IB Biology Y11
ECOLOGY: The study of the relationship between living organisms, or between living organisms and their environment
MOLECULAR BIO
CELL BIO
Respiration
Photosynthesis
Metabolic Molecules
CELL Membrane
Proteins
Lipids
Carbohydraes
Nucleic Acids
Formed due to the amphipathic properties of phospholipids ✏
Enzymes
Cell Theory
Components
- All living things are composed of cells (or cell products)
- The cell is the smallest unit of life
- Cells only arise from pre-existing cells
Phospholipids held by weak hydrophobic interactions
Species & Ecosystems
DNA
RNA
Species: a group of organisms that can potentially interbreed to produce fertile, viable offspring
DNA replication
Hybrids: offsprings produced by cross-breeding of 2 diff species --> are reproductively sterile
Integral proteins (for transport, enzymatic activity & intercellular joining)
Functions of Life
Metabolism
Reproduction
Water (H2O)
Sensitivity
Homeostasis
Excretion
Peripheral Proteins (cell to cell recognition, attachment)
Nutrition
Growth
Living things undertake essential chemical reactions
Living things produce offspring, either sexually or asexually
Population: a group of organisms of the same species living in the same area at the same time
Living things are responsive to internal and external stimuli
Living things maintain a stable internal environment
Habitat:The environment in which a species normally lives/the location of a living organism
Living things exhibit the removal of waste products
Community: group of populations living together & interacting with each other within a given area
Living things exchange materials and gases with the environment
Ecosystem: A community and its abiotic environment (i.e. habitat)
Living things can move and change shape or size
Cholesterol (reduces membrane fluidity)
Structure
Fluid Mosaic Model
FLUID
Phospholipid bilayer is viscous & phospholipids can move position
Modes of Nutrition
MOSAIC
Phospholipid bilayer is embedded with proteins, = mosaic of components
S.A : Volume ratio
Covalent bond, as there is a shari of electrons, but not shared equally between atoms.
The bigger the Cell, the bigger amount of nutrution and waste
Autotrophy - Self-feeding: Organisms which synthesize organic mol from inorganic sources
TRANSPORT
Resulting in Water as a polar molecule because of its slight charge difference across the different poles of the molecule.
Heterotrophy - other source feeding: Organisms which obtain organic mol from other organisms (living, recently killed & detritus)
SIMPLE DIFFUSION
The rate of exchange is determined by the Surface Area
OSMOSIS
FACILITATED DIFFUSION
The S.A. doesn't grow at the same rate than the volume (it is slower)
ACTIVE TRANSPORT
Photoautotroph - photosynthesis: Makes organic comp using energy derived from the sun (solar energy)
If the rate of exchange decreases --> Cell can't get waste products out fast enough --> Cell devides in order not to die
Chemoautotroph - chemosynthesis: Makes organic comp using energy derived form the oxidation of chemicals
Types - Classified by feeding pattern
Passive mov. of small hydrophobic particles ↓ a concentration gradient through a partially permeable membrane, w/out help from other substance (proteins). Driven by random movement, until reaches an equilibrium, even distribution (no net mov. of molec. from either side).
Oxygen → higher electronegativity → attracts electrons + strongly → oxygen atom slightly negative (δ–) → negative pole
Hydrogen → lower electronegativity → attracts electrons - strongly → hydrogen atoms slightly positive (δ+) → positive pole
Detritivores - earthworms, woodlice: Ingests non-living OM like detritus and humus
Saprotrophs - Decomposers like bacteria & fungi: Feeds on non-living OM by secreting digestive enzymes and absorbing the products
Magnification
Passive movement of water molecules across a semi permeable membrane from a region of ↓ solution concentration to a region of ↑ solution conc., due to differences in conc. of substances dissolved in water (solutes), until equilibrium is reached
Magnification = Image size : Actual size
Passive movement of particles through a p.p. membrane down a concentration gradient, through channels with proteins embedded in the phospholipid bilayer
Active transport of particles through a p.p membrane carried out by globular or pump proteins in the membrane, against the concentration gradient, using ATP.
