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Biology review content, Test tips & useful resources - Coggle Diagram

- - - - levels of molecular structure
        
        primary structure
        
        sequence of amino acids
        
        secondary structure
        
        patterned repitition
        
        tertiary structure
        
        3-D shape of the molecule
        
        quantemary structure
        
        inter-molecule association
      - ROOT: "glyco"-sugar
    - - ATP synthesiser -> mitochondria
      - photosynthesiser -> chloroplast
    - - plant-explicit
        
        chloroplast
        
        granum
        
        thykaloid
        
        have extensive membrane surface areas, which helps boost light absorption, despite having small spaces and low volume; faster proton accumulation
        
        different in various species' cells
        
        green colour due to the chlorophyll pigment
        
        starch grains can be found inside if it has been synthesising rapidly
        
        function: responsible for photosynthesis
        
        presence: mostly in leaf cells
        
        cell wall
      - animal-explicit
      - nucleus
        
        chromatin / chromosomes
        
        chromatin is the regular form, when DNA are "relaxed" and easily accessible: strands are wrapped around histones
        
        chromosomes are when histones stack together and form an "x" shape
        
        linear DNA, as opposed to the prokaryotic circular genetic material
        
        nucleus pore
        
        nuclear envelope
        
        has two layers
        
        facilitated diffusion: allows parts produced in the nucleus to exit into the cell if they pass the pore guards' genome-specific examination
        
        nucleolus
        
        function: manufacture site for ribosomes
        
        can become visible under the light microscope with assistance from stain
        
        has no membrane
        
        function: manages cell activity through selective gene transcription
      - plasma membrane
        
        glycoproteins (/proteins) carry out the functions (aside from compartmentalisation)
        
        serves as the hormone binding site for chemical messengers in order to carry out intercellular communication
        
        consisted of
        
        phospholipid bilayer
        
        phospholipids engage in frequent lateral movement (10^7 times/second); flip-flop (tail-head flipping inside-out) happens ~1 time/month
        
        trait: can fuse together with any other unit of bilayer membrane and break off at any point
        
        peripheral proteins
        
        definition: proteins positioned on the membrane
        
        integral proteins
        
        enables cell-to-cell adhesion, where two cells attach to each other through binding their integral proteins and exchange information through chemical messengers
        
        cholesterol
        
        though present in both plant and animal cells, are more frequently seen on animal cells
        
        function: helps membrane maintain fluidity & flexibility and prevents crystalisation, accomplished through slightly disrupting the bilayer's regular packing
        
        glycoproteins
        
        "decorates" the cell membrane, functioning as cell IDs
        
        glycolipids
        
        trait: semi-permeable
        
        function: compartmentalises the cell, separating inside from environment
        
        gates
        
        unitransporter
        
        allows only a single type of material to pass
      - cytoplasm
        
        clear, jelly-like fluid suspending organelles; contains dissolved fluids
      - endoplasmic reticulum
        
        smooth ER
        
        produces sex hormones
        
        helps with detoxication in liver cells
        
        regulates calcium levels in muscle cells
        
        rough ER
        
        folds proteins and attaches needed sugar chains to them
        
        ribosomes are attached here
        
        a system of membranes extended throughout the cytoplasm
        
        presence: found in all eukaryotes except red blood cells
      - ribosomes
        
        80s in eukaryotes
        
        site of protein synthesis, dissembles into 2 subunits when not active
      - golgi apparatus
        
        shaped as a pile of pancakes
        
        each single pancake is a cisterna (plural. cisternae), which are vesicle sacs
        
        its layers and connected and synched in motion
        
        presence: numerous (and larger) in plant cells, less (and smaller) in animal cells
        
        transportation efficiency is greater in animal than in plant cells
        
        function: transportation. Modifies and packages molecules, readying them for out-of-nucleus export. Assembles macromolecules such as glycolipids
        
        the sacs can fuse together, and bud out from the entirety to transport some items.
      - mitochondria (sing. mitochondrion)
        
        presence: present in all eukaryote cells, even mature red blood cells and sperm cells
        
        function: aerobic respiration
        
        cristae (folds in its inner membrane) increase surface area, allowing more f. particles to attach and thus increasing respiration rate
        
        matrix: the organelle's cytoplasm-like substance.
        
