A – unity and diversity

A 1.1 – water
- Covalent bond exists between atoms that share electrons, usually between non metals
- In water, hydrogen and oxygen share electrons but unequally, more orbiting around oxygen
o Oxygen has negative charge, hydrogen has positive, -> water is polar
- Each individual water molecule forms hydrogen bonds with other molecules (relatively weak
bond -> easily broken and reformed)
o Known as cohesion
o The "film" seen on the surface of lakes/water is due to the cohesion of water molecules
forming surface tension
- Negative charge of one molecule is attracted to the positive charge of another and so on
- Adhesion and cohesion occurs because of polarity
- Has ability to dissociate and reform into ions in liquid form
o 2 H2O -> H3O + OH
- Cohesion; water molecules held together by hydrogen bonds
- Adhesion; when one substance (water) clings to another (cells) de to hydrogen bonds
- Surface tension; how difficult it is to stretch or break apart the surface of a liquid
o Water has very high surface tension due to its high cohesion from hydrogen bonds
o Raft spider increases its surface tension by spreading out

Water transport in plants

- Adhesion allows the water particles to stay near the roots
- Move in through the root cells
- Allows water to move in a continuous unbroken stream because water is able to adhere to side of
cells as well as cohere to water cells around it
- Capillary action through the plant is possible due to properties of water
- High concentration of solutes at top of tree due to transpiration

Water is a versatile solvent

- Solution; homogenous solution of two or more substances (solute and solvent)
o Aqueous solutions have water as the solvent
- Ionic compounds easily dissolve in water due to its polar nature as a hydration shell forms
o Cations attracted to the partially negative oxygen
o Anions attracted to partially positive hydrogen
- Covalent
- Hydrophilic substance is one that has an affinity for water
- Hydrophobic substance is one that does not have an affinity for water
- Oil molecules are hydrophobic because they have relatively nonpolar bonds
- Hydrophobic molecules related to oils are the major ingredients of cell membranes

Formation of hydration shell

- Occurs when an ionic compound ins dissolved in water

Solubility and transport

- Watery habitat can dissolve substances that can then be absorbed by organisms
- Watery environment of cytoplasm allows for dissolved substances
- When substances are dissolved in a liquid, metabolic reactions can take place easily and
efficiently
- Blood plasma (the liquid portion of blood) is 95% water and 5% dissolved substances
- Water facilitates chemical reactions

Temperature moderation
- Kinetic energy; energy of motion that all molecules have:
o Heat; total kinetic energy
  Volume dependent
 Heat always moves from high to low (warm to cool)
o Temperature; average kinetic energy
 Volume is not a factor
- Water has high specific heat
o Due to hydrogen bonding
o Resists changes in temperature (allows entire body of water to maintain consistent
temperature)

- Heat of vaporization; amount of energy (heat) needed to change 1g of liquid to gas

- Evaporative cooling; as a liquid evaporates, the surface is left cooler because all of the "hottest"
molecules (the ones with the most kinetic energy) have escaped and turned into gas.
o Done to maintain homeostasis (includes maintaining a stable body temperature; when hot
-> sweats to cool down body)
- High temperatures can cause proteins to denature (when protein bond breaks and changes shape)

Applications of evaporative cooling

- Sweating in humans
- Plants will increase transpiration rates when in danger of over-heating
- Dogs will plant when they overheat

Sweating
- The hypothalamus in the brain controls sweating in humans
- Waters high latent heat of vaporization allows organisms to use it as a coolant. When body
temperature increases, sweat builds on the skin.
- The water molecules absorb heat from the skin until it evaporates
- this energy is carried away and the body is cooled

Density - the ratio of mass and volume of a substance

- Denser objects are more compact and tend to sin, while less dense objects are most likely to float
- Density also carries with temperature - the high the temperature, the less dense an object becomes
and vice versa
- Waters hydrogen bonds make solid ice less dense than liquid water, allowing ice to float

Buoyancy
- The Archimedes principle states that when a body is partially or totally immersed in a fluid it is
buoyed up by a force equal to the weight (volume) of the fluid that is displaced by the body
- When body is submerged it displaces water, producing the buoyancy force
- Force of gravity also acts on this body meaning that if the body is to remain in static quilibrium
(nautral buoyancy) these two forces must counterbalance one another
o Buoyancy will be positive when a body tends to rise within the fluid and…

