Bio Notes (Homeostasis, Biomolecules)Document Transcript
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1.1. Feedback loops
Positive Feedback Loop
● Positive feedback loops increases the change in the environmental condition.
● Usually do not result in homeostasis
● They almost always operate when acontinuous increase in some internal variable
● Enhance the effect of a change in the internal or external environment
● Example: initial uterine contractions during childbirth
stimulate the releaseof the
hormone oxytocin from the pituitary gland, which increases and intensifies the
contractions. When the baby is delivered, the contractions stop, which in turn stops the
production of oxytocin.
● Not likely to be tested.
Negative Feedback Loop
● Negative feedback occurs when a system responds to change by attempting to
compensate for this change.
● Homeostasis is accomplished by negative feedback mechanisms.
● A negative feedback mechanism includes three components: a sensor, which detects
changes in the body’sconditions; an integrator, which compares the sensory
information to the desired set point; and an effector, which acts to reestablish
● All animals use manynegative feedback mechanisms to maintain homeostasis, and
responses can be physiological or behavioural.
● Example 1:
→ Maintaining body temperature in animals
→ integrator = hypothalamus
→ receives information from receptors in skin and spinal cord
→ if temperature drops below setpoint
● effectors such as vasoconstriction in skin is activated (when blood flow through the skin
is reduced, less thermal energy is lost to the environment)
● Shivering, which generates body heat
● Makes us aware of the low temperature
1.2. Cell Structure
1.1.1 General information
● Parts of a cell: chloroplasts, cell membrane, cell wall, cytoplasm,cell vacuoles, nucleus,
mitochondria, ribosome, smooth and rough endoplasmic reticulum, golgi apparatus,
lysosome and cilia
● Prokaryotic cells are probably not tested.
● Eukaryotic cells have membranebound organelles and a true nucleus is present.
1.1.2. Functions and
● Cell wall
→ Usually found in plant and
→ consists of cellulose fibres
→ provides structural support
to the cell and the plant due to
its mechanical strength
→ contains chromatin which
controls cell activities
→ chromatin contain DNA (instruction for traits & characteristics and to carry out the cell’s
→ separated from cytoplasm by nuclear membrane
→ Inner membrane has many folds to increase total surface area
→ produce adenosine triphosphate (ATP) from cellular respiration
→ releases energy by oxidising glucose
→ Present in eukaryotic photosynthetic cells
→ contains chlorophyll
→ converts light energy to glucose and oxygen during photosynthesis
→ converts solar energy to chemical energy
6H20 + 6CO2
C6H12O6 + 6O2
→ Membranebound sacs for storage, digestion and waste removal
→ food vacuoles are formed by phagocytosis
→ central large vacuole helps plants to maintain shape, fluid within vacuole known as cell sap,
membrane known as tonoplast
→ free or membranebound (attached to rough ER)
→ sites of protein synthesis, newly synthesised proteins may be passed into the rough ER for
● Rough ER (endoplasmic reticulum)
→ Isolate and transport proteins synthesized by attached ribosomes
→ Proteins may undergo further folding within the rough ER
→ Abundant in cells producing proteins or enzymes, e.g.pancreatic cells, muscle cells
● Smooth ER (endoplasmic reticulum)
→ Synthesis and transport of lipids
→ E.g. Membrane phospholipids and steroid hormones
→ Abundant in cells involved in lipid synthesis, e.g. epithelial cells of small intestine, liver cells,
muscle cells, adrenal cortex
● Golgi apparatus
→ Process and packages complex molecules such as proteins and fats that are made by the
→ Transports protein and fat molecules to cell membrane for secretion
→ Other secretions include hormones, antibodies and enzymes
→ secretes by forming membranous sacs which fuse with the cell membrane (exocytosis)
→ Proteins and lipids synthesized within ER are frequently passed into GA for modification,
sorting and packaging before being released or secreted to exterior of cell.
