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Biology - Coggle Diagram

- - - - inorganic (chemolithotrophy)
      - organic - aerobic respiration (oxygen is electron acceptor) or anaerobic respiration (electron acceptor that isn't oxygen)
- - - - inhibit enzymes, some look like a substrate and get in the way, some permanently block the active site and some bind to other parts of the enzyme to stop the enzyme working properly (allosteric modulation), examples of inhibitors include poisons
- - - - Endocrine glands secrete hormones into the blood stream eg the pancreas secretes glucagon/ insulin and the pituitary gland secretes FSH/LH. Exocrine - secretion of non-messenger substances into ducts (bile, milk, semen, salvia)
- - - - Role of mitochondrial apoptosis: loss of mitochondrial membrane potential stops ATP synthesis, generation of pores in membranes, release Cytochrome C, nearly all proteins involved are from bacteria eg cytochrome C, caspases etc
- - - - Modifying amino acids involves covalent modification which is sometimes irreversible, it can alter protein structure/ function/ location/ folding etc, on top of this due to proteins being made up of many amino acids multiple modifications can happen
        
        Example modifications include: carboxylation, acetylation, hydroxylation, methylation etc
  - - - Newly synthesised proteins formed by free floating ribosomes in the cytosol remain in the cytosol, ribosomes on ER produce proteins that will be lysosomes, part of the plasma membrane or secreted and ribosomes in organelles like the mitochondria, chloroplasts or nucleus produce proteins that will stay in there
- - - - 2-oxoglutarate (5C) + CoA -> succinyl-CoA (4C) + CO2 (1C) + NADH - 2-oxoglutarate dehydrogenase complex
        
        succinyl-CoA (4C) + GDP + Pi -> succinate (4C) + GTP + CoA - succinyl-CoA ligase
        
        succinate (4C) -> fumarate (4C) + QH2 - succinate dehydrogenase
        
        fumarase - fumarate (4C) -> malate (4C) -> oxaloacetate (4C) + NADH - malate dehydrogenase
- - - - Tumour cells are a result of mutation, like constitutive mitosis, defective response to anti-mitotic signals, unscheduled proliferation and genomic/ chromosomal instability, teratoma is a tumour with teeth and eyes etc
  - - - Growth phase, S phase (synthesis/ copy DNA), prophase (trying to get chromosomes organised), metaphase (chromosomes line up at cell equator), anaphase (pair of chromosomes pull apart), telophase (chromosome move to either end of cell), cytokinesis (break the bond and you end up with two new cells with two copies of the DNA)
      - Cell cycle is controlled by 3 checkpoints which check progress, spindle assembly checkpoint - check for chromosome attachment to spindle, G1 checkpoint - check cell size, nutrients, growth factors and DNA damage, G2 checkpoint - check for cell size and DNA replication
      - The levels of cyclin change throughout the cycle, it is dangerous and has to be highly regulated by phosphorylation, inhibitory proteins and degradation. G1/S checkpoint - restriction point, ubiquitination (adding ubiquitin) and degradation of S phase inhibitor proteins. Proteasome - protein complexes which degrade ubiquitin-tagged proteins by proteolysis
      - p53 - a product of a TP53 gene (a tumour suppressor gene), 15 isoforms, often mutated in cancer, usually DNA-binding domain, loss of function, anti-cancer roles increase DNA repair, arrests cell cycle if DNA damage, G1 checkpoint, initiates apoptosis if DNA damage irreparable
      - Separase is bound to an inhibitory protein making it inactive. Once you get the signal that you need to move from metaphase into anaphase, this inhibitory protein gets degraded, separase becomes active, it breaks those cohesive rings and then you can start putting the chromosomes apart.
      - Cytokinesis - when separation occurs the contractile ring gets tighter until it splits
      - Cell cycle, the process where eukaryotic cells replicate themselves, mitotic cell division (1 x 2N cell becomes 2 x 2N cells), cycle divided into 4 phase, G1 is G0, growth factors stimulate growth
- - - - 2) Glucose-6-phosphate (aldose)-> Fructose-6-phosphate (ketose): pentagon made (so it can split equally). Powered by phosphoglucoisomerase
        
