2.2 Biological Molecules Flashcards
(288 cards)
1
Q
Properties of water
A
Medium in which all metabolic reactions take place (70%-95% of the mass of a cell is water)
Major habitat for organisms
Composed of hydrogen and oxygen, 1 oxygen atom combines with two atoms of hydrogen by covalent bonding
Water as a whole is electrically neutral but sharing of atoms is uneven
Polar molecule
2
Q
Polar molecule in water
A
sharing of electrons is uneven and oxygen attracts electrons more strongly than hydrogen atoms resulting in a weak negatively charge region on the oxygen atom and a weak positively charged region on the hydrogen atoms, resulting is asymmetrical shape
3
Q
Polar molecule
A
When one molecule has one end that is negatively charged and one end is positively charged
4
Q
Dipole
A
Separation of charge due to electrons in the covalent bonds being unevenly shared
5
Q
Why are Hydrogen bonds formed in water
A
A result of polarity of water hydrogen bonds form between positive and negatively charged regions of adjacent water molecules
6
Q
Hydrogen bond strength
A
When there are few they are weak so they are constantly breaking and reforming
When there are a large numbers present they form a strong molecule
7
Q
What properties do hydrogen bonds contribute to water
A
Excellent solvent
Relatively high specific heat capacity
Relatively high latent heat of vaporisation
Water is less dense when a solid
Water has high surface tension and cohesion
It’s acts as a reagent
8
Q
Water as a solvent
A
As its a polar molecules many ions and covalently bonded polar substances (eg glucose) will dissolve in it.
9
Q
What does water being a good solvent lead to
A
Allows chemical reactions to occur within cells (as dissolved solutes are more chemically reactive when they are free to move about)
Metabolites can be transported efficiently (except non polar molecules which are hydrophobic)
10
Q
Specific heat capacity
A
Amount of thermal energy required to raise the temperature of 1kg of a substance by 1’c
11
Q
Water specific heat capacity
A
4200j/kg’C
12
Q
Why does water have high specific heat capacity
A
Due to many hydrogen bonds present in water, its takes a lot of energy to break these bonds and a lot of energy to build them, thus them temperature of water does not fluctuate greatly
13
Q
What are the advantages of water’s high specific heat capacity for living organisms
A
Provides suitable habitats
Able to contain constant temperature as water is able to absorb a lot of heat without big temperature fluctuations which is vital in maintain temperatures that are optimal for enzyme activity
14
Q
Water in blood plasma
A
Vital in transferring heat around the body, helping to maintain a fairly constant temperature
As blood passes through more active (warmer) regions of the body, heat energy is absorbed but the temperature remains firmly constant
15
Q
Water in tissue fluid
A
Plays an important role in maintaining a constant body temperature
16
Q
High latent heat of vaporisation
A
In order to change state from liquid to gas a large amount of thermal energy must be absorbed by water to break the hydrogen bonds and evaporate
17
Q
How does high latent heat of vaporisation benefit animals
A
Only a little water is required to evaporate for the organism to lose a great amount of heat, this provides a cooling effect for living organisms, (eg transpiration from leaves or evaporation of water in sweat)
18
Q
Cohesion in water
A
Hydrogen bonds between water molecules allow for strong cohesion between water molecules
19
Q
What does cohesion between water molecules allow
A
Columns of water to move through xylem of plants through blood vessels in animals
Enables surface tension where a body of water meets the air, these hydrogen bonds occur between the top layer of water molecules to create a sort of film on the body of water (this allows insects such as pond skaters to float)
20
Q
Adhesion is water molecules
A
When water is able to hydrogen bond to other molecules which enables water to move up xylem due to transpiration
21
Q
Key molecules that are required to bold structures that enable organisms to function
A
Carbohydrates, proteins, lipids, nucleic acids, water
22
Q
Monomers
A
Smaller units from which larger molecules are made
23
Q
Polymers
A
Molecules made from a large number of monomers joined together in a chain
24
Q
Polymerisation
A
Carbon compounds can form small single subunits (monomers) that bond with many repeating subunits to form large molecules (polymers)
25
Macromolecules
Very large molecules
Contain 1000 or more atoms so high high molecular mass
Polymers can be macromolecules however not all macromolecules are polymers as the subunits of polymers have to be repeating units
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Covalent bonds
Sharing of two or more electrons between two atoms
Can be formed equally forming a non polar covalent bond
Can be formed unequally forming a polar covalent bonding
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Properties of covalent bonds
Very stable as high energy required to break bonds
Multiple pairs of electrons can be shared forming double or triple bonds
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Covalent bonds in monomers
When two monomers are close enough that their outer orbitals overlap which results in their electrons being shared and a covalent bond forming. If more monomers are added then polymerisation occurs and/or a macromolecule forms
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Condensation reaction
Occurs when monomers combine together by covalent bonds to form polymers or macromolecules and water is removed
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Hydrolysis
Breaking down a chemical bond between two molecules and involves the use of a water molecule
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Hydrolysis of polymers
Covalent bonds are broken when water is added
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Type of Covalent bonds in carbohydrates
