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Unit 1: Biological molecules - Coggle Diagram
Unit 1: Biological molecules
Carbohydrates
Monosaccharides
all carbohydrates contain the elements carbon, hydrogen, and oxygen
carbohydrate is a polymer made from monomers called monosaccharides, like glucose, frucotse, and galactose
all of these are hexose sugars
Simple sugars
Glucose
Alpha glucose
H atom on top of right side, hydroxyl group on bottom
Beta glucose
H atom on bottom of right side, hydroxyl group on top
Poor storage molecule
Can diffuse in and out of cells
soluble in water so affects the water potential of cells (causes osmosis
Main respiratory substrate
Disaccharides
Sucrose, lactose, and maltose
Simple sugars
Form through condensation reactions
Polysaccharides
Starch, glycogen, and cellulose
Test for starch:
Add iodine solution
Colour change to blue/black
Amylose
coiled
Better for storage
1,4 - glycosidic bonds
Amylopectin
Branched molecule
Easier to hydrolyse
1,6 AND 1,4 - glycosidic bonds
Glycogen has a similar structure and function to starch (amylopectin) so has many o the same adaptations except with more branches
Glycogen is formed of branched chains of alpha glucose joined by both 1,6 and 1,4 glycosidic bonds
Starch and glycogen are both alpha glucose
When digested, releases glucose for respiration
Cellulose = beta glucose
Made up of beta glucose molecules
every other molecule is inverted to form straight chains of cellulose which then form microfibrils which is what makes cellulose so strong
Cellulose is a polysaccharide made of beta glucose joined by just 1,4 - glycosisdic bonds
insoluble
won't affect water potential of cells
Storage molecules
Complex carbohydrates
Forms through condensation polymerisation
Reducing sugars
The H atom could dissociate from the carbon ring if it is a reducing sugar
Maltose = reducing sugar
Sucrose = non-reducing sugar
Sucrose + sucrose cannot form a polysaccharide as the hydrogen could not dissociate and could not form a glycosidic bond
Lactose = reducing sugar
If the H atom dissociates, it could form a glycosidic bond
Benedict's test for NON-REDUCING sugars
1) After carrying out Benedict's test and getting a negative result, hydrolyse the sugar by adding
hydrochloric acid
and heating
2)
Neutralise
the acid by adding
sodium hydrogen carbonate
3) Carry out another Benedict's test
4) solution changes colour to red/organge/yellow/green
Benedict's test for REDUCING sugars
1) Grind up food sample
2) Dissolve food sample in water
3) Measure 2cm^2 of food sample into a beaker
4) add an equal volume of Benedict's reagent
5) heat in a water bath for 5 minutes
6) Solution changes colour to red/orange/yellow/green
Lipids
Fatty acids
Saturated fatty acids
Carboxyl group
Saturated hydrocarbon chain (no C=C double bonds
Unsaturated fatty acids
Carboxyl group
Unsaturated hydrocarbon chain (contaisn C=C double bonds)
monounsaturated
just one C=C double bond
polyunsaturated
more than one C=C double bond
R group
the variable region on a fatty acid hydrocarbon chain (RCOOH)
Triglycerides
Formation of triglycerides
Glycerol + 3 fatty acids --> triglyceride + 3H2O
forms ester bond
condensation reaction
Fats are solid at room temp, oils are liquids
Fats are saturated HC chains
oils are unsaturated HC chains
contain more C=C double bonds
lower mpt is related to higher degree of unsaturation
the presence of C=C double bonds in the oil molecules distorts the long fatty acid chain (causes kinks) and as a result, the molecules cannot pack closely together, leading to weak IM forces
Roles of triglycerides
Energy storage
insulation
Protection for organs
waterproofing
Emulsion test for lipids
Grind up food sample and place into test tube
Add ethanol and shake
Decant the ethanol into distilled water
A cloudy white emulsion will appear if lipids are present
Cannot dissolve in water, but CAN dissolve in organic substances like alcohols (e.g. ethanol)
Phospholipids
Contain a phsphate group
Two fatty acid chains
Polar head
contains glycerol and a phosphate group
Hydrophyllic
attracted to water so point out towards water
Non-polar tails
Can be saturated/unsaturated
Hydrophobic
point in, away from water, forming a hydrophobic core
roles of phospholipids
main component of membranes (e.g. cell surface membranes and organelle membanes - compartmentalisation of cells.
