Module 2, Chapter 2: Biological Molecules

How many bonds can nitrogen form?
different types of atoms
How are elements distinguished?
by the number of protons in their atomic nuclei
How many known elements are they?
over 100 (only a small percent present in the world)
What are all living things primarily made of?
carbon, hydrogen, nitrogen and oxygen
2 or more atoms bonded together
What is a covalent bond?
2 atoms sharing a pair of electrons
How many bonds can carbon form?
In covalent bonds, the electrons used to from bonds.....
are unpaired and present in the outer orbitals of the atoms
How many bonds can oxygen form?
How many bonds can hydrogen form?
an atom or molecule in which the total number of electrons is not equal to the total number of protons
How does an atom become a cation?
if an atom or molecule loses one or more electrons
has a net positive charge
How does an atom become a anion?
atom gains electrons
has a net negative charge
What happens in an ionic bond?
one atom in the pair donates an electron and the other receives it
How are ionic bonds held together?
by attraction of opposite charges
ions in solutions
Roles of Calcium ions
- nerve impulse transmission

- muscle contraction
Roles of Sodium Ions
- nerve impulse transmission

- kidney function
Roles of Potassium Ions
- nerve impulse transmission

- stomatal opening
Roles of Hydrogen Ions
- catalysis of reactions

- pH determination
Roles of Ammonium Ions
- production of nitrate ions by bacteria
Roles of Nitrate Ions
- nitrate supply to plants for amino acid and protein formation
Roles of Hydrogen Carbonate Ions
maintenance of blood pH
Roles of Chloride Ions
- balance positive charge of sodium and potassium ions in cells
Roles of Phosphate Ions
- cell membrane formation

- nucleic acidando ATP formation

- bone formation
Roles of Hydroxide Ions
- catalysis of reactions

- pH determination
Biological Molecules of Carbohydrates
- carbon

- hydrogen

- oxygen
Biological Molecules of Lipids
- carbon

- hydrogen

- oxygen
Biological Molecules of Proteins
- carbon

- hydrogen

- oxygen

- nitrogen

- sulfer
Biological Molecules of Nucleic Acids
- carbon

- hydrogen

- oxygen

- nitrogen

- phosphorous
ong chain molecules composed of linked multiple individual molecules (monomers) in a repeating pattern
individual molecules that make up a polymer
What are the monomers of carbohydrates?
the monomers of a carbohydrates
What are the monomers of proteins?
amino acids
How do atoms join together to form molecules?
they make bonds with eachother
Negative electrons in covalent bonds......
- they are not always shared equally by the atoms of different elements

the electrons will spend more time closer to one of the atoms than to the other
Polar Molecules
molecules which have regions of negativity and regions of positivity
What happens when an atom has a greater share of electrons compared to the other atom in the bond?
it'll be slightly negative compared with the other atom in the bond, which will therefore be slightly positive
Examples of elements that do not share electrons equally in a covalent bond
oxygen and hydrogen
Which has a greater share of electrons in an O-H bond?
oxygen always has a much greater share of the electrons in an O-H bond
hydroxyl group
A chemical group consisting of an oxygen atom bonded to a hydrogen atom
example of hydroxyl group
Property of hydroxyl group
slightly polar
What happens in polar molecules?
interact with each other as the positive and negative regions of the molecule attract each other and form bonds
Hydrogen Bonds
relatively weak interactions which break and reform between the constantly moving water molecules
Hydrogen bonds occur....
in high numbers
Characteristics of Water
- polar

- high specific heat

- unusually high boiling point

- universal solvent

- small molecule

- much lighter than the gases carbon dioxide or oxygen

- unlike CO2 and O2, water is a liquid at room temperature
Why is water a liquid at room temperature?
- due to the hydrogen bonding between water molecules which required a lot of energy to break

- It takes a lot of energy to increase the temperature of water and cause water to become gaseous (evaporate)
Water as a solid
less dense
Why is water less dense as a solid?
- hydrogen bonds formed

- hydrogen bonds fix the positions of the polar molecules slightly further apart than the average distance in the liquid state
Structure of Ice
- giant