Properties
Autotrophs obtain inorganic nutrients from the abiotic environment - -> from the air/water/soil
Cohesion
Binding of water molecules through hydrogen bonds.
enables surface tension as in liquid resists low external forces
Water’s Dipolarity allows hydrogen bonding between the molecules. As the
*THIS FORMULA CAN ALSO BE INVERTED TO CALCULATE THE ACTUAL SIZE OF THE IMAGE
Simple inorganic substance/nutrients needed: carbon, nitrogen, hydrogen, oxygen and phosphorus
NO ENERY
NO ENZYME
Heterotrophs obtain some simple inorganic substances from env., but principally obtain their C and N from the organic mol produced by autotrophs
NO ENERY NO ENZYME
NO ENERY
Emergent Properties
They arise when the interaction of individual component produce new functions
Consumers - herbivores, carnivores, scavengers Ingests OM which is living or recently killed
Adhesion
Binding of water molecules with other polar substances by hydrogen bonds.
→ enables Capillary action as it allows water to flow against gravity
Dipolarity: Allows it to to attract other polar substances (+ or -) by hydrogen bonding.
Herbivores: consumers that feed principally on plant matter
Carnivores: consumers that feed principally on animal matter
Omnivores: consumers that have a principle diet composed of both plant and animal matter
In multicellular organisms collective actions of individual cells combine to create new synergistic effects
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Organ systems collectively carry out the life functions of the complete organism
Organs that interact may form organ systems capable of carrying out specific body functions
Organs are then formed from the functional grouping of multiple tissues
Cells may be grouped together to form tissues
Scavengers: consumer that principally feed on dead and decaying carcasses rather than hunting live prey
Thermal
Has Higher specific heat capacity (Energy needed to raise 1°C 1g)
→ High boiling point. Water can absorb much heat before changing state (good temperature regulator)
Hydrogen Bonds: For water to evaporate, its particles should start dispersing and moving quicker. For this to happen, + Energy is required to break the H-bonds. → harder
Detritus: dead, particulate OM – such as decaying organic material / fecal matter
Cell Diferentiation
Humus: decaying leaf litter intermixed within the topsoil
Do not ingest food --> use enzymatic secretion to facilitate external digestion
Differentiation is the process during development whereby newly formed cells become more specialised and distinct from one another as they mature
Cell Division
Bc saprotrophs facilitate breakdown of dead OM --> commonly referred to as decomposers
OM = Organic matter
Solvent
Can dissolve any substance hydrophilic substance (either contains ions or electronegative (polar) atoms) → considered the universal solvent.
Dipolarity: As it attracts polar atoms of either charge. Because its polar attraction in large quantities of water molecules can weaken intramolecular forces (such as ionic bonds) and result in the dissociation of the atoms.
As the slightly charged regions surround atoms of opposing charge, forming dispersive hydration shells (polar associations to draw materials apart)
All cells of an organism share an identical genome – each cell contains the entire set of genetic instructions for that organism
The activation of different instructions (genes) within a given cell by chemical signals will cause it to differentiate
MITOSIS
Gene Packing
Interphase
Within the nucleus of a eukaryotic cell, DNA is packaged with proteins to form chromatin
Density
Most substances: when frozen contract → + dense Water: when frozen expands → - dense
Hydrogen Bonds: When frozen, water stops breaking and reforming bonds. These ones freeze in a lattice of hexagonal structures.
Active genes are packaged in an expanded form called euchromatin that is accessible to transcriptional machinery
Prophase
Metaphase
Inactive genes are typically packaged in a more condensed form called heterochromatin (saves space, not transcribed)
Anaphase
Telophase
Differentiated cells will have different regions of DNA packaged as euchromatin and heterochromatin according to their specific function
DNA as uncondensed chromatin, in nucleus, organelles duplicated, cell enlarged.
