This document can be found at http://tinyurl.com/BioNotesforTA1 :)

Topics:1. Homeostasis2. BiomoleculesLink to PPTs: https://www.edmodo.com/home#/group?id=6949465&sub_view=folders

useful links:http://www.infoplease.com/cig/biology/fluid­mosaic­model­membrane­structure­function.htmlhttp://www.shmoop.com/biomolecules/

1. Homeostasis1.1. Feedback loopsPositive 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

is required. 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 thecontractions. When the baby is delivered, the contractions stop, which in turn stops theproduction 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 sensoryinformation to the desired set point; and an effector, which acts to re­establishhomeostasis.

All animals use manynegative feedback mechanisms to maintain homeostasis, andresponses 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 Structure1.1.1 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. Diagram

1.1.2. Functions andstructure

Cell wall→ Usually found in plant andbacteria cells→ consists of cellulose fibres(carbohydrates)→ provides structural supportto the cell and the plant due toits mechanical strength

Nucleus→ contains chromatin whichcontrols cell activities

→ chromatin contain DNA (instruction for traits & characteristics and to carry out the cell’sfunction)→ separated from cytoplasm by nuclear membrane

Mitochondrion→ Inner membrane has many folds to increase total surface area→ produce adenosine triphosphate (ATP) from cellular respiration→ releases energy by oxidising glucose

Chloroplast→ Present in eukaryotic photosynthetic cells→ contains chlorophyll→ converts light energy to glucose and oxygen during photosynthesis→ converts solar energy to chemical energy6H20 + 6CO2 C6H12O6 + 6O2

Vacuoles→ 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

Ribosome→ free or membrane­bound (attached to rough ER)→ sites of protein synthesis, newly synthesised proteins may be passed into the rough ER forfurther processing

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 thecell→ 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.

Lysosome→ 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)

Cytoskeleton

→ provides support for organelles→ help to direct movements of organelles inside cell→ support for cell, to maintain cell shape

Cilia→ 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 Membrane1.2.1. Fluid Mosaic model

Protein molecules scattered within a fluid phospholipid bilayer in mosaic pattern, thusname of model.

Within the phospholipid bilayer are many different types of embedded proteins andcholesterol molecules whose presence spawned the term mosaic. From scanningelectron microscope images, it was observed that the embedded molecules can movesideways throughout the membrane, meaning the membrane is not solid, but more like afluid.

Simplified diagram:

Less simplified diagram:

1.2.2. Components Phospholipids

→ Major component of membrane→ Phospholipids are lipids with phosphate groups(PO43­) that are hydrophilic while hydrocarbonchains are hydrophobic.

→ When phospholipid molecules come into contact with water, they tend to line up polar headsin water and hydrocarbon tails away from water.→ The phospholipid molecule has a water­soluble, polar “head” and two fat­soluble, nonpolar“tails.”

Proteins→ 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 themembrane entirely→ Proteins partially embedded in phospholipid bilayer: Contain both hydrophilic and hydrophobicregions to interact with polar heads and hydrocarbon tails of phospholipid bilayer respectively.

Glycoproteins→ Interspersed among phospholipids→ Consists of carbohydrate chains bound to peripheral proteins and hydrophilic regions ofintegral proteins that occur on surface of outer membrane→ Carbohydrate chains involved in recognition of same cell type or adhesion of cells toneighbouring cells for immune response.

Glycolipids→ Interspersed among phospholipids→ Consists of carbohydrate chains bound to polar head of phospholipid→ Involved in recognition of same cell type or cell signalling pathways.

Cholesterol→ 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 thatmetabolic reactions can take place without interference from other enzymes, thus increaseefficiency.→ Example: Protein synthesis occurs within the cytoplasm and/or the ER.Lysosome containsprotease 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 Cells1.3.1. 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, orderedstructure to a lower­energy, increasing randomness, or increasing entropy state of being.

Diffusion Certain molecules, such as oxygen, simply move directly through a membrane in

response to the high­to­low concentration gradient. As an example, oxygen diffuses outof the lungs and into the blood for transport to all of the cells.

Facilitated Diffusion 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 themembrane 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 numberof transport proteins embedded in the membrane.

e.g. Glucose is moved by a glucose­transporter protein as it passes through the redblood cell into a body cell.

Osmosis 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

equal. 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.Ion channels.

Protein channels 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 membranemovement.

Active Transport 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 bondswith a potassium ion, loses the phosphate group (which again changes the shape of thetransport protein), and allows for the return trip.3. The potassium is deposited inside the cell, and a sodium ion and a phosphate are attached toa 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, creatinga 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 theidentification of a receptor protein sensitive to the specific substance.→ Phagocytosis is the engulfing and digesting of substances, usually food, by vacuoles with alysosome attached (a lysosome is an organelle that contains digestive enzymes).