- rigid

- open structure

- every oxygen atom at the centre of a tetrahedral arrangement of hydrogen atoms
Why does water have cohesive properties?
- moves as one mass because the molecules are attracted to each other
How does cohesion support life on Earth?
- Cohesion creates a layer of insulation below ice (water molecules) which protects organisms below it

- plants are able to draw water up their roots
Water's adhesive properties
- where water molecules are attracted to other materials

- water molecules are more strongly cohesive to each other than they are to air, the results in water having a 'skin' of surface tension
Water in Metabolic Reactions
- Polar molecule, so it acts as a solvent in which many of the solutes in an organisms can be dissolved

- The cytosol of prokaryotes and eukaryotes is mainly water

- Many solutes are aso polar molecules, amino acids and proteins

- Water acts as a medium for chemical reactions and also helps transport dissolved compounds in and out of cells
Water as a Transport Medium
- Cohesion between water molecules means that when water is transported through the body- molecules will stick together

- Adhesion occurs between water molecules and other polar molecules and surfaces

- the effects of adhesion and cohesion result in water exhibiliting capillary action

- Capillary Action: this is the process by which water can rise up a narrow tube against the force of gravity
Capillary Action
the process by which water can rise up a narrow tube against the force of gravity
Water as a Coolant
-helping to buffer temperature changes during chemical reactions in prokaryotic and eukaryotic cells

- this is because of the large amounts of energy required to overcome hydrogen bonding

- maintaining constant temperatures in cellular environments is important as enzymes are often only active in a narrow temperature range
Why is water an effective coolant?
because it has a high specific heat capacity (absorbs lots of heat)
Water as a habitat
- the water is stable: does not change temperature or become a gas easily - constant environment

- because ice floats, it forms on the surface of ponds and lakes, rather than from the bottom up
forms an insulating layer above the water below

- aquatic organisms would not be able to survive freezing temperatures if their entire habitat froze solid

- some organisms also inhabit the surface of water

- surface tension is strong enough (due to hydrogen bonding) to support small insects such as pod skaters

- Water has a surface tension because:
-- the water molecules attract one another due to the water's polar property

--the hydrogen ends, which are positive in comparison to the negative ends of the oxygen cause water to "stick" together

--takes a certain amount of energy to break these intermolecular bonds.

- Transparency: allows aquatic plants to photosynthesise and produce oxygen and glucose for aquatic mammals

- Buoyancy: upthrust allows all organisms to stay afloat

- High SHC: stable external environment (chemical reactions, evaporation of water)
What are carbohydrates?
molecules that only contain the elements carbon, hydrogen and oxygen
What ratio do the elements appear in carbohydrates?
C: H2 : O
What are carbohydrates also known as?
- saccharides

- sugars
What is a single sugar unit called?
Examples of Monosaccharides
- glucose

- fructose

- ribose
What happens when 2 monosaccharides link together?
they form a disaccharide
Examples of disaccharides
- sucrose

- lactose
Carbohydrates that are made up of more than two monosaccharides
Examples of polysaccharides
- starch

- glycogen

- cellulose
Chemical Formula of Glucose
What is glucose?
a monosaccharide composed of six carbons and therefore is a hexose monosaccharide (hexose sugar)
Hexose Sugar
A sugar with six carbon atoms
Example of a Hexose Sugar
Which way are the carbons numbered in molecular structure diagrams?
2 structural variants of the glucose molecule
alpha and beta glucose
What is the difference between alpha and beta glucoses?
OH (hydroxyl) group on carbon 1 is in opposite positions
Glucose molecules in Water
they are soluble
Why are glucose molecules soluble in water?
due to the hydrogens to the hydrogen bonds that form between the hydroxyl groups and water molecules
Why is it important glucose is soluble in water?
because it means glucose is dissolved in the cytosol of the cell
What happens when two alpha glucose molecules are side by side?
2 hydroxyl groups interact (react)
What happens when 2 hydroxyl groups interact (react)?
bonds are broken and new bonds reformed in different places producing new molecules
What happens to the hydrogen and oxygen atoms in a Condensation Reaction?
- 2 hydrogen atoms and an oxygen atoms are removed from the glucose monomers and join to form a water molecules

- a bond forms between carbons 1 and 4 on the glucose molecules and the molecules are now joined