Origin of water
- Outgassing; volcanic gasses escaping through the core of the earth -> forming a layer which
traps water so it can't escape when evaporating
- Carbonaceous chondrite meteorites contain water -> water may have accumulated through
asteroids
A 1.2 – nucleic acids
Sugar in DNA is deoxyribose (5 carbon)
The sugar is what makes dna different from rna
DNA has oxyl group,, deoxyribose

Phosphodiester bond

Made up of many small repeating units called

nucleotide, many = polynucleotide

5 carbon sugar molecule

Bonds with phosphate

DNA vs RNA
 RNA is single strand of molecule
 RNA's sugar is ribose, 1 more oxygen
than oxygens deoxyribose (means no
oxygen "de oxy"
 RNA doesn’t contain thymine, 4th
nucleotide is base uracil

DNA and RNA

 Both organic molecles
 Both nucleic acids = made up of
nucleodtides
 Both nucleotides contain a sugar, phosphate, and base

Video notes
 rna is found in nucleus, rna found inside and outside nucleus
 Both nucleic acid, organic molecules
 Both have monomers -> nucleotide
 Antiparallel for dna
 Ribose for RNA and deoxyribose for DNA
 Dna cant code for genes without rna
 Mrna = messenger rna, carries message based off dna
 Rrna = ribosomal rna, can leave nucleus to take information to ribosome
 Trna = transfer rna, transfers amino acids to match ,,

DNA structure
The ,, on one end on the strand is unlinked on 3 prime terminal
Because c3 in the sugar is available for linking

New nucleotide is always added to 3 prime end, forms covalent bond to the phosphate on the 3 prime,
and so on
-> chain always grows in one direcion

Read from 5 -> 3 but dna is only added to the 3 prime end
Replication, transcription and translation is where the order matters
 Significance of directionality Diagram
Replication DNA polymerases and other enzymes make
copies of DNA;

Nucleotides always added to the 3' end of the

growing polymer of nucleotides. The 5'
phosphate of the free nucleotide is linked to the
deoxyribose sugar at the 3' end of the growing
polymer, thus replication is 5' to 3'

Transcription RNA polymerases makes an RNA copy of a

DNA base sequence

RNA nucleotides are always added to the 3' end

of the growing polymer of nucleotides. The 5'
phosphate of the free nucleotide is linked to the
ribose sugar at the 3' end of the growing
polymer, thus transcription is 5' to 3'
Translation Occurs at a ribosome with an RNA base
sequence determining the amino acid sequence
of a polypeptide;

Molecule of RNA carries the sequence

information for making a polypeptide by
linking amino acids together. The ribosome that
carries out a translation moves along this RNA
molecule towards the 3' end, thus translation is
5' to 3'

A.2.1 – Hershey-Chase experiment

Experiment method

Sulphur
1. Phage was produced containing radioactive sulphur
2. Phage population with s35 radioactivity in the protein coat
3. Phage attached to bacterial cell and injected dna into bacteria
4. Sulpher remained in the outside
5. Phage in cell contained no radiaoactivity, empty protein cells were removed

Phosphorous
1. Phage produced containing radioactive phosphorous
2. Phage population with p32 radioactivity and in the deoxyribose, no radioactive label in
protein
3. Phage attached to bacterial cell and injected dna into bacteria
4. Entered cell and could be found in phage subsequently produced

Demonstrated that dna carries genetic information for phague

The hershy chase experiment used transfer of radioactivity in bacterial cells with sulphur and
phosphorous to conclude that genetic information is carried in phague's dna rather than protein

A 2.2 – cell structure

All cells have cell membrane separating the inside of the cell from its environment
Cytoplasm; jelly like fluid, dna is cells genetic material
Two categories of cells:
Eucaryotic
- Organelles including nucleus and other parts
- Advanced complex such as plants and animals
Prokaryotic
- No nucleus or membrane enclosed organelles
- DNA present but not contained in the nucleus
- Always unicellular such as bacteria

Organelles means little organ

- Specialised part of cell that has unique job

Nucleus; control centre of cell

- Contains DNA/genetic material
- Dictates the purpose of the cell and how it will do it
- Chromatid - tangled spread out form of DNA found inside nuclear membrane