2. Biomolecules2.1. Carbohydrates

Contain the elements C, H, O  They are either made from single monosaccharide monomers or from several

monosaccharides joined together  general formula ­(CH2O)n

2.1.1. Monosaccharides Monosaccharides are: 

→ Trioses – C3H6O3 (e.g. glyceraldehyde) → Pentoses – C5H10O5 (e.g. deoxyribose)→ Hexoses – C6H12O6 (e.g. glucose, fructose)

2.1.2. Disaccharides

2.1.3. Polysaccharides 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

Starch

→ 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 COMPACTto store more energy for future cellular respiration.

Cellulose→ 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 carbohydrates2.1.2.1. 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

2.1.2.2. Polysaccharides Examples – starch, glycogen, cellulose Energy Storage ­ starch (plant) and glycogen(animal) Structural ­ Cellulose cell wall (plant) and Chitin(insects/crab/shrimp)

2.2. Water2.2.1 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

degrees water has high cohesion (force of attraction between like molecules) due to hydrogen

bonds 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

2.2.1.1. 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 waterThe 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 thechemistry of life

Much heat energy is needed to raisethe temperature of water(very high specific heat capacity)

∙ Aquatic environments are slow to changetemperature

Evaporation of water requires a greatdeal of heat(high latent heat of vaporisation)

∙ Evaporation of water in sweat or intranspiration causes marked cooling

∙ Much heat is lost by the evaporation of asmall quantity of water

Much heat must be removed beforefreexing occurs(very high latent heat of fusion)

∙ Contents of cells and aquatic environmentsare slow to freeze in cold weather

Ice is less dense than water, even very ∙ Ice forms on the surface of water, insulating

cold water(maximum density at 40C)

the water below∙ When surface water does freeze, aquatic

life can survive below the ice

Water molecules at surface with airorientate so that hydrogen bonds faceinwards(very high surface tension)

∙ Water forms droplets on surfaces and runsoff

∙ Certain small animals exploit surfacetension to land on and move over thesurface of water

Water molecules slide over each othervery easily(very low viscosity)

∙ Water flows readily through narrowcapillaries

∙ Mucus is used externally to aid movement inanimals (e.g. snail and earthworm). It is alsoused internally in the movement of foodalong the digestive tract or movement ofsperm along the oviduct.

(ii) The synovial fluid lubricates movement inmany vertebrate joints.(iii)  The pericardial fluid lubricates movementof the heart.

Water molecules adhere to sufaces(strong adhesive properties)

∙ With low viscosity, capillarity becomespossible, water moves through extremelynarrow spaces e.g. between soil particles,and in cell walls

∙ Large adhesive forces between cellulose incapillary and the water within them so acolumn of water can be maintained (capillaryaction)

Water column does not break or pullapart under tension(high tensile strength)

∙ Medium for chemical reactions of life

Water is colourless(high transmission of visible light)

∙ Plants can photosynthesize at depth inwater

∙ Light may penetrate deeply into livingtissues.

Light can easily penetrate the water­filledepidermis of leaves and reach the underlyingmesophyll cells, which contain chloroplasts

Metabolic role of water:∙ Water is required for the hydrolysis of many substances (for examples, proteins, lipids and

carbohydrates).∙ 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 Lipids2.3.1. Properties of Lipids

made up of carbon, hydrogen and oxygen (CH3(CH2)nCOOH) 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

2.3.2.1. 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

2.3.2.2. Glycerol

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 includemonoglyceride,diglyceride and triglyceride.

→ Triglycerides

→ 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

Phospholipid→ 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→ 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 Lipids2.3.3.1. 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, theycan be stored in large amounts. There will not be any great effect on the water potential ofcells. This can prevent it from diffusing out of cells.

2.3.3.2. 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

2.3.3.3. Other Honeycomb ­ beeswax

 2.4. Proteins

2.4.1. Properties of Proteins sensitive to pH and heat (can be

denatured) 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)

2.4.2.1. Structure of amino acids four groups bonded to a carbon, where R is the variable that determines the varieties of

amino acids

the various amino acids differ in their R group

2.4.2.2. 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

2.4.4.1. Globular Proteins Polypeptide chain folded into a compact, spherical

structure soluble in aqueous medium Enzymes, hormones (e.g. insulin), haemoglobin,

antibodies Example: Haemoglobin

→ With quaternary structure→ 2 alpha globin and 2 beta globin→ globular/spherical shape→ permits transport of oxygen in blood

2.4.4.2. Fibrous Proteins long polypeptide chains twist around each other to

form fibres 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→ insoluble

→ fibre­like/rod shaped→ found in tendons, bone, skin, teeth and connective tissue, cartilage

2.4.5. Roles of Proteins