Glycosidic
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Type of covalent bond in proteins
Peptide
34
Type of covalent bond in lipids
Ester
35
Types of covalent bond in nucleic acids
Phosphodiester
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Why are Carbon atoms key to organic compounds
Each carbon atom can form 4 covalent bonds making the compound very stable
Carbon atoms can form covalent bonds with oxygen, nitrogen and sulfur
Carbon atoms can form straight chains, branched chains or rings
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What do carbohydrates, proteins, lipids and nucleic acids contain making them organic compounds
Carbon and hydrogen
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Function of carbohydrates
Source of energy e.g. glucose is used for energy-release during cellular respiration
Store of energy e.g. glycogen is stored in the muscles and liver of animals
Structurally important e.g. cellulose in the cell walls of plants
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3 types of carbohydrates
monosaccharides, disaccharides and polysaccharides
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Monosaccharide
Single sugar monomer, all are reducing sugars
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Examples of monosaccharide
Glyceraldehyde (3c), ribose (5c), glucose (6c)
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Function of monosaccharide
Source of energy in respiration, building blocks for polymers
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Disaccharide
A sugar formed two monosaccharides joined by a glycosidic bond in a condensation reaction
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Examples of disaccharides
Maltose-(glucose+glucose)
Sucrose-(glucose+fructose)
Lactose-(glucose+galactose)
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Function of disaccharide
Sugar fund in germinating seeds (maltose)
Mammal milk sugar (lactose)
Sugar stored in sugar cane (sucrose)
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What makes up maltose
Glucose+glucose
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What makes up sucrose
Glucose+fructose
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What makes up lactose
Glucose+galactose
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Polysaccharide
A polymer formed by many monosaccharides joined by glycosidic bonds in a condensation reaction
50
Examples of polysaccharide
Cellulose (glucose)
Starch (glucose in the form of amylose and amylopectin)
Glycogen (glucose)
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What makes up cellulose
Glucose
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What makes up starch
Glucose in the form of amylose and amylopectin
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What makes up glycogen
Glucose
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Function of polysaccharides
Energy storage- (plants-starch, animals-glycogen)
Structural- cellulose cell wall
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Types of lipids
triglycerides (fats and oils), phospholipids, waxes, and steroids (such as cholesterol)
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Functions of lipids
Source of energy
Store of energy
Insulating layer
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Lipids as a source of energy
Source of energy that can be respired (lipids have a high energy yield)
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Lipids as a store of energy
lipids are stored in animals as fats in adipose tissue and in plants as lipid droplets
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Lipids as an insulating layer
thermal insulation under the skin of mammals and electrical insulation around nerve cells
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Eg of carbohydrate as source of energy
glucose is used for energy-release during cellular respiration
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Carbohydrates as store of energy
glycogen is stored in the muscles and liver of animals
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Eg of carbohydrates being structurally important
cellulose in the cell walls of plants
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Functions of proteins
Required for cell growth
Structurally important
Can act as carrier molecules in cell membrane
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Eg of proteins being structurally important
in muscles, collagen and elastin in the skin, collagen in bone and keratin in hair
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Eg of nucleic acids
DNA and rna
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Function of nucleic acids (dna and rna)
Carrying the genetic code in all living organisms
Nucleic acids are essential in the control of all cellular processes including protein synthesis
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Reducing sugars
Can donate electrons and the sugars become the reducing agent
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Examples of reducing sugars
glucose, fructose and galactose
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Non-reducing sugars
cannot donate electrons, therefore they cannot be oxidised
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Example of non reducing sugar
Sucrose
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Glucose molecular formula
C6H12O6
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Why is glucose so important
The main function of glucose is as an energy source
It is the main substrate used in respiration, releasing energy for the production of ATP
Glucose is soluble and so can be transported in water
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Penrose sugars
Sugars that contain five carbon molecules
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Learn how to draw alpha and beta glucose
Type?