        contains the enzymes needed for the first stages of link reaction & Kreb cycle( mitochondria respiration)
        
        almost identical DNA across different species of eukaryotes
      - vacuoles & vescicles
        
        vacuoles are extremely large for plant cells; smaller for animal cells
        
        function: vessels used to store food, dispel waste, and isolate toxins
        
        Clathrin protein
        
        three-legged protein; assemble to form spherical cage
        
        coats the vesicle; pull a patch of membrane inwards
      - lysosome
      - cytoskeleton
        
        function: holds up the shape of the cell
        
        allows animal cells, which don't have cell walls to help them maintain shape, to sustain a general shape
        
        consisted of microtubules (cylinder-shaped protein fibres which has some flexibility due to its lengthy shape)
        
        basal bodies (plural for centriole) form an anchor point for microtubules during cell division
        
        provides the platform for intercellular transport
        
        provides support during cell adhesion
    - - pili, cilia, flagella
        
        function: allow movement
- - - - asexual reproduction of prokaryotes
    - - definition: division of eukaryote nucleus, a key process in the asexual reproduction of eukaryotes; a reproduction for continuity
      - function: in multicellular organisms, primarily for (1) growth or (2) recovery and repair
      - result: two diploid daughter cells with genetic material identical to the mother cell's
      - mitotic index
        
        a number between 0-1, calculated from (number of cells undergoing mitosis/ total number of cells in the area)
        
        indicates the rate of growth OR level of aggression, if applied to a tumour or cancerous tissue.
      - Mutations
        
        mutagens
        
        definition: various factors which cause mutation to happen, including chemical impacts and radiation.
        
        other possible causes of mutation include random mutation and inheritance
        
        tumour (definition: an uncontrolled cell proliferation caused by genetic mutation in tumour suppresor genes or proto-oncogenes)
        
        benign
        
        tumours which stayed properly in their place; though the cells aren't performing their functions at good efficiency they are not hindering the organism's overall wellness.
        
        malignant
        
        tumours which are causing problems for the organism, threatening their health. These tumours are called cancers.
        
        situation 1: tumours cells have detached from their original positions, entered the blood circulation and ended up somewhere else in the body, where nutrition environments are not fit. This lack of nutrients causes the cell to grab whatever is available, thereby meddling with the once-proper nutrient shares, and ends up harming indigenous cells.
        
        situation 2: the tumour has grown to intrude into other spaces, taking up other tissue's places.
        
        proto-oncogenes
        
        genes that control the cell cycle
        
        tumour suppressor genes
        
        genes responsible for preventing cell proliferation and correcting errors due to DNA damage
    - - definition: devision of eukaryote nucleus, a key process for sexual reproduction of multicellular organisms; a reproduction for variation which extends the species' genetic pool
      - result: a diploid mother cell produces four haploid daughter cells which each have half a number of the mother cell's number of chromosomes and are different in each's combination of alleles
        
        definition: diploid= chromosomes come in pairs, abbreviated as "2n". Haploid= chromosomes are halved, hence do not come in pairs; abbreviated as "n"
      - process: meiosis is divided into part I and part II, structured as two sets of mitosis
        
        meiosis I
        
        prophase I
        
        metaphase I
        
        anaphase I
        
        during this phase, homologous chromosomes are separated, halving the number of chromosomes in each daughter cell.
        
        telophase I
        
        meiosis II
        
        identical with mitosis
    - - definition: division of a cell's cytoplasm to form two cells.
        
        plant cells create the new cell wall by spreading a line of vesicles containing pectin along the mother cell's equator and linking them together, forming a middle lamella; then cellulose is added on either side of the lamella to form two cell wall (one for each daughter cell. During the process of construction, this structure can be called a "cell plate").
        