Nucleolus; inside the nucleus

- Where ribosomes are made

Ribosomes
- When ribosomes leave nucleus they synthesis poteins
- may attach to er

ER
- Rough has ribosomes attached
- Smooth doesn’t
- Membrane enclosed passage way used for transporting materials such as the proteins
synthesised by ribosomes
- Proteisn emerge from the er in small vesicles where the golgi body receives them

Golgi body/apparatus
- Proteins move through golgi body customers into forms that cells can use (protein change,,
final conformation e.g. alpha helix, beta sheet, uaterny structure)
- Other materials are added such as lipids or carbs known as cofactors

Vacuole
- Sack like structure that stores different materials
- Large vacuole in plant cell,, stores water
- Smaller in animal cell
- Lysosome in animal cell collects waste such as worn out cells
- Filled with enzymes that break down cellular debris

Mitochondria
- Powerhouse of animal and plant cell as they produce energy
- Cellular respiration in mitochondria,, makes atp molecules which provides energy for all cell
activity

Cytoskeleton in animal cells

 - Maintains cells structural integrity
- Long protein fibres that extend from one side of the cell to the other
- Thread like microfilaments microtubules are thin hollow tubes
- Plants that are photoautotrophic have chrlorophase

Chloroplast
- Where photosynthases occurs
- Green due to pigmant chloraphil
- Cell wall outside of membrane, shape supports and protects
- No cell wall

Other
- In human cells,, respiratory track have cells containing cilia -> microspcopic hairs that move
in waves, traps inhaled particles and expels them in coughs
- Flagella, some bacteria, flagellum is the tail that helps a cell move or propel itself, only
human cell that has a flagellum is sperm cell

B – form and function

B 1.1 – carbs
Central Carbon in amino acids forms only 4 single bonds to each valence electron, carbon in carboxyl
group has double bond with an oxygen
Single bonds vs double bonds changes the molecule
4 single bonds allows the molecules to rotate and spin allowing in to form rings shapes
Double bonds are more rigid

When you eat your digestive system breaks down polymers into monomers
Amonio acids are monomers of proteins, amino acids put together are polypeptides

Polysaccharides - poly=many saccharide=sweet

Glucose most common polysaccharide, starch is many glucose put together

Cellulose is polysaccharide in plant walls made up of two subtypes of carbs; amylose and amylopectin
Fats don’t have repeating monomers they have two types of monomers; fatty acids and glycerol
Triglyceride is a type of monomers, saturated fats = good, unsaturated = bad

All sugars end in ose, al have ring shape - could be hexagon or pentagon (ribose and deoxyribose)
Ring is made of carbon
Pentoses [5sides] - e.g. deoxyribse
Hexoses [6sides]- e..g glucose

Glucose is typical monosaccharide and has the following properties

- Soluble in water; glucose is a polar molecule which readily dissolved in water
- Transportability; since glucose is soluble in water, it is transported within body fluids such as
the bloodstream in humans
- Chemical stability; glucose is relatively stable compound, so it does not degrade as it is being
transported
- Energy yield; glucose is the primary fuel for respiration in cells. The glucose molecule is
repeatedly oxidized to produce a net

Polysaccharides
- Condensation is required to make polysaccharides [contains a combination of 100-1000
glucose units] -> why its not transported in water nor soluble
- Great for storing energy, starch in plants and glycogenin animals
- Glucose affects osmosis and solute concentration in cells
- Formation of starch and glycogen is easily reversible through hydrolysis reactions
- Are very compact, large amounts are able to be stored in a small space, they are linear so can
be coiled, branched are already compact

Starch and glycogen

- Both starch and glycogen are composed of alpha and beta molecules
- Amylose is a linear starch, amylopectin is branched
- Carbon 1 and 4 face each other in two glucoses, easily form a peptide bond of linear glucose
molecules
- Branches are formed when carbon 1 bonds with carbon 6
o In linear molecules there are only carbon bonds between carbon 1 and 4, in branches
there are also carbon bonds between carbon 6 of a molecule in the chain with carbon
1 of an adjacent molecule
- Used for storage and not release of energy as the many many carbon bonds are not soluble in
water
- Hydrolysis of glucose molecules is easier with amylopectin as it is a branched molecule,
meaning that glucose can be broken off at any part of the chain rather than just the ends with
linear chains

