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

  1. All living things are composed of cells (or cell products)
  1. The cell is the smallest unit of life
  1. 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:

  1. Self Renewal – They can continuously divide and replicate
  1. 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

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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)

energy-transformations_med

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

pyramid-of-energy_med

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-cycle_med

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