Genes

A Cuffe
Mind Map by A Cuffe, updated more than 1 year ago
A Cuffe
Created by A Cuffe almost 4 years ago
10
1

Description

Summary of the Genes section of BIOL1020
Tags

Resource summary

Genes
1 Viruses

Annotations:

  • Replicate - only in host cell Evolve - mutation/natural selection Only one kind of Nucleic Acid - Limited amount
1.1 Structure
1.1.1
1.1.1.1 Capsid

Annotations:

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

Annotations:

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

Annotations:

  • 1. Attachment (to host) 2. Penetration 3. Uncoating (of capsid) 4. Transcription/Translation 5. Genome replication 6. Assembly 7. Release (from host)
1.2.1 Replication
1.2.1.1 ssDNA
1.2.1.2 dsRNA
1.2.1.3 dsDNA
1.2.1.4 ssRNA
1.2.1.4.1 Retrovirus
1.2.1.4.1.1 +RNA HIV
1.2.1.4.1.1.1
1.2.1.4.1.1.1.1 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
1.2.1.4.1.1.1.2 Host

Annotations:

  • Does transcription & translation
1.2.1.4.2 Positive Sense (+)

Annotations:

  • RNA strand resembles mRNA
1.2.1.4.2.1
1.2.1.4.2.1.1 Virus

Annotations:

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

Annotations:

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

Annotations:

  • RNA strand resembles template RNA
1.2.1.4.3.1 Virus

Annotations:

  • 'Injects' -RNA RNA Pol (RdRP)
1.2.1.4.3.2 Host

Annotations:

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

Annotations:

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

Annotations:

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

Annotations:

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

Annotations:

  • Inhibit cell divisionStop working can lead to cancer
2.1.1.1 p53

Annotations:

  • >50% human cancer patients have mutated p53 genep53 prevents cells with damaged DNA from replicating
2.1.1.1.1
2.1.1.1.2
2.1.2 Oncogenes

Annotations:

  • Genes that actively promote cell division.If not turned off at right times, can lead to cancer.
2.2 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 
2.2.1
2.2.1.1 Chromatin

Annotations:

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

Annotations:

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

Annotations:

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

Annotations:

  • A gene's address on a chromosome.
2.2.1.1.3
2.2.1.1.3.1 Euchromatin

Annotations:

  • - Relaxed - Transcribed
2.2.1.1.3.2 Heterochromatin

Annotations:

  • - Compact - Transcriptionly silent
2.2.1.2 Regulation

Annotations:

  • Regulation of gene expression can occur at: - Chromatin remodeling - Transcription - RNA processing - mRNA stability - Translation - Post-translation
2.2.1.2.1
2.2.1.2.1.1 Chromatin Remodeling
2.2.1.2.1.1.1 Histones

Annotations:

  • Histone structure can be modified. - Histone acetylation associated with active chromatin - Histone/DNA methylation = inactive genes
2.2.1.2.1.1.1.1
2.2.1.2.1.1.1.1.1 Acetylation

Annotations:

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

Annotations:

  • - Compacts histones & DNA - No transcription
2.2.1.2.1.2 Transcriptional Control

Annotations:

  • TF => Protein => Binds to DNA
2.2.1.2.1.2.1 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
2.2.1.2.1.2.1.1 General TF

Annotations:

  • - 'General transcription factor' - Binds to Promoter - Recruit RNA Pol & other proteins for transcription
2.2.1.2.1.2.2 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)
2.2.1.2.1.2.2.1 Specific TF

Annotations:

  • - Gene-specific transcription factors - Bind to enhancers- Control enhancer strength (Activators or Repressors)
2.2.1.2.1.2.2.1.1
2.2.1.2.1.2.2.1.2
2.2.1.2.1.2.3 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). 
2.2.1.2.1.2.3.1 Homeotic Mutations

Annotations:

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

Annotations:

  • - Encode transcription factors required for proper flower development.
2.2.1.2.1.3 Post-Transcriptional Control
2.2.1.2.1.3.1 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
2.2.1.2.1.3.1.1
2.2.1.2.1.3.1.1.1 Exons

Annotations:

  • - Exon=Exciting=Keep
2.2.1.2.1.3.1.1.2 Introns

Annotations:

  • - Intron=Intern=Doesn't get paid=Doesn't get translated
2.2.1.2.1.3.2 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.
2.2.1.2.1.4 Translational Control
2.2.1.2.1.4.1 Translational Repression
2.2.1.2.1.4.1.1 Example: Ferritin

Annotations:

  • - Stores excess iron and releases it when blood iron levels drop. - Production controlled by iron (Fe) levels by translational repression.
2.2.1.2.1.4.1.1.1
2.2.1.2.1.4.1.1.1.1 IRE

Annotations:

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

Annotations:

  • - Active => Binds to IRE => No translation - Inactive => bound to Fe => translation
2.2.1.2.1.5 Post-Translational Gene Silencing
2.2.1.2.1.5.1 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
2.2.1.2.1.5.1.1 Dicer

Annotations:

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

Annotations:

  • - Argonaute protein complex - Degrades one strand of ds miRNA.
2.2.1.2.1.5.1.3 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.
2.2.1.2.2 Cell Differentiation

Annotations:

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

Annotations:

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

Annotations:

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

Annotations:

  • Differentiation trigger by extrinsic signals. Other cells with embryo produce inductive signals. Increase and/or decrease gene expression.
2.2.1.3 Structure
2.2.1.3.1
2.2.1.3.1.1 Promoter
2.2.1.3.1.2 Coding Region
2.2.1.3.1.3 Enhancer
3 Prokaryotes

Annotations:

  • Very genetically diverse.
3.1 Transcription
3.1.1
3.1.1.1 Sigma
3.1.1.2 RNA Polymerase
3.2 Operon
3.2.1
3.2.1.1 Operator

Annotations:

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

Annotations:

  • Specific DNA sequence recognized by RNA polymerase. RNA polymerase binds to the promoter and transcription is initiated.
3.2.1.3 DNA
3.2.2 The Lac Operon
3.2.2.1 Catabolite Repression

Annotations:

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

Annotations:

  • Lactose must be present to prevent binding of the repressor to the operator
3.2.2.1.1.1.1 Lactose Absences
3.2.2.1.1.1.1.1
3.2.2.1.1.1.1.1.1 Regulatory Protein
3.2.2.1.1.1.1.1.1.1 Turns off Operator
3.2.2.1.1.1.2 Lactose Presence
3.2.2.1.1.1.2.1
3.2.2.1.1.1.2.1.1 Regulatory Protein
3.2.2.1.1.1.2.1.1.1 Bound to lactose isomer
3.2.2.1.1.1.2.1.1.1.1 Operator stays on
3.2.2.1.2 Positive Control
3.2.2.1.2.1 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
3.2.2.1.2.1.1
3.2.2.1.2.1.2 CAP

Annotations:

  • - 'Catabolite activator protein' - Regulatory protein- Binds to CAP binding site upstream of promoter with high enough levels.
3.2.2.1.2.2 Activation
3.2.2.1.2.2.1
3.2.2.1.2.3 Repression
3.2.2.1.2.3.1
3.2.3 The Trp Operon

Annotations:

  • - 'The Tryptophan Operon' - On by default - Tryptophan binds to repressor protein = Off - Repressor active only in presences of corerepressor (Tryptophan)
3.2.3.1 Trp Absence
3.2.3.1.1
3.2.3.2 Trp Presence
3.2.3.2.1
4 DNA Technology
4.1 Cloning Vectors

Annotations:

  • Molecules used to capture, amplify and express foreign DNA. Uses Restriction Enzymes
4.1.1 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
4.1.1.1 'Sticky' Ends
4.1.1.1.1
4.1.1.1.1.1 DNA ligase

Annotations:

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

Annotations:

  • No overhang
4.1.1.3 Bacteria

Annotations:

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

Annotations:

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

Annotations:

  • - Polymerase Chain Reaction - (The thing we did in our bitter gene prac)
4.2.1
Show full summary Hide full summary

Similar

DNA Basics
Sarah Juliette B
DNA (labeling) for biochem and cell biology (lecture 2)
MrSujg
DNA structure and replication
Ifeoma Ezepue
DNA questions not from the lectures
MrSujg
Biology- Genes, Chromosomes and DNA
Laura Perry
Genes, The Genetic Code, DNA and Chromosomes
Bee Brittain
Biology- Genes, Chromosomes and DNA
Jessy Toro
Biology- Genes, Chromosomes and DNA
William Sowden
Nucleic Acids
gordonbrad
Nucleic Acids
Portia O