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What Penrose sugar makes up rna and dna
Ribose-rna
Deoxyribose-dna
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What does a glycosidic bond result in
one water molecule being removed, thus glycosidic bonds are formed by condensation
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Example of Penrose and heroes monosaccharide
Pentose-ribose
Hexose-glucose
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Difference between heroes and Penrose monosaccharide
Pentose- five carbon atoms
Hexose- six carbon atoms
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How is a glycosidic bond formed
A condensation reaction between two monosaccharides forming disaccharides and polysaccharides
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How are glycosidic bonds broken down
Water is added in hydrolysis, disaccharides and polysaccharides are broken dow in hydrolysis reaction
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What happens when you heart sucrose
When sucrose is heated with hydrochloric acid this provides the water that hydrolyses the glycosidic bond resulting in two monosaccharides that will produce a positive Benedict's test
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What result does sucrose give in Benedict test when not heated
Sucrose is a non-reducing sugar which gives a negative result
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Condensation reaction
two molecules join together via the formation of a new chemical bond (glycosidic bond), with a molecule of water being released in the process
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How to calculate chemical formula of disaccharide
you add all the carbons, hydrogens and oxygens in both monomers then subtract 2x H and 1x O (for the water molecule lost)
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Examples of disaccharides
Maltose, sucrose and lactose
All three of the common examples above have the formula C12H22O11
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Maltose
The sugar formed in the production and breakdown of starch
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Sucrose
The main sugar produced in plants
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Lactose
A sugar found only in milk
89
Monosaccharide components of maltose
Glucose + glucose
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Monosaccharide components of sucrose
Glucose + fructose
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Monosaccharide components of lactose
Glucose + galactose
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What are Starch, glycogen and cellulose
Polysaccharides
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What are polysaccharides
macromolecules (polymers) that are formed by many monosaccharides joined by glycosidic bonds in a condensation reaction to form chains
These chains may be:
Branched or unbranched
Folded (making the molecule compact which is ideal for storage eg. starch and glycogen)
Straight (making the molecules suitable to construct cellular structures e.g. cellulose) or coiled
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What two polysaccharides construct starch
Amylose
Amylopectin
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Amylose in starch
(10 - 30% of starch)
Unbranched helix-shaped chain with 1,4 glycosidic bonds between α-glucose molecules
The helix shape enables it to be more compact and thus it is more resistant to digestion
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Amylopectin in starch
(70 - 90% of starch)
1,4 glycosidic bonds between α-glucose molecules but also 1,6 glycosidic bonds form between glucose molecules creating a branched molecule
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What makes up glycogen
It is made up of α-glucose molecules
There are 1,4 glycosidic bonds between α-glucose molecules and also 1,6 glycosidic bonds between glucose molecules creating a branched molecule
Glycogen has a similar structure to amylopectin but it has more branches
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Monomer in amylose, amylopectin and glycogen
Glucose for all of them
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Branched feature in amylose, amylopectin and glycogen
Amylose- no
Amylopectin- yes (every 20 monomers)
Glycogen-yes (every 10 monomers)
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Do amylose, amylopectin and glycogen have a helix (coiled) shape
Amylose- yes
Amylopectin- no
Glycogen- no
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Glycosidic bonds present in amylose, amylopectin and glycogen
Amylose- 1,4
Amylopectin- 1,4 and 1,6
Glycogen- 1,4 and 1,6
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Cellulose
polysaccharide found in plants
It consists of long chains of β-glucose joined together by 1,4 glycosidic bonds
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Why is cellulose strong
β-glucose is an isomer of α-glucose, so in order to form the 1,4 glycosidic bonds consecutive β-glucose molecules must be rotated 180° to each other
Due to the inversion of the β-glucose molecules, many hydrogen bonds form between the long chains giving cellulose its strength
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Why are starch and glycogen storage polysaccharides
they are:
Compact
So large quantities can be stored
Insoluble
So they will have no osmotic effect, unlike glucose which would lower the water potential of a cell causing water to move into cells
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What is starch stored as in plants
It is stored as granules in plastids such as amyloplasts and chloroplasts
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Plastids
Plastids are membrane-bound organelles that can be found in plant cells. They have a specialised function eg. amyloplasts store starch grains
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Why does starch take longer to digest than glucose
Due to the many monomers in a starch molecule
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How can amylopectin in starch help the plant
has branches that result in many terminal glucose molecules that can be easily hydrolysed for use during cellular respiration or added for storage
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Glycogen
the storage polysaccharide of animals and fungi, it is highly branched and not coiled
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Glycogen in liver and muscles cells
have a high concentration of glycogen, present as visible granules, as the cellular respiration rate is high in these cells (due to animals being mobile)
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Benefits of glycogen being more branched than amylopectin
