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IB Biology Concepts - Coggle Diagram

- - - - Contains cells whose nuclei only has pairs of chromosomes
  - - - Mendelian laws
        
        Law of Dominance and Uniformity
        
        Variants of genes found in loci are either dominant or recessive. if there is a dominant allele, its phenotype is expressed over recessive alleles
        
        Law of Segregation
        
        Two alleles from each gene separate during gametogenesis - parents only pass one down
        
        Monohybrid cross
        
        Law of Independent Assortment
        
        Alleles of genes are separated independently - and are inherited independently of each other
        
        Gene bahaviour
        
        Dihybrid cross
        
        Established in Metaphase 1
        
        Exceptions - linked chromosomes
        
        Rarely cross over separately
    - - Parent generation
    - - Offspring 1
    - - Offspring 2
  - - - One from each parent
      - Chromosomes have stretches of DNA called genes
        
        Encode for specific proteins
        
        Are in identical positions - individuals have two copies
        
        Different forms of genes called alleles
        
        Allele combination - Genotype
        
        Heterozygous
        
        Bb
        
        Homozygous
        
        Dominant
        
        BB
        
        Recessive
        
        bb
        
        Allele combinations
        
        SNP mutations
        
        Multiple alleles
        
        Blood type - (Ia, Ib, i)
        
        Co - dominance
        
        Neither is dominant over the other - both genes are expressed
        
        Incomplete dominance
        
        Neither is dominant over the other completely - a blend of both is expressed
    - - Phenotypic plasticity
        
        Ability to express variations in physical characteristics in response to changes in environment
        
        Polyphenism
        
        Environmental pressures result in two or more distinct phenotypes of one organism
- - - - Elongation
        
        RNA polymerase builds a molecule on one strand of DNA
        
        Template / Anti-sense strand
        
        Other strand is called sense strand
        
        RNA polymerase moves along DNA, adds RNA nucleotides 1 at a time, complimentary base paired
      - Termination
        
        Terminator sequence is reached
        
        mRNA released
        
        DNA joins back together again
      - Initiation
        
        RNA polymerase binds to DNA at the start of a gene
        
        Separates two strands by breaking H bonds
    - - G with C
      - C with G
        
        3 H bonds
      - A with U
        
        2 H bonds
      - T with A
  - - - mRNA
        
        Brings code from nucleus
        
        3 - base combinations
        
        Codons
        
        Stop
        
        UGA
        
        UAA
        
        UAG
        
        Start
        
        AUG
      - tRNA
        
        Single-stranded RNA molecule
        
        Folds on itself to have a clover-lead structure with double stranded regions
        
        Has three hairpin loops
        
        Has specific corresponding amino acid attached
        
        Has specific amino acid attached
        
        Recognizes, binds to corresponding codon
        
        Transfers acid to end of growing polypeptide chain, peptide bond is formed
        
        3 - base combinations
        
        Anti-codons
        
        Complementary in nature
      - Ribosomes
        
        Enzyme thing with multiple active sites
        
        80S and 70S
        
        Eukaryotic 80S
        
        Small 40S subunit
        
        Large 60S subunit
        
        Prokaryotic 70S
        
        Small 30S subunit
        
        Large 50S subunit
        
        Proteins and rRNA
        
        3 Binding sites for tRNA
        
        Aminoacyl-tRNA binding site
        
        Peptidyl-tRNA binding site
        
        Exit
        
        2 subunits
        
        Large subunit - 2 tRNAs bind at a time
        
        Small subunit - mRMA binds
    - - Degeneracy
        
        different codons code for the same amino acid
      - 20 Amino acids in total
      - Universal - Every organism has the same system
    - - Elongation
        
        Ribosome moves along mRNA 1 codon at a time
        
        New codon - new tRNA attaches
        
        New acids delivered. Condensation reaction catalysed, peptide bonds formed
        
        Begins with tRNA binding to A site
        
        Reaction catalysed by large subunit
        
        Forms peptide bond with P site amino acid
        
        Once bond forms, tRNA translocates by one codon
        
        tRNA in P site moves to E site, exits ribosome
        
        tRNA in A site moves to P site
        
        2 more items...
        