- a covalent bond called a glycosidic bond is formed between 2 glucose molecules
Why is it called a Condensation Reaction?
because a water molecules is formed as one of the products of the reaction
a disaccharide formed from two units of glucose joined with an α(1→4) bond
- naturally occurs in fruit

- often in combination with glucose forming the disaccharide, sucrose

- commonly known as cane sugar or just sugar
- galactose and glucose form the disaccharide lactose

- lactose is commonly found in milk and milk products
Pentose Monosaccharides
Sugars that contain five carbon atoms
he sugar present in RNA nucleotides
the sugar present in DNA molecules
How is starch formed?
many alpha glucose molecule can be joined by glycosidic bonds to form 2 slightly different polysaccharides
one of the polysaccharides in starch is called amylose
How is Amylose formed?
formed by alpha glucose molecules joined together only by 1-4 glycosidic bonds
What shaped does glucose twist into?
- helix (due to the angle of the bond)

- which is further stabilised by hydrogen bonding within the molecule
Benefits of a Polysaccharide having a helix shape?
makes the polysaccharide more compact and much less soluble, than the glucose molecules used to make it
How is amylopectin formed?
when glycosidic bonds form in condensation reactions between carbon 1 and carbon. 6 on 2 glucose molecules

- made 1 -4 glycosidic bonds between alpha glucose molecules
Difference between amylose and amylopectin formation
- But (unlike amylose) in amylopectin there are also some glycosidic bonds formed by condensation reactions between carbon 1 and carbon 6 on two glucose molecules

- amylopectin has a branched structure, which the 1-6 branching points occurring approximations in every 25 glucose subunits
Storage form of glucose
Why is glycogen more compact than amylopectin?
- forms more branches that amylopectin

- it is more compact and less space is needed for it to be stored
Why is the glycogen structure important?
animals are mobile, unlike plants
Which polysaccharide has more branches?
What does more branching mean for the glucose molecules?
many free ends where glucose molecules can be added or removed
What do the many free ends in glucose molecules do?
speeds up the process of storing or releasing glucose molecules required by the cell
Key Properties of Amylopectin and Glycogen
- insoluble

- branches


which make it suitable for storage roles
How is glucose released for respiration?
starch or glycogen undergo hydrolysis reactions ( requiring the addition of water molecules )
How are hydrolysis reactions catalysed?
by enzymes
What is formed in hydrolysis?
glycosidic bonds
Why can't the hydroxyl groups n carbon 1 & carbon 4 react?
they are too far away
How do beta glucose molecules join together?
if alternate beta glucose molecules are turned upside down
What do beta glucose molecules form?
a polymer
What is a straight chain molecule called?
Why is cellulose formed when beta glucose molecules react?
because the polysaccharide is unable to coil or form branches
What do cellulose molecules make?
hydrogen bonds (forming microbrils)
when microfibrils join together
Properties of Macrofibrils
- insoluble

- used to make cell walls
Why is cellulose an important part of our diet?
forms fibre necessary for a healthy digestive system
Monosaccharides that make Maltose
2 alpha glucose
Monosaccharides that make Sucrose
glucose and fructose
Monosaccharides that make Lactose
glucose and galactose
gain of electrons
What reduces sugars?
- all monosaccharides

- some disaccharides (e.g. maltose)
How do monosaccharides reduce sugars?
hat they can donate electron or reduce another molecule of chemical
Chemical in the Test for Reducing Sugars
Benedict's Reagent
What's Benedict's Reagent
an alkaline solution of copper(II)sulfate
How is the Benedict's test carried out?
1. Place the sample to be tested in a boiling tube. If it is not in liquid form, grind it up or blend it in water

2. Add an equal volume of Benedict's Reagent

3. Heat the mixture gently in boiling water bath for 5 minutes
Results of Reducing Sugars with Benedict's Reagent
- reducing sugars will react with the copper ions in Benedict's reagent

- this results in addition of electron to the blue Cu2+ ions, reducing them to brick red Cu+ ions

- when a reducing sugar is mixed with Benedict's reagent and warmed, a brick - red precipitate is formed indicating a positive result
The ore the Reducing Sugar present....
- the more precipitate formed and the less blue Cu2+ ions are left in solution

- so the actual colour seen will be a mixture of brick red (precipitate) and blue (unchanged copper ions) and will depend on the concentration of the reducing sugar present