Makes it more compact which animals store more
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Branching in glycogen
The branching enables more free ends where glucose molecules can either be added or removed allowing for condensation and hydrolysis reactions to occur more rapidly – thus the storage or release of glucose can suit the demands of the cell
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Cellulose
main structural component of cell walls due to its strength which is a result of the many hydrogen bonds found between the parallel chains of microfibrils
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What does the high tensile strength of cellulose allow
it to be stretched without breaking which makes it possible for cell walls to withstand turgor pressure
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How does cellulose increase strength of the cell walls
The cellulose fibres and other molecules (eg. lignin) found in the cell wall forms a matrix
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What do cell walls do
The strengthened cell walls provide support to the plant
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Permeability of cellulose fibres
Cellulose fibres are freely permeable which allows water and solutes to leave or reach the cell surface membrane
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Benedict’s test for reducing sugars method
Add Benedict's reagent (which is blue as it contains copper (II) sulfate ions) to a sample solution in a test tube
Heat the test tube in a water bath or beaker of water that has been brought to a boil for a few minutes
If a reducing sugar is present, a coloured precipitate will form as copper (II) sulfate is reduced to copper (I) oxide which is insoluble in water
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Why is it important there is an excess of Benedict’s solution
so that there is more than enough copper (II) sulfate present to react with any sugar present
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Benedict’s reagent
Benedict’s reagent is a blue solution that contains copper (II) sulfate ions (CuSO4 ); in the presence of a reducing sugar copper (I) oxide forms
Copper (I) oxide is not soluble in water, so it forms a precipitate
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Colour change in Benedict’s test for reducing sugars
A positive test result is a colour change somewhere along a colour scale from blue (no reducing sugar), through green, yellow and orange (low to medium concentration of reducing sugar) to brown/brick-red (a high concentration of reducing sugar)
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Examples of reducing sugars
Galactose, glucose, fructose and maltose
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Example of non-reducing sugars
Sucrose (only one need to know)
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Test for non-reducing sugars
Add dilute hydrochloric acid to the sample and heat in a water bath that has been brought to the boil
Neutralise the solution with sodium hydrogencarbonate
Use a suitable indicator (such as red litmus paper) to identify when the solution has been neutralised, and then add a little more sodium hydrogencarbonate as the conditions need to be slightly alkaline for the Benedict’s test to work
Then carry out Benedict’s test as normal
Add Benedict’s reagent to the sample and heat in a water bath that has been boiled – if a colour change occurs, a reducing sugar is present
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Why do we add hydrochloride acid to test non-reducing sugars
The addition of acid will hydrolyse any glycosidic bonds present in any carbohydrate molecules
The resulting monosaccharides left will have an aldehyde or ketone functional group that can donate electrons to copper (II) sulfate (reducing the copper), allowing a precipitate to form
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Iodine test for starch
Iodine- orange/black
If starch is present, iodide ions in the solution interact with the centre of starch molecules, producing a complex with a distinctive blue-black colour
127
Why do iodine test
To show starch in a sample has been digested by enzymes
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Lipids
macromolecules that contain carbon, hydrogen and oxygen atoms. Unlike carbohydrates, lipids contain a lower proportion of oxygen
Lipids are non-polar and hydrophobic (insoluble in water)
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2 groups of lipids
Triglycerides (the main component of fats and oils)
Phospholipids
130
What do lipids pay a role in
Lipids play an important role in energy yield, energy storage, insulation and hormonal communication
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Triglycerides
Triglycerides are non-polar, hydrophobic molecules
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What monomers make up tryglycerides
Glycerol and fatty acids
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How can fatty acids vary
Length of the hydrocarbon chain (R group)
The fatty acid chain (R group) may be saturated (mainly in animal fat) or unsaturated (mainly vegetable oils, although there are exceptions e.g. coconut and palm oil)
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Phospholipids
a type of lipid, therefore they are formed from the monomers glycerol and fatty acids
Unlike triglycerides, there are only two fatty acids bonded to a glycerol molecule in a phospholipid as one has been replaced by a phosphate ion (PO43-)
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Polarity of phospholipids
As the phosphate is polar it is soluble in water (hydrophilic)
The fatty acid ‘tails’ are non-polar and therefore insoluble in water (hydrophobic)
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Amphipathic
Eg. Phospholipids
Have both hydrophobic and hydrophilic parted
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What do phospholipids having hydrophobic and hydrophilic parts lead to
phospholipid molecules form monolayers or bilayers in water
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Function of phospholipids
Cell membrane component
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Function of triglycerides
Energy storage
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How are triglycerides formed
Esterification
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How do ester bonds form
when a hydroxyl (-OH) group from the glycerol bonds with the carboxyl (-COOH) group of the fatty acid
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Process of esterification
An H from glycerol combines with an OH from the fatty acid to make water