Disaccharides
Stem Cells
DNA supercoils & chromosomes condense & comprise into chromatids, centrosomes move to opposite poles & form spindle fibers, nucleus dissolves.
Stem cells are unspecialised cells that have two key qualities:
- Self Renewal – They can continuously divide and replicate
- Potency – They have the capacity to differentiate into specialised cell types
MESOCOSMS: enclosed env that allow a small part of a natural environment to be observed under controlled conditions
Microtubule spindle fibres from both centrosomes connect to centromere of chromosomes. Chromosomes align in the metaphase plate
Carbons 1 & 4 participate in reaction using E to form oxygen bridge/glycosidic bond.
Contraction of spindle fibres. Sister chromatids separate, & are now considered an individual chromosome. The chromosomes move to the opposite poles of the cell
Monosacharides
Glucose
Alpha Glucose has the hydrocyl goup of C1 below
Once the 2 chromosome sets arrive at poles, spindle fibres dissolve. Chromosomes decondense (no longer visible under light microscope). Nuclear membranes reform around each chromosome set. Cytokinesis occurs concurrently, splitting the cell into 2.
They can have different types of potencies:
Beta-Glucose has the hydrohyl group of C1 above
Totipotent – Can form any cell type, as well as extra-embryonic (placental) tissue (e.g. zygote)
Pluripotent – Can form any cell type (e.g. embryonic stem cells)
Multipotent – Can differentiate into a number of closely related cell types (e.g. haematopoeitic adult stem cells)
Unipotent – Can not differentiate, but are capable of self renewal (e.g. progenitor cells, muscle stem cells)
Starch
CYTOKINESIS
ANIMAL
PLANT
AROBIC
ANAEROBIC
NO Oxygen
ANIMALS: pyruvate is converted into lactic acid
PLANTS & YEASTS: pyruvate converted into ethanol & Carbon Dioxide
Oxygen
link reaction, citric acid cycle (or Krebs cycle) and the electron transport chain
LARGER ATP FIELD
SMALLER ATP FIELD
process by which cells synthesise organic compounds (e.g. glucose) from inorganic molecules (CO2 and H2O) in the presence of sunlight
CHLOROPHYLL
Green light reflected, Blue & red are the optimum
green pigment found in photosynthetic organisms that is responsible for light absorption
ABSORPTION SPECTRUM
ACTION SPECTRUM
Indicates the wavelengths of light absorbed by each pigment (e.g. chlorophyll)
Indicates the overall rate of photosynthesis at each wavelength of light
CHROMATOGRAPHY
The different components of the mixture travel at different speeds, causing them to separate
A retardation factor can then be calculated (Rf value = distance component travels ÷ distance solvent travels
An experimental technique by which mixtures can be separated. A mixture is dissolved in a fluid & passed through a static material.
