Mindmap

Genes

A Cuffe 2016 Englisch

Inhalt der Mindmap

Genes

Viruses
- Replicate - only in host cell Evolve - mutation/natural selection Only one kind of Nucleic Acid - Limited amount
- Structure
  - - Capsid
      - - Protein shell that encloses the viral genome Protects from:  - Physcial damage  - Chemical damage  - Enzymatic damage
    - Envelope
      - - Membrane derived from host cell - Only sometimes present (not all cases)
- Lifecycle
  - 1. Attachment (to host) 2. Penetration 3. Uncoating (of capsid) 4. Transcription/Translation 5. Genome replication 6. Assembly 7. Release (from host)
  - Replication
    - ssDNA
    - dsRNA
    - dsDNA
    - ssRNA
      - Retrovirus
        +RNA HIV
        Virus
        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
        Host
        Does transcription & translation
      - Positive Sense (+)
        RNA strand resembles mRNA
        Virus
        'Injects' +RNA & RNA dependent RNA Pol (RdRP) RdRP copies +RNA to produce -RNA
        Host
        Uses -RNA for more +RNA Translates RNA into proteins (for capsids)
      - Negative Sense (-)
        RNA strand resembles template RNA
        Virus
        'Injects' -RNA RNA Pol (RdRP)
        Host
        Makes +RNA from -RNA Replicates RNA  > -RNA for progeny virus  > +RNA for translation Translates RNA into proteins
  - Lysogenic Cycle
    - Phage remain dormant in a genome for an indefinite time before rejoining lytic cycle.
  - Lytic Cycle
    - Phages replicate. New viral particles are produced and released soon after infection, killing the host bacterium by lysis.
Eukaryotes
- Cancer
  - Loss of cell cycle control = cancer Cancer cells do not respond naturally to the body's control mechanisms.
  - Tumor Suppressor Genes
    - Inhibit cell divisionStop working can lead to cancer
    - p53
      - >50% human cancer patients have mutated p53 genep53 prevents cells with damaged DNA from replicating
  - Oncogenes
    - Genes that actively promote cell division.If not turned off at right times, can lead to cancer.
- DNA
  - Both strands of DNA can be either coding or template strands, depending on where the gene is. Interphase = dispersed in nucleus metaphase = super compacted 
  - - Chromatin
      - Compacted DNA wrapped around histones. Prokayotes don't have histones or chromatin
      - Histones
        Small positively charged proteins that associate with negatively changed DNA backbones. DNA wraps around histones
      - Chromosomes
        Unreplicated chromosome contains  one continuous DNA molecule wrapped around histones. Replicated chromosome consists of two sister chromatids connected by a centromere.
        Locus
        A gene's address on a chromosome.
      - Euchromatin
        - Relaxed - Transcribed
        Heterochromatin
        - Compact - Transcriptionly silent
    - Regulation
      - Regulation of gene expression can occur at: - Chromatin remodeling - Transcription - RNA processing - mRNA stability - Translation - Post-translation
      - Chromatin Remodeling
        Histones
        Histone structure can be modified. - Histone acetylation associated with active chromatin - Histone/DNA methylation = inactive genes
        Acetylation
        - Allows histone to relax hold on DNA - Makes DNA available for transcription
        Methylation
        - Compacts histones & DNA - No transcription
        Transcriptional Control
        TF => Protein => Binds to DNA
        Basal/Core Promoter
        - 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
        General TF
        - 'General transcription factor' - Binds to Promoter - Recruit RNA Pol & other proteins for transcription
        Enhancer
        - 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)
        Specific TF
        - Gene-specific transcription factors - Bind to enhancers- Control enhancer strength (Activators or Repressors)
        Hox Genes/TF
        - 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). 
        Homeotic Mutations
        Mutation in which one body part is replaced by another
        MADS Box Genes
        - Encode transcription factors required for proper flower development.
        Post-Transcriptional Control
        Gene Splicing