The formation of an ester bond is a condensation reaction
For each ester bond formed a water molecule is released
Three fatty acids join to one glycerol molecule to form a triglyceride
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How many water molecules are released when one triglyceride is formed
3
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What makes up tryglycerides
Fatty acid and glycerol molecules
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What are tryglycerides
Fats and oils
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Functions of fats and oils (tryglycerides)
energy storage, insulation, buoyancy, and protection
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Why do tryglycerides store more energy per gram than carbs and proteins
The long hydrocarbon chains in triglycerides contain many carbon-hydrogen bonds with little oxygen (triglycerides are highly reduced)
So when triglycerides are oxidised during cellular respiration this causes these bonds to break releasing energy used to produce ATP
148
Why can tryglycerides store more
As triglycerides are hydrophobic they do not cause osmotic water uptake in cells so more can be stored
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Why would mammals store tryglycerides
Mammals store triglycerides as oil droplets in adipose tissue to help them survive when food is scarce (e.g. hibernating bears)
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How do triglycerides link to water
The oxidation of the carbon-hydrogen bonds releases large numbers of water molecules (metabolic water) during cellular respiration
Desert animals retain this water if there is no liquid water to drink
Bird and reptile embryos in their shells also use this water
151
How do triglycerides act as an insulator
Triglycerides compose part of the adipose tissue layer below the skin which acts as insulation against heat loss (eg. blubber of whales)
Triglycerides are part of the composition of the myelin sheath that surrounds nerve fibres
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How do triglycerides lead to buoyancy
The low density of fat tissue increases the ability of animals to float more easily
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How do triglycerides protect mammals
The adipose tissue in mammals contains stored triglycerides and this tissue helps protect organs from the risk of damage
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What forms phospholipids
they are formed from the monomer glycerol and fatty acids
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How do phospholipids create a barrier to water soluble molecules
Due to the presence of hydrophobic fatty acid tails, a hydrophobic core is created when a phospholipid bilayer forms
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Compartmentalisation in cells
Compartmentalisation enables cells to organise specific roles into organelles, helping with efficiency
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How do phospholipids link to cell membranes
Phospholipids are the main component (building block) of cell membranes
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How do phospholipids allow the cell membrane to be used to compartmentalise
The hydrophilic phosphate heads form H-bonds with water allowing the cell membrane to be used to compartmentalise
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How does the composition of phospholipids contribute to the fluidity of the cell membrane
If there are mainly saturated fatty acid tails then the membrane will be less fluid
If there are mainly unsaturated fatty acid tails then the membrane will be more fluid
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How do phospholipids control protein orientation
Weak hydrophobic interactions between the phospholipids and membrane proteins hold the proteins within the membrane but still allow movement within the layer
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Cholesterol molecules
cholesterol molecules have hydrophobic and hydrophilic regions
Their chemical structure allows them to exist in the bilayer of the membrane
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Where of molecules of cholesterol synthesised
Molecules of cholesterol are synthesised in the liver and transported via the blood
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How does cholesterol affect the fluidity and permeability of the cell membrane
It disrupts the close-packing of phospholipids, increasing the rigidity of the membrane (makes the membrane less flexible)
It acts as a barrier, fitting in the spaces between phospholipids. This prevents water-soluble substances from diffusing across the membrane
164
What are molecules of cholesterol used to produce
steroid-based hormones such as oestrogen, testosterone and progesterone
165
Lipid test method
Add ethanol to the sample to be tested
Shake to mix
Add the mixture to a test tube of water
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Lipid test results
If lipids are present, a milky emulsion will form (the solution appears ‘cloudy’); the more lipid present, the more obvious the milky colour of the solution
If no lipid is present, the solution remains clear
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What are proteins
Proteins are polypeptides (and macromolecules) made up of monomers called amino acids
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What are proteins important for
cell growth, cell repair and structure
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What do proteins form
Enzymes
Cell membrane proteins (eg. carrier)
Hormones
Immunoproteins (eg. immunoglobulins)
Transport proteins (eg. haemoglobin)
Structural proteins (eg. keratin, collagen)
Contractile proteins (eg. myosin)
170
Amino acids
Monomers of polypeptides
171
Bonds between amino acids
Peptide
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What type of bond are peptide bonds
Covalent bonds
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How is a peptide bond formed
a hydroxyl (-OH) is lost from the carboxylic group of one amino acid and a hydrogen atom is lost from the amine group of another amino acid
The remaining carbon atom (with the double-bonded oxygen) from the first amino acid bonds to the nitrogen atom of the second amino acid
This is a condensation reaction so water is released
174
Dipeptides
formed by the condensation of two amino acids
175
Polypeptides
formed by the condensation of many (3 or more) amino acids
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What happens during hydrolysis reaction of polypeptides
During hydrolysis reactions, the addition of water breaks the peptide bonds resulting in polypeptides being broken down to amino acids