→ Originated from the GA
→ Can be found in most plant and animal cells, especially phagocytic cells
→ Breaks down worn out organelles within the cell
→ Digests materials taken in through endocytosis (e.g.amoeba feeding) or phagocytosis
(ingestion of bacteria by white blood cells)
→ provides support for organelles
→ help to direct movements of organelles inside cell
→ support for cell, to maintain cell shape
→ for cell mobility
→ hairlike projections
→ line the primary bronchus to remove microbes and debris from the interior of the lungs
● Cell membrane
→ covered in detail later
1.1.3. Differences between animal and plant cells
1.2. Cell Membrane
1.2.1. Fluid Mosaic model
● Protein molecules scattered within a fluid phospholipid bilayer in mosaic pattern, thus
name of model.
● Within the phospholipid bilayer are many different types of embedded proteins and
cholesterol molecules whose presence spawned the term mosaic. From scanning
electron microscope images, it was observed that the embedded molecules can move
sideways throughout the membrane, meaning the membrane is not solid, but more like a
● Simplified diagram:
Less simplified diagram:
→ Major component of membrane
→ Phospholipids are lipids with phosphate groups(PO43) that are hydrophilic while hydrocarbon
chains are hydrophobic.
→ When phospholipid molecules come into contact with water, they tend to line up polar heads
in water and hydrocarbon tails away from water.
→ The phospholipid molecule has a watersoluble, polar “head” and two fatsoluble, nonpolar
→ peripheral/extrinsic proteins and integral/intrinsic proteins
→ peripheral/extrinsic proteins are attached at polar surface of phospholipid bilayer
→ Integral / intrinsic proteins are either partially penetrating the phospholipid bilayer or span the
→ Proteins partially embedded in phospholipid bilayer: Contain both hydrophilic and hydrophobic
regions to interact with polar heads and hydrocarbon tails of phospholipid bilayer respectively.
→ Interspersed among phospholipids
→ Consists of carbohydrate chains bound to peripheral proteins and hydrophilic regions of
integral proteins that occur on surface of outer membrane
→ Carbohydrate chains involved in recognition of same cell type or adhesion of cells to
neighbouring cells for immune response.
→ Interspersed among phospholipids
→ Consists of carbohydrate chains bound to polar head of phospholipid
→ Involved in recognition of same cell type or cell signalling pathways.
→ Interspersed among phospholipids
→ Essential in maintaining membrane fluidity
1.2.3. Functions of cell membranes
● To compartmentalise the cell
→ Different metabolic processes require different enzymes that must be separated so that
metabolic reactions can take place without interference from other enzymes, thus increase
→ Example: Protein synthesis occurs within the cytoplasm and/or the ER.Lysosome contains
protease that breaks down proteins.
→ prevent autolysis
● Controls entry and exit of substances
→ Separates cytoplasm from external environment maintaining constant environment inside cell.
● Increases surface area for exchange of substances
→ E.g. Microvilli of intestinal cells making up the villi
● Site of chemical reactions
→ E.g. light reactions of photosynthesis take place on membranes found in chloroplasts.
1.3 Transport in Cells
1.3.1. Passive Transport
● no energy is required to move a substance (such as water or carbon dioxide)
● from an area of high concentration to an area of low concentration until the concentration
is equal, sometimes across a membrane.
● The hightolow concentration gradient is the driving force for passive transport because
it fulfills a fundamental law of nature: Things tend to move from a highenergy, ordered
structure to a lowerenergy, increasing randomness, or increasing entropy state of being.
● Certain molecules, such as oxygen, simply move directly through a membrane in
response to the hightolow concentration gradient. As an example, oxygen diffuses out
of the lungs and into the blood for transport to all of the cells.
● Substances are sometimes too large to move freely through a membrane, or they need
to move against a concentration gradient so transport proteins embedded in the
membrane assist with the passage.
● Transport protein creates a chemical channel for the passage of a specific substance.
Because no energy is expended, the rate of facilitated diffusion depends on the number
of transport proteins embedded in the membrane.
● e.g. Glucose is moved by a glucosetransporter protein as it passes through the red
blood cell into a body cell.
● similar to diffusion
● refers only to water diffusing through a permeable membrane.
● Water as a solvent moves from an area of high to low concentration.
● water flows from a lowsolute to a highsolute concentration until the concentration is
● The solution that has a highsolute concentration is a hypotonic solution relative to
another lowersolute concentration or hypertonic solution.