- this makes the qualitative
Non Reducing Sugars and Benedict's solution
- do no react with Benedict's solution

- the solution will remain blue after warming

- indicating a negative result
The Most Common Non Reducing Sugar
What happens is the sucrose is first boiled with HCl and then warmed with Benedict's solution?
- it will then give a positive result
Why does it give a positive result when the sucrose is first boiled with HCl before warming the Benedict's solution?
ecause the sucrose has been hydrolysed by the acid to glucose and fructose, both reducing sugars
What is the Iodine Test used for?
to detect the presence of starch
How to Carry out an Iodine Test
add a few drops of iodine dissolved in potassium iodine solution are mixed with a sample
Positive Results of Iodine Test
solution changes colour from yellow/brown to purple/black starch is present in the sample
Negative Results of Iodine Test
iodine solution remains yellow/brown
What are Reagent Strips used for?
to test for the presence of reducng sugars, most commonly glucose
Advantage of Reagent Strips
with the use of colour coded chart, the concentration of the sugar can be determined
complex molecules with a relatively large molecule mass
Chemical Elements in Triglycerides
- carbon

- hydrogen

- oxygen
What are triglycerides made of?
Glycerol and three fatty acids.
What do fatty acids have?
long tails made of hydrocarbons
What makes lipids insoluble in water?
What are triglycerides synthesised by?
the formation of an ester bond between fatty acid and the glycerol molecule
How is an ester bond formed?
a condensation reaction (in which a water molecule is released)
the process of which triglycerides are synthesized
What happens in a hydrolysis reaction in an ester bond?
- triglycerides break down then the easter bonds are broken

- Each easter bond is broken in a hydrolysis reaction
Saturated Fatty Acids
- don't have any double bonds between their carbon atoms

- their fatty acid is saturated with hydrogen
General Formula of Fatty Acids
Unsaturated Fatty Acid
have at least one double bond between carbon atoms, which cause the chain to kink
- macromolecules

- similar to triglycerides, apart from one of the fatty acids molecules is replaced by phosphate group
Phosphate Group in Phospholipids is.....
water loving
Water fearing
Fatty Acid tail in Phospholipids is.....
Functions of Triglycerides in animals and plants
mainly used as energy storage molecules
What do bacteria use triglyceride for?
store both energy and carbon
Why are Triglyceride good for storage?
- the long hydrocarbon tails of the fatty acids contain lots of chemical energy

- they're insoluble, so they don't cause water to enter the cells by osmosis = swell
Why is loads of energy released when triglycerides are broken down?
because of these tails, lipids contain about twice as much energy per gram as carbohydrates
Why are triglycerides insoluble?
- the triglyceride bundle together as insoluble droplets in cells because the fatty acid tails are hydrophobic`

- the tails face inwards, shielding themselves from water with their glycerol head
Why do the triglycerides bundle together?
because the fatty acid tails are hydrophobic
Where are phospholipids found?
in the cell membranes of all eukaryotes and prokaryoes
Why do phospholipids form a double layer?
- Phospholipid heads are hydrophilic and their tails are hydrophobic

- their heads facing out towards the water on either side
Why is the centre of the bilayer hydrophobic?
so water soluble substances can't easily pass through it
has a hydrocarbon ring structure attached to a hydrocarbon
Structure of Cholesterol
has a hydrocarbon ring structure attached to a hydrocarbon
Ring Structure of Cholesterol
a polar hydroxyl (OH) group attached to it
Function of Cholesterol Molecules in Eukaryotic Cells
cholesterol molecules help strengthen the cell membrane by interacting with the phospholipid bilayer
Shape of Cholesterol
- small size

- flattened shape
What does the shape of a molecule allow?
cholesterol to fit in between the phospholipid molecules in the membrane
What are proteins made of?
long chains of amino acids
What are the monomers in proteins?
amino acids
formed when 2 amino acids join together
General Structure of Amino Acids
- a carboxyl group (-COOH)

- an amino group (-NH2) attached to a carbon atom
What is the difference between different amino acids?
the variable group they contain
Forming Dipeptides
- condensation reaction

- molecule of water is released
Primary Structure of Proteins
- this is the sequence of amino acids in the polypeptide chain