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4 levels of protein structure
Primary, secondary, tertiary, quaternary
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Primary protein structure
The sequence of amino acids bonded by covalent peptide bonds is the primary structure of a protein
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How is primary structure of a protein determined
The DNA of a cell determines the primary structure of a protein by instructing the cell to add certain amino acids in specific quantities in a certain sequence. This affects the shape and therefore the function of the protein
180
Specificity of primary structure
The primary structure is specific for each protein (one alteration in the sequence of amino acids can affect the function of the protein)
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Secondary structure of a protein
The secondary structure of a protein occurs when the weak negatively charged nitrogen and oxygen atoms interact with the weak positively charged hydrogen atoms to form hydrogen bonds
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What two shapes can form within proteins due to hydrogen bongs
Helix
Pleated sheet
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When does a helix shape occur
when the hydrogen bonds form between every fourth peptide bond (between the oxygen of the carboxyl group and the hydrogen of the amine group)
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When does a pleated sheet shape occur
The β-pleated sheet shape forms when the protein folds so that two parts of the polypeptide chain are parallel to each other enabling hydrogen bonds to form between parallel peptide bonds
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What does secondary structure only relate to
The secondary structure only relates to hydrogen bonds forming between the amino group and the carboxyl group (the ‘protein backbone’)
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How can hydrogen bonds be broken
High temperatures and pH changes
187
Tertiary structure
Further conformational change of the secondary structure leads to additional bonds forming between the R groups (side chains)
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Additional bonds (tertiary structure)
Hydrogen (these are between R groups)
Disulphide (only occurs between cysteine amino acids)
Ionic (occurs between charged R groups)
Weak hydrophobic interactions (between non-polar R groups)
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Disulphide bonds
strong covalent bonds that form between two cysteine R groups (as this is the only amino acid with a sulphur atom)
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Disulphide bonds strength
These bonds are the strongest within a protein but occur less frequently, and help stabilise the proteins
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How can disulphide bonds be broken
Oxidation
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Where are Disulphide bonds common
This type of bond is common in proteins secreted from cells eg. insulin
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Ionic bonds
Ionic bonds form between positively charged (amine group -NH3+) and negatively charged (carboxylic acid -COO-) R groups
194
Ionic bond strength
Ionic bonds are stronger than hydrogen bonds but they are not common
195
How can ionic bonds be broken
By ph changes
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Hydrogen bongs
Hydrogen bonds form between strongly polar R groups. These are the weakest bonds that form but the most common as they form between a wide variety of R groups
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Hydrophobic interactions
Hydrophobic interactions form between the non-polar (hydrophobic) R groups within the interior of proteins
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Why will polypeptide chain fold differently
A polypeptide chain will fold differently due to the interactions (and hence the bonds that form) between R groups
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Why is there a vast range of protein configurations and therefore functions
Each of the twenty amino acids that make up proteins has a unique R group and therefore many different interactions can occur creating a vast range of protein configurations and therefore functions
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Quaternary structure
Quarternary structure exists in proteins that have more than one polypeptide chain working together as a functional macromolecule, for example, haemoglobin
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What is each polypeptide chain in a quaternary structure referred to as
A subunit of a protein
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Bonds in primary structure
Peptide
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Bonds in secondary structure
Peptide and hydrogen
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Bonds in tertiary structure
Peptide, hydrogen, disulphide, ionic, hydrophobic interactions
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Features of globular proteins
Globular proteins are compact, roughly spherical (circular) in shape and soluble in water
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Why do globular proteins form spherical shape when folding into their tertiary structure
their non-polar hydrophobic R groups are orientated towards the centre of the protein away from the aqueous surroundings and
their polar hydrophilic R groups orientate themselves on the outside of the protein
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How does orientation of globular proteins enable them to be generally soluble in water
the water molecules can surround the polar hydrophilic R groups
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What does solubility in globular proteins mean
they play important physiological roles as they can be easily transported around organisms and be involved in metabolic reactions
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How do globular proteins have specific shapes
The folding of the protein due to the interactions between the R groups results in globular proteins having specific shapes
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What does globular proteins having specific shape enable
enables globular proteins to play physiological roles, for example, enzymes can catalyse specific reactions and immunoglobulins (antibodies) can respond to specific antigens
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Conjugated protein
A protein that contains a non-protein chemical group such as a prosthetic group or cofactor.