Cellulose
- Carbs in plants are stored in the form of cellulose
- Cellulose molecules consists of long chains of beta glucose molecules with linkages between
carbon 1 and 4
- Each second molecule is flipped, resulting in a straight chain of molecules
- Cellulose molecules form groups known as microfibrils which are held together by hydrogen
bonds
 o Have high tensile strength, allowing them to maintain the structural integrity of plant
cell walls
- Not digestible by humans as they can only digest alpha glucose, cellulose consists of beta
glucose

Glycoproteins
- Integral proteins in the phospholipid bilayer of cells
- Composed of polypeptides and have a chain of carbohydrates attached
- Carbohydrates on the glycoprotein have a specific shape and can act as an antigen
- Acts as antigens if the glycoprotein is not recognised as their own

Roles of glycoproteins
- Adhesion between cells; interact with the glycoproteins on neighbouring cells -> allows the
formation of tissues
o Sperm and egg
- Receptors; act as receptors for hormones, when a hormone binds to a specific glycoprotein
receptor the metabolism within a cell is changed
o Insulin (glucose regulation)
- Communication between cells; neurotransmitters bind to glycoproteins which allows
communication between cells
o Dopamine
- Immune response; glycoproteins act as markers on cells allowing the immune system to
distinguish between their own cells and outside cells
o Antigen

- Monomer of lipid is glycerol and fatty acid

- Hydrophobic, contain a significant hydrophobic component
- All cells have membranes, made up of lipids, source of long term energy storage
- When carbs are used up, lipids store energy that organisms can use
- Insulation, helping cells to carry electrical impulses
- E.g. myelin sheath in neurons

- Osmosis; travel of water through semipermeable membrane

Triglycerides
- (3 tails) are composed of 1 glycerol molecule and 3 fatty acid molecules
- These molecules form condensation reactions, releasing a byproduct of 3 water molecules

Phospholipids
- (2 tails) composed of 1 glycerol attached to 2 fatty acids and 1 phosphate (what makes it
polar)
- Formed through condensation reaction between the molecules

Fats and oils

- Fats are tryglycerides, solid at room temperature, high melting point, fatty acids in fats are
usually saturated (more hydrogen atoms)
- Oils are triglycerides, liquid at room temperature, low melting points, fatty acids in oils are
unsaturated
- Many carbon bonds within fats and oils

Saturated vs unsaturated
Saturated; maxed out / saturated with hydrogen bonds
- Determined by lack of double bonds
Unsaturated; determined by presence of at least one double bond (one double bond = mono saturated
fat, more than one = poly saturated bond)
- Double bonds between carbons means that it cant bond to a hydrogen = less hydrogens than
saturated fats
- Hydrogens on same side as double bonds causes the molecule to bend, -> why its an oil, not
as rigid and straight, lower melting point, liquid at room temp

Cholesterol helps regulate phospholipid bilayer

- Not enough = too fluid, too much = too rigid
- Stored long term, when you eat and body breaks down carbs into glucose, it uses it for energy
and stores it as glycogen
- Cell respiration chain, converts,,into glucose, stores it as atp

Adipose tissue
- Fats have low thermal conductivity and act as an insulator, helps endotherm maintain a
constant body temperature

Formation of phospholipid bilaers as a consequence of the hydrophobic and hydrophilic regions

Amphipathic - part hydrophobic part hydrophilic
- E.g. soap trees, used by indigenous groups to wash themselves
- Structural component of cell membranes

Hydrophilic part is form phosphate group and hydrophobic is from the chains

Steroids are lipids with a characteristic shape, 4 carbon rings and a hydrocarbon chain