        3) Fructose-6-phosphate -> fructose-1,6-bisphosphate: ATP goes to ADP for Pi to bond to the carbon 1. Powered by Mg^2+ hexokinase (kinase)
        
        4) Fructose-1,6-bisphosphate -> GAP (aldose) or DHAP (ketose) (DHAP then goes to GAP)
        
        5) GAP -> 2 x 1,3-bisphosphoglycerate: NAD^+ and Pi involved, NADH + H^+ left over. Phosphate added GAP dehydrogenase and triose phosphate isomerase
        
        6) 2 x 1,3-bisphosphoglycerate -> 2 x 3-phosphoglycerate: involves ADP to ATP reaction, phosphate removed to go to ADP to make ATP. phosphoglycerokinase Mg^2+
        
        7) 2 x 3-phosphoglycerate -> 2 x 2-phosphoglycerate: phosphate moves, phosphoglyceromutase
        
        1 more item...
  - - - Metabolites containing phosphate groups hydrolyse in water, the extent of hydrolysing differs
      - Energy changes are additive (Endergonic reaction driven forwards by coupling it to strongly exergonic reaction)
  - - - Active skeletal muscle
      - Poor oxygen supply
      - High ATP demand
      - NADH by pyruvate -> NAD^+ + lactate
      - Lactic acid -> lactate + H^+
      - H^+ can build up causing muscle cramps
- - - - RuBisCO catalyses the oxygenation of RuBP: D - ribulose 1,5-bisphosphate + O2 → 3-phospho-D-glycerate +
        2-phospho-D-glycolate + 2H^+
- - - - 2) Electrons from this reaction go to the quinone pool and then to cytochrome c after the electrons pass the proton carriers carry protons (H^+) through the membrane (4H^+ in two proton carriers and 2 in one (QH2 + 2cyt c (ox) -> Q + 2cyt c(red) + 2H^+))
        
        3) Because of the moving electrons and protons in the mitochondrial matrix this reaction happens: 4H^+ + O2 -> 2H2O (4cyt c(red) + O2 + 8H^+ -> 4cyt c(ox) + 2H2O + 4H^+)
        
        4) Unplugging the quinone pool from getting build up from being reduced too much 2QH2 + O2 → 2H2O + 2Q
        
        Uncoupling agents (ATP synthase) exist, they stop Δp build up (ps sometimes ATP synthase reverses)
        
        Natural: used to generate heat eg thermogenin
        
        Synthetic: lipid soluble proton carriers that carry protons back through the membrane eg 2,4 - dinitrophenol (DNP), FCCP, CCCP, some of them are illegal dietary aids
- - - - Microfilaments
        
        Made of actin filaments (contain a protein called actin) common in eukaryotes, it exists as G (globular) actin, they bind to ATP forming F-actin then they oligomerise and then form the nucleus
        
        labile/ changeable
        
        concentrated under plasma membrane
        
        Scaffolding - cell movement
        
        many other associated proteins
        
        used in cell-cell adhesion (cells sticking together), a lot of weak interactions make a stronger interaction, Ca^2+ adherence proteins are cadherins and they're attached to the cytoskeleton and connect with other E-cadherins to stick (velco-like)
      - Microtubules
        
        Made of alpha and beta tubulin heterodimer units, alpha and beta tubulins are homologous but not identical, alpha binds to GTP and beta hydrolyses GTP to GDP + Pi and then exchanges GDP for GTP. Microtubules grow from the centrosome/ mitotic spindle and they track chromosome segregation, together alpha and beta form long filaments
        
        Dynein and Kinesin "walk" (one foot attaches to microtubule other foot detaches from microtubule then swings in front of first foot and attach to microtubule then the first foot moves in front of the other foot etc (detachment and attachment is due to ATP binding to microtubule, ADP is detached )) this process depends on ATP and is used to move cargo etc
      - Intermediate filaments
        
        Heteropolymers include lamins (nuclear, provide structural support (can see by radiation in nucleus)), keratins (acidic/basic), vimentin, desmin, NF proteins (neuronal)
        