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Simple proteins
Proteins that just contain amino acids
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Prosthetic group
A permanent, non protein part of a protein molecule eg. A haem group in haemoglobin
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Example Globular proteins as conjugated proteins
haemoglobin which contains the prosthetic group called haem
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Haemoglobin
a globular protein which is an oxygen-carrying pigment found in vast quantities in red blood cells
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Structure of haemoglobin
It has a quaternary structure as there are four polypeptide chains. These chains or subunits are globin proteins (two α–globins and two β–globins) and each subunit has a prosthetic haem group
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What bonds the 4 globin subunits
Disulphide bonds
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How are the 4 globin subunits arranged
arranged so that their hydrophobic R groups are facing inwards (helping preserve the three-dimensional spherical shape) and the hydrophilic R groups are facing outwards (helping maintain its solubility)
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Why is the arrangement of the R groups important to the functioning of haemoglobin
If changes occur to the sequence of amino acids in the subunits this can result in the properties of haemoglobin changing
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Example of sequence of amino acids in subunits of haemoglobin changin
This is what happens to cause sickle cell anaemia (where base substitution results in the amino acid valine (non-polar) replacing glutamic acid (polar) making haemoglobin less soluble)
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How is oxyhaemoglobin formed
The prosthetic haem group contains an iron II ion (Fe2+) which is able to reversibly combine with an oxygen molecule
Therefore Each haemoglobin with the four haem groups can carry four oxygen molecules (eight oxygen atoms)
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What is haemoglobin responsible for
binding oxygen in the lung and transporting the oxygen to tissue to be used in aerobic metabolic pathways
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How does haemoglobin lead to oxygen being carried around the body more efficiently
As oxygen is not very soluble in water and haemoglobin is, oxygen can be carried more efficiently around the body when bound to the haemoglobin
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How does structure change in haemoglobin affect its affinity for oxygen
The presence of the haem group (and Fe2+) enables small molecules like oxygen to be bound more easily because as each oxygen molecule binds it alters the quaternary structure (due to alterations in the tertiary structure) of the protein which causes haemoglobin to have a higher affinity for the subsequent oxygen molecules and they bind more easily
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How is oxygen allowed to reversible bind
The existence of the iron II ion (Fe2+) in the prosthetic haem group also allows oxygen to reversibly bind as none of the amino acids that make up the polypeptide chains in haemoglobin are well suited to binding with oxygen
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How are enzymes biological catalysts
Biological’ because they function in living systems
‘Catalysts’ because they speed up the rate of chemical reactions without being used up or changed
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What type of proteins are enzymes
Globular
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Insulin
globular protein produced in the pancreas. It plays an important role in the control of blood glucose concentration
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How many polypeptide chains in insulin
It consists of two polypeptide chains
Polypeptide A has 21 amino acid residues
Polypeptide B has 30 amino acid residues
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what are the polypeptide chains in insulin held together by
The two polypeptide chains are held together by three disulfide bridges
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Fibrous proteins
long strands of polypeptide chains that have cross-linkages due to hydrogen bonds
These proteins have little or no tertiary structure
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Solubility of fibrous proteins
Due to a large number of hydrophobic R groups, fibrous proteins are insoluble in water
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Why is the sequence of fibrous proteins highly repetitive
Fibrous proteins have a limited number of amino acids
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What does the highly repetitive sequence in fibrous proteins mean
creates very organised structures that are strong and this along with their insolubility property, makes fibrous proteins very suitable for structural roles
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Examples of fibrous proteins
Keratin, elastin, collagen
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Keratin
makes up hair, nails, horns and feathers (it is a very tough fibrous protein)
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Elastin
is found in connective tissue, tendons, skin and bone (it can stretch and then return to its original shape)
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Collagen
is a connective tissue found in skin, tendons and ligaments
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Shape of globular and fibrous proteins
Globular- roughly circular
Fibrous- long strands
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Amino acid sequence of globular and fibrous proteins
Globular- irregular ad wide range of R groups
Fibrous- repetitive with a limited range of R groups
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Function of globular and fibrous proteins
Globular- physiological/functional
Fibrous- structural
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Examples of globular and fibrous proteins
Globular- haemoglobin, enzymes, insulin, immunoglobulin
Fibrous- collagen, keratin, myosin, actin, fibrin
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Solubility of globular and fibrous proteins
Globular- generally soluble in water
Fibrous- generally insoluble in water
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Collagen
most common structural protein found in vertebrates
It provides structural support
It’s an insoluble fibrous protein
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Function a collagen
flexible structural protein forming connective tissues
great tensile strength. This enables collagen to be able to withstand large pulling forces without stretching or breaking
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Solubility of collagen
The length of collagen molecules means they take too long to dissolve in water (making it insoluble in water)
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Number of polypeptide chains in collagen and haemoglobin
Collagen-3
Haemoglobin- 4
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Shape of collagen and haemoglobin