● Water will continue to osmotically move from the lowsolute/highsolvent concentration
toward the highsolute/lowsolvent concentration until both sides are isotonic, or equal.
● These are membrane proteins that allow the passage of ions that would ordinarily be
stopped by the lipid bilayer of the membrane.
● These small passageways are specific for one type of ion, such that a calcium ion could
not pass through an iron ion channel.
● The ion channels also serve as gates because they regulate ion flow in response to two
environmental factors: chemical or electrical signals from the cells and membrane
● Sometimes substances must be pumped against a concentration gradient, such as the
sodium ions (Na+) and potassium ions (K+) pump.
● So a transport protein and energy, usually adenosine triphosphate (ATP), the energyrich
compound, are needed to push the ions against the gradient.
● In the case of sodium and potassium ions, maintaining sodium outside and potassium
inside the cell is crucial to the functioning of muscles and nerves.
● The following mechanism illustrates an active transport mechanism:
1. Sodium ions inside the cell bind to the transport protein as a phosphate is added from an ATP,
which changes the shape of the transport protein.
2. The new transport protein structure carries and deposits the sodium to the exterior and bonds
with a potassium ion, loses the phosphate group (which again changes the shape of the
transport protein), and allows for the return trip.
3. The potassium is deposited inside the cell, and a sodium ion and a phosphate are attached to
a transport protein to repeat the process.
Endocytosis and exocytosis
● for big molecules, such as long protein chains or ringed structures, as well as the bulk
volume of small molecules.
● In endocytosis, substances such as food are brought into the cell in a process in which
the cell membrane surrounds the particle and moves the particle inside the cell, creating
a vacuole or vesicle as a membraneenclosed container. I
● n exocytosis, waste products or hormones, which are contained in vacuoles or vesicles,
exit the cell and their containing membrane is absorbed and added to the cell membrane.
● There are three types of endocytosis:
→ Pinocytosis occurs when the cell absorbs fluid from the exterior, creating a fluid vacuole.
→ Receptormediated endocytosis is a special type of pinocytosis that is activated by the
identification of a receptor protein sensitive to the specific substance.
→ Phagocytosis is the engulfing and digesting of substances, usually food, by vacuoles with a
lysosome attached (a lysosome is an organelle that contains digestive enzymes).
● Contain the elements C, H, O
● They are either made from single monosaccharide monomers or from several
monosaccharides joined together
● general formula (CH2O)n
● Monosaccharides are:
→ Trioses – C3H6O3 (e.g. glyceraldehyde)
→ Pentoses – C5H10O5 (e.g. deoxyribose)
→ Hexoses – C6H12O6 (e.g. glucose, fructose)
● Many monosaccharides are joined in a chain to form polysaccharides.
● Glycogen and starch are storage carbohydrates in animals and plants respectively.
● Joined by condensation reaction.
● n molecules joined together produces n1 molecules of water
● the bond is called glycosidic bond
→ polymer of glucose molecules
→ made up of amylose and amylopectin
→ has a complex 3 dimensional structure that is insoluble in water
→ amylose chain is coiled into a helix to make it easier to store
→ amylopectin is long and extensively branched so that it is more compact
● Starch and glycogen are INSOLUBLE to stop interference with osmosis, and COMPACT
to store more energy for future cellular respiration.
→ long, straight, unbranched chains of glucose
→ chains held together by hydrogen bonds to form strong fibrils
→ chemically inert and insoluble, thus difficult to digest
→ only some bacteria, fungi and a very small number of animals can secrete cellulase
2.1.2.Functions of carbohydrates
126.96.36.199. Monosaccharides and disaccharides
● Building blocks for larger molecules (e.g. DNA,cellulose, starch, glycogen)
● Source of respiratory energy (glucose)
● Transport compound (sucrose in plant phloem)
● Infant milk (lactose)
● Attraction – flower nectar, fruit (fructose)
● Honey – Bees food storage
● Examples – starch, glycogen, cellulose
● Energy Storage starch (plant) and glycogen(animal)
● Structural Cellulose cell wall (plant) and Chitin(insects/crab/shrimp)
2.2.1 Properties of water
● high heat capacity
● high heat of vapourisation
● high heat of fusion
● most dense at 0 degrees Celsius
● density of water decreases as the temperature increases when the temperature is above
0 degrees Celsius
● density of water decreases as the temperature of water decreases from 4 degrees to 0
● water has high cohesion (force of attraction between like molecules) due to hydrogen
● an effect of high cohesion is high surface tension
● In clear water, red and yellow light can reach a depth of 50 metres while blue and violet
light can penetrate 200metres deep.