        Uses GTP
        
        Termination
        
        Ribosome reaches stop codon, releases polypeptide chain
        
        Polypeptides delivered via vesicles into golgi apparatus for modification and transport
      - All proteins start with Met - start codon
        
        5′ terminal of the mRNA binds to the small ribosomal subunit
        
        Ribosome moves along until it binds AUG
        
        anticodon of initiator tRNA binds to codon
        
        Large subunit joins, completes assembly of translation complex
    - - Point mutation
        
        Mutations occurring onto one nucleotide
        
        Frameshift
        
        Insertion
        
        Nucleotide added
        
        Deletion
        
        Nucleotide deleted
        
        Substitution
        
        Nucleotide changed for another
        
        Sickle Cell Anemia
        
        Silent
        
        Changes in structure, but no change in expression
  - - - Promoter has transcription factors that bind
        
        No transcription factors - no transcription
  - - - Promoters
      - Enhancers
        
        Increase rate of transcription
      - Silencers
        
        Decrease rate of transcription
    - - Sequences that get removed at the end of transcription
    - - Repetitive sequences that protect the ends of the chromosome - ensure that DNA is replicated correctly. With every cell division, short stretches of DNA are lost from the telomeres.
    - - Codes for RNA molecules that do not fold to form proteins
  - - - Codes for polypeptides
    - - Transcription - synthesis of pre-mRNA
        
        Addition of 5'cap and poly A-tail
        
        Prevents mRNA degradation
        
        Splicing
        
        Excising introns, Ligating exons
        
        snRNP (Small nuclear ribonuclearproteins) forms base pairs with ends of intron
        
        Spliceosome and looped intron form
        
        1 more item...
        
        mRNA
- - - - Actin and Myosin proteins form contractile ring
        
        Pinches cell membrane together, forms cleavage furrow
        
        Gradually deepens, splits membrane in half
        
        Separates cytoplasm into two daughter cells
        
        Important proteins involved in muscle contraction
    - - Assembly of cell plate
        
        Vesicles containing cell wall materials fusing
        
        Cell plate grows outwards, dividing cytoplasm into two daughter cells
    - - Oogenesis
        
        Formation of egg cells
        
        Produces first polar body, and secondary oocyte
        
        If fertilisation occurs, second polar body produced, mature oocyte is made
      - Budding
        
        Growth of a genetically identical daughter from parent
        
        Daughter smaller than parent, receives half or less of cytoplasm
        
        Parent left with scars when separated
  - - - Chromatin condenses into chromosomes
      - Nuclear membrane breaks down
      - Spindle fibres form
      - Microtubule organising centres head towards opposing ends - centrosomes containing centrioles in animal cells
      - Metaphase
        
        Anaphase
        
        Telophase
        
        Chromosome decondenses, nuclear membrane reforms
        
        Spindle fibres disintegrate, cell elongates
        
        Spindle fibres shorten, splits centromere, pulling sister chromatids apart
        
        Sister chromatids line up on metaphase plate
        
        Spindle fibres bind to centromeres, moving them into position
  - - - Prophase I
        
        Sister chromatids form tetrads / Bivalent pairs
        
        Homologous pairs form
        
        Same genes at the same loci
        
        Crossing over
        
        Swaps alleles for the same gene
        
        Can occur multiple times in the same bivalent
        
        Crossing over occurs between two non-sister chromatids over the chiasmata
        
        Different places each time meiosis occurs
        
        Chromatids not crossed over are called non-recombinant
        
        Chromatids that cross over are recombinant
      - Anaphase I
        
        Sister chromatids remain connected
        
        Homologous pairs separated
      - Telophase I
        
        Chromosomes decondense, cytokinesis occurs, followed by interkinesis
        
        Two non-identical haploid daughter cells
      - Metaphase I
        
        Random orientation
        
        Orientation of one independent of the other
    - - Prophase II
        
        Nothing special
      - Metaphase II
        
        Fibres attach to centromeres
      - Anaphase II
        
        Sister chromatids separated, they're now called chromosomes
      - Telophase II
        
        Chomosomes decondense, nuclear membrane reforms
        
        Four haploid daughter cells
    - - Failure of sister chromatids to separate
        
        Gamete with three chromatids, and one
        
        Trisomy
        
        Monosomy
        
        Trisomy 21 - Down's Syndrome
    - - Crossing over
      - Independent assortment, Random orientation
      - Random fusion during sexual reproduction
        