        animal cells have actin and myosin proteins, which are usually randomly positioned, arrange in parallel in a ring around the equator of the cell and forming a contractile ring. The ring exerts tension to pull the membrane inwards, forming a cleavage furrow and eventually splitting the cell. During this process, the plasma membrane is moved.
      - occurrence: happens after mitosis and in different ways in plant vs. animal cells
        
        in rarer, occasions, when cytokinesis happens before (without) DNA duplication, an anucleated daughter cell is produced. The anucleated : cell will not be able to synthesise its own proteins
        
        example: red blood cell
      - usually equal division. However, unequal division may also happen with some limitation: the daughter cell receives (1) its own nucleus and (2) a mitochondria
        
        example 1 (mitosis): yeast budding
        
        example 2 (meiosis): oocyte (egg) production
  - - - fertilization
        
        definition: fusion of male and female gamete to produce a zygote
      - cell repeat divide -> embryo
      - vitosis
        
        ensure all the cells in membrane has the gene in the genome
      - early stage cell are Unspecialized
        
        Grow and specialized
        
        concentrations of morphogens
        
        indicate cell position
        
        determine the differiation it follow
    - - Two key properties
        
        self-replicating
        
        undifferentiated
      - Types of stem cell
        
        Pluripotent
        
        during the development of cell
        
        can differentiate to many but not all
        
        Multipotent
        
        only can differentiate to few types of cell
        
        in adult tissue
        
        Totipotent
        
        early stage
        
        can differentiate to any cell
      - stem cell niches
        
        All cell in embryo are stem cell
        
        precise location of stem cell is called stem cell niche
        
        Definition: microenvironment with conditions needed to make stem cell inactive & undifferentiated
        
        Examples
        
        Hair follicles
        
        pores in the skin that hold hair
        
        SC locate ot the base
        
        blood capillaries supply nutrition
        
        Bone marrow
        
        soft, spongy tissue in the middle of bones
        
        haematopoictic stem cells are produced
        
        red & white blood cells
        
        platelets
        
        Blood provide necessary components
    - - red blood cell
        
        small (7um)
        
        narrow capillaries & large surface area
      - female gametes
        
        110 um
        
        large volumn of cytoplasm -> enough food
      - strated muscle fibres
        
        20-100um
        
        large & powerfyl muscle contractiosn
      - white blood cells
        
        10-12 um
        
        produce antibodies
      - male gametes
        
        3um wide
        
        allow sperm to swim to egg
      - neurons
        
        20um
        
        can extend for meter or longer
    - - surface area-to-volumn ratio of cells decrease as cell grow larger
      - rate of materials enter & leave cell depends on surface area
      - rate of materials are used or produced depends on the volumn
      - surface area - to - volumn limits how big a cell can grow
    - - cell specialized for exchange process
      - flattening
        
        make cell very wide & thin
        
        e.g. red blood cell
      - microvilli
        
        finger-liked projections on the exposed surface of epithelial cell
        
        reabsorb glucose and other useful substance
      - invagination
        
        infolding of the plasma membrane to form tubules/ folds or sacs
    - - the alveoli of the lungs -> air sacs
        
        gas exchange happen
        
        wall is epithelium
        
        one cell thick
        
        contains two cell types with different structure
        
        for different functions
      - Type I pneunocytes
        
        make up 95% alveolus wall
        
        little cytoplasm, thin and permeable
      - type II pneunocytes
        
        rest 5% of alveolus
        
        dense cytoplasm with many vesicles
        
        secrete fluid that keeps the alveoli moist and reduce surface tension (using a natural detergent)
        
        prevent alveoli from sticking together
    - - muscle tissue exerts pulling forces as it contracts
      - study guide p79
    - - Male gametes travel to female gametes
        
        different adaptations
      - male gametes
        
        mortile
        
        can swim
        
        more faster -> more chance to fertilizing
        
        small size & efficient propulsion system
        
        larger numbers are produced compare to female
        
        increase chance to fetilize egg
      - female gametes are much larger
        
        all the food are reserved in it
        
        smaller number gametes are produce than male
      - Diagrams
        
        study guide page 79
  - - - 1) interphase
        
        1) G_1 phase
        
        2) S phase
        
        3) G_2 phase
      - 2) division
- - - - *bond formation releases energy, more solute, lower SP (greater the effect)
      - Max: 0; get more negative
      - reduction in PE of the water due to solute-water bonds
    - - Higher pressure, greater PE
      - can be positive (turgid) or negative (xylem)
    - - osmosis: higher WP to lower WP
      - values are relative, pure water at standard atmospheric pressure and 20˚C is 0
      - Measurement of P.E. per unit V
      - Max: 0; WP can only be more negative
      - WP = SP + PP
    - - Fully turgid: WP=0, -S=P
      - Partially turgid: P is still positive, yet -S>P
      - Flaccid: P=0, WP=SP
      - Xylem vessel: P is negative, WP is extremely negative
  - - - differences in concentration
      - plasma membrane
        