        In terms of cell-cell adhesion cadherins are involved (desmoglein/ desmocollin) and they interact with each other in between the membranes, cytoplasmic plaque (plakoglobin/ desmoplakin) is on the other side of the membrane (in the cell), intermediate filaments are keratin and they are attached to plectin within the plaque, the whole structure of this is called a desmosome or hemidesmosomes
      - These filaments are involved in muscle contraction, (thin (actin) filament move over thick (myosin) filament when contracting) myosin binds, ATP hydrolyses causing the movement required for the activity, ATP is released and the cycle continues
- - - - There are multiple DNAs: B-DNA (this is the main DNA, right hand helix 2.0 nm diameter and is the most abundant form in nature, when at pH 7 it spontaneously coils, distance of one wavelength of helix is 3.4nm, distance from base to base is 0.34nm, in this DNA there is hydrogen bonding between bases and even between sugars in backbone, ionic bonding, hydrophobic interactions, van der Waals interactions), A-DNA (right hand helix 2.6 nm diameter, formed when B-DNA is dehydrated and is found in bacteria, archaea and viruses), Z-DNA (left hand helix 1.8 nm diameter, found in eukarya when being transcribed into mRNA), C-DNA (not in nature) and H-DNA (triple stranded)
      - In bacteria and archaea the majority of taxa in these two domains don't have membrane bound nuclei so DNA is naked in the cytosol, there's no histones, the DNA is circular, supercoiled and has 1 - 2 chromosomes. Mitochondria and plastids were once bacteria so have same DNA properties in their genomes as bacteria have.
  - - - mRNA (messenger RNA) - used in transfer of information from DNA to ribosome for protein synthesis
      - rRNA (ribosomal RNA) - forms the part of the structure of the ribosome and catalyses the formation of peptide bonds
      - tRNA (transfer RNA) - moves amino acids around the cell to the ribosome
      - Other: siRNA (small interfering RNA), ribozymes (RNA molecules with enzyme like catalytic abilities) and viroids (double looped RNA that acts as a plant pathogen)
    - - 1) Information from DNA is copied into a strand of mRNA (the mRNA strand is complementary to DNA but instead of T it's U) 2) mRNA code sequence is in triplets/ codons (each codon encodes an amino acid for the genetic code the code is not universal) The code sequence has exons (regions that code for a polypeptide) and introns (regions that don't code for a polypeptide but act as a filler to protect the genes if DNA is damaged) (mRNA that has introns and exons is called the primary transcript) splicing is done to cut the introns out to make the final transcript (in bacteria and archaea they have rarely have introns but they have inteins which are like introns but they remove themselves out)
    - - In Eukarya DNA is linear within a membrane bound nuclei, DNA is protein-associated and only chromosomal DNA is in the nucleus.
      - Chromatin is a protein-DNA complex, the outer nucleus has heterochromatin and inner nucleus has euchromatin
      - Most protein content is histones (histones are written as H1, H2a, H2b, H3 and H4), at 20nm spacing along DNA strand are nucleosomes (DNA wrapped around histones), the nucleosomes are separated by linker DNA, several nucleosomes and linker DNA are termed a polynucleosome, polynucleosomes coil to forma 30nm thick fibre, the fibre is supported by scaffold proteins to form a 300nm strand with loops and it folds even more to make an active chromosome (700nm), the X shaped chromosomes form at metaphase and require scaffold proteins
      - Degeneracy of code - different codes can code for the same thing
      - gene - region of DNA that begins with a start codon and ends with a stop codon
      - Operon - region of DNA that's transcribed as a single mRNA strand (in diagrams of operons genes are shown as arrows eg -====>|==========>|=>|=>)
      - Gene cluster/ putative operon - group of genes close together
    - - This happens on the ribosome (fyi ribosomes are subcellular particles and are not organelles ribosomes are made for 60% rRNA and 40% protein both of which make the subunits (units in Svedberg), the ribosomes are bound to the rough endoplasmic reticulum in eukarya but in bacteria and archaea they roam free in the cytosol and in the mitochondria's case the matrix), codons can be start codons and stop codons which control the start and end of translation, as the ribosome has rRNA the bases of rRNA interact with the mRNA transcript and the tRNA molecules (tRNA molecules are r-shaped and are there for each structural amino acid, it has an anti-codon loop that has the anti-codon sequence (complementary to the codon), it has a D loop, an anticodon loop and a TΨC loop), mRNA binds to rRNA using the cap and start codons as recognition sites, start codons bind to the anti-codon and tRNA stays bound to ribosomes, until the amino acid that is attached to the other amino acids, rRNA catalyses the peptide bond formation between the amino acids
- - - - site of respiratory chain - happens in the inner membrane, proton motive force (Δp) develops in the intermembrane space and is used to drive ATP biosynthesis by ATP synthase
      - site of Krebs cycle - pyruvate produced is translocated into the mitochondrial matrix by active transport (link reaction converts it to acetyl CoA)
      - site of fermentation - pyruvate is fermented into lactate to generate NADH
      - site of non-shivering thermogenesis - take Δp and uncouples it from ATP biosynthesis
      - site of calcium homeostasis - Ca^2+ is used in signal transduction, mitochondria take up and release Ca^2+ ions acting as storage vessels for them keeping them in the matrix
      - site of regulation of cell division: mitochondrial production of molecules to regulate cell division
      - other - regulate apoptosis, biosynthesis of steroids, biosynthesis of heme cofactors, hormonal signalling
    - - black dots are ribosomes, gaps are matrix, inner and outer membranes separated by intermembrane space, circular mitochondrial genomic DNA, cristae within thin dark lines
    - - Membrane
        
