Genes

Annotations:

• Replicate - only in host cell Evolve - mutation/natural selection Only one kind of Nucleic Acid - Limited amount

1. Structure
   1. 1. Capsid

         Annotations:

         • - Protein shell that encloses the viral genome Protects from:  - Physcial damage  - Chemical damage  - Enzymatic damage
      2. Envelope

         Annotations:

         • - Membrane derived from host cell - Only sometimes present (not all cases)
2. Lifecycle

   Annotations:

   • 1. Attachment (to host) 2. Penetration 3. Uncoating (of capsid) 4. Transcription/Translation 5. Genome replication 6. Assembly 7. Release (from host)
   1. Replication
      1. ssDNA
      2. dsRNA
      3. dsDNA
      4. ssRNA
         1. Retrovirus
            1. +RNA HIV
               1. 1. Virus

                     Annotations:

                     • Provides:  > +RNA  > Reverse Transcriptase (uses +RNA to made DNA)  > Integrase (enzyme that enables genetic material to be integrated into host DNA) Makes ds DNA with host nucleotides & intergrates into host DNA
                  2. Host

                     Annotations:

                     • Does transcription & translation
         2. Positive Sense (+)

            Annotations:

            • RNA strand resembles mRNA
            1. 1. Virus

                  Annotations:

                  • 'Injects' +RNA & RNA dependent RNA Pol (RdRP) RdRP copies +RNA to produce -RNA
               2. Host

                  Annotations:

                  • Uses -RNA for more +RNA Translates RNA into proteins (for capsids)
         3. Negative Sense (-)

            Annotations:

            • RNA strand resembles template RNA
            1. Virus

               Annotations:

               • 'Injects' -RNA RNA Pol (RdRP)
            2. Host

               Annotations:

               • Makes +RNA from -RNA Replicates RNA  > -RNA for progeny virus  > +RNA for translation Translates RNA into proteins
   2. Lysogenic Cycle

      Annotations:

      • Phage remain dormant in a genome for an indefinite time before rejoining lytic cycle.
   3. Lytic Cycle

      Annotations:

      • Phages replicate. New viral particles are produced and released soon after infection, killing the host bacterium by lysis.

1. Cancer

   Annotations:

   • Loss of cell cycle control = cancer Cancer cells do not respond naturally to the body's control mechanisms.
   1. Tumor Suppressor Genes

      Annotations:

      • Inhibit cell divisionStop working can lead to cancer
      1. p53

         Annotations:

         • >50% human cancer patients have mutated p53 genep53 prevents cells with damaged DNA from replicating
   2. Oncogenes

      Annotations:

      • Genes that actively promote cell division.If not turned off at right times, can lead to cancer.
2. DNA

   Annotations:

   • Both strands of DNA can be either coding or template strands, depending on where the gene is. Interphase = dispersed in nucleus metaphase = super compacted 
   1. 1. Chromatin

         Annotations:

         • Compacted DNA wrapped around histones. Prokayotes don't have histones or chromatin
         1. Histones

            Annotations:

            • Small positively charged proteins that associate with negatively changed DNA backbones. DNA wraps around histones
         2. Chromosomes

            Annotations:

            • Unreplicated chromosome contains  one continuous DNA molecule wrapped around histones. Replicated chromosome consists of two sister chromatids connected by a centromere.
            1. Locus

               Annotations:

               • A gene's address on a chromosome.
         3. 1. Euchromatin

               Annotations:

               • - Relaxed - Transcribed
            2. Heterochromatin

               Annotations:

               • - Compact - Transcriptionly silent
      2. Regulation

         Annotations:

         • Regulation of gene expression can occur at: - Chromatin remodeling - Transcription - RNA processing - mRNA stability - Translation - Post-translation
         1. 1. Chromatin Remodeling
               1. Histones

                  Annotations:

                  • Histone structure can be modified. - Histone acetylation associated with active chromatin - Histone/DNA methylation = inactive genes
                  1. 1. Acetylation

                        Annotations:

                        • - Allows histone to relax hold on DNA - Makes DNA available for transcription
                     2. Methylation

                        Annotations:

                        • - Compacts histones & DNA - No transcription
            2. Transcriptional Control

               Annotations:

               • TF => Protein => Binds to DNA
               1. Basal/Core Promoter

                  Annotations:

                  • - Essential for transcription - Required for binding of General TF - Specify/Recognise transcription start site & recruit other proteins required for initial of transcription (e.g. RNA Pol) - Must directly preceide gene
                  1. General TF

                     Annotations:

                     • - 'General transcription factor' - Binds to Promoter - Recruit RNA Pol & other proteins for transcription
               2. Enhancer

                  Annotations:

                  • - Gene specific regions recognised & bound by Specific TF. - Provide high levels of cell type-specific gene expression. - Position does not matter. - Not always just 1 per gene (Can be shared/multiple)
                  1. Specific TF

                     Annotations:

                     • - Gene-specific transcription factors - Bind to enhancers- Control enhancer strength (Activators or Repressors)
               3. Hox Genes/TF

                  Annotations:

                  • - Conserved family of transcription factors called Homeobox genes. - Encode proteins with a Homeodomain (helix-turn-helix protein domain -specifically structured part of a protein-) - Expressed early in embryo development in animals. Specify head-to-tail development (necessary for proper expression of thousands of genes required to build body parts). 
                  1. Homeotic Mutations

                     Annotations:

                     • Mutation in which one body part is replaced by another
               4. MADS Box Genes

                  Annotations:

                  • - Encode transcription factors required for proper flower development.
            3. Post-Transcriptional Control
               1. Gene Splicing

                  Annotations:

                  • - Different exons from the same gene can be spliced together to give rise to different mRNAs and proteins. - Increases diversity of proteins
                  1. 1. Exons

                        Annotations:

                        • - Exon=Exciting=Keep
                     2. Introns

                        Annotations:

                        • - Intron=Intern=Doesn't get paid=Doesn't get translated
               2. mRNA Degradation

                  Annotations:

                  • mRNA stability associated with poly(A) tail length. Shortened tail may trigger enzymes to remove 5' cap. Without cap, nucleus enzymes degrade RNA.
            4. Translational Control
               1. Translational Repression
                  1. Example: Ferritin

                     Annotations:

                     • - Stores excess iron and releases it when blood iron levels drop. - Production controlled by iron (Fe) levels by translational repression.
                     1. 1. IRE

                           Annotations:

                           • - Iron-Response element. - Stops translation when bound by active binding protein.
                        2. IRE Binding Protein

                           Annotations:

                           • - Active => Binds to IRE => No translation - Inactive => bound to Fe => translation
            5. Post-Translational Gene Silencing
               1. miRNA

                  Annotations:

                  • - MicroRNA (Non=coding RNA) - Transcribed from genes in DNA. Processed into smaller looped RNA fragments. - Influence stability of mRNA or blocks translation - execute post-transcriptional gene silencing
                  1. Dicer

                     Annotations:

                     • In cytoplasm, Dicer enzyme removes hairpin loop of miRNA and transfers it to AGO protein complex forming RISC.
                  2. AGO

                     Annotations:

                     • - Argonaute protein complex - Degrades one strand of ds miRNA.
                  3. RISC

                     Annotations:

                     • - RNA-induced silencing complex - Guided by sequence of complimentarity of its miRNA to targets (mRNA transcripts) which are either cleaved or translation inhibited.
         2. Cell Differentiation

            Annotations:

            • Embryonic cell are provided with signals that indicate their location in the body.
            1. Signals
               1. Gene Expression
               2. Cytoplasmic Determinants

                  Annotations:

                  • Include proteins, RNA, organelles in cytoplasm of embryonic cell. Govern cell's gene expression & differentiation.
               3. Extrinsic

                  Annotations:

                  • Come from outside the cell. Membrane receptors detect substance & signal cascade begins that promotes or blocks gene transcription.
                  1. Induction

                     Annotations:

                     • Differentiation trigger by extrinsic signals. Other cells with embryo produce inductive signals. Increase and/or decrease gene expression.
      3. Structure
         1. 1. Promoter
            2. Coding Region
            3. Enhancer

Annotations:

• Very genetically diverse.

1. Transcription
   1. 1. Sigma
      2. RNA Polymerase
2. Operon
   1. 1. Operator

         Annotations:

         • Specific DNA sequence binds corresponding regulatory protein. Can 'turn on/off' genes by interfering with RNA Pol activity.
      2. Promoter

         Annotations:

         • Specific DNA sequence recognized by RNA polymerase. RNA polymerase binds to the promoter and transcription is initiated.
      3. DNA
   2. The Lac Operon
      1. Catabolite Repression

         Annotations:

         • Repression of the synthesis of catabolic enzymes in order to use a preferred energy source first
         1. Negative Control
            1. Lactose+Repressor Binding

               Annotations:

               • Lactose must be present to prevent binding of the repressor to the operator
               1. Lactose Absences
                  1. 1. Regulatory Protein
                        1. Turns off Operator
               2. Lactose Presence
                  1. 1. Regulatory Protein
                        1. Bound to lactose isomer
                           1. Operator stays on
         2. Positive Control
            1. Cyclin AMP

               Annotations:

               • The level of cyclin AMP must be high enough so that the catabolite activator proteins (CAP) binds to the CAP binding site upstream of the promoter
               2. CAP

                  Annotations:

                  • - 'Catabolite activator protein' - Regulatory protein- Binds to CAP binding site upstream of promoter with high enough levels.
            2. Activation
            3. Repression
   3. The Trp Operon

      Annotations:

      • - 'The Tryptophan Operon' - On by default - Tryptophan binds to repressor protein = Off - Repressor active only in presences of corerepressor (Tryptophan)
      1. Trp Absence
      2. Trp Presence

1. Cloning Vectors

   Annotations:

   • Molecules used to capture, amplify and express foreign DNA. Uses Restriction Enzymes
   1. Restriction Enzymes

      Annotations:

      • 'Cuts' DNA backbone in specific spots on specific DNA recognision sequence depending on the enzyme  - Found in bacteria = defense mechanism against viral infection
      1. 'Sticky' Ends
         1. 1. DNA ligase

               Annotations:

               • Is used to repair backbone and properly connect sticky ends
      2. Blunt Ends

         Annotations:

         • No overhang
      3. Bacteria

         Annotations:

         • Restriction enzymes = defense mechanism against viral infection. Protects own DNA with methylase
   2. Plasmids

      Annotations:

      • Prefer plasmids: - Small - Independent replication - strong promoter - numerous restriction enzyme recognition sites
2. PCR

   Annotations:

   • - Polymerase Chain Reaction - (The thing we did in our bitter gene prac)