Phospholipid bilayers
hydrophobic core
Fluidity of membranes
Phospholipids with mainly unsaturated atty acid tails
more kinks in the hydrocarbon chains
weaker intermolecular forces
phospholipid bilayer/membrane is more fluid
more double bonds in hydrocarbon chains
phospholipids with mainly aturated fatty acid tails
More saturated hydrocarbon chains
Fewer kinks in hydrocarbin chain
Stronger intermolecular forces
Phsopholipid bilayer/membrane less fluid
Proteins
Amino acids
All amino acids have:
A central carbon atom
An amine group (NH2)
A carboxyl group (COOH)
An R group/variable group/side group
This varies in size and charge
There are 20 different amino acids found in all organisms
Dipeptides
Form through condensation reactions
2 amino acids join
Peptide bond is formed
Water is also produced
Polypeptides
Many amino acids join together
condensation polymerisation
forming peptide bonds
water is also formed
Protein structure
primary structure
The sequence of amino acids in a polypeptide (different for each protein)
Secondary structure
Alpha helix or beta pleated sheet (only aplha helix on spec)
Maintained by hydrogen bonds (between N-H and C=O groups on different aminoa cids
Tertiary structure
Specific 3D shape (different for each protein)
Maintained by bonds between R groups
Hydrogen bonds
Ionic bonds
Disulphide bridges (covalent bonds
Factors affecting tertiary structure of a protein/enzyme
Primary structure
Temperatures above 40 degrees celcius
Change in pH
Another molecule binding (sticking to/temporarily bonding to) the protein
Phosphorylation
The addition of a phosphate group to a protein
Quaternary structure
Several polypeptides
Maintained by bonds between polypeptides
Lots of hydrogen bonds (weak)
Ionic bonds
Disulphide bridges (covalent bonds)
May be non-protein (prosthetic) groups, E.g. haem groups in haemoglobin
Globular
Metabolic functions (e.g. enzyes, receptor molecules, and transport proteins in plasma membranes
Fibrous
Structural (e.g. keratin in our hair and collagen in connective tissue
Biruet test
Add sodium hydroxide to food sample
Add cooper sulfate solution
Colour change from blue to purple if protein is present
Enzymes
Early model: Lock and key
Substrate complimentary to the shaoe of active site
Substrate binds to active site
Enzyme-substrate complex is formed
Induced fit model of enzyme action (the one we use at A level)
Substrate binds to active site
Active site changes shape slightly (to form the functional active site) so it is complimentary to the substrate
Enzyme-substrate complex is formed
How enzymes work as catalysts
1) Substrate binds to the active site of the enzyme
2) The active site changes shape so it is complimentary to the substrate (induced fit model)
3) Enzyme-substrate complex is formed
4) This puts strain on bonds in substrate molecule
5) this causes bonds in substrate to break more easily
6) Enzymes lower the activation energy (the energy needed to start a reaction)
Rates of reaction
Measuring RoR
Use of reactant/time
Production of product/time
Change in mass/time
Temperature/time
Ph and temperature:
Temperature
when temperatures reach 40 degrees celcius or over, the hydrogen bonds maintaining the tertiary structure of the enzyme break
This means the tertiary stucture of the enzyme changes and the substrate cannot bind (or binds less easily) to the active site
Less/no enzyme-substrate complexes are formed (enzyme is denatured)
pH
Change in pH from optimun means a change in the concentration of hydrogen ions
Hydrogen and ionic bonds which maintain the tertiary structure of the enzyme break
change in the tertiary structure of enzyme
Substrate does not bind (or binds less easily) to the active site
Less/no enzyme-substrate complexes are formed
Enzyme and substrate concentrations
Increase in substrate concentration
increase in enzyme-substrate complexes
Increase in rate or reaction
Once all active sites have been filled by substrates...
Increase in substrate concentration will not cause an increase in enzyme-substrate complexes so no increase in rate of reaction
Increase in enzyme concentrations
Free substrate molecules
more enzyme-substrate complexes
increase in rate of reaction
No more free substrate molecules
No increase in enzyme-substrate complexes
No increase in rate of reaction
Inhibitors
non-competitive inhibitors
Shape is different to the substrate
binds onto an alternative (allosteric) site on the enzyme (not the active site)
Changes the enzyme's tertiary structure
Active site no longer complimentary to substrate
Less enzyme-substrate complexes formed
Lower rate of reaction
After adding a noncompetitive inhibitor and increasing the substrate concentration, the rate of reaction is unaffected as the same number of enzymes are available so there is no increase in the number of enzyme-substrate complexes formed.