B1.2 – proteins
Protein is organic molecules defined by the presence of carbon (and hydrogen and oxygen)
DNA used to make proteins
- Gene expression (each gene in DNA codes for different protein)
- There are no subprocesses: transcription and translation
- Convert DNA to RNA
- Put together (translation) in cytoplasm
Shape changes function of protein
Proteins have many structures -> wide variety of functions
Does majority of work in cells and act as enzymes
Are made of monomers called amino acids ->
- Amino acids = monomer, protein = polymer
What proteins do
- Enzyme (pepsin, DNA polymerase)
- Structure (keratin, collagen)
- Carriers and transport (haemoglobin, aquaporins)
- Cell communication
 Signals (insulin and other hormones)
 Receptors
- Defence (antibodies)
- Movement (actin and myosin)
- Storage (bean seed proteins)
Proteins are polypeptides because there are many peptide bonds
Amino acids in diet
- When you combine amino acids in different ways, you make different proteins.
- Your body needs amino acids but can't make 9/20. You have to eat foods with these 9 (called
essential amino acids)
Where can you find amino acids
- Beef, poultry, eggs
  Animal proteins are most easily absorbed and used in body
- Foods that have all 9 essential amino acids are called complete proteins
 Beef, poultry, fish, eggs, dairy, soy, quinoa, buckwheat
- If they contain some of the essential ones, they are called incomplete proteins
 Nuts, seeds, beans, some grains

Variety of peptide chains!!

- Most proteins have between 50-2000
- Residues? _____
- Spends a large amount of time in the Golgi body.
 This is where the proteins get converted in different shapes
- They can then be used in the cells itself, or sent out of the cell through exocytosis (packaged
in vesicle to do so, since it's big.
Structure determines structures
o How can we change the shape of a protein so it might not do its job?
- Remember that proteins have different structures; interactions depending on their R-groups
Protein denaturation!!
- Unfolding a protein
- Conditions that disrupt H bonds, ionic bonds, and disulphide bridges include:
 Temperature (when you have a fever, your proteins denature)
 pH
 Salinity
- It destroys functionality
- Renaturation: going back to same shape after denaturing
 Only some proteins can do this

Protein structure
1. Primary structure (polypeptide, what comes out of the ribosome, peptide bonds between
amino acids, very long chain of amino acids (not folded).
 Properties of amino acids; hydrophobic, hydrophilic (acidic or basic)(charged or uncharged)

2. Secondary structure : 2 ways in which it can fold, alpha helix or beta pleated sheet, depends
on the amino acid arrangements.

3. Tertiary structure : overall 3d shape of a polypeptide, more folding, r group can define amino
acids and make it function a certain way, when protein folding happens, amino acids that are
hydrophilic orient on the outside whereas hydrophobic interactions orient in the inside of the
protein to make the protein soluble since cytoplasm is water based.
 Results from interactions between amino acids and r groups creating disulphide
bonds/bridges (only form between one amino acid called cysteine ;contains sulphur, 2
cysteine form disulphide bonds) (strongest of all bonds in the protein)
 Interaction between side chain atoms of amino acids and the water molecules in the
surrounding environment

4. Quaternary - protein consisting of more than one polypeptide chain bonded together e.g.
Hemoglobin hem refers to ion, globin refers to protein.
 Each proteins fold into secondary/tertiary structure than come together to form a quaternary
structure. Collagen, forms a triple helix with 3 unfolded polypeptide chain from a primary
structure to quaternary structure

Bonds that form in secondary, tertiary and quaternary structures

 Hydrogen bonds
 Ionic bonds
  Disulphide bridges

Protein folding problem

 Most proteins usually go through several intermediate states on their way to a stable
conformation
 Denatured proteins cannot function in their unfolded condition
 Conformation - final shape in which they function in
 Proteins specific conformation(shape) determines how it functions

Chaperonins - protein molecules that assist in the proper folding of other proteins
 The polypeptide enters chaperonin where the cap attaches causing cylinder (chaperonin) to
change shape in a way which creates a hydrophilic environment for the folding of the
polypeptide. The cap then comes off releasing the folded polypeptide.

 Repeating sequence of N-C-C is the polypeptide backbone that can only grown in one
direction
 The nH2 end is known as the N-terminus
 The COOH end is known as the C-terminus

Sickle cell anemia

 Results from a single amino acids substitution in the protein haemoglobin (change of one
amino acid in the haemoglobin)
 Blood cells are sickle shaped
 Cause blood clotting
 Can't carry oxygen

