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Biochem exam topics - Coggle Diagram

- - - - Adrenaline
    - - Steroid hormones
    - - Thyroid hormones
- - - - Histones
      - Euchromatin and heterochromatin
      - Chromatin remodelling complexes and modifications
      - Nucleosome
    - - Initiation
      - Elongation
      - Termination
      - Enzymes involved and their roles
      - Regulation
  - - - Pre-initiation complex
      - Transcription factors
  - - - tRNA
      - mRNA
      - rRNA
  - - - Raf
      - RTK
      - Ras
      - HER2
    - - p53
      - BCR-ABL
  - - - X-linked recessive/dominant
        
        Dominant maternal X chromosome
        
        All boys inherit, daughters carriers
        
        Dominant paternal X chromosome
        
        All daughters inherit, boys do not (receive X from mom)
      - Autosomal recessive
        
        25% chance for child to inherit if both parents carriers
      - Y-linked
        
        only in boys
      - Autosomal dominant
        
        Inherited in every generation
      - Mendel's laws
        
        Law of dominance and uniformity: Some alleles are dominant while others are recessive; an organism with at least one dominant allele will display the effect of the dominant allele
        
        Law of independent assortment: Genes of different traits can segregate independently during the formation of gametes.
        
        Law of segregation: Each trait inherited independently of others
    - - Codominant
        
        Blood types
      - Intermediary
        
        phenotype mixture of both alleles
      - Mitochondrial
        
        only in maternal lines
  - - - Acetylation
      - Methylation
    - - miRNAs
- - - - A=ecl
        
        Concentration of substance is proportional to its absorbance
    - - NADH has peak at 340nm, NAD+ does not - appearance of this peak can be used to estimate enzyme reaction rate in reactions where NAD+ is involved
      - Conversely, disappearance of 340 nm absorption peak can be used to track conversion of NADH to NAD+
      - The change in absorbance per minute (A min-1) is a measure of the enzyme activity because the change in absorbance per minute is a measure of how fast NADH is produced
  - - - Km
        
        Substrate concentration needed to reach 1/2 Vmax, measure of enzyme affinity for substrate
        
        Large = low affinity, lots of substrate needed
        
        Low = High affinity, not much substrate needed
      - Vmax
        
        Maximal reaction rate
      - Ki
        
        the inhibitor constant, the dissociation constant of the enzyme-inhibitor complex, comparable to Ks
      - Ks
        
        the dissociation constant of the enzyme-substrate complex
    - - Uncompetitive inhibition
        
        I binds to the enzyme substrate complex and in doing so renders the enzyme catalytically inactive, preventing product formation
        
        Y-intercept increases as Vmax is reduced as E-S complex is locked and cannot form product no matter how much substrate is added (= increase in 1/Vmax)
        X-intercept moves to left as Km decreases (= increase in -1/Km)
        Slope stays the same, because both Km and Vmax decrease
      - Noncompetitive inhibition
        
        inhibitor binds to allosteric site, changes enzyme conformation and its activity --> reduction of enzyme’s ability to convert substrates into products in the active site
        
        Y-intercept: increases as Vmax is reduced (increase in 1/Vmax)
        Slope increases as Vmax s reduced but Km unchanged (slope = Km/Vmax)
        X-intercept: stays the same as Km is unchanged (enzyme can still bind substrate but not form product)
      - Competitive inhibition
        
        A competitive inhibitor will increase the apparent Km of the enzyme for substrate i.e., cause it to require a higher substrate concentration to achieve Vmax
        --> Vmax can still be achieved if enough substrate is added to outcompete inhibitor
        
        Y-intercept: stays the same as no change in Vmax
        X-intercept: moves to right as Km increases
        Slope increases as Km increases (Km/Vmax)
    - - Y-axis: 1/v0
        Negative X-axis: -1/Km
        Positive X-axis: 1/[S]
        Slope = Km/ Vmax
        Y-intercept: 1/Vmax
        X-intercept: -1/Km
  - - - specific enzyme activity * total amount of protein
    - - enzyme activity in cuvette/mg of protein in cuvette
    - - DF = Final volume / Added volume
        DF = Stock concentration / Final concentration
      - c1V1=c2V2
    - - Triton X-100
    - - o High activity in the cytosol fraction + cytosol enzyme
        o High activity in the mitochondrial + triton fraction – mitochondrial enzyme
    - - total fraction activity *100 / total F1 triton activity
      - Total fraction activity= refers to the fraction of interest - E.g. the question asks for yield of F2 fraction, plug in the total enzyme activity there and the total enzyme activity for the F1 + triton goes on the bottom
  - - - State 3 (fast): State 4(slow)
      - Measure of the degree of coupling, ratio of oxygen consumption rates in different states
      - Oxygen consumption in different states
        
        State 1
        
        Mitochondria + medium added to oxygen electrode
        
        State 2
        
        Substrate added to mitochondria in state 1
        
        State 3
        
        ADP added to mitochondria in State 2
        
        State 4
        
        Slow rate of O consumption after all ADP has been phosphorylated to ATP
    - - How much ATP synthesized / How much oxygen consumed, will depend on substrate used
    - - Complex I
        
        rotenone
        
        Substrate: glutamate/malate (NADH)
      - Complex II
        
        Substrate: succinate (FADH2)
        
        3-NP
      - Uncouplers
        
        2,4-DNP
      - Complex III
        
        antimycin
      - Complex IV
        
        cyanide
      - Complex V (ATP synthase)
        
        oligomycin
- - - - HMG CoA reductase
  - - - Chylomicron lifecycle
      - VLDL to LDL pathway
      - HDLs and reverse cholesterol transport