LIMITING FACTORS
Temperature
Light Intensity
Carbon Dioxide Concentration
The controlled release of energy from organic compounds to produce ATP
Vesicles fuse to form a cell plate
Contractile ring of microfilaments cause constriction at all centre
MITOTIC INDEX
ratio between the number of cells in mitosis and the total number of cells
CYCLINS
A family of regulatory proteins that control the progression of the cell cycle
FATTY ACIDS
Long hydrocarbon chains that are found in certain types of lipids (triglycerides & phospholipids)
Polyunsaturated (+1 double bond)
Unsaturated (1 Double bond)
Saturated (No double bonds)
TRYGLICERIDES
largest class of lipids and function primarily as long-term energy storage molecules
Animals tend to store triglycerides as fats (solid), while plants tend to store triglycerides as oils (liquid)
HEALTH RISKS
High cholesterol levels
Discfunctioning cells
Clogging of arteries
Coronary Heart Disease
BODY MASS INDEX
Mass in kg/(height in m^2)
POLYSACCHARIDES
cellulose, glycogen, starch
Chains of nucleotides
more versatile single stranded form that transfers the genetic information for decoding
more stable double stranded form that stores the genetic blueprint for cells
Ribose
Deoxyribose
Has Uracil
Has Thymine
Double Stranded
Single Stranded
Two polynucleotide chains of DNA are held together via hydrogen bonding between complementary nitrogenous bases
is a semi-conservative process, because when a new double-stranded DNA molecule is formed; One strand will be newly synthesised & one strand will be from the original template molecule
ENZYMES
HELICASE
DNA POLYMERASE
unwinds the double helix and separates the two polynucleotide strands by breaking the hydrogen bonds that exist between complementary base pairs
synthesises new strands from the two parental template strands. Free deoxynucleoside triphosphates (nucleotides with 3 phosphate groups) align opposite their complementary base partner. DNA polymerase cleaves the two excess phosphates and uses the energy released to link the nucleotide to the new strand
The polymerase chain reaction (PCR)
an artificial method of replicating DNA under laboratory conditions
TRANSCRIPTION
TRANSLATION
process by which an RNA sequence is produced from a DNA template
RNA polymerase separates DNA strands and synthesises a complementary RNA copy from one of the DNA strands. When the DNA strands are separated, ribonucleoside triphosphates align opposite their exposed complementary base partner. RNA polymerase removes the additional phosphate groups and uses the energy from this cleavage to covalently join the nucleotide to the growing sequence. Once the RNA sequence has been synthesised, RNA polymerase detaches from the DNA molecule and the double helix reforms.
CODONS
a sequence of three nucleotides which together form a unit of genetic code in a DNA or RNA molecule. Each codon codes for one amino acid with a polypeptide chain
GENETIC CODE
the set of rules by which information encoded within mRNA sequences is converted into amino acid sequences (polypeptides) by living cells. The genetic code identifies the corresponding amino acid for each codon combination
64 codon possibilities (43)
process of protein synthesis in which the genetic information encoded in mRNA is translated into a sequence of amino acids on a polypeptide chain
Ribosomes bind to mRNA in the cytoplasm and move along the molecule in a 5’ – 3’ direction until it reaches a start codon (AUG). Anticodons on tRNA molecules align opposite appropriate codons according to complementary base pairing (e.g. AUG = UAC). Each tRNA molecule carries a specific amino acid (according to the genetic code). Ribosomes catalyse the formation of peptide bonds between adjacent amino acids (via condensation reactions). The ribosome moves along the mRNA molecule synthesising a polypeptide chain until it reaches a stop codon. At this point translation ceases and the polypeptide chain is released
Amino Acids structure
Amino acids all share a common basic structure, with a central carbon atom bound to:
An amine group (NH2)
A carboxylic acid group (COOH)
A hydrogen atom (H)
A variable side chain (R)
Proteins are comprised of long chains of recurring amino acids
Amino acids are joined together on the ribosome by peptide bonds to form polypeptides.
This condensation reactions can form the primary, secondary, tertiary or quartenary structure of proteins
DENATURATION
A structural change in a protein that results in the loss (usually permanent) of its biological properties,
because the way a protein folds determines its function, any change or abrogation of the tertiary structure will alter its activity.
Can happen due to too extreme pH or temperature values
PROTEOME
The totality of proteins expressed within a cell, tissue or organism at a certain time. The proteome of any given individual will be unique, as protein expression patterns are determined by an individual’s genes
FUNCTIONS
Structure – e.g. collagen, spider silk
Hormones – e.g. insulin, glucagon
Immunity – e.g. immunoglobulins
Transport – e.g. haemoglobin
Sensation – e.g. rhodopsin
Movement – e.g. actin, myosin
Enzymes – e.g. Rubisco, catalase
a globular protein which acts as a biological catalyst by speeding up the rate of a chemical reaction
The active site is the region on the surface of the enzyme which binds to the substrate molecule. It complements the substrate in terms of shape and chemical properties, so a particular substrate has to bind to the enzyme.
