicated while a gene is transcribed
- The scale of synthesis in DNA replication is much larger than the scale of synthesis in
transcription
- Genes in multiple forms called alleles
- Genes confer phenotypes
- Genetic info is within RNA and DNA
- Genes are located on chromosomes
- Chromosomes separate in the processes of mitosis and meiosis in eukaryotes
- Genetic info is transferred from DNA to RNA to protein
- Eukaryotes:
- Unique sequence DNA: 25-30% of the genome (for polypeptides/mRNA genes)
- Moderately repetitive DNA: 30-45% of the genome (for tRNA, rRNA, small RNA genes)
- Mutations are permanent changes in genetic info that can be passed from cell to cell or from
parent to o spring
- Many traits are a ected by many factors
- Actions of other genes and their products
- Genotype (Genetic constitution)
- Environmental in uences
- Evolution is genetic change
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 Week 3 | 1.24
- Bacteria and Viruses:
- Types of viruses:
- Bacteriophages
- Plant viruses
- Animal viruses
- Common characteristics of viruses:
- A virion: a virus particle
- Small genome (RNA or DNA)
- Contains genes needed for entry and replication
- Protein shell encloses the nucleic acid genome (capsid/nucleocapsid - protection)
- Insertion of genome into host cell
- Replication of virus genome and production of new viral progeny (virions) using host cell

- Animal Viruses: Genome - DNA or RNA

- Coronavirus:
- RNA virus
- ssRNA (continuous genome molecule)
- Structure:
- Spikes, Nucleocapsid, Membrane, Envelope, ssRNA
- 1960s
- In uenza A virus:
- RNA virus
- 8 ssRNA strands (separate genome molecules)
- Structure:
- Nucleocapsid, membrane envelope, membrane proteins, 8 ssRNA
- 1930s
- HIV:
- RNA virus
- retrovirus: reverse transcriptase (the virus carries proteins as well - unique to HIV)
- Two layers of capsids
- Structure:
- Envelope proteins, Lipid membrane, major Capsid, RNA, Protease, Reverse
Transcriptase, Integrase
- 1980 and 1981
- Others: DNA viruses: Smallpox, Herpes Simplex, Adenovirus
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 - Bacteriophage: Genome - DNA or RNA
- No lipid membrane or membrane proteins in bacteriophages
- Head (capsid, RNA) + Tail sheath
- Lytic viruses:
- T4 and T2 viruses, MS2 RNA viruses
- Lysogenic Viruses:
- Lambda bacteriophage: DNA virus
- Plant viruses:
- Tobacco mosaic virus - 1890s
- A single long ssRNA strand coated with proteins (nucleocapsid) in the helical shape

- Viral Genome: Types of genes:

- SARS CoV-2:
- Genome: ssRNA, one molecule
- Papain-like protease, 3CL-protease, Replicase, Helicase, Endoriboneuclease, Spikes
- In uenza A:
- Each ssRNA strand produces one protein -> 8 proteins
- HIV
- Tobacco Mosaic Virus
- Common proteins coded by viral genome:
- Replication protein, Capsid protein, Membrane protein

- Virus life cycle:

- 1. Genome enters the host cell
- Bacteriophages:
- Attachment through virus-host recognition by the long contractile tail
- Release of viral genome into the host cell (capsid becomes empty and stays outside)
- Animal viruses:
- Entry - Attachment through binding to the host cell membrane receptors
- Endocytic route:
- Virus taken in a vesicle (both genome and capsid)
- SAR-CoV-2: Spike binds with ACE2 receptors
- Non-endocytic route
- Virus fused at the cell surface (only genome)
- In uenza A: endocytic route
- HIV: non-endocytic route
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 - Spike Env binds to CD4 membrane receptors on immune cells
- Plant viruses:
- Cell wall -> membrane -> cytoplasm
- Entry: both genome and nucleocapsids
- Preexisting injury on the host cell
- Punctures by other organisms
- Cell to cell tra cking through plasmodesmata
- 2. Genome is replicated
- 3. Viral proteins are translated
- 4. Proteins and virions are assembled
- 5. Virions are released from the cell
- Bacteriophages:
- Lytic cycle:
- Circularization of linear viral DNA once inserted into host cell
- Host DNA disintegrated by the viral proteins
- Viral DNA replicated and viruses released from the host cell through burst
- Lysogenic cycle:
- Circularization of linear viral DNA once inserted into host cell by the cohesive ends
- Integration into the host DNA
- Normal cell division -> daughters cells carry the viral genome
- Exposure to induction event can caused lysogenic cycle turn into lytic cycle
- Animal Virus:
- Coronavirus and In uenza A Virus
- Genetic material brought to the nucleus and translated into polypeptide using host
cell ribosomes
- Packaged into new viruses
- HIV/retrovirus:
- RNA -> cDNA -> nucleus -> replication
- Plant Virus:
- TMV: Disassembly of genome and capsids -> translation -> repcication -> cell to cell
tra cking
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 Week 4 | 1. 31
- Genetic Variants:
- Mutations: SARS-CoV2: mutations in genes encoding for spikes -> enhancing viral
infections
- Recombination: collection of ssRNA from di erent genomes of multiple viruses when
packaged and released
- Recombination of genomes of di erent multiple viruses
- Testing for Viruses:
- Antibody test:
- Sample collection: antibody binds sample antigen and linked to detector molecule
(labeled)
- Primary antibody (for virus testing): recognizes the viral proteins on the antigen
- Secondary antibody (for control) : recognizes the labels on the antigen
- PCR test:
- RT-qPCR: reverse transcription quantitative PCR
- RNA extracted from sample -> reverse transcriptase + DNA primers -> cDNA (copy/
complimentary DNA) ampli ed by primers
- cDNA - amplify through heat-resistant DNA polymerase -> more DNA + speci c DNA
primers and uorescent probes
- Detection and Quanti cation
- COVID-19 PCR: detects and ampli es the N gene
- One step: All material in one tube (RNA template, primers, reverse transcriptase, DNA
polymerase, dNTPs)
- Two step: 1st- RNA template, dNTPs, reverse transcriptase; 2nd- primers, DNA
polymerase, dNTPs
- mRNA vaccines:
- Vaccine includes key spike proteins mRNA -> enter cells -> spike protein produced -> B
cell produces neutralizing antibodies -> bind and block the real virus from binding to cell
receptors
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 Week 5 | 2.7
Regulation of Gene Expression:
- Types of genes:
- Protein coding genes
- Transcribed into mRNA
- RNA coding genes
- siRNA, snRNA, tRNA, etc
- Virus has only protein coding genes

- Gene Regulation and Phenotype Variation:

- King and Wilson: Changes in a relatively small number of regulatory sequences help
produce the large phenotypic di erences between humans and chimpanzees
- Anatomy of a gene:
- Downstream: relative to the transcriptional start site: the direction of transcription
- Upstream: opposite to the direction of transcription
- Template strand from Upstream to Downstream (3’ - 5’):
- Promoter, start site (speci c nucleotides), RNA-coding region, termination site (speci c
nucleotides), Terminator
- Promoter: transcription factors and RNA polymerase
- RNA-coding region: transcribed sequence
- 3’ - 5’: template strand -> RNA transcript is always complementary to it
- 5’ - 3’: non-template strand

- Gene expression in eukaryotes and prokaryotes:

- Prokaryotes:
- Transcriptional control
- Translational control
- Eukaryotes:
- Gene silencing:
- Histone modi cation
- DNA methylation
- Transcriptional control:
- RNA polymerase binding
- Post-transcriptional control:
- Slicing
- RNA processing control
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 - Nuclear transport control
- Translational control:
- Ribosome binding
- Protein modi cation control/ Post-translational control:
- Phosphorylation

- Transcriptional Regulation:
- Positive regulation of gene transcription:
- Activator: assists RNA polymerase binding, promotes transcription
- Negative regulation of gene transcription:
- Repressor: inhibits RNA polymerase binding, represses transcription
- Trans factors: gene activator/ repressor
- Binds to the cis element/response element on the promoter
- Prokaryote: polycistronic: entire mRNA transcribed
- Eukaryote: Each gene encodes for an individual mRNA
- Basal Transcriptional Apparatus at core promoter
- Core promoter sequence: next to the transcription start site
- TATA box (cis element)
- Assembles the basal transcriptional apparatus
- RNA polymerase + TFs
- Regulatory promoter sequence (containing cis elements) : upstream of the core
promoter
- Enhancer(bind activator proteins), Silencer(bind repressor proteins): cis elements
- Interacts with basal transcription apparatus through mediator
- Each promoter attracts a unique combination of transcription factor for their
combination of cis elements
- Enhancer: cis elements and trans factors
- Basal levels of expression: without the e ect of regulatory proteins
- Multiple Control Elements:
- Insulator sequences: in between two enhancers for two di erent genes, regulates
which enhancer can a ect which gene
- DNA-binding proteins/ Trans factors can be grouped into several types of structures
- Regulation of Transcriptional Stalling and Elongation:
- RNA polymerase starts reading and stalls/pauses at certain genes (repression or set up
for rapid reading)
- Regulatory factors a ect stalling and elongation of transcription
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 - Co-ordinated Gene Expression: (only in Eukaryotes)
- Combinatorial gene expression
- Involves response elements and associated trans factors
- Estrogen-responsive genes: hormone response pathway
- Inactive - chemical trigger binds to activator -> Active (high transcription)
- Promoters of Animal Viruses:
- Similar to eukaryote promoters