        Offspring inherit a random combination of alleles
  - - - Forms chromosomes
    - - Long, thing cylindrical fibrous proteins that form spindle apparatus
        
        Motors attach to microtubules, hydrolyze ATP for movement
  - - - Growth
        
        Increase in cell number / organism size
        
        In plants
        
        Meristematic tissue
        
        Regions of undifferentiated cells
        
        Stimulated by auxin
        
        Actively divide and differentiate
        
        Cell at apex, the tip, remain undifferentiated
        
        In animals
        
        Embryonic division
        
        Cleavage
        
        Division of zygote into totipotent stem cells
        
        1 more item...
        
        Cell replacement
        
        Skin turnover
        
        Skin cells formed from epithelial cells
        
        Asymetric division
        
        1 Undifferentiated, 1 Differentiated
        
        Mature skin cells move upwards through epidermis to replace dead skin cells
      - Tissue repair
        
        When wounded, cells surrounding rapidly divide
        
        Healing rate depends on cell turnover rate - some are non-dividing, and need to be stimulated
    - - Interphase
        
        G1 (Gap 1)
        
        Happens in cytoplasm
        
        Cell grows in size
        
        Mitochondria and chloroplasts divide through binary fission
        
        Supports endosymbiotic theory
        
        Cell doubles in size
        
        Checks internal environment for ability to synthesize DNA
        
        S (Synthesis)
        
        DNA replication occurs
        
        Doubles amount of DNA
        
        G2 (Gap 2)
        
        Grows and prepares for Mitosis
        
        Synthesizes microtubules and other proteins requires for mitosis
        
        Acts as checkpoint to ensure DNA replication is properly carried out
        
        Most active, longest phase of cell cycle
    - - Cyclins
        
        Family of proteins that regulate the cell cycle
        
        Binds to and activates CDKs - Cyclin dependent kinases
        
        Enzymes that phosphorylate specific proteins to drive the cell forwards
        
        Each cyclin only active in a specific stage
        
        DEAB
        
        Certain concentration (Threshold) must be reached before new stage can continue
- - - - Formulate H0 and HA
        
        H0 - There is no statistical significance between the expected and observed values
        
        Genes unlinked
        
        HA - There is a statistically significant difference between the expected and observed values
        
        Genes linked
      - Determine expected / observed values
      - Identify no. alleles
    - - Degrees of freedom - # of categories - 1
      - Find critical value - use p=0.05
        
        X^2 < critical value, there IS NO statistical significance
        
        X^2 > critical value, there IS statistical significance
- - - - Forms Nucleosomes
    - - Breaks Hydrogen bond between strands, separating them
    - - DNA made up of phosphodiester bonds attached to 5' Carbon
      - DNA polymerase III adds to the 3' end of the previous molecules - 3' - 5' directionality
        
        Can ONLY do so in said direction due to shape
      - Lagging strand
        
        Discontinuous replication
        
        Oriented 5' to 3'
      - Leading strand
        
        Continuous replication
        
        Oriented 3' to 5'
      - Enzymes of DNA replication (HL)
        
        DNA polymerase :
        
        DNA polymerase III
        
        Leading strand
        
        Replicates continuously
        
        Lagging strand
        
        Replicates in intervals - Okazaki fragments
        
        5' to 3' directionality
        
        Proofreads DNA strands for errors, fixes them
        
        DNA polymerase I
        
        Removes RNA primers, replaces with DNA
        
        DNA ligase
        
        Catalyses phosphodiester bonds between Okazaki fragments and primers - Turns lagging strand into a single strand
        
        Helicase
        
        Unwinds / Unzips DNA molecule
        
        Breaks H bonds holding bases together
        
        Forms replication fork
        
        Strands kept from rejoining via single-strand binding proteins
        
        Gyrase
        
        Goes in front of Helicase, relieves pressure from unwinding DNA; controls topological transition
        
        DNA primase
        
        Attaches RNA primers to template strand
        
        Lets DNA polymerase begin replication
        
        Single primer required for leading strand
        
        Multiple needed on lagging due to discontinuous nature
  - - - Resuspension buffer (RSB) added to DNA sample, separates from beads
        