- different proteins have different sequences of amino acids in their primary structure

- a change in just one amino acid may the change the structure of the whole protein
Secondary Structure of Proteins
the polypeptide chain doesn't remain flat and straight

hydrogen bonds form between nearby amino acids in the chain

this makes it automatically cell into an alpha helix or fold into a beta pleated sheet
Tertiary Structure - Proteins
the cooled or folded chain amino acids is often coiled and folded further

more bonds form between different parts of the polypeptide chain

for protein made from a single polypeptide chain, the tertiary structure forms their final 3D structure
Quaternary Structure
some proteins are made of several different polypeptide chains held together by bonds

the Quaternary Structure is the way these polypeptide chains are assembled together

for proteins made from more than one polypeptide chain, the quaternary structure is the protein's final 3D
What can create 3D interactive images of proteins
Computer Modelling - this is useful for investigating the different levels of structure in a protein molecule
Bonds in Primary Structure
held together by peptide bonds between amino acids
Bonds in Secondary Structure
held together by hydrogen bonds
Tertiary Structure
- ionic bonds

- disulfiide bonds

- hydrophobic and hydrophilic interactions

- hydrogen bonds
Ionic Bonds
attractions between negatively charged R groups and positively charged R groups on different kinds of bonds
Disulphide Bonds
whenever 2 molecules of the amino acid, cysteine, come close together, the sulfur atom in one cysteine, bonds to the sulfur in the other cysteine, forming a disulfide bond
Hydrophobic and Hydrophilic Interactions
- when hydrophobic R groups are close together in the protein, they tend to clump together

- Hydrophilic R groups are more likely to be pushed to the outside = affects how protein folds up into its final structure
Hydrogen Bonds in Tertiary Structure
- these weak bonds form between slightly positively charged hydrogen atoms in some R groups and slightly negatively charged atoms in other R groups on the polypeptide chain
Globular Proteins shape
round and compact
Why are globular proteins soluble?
- hydrophilic R groups on the amino acids tend to be pushed to the outside of the molecule

- this is caused by the hydrophobic and hydrophilic interactions in the protein's tertiary structure
Why is it good that globular proteins are soluble?
easily transported in fluids
Examples of Globular Proteins
- haemoglobin

- insulin

- amylase
What is haemoglobin?
- Globular protein that carries oxygen around the body in red blood cells

- conjugated protein
Conjugated Protein
a protein with a non protein group attached
The Non Protein in a Conjugated Protein is called....
a prosthetic group
What does each of the four polypeptide chains in haemoglobin have?
a prosthetic group called haem
What does a haem group contain?
What is insulin?
a hormone secreted by the pancreas
Insulin Function
helps to regulate the blood glucose level
Why is insulin's solubility important?
it can be transported in the blood to the tissues where it acts
How many polypeptide chains does insulin have?
What are the polypeptide chains held together by in insulin?
disulphide bonds
What is amylase
an enzyme that catalyses the breakdown of starch in the digestive systems
What is amylase's secondary structure?
both alpha-helix and beta-pleated sheet sections
What type of protein is amylase?
globular protein
Properties of Fibrous Proteins
- tough

- rope shaped

- insoluble

- strong

- structural proteins

- fairly unreactive
Examples of Fibrous Proteins
- collagen

- keratin

- elastic
Where is Collagen found?
in animal connective tissues, such as bone, skin and muscle
What does collagen do?
bind to the protein to increase its rigidity
Where is Keratin found?
found in many of the external structures of animals, such as skin, hair, nails, feathers and horns
Properties of Keratin
- it can either be flexible (skin)

- hard and tough (nails)
Where is Elastic found?
found in elastic connective tissues, such as skin, large blood vessels and some ligaments
Functions of Elastic
It is elastic, so it allows tissues to return to their original shape after they have been stretched
In-organic Ion
one which doesn't contain carbon (although there are few exceptions to this rule)
What Role does Calcium have in Biological Processes?
- important for generating nerve impulses

- important for muscle contraction

- for regulating fluid balance in the body
What Role does Sodium have in Biological Processes?
- transmission of nerve impulses

- release of insulin from the pancreas

- acts as a cofactor for many enzymes (blood clotting)