● The ability of light to penetrate water enables photosynthetic organisms to occupy the
vast volumes of lakes and oceans
● water has low viscosity
188.8.131.52. Water as a solvent
● many substances are dissolved in the water of biological fluids (e.g. blood plasma)
● Hydrophilic substances dissolve in water
2.2.2. Uses of water
The significance of the physical properties of water
Properties of water
Significance for living things
Liquid at room temperature
∙ Liquid medium for living things and for the
chemistry of life
Much heat energy is needed to raise
the temperature of water
(very high specific heat capacity)
∙ Aquatic environments are slow to change
Evaporation of water requires a great
deal of heat
(high latent heat of vaporisation)
∙ Evaporation of water in sweat or in
transpiration causes marked cooling
∙ Much heat is lost by the evaporation of a
small quantity of water
Much heat must be removed before
(very high latent heat of fusion)
∙ Contents of cells and aquatic environments
are slow to freeze in cold weather
Ice is less dense than water, even very
∙ Ice forms on the surface of water, insulating
(maximum density at 40C)
the water below
∙ When surface water does freeze, aquatic
life can survive below the ice
Water molecules at surface with air
orientate so that hydrogen bonds face
(very high surface tension)
∙ Water forms droplets on surfaces and runs
∙ Certain small animals exploit surface
tension to land on and move over the
surface of water
Water molecules slide over each other
(very low viscosity)
∙ Water flows readily through narrow
∙ Mucus is used externally to aid movement in
animals (e.g. snail and earthworm). It is also
used internally in the movement of food
along the digestive tract or movement of
sperm along the oviduct.
(ii) The synovial fluid lubricates movement in
many vertebrate joints.
(iii) The pericardial fluid lubricates movement
of the heart.
Water molecules adhere to sufaces
(strong adhesive properties)
∙ With low viscosity, capillarity becomes
possible, water moves through extremely
narrow spaces e.g. between soil particles,
and in cell walls
∙ Large adhesive forces between cellulose in
capillary and the water within them so a
column of water can be maintained (capillary
Water column does not break or pull
apart under tension
(high tensile strength)
∙ Medium for chemical reactions of life
Water is colourless
(high transmission of visible light)
∙ Plants can photosynthesize at depth in
∙ Light may penetrate deeply into living
Light can easily penetrate the waterfilled
epidermis of leaves and reach the underlying
mesophyll cells, which contain chloroplasts
Metabolic role of water:
Water is required for the hydrolysis of many substances (for examples, proteins, lipids and
All biochemical reactions in cells occur in an aqueous medium.
Water is needed for the diffusion of materials across surfaces such as in leaf cells
Water acts as a substrate for photosynthesis
2.3.1. Properties of Lipids
● made up of carbon, hydrogen and oxygen
● have much less oxygen than hydrogen
● insoluble in water
● soluble in organic solvents
● in solid state at 20 degrees Celsius fats
● in liquid state at 20 degrees Celsius oils
● identified using emulsion test
● Classification: simple lipids (triglycerides, waxes), compound lipids (phospholipid, glycolipid),
steroids and sterols (cholesterol)
2.3.2. Structure of Lipids
● the components of lipids are fatty acids and glycerol
● glycerol bonds with 3 fatty acids
Food test: white emulsion from ethanol/water + oil
184.108.40.206. Fatty acids
● A fatty acid consists of a hydrocarbon chain and a hydroxyl group (COOH), i.e. RCOOH, R
being the hydrocarbon chain
● Fatty acids may be saturated or unsaturated
● Saturated fatty acid (e.g. stearic acid)
→ does not contain carboncarbon double bond in hydrocarbon chain
→ have the maximum number of hydrogen atoms
● Unsaturated fatty acid (e.g. oleic acid)
→ contains carboncarbon in double bond hydrocarbon chain
→ kinks in fatty acid tail
Glycerol’s molecular formula is C3H8O3
2.3.3. Classification of Lipids
● Simple Lipids
→ formed by joining fatty acids to an alcohol (e.g. glycerol) by ester linkages
→ Fats are formed by joining fatty acids to a glycerol molecule.Examples of fats include
monoglyceride,diglyceride and triglyceride.