        DNA is left in supernatant, BLT pulled down by magnet
    - - Add ethanol
        
        Beads and DNA pulled downwards
        
        Supernatant, PCR reagents, and ethanol removed
    - - Concentrated solution has more beads
        
        Medium-sized fragments bind to BLT
        
        Same as large fragments
    - - Sequencer works best with medium sized DNA fragments
        
        Large fragments bind with BLT first in diluted solution
        
        Magnet pulls BLT with large DNA downwards, transfer small and medium fragments to another tube
    - - Add index - Unique index added to each sample for identification by sequencer
        
        Temperature increased to denature DNA
        
        Primers added to ends of DNA strands
        
        Extension begins from primers, copies of DNA are produced
        
        Desired DNA placed in chamber that contains
        
        Primers for replication
        
        Taq polymerase
        
        Found in Hot springs bacteria
        
        Does not denature in high temp
        
        Replicates DNA
        
        Free Nucleoside Triphosphates
        
        Annealing
        
        Temperature lowered to 60C
        
        Primers bind to complementary strands of DNA
        
        Denaturation
        
        Occurs at 98C
        
        DNA heated until denatures
        
        Extention
        
        Taq polymerase goes through DNA with primer as start point
        
        Once replicated, begin Denaturation again
    - - Removes enzymes used for tagmentation
        
        Tagmentation wash buffer (TWB is used)
        
        Magnet pulls BLT towards the bottom, enzymes remain in supernatant
    - - Stops enzymes from cutting DNA
        
        Prevents DNA getting too small
        
        Tagmentation stop buffer (TSB) is added
    - - Rise in temperatures allow enzymes to cut DNA into smaller pieces
      - DNA is tagged with adapters
        
        DNA binds with Bead-linked Transposomes (BLT), "tagged" with adapters
- - - - One nucleotide is replaced with another
      - Synonymous
        
        No effect - no changes in protein
      - Non-synonymous
        
        Changes protein
    - - Insertion
      - Deletion
      - Frameshift
    - - Causes
        
        Mutagens
        
        Chemical mutagens
        
        DNA breaking
        
        Single-strand break
        
        Impedes replication fork movement
        
        Replication errors / Halt of replication
        
        Double-strand break
        
        Completely halts DNA replication
        
        Radiation
        
        Errors in DNA replication and repair
    - - Some bases more likely to cave under mutagens
        
        Cytosine can deanimate - amino group is removed
      - Environmental factors can contribute to mutation rate and frequency
        
        Environment can favour specific mutations
    - - Somatic cells
        
        Within a person's lifetime, inheritable
        
        Mutations that happen in genes controlling cell cycle
        
        Occurs in proto-oncogene
        
        Uncontrolled cell division
        
        Proto-oncogene becomes oncogene
        
        1 more item...
        
        Tumour suppressor genes
        
        Codes for proteins that slow / prevent cell division
        
        Promote apoptosis (programmed cell death)
        
        1 more item...
      - Germ cells
        
        Heritable
      - Types
        
        Silent
        
        Occurs in coding sections, does not alter amino acids
        
        Harmful
        
        Have harmful consequences on organism
        
        Beneficial
        
        Increases fitness in a particular environment
        
        Neutral
        
        Occurs in non-coding sections
  - - - Cas9 - Enzyme that cuts DNA at specific target sites
      - CRISPR
        
        Clustered Regularly Interspaced Short Palindromic Repeats
        
        Specific regions found in bacteria that contain short repeated and unique spacer sequences
      - Bacterial uses
        
        When foreign DNA matches a CRISPR spacer, a corresponding RNA sequence (CRISPR RNAs) bind to the DNA
        
        Cas9 is guided to make precise cuts into the DNA
        
        Induces double strand breaks that can be repaired by cell's repair system
      - Human uses
        
        Single-guide RNAs
        
        Targets a specific DNA sequence
        
        Marks DNA for cutting
        
        Lets scientists add or delete or modify sequences
        
        Gene therapy
        
        Agriculture
        
        Disease modelling
        
        Genetic engineering of microorganisms
    - - Specific gene is intentionally removed
      - Determines function of gene