        holds useful inside the cell
        
        prevents harmful substances
      - examples
        
        large molecules: proteins, starch
        
        Polar molecules: glucose, amino acids
        
        Ions: chloride, sodium
  - - - simple diffusion
        
        does not happen in solids
        
        small non-polar molecules can diffuse across membranes
        
        concentration of it is same on 2 side of membrane
        
        move in both direction
        
        rate -> depends on their concentration
        
        higher concentration -> more molecules move
        
        higher concentration on one side of membrane -> move in both directions
        no special structures are required in the membrane
        
        Example
        
        CO2: non polar
        
        oxygen : non polar
        
        passive: natural consequences
        
        net movement from higher concentration to lower concentration
      - facilitated diffusion
        
        Ions & polar molecules only pass between the phospholipids in membrane at a slow rate
        
        channel proteins are needed
        
        a pore -> allow particle to pass membrane in either directions
        
        some of these can open & close pore
        
        passive movement of particles across membrane from high to low concentration vio channel proteins
    - - Water is solvent
        
        particles dissolve in water
        
        forming hydrogen bonds
        
        other intermolecular interactions
      - membranes very permeable to water
        
        across membrane rapidly
        
        move in either direction
      - net movement from low concentration to high concentration area (water)
      - concerntration of solutes causes movement of water
      - Osmosis is a passive movement of water molecoles
        
        from low to high concentration & across permeable membrane
      - plasma membrane
        
        all permeable
        
        increased by placing aquaporins
        
        aquaporins do not use energy
        
        the properties of pore prevent other particles
        
        water molecules are never pumped
    - - semi-permeable & partially permeable
        
        membrane are described as this since allow substance to go through
      - active transport are selectively oermeable
  - - - tail: hydrophobic
      - head: hydrophilic
    - - saturated fatty acid: all the carbon stoms are connected by single covalent bonds
      - monounsaturated fatty acids: double bond between
      - polyunsaturated fatty acids
        
        has two or more bonds
      - triglycerides: oil in plant / fat in animal
  - - - protein pumps carry out active transport
      - low to high concentration
      - specific direction
        
        pump on one side and exit on another side
      - ATP -> more stable
      - movement of substance across membrane using energy (ATP)
    - - Gated ion channels
        
        can open and close and allow ions to go through
        
        used in berve impulses & synapic transmission
      - Voltaged-gated sodium & potassium channels
        
        use in nerve impulse
        
        membrane proteins can change shape to change voltage
        
        since inside are less positive than out side, voltage go through
        
        open & close a pore
      - nerve impulse
        
        brief movement of sodium
        
        -50 mv -> NA+ & K+ channel close
        -50-40 mv -> NA+ open, voltage rise
        40+ mv -> K+ channel open, return to orginal level of -70 mv
      - Nicotinic acetylcholine receptors
        
        use at synapses
        
        proteins in the postsynaptic membrane in both receptor & channel
      - Binding
        
        binding sites are vacant so the pore is closed
        
        binding of acetylcholine causes the pore to open
    - - Exchange treansporters -> multi-taskers
        
        transport different substances in opposite directions
      - generates concentration gradients
        