MODELS OF ACTION
Lock & Key model
Induced Fit Model
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Biofuels
Medicine
Biotechnology
Food production
Textiles
Paper
Quick source of energy
Cellulose
Glycogen
extra 1-6 Hydrogen bonds for branch
Branched (~per 10 subunits)
Main Energy storage of glucose in animals & humans.
Energy storage found in plants
Amylose
Nutrient Cycling: supply of inorganic nutrients (which is finite) is maintained by nutrient cycling. --> thus, chemical elements are constantly recycled
Linear and Straight Structure
Indigestible (bc of β-glucose) for most animals → lack enzyme
Linear, Helical structure. Harder to digest and less soluble, however, as it takes up less space, is the preferred storage form in plants
Amylopectin
formed by the bonding of 2 monosaccharides via a condensation reaction, to form a glycosidic bond and water as a by-product.
Nutrient = material required by an organism. Include: carbon/nitrogen/phosphorus.
Autotrophs get inorganic nutrients from the air/water/soil --> convert into organic comp.
Heterotrophs ingest these organic comp. --> use for growth and respiration, releasing inorganic byproducts
Saprotrophs decompose the remains of dead organisms --> free inorganic materials into soil
Return of inorganic nutrients to soil ensures the continual supply of raw materials for the autotrophs
extra 1-6 hydrogen bonds for branch
Branched (~per 20 subunits)
3 main components for sustainability in an ecosystem:
Energy availability: light from the sun provides the initial energy source for almost all communities
Nutrient availability: saprotrophic decomposers ensure constant recycling of inorganic nutrients within env
Recycling of wastes: bacteria detoxify harmful waste byproducts
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Climate Change
Greenhouse gasses: absorb and emit long-wave (infrared) radiation, thereby trapping and holding heat within the atmosphere
Types
Other gases including methane and nitrogen oxides have less impact
Co2 and water vapour are the most significant greenhouse gases
Methane = emitted from waterlogged habitats (like marshes) and landfills – it is also a gaseous waste produced by ruminants
Nitrogen oxides = released naturally by certain bacteria and also is emitted in the exhaust by certain vehicles
Impact of gas depends on:
- ability to absorb long wave radiation --> + capacity = greater impact per mol
- Gas conc. in atmosphere --> + conc = more impact. Conc depends on rate of release/persistance in atmosphere
Co2 made by cell respiration & burning fossil fuels –> removed via photosynthesis & absorption by oceans
Greenhouse effect: natural process whereby the atmos. behaves like a greenhouse to trap & retain heat --> ensures Earth maintains moderate temp needed by organisms to maintain life processes (homeostasis)
Recent increases in atmospheric CO2: largely due to increases in the combustion of fossilised organic matter.
Main activities that emit green house gasses: deforestation/increased farming & agriculture
Ocean acidification: oceans are major carbon sink & absorb ≈1/3 of all human produced (atmos.) CO2 emission
CO2 solubility is temp dependent (+ soluble when cooler) --> less CO2 will be absorbed as temp rise
When oceans absorb atmospheric CO2, some of it will remain dissolved in a gaseous state but most will be chemically modified:
Ocean -Atmosphere carbon dioxide exchange
CO2 + H20 --> carbonic acid
dissociates into hydrogen ions and hydrogen carbonate
Acidification: H+ ions lower ocean pH
H+ ions + free carbonate ions --> form more hydrogen carbonate
There is - free carbonate ions in water = marine organisms - able to produce calcium carbonate (via calcification)
Calcium carbonate used to form the hard exoskeleton of coral and is also present in the shells of certain molluscs
Thus, + concc of dissolved CO2 threatens viability of coral reefs and certain molluscs
Energy
Energy Source
Sunlight: used by photoautotrophic animals (all green plants and some bacteria)
Initial source of energy for almost all communities
Light energy absorbed by photoautotrophs and is converted into chemical energy via photosynthesis
Light energy used to make: organic comp from inorganic sources
Heterotrophs ingest organic comp and break them down vua respiration --> derive ATP (chemical energy) for metabolic process
Energy Flow:
Energy Loss
Energy Efficency
Pyramids of Energy: graphical representation of E at each trophic level
Chemical energy stored in carbon comp flows through food chains by feeding:
Trophic levels (TL): position an organism occupies within feeding sequence
1 TL: Producers - E enters ecosystem as sun --> converted into chemical E by producers through photosynthesis.
2 TL: Primary Consumers - feed on producers
Further Consumers occupy subsequent trophic levels:
TL 3: Secondary Consumer
TL 4: Tertiary Consumer
Food Chain: shows linear feeding relationships between species in a community
Arrows = transfer of energy & matter through feeding (point in direction of E flow)
1 organism is always a producer, followed by consumers
Not all E is transferred through feeding --> chemical E lost by:
- excretion through faeces
- unconsumed/uneaten portions of food
- Heat (byproduct of exothermic reactions in organisms) --> heat lost in ecosystem not recycled --> thus ecosystems require continues entry of E from external sources like sun
E stored in organic mol --> released by cell respiration to produce ATP (used for metabolic reactions for growth & homeostasis) & byproduct heat (thermal E --> organisms ccannot turn heat to other forms of usable E)
E losses between trophic levels restrict length of food chains & biomass of higher trophic levels
E transformations are ~10% efficient, ~90% of available E lost between trophic levels
Biomass: total mass of a group of organisms – consisting of the carbon compounds contained in the cells and tissues
It diminishes along food chains with loss of CO2, H20 and waste products to the environment
units of energy per area per time: kJ m–2 year–1)
Characteristic:
- never appear inverted as E stored in one source is always lost upon transfer
- Each level is roughly 1/10 the size of the preceding level (E transformations = ~10% efficient)
- Bottom level = producers
- Subsequent levels = consumers
Carbon cycling: biogeochemical cycle where carbon is exchanged between the different 4 spheres of the Earth
4 spheres:
- Atmosphere (air)
- Lithosphere (ground)
- Hydrosphere (water/oceans)
- Biosphere (living things)
Carbon exchanged in diff forms:
- Atmospheric gases: mostly CO2 & also CH4
- Oceanic carbonates bicarbonates dissolved in the H2O & calcium carbonate in corals/shells
- As organic materials: carbs, lipids & proteins found in all living things
- As non-living remains: detritus/fossil fuels
Carbon Comp.
Autotrophs convert inorganic CO2 into organic comp. (carbs, lipids, proteins) via photosynthesis
Autotrophs use Co2 for photosynthesis --> levels of co2 within organism should always be low --> co2 should always be at a higher conc in atmosph. (or water)
- Concentration gradient ensures co2 will passively diffuse into the autotrophic organism as required
- In aquatic producers, CO2 can usually diffuse directly into the autotroph; whereas in terrestrial plants, diffusion occurs at stomata
Heterotrophs cannot synthesise their own organic mol. --> instead obtain carbon comp via feeding
All organisms produce the chemical E (ATP) required to power metabolic processes via the cell respiration
- Respiration = breakdown of organic mol (e.g. sugars) & produces co2 as by-product
- Build up of CO2 in respiring tissues creates concentration gradient --> removed by passive diffusion
Compensation point: at which the net co2 assimilation is zero (intake = output) --> this is when uptake of CO2 by photosynthesis is balanced by the production of CO2 by respiration
Similarly, the amount of carbon dioxide in the environment will be determined by the level of these two processes:
more net photosynthesis than cell respiration occuring in biosphere = atmospheric carbon dioxide levels drop
more net respiration than overall photosynthesis occuring = atmospheric carbon dioxide levels should increase
Methane
Fossil Fuels
Combustion
Carbon Fluxes
Methanogens: archaean microorganisms that produce CH4 as a metabolic by-product in anaerobic conditions
Anaerobic conditions:
- Wetlands
- Marine sediments
- Digestive tract of ruminant animals