Collagen-long,thin
Haemoglobin-spherical,round
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What type of protein is collagen and haemoglobin
Collagen-fibrous
Haemoglobin-globular
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Main function of collagen and haemoglobin
Collagen- structural (connective tissue eg. Tendons, skins)
Haemoglobin- functional (transport of oxygen)
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Elastin
allows tissues in your body to stretch out and shrink back
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Keratin
Protects epithelial cells, strengthens the skin, strengthens internal organs, controls the growth of epithelial cells, and maintains the elasticity in the skin
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Ion
An atom that has an electrical charge
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Cation
Ion with positive charge
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Anion
Ion that has negative charge
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Inorganic ion
Does not contain carbon
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Cofactors
Non- protein chemical compounds that are required for a protein to function
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Hydrogen ions
H+
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Calcium ions
CA2+
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Iron ions
Fe2+/Fe3+
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Sodium ions
Na+
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Potassium ions
K+
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Ammonium ions
NH4+ (4 belongs to H)
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Nitrate ions
NO3- (3 belongs to o)
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Hydrogen carbonate ions
HCO3- (3 belongs to o)
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Chloride ions
Cl-
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Phosphate ions
PO4 3- (4 belongs to o)
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Hydroxide ions
OH-
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What chemical is used to test proteins
Biuret
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Method biuret test
Add sodium hydroxide to the food solution sample to make the solution alkaline
Add few drops of Biuret ‘reagent’ contains an alkali and copper (II) sulfate
Repeat steps 1 and 2 using the control solution
Compare the colours of the control solution and the food sample solution
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Results biuret test
If a colour change is observed from blue to lilac/mauve, then protein is present.
If no colour change is observed, no protein is present
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What to do when colour change is very subtle
hold the test tubes up against a white tile when making observations
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Limitations of biuret tes
it does not give a quantitative value as to the amount of protein present in a sample
If the sample contains amino acids or dipeptides, the result will be negative (due to lack of peptide bonds)
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Colour change to represent sugar concentration
The intensity of any colour change seen relates to the concentration of reducing sugar present in the sample
A positive test is indicated along a spectrum of colour from green (low concentration) to brick-red (high concentration of reducing sugar present)
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Colorimeter
A colorimeter is an instrument that beams a specific wavelength (colour) of light through a sample and measures how much of this light is absorbed (arbitrary units)
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How do colorimeter work
They contain different wavelengths or colour filters (depends on the model of colorimeter), so that a suitable colour can be shone through the sample and will not get absorbed. This colour will be the contrasting colour (eg. a red sample should have green light shone through)
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What must be done when using colorimeter
Colorimeters must be calibrated before taking measurements
This is completed by placing a blank into the colorimeter and taking a reference, it should read 0 (that is, no light is being absorbed)
This step should be repeated periodically whilst taking measurements to ensure that the absorbance is still 0
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Chromatography
a technique that can be used to separate a mixture into its individual components
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Two phases of chromatography
All chromatography techniques use two phases:
The mobile phase
The stationary phase
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What does chromatography rely on
Chromatography relies on differences in the solubility of the different chemicals (called ‘solutes’) within a mixture
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How is the distance travelled different
Differences in the solubility of each component in the mobile phase affects how far each component can travel
Those components with higher solubility will travel further than the others
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Why do components with higher solubility travel further
they spend more time in the mobile phase and are thus carried further up the paper than the less soluble components
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The mobile phase in Paper chromatography
The mobile phase is the solvent in which the sample molecules can move, which in paper chromatography is a liquid e.g. water or ethanol
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The stationary phase in paper chromatography
The stationary phase in paper chromatography is the chromatography paper
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Paper chromatography method
A spot of the mixture (that you want to separate) is placed on chromatography paper and left to dry
The chromatography paper is then suspended in a solvent
As the solvent travels up through the chromatography paper, the different components within the mixture begin to move up the paper at different speeds
Larger molecules move slower than smaller ones
This causes the original mixture to separate out into different spots or bands on the chromatography paper
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Using chromatography to separate a mixture of monosaccharides methd
Use a stain if needed
Spots of solution of different monosaccharide placed on a line beside the sample spot
The chromatography paper is then suspended in a solvent
As the solvent travels up through the chromatography paper, the different monosaccharides within the mixture separate out at different distances from the line
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Rf equation
Rf = distance moved by solute ÷ distance moved by solvent
Always lower than one
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What does Rf Value demonstrates
The Rf value demonstrates how far a dissolved molecule travels during the mobile phase
A smaller Rf value indicates the molecule is less soluble and larger in size