Competitive inhibitors
Shape is similar to that of the substrate
Binds temporarily to the active site of the enzyme
Prevents substrate from binding
Less enzyme-substrate complexes formed
Lower rate of reaction
After adding a competitive inhibitor and increasing the substrate concentration, the rate of reaction increases as there is more chance of a substrate molecule colliding with an active site so more enzyme-substrate complexes formed
Nucleic acids
Fromation of a polynucleotide
Nucleotides join together by a condensation reaction (between the phosphate group of one nucleotide and the pentose sugar of another)
A phosphodiester bond/linkage is formed
water is produced
DNA
Contain deoxyribose sugar
Contains adenine (A), cytosine (C), guanine (G), and
thymine (T)
Double stranded
Longer than RNA molecule
RNA
Contains ribose sugar
Contains adenine (A), cytosine (C), guanine (G), and
uracil (U)
Single stranded
Shorter than DNA molecule
mRNA:
Messenger RNA
transfers genetic information from DNA to ribosomes
tRNA:
Tranfer RNA
brings specific amino acids to the riboosome during protein synthesis
rRNA:
Ribosomal RNA
The ribosome itself is made of RNA and proteins
Nucleotides
All nucleotides contain a phosphate group, a pentose sugar (either deoxyribose or ribose), and a nitrogen containing base (adening, cytosine, guanine, and either thymine (DNA nucleotide) or uracil (RNA nucleotide)
Guanine is complimentary to cytosine
Adenine is complimentary to thymine (DNA molecule)
Adenine is complimentary to uracil (RNA molecule)
DNA replication:
1) DNA helicase breaks hydrogen bons between DNA strands. DNA strands spearate and unwind
2) Both strands can now act as a template for the formation of a new strand
3) Free DNA nucleotides (in the nucleus) are attracted to exposed bases on the template strands and form complimentary base pairs
4) Dna polymerase joins adjacent nucleotides by condensation reactions forming phosphodiester bonds
5) This is called semiconservative replication as each new DNA molecule contains one new and one original strand
Monomers and Polymers
Most carbohydrates, proteins and nucleic acids are polymers
Examples of monomers include monosaccharides, amino acids, and nucleotides
Condensation polymerisation reactions are used to make polymers
Hydrolysis reactions break down polymers back into their originial monomers
Form water as a byproduct
ATP
ATP is a nucleotide derivative
Structure
Three phosphate groups (hence adenosine
tri
phosphate)
Pentose sugar (ribose)
Nitrogenous base is ALWAYS adenine for ATP
Hydrolysis of ATP
ATP is hydrolysed into ADP (adenosine diphosphate) and an inorganic phosphate ion (Pi)
catalysed by ATP hydrolase
Exothermic reaction (releases energy)
Uses of ATP:
ATP hydrolysis releases energy that can be used for an energy-requiring reaction or process
Anabolic/synthesis/condensation reactions (e.g. synthesis of DNA/proteins)
Active transport (including pumping of ions and exocytosis)
Cell division (mitosis/meiosis)
muscle contraction in animals
The inorganic phosphate ion released during hydrolysis may be used to phosphorylate another compound (stick a phosphate group onto it)
Suggest how phsphorylation of an enzyme could "activate" the enzyme (cause it to become functional) (3 marks)
1) Phosphorylation of an enzyme changes its tertiary structure
2)Active site becomes complimentary to substrate
3) enzyme-substrate complex can form
4) Enzyme is activated
Why is ATP a good energy molecule?
ATP can be hydrolysed ina single reaction - releasing energy quickly.
Hydrolysis of ATP only releases a small amount of energy at a time - less energy wasted as heat which also stops cell from overheating
ATP is small and can diffuse easily around the ell
ATP is polar and cannot diffuse out of the cell
ATP synthesis
ADP + Pi --> ATP +H2O
ADP and an inorganic phosphate ion join in a condensation reaction form ATP and a water molecue
This reacion is endothermic and is catalysed by ATP synthase
Water
Water molecules are polar. This means that there is no overall charge on a water molecule but one part is postively charged and another is negative
Hydrogen bonds are intermolecular forces tha form between hydrogen atoms and other elements
Weak copared to ionic or covalent bonds
Strong compared to other intermolecular forces
Can form between water molecules (cohesion)
Can form between water molecules and other substances (adhesion)
Water is almost a universal indicator:
Any molecule that is charged or polar will dissolve in water
Makes water a good site for metabolic reactions
Water is an important metabolite (reactant/product):
e.g. photosynthesis
Carbon dioxide + water --> glucose + oxygen
Hydrolysis
Sucrose + water --> glucose + fructose
Condensation:
lucose + fructose --> sucrose + water
Respiration:
glucose + oxygen --> water +carbon dioxide
Water has a high thermal capacity (due to hydrogen bonding between water molecules:
This means that it takes a lot fo energy to change the temperature of the water
This is important because it buffers changes in temperature in organisms and it remains a liquid in most environments on earth
Water has a high latent heat of vaporisation:
This means it takes a lot of energy to evaporate water
this is important because it cools plants and animals as it eaporates
Water is cohesive:
This allows water to be pulled up the xylem tissue in plants in an unbroken colomn
This results in surface tension which allows small organisms to love on the surface of water
Water is less dense as a solid
Ice floats on water (e.g. ponds/rivers)
ince insulates the water below that doesn't freeze so fish etc don't die
Inorganic ions
Fe 2+ is part of haemoglobin which oxygen binds to in order to transport oxygen around the body
Inorganic phosphate ions are a component of DNA, RNA, ATP, and phospholipids
H+ ions determine pH
Na+ ions aid the absorption of glucose and amino acids via co-transport
Ca+ ions help the function of synapses and muscle contraction
Mg+ ions are responsible for absorbing light in chlorophyll
Na+ ions are also responsible for transmitting impulses along nerve cells
Ca+ ions are also in charge of aiding blood clotting