        Na + K across membrane allows a nerve impulse
    - - movement of glucose in to cell
        
        concentration of Na+ are not equal
        
        energy drives the movement of glucose
        
        ATP pump our Na+ out of cell to maintain balance of concentration
        
        sodium-glucose move Na+ & glucose into a cell
  - - - polypeptides with carbonhydrate attached
      - partly proteins & partly carbohydrate
    - - lipids with carbohydrates attached
    - - cell adhesion
        
        together form a carbohydrate-rich layer on plasma membrane
        
        the layer is glycocalyx
      - cell recognition
        
        differences between 2 G -> recgonize other cell
  - - - unsaturated fatty acids more loosely -> fluid, flexible & permeable
      - satuurated fatty acid lead to more stable structure with low fludity
    - - maintain orderly arrangement
      - prevents membrane too fluid
    - - do not solidify
      - membrane become viscous & inflexible
      - restrict movement & cell likely to burst
  - - - formation of vesicle
      - contain water and solutes from outside of cell
      - contain larger molecules
    - - fusion of vesicle
    - - small spherical sac of membrane with a droplet of fluid inside
      - dynamic feature
      - move materials around inside cell
- - - - ribose or deoxyribose as pentose sugar
  - - - catalysis: chemical reactions
      - self-replication of molecules: inheritance and evolution
      - self-assembly: spontaneous building of macromolecules
      - compartmentalisation: distinction of cell from environment
      - seven functions of life
        
        metabolism
        
        homeostasis
        
        growth
        
        nutrition
        
        reproduction
        
        excretion
        
        response
    - - primordial soup theory
  - - - a simple simulation of conditions believed to exist on early Earth, producing organic compounds in the sample taken; supports spontaneous origin of life
  - - - Last Universal Common Ancestor
      - all organisms use LUCA
      - 64 codons
    - - fossils
      - Isotope ratios in rock
      - Genomic information
    - - 350 types of protein was proved are form by LUCA's genome
      - LUCA lived in environment with high concentration of hydrogen, carbon dioxide & iron
- - - - can be DNA or RNA
      - single or double stranded
      - linear or circular
      - positive sense or negative sense
    - - some enveloped during lysis, helps to make contact with host cell and infect it
      - non-enveloped: do not become enclosed in membrane
      - animal cell are envelop and plants / bacteria are not
  - - - Influnza
      - HIV
- - - - freeze-fracture
  - - - applies stains to increase visibility
        
        direct attachment
        
        indirect attachment
  - - - meters
        
        centimeters
        
        millimeters
        
        nanometers
    - - measured size of image/ actual size of specimen
    - - size of image/ magnification
- - - - alcohol
        
        a hydroxyl group
      - icetone
      - carboxylic acid
      - ester
      - amine
      - amide
    - - monosaccharides
        
        carbon ring isomers
        
        triose
        
        tetrose
        
        pentose
        
        ribose
        
        deoxyribose
        
        hexose
        
        glucose
        
        the most common form
        
        alpha glucose
        
        1 more item...
        
        beta glucose
        
        1 more item...
        
        fructose
        
        galactose
        
        "ga"=half, half of lactose
        
        "isomers" definition: molecules with identical molecular formula but different structural formulae
        
        definition: a monomer sugar
      - disaccarides
        
        maltose
        
        glucose + glucose
        
        sucrose
        
        glucose + fructose
        
        lactose
        
        glucose + galactose
        
        formed through condensation reaction of monosaccharides, which are bonded by a glycosidic bond
        
        definition: a polymer sugar consisted of two monomers
      - polysaccharides
        
        starch
        
        amylose
        
        amylopectin
        
        presence: found in plant cells only
        
        composed of alpha glucose
        
        glycogen
        
        needed for cellular respiration, hence present in rapidly metabolising cells; found in liver and muscle cells
        
        presence: found in animals only
        
        composed of alpha glucose
        
        cellulose
        
        presence: found in plants' cell walls only
        
        composed of beta glucose
  - - - = two smaller molecules combining into a single macromolecule, eliminating a H_2O during the process
      - can be reversed by applying a reducing agent, thereby triggering hydrolysis
      - can be carried out by an oxidising agent coming into contact with an oxidised molecule
        
        the oxydising agent contributes an oxygen and takes away one positive hydrogen ion and one electron
    - - a reducing agent takes an oxygen from the reduced molecule and gives it, separately, one positive hydrogen ion and one electron (which combines into a regular hydrogen atom)
        
        all mono & disaccharides are reducing sugars, except for sucrose
        
        Benedict's reagent (CuSO_4, copper sulphate in NaOH alkaline solution; apply heat to produce Cu^2+)