- important for bone formatioN
What Role do Potassium ions have in Biological Processes?
- important for generating nerve impulses

- for muscle contraction

- for regulating fluid balance

- activates essential enzymes needed for photosynthesis in plant cells
What Role do Hydrogen ions have in Biological Processes?
- affects the pH of substances (more H+ ions from OH- ions in a solution creates of acid

- also important for photosynthesis reaction that occur in the thylakoid membranes inside chloroplasts
What Role do Ammonium ions have in Biological Processes?
- absorbed from the soil by plants

- an important source of nitrogen (make amino acids and nucleic acids)
What Role do Nitratre ions have in Biological Processes?
- absorbed from the soil by plants

- is an important source of nitrogen (make amino acids and nucleic acids)
What Role do Hydrogencarbonate ions have in Biological Processes?
- acts as a buffer

- helps maintain the pH of the blood
What Role do Chloride ions have in Biological Processes?
- involved in the chloride shift (helps maintain the pH of the blood during gas exchange

- acts as a cofactor for the enzyme amylase

- also involved in some nerve impulses
What Role do Phosphate ions have in Biological Processes?
- photosynthesis and respiration reactions

- needed for the synthesis of many biological molecules, such as nucleotides



--Calcium phosphate
What Role do Hydroxide ions have in Biological Processes?
- affects the pH of substances (more OH- ions than H+ ions in a solution creates an alkali)
is a device that uses a biological molecule, such as an enzyme to detect a chemical
How does a biosensor work?
- he biological molecule produces a signal (e.g. a chemical signal) which is converted to an electrical signal by a transducer (another part of the biosensor)

- the electrical signal is then processed and can be used to work out other information
What is a glucose biosensor?
used to determine the concentration of glucose in a solution
How does a glucose biosensor work?
- it does this using the enzyme oxidase and electrode

- the enzyme catalyses the oxidation of glucose at the electrodes - this creates a charge, which is converted into an electrical signal by the electrodes (transducer)

- the electrical signal is then processed to work out the initial glucose concentration
What is Chromatography used for?
is used to separate stuff in a mixture
What are the 2 types of chromotography?
- paper chromatography

- thin layer chromatography
Mobile Phase
- where the molecules can move

- liquid solvent (ethanol or water)
Stationary Phase in Paper
chromatography paper
Stationary Phase in Thin Layer
thin layer of solid on a glass or plastic plate
Stationary Phase
where the molecules can't move
Components that spend longer in the mobile phase..
travel faster or further
Paper Chromatography Method
1. Draw a pencil line near the bottom of a piece of chromatography paper and put a concentrated spot of the mixture of amino acids on it

2. Add a small amount of prepared solvent (a mixture of butan - 1 - ol, glacial ethanoic acid and water is usually used for amino acids) to a beaker and dip the bottom of the paper into it
(this should be done in a fume cupboard)

3. As the solvent spreads up the paper, the different amino acids (solutes) move with it, but at different rates, so they seperate out

4. When solvent nearly reaches the top, take the paper out and mark the solvnt front with a pencil

5. Leave to dry

6. Amino acids aren't coloured, so you won't be able to see them on the paper, so before you can analyse them, you have to spray the paper with ninhydrin solution to turn the amino acids purple

(Be done in a fume cupboard and gloves should be born)

7. You then use Rf values to identify the separate molecule
Rf Value
the ratio of the distance travelled by a solute to the distance travelled by solvent, you can calculate it using this formula
Rf value of amino acids=
distance travelled by solute / distance travelled by solvent
How can we work out what was in a chromatography mixture?
by calculating an R1 value for each slute and looking each Rf value up in database
Reducing Sugar
all monosaccharides and some disaccharides (e.g. maltose and lactose)
Test for Starch
add iodine dissolved in potassium iodide solution
Test for Glucose
- can be tested using test strips coated in a reagent

- they are dipped in a test solution and change colour if glucose is present
Test for Proteins
Biuret test

- test solution needs to be alkaline = add few drops of sodium hydroxide solution

- add some copper (II) sulfate solution
Test for Lipids
Emulsion test
- shake the test with ethanol then pour the solution into the water
Positive Test for Starch
orangey brown to black - blue
Positive Test for Proteins
blue to purple