→ These are NOT made from monomers
→ Each contains 1 glycerol and 3 fatty acid molecules(elements: C, H, O)
→ They are linked by ester bonds
→ These form during condensation reactions
→ Fats (solid at room temp.) contain saturated fatty acid chains
→ Oils (liquid at room temp.) have unsaturated chains
→ Consist of organic group, phosphate group,glycerol and fatty acid.
→ The bonds between the glycerol and fatty acid are broken by hydrolysis.
→ Major component of the plasma membrane, because they form a bilayer.
→ Hydrophilic heads outside, hydrophobic tail inside.
→ One fatty acid in triglyceride swapped for phosphate base
→ Waxes are formed by joining fatty acids to highmolecular weight alcohols. (nonglycerides)
→ Waxes are found in the cuticles of leaves
2.3.3. Functions of Lipids
220.127.116.11. In Mammals
● Water repellent properties – waterproof fur and skin.
● Structural Cell membranes, phospholipids and polar nature
● Electrical insulation – myelin, insulates neurones, impulse transmission more rapid.
● Hormones – steroids e.g. testosterone and oestrogen
● Physical protection – shock absorb, found round delicate organs e.g. kidneys
● Thermal insulation – conducts heat poorly, so insulates. Blubber in diving animals.
● Energy storage: yield twice as much energy compared with carbohydrates and also yield
metabolic water during respiration.
→ Why is triglyceride able to store energy?
A triglyceride molecule is large and uncharged. It is also insoluble in water: Being insoluble, they
can be stored in large amounts. There will not be any great effect on the water potential of
cells. This can prevent it from diffusing out of cells.
18.104.22.168. In Plants
● Attraction – plant scents contain fatty acids
● Waterproofing – wax for the cuticle (not glycerol,different alcohol used)
● Energy storage – Oil droplets in plant cells
● Honeycomb beeswax
2.4.1. Properties of Proteins
● sensitive to pH and heat (can be
● shape determines its function (e.g.
active site in enzymes)
● contains H, C, H, S
● Made up of amino acids
● there are about 20 types of amino
acids in proteins
2.4.2. Structure of Proteins (I)
22.214.171.124. Structure of amino acids
● four groups bonded to a carbon, where R is the variable that determines the varieties of
the various amino acids differ in their R group
126.96.36.199. How polypeptides are formed
● amino acids join together to form polypeptides
● Two amino acids become joined by a peptide bond to form a dipeptide via condensation
and water is formed as a byproduct
● Reaction is between amino group & carboxyl group
● Continued condensation leads to the addition of further amino acids resulting in the
formation of a long chain called a polypeptide.
● n amino acids/polypeptides joined together yield (n1) molecules of water
2.4.3. Structure of Proteins (II)
2.4.4. Classification of Proteins based on Structure
● Proteins can be classified under globular and fibrous
188.8.131.52. Globular Proteins
● Polypeptide chain folded into a compact, spherical
● soluble in aqueous medium
● Enzymes, hormones (e.g. insulin), haemoglobin,
● Example: Haemoglobin
→ With quaternary structure
→ 2 alpha globin and 2 beta globin
→ globular/spherical shape
→ permits transport of oxygen in blood
184.108.40.206. Fibrous Proteins
● long polypeptide chains twist around each other to
● insoluble and provide high tensile strength
● Examples: Collagen and elastin (structural component of skin and blood vessels),
myosin, keratin (in nail, horn, hair, feather).
● Detailed example: Collagen
→ with quaternary structure
→ triple helix
→ fibrelike/rod shaped
→ found in tendons, bone, skin, teeth and connective tissue, cartilage
2.4.5. Roles of Proteins