        - Different exons from the same gene can be spliced together to give rise to different mRNAs and proteins. - Increases diversity of proteins
        Exons
        - Exon=Exciting=Keep
        Introns
        - Intron=Intern=Doesn't get paid=Doesn't get translated
        mRNA Degradation
        mRNA stability associated with poly(A) tail length. Shortened tail may trigger enzymes to remove 5' cap. Without cap, nucleus enzymes degrade RNA.
        Translational Control
        Translational Repression
        Example: Ferritin
        - Stores excess iron and releases it when blood iron levels drop. - Production controlled by iron (Fe) levels by translational repression.
        IRE
        - Iron-Response element. - Stops translation when bound by active binding protein.
        IRE Binding Protein
        - Active => Binds to IRE => No translation - Inactive => bound to Fe => translation
        Post-Translational Gene Silencing
        miRNA
        - 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
        Dicer
        In cytoplasm, Dicer enzyme removes hairpin loop of miRNA and transfers it to AGO protein complex forming RISC.
        AGO
        - Argonaute protein complex - Degrades one strand of ds miRNA.
        RISC
        - RNA-induced silencing complex - Guided by sequence of complimentarity of its miRNA to targets (mRNA transcripts) which are either cleaved or translation inhibited.
      - Cell Differentiation
        Embryonic cell are provided with signals that indicate their location in the body.
        Signals
        Gene Expression
        Cytoplasmic Determinants
        Include proteins, RNA, organelles in cytoplasm of embryonic cell. Govern cell's gene expression & differentiation.
        Extrinsic
        Come from outside the cell. Membrane receptors detect substance & signal cascade begins that promotes or blocks gene transcription.
        Induction
        Differentiation trigger by extrinsic signals. Other cells with embryo produce inductive signals. Increase and/or decrease gene expression.
    - Structure
      - Promoter
        Coding Region
        Enhancer
Prokaryotes
- Very genetically diverse.
- Transcription
  - - Sigma
    - RNA Polymerase
- Operon
  - - Operator
      - Specific DNA sequence binds corresponding regulatory protein. Can 'turn on/off' genes by interfering with RNA Pol activity.
    - Promoter
      - Specific DNA sequence recognized by RNA polymerase. RNA polymerase binds to the promoter and transcription is initiated.
    - DNA
  - The Lac Operon
    - Catabolite Repression
      - Repression of the synthesis of catabolic enzymes in order to use a preferred energy source first
      - Negative Control
        Lactose+Repressor Binding
        Lactose must be present to prevent binding of the repressor to the operator
        Lactose Absences
        Regulatory Protein
        Turns off Operator
        Lactose Presence
        Regulatory Protein
        Bound to lactose isomer
        Operator stays on
      - Positive Control
        Cyclin AMP
        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
        CAP
        - 'Catabolite activator protein' - Regulatory protein- Binds to CAP binding site upstream of promoter with high enough levels.
        Activation
        Repression
  - The Trp Operon
    - - 'The Tryptophan Operon' - On by default - Tryptophan binds to repressor protein = Off - Repressor active only in presences of corerepressor (Tryptophan)
    - Trp Absence
    - Trp Presence
DNA Technology
- Cloning Vectors
  - Molecules used to capture, amplify and express foreign DNA. Uses Restriction Enzymes
  - Restriction Enzymes
    - 'Cuts' DNA backbone in specific spots on specific DNA recognision sequence depending on the enzyme  - Found in bacteria = defense mechanism against viral infection
    - 'Sticky' Ends
      - DNA ligase
        Is used to repair backbone and properly connect sticky ends
    - Blunt Ends
      - No overhang
    - Bacteria
      - Restriction enzymes = defense mechanism against viral infection. Protects own DNA with methylase
  - Plasmids
    - Prefer plasmids: - Small - Independent replication - strong promoter - numerous restriction enzyme recognition sites
- PCR
  - - Polymerase Chain Reaction - (The thing we did in our bitter gene prac)