2 categories of proteins based on their job

 Fibrous - elongated shape, don't always become folded into tertiary structures, form structural
components of the cell e.g. Integral protein, melanin,
 Globular - functional proteins, physically do something e.g. Hemoglobin, insulin, all enzymes
 C – interaction and interdependence
C1.1 – enzymes
Catalysts
- Activation energy is the level of energy required to activate a reaction
o Law of conservation of energy; energy cannot be created nor destroyed
- Catalyst is a substance that lowers the activation energy needed to run a reaction
- Speeds up the reaction but do not change the outcome of the reaction or become part of the
reaction
- Bonds between atoms are broken down, rearranged, and rebuilt, recombining atoms into new
molecules
o Catalyst lowers the activation energy required for atoms to be rebuilt into new
molecules

Enzymes
- Enzymes are catalysts that are produced by living organisms and are therefore often referred
to as biological cayalysts
o They are globular proteins which act as catalysts in chemical reactions in organisms
- Allows chemical reactions to occur under tightly controlled conditions
- Are needed for almost all processes in living things
o All enzymes are catalysts but not all catalysts are enzymes
- Fastest known enzyme is catalyse and is found in tissue

Enzyme key terms

- Substrate
o Reactant which binds to enzyme
o Enzyme-substrate complex; temporary association
o Site where the enzyme acts on
o Each enzyme only has one substrate, temporary hydrogen bond while enzyme forms
its function
o Enzyme is reusable, unchanged after reaction, hydrogen bond is broken after
catabolism and enzyme is released back into body
- Product; end result of a reaction
o Depends on type of enzyme
- Active site; enzymes catalytic site; substrate fits into active site
o Location on the enzyme where the bond with substrate forms
o Substrate (the substance to be broken down) attaches to active site

How enzymes lower activation energy

- Changing relative positions of atoms in the reacctants, making it easier for them to form the
products
- Stabilizing the intermediate products or transition states, making the reaction proceed more
smoothly
- Providing an alternative and more favourable transition state for the reaction to proceed

Metabolism
- Metabolism refers to every chemical reaction that occurs in the body, including dna
replicaiton, transcription, protein synthesis
- Metabolism is the complex network of interdependent and interactive … in living organisms
- A coordinated series of chemical reactions
- An enzyme may act upon one substrate to break it into two products or it may act upon two
substrates to create one product
- Catabolic metabolism breaks one substrate into two
- Anabolic metabolism creates one product from two substrates
 - Carbohydrate into mouth -> in stomach becomes glucose, fructose, etc. this is an example of
catabolism
- Peptide bond between two amino acids makes protein, example of anabolism

Lock and key mechanism

- A perfect lock and key. If they did not fit they could not work, but THIS IS WRONG!
- We know now that the shape of the active site can be altered, by ph, temp. Bad changes can
end up with denaturation, but enzymes can be induced to change (whether its throgh ph, temp,
chemicals, drugs that bind to enzymes and cause active sit eto chnage).

Induced fit model

- More accurate model of enzyme action
- 3d structure of enzyme fits substrate
- Substrate binding causes enzyme to change shape leading to tighter fit
- "Conformational change"
- Bring chemical groups in position to catalyse reaction
- Enzymes are highly specific and …

Biomolecules
- Biomolecules are broken down in digestion
- Amylase breaks down carbs by breaking the starch bonds
- Lipase breaks the ester bonds in triglyceride

Cofactors and coenzymes

- Permanent or temporary depending on how theyre bonded
- Sits in active sites, helps with the binding of enzyme
- Non competitive/allosteric inhibition, binded somewhere else but still changes shape of active
site
- Competitive are in the active site and block the substrates
- Non competitive binds to another area of the enzyme that’s not the active site (allostreic site)
- Enzyme has conformational change but active site is not blocked
- Feedback inhibition,, enzymes that
- Overproduction of an substrate,, may be a non competitive inhibitor and bind to the first
enzyme f the metabolic pathway, causes a conformational change in the first enzyme

Metabolic pathways
- Not simple, convoluted but at every stage they are regulated by enzymes
- "-lysis" means to split,, glycolysis is glucose being split
- When two reactions are connected through a common intermediate, they are said to be
coupled

Intracellular enzymes
- May be present freely in the cytoplasmic fluid of the cell or they may be bound to some
organelles such as ribosomes
- Enzymes may also present within the membrane bound organelles within the cell

Allosteric regulation
- Inhibitor is binding away from the active site but still causes conformational change

Competitive inhibitor
- Inhibitor and substrate compete for acctive site
- Can overcome by increasing substrate concentration