        inner membrane - site of respiratory chain, H^+ transporting two-sector ATPase, intermembrane space is the site in which Δp develops, lots of cardiolipin
        
        outer membrane - contains porins, gated ion channels, if broken kill the cell, contains enzymes monoamine oxidase and CoA ligase
      - Matrix
        
        Contents: herein makes up 60% of soluble protein content, pyruvate oxidation and Krebs cycle enzymes, contains mitochondrial ribosomes, mtDNA (mitochondrial genome)
  - - - Plant immunity - chloroplasts trigger apoptosis and release defence signals
      - Fatty acid biosynthesis - chloroplasts make all plant cell fatty acids
      - Site of phototrophic electron transport chain - where Δp is generated (from stroma to thylakoid lumen) and used to drive ATP biosynthesis by H^+ transporting two sector ATPase
      - Sugar and starch biosynthesis - chloroplasts generate hexoses from glyceraldehyde 3-phosphate which are then assembled into sucrose or starches
    - - Stroma is the space with no grana (stack of thylakoids), lamella/ structural thylakoids link grana together, chloroplast DNA (cpDNA), starch granules, plastoglobules, inner and outer membranes with inner membrane space
- - - - Alkaloids: c 12000 known compounds, characterised by a basic N in a heterocycle, synthesis from amino acids, often stored in seeds as a N store and can be toxic/ hallucinogenic eg morphine
      - Phenolics: structural role (lignin), defence (tannins), communication, antioxidants, guaiacol, aspirin (salicylic acid)
      - Flavonoids: influence the colours of things like flowers
      - Terpenoids/ isoprenoids: isoprene pyrophosphate, volatile and hydrophobic, "sticking things together", found in pine scent, menthol etc
      - Steroids: eg testosterone, estrogen, alarm pheromones in honey bees, mating pheromones in moths, pollutants can interfere as they mimic, capsicum
- - - - Fatty acid naming methods
        
        Omega nomenclature - numbers from terminal end of tail until C=C eg ω6c ω is omega/ terminal carbon, 6c is the number from the terminal carbon where C=C is (this method only names 1 specific C=C)
        
        Delta nomenclature - is from the beginning/ COOH end of the chain instead, it's written as cis-Δ^14 where 14 is the number carbon the C=C is
        
        C20:4 (the 20:4 is small, 20 is the number of carbons and 4 is the number of C=C)
      - It's unusual to have an odd chain length in Eukarya and it is also odd to have branches, branched fatty acids have the prefixes like iso- and anteiso-, branched fatty acids also have lower melting points
      - Fatty acids take the forms of esters (left) via condensation reactions, Archaea have ether (right) linkages which are stronger
    - - forms bilayer, hydrophobic heads face outwards, hydrophilic tails face each other inwards, makes plasma membrane in eukarya, flippases move phospholipids to the inner leaflet/layer closest to cell, and floppases move phospholipids to the extracellular layer (outer leaflet), both processes require ATP as it's thermodynamically unfavourable