- Post-transcriptional control:
- Through sequence of RNA: alternative splicing or RNA editing
- Through concentration of RNA: RNA stability and transport
- P bodies are activated
- Alternative Splicing:
- Mechanism of intron splicing:
- 5’ splice site: 5’ consensus sequence (GU A/G GU) - U1 binding site
- Branch point - U2 binding site
- 3’ splice site: 3’ consensus sequence (CAG)
- Spliceosomes: proteins involved in the splicing process (snRNPs)
- Alternative Splicing: Intron and Exon may be spliced -> production of more alternate proteins
- Same pre-mRNA produces di erent proteins
- Human genome: 95% of multi-exotic genes alternative splices
- Virus RNAs undergo alternative splicing
- Post-transcriptional control: Manipulate RNA concentration
- Deadenylation-dependent mRNA decay
- Deadenylation -> enzymes take o the poly-A-tail
- Other enzymes attach to the RNA and degrade the RNA (both 3-5 and 5-3( rst decap)
directions)
- P-bodies: processing mRNA decay
- cluster of proteins needed in the degradation process of RNA
- 5-cap removal, shortening of poly-A-tail, degrading of 5 utr, coding sequence, and 3utr,
involves RNAse and P-bodies
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Week 6 | 2.14
- Post-transcriptional control: Manipulate RNA concentration
- Deadenylation-dependent mRNA decay
- Deadenylation -> enzymes take o the poly-A-tail
- Other enzymes attach to the RNA and degrade the RNA (both 3-5 and 5-3( rst decap)
directions)
- P-bodies: processing mRNA decay
- cluster of proteins needed in the degradation process of RNA
- 5-cap removal, shortening of poly-A-tail, degrading of 5 utr, coding sequence, and 3utr,
involves RNAse and P-bodies
- Translational Control: Manipulate protein concentration
- Initiation Factors Control (eIFs)
- Ribosomal subunit binding
- More initiation factors, more e cient ribosome binding, increased translation rate
- RNA interference (siRNA and miRNA)
- Sequence-speci c gene silencing mediated by small dsRNAs (siRNA and miRNA)
- Most post-transcriptional
- First hint of gene silencing:
- 1990: Richard Jorgensen
- Inserted a gene for increased expression, outcome was silenced phenotype
- Co-suppression: an extra copy of the gene silences the gene expression
- 1998: Andrew Fire, Craig Mello: dsRNA can silence genes with speci city
- siRNA processing and prevention of translation
- Targets double stranded RNA (made up of two RNA molecules )
- Dicer: processing enzyme, cuts dsRNA into single stranded small fragments
- RISC: RNA-Induced Silencing Complex, combines with small siRNA fragments
- RISC-siRNA complex cuts and causes mRNA degradation (siRNA is fully
complementary to mRNA)
- No mRNA for translation
- miRNA processing and prevention of translation
- Targets one RNA molecule with complementary region
- Dicer: processing enzyme, cuts dsRNA into single stranded small fragments
- RISC combines with small miRNA fragments
- miRNA sequence is not fully complementary to mRNA
- RISC-miRNA combines with the mRNA, Ribosomes cannot access mRNA
- No translation
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 - RNA interference and DNA methylation:
- siRNA-RITS complex: attracts DNA methylating enzyme to reduce transcription of the
gene
- Post-translational control: protein folding and modi cation:
- A ects concentration of protein, protein function, activation of a protein
- Chaperoning-mediated protein folding
- Ubiquitination- Addition of Ubiquitin protein to other proteins
- A large amount of ubiquitin: Attracts 26S proteasome and leads to protein degradation
- A moderate amount: Altered protein-protein interactions
- Activation of the p53 protein for cell cycle arrest:
- DNA damage: serine residues are phosphorylated
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